Additional File 5 - Recombination Mediated Deletions Truncated L1HS Elementsreference

Additional file 5 - Recombination mediated deletions – Truncated L1HS elementsReference human genome comparison with Chimpanzee, Celera and HuRef genomes.

Note that premasked files were available only for reference human and Chmpanzee. These were directly parsed to extract repeat masker annotation of the repeat locus in the reference human genome and of the ortholog in the comparative genome. However, for Celera and HuRef genomes, the orthlog and flanking sequence was retrieved and annotated by RepeatMasker online.

Repeat masker annotation of the locus in the main genome and its flanks is listed first, followed by the Repeat masker annotation of the identified ortholog in the comparative genome and its flanks.

R1,R2 – PUTATIVE REGIONS OF HOMOLOGY WHICH RECOMBINE TO GIVE R12 (M_INTER_RMD or C_INTER_RMD).

In case of disruptions, R1 and R2 represent disrupted halves of the parent repeat, R represents undisrupted repeat and D represents the disruptive sequence. (M_DISRUPTED OR C_DISRUPTED).

In case of intra element recombination (M_INTRA_RMD or C_INTRA_RMD), R12 represent the 2 resulting copies arising out of intra element recombination and R represents the intact repeat.

Reference human Vs Chimpanzee

L1HS_1_1356327899-56330505M_INTRA_RMD

5632453956325159+L1M5LINE/L150985727

5632517356325278+L1ME3BLINE/L146004701

5632527956325647+L1PA11LINE/L157946173

5632564856325687+L1ME3BLINE/L147024740

5632571856325808+L1ME3BLINE/L157555857

5632580956326103CAluSpSINE/Alu2971

5632610456326302+L1ME3BLINE/L158586096

5632639656327164CL1MD2LINE/L11521651

5632722356327517+AluSxSINE/Alu1296

5632757556327876+AluSxSINE/Alu1303

5632789956330505+L1HSLINE/L122607 ( L1HS_1_13 ) (R12)

5633050756331226+L1PA3LINE/L155696288 (R12)

5633140456331500CL1MD2LINE/L1408313

5633172056332173+LTR16CLTR/ERVL11488

5633222856332410+MIRbSINE/MIR8204

5633284956332932CMIR3SINE/MIR197116

5633296156333266+L3LINE/CR141444486

5633362656334033+LTR16BLTR/ERVL39452

5633451456334934CMLT1FLTR/MaLR4793

Ortholog in Chimp57100076-57106538PlusNscore 0.34

N positions 57103775-57103784; 57103806-57103807; 57105481-57105490;

5709669557097335+L1M5LINE/L150745727

5709734957097454+L1ME3BLINE/L146004701

5709745557097823+L1PA11LINE/L157946173

5709782457097863+L1ME3BLINE/L147024740

5709789457097984+L1ME3BLINE/L157555857

5709798557098281CAluSpSINE/Alu2991

5709828257098483+L1ME3BLINE/L158586095

5709858057099345CL1MD2LINE/L11507651

5709940457099698+AluSxSINE/Alu1296

5709975657100066+AluSxSINE/Alu1312

5710007657105480+L1PtLINE/L125020 (R1,R2)

5710550157107124+L1PA3LINE/L145156155 (R1,R2) Broken due to Ns, overlap at Ns

5710715257107182+(TAAA)nSimple_repeat232

5710719357107226+(A)nSimple_repeat134

5710722757107348CL1MD2LINE/L1408291

5710743357107557CL1MD2LINE/L1408286

5710774957108201+LTR16CLTR/ERVL11488

5710825657108438+MIRbSINE/MIR8204

5710887757108960CMIR3SINE/MIR197116

5710898957109294+L3LINE/CR141444486

5710965457110059+LTR16BLTR/ERVL39449

5711054457110963CMLT1FLTR/MaLR4793

______

L1HS_1_2873431855-73433278C_DISRUPTED_M_INTER_RMD

7342903473429396CTHE1BLTR/MaLR3641

7342939773429422CMLT1A0-intLTR/MaLR16741653

7342954373429964+MLT-intLTR/MaLR9721456

7342996273430118C7SKRNA23859

7343012473430383+MLT1A0-intLTR/MaLR14381706

7343037173430635+MLT1A0LTR/MaLR97365

7343063773430937CMLT1A0-intLTR/MaLR2982

7343093973431280CMLT1A0LTR/MaLR36517

7343128373431337CMLT1A0LTR/MaLR551

7343144373431859+L1ME1LINE/L142614694

7343185573433278+L1HSLINE/L117163139 ( L1HS_1_28 ) (R12)

7343330873433655CMLT1ELTR/MaLR654284

7343375273434067CAluYSINE/Alu3101

7343408773434147CMLT1F2LTR/MaLR601

7343414973434201+L1MDLINE/L146534708

7343420273434510+AluSxSINE/Alu1311

7343451173434774+L1ME1LINE/L147825068

7343477573435069+AluJbSINE/Alu12306

7343507073436159+L1ME1LINE/L150696233

Ortholog in Chimp74467496-74470238PlusNscore 0.36

N positions 74469657-74469666;

7446467474465036CTHE1BLTR/MaLR3641

7446503774465062CMLT1A0-intLTR/MaLR16741653

7446518274465607+MLT-intLTR/MaLR9671456

7446560574465760C7SKRNA23859

7446576674466025+MLT1A0-intLTR/MaLR14381706

7446601374466277+MLT1A0LTR/MaLR97365

7446627974466579CMLT1A0-intLTR/MaLR2982

7446658174466922CMLT1A0LTR/MaLR36517

7446692574466979CMLT1A0LTR/MaLR551

7446710974467500+L1ME1LINE/L142154621

7446749674469656+L1PtLINE/L117173881 (R1)

7446963974470238+L1P1LINE/L126633262 (R2)

7447026874470726CMLT1ELTR/MaLR59379

7447072774471043CAluYSINE/Alu3111

7447104474471123CMLT1ELTR/MaLR781

7447112574471177+L1MDLINE/L146534704

7447117874471486+AluSxSINE/Alu1309

7447148774471749+L1ME1LINE/L147044995

7447175074472044+AluJbSINE/Alu12306

7447204574473135+L1ME1LINE/L149966160

______

L1HS_1_40c90456915-90457988C_DISRUPTED_M_INTER_RMD

9045070290451006CAluSxSINE/Alu2981

9045100790452796CL1MEcLINE/L1189216

9045284090456910CL1PA3LINE/L161842110

9045691590457988CL1HSLINE/L110825 ( L1HS_1_40c ) (R12)

9045897890459074CMIR3SINE/MIR15457

9046007590460172CMER91ADNA/Tip10012933

9046057990460648+MIRSINE/MIR270

9046063690461034+L2LINE/L225292958

9046104290461887CMER21BLTR/ERV186215

9046188890461917+(CATATA)nSimple_repeat433

9046193390462220+L2LINE/L229603268

9046226190462541CAluSxSINE/Alu30727

9046258590462952+THE1BLTR/MaLR3364

9046295390464421+THE1B-intLTR/MaLR11516

Ortholog in Chimp91675231-91676492MinusNscore 0.79

N positions 91676234-91676243;

9166837791669250CL1MEcLINE/L126911893

9166925191669560CAluSxSINE/Alu3001

9166956191671350CL1MEcLINE/L1189216

9167143591675226CL1PA3LINE/L161392110

9167523191676233CL1PtLINE/L1108376 (R2)

9167624491676492CL1PtLINE/L12555 (R1)

9167748291677578CMIR3SINE/MIR15457

9167857991678669CMER91DNA/Tip10012938

9167908391679152+MIRSINE/MIR270

9167914091679538+L2LINE/L225292958

9167954691680380CMER21BLTR/ERV186227

9168038191680405+(TA)nSimple_repeat125

9168040691680443+(CA)nSimple_repeat240

9168046091680742+L2LINE/L229603268

9168078391680859CAluSINE/Alu295221

9168159591683042+THE1B-intLTR/MaLR181516

______

L1HS_1_4593747746-93749829 M_DISRUPTED

9374336093743922CLTR10CLTR/ERV15911

9374392393744121CAluSgSINE/Alu1991

9374423793744287+AT_richLow_complexity151

9374520293745253+(CA)nSimple_repeat253

9374525493745315+(TC)nSimple_repeat162

9374579493746093CAluSxSINE/Alu3001

9374609793746119+AT_richLow_complexity123

9374621293746497+AluSxSINE/Alu1286

9374689493747189CMLT1KLTR/MaLR591233

9374727593747369CMLT1ILTR/MaLR409315

9374774693749829+L1HSLINE/L1 42093 ( L1HS_1_45 ) (R1)

9374983093750133+AluYa5SINE/Alu1304 (D)

9375013493754072+L1PA3LINE/L1 20946032 (R2)

9375442093754494CtRNA-Cys-TGYtRNA741

9375467993754863+AluSqSINE/Alu1195

9375513293755172+CT-richLow_complexity343

9375517493755455CAluSxSINE/Alu31135

9375546793755635CFRAMSINE/Alu1661

9375571293755812CMER58ADNA/MER1_type14139

9375599393756176+MIRbSINE/MIR50257

Ortholog in Chimp95008405-95010448PlusNscore 0.59 (94008405-95015146 - Nscore 17.87)

N positions 95008965-95008965; 95008975-95008975; 95009015-95009024;

9500357695004138CLTR10CLTR/ERV15911

9500413995004337CAluSgSINE/Alu1991

9500445395004503+AT_richLow_complexity151

9500541495005463+(CA)nSimple_repeat251

9500546495005497+(TC)nSimple_repeat134

9500597695006275CAluSxSINE/Alu3001

9500697695007162+AluSg/xSINE/Alu108293

9500755295007847CMLT1KLTR/MaLR591233

9500840595012316+L1PtLINE/L143983 (R) (BROKEN BECAUSE OF Ns)

9501353195015146+L1PA3LINE/L143966032 (R)

9501549395015567CtRNA-Cys-TGYtRNA741

9501575295015936+AluSqSINE/Alu1195

9501622995016273+CT-richLow_complexity245

9501627495016555CAluSxSINE/Alu31135

9501656795016735CFRAMSINE/Alu1661

9501681295016912CMER58ADNA/MER1_type14139

9501709395017276+MIRbSINE/MIR50257

______

L1HS_1_4898826806-98830180M_INTRA_RMD

9882069098820880CL1PLINE/L153195130

9882088198820924+(TG)nSimple_repeat144

9882092598821635CL1PLINE/L151294407

9882164198821891+Tigger2DNA/MER2_type87343

9882189298824268+L1PA10LINE/L133725788

9882426998824578+AluSgSINE/Alu1306

9882457998824964+L1PA10LINE/L157896167

9882497398825717+Tigger2DNA/MER2_type339337

9882571898826033+AluJoSINE/Alu1304

9882603498826411+Tigger2DNA/MER2_type338694

9882641298826702CAluJoSINE/Alu2851

9882670398826795+Tigger2DNA/MER2_type695786

9882680698830180+L1HSLINE/L1123389 ( L1HS_1_48 )

9883017798831188+L1PA2LINE/L151466155

9883119698832387+Tigger2DNA/MER2_type7752718

9883238898832434+MLT2B1LTR/ERVL521567

9883243598832870CL1MDLINE/L128632429

9883290398833632CL1MA3LINE/L163055592

9883363398833939CAluSxSINE/Alu3061

9883394098834354CL1P4LINE/L156075199

9883513398835466+L1M5LINE/L144254739

9883547298835563+(TA)nSimple_repeat191

9883600898836123+MLT1ILTR/MaLR12131

9883625698836469CMIRSINE/MIR2377

9883648498836834+MLT1A0LTR/MaLR1365

9883832798838685CMSTDLTR/MaLR3961

9883913898839165+AT_richLow_complexity128

Ortholog in Chimp100150551-100158165PlusNscore 9.51

N positions 100151331-100151340; 100153307-100154020;

100145534100145563+(TG)nSimple_repeat130

100145564100146250CL1PLINE/L151264429

100146251100146528+Tigger2DNA/MER2_type66343

100146529100147954+L1P3LINE/L133724802

100149224100149455+Tigger2DNA/MER2_type107330

100149456100149776+AluJoSINE/Alu1308

100149777100150155+Tigger2DNA/MER2_type331694

100150156100150446CAluJoSINE/Alu2852

100150447100150540+Tigger2DNA/MER2_type695786

100150552100151330+L1PtLINE/L113792 (R1)

100151341100151987+L1PA11LINE/L151355788 (D)

100151988100152303+AluSgSINE/Alu1302 (D)

100152304100152692+L1PA11LINE/L157896172 (D)

100152701100153302+Tigger2DNA/MER2_type339195 (D)

100154021100159175+L1PA2LINE/L18806032 (R2)

100159181100160374+Tigger2DNA/MER2_type7752718

100160375100160421+MLT2B1LTR/ERVL521567

100160422100160857CL1MDLINE/L128632431

100160892100161599CL1MA3LINE/L163055592

100161620100161926CAluSxSINE/Alu3061

100161927100162343CL1MA3LINE/L156075199

100162787100162816+AT_richLow_complexity130

100163121100163265+L1M5LINE/L144254572

100163266100163295+(TA)nSimple_repeat231

100163296100163458+L1M5LINE/L145734738

100163464100163555+(TA)nSimple_repeat191

100163989100164114+MLT1ILTR/MaLR1131

100164247100164460CMIRSINE/MIR2377

100164475100164824+MLT1A0LTR/MaLR1365

100166328100166686CMSTDLTR/MaLR3961

100167138100167165+AT_richLow_complexity128

______

L1HS_1_61106769783-106770468C_INTER_RMD_M_DISRUPTED

106760330106761102CL2LINE/L223981467

106761926106762021CLTR52LTR/ERVL14749

106762031106765236+L1MA2LINE/L1173174

106765237106765275+(TTA)nSimple_repeat240

106765276106765301+L1MA2LINE/L131753178

106765302106765324+(TG)nSimple_repeat224

106765325106765526+L1MA2LINE/L131793343

106765527106765878+L1PA10LINE/L157946152

106765879106766113+L1MA2LINE/L133443523

106766108106766884+L1MA2LINE/L141995166

106766885106767174+AluYSINE/Alu7296

106767175106769661+L1MA2LINE/L151677671

106769665106769782+AluSpSINE/Alu1120

106769783106770468+L1HSLINE/L154776155 ( L1HS_1_61 ) (R1)

106770520106770543+(TAAAA)nSimple_repeat225

106770564106770944+L1PA5LINE/L157706151 (R2)

106770950106771074+AluSg/xSINE/Alu130254

106771075106771353+(TA)nSimple_repeat1277

106771354106771793+THE1B-intLTR/MaLR11461580

106771794106772146+THE1BLTR/MaLR1364

106772194106773238CL1MEcLINE/L124751393

106773271106773296+AT_richLow_complexity126

106773380106773743CTHE1BLTR/MaLR3641

106774718106775121+MLT2A2LTR/ERVL1413

106775127106775270+(TA)nSimple_repeat2155

106775287106775591+(TA)nSimple_repeat1334

106775679106776246CMLT1GLTR/MaLR5952

106776399106776484+AluScSINE/Alu212297

106776486106777147CL2LINE/L230952367

106777875106777909+AT_richLow_complexity135

106778027106778274+MIRSINE/MIR7241

106778658106778848CMIRbSINE/MIR23947

106779103106779392+AluSxSINE/Alu1290

106779424106779833CMER57ALTR/ERV14033

Ortholog in Chimp108095368-108095651PlusNscore 0.00

N positions

108085925108086697CL2LINE/L223981467

108087521108087616CLTR52LTR/ERVL14749

108087626108090828+L1MA3LINE/L1173174

108090829108090861+(TTA)nSimple_repeat234

108090862108090887+L1MA3LINE/L131753178

108090888108090916+(TG)nSimple_repeat230

108090917108091118+L1MA3LINE/L131793343

108091119108091466+L1PA10LINE/L157946152

108091467108091700+L1MA3LINE/L133443523

108091695108092470+L1MA3LINE/L141995165

108092471108092761+AluYSINE/Alu1292

108092762108095246+L1MA3LINE/L151667671

108095254108095367+AluSpSINE/Alu5120

108095368108096033+L1PA5LINE/L154776152 (R12)

108096034108096161+AluSpSINE/Alu121252

108096162108096283+(TA)nSimple_repeat1121

108096288108096733+THE1B-intLTR/MaLR11391580

108096734108097084+THE1BLTR/MaLR1364

108097132108098114CL1MEcLINE/L124751462

108098213108098238+AT_richLow_complexity126

108098322108098684CTHE1BLTR/MaLR3641

108099657108100050+MLT2A2LTR/ERVL1399

108100062108100390+(TA)nSimple_repeat1357

108100396108100479+(TTATA)nSimple_repeat184

108100480108100656+(TATAA)nSimple_repeat1179

108100673108100818+(TATAA)nSimple_repeat4159

108100819108100845+AT_richLow_complexity127

108100846108100900+MLT2A2LTR/ERVL506560

108100912108100960+AT_richLow_complexity149

108100973108101124+L1P3LINE/L148905032

108101601108102167CMLT1GLTR/MaLR5952

108102320108102405+AluScSINE/Alu212297

108102407108103099CL2LINE/L230952322

108103795108103829+AT_richLow_complexity135

108103941108104229+MIRSINE/MIR5272

108104557108104765CMIRbSINE/MIR26047

______

L1HS_1_63113685753-113689935C_INTER_RMD_M_DISRUPTED

113676749113676954+MIRbSINE/MIR2232

113677097113677430+L2LINE/L230543378

113679033113679160+L1M5LINE/L156915823

113679198113680003CTigger1DNA/MER2_type24181589

113680004113680303CAluSpSINE/Alu3042

113680304113681904CTigger1DNA/MER2_type15881

113682091113682392CAluSpSINE/Alu2991

113683352113683405+(TG)nSimple_repeat255

113683409113683483+L2LINE/L233013374

113683523113683577+AluSxSINE/Alu245299

113683579113684447+L1MB2LINE/L152306135

113685480113685748CL2LINE/L233523083

113685753113689935+L1HSLINE/L119956155 ( L1HS_1_63 ) (R1)

113689938113690958+L1PA4LINE/L151286155 (R2)

113690974113691114CL2LINE/L230612910

113691263113691538CAluSgSINE/Alu30311

113691591113691900CAluJoSINE/Alu3011

113692262113692340+MIRSINE/MIR178

113692671113692720+(TGGA)nSimple_repeat453

113693058113693159+AluSg/xSINE/Alu135236

113693161113693323+MIRSINE/MIR50231

113693398113693651CL2LINE/L229642711

113693652113693960CAluYSINE/Alu3061

113695067113695163CMIRmSINE/MIR255157

113696363113696683+MER44ADNA/MER2_type1336

113697350113697992CL1MD3LINE/L179957346

113698870113699175+AluJbSINE/Alu1308

Ortholog in Chimp124346587-124349743MinusNscore 0.00

N positions

124337354124337657CAluJbSINE/Alu3081

124338535124339172+L1MD3LINE/L173467995

124339839124340159CMER44ADNA/MER2_type3361

124341353124341441+L2LINE/L232523341

124342563124342869+AluYSINE/Alu1304

124342870124343150+L2LINE/L227113008

124343182124343373CMIRbSINE/MIR27357

124343375124343476CAluSg/xSINE/Alu236135

124343814124343863+(TCCA)nSimple_repeat453

124344194124344272CMIRSINE/MIR781

124344634124344941+AluJoSINE/Alu1301

124344994124345260+AluSgSINE/Alu11294

124345406124345554+L2LINE/L229073066

124345565124349744CL1PA4LINE/L161551995 (R12)

124349749124350017+L2LINE/L230833352

124351050124351918CL1MB2LINE/L161355230

124351920124351974CAluSINE/Alu299245

124352014124352088CL2LINE/L233743301

124352092124352129+(CA)nSimple_repeat239

124353091124353394+AluSpSINE/Alu1300

124353581124355008+Tigger1DNA/MER2_type11415

124355432124355508+Tigger1DNA/MER2_type15131588

124355509124355809+AluSpSINE/Alu1304

124355810124356615+Tigger1DNA/MER2_type15892418

124356653124356780CL1M5LINE/L158235691

124358386124358717CL2LINE/L233783054

______

L1HS_2_32240463-2242344C_INTER_RMD_M_DISRUPTED

22297962233590+L1MA2LINE/L121116304

22336742233737+AT_richLow_complexity164

22346132234727+GA-richLow_complexity2117

22357412235764+AT_richLow_complexity124

22359002235946+A-richLow_complexity147

22373032237403+MIRSINE/MIR158262

22391242239340+MER58ADNA/MER1_type1224

22398012239947CMER5ADNA/MER1_type1576

22401832240247+AluSINE/Alu973

22402532240432+L1MA9LINE/L160046183

22404242240473CL1HSLINE/L144314384

22404632242344+L1HSLINE/L144326312 ( L1HS_2_3 )

22425342242730+MIRbSINE/MIR32220

22429542243086+MIRSINE/MIR60192

22439022243953+(TG)nSimple_repeat253

22448822244964+L2LINE/L233363419

22451102245165+AluYc3SINE/Alu238293

22451662245178+AluYc3SINE/Alu272283

22451902245488+AluYSINE/Alu1298

22456952245734+(TA)nSimple_repeat241

22466872246744+L1PA5LINE/L160926150

22468092246924CMIRbSINE/MIR14616

22477082247800+MIRbSINE/MIR26120

22478012248086CAluSqSINE/Alu3041

22480872248230+MIRbSINE/MIR121267

22484292248564+MIRSINE/MIR84237

22488422249077CMIRbSINE/MIR2382

22494102249769+THE1BLTR/MaLR1364

22499932250209CMIRSINE/MIR23221

Ortholog in Chimp2221514-2221647PlusNscore 0.00

N positions

22124892212614+GA-richLow_complexity2129

22132602213392+GA-richLow_complexity2137

22144052214427+AT_richLow_complexity123

22145632214610+(A)nSimple_repeat145

22159362216036+MIRSINE/MIR158262

22164122216463CL4LINE/RTE19481897

22177562217972+MER58ADNA/MER1_type1224

22184332218579CMER5ADNA/MER1_type1576

22188152219107+AluScSINE/Alu9300

22197072219850CAluScSINE/Alu309166

22198522220599+L1PA7LINE/L154056154

22210692221647+L1MA9LINE/L157306312

22218372222033+MIRbSINE/MIR32220

22222482222453+MIR_MarsSINE/MIR57260

22232022223251+(TG)nSimple_repeat251

22239582223978+AT_richLow_complexity121

22241432224262+L2LINE/L233073419

22244082224463+AluSINE/Alu238293

22244642224480+AluSINE/Alu272287

22244842224783+AluYSINE/Alu1300

22259852226042+L1PA5LINE/L160926150

22261072226222CMIRbSINE/MIR14616

22270072227099+MIRbSINE/MIR26116

22271002227380CAluSqSINE/Alu2991

22273812227525+MIRbSINE/MIR117268

22277242227859+MIRSINE/MIR84237

22281372228372CMIRbSINE/MIR2382

22287052229064+THE1BLTR/MaLR1364

22292882229504CMIRSINE/MIR23221

______

L1HS_2_1549162749-49166150C_INTRA_RMD

4915657549156823+L1ME3BLINE/L133503590

4915682449157178CTHE1BLTR/MaLR3641

4915717949158723CMLT-intLTR/MaLR17352

4915872649159024CTHE1BLTR/MaLR36471

4915904649161311+L1ME3BLINE/L135885946

4916131249161877+MER74ALTR/ERVL1558

4916187849161951+L1ME3BLINE/L159476028

4916265749162754+L1HSLINE/L1198

4916274949166150+L1HSLINE/L16154029 ( L1HS_2_15 ) (R1,R2)

4916614949166192CL1P1LINE/L127472704

4916619349166764+L1PA4LINE/L155786150

4916682849167075+Charlie8DNA/MER1_type19271

4916716249167270CMER5BDNA/MER1_type17866

4916727149167576CAluSqSINE/Alu3121

4916757749167641CMER5BDNA/MER1_type651

4916771449167741+(T)nSimple_repeat128

4916806249168204CL2LINE/L234193267

4916841449168584CL2LINE/L234193239

4916859549168810CMIRbSINE/MIR24930

4916928949169348+L3LINE/CR138253884

4916973749169757+(TATAA)nSimple_repeat323

4917063349170717CMIRbSINE/MIR261177

4917076849170809+(TG)nSimple_repeat243

4917081249171959CL1ME1LINE/L161104951

4917196049172239CAluJbSINE/Alu2871

Ortholog in Chimp50257934-50261219PlusNscore 0.30

N positions 50258721-50258730;

5025179050252034+L1ME3BLINE/L133493589

5025203650252393CTHE1BLTR/MaLR3641

5025239450253933CMLT-intLTR/MaLR17352

5025393650254234CTHE1BLTR/MaLR36471

5025438550256495+L1ME3BLINE/L137645944

5025649650257061+MER74ALTR/ERVL1558

5025706250257135+L1ME3BLINE/L159456028

5025784250257939+L1PtLINE/L1198

5025790950261219+L1PtLINE/L15794029 (R12) (NOTE THAT THE LENGTH IS SMALLER THAN THE HUMAN ORTHOLOG)

5026121850261261CL1P1LINE/L127472704

5026126250261834+L1PA4LINE/L155786150

5026191750262145+Charlie8DNA/MER1_type28260

5026223850262346CMER5BDNA/MER1_type17866

5026234750262668CAluSxSINE/Alu3121

5026266950262733CMER5BDNA/MER1_type651

5026280850262845+(T)nSimple_repeat138

5026316750263309CL2LINE/L234193267

5026351950263689CL2LINE/L234193239

5026370050263915CMIRbSINE/MIR24930

5026439450264453+L3LINE/CR138253884

5026484250264867+AT_richLow_complexity126

5026572750265811CMIRbSINE/MIR261177

5026586250265885+(TG)nSimple_repeat225

5026588850267027CL1ME1LINE/L161104951

5026702850267308CAluJbSINE/Alu2881

______

L1HS_3_7c11505147-11508964C_INTER_RMD_M_DISRUPTED

1149612811496162+(TAAAAA)nSimple_repeat235

1149640411496704CAluYSINE/Alu2971

1149672811497061+AluJoSINE/Alu3300

1149757311497644CL2LINE/L233733296

1149765011497823+L1MB3LINE/L160066182

1149820911498442+MIRbSINE/MIR14254

1149926911499477CL1ME3LINE/L161625953

1150058611500894+AluSxSINE/Alu1312

1150091711500993+L3LINE/CR135253606

1150102411503297CL1PA3LINE/L161553867 (R2)

1150330211504773CSVAOther1386393 (D)

1150514711508964CL1HSLINE/L137581 ( L1HS_3_7c ) (R1)

1150896711510066CLTR1DLTR/ERV19781

1151007611510511+L3LINE/CR136354178

1151051211510993CLOR1aLTR/ERV14971

1151099411511265+L3LINE/CR141794432

1151126611511563+AluSgSINE/Alu1292

1151156411511615+L3LINE/CR144334484

1151241411512549CMIRSINE/MIR23999

1151287811512915+CT-richLow_complexity440

1151332211513624CAluSxSINE/Alu3121

1151370411513831+AluSxSINE/Alu1128

1151383211513866+(TA)nSimple_repeat236

1151386711514029+AluSxSINE/Alu129303

1151461411514655+(CATA)nSimple_repeat144

Ortholog in Chimp11804325-11808145MinusNscore 0.00

N positions

1179498711795444CMLT1KLTR/MaLR587154

1179635711796399+(CA)nSimple_repeat244

1179701211797046+(TAAAAA)nSimple_repeat235

1179728811797601CAluYSINE/Alu3081

1179762511797960+AluJoSINE/Alu3302

1179855111798724+L1MB3LINE/L160066182

1179910211799322+MIRbSINE/MIR14241

1180016111800368CL1ME3LINE/L161625953

1180161111801916+AluSxSINE/Alu1309

1180193811802014+L3LINE/CR135253606

1180203011802057+(TTTTA)nSimple_repeat532

1180206411808145CL1PA3LINE/L161401 (R12)

1180814811809237CLTR1DLTR/ERV19781

1180924711809457+L3_MarsLINE/CR135633789

1180958011809682+L3LINE/CR139994103

1180968311810163CLOR1aLTR/ERV14971

1181016411810436+L3LINE/CR141044357

1181043711810734+AluSgSINE/Alu2293

1181073511810786+L3LINE/CR143584409

1181160311811745CMIRSINE/MIR21685

1181205011812086+CT-richLow_complexity136

1181248911812791CAluSxSINE/Alu3121

1181287111813179+AluSxSINE/Alu1303

1181376411813801+(CATA)nSimple_repeat340

______

L1HS_3_14c22066888-22069693C_INTER_RMD_M_DISRUPTED

2205771922057907CMLT1KLTR/MaLR27369

2205798122058465+L3LINE/CR137484243

2205864722058850+MIRSINE/MIR35262

2206001922060131CL2LINE/L234073288

2206013522060437+MLT1F2LTR/MaLR4323

2206044722060600CL2LINE/L219571803

2206093722060963+(CAAAAA)nSimple_repeat430

2206106522061330CL2LINE/L217521458

2206145222061522+AluSp/qSINE/Alu226296

2206152322061584CL1M2LINE/L143264264

2206161622061797CL1M2LINE/L151334941

2206360222065510CL1MA8LINE/L162894316

2206551122065836+AluSqSINE/Alu1327

2206583722066576CL1MA8LINE/L143153551

2206658022066854+AluJoSINE/Alu1279

2206685522066887+(CAAA)nSimple_repeat133

2206688822069693CL1HSLINE/L13437329 ( L1HS_3_14c )

2206969222072804+L1HSLINE/L130646176

2207318722073315CMLT1HLTR/MaLR533406

2207340422073481CMLT1H2LTR/MaLR16184

2207362222073874+MIRbSINE/MIR14262

2207401022074309CAluSxSINE/Alu2961

2207449122074521+(TGAA)nSimple_repeat333

2207511322075135+AT_richLow_complexity123

2207517622075197+AT_richLow_complexity122

2207581622075885CMER5BDNA/MER1_type744

2207596322076050CCharlie2DNA/MER1_type263176

2207607722076177CCharlie2DNA/MER1_type1105

2207618022076259+L2LINE/L233023387

2207626022076829+MLT2B2LTR/ERVL1515

2207683022076860+L2LINE/L233883419

2207719522077229+AT_richLow_complexity135

2207740322077456+AT_richLow_complexity154

2207761322077635+(TTAAA)nSimple_repeat426

2207781622078127+L2LINE/L226262965

2207816822078487+L2LINE/L231273415

2207854322078851CAluJbSINE/Alu2911

Ortholog in Chimp22610755-22611218MinusNscore 0.00

N positions

2260181722602300+L3LINE/CR137484243

2260241522602639+MIRSINE/MIR11262

2260381022603922CL2LINE/L234073288

2260395222604264+MLT1F2LTR/MaLR4381

2260426922604416CL2LINE/L219511803

2260475222604778+(CAAAAA)nSimple_repeat430

2260487922605144CL2LINE/L217521458

2260526622605336+AluSp/qSINE/Alu226296

2260533722605398CL1M2LINE/L143264264

2260543022605609CL1M3LINE/L151304938

2260712722607147+AT_richLow_complexity121

2260741122609319CL1MA8LINE/L162894313

2260932022609635+AluSqSINE/Alu1317

2260963622610453CL1MA8LINE/L143123559

2261045422610753+AluJoSINE/Alu1305

2261075422610966CL1MA8LINE/L135583376

2261108922611152+AT_richLow_complexity164

2261159822611726CMLT1HLTR/MaLR533406

2261181522611915CMLT1H2LTR/MaLR16165

2261203922612266+MIRbSINE/MIR27248

2261241522612713CAluSxSINE/Alu2951

2261289522612925+(TGAA)nSimple_repeat333

2261351722613539+AT_richLow_complexity123

2261358022613601+AT_richLow_complexity122

2261422022614289CMER5BDNA/MER1_type744

2261436722614454CCharlie2DNA/MER1_type263176

2261448122614581CCharlie2DNA/MER1_type1105

2261458422614663+L2LINE/L233023387

2261466422615233+MLT2B2LTR/ERVL1515

2261523422615264+L2LINE/L233883419

2261559922615633+AT_richLow_complexity135

2261619622616505+L2LINE/L226262965

2261654922616861+L2LINE/L231303415

2261691722617218CAluJbSINE/Alu2911

2261744622617958+MLT1F1LTR/MaLR1567

2261801022618148+MIRbSINE/MIR89229

2261847622618903+LTR16ALTR/ERVL13450

2261891222619111CERVL-B4LTR/ERVL930727

2261928222619776+L1MA7LINE/L156296119

2261984222619965+MIRSINE/MIR1126

______

L1HS_3_17c25715952-25718569C_INTER_RMD_M_DISRUPTED

2571137025711583CL1PREC2LINE/L146844481

2571161925711889+AluJbSINE/Alu24293

2571245225712533+MIRSINE/MIR54138

2571262725712934CAluJbSINE/Alu3071

2571308725713107+AT_richLow_complexity121

2571330825713524CMIRbSINE/MIR24910

2571362125713702+GA-richLow_complexity381

2571474125715218CL1PA3LINE/L161545677 (R2)

2571523125715252+AT_richLow_complexity122

2571531525715468CERVL-ELTR/ERVL52765122

2571550025715921CERVL-ELTR/ERVL50324590

2571595225718569CL1HSLINE/L161553538 ( L1HS_3_17c ) (R1)

2572046625720773+AluSxSINE/Alu1309

2572136025721402+AT_richLow_complexity143

2572143525721547+L1ME4aLINE/L159786100

2572156725721605+AT_richLow_complexity139

2572187825722037CMIRbSINE/MIR25885

2572252925722729+L2LINE/L232253419

2572355425723641CMIRmSINE/MIR247156

2572364425723741CL2LINE/L219841887

2572399425724078+MIR3SINE/MIR70159

2572408025724260CMER5ADNA/MER1_type1898

2572540225725432+(T)nSimple_repeat131

2572561725726320+L1ME3BLINE/L152175976

2572640325726679+AluJbSINE/Alu1306

2572669225726874+THE1CLTR/MaLR1183

2572687525727157CAluSxSINE/Alu2951

2572715825727346+THE1CLTR/MaLR184375

Ortholog in Chimp26317977-26320115MinusNscore 0.00

N positions

2631412826314350CL1PREC2LINE/L146904465

2631437326314643+AluJbSINE/Alu24293

2631520626315287+MIRSINE/MIR54138

2631538226315694CAluJbSINE/Alu3121

2631584726315867+AT_richLow_complexity121

2631606826316281CMIRbSINE/MIR24914

2631638126316462+GA-richLow_complexity384

2631750026320115CL1PA3LINE/L161543538 (R12)

2632201826322321+AluSxSINE/Alu1305

2632290826322950+AT_richLow_complexity143

2632298326323095+L1ME4aLINE/L159786100

2632310626323153+AT_richLow_complexity148

2632342726323585CMIRbSINE/MIR25785

2632407726324277+L2LINE/L232253419

2632519126325288CL2LINE/L219841887

2632553426325625+MIR3SINE/MIR73159

2632562726325807CMER5ADNA/MER1_type1898

2632694226326963+(TTTA)nSimple_repeat223

2632715026327856+L1ME3BLINE/L152175976

2632793926328219+AluJbSINE/Alu1310

2632822626328408+THE1CLTR/MaLR1182

2632840926328690CAluSxSINE/Alu2952

2632869126328880+THE1CLTR/MaLR183375

______

L1HS_3_20c29124607-29128608M_INTRA_RMD

2912036429120583CMER58ADNA/MER1_type2221

2912114129121161+AT_richLow_complexity121

2912212229122328+MIRSINE/MIR1208

2912234529122484CMER5A1DNA/MER1_type1461

2912253229122576+(CAT)nSimple_repeat145

2912276429122891+L2LINE/L223262460

2912330529123954+L1M1LINE/L143074955

2912395529123994+(TC)nSimple_repeat140

2912399529124608+L1M1LINE/L149565607

2912460729128608CL1HSLINE/L140242 ( L1HS_3_20c )

2912861529128711CL1MEcLINE/L115461450

2912877929129448CHAL1LINE/L11344640

2912956529129886CHAL1LINE/L141783

2912989329130196+AluSxSINE/Alu1302

2913059229130645+(TG)nSimple_repeat154

2913134629131591CMIRSINE/MIR2625

2913260729132875+AluSgSINE/Alu14292

2913289129132913+AT_richLow_complexity123

2913297629133271+MLT1A0LTR/MaLR1326

2913361229133796CLTR33ALTR/ERVL496299

Ortholog in Chimp29782380-29788390MinusNscore 0.00

N positions

2977813929778358CMER58ADNA/MER1_type2221

2977891529778935+AT_richLow_complexity121

2977989429780103+MIRSINE/MIR1218

2978010429780256CMER5A1DNA/MER1_type1591

2978025729780315+THER1_MDSINE/MIR219274

2978039529780458+L2LINE/L232773341

2978078129780804+(A)nSimple_repeat124

2978108229782381+L1MA4LINE/L143075607

2978238029784999CL1PA3LINE/L141471528

2978499529787017+L1PA3LINE/L141326155

2978702129787410+L1MA4LINE/L155955991

2978742229787447+AT_richLow_complexity126

2978757829789226CHAL1LINE/L12393640

2978934329789664CHAL1LINE/L141783

2978967129789975+AluSxSINE/Alu1307

2979037329790418+(TG)nSimple_repeat146

2979111929791361CMIRSINE/MIR2628

2979238029792651+AluSgSINE/Alu14295

2979266529792687+AT_richLow_complexity123

2979275029793045+MLT1A0LTR/MaLR1326

2979338329793471CLTR33ALTR/ERVL496393

______

L1HS_3_24c36637972-36641523C_INTRA_RMD

3663433936634515CMIRbSINE/MIR19714

3663547036635695CMER46CDNA/MER2_type330100

3663714236637402CL1PA5LINE/L161545894

3663742436637492+Tigger1DNA/MER2_type23512418

3663797236641523CL1HSLINE/L161542621 ( L1HS_3_24c ) (R1,R2)

3664156036641641+L1MC4LINE/L179558037

3664178036641925+MIRbSINE/MIR101236

3664423236644269+GA-richLow_complexity138

3664454136644671+AluJbSINE/Alu179311

3664468436644726+(GAAA)nSimple_repeat242

Ortholog in Chimp37462401-37462886MinusNscore 0.00

N positions

3745756137457659+(TA)nSimple_repeat297

3745871637458953CMIRbSINE/MIR26413

3745991637460129CMER46CDNA/MER2_type317100

3746158037461849CL1PA5LINE/L161545887

3746186137461929+Tigger1DNA/MER2_type23512418

3746239737462754CL1PA3LINE/L161555837 (R12)

3746275937462898CL1P1LINE/L127492611 (R12)

3746292337463004+L1MC4LINE/L179558037

3746314337463288+MIRbSINE/MIR101236

3746559437465631+GA-richLow_complexity138

3746590337466032+AluJbSINE/Alu179312

3746604637466092+(GAAA)nSimple_repeat246

______

L1HS_3_5498842962-98846616M_INTRA_RMD

9883402498834112+L2LINE/L232913377

9883561898835839+MIRSINE/MIR13262

9883608898836397+LTR16ALTR/ERVL52379

9883639798836703CCharlie1aDNA/MER1_type33442

9883692598837366+L1MB8LINE/L157156178

9883754998837674CMIRbSINE/MIR262115

9883851298838534+AT_richLow_complexity123

9883992298839943+AT_richLow_complexity122

9884113198841154+AT_richLow_complexity124

9884201898842329+AluSpSINE/Alu1298

9884235998842637CL2LINE/L227792502

9884296298846616+L1HSLINE/L113661 ( L1HS_3_54 ) (R12)

9884661798847212+L1PA2LINE/L155596155 (R12)

9884795298848006CCharlie7DNA/MER1_type9738

9884810398848747CMER70BLTR/ERVL5781

9885061198850959CTHE1BLTR/MaLR3633

9885129998851326+(CA)nSimple_repeat128

9885228698852409+AluSg/xSINE/Alu178301

9885301498853038+AT_richLow_complexity125

9885337698853613CL1PA16LINE/L161635924

9885415298854445+MLT1LLTR/MaLR314615

9885467298855821+L1MA9LINE/L151146311

Ortholog in Chimp101503376-101508555PlusNscore 0.39

N positions 101503886-101503895; 101504930-101504939;

101494430101494518+L2LINE/L232913377

101496028101496249+MIRSINE/MIR13262

101496418101496493CLTR16ALTR/ERVL445364

101496497101496806+LTR16ALTR/ERVL52379

101496806101497113CCharlie1aDNA/MER1_type33442

101497335101497776+L1MB8LINE/L157156178

101497955101498076CTHER1_MDSINE/MIR273127

101498924101498946+AT_richLow_complexity123

101500330101500351+AT_richLow_complexity122

101501538101501561+AT_richLow_complexity124

101501878101501907+AT_richLow_complexity130

101502425101502742+AluSpSINE/Alu1299

101502772101503050CL2LINE/L227792502

101503377101503901+L1PtLINE/L12520 (R1,R2)

101503903101504929+L1PtLINE/L113512377 (R1,R2)

101504942101509144+L1PA2LINE/L118236032 (R1,R2)

101509886101509940CCharlie7DNA/MER1_type9738

101510037101510676CMER70BLTR/ERVL5781

101512541101512889CTHE1BLTR/MaLR3633

101514209101514340+AluSg/xSINE/Alu178309

101514945101514969+AT_richLow_complexity125

101515307101515543CL1PA16LINE/L161635924

101516136101516429+MLT1LLTR/MaLR314615

101516663101517812+L1MA9LINE/L151146311

______

L1HS_3_57104434312-104435487M_DISRUPTED

104421983104428010+L1PA2LINE/L146032

104430325104430656CMLT1CLTR/MaLR3544

104430910104430961+AT_richLow_complexity152

104431063104431298CMIRSINE/MIR2395

104431354104431383+AT_richLow_complexity130

104434173104434311+AluYSINE/Alu1138

104434312104435487+L1HSLINE/L117862961 ( L1HS_3_57 ) (R1)

104435488104435796+AluYSINE/Alu1307 (D)

104435797104438873+L1PA2LINE/L130856155 (R2)

104438883104439059+AluYSINE/Alu127303

104440589104441054CLTR40bLTR/ERVL4623

104441811104441845+AT_richLow_complexity135

104442215104442346CCharlie8DNA/MER1_type271139

104444037104444621CMER77LTR/ERVL6071

Ortholog in Chimp107247821-107248983PlusNscore 0.00

N positions

107239052107239072+AT_richLow_complexity121

107239080107239588CL2LINE/L234192878

107240299107240369+A-richLow_complexity274

107240440107241063+HAL1bLINE/L17421394

107243841107244166CMLT1CLTR/MaLR3544

107244420107244471+AT_richLow_complexity152

107244576107244808CMIRSINE/MIR2365

107244864107244893+AT_richLow_complexity130

107247682107247820+AluYSINE/Alu1138

107247821107252062+L1PA3LINE/L119096155 (R)

107252066107252246+AluYSINE/Alu127307

107253777107254236CLTR40bLTR/ERVL4623

107254992107255027+AT_richLow_complexity136

107257217107257801CMER77LTR/ERVL6071

______

L1HS_3_83133338444-133343287M_INTRA_RMD

133328875133330099+L1PA3LINE/L149296155

133330175133330423+MLT1HLTR/MaLR23262

133330486133330621+MLT1HLTR/MaLR410542

133330754133331201+MLT2B2LTR/ERVL3514

133332122133332333CMIRbSINE/MIR25340

133332874133333048CMIRbSINE/MIR25845

133333776133334318+L1ME3BLINE/L153535888

133336710133336835+L1MB8LINE/L160446167

133336854133336880+AT_richLow_complexity127

133336939133337151+MIRbSINE/MIR41253

133338147133338355+L1ME4aLINE/L155755804

133338444133343287+L1HSLINE/L1424892 ( L1HS_3_83 ) (R12)

133343288133343603+AluYa5SINE/Alu1310 (D)

133343604133344755+L1PA3LINE/L150166152 (R12)

133344868133344896+AT_richLow_complexity129

133345490133345524+(A)nSimple_repeat135

133345559133345714+L1ME4aLINE/L159576120

133345734133346009+AluScSINE/Alu34302

133346011133346328+AluSgSINE/Alu1317

133346678133346790CL2LINE/L233453233

133346791133347015CMER20DNA/MER1_type2191

133347016133347281CL2LINE/L232322942

133347443133347902+MLT1J1LTR/MaLR2444

133348707133348826CMER112DNA/MER1_type19674

133348836133349581+L1ME2LINE/L153016113

133349883133349966CMIRbSINE/MIR197118

133350914133351052+MIRbSINE/MIR77215

133351153133351257CL2LINE/L234183309

133351366133351699+LTR16ALTR/ERVL97428

133351700133352065+MLT2DLTR/ERVL1360

133352087133352139+(TC)nSimple_repeat153

133352140133352178+(TG)nSimple_repeat240

Ortholog in Chimp136680168-136686781PlusNscore 0.15

N positions 136683001-136683010;

136670599136671824+L1PA3LINE/L149296154

136671990136672136+MLT1HLTR/MaLR108249

136672477136672922+MLT2B2LTR/ERVL3514

136673842136674053CMIRbSINE/MIR25340

136674599136674813CMIRbSINE/MIR2589

136675502136676044+L1ME3BLINE/L153535888

136677958136678035CL2LINE/L231623083

136678435136678560+L1MB8LINE/L160446167

136678579136678605+AT_richLow_complexity127

136678664136678876+MIRbSINE/MIR41253

136679872136680079+L1ME4aLINE/L155755804

136680167136683000+L1PtLINE/L1412878 (R) (BROKEN DUE TO Ns)

136683011136687931+L1PA3LINE/L111046029 (R) (Overlap at Ns)

136688044136688072+AT_richLow_complexity129

136688668136688689+(A)nSimple_repeat122

136688729136688829+L1ME4aLINE/L159576055

136688904136689195+AluScSINE/Alu34318

136689197136689502+AluSgSINE/Alu1307

136689885136689963CL2LINE/L233083233

136689964136690188CMER20DNA/MER1_type2191

136690189136690454CL2LINE/L232322942

136690616136691075+MLT1J1LTR/MaLR2444

136691880136692026CMER112DNA/MER1_type19648

136692027136692788+L1ME2LINE/L153196294

136693071136693202CMIRbSINE/MIR19842

136694098136694236+MIRbSINE/MIR77215

136694337136694441CL2LINE/L234183309

136694550136694883+LTR16ALTR/ERVL97428

136694884136695236+MLT2DLTR/ERVL1349

136695302136695326+(TG)nSimple_repeat226

136695443136695725+MER45BDNA/Tip1001308

136695723136695780+MER45BDNA/Tip100251308

136695778136696143+MER45BDNA/Tip100251607

______

L1HS_3_88c136203780-136207508M_INTRA_RMD

136197368136197470CL1ME4aLINE/L161015985

136197720136198018CAluJbSINE/Alu3051

136198025136198364CL1ME4aLINE/L156645313

136198839136199105CHAL1bLINE/L1988711

136200295136200341+L2LINE/L232993345

136203267136203458CL1MC4aLINE/L158985703

136203460136203681+L1MB4LINE/L156505869

136203689136203779+MSTALTR/MaLR1100

136203780136207508CL1HSLINE/L1373010 ( L1HS_3_88c ) (R12)

136207509136207740+THE1DLTR/MaLR146381

136207743136208035+L1MB4LINE/L158696179

136208091136208210+FLAM_ASINE/Alu11130

136208220136208499CL1MC4aLINE/L157095409

136209213136209439CL3LINE/CR137363512

136209759136209980CMIRSINE/MIR26213

136210660136210749CMER5BDNA/MER1_type17783

136210804136210881CMER5BDNA/MER1_type761

136211422136211732CHAL1bLINE/L119901648

136211801136211974CHAL1bLINE/L115111321

Ortholog in Chimp139591280-139597362MinusNscore 0.00

N positions

139584872139584977CL1ME4aLINE/L161015985

139585131139585225CL1MCLINE/L157495658

139585226139585524CAluJbSINE/Alu3051

139585531139585869CL1M5LINE/L156645313

139585964139586250CL1M5LINE/L151554860

139586334139586610CHAL1bLINE/L11002711

139587795139587855+L2LINE/L232993363

139590767139590958CL1MC4aLINE/L158985703

139590960139591181+L1MB4LINE/L156505869

139591189139591335+THE1DLTR/MaLR1168

139591345139597362CL1PA3LINE/L1603210 (R1,R2)

139597363139597594+THE1DLTR/MaLR146381

139597597139597889+L1MB4LINE/L158696179

139597945139598064+FLAM_ASINE/Alu11130

139598074139598351CL1MC4aLINE/L157095409

139599066139599296CL3LINE/CR137363512

139599459139599520+L3LINE/CR122072268

139599616139599838CMIRSINE/MIR26213

139600518139600608CMER5BDNA/MER1_type17783

139600663139600740CMER5BDNA/MER1_type761

139601278139601588CHAL1bLINE/L119901648

139601657139601829CHAL1bLINE/L115111321

139601838139601935CMER5A1DNA/MER1_type16074

139601936139602239CAluSqSINE/Alu3061

139602240139602313CMER5A1DNA/MER1_type737

139602414139602740CHAL1bLINE/L11251958

139605770139605837+LTR67LTR/ERVL490557

139605942139606055CL2LINE/L234143235

______

L1HS_3_118189836527-189837415M_INTRA_RMD

189827412189827578CArthur1DNA/Tip10037853597

189827581189831676+L1PA11LINE/L124616701

189831129189831184CMADE1DNA/Mariner8025

189831692189831868CArthur1DNA/Tip10036093431

189831902189832525CArthur1DNA/Tip10074135

189832791189832910CL2LINE/L231843064

189834752189834920CMIRmSINE/MIR27684

189834921189835444+MER1ADNA/MER1_type1529

189835445189835471CMIRmSINE/MIR8360

189835606189835628+AT_richLow_complexity123

189836239189836294+L2LINE/L233203374

189836527189837415+L1HSLINE/L13889 ( L1HS_3_118 ) (R12)

189837418189840995+L1PA3LINE/L125616137 (R12)

189840996189841020+(TAA)nSimple_repeat327

189843137189843433+AluSpSINE/Alu1298

189843600189843755CMIR3SINE/MIR20238

189844608189844785CL2LINE/L231582973

189845372189845603+MIRbSINE/MIR29267

189845616189845692CL3LINE/CR143664280

189845818189846030CL3LINE/CR141773951

Ortholog in Chimp194235028-194237447PlusNscore 0.00

N positions

194225824194226088CArthur1DNA/Tip10038503597

194226091194230183+L1PA11LINE/L124616701

194229637194229692CMADE1DNA/Mariner8025

194230198194230370CArthur1DNA/Tip10036093431

194230404194231027CArthur1DNA/Tip10074135

194231293194231412CL2LINE/L231843064

194233253194233421CMIRmSINE/MIR27684

194233422194233945+MER1ADNA/MER1_type1529

194233946194233972CMIRmSINE/MIR8360

194234107194234129+AT_richLow_complexity123

194234719194234786+MIRSINE/MIR184256

194235028194241022+L1PA3LINE/L136014 (R1,R2)

194241023194241044+(TAA)nSimple_repeat324

194243155194243459+AluSpSINE/Alu1306

194243626194243754CMIR3SINE/MIR20267

194244634194244811CL2LINE/L231582973

194245393194245624+MIRbSINE/MIR29267

194245637194245709CL3LINE/CR143664284

194245793194246044CL3LINE/CR142333951

194246306194246336+(A)nSimple_repeat131

______

L1HS_4_4c13275194-13275977M_INTRA_RMD

1326861413268953+MER113DNA/MER1_type49416

1326895413269218+AluYSINE/Alu30294

1326921913269309+MER113DNA/MER1_type417511

1326931213269602+AluJbSINE/Alu1288

1326971813269826CMIR3SINE/MIR20282

1326985113269899+(TG)nSimple_repeat250

1327107113271160CMIRSINE/MIR261166

1327173613271873CMIRbSINE/MIR21583

1327194713271974+(TTA)nSimple_repeat330

1327197513275190CL1PA3LINE/L161372919 (R12)

1327519413275977CL1HSLINE/L17853 ( L1HS_4_4c ) (R12)

1327606913276432CMLT1A0LTR/MaLR3651

1327644013277080CMLT1A0-intLTR/MaLR1727880

1327708713277599+LTR3B_LTR/ERVK1492

1327766813278507CMLT1A0-intLTR/MaLR8452

1327850813278879CMLT1A0LTR/MaLR3631

1327897213278999+AT_richLow_complexity128

1327900213279137CMIRSINE/MIR14510

1327998413280286CAluYSINE/Alu3011

1328036013280381CMIRbSINE/MIR262245

1328038213280739CMLT1A0LTR/MaLR3651

Ortholog in Chimp13519378-13522161MinusNscore 0.00

N positions

1351341313513481+MER113DNA/MER1_type417489

1351350613513806+AluJbSINE/Alu1298

1351391213514020CMIR3SINE/MIR20282

1351404513514093+(TG)nSimple_repeat250

1351477913514827+L2LINE/L233693417

1351487213515028+MIRSINE/MIR34193

1351505113515159CL2LINE/L233783243

1351526513515354CMIRSINE/MIR261166

1351593013516067CMIRbSINE/MIR21583

1351614113516162+(TTA)nSimple_repeat324

1351616313522161CL1PA3LINE/L160143 (R1,R2)

1352225313522616CMLT1A0LTR/MaLR3651

1352262413523264CMLT1A0-intLTR/MaLR1727880

1352327113523783+LTR3B_LTR/ERVK1492

1352391713524391CMLT1A0-intLTR/MaLR801303

1352442113524782CMLT1A0LTR/MaLR3531

1352490513525040CMIRSINE/MIR14510

1352558413525755CL2LINE/L231672989

1352588513526191CAluYSINE/Alu3051

1352626513526286CMIRbSINE/MIR262245

1352628713526644CMLT1A0LTR/MaLR3651

______

L1HS_4_513409700-13411042M_INTRA_RMD

1340463813405125CCharlie1bDNA/MER1_type5232

1340514113405296+MIRSINE/MIR65244

1340551213405705CMIRbSINE/MIR2113

1340629813406539CMIRbSINE/MIR2542

1340696213406995+AT_richLow_complexity134

1340738213407549CMIRbSINE/MIR19614

1340858013408841+GA-richLow_complexity1259

1340925513409565CL4LINE/RTE17151417

1340970013411042+L1HSLINE/L111334 ( L1HS_4_5 ) (R12)

1341103113415298+L1PA3LINE/L119016168 (R12)

1341567013415954CAluScSINE/Alu30420

1341614513416312CMER5ADNA/MER1_type18621

1341633113416420CL4LINE/RTE13681268

1341643113416542CMIRbSINE/MIR265162

1341659113416724CMIRSINE/MIR16821

1341683213417007CMER58ADNA/MER1_type22447

1341726513417402+L2LINE/L227422891

1341825613418514+L2LINE/L231203358

Ortholog in Chimp13672242-13674030PlusNscore 0.00

N positions

1366724613667734CCharlie1bDNA/MER1_type5232

1366775013667922+MIRSINE/MIR65272

1366813313668314CMIRbSINE/MIR1993

1366890713669147CMIRbSINE/MIR2542

1366957013669591+AT_richLow_complexity122

1366970113669728+(T)nSimple_repeat128

1367112013671383+GA-richLow_complexity1261

1367179713672107CL4LINE/RTE17151417

1367224213678285+L1PA3LINE/L116045 (R1,R2)

1367840613678427+AT_richLow_complexity122

1367867213678961CAluScSINE/Alu30920

1367915413679319CMER5ADNA/MER1_type18421

1367933813679427CL4LINE/RTE13681268

1367944113679553CMIRSINE/MIR258152

1367959813679726CMIRbSINE/MIR17221

1367974913679806CL4LINE/RTE12181162

1367983413680009CMER58ADNA/MER1_type22447

1368027413680411+L2LINE/L227422891

1368152313682028+(TA)nSimple_repeat1511

______

L1HS_4_5170564317-70567872C_INTRA_RMD

7055810570558785CLTR12DLTR/ERV16873

7055878670561025+L1PBaLINE/L18573356

7056102670561074+(TAGA)nSimple_repeat452

7056107570561194+L1PBaLINE/L133573489

7056119370562034CL1P2LINE/L188827

7056202270564314+L1P2LINE/L18893191

7056431770567872+L1HSLINE/L123559 ( L1HS_4_51 ) (R1,R2)

7056813670568193+L1MCLINE/L144014458

7056882970570087+L1MA1LINE/L1171272

7057008870570396+AluJbSINE/Alu1309

7057039770574608+L1MA1LINE/L112735378

Ortholog in Chimp60959220-60962534MinusNscore 2.41

N positions 60961648-60961727;

6095248960956702CL1MA1LINE/L153781273

6095670360957012CAluJbSINE/Alu3101

6095701360958270CL1MA1LINE/L1127217

6095922260961609CL1PtLINE/L135571148 (R12)

6096172860962534CL1PtLINE/L18092 (R12)

6096253760963133CL1P1LINE/L131912595

6096319560964100CL1P1LINE/L123041396

6096446560965157CL1P2LINE/L11604889

6096514560965986+L1P2LINE/L127888

6096598560966104CL1PBaLINE/L134913372

6096610560966150+(TCTA)nSimple_repeat348

6096615160968388CL1PBaLINE/L13371857

6096838960969069+LTR12DLTR/ERV13686

______

L1HS_4_52c70915703-70919982M_INTRA_RMD

7090769670907840+MER5A1DNA/MER1_type9157

7090823070908250+AT_richLow_complexity121

7090903670909436CMER92ALTR/ERV13991

7091011770910475CL1PB1LINE/L168676509

7091047670910544+(TA)nSimple_repeat169

7091054570914128CL1PB1LINE/L165082906

7091412970914444CAluScSINE/Alu2811

7091444570915703CL1PB1LINE/L129051563

7091570370919982CL1HSLINE/L142801 ( L1HS_4_52c )

7092006170920218CMIRbSINE/MIR19530

7092026470920744CMLT1DLTR/MaLR5021

7092167270922926+L1PA4LINE/L149306152

7092371070924244CL2LINE/L234142802

7092497670925061+AT_richLow_complexity186

7092525870925371+L2LINE/L222452361

7092571170925792+GA-richLow_complexity182

7092654970926841+AluJoSINE/Alu6293

7092720670927228+AT_richLow_complexity123

7092737570927583CL1PA8LINE/L161715954

7092766070927838CMER5ADNA/MER1_type1831

Ortholog in Chimp60593498-60600888PlusNscore 0.00

N positions

6058569060585868+MER5ADNA/MER1_type1183

6058594560586153+L1PA8LINE/L159546171

6058629560586317+AT_richLow_complexity123

6058668260586972CAluJoSINE/Alu2936

6058705660587125+T-richLow_complexity269

6058772660587807+CT-richLow_complexity182

6058814760588257CL2LINE/L223562245

6058850960588538+AT_richLow_complexity130

6058927260589804+L2LINE/L228023414

6059058960591810CL1PA4LINE/L161524930

6059253160592646CL3LINE/CR144854366

6059273760593218+MLT1DLTR/MaLR1502

6059326460593464+MIRbSINE/MIR30243

6059349860599515+L1PA3LINE/L116032

6059979960599969CMIRbSINE/MIR24559

6060000260600042+(TG)nSimple_repeat242

6060030160600363+(TA)nSimple_repeat162

6060054060600719+L1PB1LINE/L13439

6060071860602148+L1PB1LINE/L113932905

6060214960602470+AluScSINE/Alu1285

6060247160606070+L1PB1LINE/L129066508

6060607160606219+(TA)nSimple_repeat2150

6060622060606413+L1PB1LINE/L165096730

6060651060606793+L1PB1LINE/L165846867

6060748360607556+MER92ALTR/ERV1174

6060757660607976+MER92ALTR/ERV11399

6060876660608786+AT_richLow_complexity121

6060917760609321CMER5A1DNA/MER1_type1579

______

L1HS_4_5982293934-82295070C_INTER_RMD_M_DISRUPTED

8228478982285431CL1PA5LINE/L161515509

8228614382286225+LTR33LTR/ERVL192

8228681482287000CL2LINE/L234113230

8228704382287165CMER94DNA/AcHobo1341

8228789082287959+MIR3SINE/MIR93170

8228796082288174+L1MC5LINE/L176387860

8228820382288238+AT_richLow_complexity136

8228962782289761+MER104DNA/Tc218162

8229025482290343+(CAGAGA)nSimple_repeat292

8229147182291499+AT_richLow_complexity129

8229290182292925+AT_richLow_complexity125

8229351082293617CMIR3SINE/MIR20186

8229393482295070+L1HSLINE/L131137 ( L1HS_4_59 ) (R1)

8229507182295375+AluYa5SINE/Alu1301 (D)

8229537682300322+L1PA3LINE/L111386054 (R2)

8230154082302147CMLT1E2LTR/MaLR6251

8230227482302419+MIRbSINE/MIR119263

8230247482302796+MLT1J1LTR/MaLR58471

8230358282303720CCharlie9DNA/MER1_type26592528

8230404282304081+(CA)nSimple_repeat241

Ortholog in Chimp49246821-49247947MinusNscore 0.00 (49241166-49247947 - Nscore 0.15)

N positions

4923776949237907+Charlie9DNA/MER1_type25282659

4923837949238449+MIRmSINE/MIR108181

4923869149239015CMLT1J1LTR/MaLR47358

4923906949239215CMIRbSINE/MIR264119

4923934249239949+MLT1E2LTR/MaLR1625

4924116649242424CL1PA3LINE/L161774892

4924245749247947CL1P1LINE/L154983 (R BROKEN DUE TO Ns)

4924831149248371+L3LINE/CR144224486

4924895649248980+AT_richLow_complexity125

4925009549250128+AT_richLow_complexity134

4925153749251626+(TCTCTG)nSimple_repeat292

4925211949252253CMER104DNA/Tc216218

4925364149253676+AT_richLow_complexity136

4925370549253919CL1MC5LINE/L178607638

4925392049253989CMIR3SINE/MIR17093

4925471449254836+MER94DNA/AcHobo1134

4925487949255065+L2LINE/L232303411

4925565449255736CLTR33LTR/ERVL921

4925644849257090+L1PA5LINE/L155096151

______

L1HS_4_84c111550299-111552050C_DISRUPTED_M_INTER_RMD

111544803111545232CTigger2aDNA/MER2_type4342

111545834111546453+MER4ALTR/ERV11625

111546455111550299CL1PA2LINE/L161552309

111550299111552050CL1HSLINE/L117564 ( L1HS_4_84c )

111552058111552113+MER4ALTR/ERV1609664

111553245111553302+MIRbSINE/MIR201260

111553311111553733CMLT1E2LTR/MaLR618146

111553777111554193CMLT1CLTR/MaLR46786

111554194111554501CAluSxSINE/Alu3121

111554502111554555CMLT1CLTR/MaLR8536

111555367111555535+MIRbSINE/MIR27198

111555625111555645+AT_richLow_complexity121

111555801111555846CtRNA-Gln-CAGtRNA461

111555911111556211CAluJoSINE/Alu3061

111556614111556867+AluYSINE/Alu39302

Ortholog in Chimp113857858-113859756MinusNscore 6.79

N positions 113858597-113858724; 113858525-113858525;

113851877113852184CAluSgSINE/Alu3091

113852255113852392CMIRbSINE/MIR21271

113853117113853546CTigger2aDNA/MER2_type4342

113854148113854766+MER4ALTR/ERV11624

113854767113854863CL1PtLINE/L161536056

113855310113855662+L1ME3BLINE/L155475916

113855746113857062CL1PA5LINE/L161414824

113857537113857858CL1PA5LINE/L126302309

113857858113859756CL1PA5LINE/L118794 (OCCUPIED)

113859764113859819+MER4ALTR/ERV1609664

113860088113860146+L3_MarsLINE/CR130333098

113860955113861010+MIRSINE/MIR200257

113861018113861440CMLT1E2LTR/MaLR618146

113861484113861898CMLT1CLTR/MaLR46786

113861899113862206CAluSxSINE/Alu3121

113862207113862260CMLT1CLTR/MaLR8536

113865341113865651CAluYSINE/Alu3111

______

L1HS_4_114147803889-147804215C_INTER_RMD_M_DISRUPTED

147795751147795788+GC_richLow_complexity138

147797462147797546+(TA)nSimple_repeat286

147797547147797572+(TG)nSimple_repeat228

147798137147798385+MER112DNA/MER1_type10261

147798711147799004CL1PA16LINE/L161655858

147799086147799248+L2LINE/L232273408

147799513147799849+L4LINE/RTE15101871

147799887147800130+MIRbSINE/MIR9265

147803253147803289+CT-richLow_complexity339

147803397147803445+AT_richLow_complexity149

147803675147803811CMIR3SINE/MIR20455

147803889147804215+L1HSLINE/L11327 ( L1HS_4_114 ) (R1)

147804216147804524+AluYa5SINE/Alu1309 (D)

147804525147810242+L1PA3LINE/L13286032 (R2)

147811081147811224CL1ME4aLINE/L161195959

147811225147811542CAluSxSINE/Alu3021

147811543147811722CL1ME4aLINE/L159585768

147811759147811856CFLAM_ASINE/Alu11013

147812215147812417+MLT1KLTR/MaLR218417

147812439147812535+GA-richLow_complexity194

Ortholog in Chimp150706845-150707155PlusNscore 0.00

N positions

150698592150698629+GC_richLow_complexity138

150700475150700511+(TA)nSimple_repeat238

150701089150701339+MER112DNA/MER1_type8261

150701661150701955CL1PA16LINE/L161665858

150702037150702199+L2LINE/L232273408

150702464150702672+L4LINE/RTE15101738

150702838150703081+MIRbSINE/MIR9265

150706211150706247+CT-richLow_complexity339

150706631150706767CMIR3SINE/MIR20455

150706845150709686+L1PtLINE/L112843 (R) BROKEN DUE TO Ns

150709681150714057+L1PA3LINE/L114276032 (R) OVERLAP AT Ns

150714905150715050CL1ME4aLINE/L161215970

150715051150715371CAluSxSINE/Alu3051

150715372150715551CL1ME4aLINE/L159695768

150715552150715683CFLAM_ASINE/Alu14013

______

L1HS_4_129168008182-168009360M_INTRA_RMD

168002082168002348+MLT2DLTR/ERVL1293

168002349168002373+(TCTG)nSimple_repeat226

168002382168002475+(TA)nSimple_repeat295

168002477168002561+MLT2B3LTR/ERVL479555

168003537168003921CMER7ADNA/MER2_type3462

168005374168005407+(TA)nSimple_repeat134

168007105168007154CMADE1DNA/Mariner7734

168007309168008050CL1MB2LINE/L161685421

168008182168009360+L1HSLINE/L131180 ( L1HS_4_129 ) (R12)

168009361168010031+L1PA3LINE/L154806150 (R12)

168010064168010330+MER72LTR/ERV148329

168010321168010494+MER72LTR/ERV1546722

168011327168011626+AluSxSINE/Alu1301

168011727168011804+MADE2DNA/Mariner180

168012627168012799+LTR29LTR/ERV12195

168012858168012923+LTR49LTR/ERV1522591

168013432168013606CMER5ADNA/MER1_type16710

Ortholog in Chimp171182353-171187702PlusNscore 0.00

N positions

171176274171176540+MLT2DLTR/ERVL1293

171176541171176565+(TCTG)nSimple_repeat226

171176620171176638+RickshaDNA/MuDR848863

171176639171176692+(TCTA)nSimple_repeat154

171176693171176734+RickshaDNA/MuDR864906

171177711171177966CTigger3(Golem)DNA/MER2_type30282771

171177964171178103CTigger3(Golem)DNA/MER2_type1422

171179548171179577+(TA)nSimple_repeat130

171181481171182222CL1MB2LINE/L161685421

171182223171182243+AT_richLow_complexity121

171182353171188376+L1PA3LINE/L136032 (R1,R2)

171188389171188655+MER72LTR/ERV148329

171188646171188819+MER72LTR/ERV1546722

171189649171189951+AluSxSINE/Alu1304

171190052171190129+MADE2DNA/Mariner180

171190950171191122+LTR29LTR/ERV12195

171191181171191246+LTR49LTR/ERV1522591

171191756171191936CMER5ADNA/MER1_type16710

171191937171192014CL2LINE/L233723290

171192031171192088+L1MA6LINE/L158475911

171192119171192518+L1MA6LINE/L158946296

171192538171192823+AluScSINE/Alu1286

171192825171192935+(TCTA)nSimple_repeat4114

171194161171194230+MIRmSINE/MIR205275

171194990171195369+MER7ADNA/MER2_type1331

______

L1HS_4_130c168506431-168507287C_INTER_RMD_M_DISRUPTED

168497339168497642+AluSgSINE/Alu1302

168497686168498525+L1MCcLINE/L118332753

168498536168498691+FRAMSINE/Alu1156

168498711168499078+Tigger5bDNA/MER2_type22418

168499227168499630+L1MCcLINE/L129283341

168499691168499808CAluJbSINE/Alu1181

168499809168499856+L1MCcLINE/L134303482

168500210168500592CMSTALTR/MaLR4281

168500680168501238CL1PA16LINE/L161575593

168501243168506404CL1PA3LINE/L16032858 (R2)

168506405168506430+(ATG)nSimple_repeat126 (D)

168506431168507287CL1HSLINE/L18572 ( L1HS_4_130c ) (R1)

168507287168508598CL1PA16LINE/L156084332

168509114168509167+AT_richLow_complexity154

168509324168509618CAluSgSINE/Alu2971

168509835168510096CAluYSINE/Alu29940

168510563168510818+Tigger7DNA/MER2_type1267

168510818168510914+Tigger7DNA/MER2_type23942490

168511304168511347CL1P5LINE/L156865643

168511348168511445+L1PB1LINE/L160526150

168511784168511854+AluYSINE/Alu234304

168511858168511913+L1ME4aLINE/L160636118

168511925168512043+L1M5LINE/L133313450

168512187168512225CTigger1DNA/MER2_type22382208

168512226168512524+AluSgSINE/Alu1303

168512525168513222CTigger1DNA/MER2_type22071524

168513288168513312+AT_richLow_complexity125

168513369168513419+L1M1LINE/L137043754

168513418168513929CL1MEcLINE/L127602241

168513931168514132CL1MEcLINE/L122342033

168514195168514322+(TA)nSimple_repeat1129

168514440168514557CL1MEcLINE/L113621246

168514652168514808CL1MEcLINE/L11034873

168514798168515593+L1M3LINE/L123903077

168515594168515617+(TAAAA)nSimple_repeat225

168515618168516847+L1M3LINE/L130784329

Ortholog in Chimp171691526-171692393MinusNscore 0.00 (17686135-171692393 Nscore -27)

N positions

171682410171682768CMLT1DLTR/MaLR505132

171682796171683098+AluSgSINE/Alu1301

171683142171683980+L1MCcLINE/L118332753

171683991171684146+FRAMSINE/Alu1156

171684166171684534+Tigger5bDNA/MER2_type22418

171684682171685066+L1MCcLINE/L129343303

171685145171685262CAluJbSINE/Alu1181

171685263171685310+L1MCcLINE/L134303482

171685664171686047CMSTALTR/MaLR4281

171686135171686630CL1PA16LINE/L161575659 (R)

171687457171689877CL1P1LINE/L153962927 (R) BROKEN DUE TO Ns

171690794171692393CL1PtLINE/L116012 (R)

171692393171693704CL1PA16LINE/L156084332

171694220171694273+AT_richLow_complexity154

171694430171694724CAluSgSINE/Alu2971

171694936171695196CAluYSINE/Alu29940

171695658171695913+Tigger7DNA/MER2_type1267

171695913171696009+Tigger7DNA/MER2_type23942490

171696398171696441CL1P5LINE/L156865643

171696442171696539+L1PB1LINE/L160526150

171696877171696938+AluSINE/Alu234295

171696942171696997+L1ME4aLINE/L160636118

171697009171697127+L1M5LINE/L133313450

171697271171697309CTigger1DNA/MER2_type22382208

171697310171697608+AluSgSINE/Alu1303

171697609171698307CTigger1DNA/MER2_type22071524

171698373171698397+AT_richLow_complexity125

171698454171698504+L1P3LINE/L137043754

171698503171699014CL1MEcLINE/L127602241

171699016171699217CL1MEcLINE/L122342033

171699280171699409+(TA)nSimple_repeat1131

171699528171699647CL1MEcLINE/L113621244

171699740171699896CL1MEcLINE/L11034873

171699868171700686+L1P4LINE/L123753071

171700687171700710+(TAAAA)nSimple_repeat225

171700711171701918+L1M2LINE/L130684317

______

L1HS_4_134177849935-177850260C_INTER_RMD_M_DISRUPTED

177840798177841103+AluSxSINE/Alu1306

177841188177841221+AT_richLow_complexity134

177842886177843172CAluSxSINE/Alu2883

177844224177844731CL2LINE/L222021616

177846397177846617CL1ME4aLINE/L158845663

177846726177846801+CT-richLow_complexity377

177846928177847123CL1MC4aLINE/L168156618

177848493177848633CL1MC4aLINE/L160045849

177849060177849184+Charlie9DNA/MER1_type1123

177849935177850260+L1HSLINE/L12326 ( L1HS_4_134 ) (R1)

177850261177850577+AluYa5SINE/Alu1317 (D)

177850578177856277+L1PA3LINE/L13276014 (R2)

177856278177856315+(TAA)nSimple_repeat340

177856548177856579+(CATATA)nSimple_repeat334

177856591177857034CL1MA9LINE/L163125827

177858283177858573+AluSxSINE/Alu1295

177859083177859428+L1MC2LINE/L159766344

Ortholog in Chimp181177517-181177827PlusNscore 0.00 (181177517-181184605 Nscore 5.78)

N positions

181168392181168693+AluSxSINE/Alu1303

181168778181168812+AT_richLow_complexity135

181170475181170760CAluSxSINE/Alu2884

181171811181172305CL2LINE/L222021632

181173982181174203CL1ME4aLINE/L158855663

181174312181174391+CT-richLow_complexity381

181174518181174720CL1MC4aLINE/L168156605

181176069181176212CL1MC4aLINE/L160045849

181176642181176766+Charlie9DNA/MER1_type1123

181177517181180702+L1PtLINE/L123162 (R) (BROKEN DUE TO Ns)

181180691181184605+L1PA3LINE/L122326137 (R) (OVERLAP AT Ns)

181184606181184643+(TAA)nSimple_repeat340

181184878181184909+(TA)nSimple_repeat132

181184921181185366CL1MA9LINE/L163125825

181186614181186905+AluSxSINE/Alu1296

______

L1HS_5_5266081868-66085803M_INTRA_RMD

6607263166072977+L2LINE/L229713370

6607297866073167CMER58ADNA/MER1_type2241

6607400366074032+AT_richLow_complexity130

6607457566074785+L2LINE/L230133243

6607540066075429+AT_richLow_complexity130

6607558966075692+CT-richLow_complexity3106

6607604266076444CMSTALTR/MaLR4281

6607660566076808CMIRbSINE/MIR24813

6607734366077456+L2LINE/L232573410

6607755566077745+MIR3SINE/MIR16208

6607794666078104+MIRbSINE/MIR5175

6607868266078729+(TG)nSimple_repeat249

6607930966079477CMER20DNA/MER1_type21929

6607974966079884+L2LINE/L232883419

6607996466080061+CT-richLow_complexity198

6608006266080371CAluScSINE/Alu3091

6608047166080563CL4LINE/RTE14291334

6608096666081179CL4LINE/RTE1004790

6608120666081388CMIRSINE/MIR25867

6608186866085803+L1HSLINE/L113934 ( L1HS_5_52 ) (R12)

6608606766086104+AT_richLow_complexity138

6608617666086910CL2LINE/L234192500

6608722966087415CL1MA8LINE/L162886091

6608909766089166CL4LINE/RTE19541889

6608953766089647CL4LINE/RTE16211510

6608995566090001+AT_richLow_complexity147

6609000266090164CFRAMSINE/Alu1631

6609017766090377CL4LINE/RTE1036851

6609086666091080CMER112DNA/MER1_type2401

6609162866091661CL1ME2LINE/L161536126

6609166266091710+(TTTA)nSimple_repeat250

6609171166091997CAluScSINE/Alu2821

6609199866092305CL1ME2LINE/L161255827

6609230566092327CL1ME2LINE/L156105593

6609232866092557+L1MA5ALINE/L160636296

6609255866092846CL1ME2LINE/L155925305

6609452266094776CMIRSINE/MIR2621

Ortholog in Chimp48901404-48908030MinusNscore 2.57

N positions 48904385-48904544; 48902987-48902996;

4889242948892683+MIRSINE/MIR1262

4889435848894646+L1ME2LINE/L153055592

4889464748894879CL1MA5ALINE/L162966058

4889488048894893+L1ME2LINE/L155935606

4889489748895204+L1ME2LINE/L158276125

4889520548895526+AluScSINE/Alu1317

4889552748895558+L1ME2LINE/L161266153

4889610648896310+MER112DNA/MER1_type1223

4889680948897009+L4LINE/RTE8511036

4889702248897184+FRAMSINE/Alu1163

4889718548897231+AT_richLow_complexity147

4889753948897649+L4LINE/RTE15101621

4889781548898000CL1MC4LINE/L180167803

4889800648898075+L4LINE/RTE18891954

4889977448899974+L1MA8LINE/L160766288

4890029548901031+L2LINE/L225003419

4890146448902986CL1PA2LINE/L161534630 (R1,R2) (Overlap at Ns)

4890300148904309CL1P1LINE/L152583915 (R1,R2) (Broken due to Ns)

4890454548908030CL1PtLINE/L134951 (R1,R2)

4890848648908697+MIRSINE/MIR51260

4890933348909425+L4LINE/RTE13341429

4890952548909839+AluScSINE/Alu1309

4890984048909858+(GGAA)nSimple_repeat119

4890985948910036+(GGGA)nSimple_repeat1178

4891003748910080+(GGAA)nSimple_repeat446

4891016048910295CL2LINE/L234193288

4891052548910735+MER20DNA/MER1_type1219

4891132048911339+(CA)nSimple_repeat221

4891191748912061CMIRbSINE/MIR17519

4891227648912446CMIR3SINE/MIR20834

4891321348913416+MIRbSINE/MIR13248

4891358048913982+MSTALTR/MaLR1428

4891433248914435+GA-richLow_complexity3106

4891459548914624+AT_richLow_complexity130

4891523048915440CL2LINE/L232433013

4891598348916012+AT_richLow_complexity130

4891684848917037+MER58ADNA/MER1_type1224

______

L1HS_5_54c77916886-77917213C_INTER_RMD_M_DISRUPTED

7790759377907893+AluYSINE/Alu1301

7790834177908403CL1PA15LINE/L161656103

7790892977908979CL3bLINE/CR143934342

7791016577910200+(CA)nSimple_repeat136

7791081277910853+GA-richLow_complexity142

7791092177916574CL1PA3LINE/L16032328 (R2)

7791657577916885CAluYa5SINE/Alu3101 (D)

7791688677917213CL1HSLINE/L13271 ( L1HS_5_54c ) (R1)

7791726977917292+(CAT)nSimple_repeat326

7791729677917419CMIRbSINE/MIR253129

7791742077917445+(TTGGGG)nSimple_repeat227

7791744677917496CMIRbSINE/MIR12871

7791776577917870+MIRbSINE/MIR96201

7791975177919914CFRAMSINE/Alu1591

7791999877920097+MIRSINE/MIR37135

7792027677920406+MIRSINE/MIR97230

7792055777920712CMIRbSINE/MIR1997

7792076877921062+AluScSINE/Alu1295

7792129677921432+L2LINE/L232393378

7792178177921806+(CAA)nSimple_repeat227

7792425077924276+(CA)nSimple_repeat228

7792430777924333+(CA)nSimple_repeat228

7792444277924607+L1MB3LINE/L160006181

7792559877925714CMIRSINE/MIR19461

7792591277925943+MIRSINE/MIR77108

Ortholog in Chimp37241511-37241822PlusNscore 0.00

N positions

3723292437232955CMIRSINE/MIR10877

3723311737233333+MIRSINE/MIR2271

3723426037234425CL1MB3LINE/L161816000

3723690737236929+(TTG)nSimple_repeat224

3723727837237414CL2LINE/L233783239

3723764837237950CAluScSINE/Alu3031

3723800637238161+MIRbSINE/MIR7199

3723827837238437CMIRbSINE/MIR274104

3723861637238715CMIRSINE/MIR13537

3723880037238965+FRAMSINE/Alu1166

3724084837240953CMIRbSINE/MIR20196

3724122237241272+MIRbSINE/MIR70127

3724127337241298+(CCCCAA)nSimple_repeat227

3724129937241422+MIRbSINE/MIR128252

3724144837241475+(GGA)nSimple_repeat229

3724151137246779+L1PtLINE/L115272 (R)

3724679037247526+L1PtLINE/L15071241 (DISRUPTED IN CHIMP AS WELL)

3724753737248328+L1PA3LINE/L153626155 (R)

3724839337248434+CT-richLow_complexity142

3724904637249077+(TG)nSimple_repeat132

3725026237250312+L3bLINE/CR143424393

______

L1HS_5_93c161890327-161891261M_INTRA_RMD

161881102161881412CL1MA4ALINE/L162995984

161881415161882530CL1M2LINE/L140262908

161882531161882553+(TTTG)nSimple_repeat224

161882554161882877CL1M2LINE/L129072585

161882878161883176CAluYSINE/Alu2991

161883177161885911CL1M2LINE/L1258413

161885919161885944+AT_richLow_complexity126

161885945161886066CAluYSINE/Alu1221

161886179161886485CAluSxSINE/Alu2971

161886872161887046CMIRbSINE/MIR20126

161887972161888194+MIRbSINE/MIR23252

161888434161888755CL2LINE/L234063025

161889081161889328+L1M4bLINE/L146304

161889414161889605+L1M4bLINE/L1762947

161890099161890324+L1M4bLINE/L112051449

161890327161891261CL1HSLINE/L19374 ( L1HS_5_93c )

161891262161892684+L1M3LINE/L126244076

161892685161892999+AluSgSINE/Alu1308

161893000161893054+L1M3LINE/L140774091

161893055161893430CL1MA5ALINE/L162875912

161893431161893926+L1M3LINE/L140924598

161893924161894487+L1M4LINE/L138164487

161894547161894697CL1M5LINE/L153795217

161894740161894817+L2LINE/L229473032

161894818161895106+AluYSINE/Alu1305

161895107161895477+L2LINE/L230333410

Ortholog in Chimp164654248-164660125MinusNscore 1.70

N positions 164655385-164655484;

164645008164645318CL1MA4ALINE/L162995984

164645321164646791CL1M2LINE/L140262585

164646792164647090CAluYSINE/Alu2991

164647091164649817CL1M2LINE/L1258413

164649840164649969CAluYSINE/Alu1301

164650083164650391CAluSxSINE/Alu3001

164650657164650769CMER117DNA/MER1_type16955

164650802164650976CMIRbSINE/MIR20126

164651902164652124+MIRbSINE/MIR23252

164652360164652681CL2LINE/L234063025

164653007164653254+L1M4bLINE/L146304

164653340164653531+L1M4bLINE/L1762947

164654022164654264+L1M4bLINE/L112051467

164654307164654633+L1M4bLINE/L115873495

164654635164655382CL1PA2LINE/L160325284

164655485164660125CL1PA2LINE/L146464

164660126164661553+L1M4bLINE/L134844936

164661554164661871+AluSgSINE/Alu1310

164661872164661914+L1M4bLINE/L149374956

164661915164662303CL1MA5ALINE/L162945911

164662304164662798+L1M4bLINE/L149575458

164662796164663189+L1M4LINE/L138164230

164663209164663359+L1M4LINE/L143344487

164663611164663689+L2LINE/L229463032

164663690164663959+AluYSINE/Alu1295

164663960164664331+L2LINE/L230333410

______

L1HS_6_19c50719695-50724460C_INTER_RMD_M_DISRUPTED

5071055450711127+L1MCcLINE/L151226930

5071113850711283+GA-richLow_complexity1147

5071196550712203CL1MA5LINE/L159455705

5071220450712418+L1MA5LINE/L160836297

5071242250712615+MIRbSINE/MIR60260

5071473750714813CHAL1LINE/L1833757

5071663050716834+MLT1J2LTR/MaLR241448

5071697850717054CMIRbSINE/MIR253183

5071841450718717+L1PB4LINE/L158466153

5071873850719035+AluYSINE/Alu1297

5071930650719679CL1PA6LINE/L161435770 (R2)

5071969550724460CL1HSLINE/L161551427 ( L1HS_6_19c ) (R1)

5072460850724950+THE1BLTR/MaLR5362

5072495350726539+THE1B-intLTR/MaLR11580

5072654050726900+THE1BLTR/MaLR1361

5072693350727909CL2LINE/L21225223

5073016050730302+L3bLINE/CR141094261

5073055750730973+MSTBLTR/MaLR4426

5073111250731344CMLT1J1LTR/MaLR432205

5073217850732206+(TTTTTG)nSimple_repeat231

5073227450732334+L2LINE/L233503419

5073339250733491CL2LINE/L233643260

Ortholog in Chimp51790403-51794773MinusNscore 0.00

N positions

5178097751781437+L1MCcLINE/L151235508

5178143451781549+L1MA9LINE/L160236135

5178156051781701+GA-richLow_complexity1143

5178238351782621CL1MA5LINE/L159455705

5178262251782836+L1MA5LINE/L160836297

5178284051783033+MIRbSINE/MIR60260

5178543851785514CHAL1LINE/L1833757

5178733351787537+MLT1J2LTR/MaLR241448

5178768151787757CMIRbSINE/MIR253183

5178914351789439+L1PB4LINE/L158516153

5178946151789758+AluYSINE/Alu1297

5179003051794773CL1PA6LINE/L161421427 (R12)

5179492151795263+THE1BLTR/MaLR5362

5179526751796853+THE1B-intLTR/MaLR21580

5179685451797213+THE1BLTR/MaLR1361

5179724651798265CL2LINE/L21225178

5180047451800616+L3bLINE/CR141094261

5180087151801286+MSTBLTR/MaLR4426

5180142551801657CMLT1J1LTR/MaLR432205

5180257051802630+L2LINE/L233503419

5180368851803787CL2LINE/L233643260

______

L1HS_6_3875251034-75255225C_INTER_RMD_M_DISRUPTED

7524191675242367+L1PA13LINE/L157086159

7524237175242395+AT_richLow_complexity125

7524255875242632+L2LINE/L233003378

7524267575243050CL2LINE/L234193026

7524338675243483+L2LINE/L232763405

7524373975243779+AT_richLow_complexity141

7524457375244776+MIRSINE/MIR15253

7524495775245168+L2LINE/L231673402

7524527275245326+AT_richLow_complexity155

7524596675246139CHSAT4Satellite/centr1781

7524671875247363+MER82DNA/MER2_type6652

7524749175247514+AT_richLow_complexity124

7524770575247752+AT_richLow_complexity148

7524840775248535CMIRSINE/MIR17014

7524878675248823+(TG)nSimple_repeat239

7524910675249327CMLT1BLTR/MaLR344137

7524933075250437CL1MC1LINE/L164725412

7525043975250726CL1MC1LINE/L139073597

7525070375250966CL1MC1LINE/L115881305

7525096875251064+L1HSLINE/L1298

7525103475255225+L1HSLINE/L15784792 ( L1HS_6_38 ) (R1)

7525523775256021+SVAOther6311422 (D)

7525602275257275+L1PA3LINE/L149066155 (R2)

7525727675258582CL1MC1LINE/L113181

7526023575260275+(TAGA)nSimple_repeat445

7526047275260832CL1ME3ALINE/L161445756

7526090675261133+(TA)nSimple_repeat1231

7526114075261574CL1ME3ALINE/L153614927

7526157375264191CL1PA5LINE/L161543557

7526419075264448CL1ME3ALINE/L149124655

Ortholog in Chimp75328425-75332666PlusNscore 0.00

N positions

7531931475319765+L1PA13LINE/L157086159

7531976975319793+AT_richLow_complexity125

7531995675320030+L2LINE/L233003378

7532007375320448CL2LINE/L234193029

7532078075320877+L2LINE/L232763405

7532113375321173+AT_richLow_complexity141

7532196775322169+MIRSINE/MIR15253

7532234975322560+L2LINE/L231663402

7532266475322722+AT_richLow_complexity159

7532323975323361CL1MEcLINE/L119061772

7532336275323535CHSAT4Satellite/centr1781

7532411875324763+MER82DNA/MER2_type6652

7532488675324909+AT_richLow_complexity124

7532510075325146+AT_richLow_complexity147

7532580375325931CMIRSINE/MIR17014

7532618075326215+(TG)nSimple_repeat237

7532647675326499+(T)nSimple_repeat124

7532650075326724CMLT1BLTR/MaLR344137

7532672775327833CL1MC1LINE/L164725412

7532783575328117CL1MC1LINE/L139073597

7532811675328357CL1MC1LINE/L115611305

7532836075328455+L1PtLINE/L1398

7532845075333911+L1PA3LINE/L16166032 (R)

7533391675335228CL1MC1LINE/L113161

7533687575336915+(TAGA)nSimple_repeat445

7533711275337464CL1ME3ALINE/L148494469

7533748275337586+(TATG)nSimple_repeat3108

7533759375337768+(TA)nSimple_repeat1177

7533777575338206CL1ME3ALINE/L140663632

7533820575340780CL1PA5LINE/L161543557

7534077975341029CL1ME3ALINE/L136173359

7534103875341151CL1MB1LINE/L161636044

7534136875345986CL1PA2LINE/L160321358

______

L1HS_6_4179549565-79552974C_INTER_RMD_M_DISRUPTED

7954057079541416+HAL1LINE/L19931920

7954161779542065CLTR16BLTR/ERVL46428

7954223779542257+AT_richLow_complexity121

7954345379543692CMLT1JLTR/MaLR2554

7954428979544342+AT_richLow_complexity154

7954476679544800+AT_richLow_complexity135

7954560279545912CL3LINE/CR122921958

7954613779546227CMIRSINE/MIR262172

7954688279549075+L1PBa1LINE/L112237

7954907379549563+L1PBa1LINE/L130183508

7954956579552974+L1HSLINE/L123413 ( L1HS_6_41 )

7955297279553040+L1M5LINE/L143244371

7955304179553685CL1PA8LINE/L161625519

7955368679554524+L1M5LINE/L143725280

7955452579554571CMLT2FLTR/ERVL563517

7955457279554649+(TA)nSimple_repeat279

7955465079554861CMLT2FLTR/ERVL616376

7955489079555345CMLT1CLTR/MaLR4679

7955535479555661CMLT2FLTR/ERVL3271

7955566279555883+L1M5LINE/L152855501

7955603079556530+MLT1DLTR/MaLR7505

7955681979556947+AluJoSINE/Alu2130

7955696279559065+L1PA13LINE/L140476156

7955906679559221+AluJoSINE/Alu129293

7955928279559591CAluSxSINE/Alu3092

7956005379560114+MER91CDNA/Tip10040105

7956039079560768CL1PREC2LINE/L157215340

7956077279561566+L1PA3LINE/L153586152

7956157579561718CL1PA13LINE/L159705826

7956172079562057+MER1BDNA/MER1_type1331

Ortholog in Chimp79777832-79778610PlusNscore 0.00

N positions

7976883379769679+HAL1LINE/L19931920

7976988079770328CLTR16BLTR/ERVL46428

7977050079770520+AT_richLow_complexity121

7977171579771954CMLT1JLTR/MaLR2554

7977255179772604+AT_richLow_complexity154

7977383179774180CL3LINE/CR122271849

7977440479774494CMIRSINE/MIR262172

7977514979777342+L1PBa1LINE/L162487

7977734079777831+L1PBa1LINE/L132683759

7977783179778605+L1PtLINE/L11772

7977860879778989CL1PA8LINE/L159005519

7977899179779836+L1MDLINE/L143575280

7977983779780139CMLT2FLTR/ERVL663374

7978016879780623CMLT1CLTR/MaLR4679

7978063279780939CMLT2FLTR/ERVL3271

7978094079781161+L1M5LINE/L152855501

7978130879781808+MLT1DLTR/MaLR7505

7978181079781963CMIR_MarsSINE/MIR1692

7978209779782225+AluJoSINE/Alu2130

7978224079784343+L1PA13LINE/L140476156

7978434479784499+AluJoSINE/Alu129293

7978456279784874CAluSxSINE/Alu3122

7978533679785397+MER91CDNA/Tip10040105

7978567379785946CL1PREC2LINE/L157215447

7978649579786585CL1PLINE/L160495956

7978658479787396+L1PA3LINE/L153406152

7978740579787548CL1PLINE/L159705826

7978755079787887+MER1BDNA/MER1_type1331

______

L1HS_6_71117244380-117246108C_INTER_RMD_M_DISRUPTED

117235506117235694CMER58CDNA/MER1_type2151

117235822117235866+T-richLow_complexity145

117235881117235944+MIRbSINE/MIR874

117236764117236962+L2LINE/L228333037

117238059117238147+L2LINE/L233303418

117238264117238391+L2LINE/L229313082

117238410117238432+AT_richLow_complexity123

117238578117238658+AT_richLow_complexity181

117238668117240498+L1MA4ALINE/L110922896

117240498117242623+L1PA6LINE/L140246154

117242625117243056+L1MA4ALINE/L128783308

117243057117243345+AluSxSINE/Alu1289

117243346117243688+L1MA4ALINE/L133093655

117243693117243936CMSTALTR/MaLR428184

117243939117244310CMSTA-intLTR/MaLR16511274

117244380117246108+L1HSLINE/L111735 ( L1HS_6_71 ) (R1)

117246109117246418+AluYa5SINE/Alu1310 (D)

117246419117250728+L1PA2LINE/L117366031 (R2)

117250748117250777+(A)nSimple_repeat130

117250778117250943CMSTA-intLTR/MaLR723534

117250944117250969+(TTTG)nSimple_repeat228

117250970117251505CMSTA-intLTR/MaLR5331

117251506117251922CMSTALTR/MaLR4281

117251923117255206+L1MA4ALINE/L136557002

Ortholog in Chimp118793866-118795582PlusNscore 0.00 (118793866-118799869 Nscore 8.31)

N positions

118784844118784907+MIRbSINE/MIR874

118785727118786019+L2LINE/L228333165

118787239118787327+L2LINE/L233303418

118787927118787953+AT_richLow_complexity127

118788095118788175+AT_richLow_complexity181

118788185118790008+L1MA4ALINE/L110922896

118790008118792110+L1PA6LINE/L140246154

118792112118792543+L1MA4ALINE/L128783308

118792544118792832+AluSxSINE/Alu1289

118792833118793175+L1MA4ALINE/L133093655

118793180118793423CMSTALTR/MaLR428184

118793426118793796CMSTA-intLTR/MaLR16511274

118793866118798663+L1PtLINE/L114805 (R)

118799167118799869+L1PA2LINE/L154536154 (R) BROKEN DUE TO Ns

118799888118799907+(A)nSimple_repeat120

118799908118800631CMSTA-intLTR/MaLR7231

118800632118801048CMSTALTR/MaLR4281

118801049118804331+L1MA4ALINE/L136557002

118804410118804517+L2LINE/L233023412

______

L1HS_7_19c43421104-43423176M_INTRA_RMD

4341205243412488+LTR47BLTR/ERVL1443

4341276043413040+AluSxSINE/Alu1290

4341455743414831+AluJbSINE/Alu33304

4341492943415070+MIRbSINE/MIR2140

4341582943415947CMIRbSINE/MIR1293

4341631343416661CMLT1ALTR/MaLR3351

4341667943418549CL1MEbLINE/L135601698

4341855043418584+(TTTA)nSimple_repeat236

4341858843421102CL1PA2LINE/L161443630 (R12)

4342110443423176CL1HSLINE/L120763 ( L1HS_7_19c ) (R12)

4342317843423473CAluSqSINE/Alu2971

4342347443423705CL1MEbLINE/L116181402

4342370643423827+FLAM_ASINE/Alu1123

4342382843424005CL1MEbLINE/L114011232

4342400643424444CMLT1CLTR/MaLR4671

4342444543425442CL1MEbLINE/L11231156

4342567243425835+L1M5LINE/L138263989

4342583643426424CLTR10CLTR/ERV15911

Ortholog in Chimp40791320-40794823PlusNscore 0.00

N positions

4078808140788669+LTR10CLTR/ERV11591

4078867040788830CL1M5LINE/L139893829

4078906340790060+L1MEbLINE/L11561231

4079006140790498+MLT1CLTR/MaLR1467

4079049940790667+L1MEbLINE/L112321401

4079066840790789CFLAM_ASINE/Alu1231

4079079040790994+L1MEbLINE/L114021591

4079102240791318+AluSqSINE/Alu1297

4079132040797334+L1PA2LINE/L136021 (R1,R2)

4079733840797368+(TAAA)nSimple_repeat232

4079736940799233+L1MEbLINE/L116983560

4079935740799658+MLT1ALTR/MaLR26335

4080001540800142+MIRbSINE/MIR6129

4080090040801041CMIRbSINE/MIR1402

4080113940801450CAluJbSINE/Alu3041

4080295440803235CAluSqSINE/Alu2921

4080350740803943CLTR47BLTR/ERVL4431

______

L1HS_7_2146826880-46831780C_INTER_RMD_M_DISRUPTED

4681888946818917+AT_richLow_complexity129

4682126946821319+(GAAA)nSimple_repeat252

4682152246821834+AluSqSINE/Alu1312

4682189146821935+AT_richLow_complexity145

4682200146822145CMER5A1DNA/MER1_type1527

4682218746822323+MER58ADNA/MER1_type30167

4682248346822875+MLT1ALTR/MaLR9374

4682309646823179+GA-richLow_complexity281

4682323846823455+L1MC4LINE/L112071421

4682349346823578+MER94DNA/AcHobo49134

4682358146824011+L1MC4LINE/L114981939

4682418446824580CLTR16CLTR/ERVL49181

4682463946824676+(TA)nSimple_repeat239

4682476446824845+L1MDaLINE/L1888

4682484646824904+(TA)nSimple_repeat159

4682490546825910+L1MDaLINE/L1891212

4682591146826879CLTR13ALTR/ERVK9661

4682688046831780+L1HSLINE/L112136545 ( L1HS_7_21 ) (R1)

4683177846832208+L1MDaLINE/L116142076 (R2)

4683223746833223+L1MLINE/L11271161

4683322346833376+L1MLINE/L125302673

4683339546833598+L1PB1LINE/L13200

4683359946837052+L1PB1LINE/L16344462

4683705846837152+L1PB1LINE/L164026519

4683715346837209+(TAGA)nSimple_repeat460

4683721046837554+L1PB1LINE/L165206865

4683755546837588+AT_richLow_complexity134

4683767246837943+L1MLINE/L127142994

4683802146838250+L1MLINE/L154535688

4683825146838961+MER44DDNA/MER2_type1704

4683896246839815+L1MC3LINE/L152716116

4683983746839920CMER34LTR/ERV1537451

4683994246840145+THE1BLTR/MaLR1212

4684015346840496CMER34-intLTR/ERV1968640

4684050246841551+L1MC3LINE/L161377214

Ortholog in Chimp47596826-47597521PlusNscore 0.00

N positions

4759127347591312+(A)nSimple_repeat140

4759151347591827+AluSqSINE/Alu1313

4759190247591944+AT_richLow_complexity143

4759201047592154CMER5A1DNA/MER1_type1527

4759219647592332+MER58ADNA/MER1_type30167

4759249247592884+MLT1ALTR/MaLR9374

4759300447593134+MER58CDNA/MER1_type6132

4759314547593188+(GAA)nSimple_repeat142

4759324747593464+L1MC4LINE/L112071421

4759350247593587+MER94DNA/AcHobo49134

4759359047594020+L1MC4LINE/L114981939

4759419347594595CLTR16CLTR/ERVL49172

4759464547594669+AT_richLow_complexity125

4759474947595856+L1MLINE/L181212

4759585747596825CLTR13ALTR/ERVK9661

4759682647597543+L1MLINE/L112131968 (R12)

4759752747597730+L1PB1LINE/L13200

4759773147601211+L1PB1LINE/L16344462

4760121747601311+L1PB1LINE/L164026519

4760131247601375+(TAGA)nSimple_repeat468

4760137647601721+L1PB1LINE/L165206865

4760172247601757+AT_richLow_complexity136

4760187147602111+L1MLINE/L127222967

4760217047602194+(CA)nSimple_repeat125

4760219547602424+L1MLINE/L154265661

4760242547603135+MER44DDNA/MER2_type1704

4760313647603990+L1MC3LINE/L152716116

4760401247604095CMER34LTR/ERV1537451

4760411747604321+THE1BLTR/MaLR1212

4760432947604672CMER34-intLTR/ERV1968640

4760467847605727+L1MC3LINE/L161377214

4760579247605899+L1MC3LINE/L172017299

4760592347606576+MER21CLTR/ERV1120795

______

L1HS_7_67140106910-140108875C_INTER_RMD_M_DISRUPTED

140097809140097976CMIR3SINE/MIR1993

140098220140098460CCharlie1DNA/MER1_type27592504

140098484140098593CFLAM_ASINE/Alu1197

140098607140098724CCharlie1DNA/MER1_type24832366

140101301140101400CAluSg/xSINE/Alu282183

140101402140101495+L2LINE/L233213414

140103215140103393CL3LINE/CR140103831

140103568140103856CAluScSINE/Alu2891

140104127140104281CL3LINE/CR134683303

140104731140105013CAluJoSINE/Alu29311

140105047140105641CL1ME2LINE/L161535487

140105662140105954CAluSpSINE/Alu2941

140106002140106074CL2LINE/L222092122

140106075140106225CMER5A1DNA/MER1_type1601

140106226140106399CL2LINE/L221211980

140106400140106708+AluSxSINE/Alu1309

140106709140106877CL2LINE/L219791817

140106910140108875+L1HSLINE/L111163083 ( L1HS_7_67 ) (R1)

140108876140109778CSVAOther1386508 (D)

140109779140112719+L1PA3LINE/L132036153 (R2)

140112752140112822CL1MC4LINE/L180017931

140112860140113118CAluJbSINE/Alu2921

140113140140113259CFLAM_CSINE/Alu1223

140113269140113572CAluJbSINE/Alu3041

140113588140113956CL2LINE/L217671338

140114020140114178+MIRSINE/MIR79240

140114394140114510+L1ME4aLINE/L159746099

140114620140114765+MSTB2LTR/MaLR1185

140114766140115065CAluJoSINE/Alu2961

140115066140115342+MSTB2LTR/MaLR186456

140115352140115646CAluSxSINE/Alu2941

140115819140115973CL1MC4aLINE/L158935723

140116007140116141CAluJbSINE/Alu1363

140116310140116421CL1MC4aLINE/L155215405

140116923140117228+AluSxSINE/Alu1311

140117468140117760CAluJbSINE/Alu2973

Ortholog in Chimp141421553-141423507PlusNscore 0.00 (141421553-141426103 - Nscore 16.3)

N positions

141412459141412626CMIR3SINE/MIR1993

141412870141413131CCharlie1DNA/MER1_type27592491

141413132141413247CFLAM_ASINE/Alu1191

141413248141413372CCharlie1DNA/MER1_type24902366

141415953141416052CAluSg/xSINE/Alu282183

141416054141416147+L2LINE/L233213414

141416748141416822CL2LINE/L217101632

141417839141418046CL3LINE/CR139633756

141418221141418509CAluScSINE/Alu2891

141418780141418934CL3LINE/CR133933228

141419382141419664CAluJoSINE/Alu29311

141419698141420288CL1ME2LINE/L161535487

141420309141420601CAluSpSINE/Alu2941

141420629141420721CL2LINE/L222282122

141420722141420872CMER5A1DNA/MER1_type1601

141420873141421046CL2LINE/L221211980

141421047141421351+AluSxSINE/Alu1304

141421352141421520CL2LINE/L219791817

141421553141424433+L1PtLINE/L111173994 (R)

141425379141426103+L1PA3LINE/L154156153 (R) - BROKEN DUE TO Ns

141426136141426206CL1MC4LINE/L180017931

141426245141426499CAluJbSINE/Alu2914

141426524141426643CFLAM_CSINE/Alu1223

141426653141426956CAluJbSINE/Alu3041

141426972141427340CL2LINE/L217671338

141427404141427562+MIRSINE/MIR79240

141427778141427894+L1ME4aLINE/L159746099

141428003141428148+MSTB2LTR/MaLR1185

141428149141428448CAluJoSINE/Alu2961

141428449141428706+MSTB2LTR/MaLR186452

141428757141428966+MIRSINE/MIR28240

141429182141429298+L1ME4aLINE/L159746099

141429407141429552+MSTB2LTR/MaLR1185

141429553141429853CAluJoSINE/Alu2961

141429854141430130+MSTB2LTR/MaLR186456

141430140141430436CAluSxSINE/Alu2961

141430610141430763CL1ME3BLINE/L158945725

141430797141430931CAluJbSINE/Alu1363

141431100141431211CL1ME3BLINE/L155215405

141431709141432016+AluSxSINE/Alu1311

141432259141432551CAluJbSINE/Alu2973

______

L1HS_7_73144889523-144892621C_DISRUPTED_M_INTER_RMD

144883301144883656CL1ME3BLINE/L153855027

144884223144884596+MLT2C1LTR/ERVL1397

144884664144884869CHAL1LINE/L11054844

144885344144885877CL1MA8LINE/L162915769

144885879144886493CL1M3eLINE/L16385

144887193144889526CL1PA3LINE/L161553824

144889523144892621+L1HSLINE/L15943697 ( L1HS_7_73 )

144892971144892991+AT_richLow_complexity121

144893526144893822CAluSgSINE/Alu2971

144894215144894254+AT_richLow_complexity140

144894288144894582+L2LINE/L229303251

144894589144894811CMER58ADNA/MER1_type2241

144895983144896569CMLT1E2LTR/MaLR6171

144896815144896842+AT_richLow_complexity128

144896885144897000+FLAM_CSINE/Alu3119

144897002144897029+(TAA)nSimple_repeat331

144897411144897773CMER46BDNA/MER2_type2311

144897782144897909+L3LINE/CR139954133

144898014144898034+AT_richLow_complexity121

144898110144898305CL2LINE/L234123251

Ortholog in Chimp146100140-146103474PlusNscore 0.33

N positions 146102292-146102292; 146102372-146102381;

146093889146094279CL1MLINE/L154265027

146094846146095219+MLT2C1LTR/ERVL1397

146095316146095492CHAL1LINE/L11031844

146095968146096495CL1MA8LINE/L162915769

146096497146097111CL1M3eLINE/L16385

146097812146100143CL1PA3LINE/L161553824

146100140146103474+L1PtLINE/L15953697 (OCCUPIED)

146103826146103846+AT_richLow_complexity121

146104375146104394+(TTA)nSimple_repeat221

146104395146104688CAluSgSINE/Alu2941

146105081146105120+AT_richLow_complexity140

146105154146105405+L2LINE/L229303198

146105455146105677CMER58ADNA/MER1_type2241

146106849146107438CMLT1E2LTR/MaLR6171

146107684146107729+AT_richLow_complexity146

146107754146107869+FLAM_CSINE/Alu3119

146107871146107907+(TAA)nSimple_repeat340

146108289146108651CMER46BDNA/MER2_type2311

146108660146108787+L3LINE/CR139954133

146108895146108915+AT_richLow_complexity121

146108991146109186CL2LINE/L234123251

______

L1HS_8_516572000-16575946M_INTRA_RMD

1656630216566502+MLT1E1ALTR/MaLR27254

1656650316566812CAluJbSINE/Alu3125

1656681316567197+MLT1E1ALTR/MaLR255697

1656721216567334CL2LINE/L221522017

1656771616567744+(CA)nSimple_repeat230

1656790816567949+(CA)nSimple_repeat142

1656913916569247+GA-richLow_complexity2108

1656924916569585CMLT2C1LTR/ERVL3491

1657050416570727+AluJoSINE/Alu12237

1657137316571393+AT_richLow_complexity121

1657160216571719+L1PB3LINE/L160326147

1657174116571911+L1ME4aLINE/L157095887

1657200016575946+L1HSLINE/L123954 ( L1HS_8_5 ) (R12)

1657593716577170+L1PA2LINE/L149216154 (R12)

1657718616577219+AT_richLow_complexity134

1657758516577662+(CA)nSimple_repeat178

1657884716579178CMLT1J2LTR/MaLR3802

1657920616579728+L1ME4aLINE/L152965840

1658044716580659CMIRSINE/MIR23015

1658100116581027+(TG)nSimple_repeat228

1658190816581942+AT_richLow_complexity135

1658241716582535+MER5BDNA/MER1_type4127

Ortholog in Chimp12834553-12839345PlusNscore 0.00

N positions

1282935212829737+MLT1E1ALTR/MaLR255697

1282975212829874CL2LINE/L221522017

1283045412830489+(CA)nSimple_repeat237

1283169612831804+GA-richLow_complexity2108

1283180612832142CMLT2C1LTR/ERVL3491

1283306112833284+AluJoSINE/Alu12237

1283415412834271+L1PB3LINE/L160326147

1283429312834464+L1ME4aLINE/L157095887

1283455312840566+L1PA2LINE/L126032 (R1,R2)

1284057012840603+AT_richLow_complexity134

1284098012841059+(CA)nSimple_repeat180

1284223712842574CMLT1J2LTR/MaLR3252

1284275212842781+AT_richLow_complexity130

1284281512843124+L1ME4aLINE/L155235840

1284381512844053CMIRSINE/MIR27215

1284439512844415+(TG)nSimple_repeat222

1284529612845330+AT_richLow_complexity135

1284580112845919+MER5BDNA/MER1_type4127

1284592012845946+AT_richLow_complexity127

1284670312846948+AluSxSINE/Alu58303

1284696712847433CMLT1CLTR/MaLR4671

1284753812847654+MIRbSINE/MIR92221

1284767412847841CMIR3SINE/MIR1631

1284806512848103+(TG)nSimple_repeat138

______

L1HS_8_1940837918-40839258C_INTER_RMD_M_DISRUPTED

4082884240828965CL1MA5ALINE/L160455929

4082896640829014+L1MD3LINE/L179427988

4082901640829950CCharlie1aDNA/MER1_type1245302

4082995140830255+AluSgSINE/Alu1304

4083025640830519CCharlie1aDNA/MER1_type30151

4083052040830891CMSTBLTR/MaLR4261

4083089240830939CCharlie1aDNA/MER1_type503

4083235640832666CAluJoSINE/Alu2981

4083390640834063+FAMSINE/Alu144

4083413740834832+L1ME2LINE/L154316155

4083613040836165+(CA)nSimple_repeat237

4083666740836820+MIRSINE/MIR4172

4083764140837909+L2LINE/L231163415

4083791840839258+L1HSLINE/L148156154 ( L1HS_8_19 ) (R1)

4083927540839660+L1PA5LINE/L157706154 (R2)

4083966540840303CL2LINE/L230662401

4084060540840727+L2LINE/L232553373

4084228940842462CMIRbSINE/MIR18711

4084346740843546+(CATA)nSimple_repeat484

4084366740843831+L2LINE/L225612765

4084383240844043CMER30DNA/MER1_type2301

4084404440844523+L2LINE/L227663264

4084452440844619+L1PA8LINE/L160776172

4084462040844752+L2LINE/L232653401

4084609040846254+MIRbSINE/MIR34200

4084626840846334+L2LINE/L233063385

4084642240846538CL3bLINE/CR142544132

4084662740847165+MER34C_LTR/ERV11585

Ortholog in Chimp37586064-37587019PlusNscore 0.00

N positions

3757696337577086CL1MA5ALINE/L160455929

3757708737577135+L1MD3LINE/L179427990

3757713737578073CCharlie1aDNA/MER1_type1245302

3757807437578378+AluSgSINE/Alu1304

3757837937578644CCharlie1aDNA/MER1_type30151

3757864537579016CMSTBLTR/MaLR4261

3757901737579064CCharlie1aDNA/MER1_type503

3757973137579756+(CA)nSimple_repeat126

3758048737580798CAluJoSINE/Alu2991

3758203837582200+FAMSINE/Alu149

3758228137582976+L1ME2LINE/L154316155

3758427437584311+(CA)nSimple_repeat239

3758481337584966+MIRbSINE/MIR4176

3758578737586055+L2LINE/L231163415

3758609237587404+L1PA5LINE/L148366153 (R12)

3758740837588045CL2LINE/L230662401

3758834737588458+L2LINE/L232553364

3759003137590204CMIRbSINE/MIR18711

3759120737591282+(CATA)nSimple_repeat480

3759140337591566+L2LINE/L225612765

3759156737591783CMER30DNA/MER1_type2301

3759178437592263+L2LINE/L227663264

3759226437592359+L1PA8LINE/L160776172

3759236037592495+L2LINE/L232653401

3759382137594027+MIRbSINE/MIR23226

3759401137594077+L2LINE/L233063385

3759417437594282CL3bLINE/CR142464132

3759437137594909+MER34C_LTR/ERV11585

______

L1HS_8_3590592964-90595078C_DISRUPTED_M_INTER_RMD

9058694990587009+L1ME3BLINE/L114431504

9058731290587693+L1ME3BLINE/L119802513

9058768590587761+L1ME3BLINE/L148994975

9058780390588820+L1ME3BLINE/L150976161

9058882190589116+AluJoSINE/Alu1296

9058911790589909+L1ME3BLINE/L161657007

9059035990590668+AluYa5SINE/Alu1310

9059069990590872+L2LINE/L229803160

9059095090592968CL1PA3LINE/L161544128

9059296490595078+L1HSLINE/L111713285 ( L1HS_8_35 ) (R12)

9059508390595265+L2LINE/L232413417

9059531590595362+AT_richLow_complexity148

9059653790596560+(T)nSimple_repeat124

9059679890596922CL2LINE/L234173289

9059700490598009+L2LINE/L217532860

9059826990598476CL2LINE/L223242107

9059857090599001+Tigger2aDNA/MER2_type2433

9059924490599396CL1ME3BLINE/L159235767

9059939790599742CMLT1ALTR/MaLR3741

9059974390600207CL1ME3BLINE/L157665283

9060028190600730CMLT1CLTR/MaLR4673

Ortholog in Chimp88297893-88300710PlusNscore 0.39

N positions 88300002-88300011; 88300034-88300034;

8829218288292558+L1ME3BLINE/L119802507

8829255688292632+L1ME3BLINE/L148994975

8829267488293691+L1ME3BLINE/L150976161

8829369288293987+AluJoSINE/Alu1296

8829398888294778+L1ME3BLINE/L161657007

8829525288295412+L2LINE/L229803150

8829550288296045CL1PA3LINE/L161555610

8829640488297897CL1PA3LINE/L156294128

8829789388299944+L1PtLINE/L111723233 (R1)

8830001288300710+L1P1LINE/L127113408 (R2)

8830071588300897+L2LINE/L232413417

8830094788300994+AT_richLow_complexity148

8830211588302141+(TC)nSimple_repeat127

8830217588302207+(TAGA)nSimple_repeat133

8830245788302581CL2LINE/L234173289

8830342888303454+(TC)nSimple_repeat127

8830348888303532+(TAGA)nSimple_repeat145

8830378288303906CL2LINE/L234173289

8830399188304995+L2LINE/L217532860

8830525588305427CL2LINE/L223242142

8830555788305988+Tigger2aDNA/MER2_type2433

8830623188306383CL1ME3BLINE/L159235767

8830638488306729CMLT1ALTR/MaLR3741

______

L1HS_8_50c122411300-122416228M_INTRA_RMD

122407492122407551CL2LINE/L220121953

122407710122408010CAluSqSINE/Alu3021

122409019122409053+AT_richLow_complexity135

122409104122409212+MIR3SINE/MIR83204

122409510122409724+MIRSINE/MIR8238

122410186122410258+LTR33ALTR/ERVL441523

122410347122410435+L2LINE/L231123229

122410436122410737CAluSgSINE/Alu3011

122410738122410928+L2LINE/L232303418

122410930122411058CMIRSINE/MIR242114

122411300122416228CL1HSLINE/L1493213 ( L1HS_8_50c )

122417739122418033CAluSxSINE/Alu3013

122419233122419408CAluJbSINE/Alu311137

122419453122419555+MIR3SINE/MIR54162

122421942122422246CLTR16BLTR/ERVL46498

122422363122423080CL1MA8LINE/L162885563

122423566122423613CMER53DNA12982

122423614122423634+(CAAA)nSimple_repeat121

122423635122423714CMER53DNA812

122424221122424341CL2LINE/L234193293

122424608122424640+AT_richLow_complexity133

122424794122425120CL2LINE/L233783032

Ortholog in Chimp120844736-120852156MinusNscore 0.00

N positions

120840924120840984CL2LINE/L220121952

120841142120841443CAluSqSINE/Alu3021

120841712120841797+L3LINE/CR111031187

120842450120842484+AT_richLow_complexity135

120842535120842643+MIR3SINE/MIR83204

120842949120843155+MIRSINE/MIR16238

120843618120843690+LTR33ALTR/ERVL441523

120843868120844173CAluSgSINE/Alu3051

120844178120844364+L2LINE/L232343419

120844366120844494CMIRSINE/MIR242114

120844650120844771CMIR_MarsSINE/MIR14122

120845381120845408+(CAAAA)nSimple_repeat330

120845885120846015+MIRbSINE/MIR21153

120846051120846100+(CA)nSimple_repeat150

120846113120846142+AT_richLow_complexity130

120846143120852156CL1PA3LINE/L1602913

120853667120853961CAluSxSINE/Alu3013

120855165120855340CAluJbSINE/Alu311137

120855385120855487+MIR3SINE/MIR54162

120857875120858037CLTR16BLTR/ERVL464275

120858296120859013CL1MA8LINE/L162885563

120859575120859644CMER53DNA701

120860151120860271CL2LINE/L234193293

120860539120860571+AT_richLow_complexity133

120860743120861055CL2LINE/L233563032

120861125120861246CL2LINE/L229022768

______

L1HS_9_5c7853205-7857520M_INTRA_RMD

78438237844272CMER31BLTR/ERV14661

78442737844309+(TCCA)nSimple_repeat138

78448267845081CMIRbSINE/MIR2564

78455067845676CMIRbSINE/MIR22248

78457977845982+MER104DNA/Tc23179

78462297846528+AluSqSINE/Alu1302

78469397847097+MIRbSINE/MIR64193

78475167847596+L2LINE/L232823378

78488777849112+MIRbSINE/MIR3239

78491147849152+(TTCA)nSimple_repeat139

78494457849632+MER5ADNA/MER1_type3189

78508487850992CL2LINE/L233783229

78517067851939+MIRSINE/MIR41262

78520207852285+L1M5LINE/L139594228

78522867852643+Charlie3DNA/MER1_type242712

78526447852831+L1M5LINE/L142254432

78528907853195+AluYSINE/Alu1303

78532057857520CL1HSLINE/L14971612 ( L1HS_9_5c ) (5' end of Twin primed L1)

78575057858562+L1PA3LINE/L150956154 (3 ' end)

78586307858755CL1M5LINE/L147424603

78591567859343+MLT1J2LTR/MaLR1209

78595507859757+L1MEdLINE/L110251233

78602427860297+AT_richLow_complexity156

78603447860504+(TA)nSimple_repeat1170

78605147860585+(ATATG)nSimple_repeat475

78606117860716+(TA)nSimple_repeat1110

78622067862276+Charlie9DNA/MER1_type273

78628567863038CMIRbSINE/MIR2001

78637977864111CAluSxSINE/Alu3121

78656497866025+THE1DLTR/MaLR1381

78660287867650+MLT1D-intLTR/MaLR21735

Ortholog in Chimp7984340-7989203MinusNscore 4.26

N positions 7988151-7988357;

79752927975547CMIRbSINE/MIR2564

79756487975668+AT_richLow_complexity121

79759227976131CMIRbSINE/MIR26048

79762527976437+MER104DNA/Tc23179

79766847976982+AluSqSINE/Alu1301

79773947977552+MIRbSINE/MIR64193

79779717978051+L2LINE/L232823378

79800327980263+MIRbSINE/MIR7239

79802657980299+(TTCA)nSimple_repeat135

79805897980755+MER5ADNA/MER1_type3168

79813437981362+(CA)nSimple_repeat221

79819957982139CL2LINE/L233783229

79828537983086+MIRSINE/MIR41262

79831677983432+L1M5LINE/L139594228

79834337983790+Charlie3DNA/MER1_type242712

79837917983977+L1M5LINE/L142254432

79840367984366+AluYSINE/Alu1328

79843727988148CL1PtLINE/L149701151

79883847989203CL1PtLINE/L11467613 (OCCUPIED - complications due to Ns)

79891887990243+L1PA3LINE/L150956153

79903357990467CL1M5LINE/L147184559

79908367991023+MLT1J2LTR/MaLR1209

79912287991437+L1MEdLINE/L110231233

79919227991974+AT_richLow_complexity153

79920007992165+(TA)nSimple_repeat2178

79922117992398+(TATAA)nSimple_repeat1179

79924497992554+(TA)nSimple_repeat1110

79930777993385CAluYSINE/Alu3091

79943517994421+Charlie9DNA/MER1_type273

79950037995189CMIRbSINE/MIR2004

79959497996263CAluSxSINE/Alu3121

79978027998178+THE1DLTR/MaLR1381

79981817999802+MLT1D-intLTR/MaLR21735

______

L1HS_9_2567998937-68001980C_DISRUPTED_M_INTER_RMD

6799304667993138+MER63DDNA/AcHobo3311061

6799318867993455+L2LINE/L228583155

6799345667993787CMLT1DLTR/MaLR50570

6799382767994103+L2LINE/L231513419

6799431967994443CFLAM_CSINE/Alu1251

6799751267997628+MARNADNA/Mariner94220

6799765967997852+MIRbSINE/MIR16228

6799866467998710+(TTCA)nSimple_repeat348

6799893768001980+L1HSLINE/L143047 ( L1HS_9_25 ) (R12)

6800199668003998CCERSatellite20051

Ortholog in Chimp136131508-136145140MinusNscore 1.29

N positions 136136565-136136740;

136123889136127297+CERSatellite13397

136127918136131492+CERSatellite13588

136131508136132412CL1P1LINE/L131702266 (R2)

136132414136133526+L1PA4LINE/L150346147

136133544136133799CL2LINE/L231152800

136133800136134041+AluSxSINE/Alu58300

136134042136134595CL2LINE/L227992213

136135323136135468CL2LINE/L229442799

136136093136136547+L1P1LINE/L149515403

136136755136137952+L1PA3LINE/L149516155

136137964136137984+AT_richLow_complexity121

136139093136139117+AT_richLow_complexity125

136139123136145138CL1PA3LINE/L160276 (R1)

136145367136145413+(TGAA)nSimple_repeat348

136146225136146418CMIRbSINE/MIR22816

136146445136146565CMARNADNA/Mariner22494

136147870136147892+(CA)nSimple_repeat224

136147893136147916+(GA)nSimple_repeat226

136149322136149347+(A)nSimple_repeat126

136149646136149769+FLAM_CSINE/Alu2125

136149985136150261CL2LINE/L234193151

136150301136150563+MLT1DLTR/MaLR70347

136150566136150632+MLT1E2LTR/MaLR560626

136150633136150735CL2LINE/L231553052

136150950136151042CMER63DNA/AcHobo1061957

______

L1HS_9_44105039589-105043574M_INTRA_RMD

105034132105034187+L1MB5LINE/L161186173

105034675105034699+(T)nSimple_repeat125

105035510105035551+L2LINE/L229412984

105035552105035585+(TTTA)nSimple_repeat235

105035594105035852CAluSxSINE/Alu2601

105035853105035942+L2LINE/L229903075

105036068105036370CAluSxSINE/Alu3051

105036748105036885CL2LINE/L232453106

105036886105037190+AluSgSINE/Alu1303

105037191105037852CL2LINE/L231052393

105038475105038500+(TG)nSimple_repeat126

105038947105039051CL2LINE/L223732275

105039361105039584+L1PA13LINE/L158916122

105039589105043574+L1HSLINE/L123987 ( L1HS_9_44 ) (R12)

105043587105043727+L1PA2LINE/L160506190 (R12)

105043728105043771+L1PREC2LINE/L161126160

105044754105044822CL2LINE/L233533285

105045010105045190CLTR16DLTR/ERVL325140

105045925105045945+AT_richLow_complexity121

105046049105046600CMER41ALTR/ERV15541

105046863105046913+(TG)nSimple_repeat252

105046941105046983+MIRSINE/MIR118156

105047029105047085+Tigger5DNA/MER2_type23452401

105047086105047164CTigger5DNA/MER2_type791

105048458105048732+L1ME3ALINE/L158816162

Ortholog in Chimp102541038-102547579PlusNscore 0.17

N positions 102543959-102543959; 102543999-102544008;

102535601102535656+L1MB5LINE/L161186173

102536956102537009+L2LINE/L229282984

102537010102537043+(TTTA)nSimple_repeat235

102537052102537310CAluSxSINE/Alu2601

102537311102537399+L2LINE/L229903075

102537525102537826CAluSxSINE/Alu3041

102538200102538337CL2LINE/L232453106

102538338102538638+AluSgSINE/Alu1299

102538639102539300CL2LINE/L231052393

102540396102540500CL2LINE/L223732275

102540810102541033+L1PA13LINE/L158916122

102541038102543992+L1PtLINE/L122926 (R1,R2)

102544014102547683+L1PA2LINE/L124646155 (R1,R2) (BREAK DUE TO Ns, OVERLAP AT Ns)

102547684102547714+AT_richLow_complexity131

102548746102548814CL2LINE/L233533285

102549002102549182CLTR16DLTR/ERVL325140

102550038102550589CMER41ALTR/ERV15541

102550837102550918+(TATATG)nSimple_repeat282

102550937102550979+MIRSINE/MIR118156

102551075102551424CMER41ALTR/ERV13491

102551672102551753+(TA)nSimple_repeat284

102551772102551814+MIRSINE/MIR118156

102551860102551916+Tigger5DNA/MER2_type23452401

102551917102551995CTigger5DNA/MER2_type791

102553289102553564+L1ME3ALINE/L158816162

______

L1HS_10_29c83191402-83191711M_INTRA_RMD

8318363583183677+AT_richLow_complexity143

8318370783183974CL1ME3ALINE/L161585891

8318397283184552+L1MD2LINE/L157786356

8318497283185487+L1MC4LINE/L164587059

8318548283185613+L1MC4LINE/L173387479

8318561483185982CTHE1BLTR/MaLR3621

8318598383186390+L1MC4LINE/L174807899

8318706083187363+AluYSINE/Alu10313

8318777983188064CHAL1LINE/L116391365

8318812183188312CL1MA4LINE/L163006104

8318839883188438+AT_richLow_complexity141

8318859383189130CL1MC4aLINE/L178087230

8318913883189408CMLT1ELTR/MaLR593318

8318951583190084CL1MC4aLINE/L158555254

8319009983190342CL1MC4aLINE/L152284993

8319034683191410CL1PA2LINE/L161835118 (R12)

8319140283191711CL1HSLINE/L132113 ( L1HS_10_29c ) (R12)

8319171183191949CL1MC4aLINE/L149954768

8319195083192248CAluSgSINE/Alu2981

8319224983192521CL1MC4aLINE/L147674491

8319259883192770CL1M1LINE/L140013829

8319285483194017CL1MA2LINE/L177236570

8319401883194437+MER61CLTR/ERV11428

8319443883194478CL1MA2LINE/L165696525

8319447283194618CL1MA2LINE/L159065760

8319461583197667CL1MA2LINE/L165153668

8319766883197973CAluSxSINE/Alu3081

8319797483198286CL1MA2LINE/L136673361

8319830383199170CL1MA2LINE/L126381756

8319917183199468CAluSpSINE/Alu3002

8319946983201165CL1MA2LINE/L1175513

Ortholog in Chimp81473574-81479354MinusNscore 1.70

N positions 81478627-81478636; 81474015-81474102;

8146563881465680+AT_richLow_complexity143

8146571081465969CL1ME3ALINE/L161585899

8146598181466418+L1MD2LINE/L157836227

8146671681466755+AT_richLow_complexity140

8146722681467666+L1MC4LINE/L165147059

8146766181467792+L1MC4LINE/L173387479

8146779381468161CTHE1BLTR/MaLR3621

8146816281468569+L1MC4LINE/L174807899

8146923981469540+AluYSINE/Alu10311

8146995581470240CHAL1LINE/L116391365

8147029781470488CL1MA4LINE/L163006104

8147057481470614+AT_richLow_complexity141

8147076981471306CL1MC4aLINE/L178087230

8147131481471584CMLT1ELTR/MaLR593318

8147169181472260CL1MC4aLINE/L158555254

8147226481472526CL1MC4aLINE/L152344981

8147254981474014CL1PA2LINE/L160294563 (R1,R2) (Broken due to Ns)

8147410481478012CL1PA2LINE/L139093 (R1,R2)

8147863781479354CL1PtLINE/L172713

8147935481479586CL1MC4aLINE/L149954768

8147958781479883CAluSgSINE/Alu2961

8147988481480156CL1MC4aLINE/L147674491

8148023281480404CL1M1LINE/L140013829

8148048881481651CL1MA2LINE/L177236570

8148165281482071+MER61CLTR/ERV11428

8148207281482116CL1MA2LINE/L165696525

8148211081482256CL1MA2LINE/L159065760

8148225381485311CL1MA2LINE/L165153668

8148531281485616CAluSxSINE/Alu3071

8148561781485932CL1MA2LINE/L136673361

8148594981486809CL1MA2LINE/L126381770

8148681081487110CAluSpSINE/Alu3032

8148711181488809CL1MA2LINE/L1176913

______

L1HS_10_30c83518118-83522977C_INTRA_RMD

8351201583512817+L1M5LINE/L131183878

8351285183512880+AT_richLow_complexity130

8351297783518073CL1PA8ALINE/L163141135

8351807483518103+(TTG)nSimple_repeat130

8351811883522977CL1HSLINE/L148621 ( L1HS_10_30c ) (R1,R2)

8352298283523223CL1M5LINE/L132272972

8352391083523939+AT_richLow_complexity130

8352396583524242CAluSxSINE/Alu2761

8352478483525096CAluSxSINE/Alu3121

8352725983527408+MER5BDNA/MER1_type28177

8352779183528487+MER44CDNA/MER2_type1733

Ortholog in Chimp81799614-81803737MinusNscore 0.24

N positions 81802138-81802147;

8179302881793825+L1MDLINE/L131183873

8179386481793893+AT_richLow_complexity130

8179469781798197CL1PA8ALINE/L161022501

8179819881798220+(TTTA)nSimple_repeat224

8179822181799569CL1PA8ALINE/L125001135

8179957081799599+(TTG)nSimple_repeat130

8179961481802137CL1PtLINE/L148622336 (R12)

8180213781803737CL1PtLINE/L116091 (R12)

8180467381804702+AT_richLow_complexity130

8180474181805019CAluSxSINE/Alu2761

8180572181805779+(T)nSimple_repeat155

8180578081805874CSVA_BOther854760

8180588881806188CAluSxSINE/Alu3001

8180835081808499+MER5BDNA/MER1_type28177

8180888081809567+MER44CDNA/MER2_type1733

8180961281809637+(TTTG)nSimple_repeat227

______

L1HS_10_39109213285-109214060M_INTRA_RMD

109211688109212086CMLT1E2LTR/MaLR4021

109212128109212162+(CA)nSimple_repeat135

109212196109212263+L1MEcLINE/L112141274

109212264109212570+AluSxSINE/Alu1307

109212571109212817+L1MEcLINE/L111461488

109212846109213213+L1MEcLINE/L114801886

109213285109214060+L1HSLINE/L11767 ( L1HS_10_39 ) (R12)

109214058109214132+L1PA2LINE/L127672841 (R12)

109214133109214446+AluYb8SINE/Alu1314 (D)

109214447109217770+L1PA2LINE/L128426155 (R12)

109217810109218151+L1MDLINE/L139764367

109218727109218822+ERVL-ELTR/ERVL462557

109218961109219635CMER54BLTR/ERVL793114

109219817109220098+AluSpSINE/Alu1281

109220100109220122+(TAAA)nSimple_repeat224

109220498109220659CMER58ADNA/MER1_type1671

109220939109221568CLTR9BLTR/ERV16441

109222681109222820+MIRbSINE/MIR107257

109222908109223047+MER5ADNA/MER1_type35186

109223053109223347CL3LINE/CR144474129

Ortholog in Chimp108013378-108016078PlusNscore 0.00

N positions

108011778108012175CMLT1E2LTR/MaLR4021

108012217108012251+(CA)nSimple_repeat135

108012288108012355+L1M4cLINE/L111221176

108012356108012662+AluSxSINE/Alu1307

108012663108013305+L1M4cLINE/L111771947

108013377108019406+L1PA2LINE/L116032 (R) -no disruption

108019445108019788+L1MDLINE/L139764367

108020366108020461+ERVL-ELTR/ERVL462557

108020602108021277CMER54BLTR/ERVL793114

108021459108021764+AluSpSINE/Alu1306

108022140108022301CMER58ADNA/MER1_type1671

108022581108023209CLTR9BLTR/ERV16441

108024323108024462+MIRbSINE/MIR107257

108024550108024689+MER5ADNA/MER1_type35186

108024695108025010CL3LINE/CR144474112

______

L1HS_11_45892300-5896254C_DISRUPTED_M_INTER_RMD

58824065886820CL1PB1LINE/L168672393

58868215886850+(TTAG)nSimple_repeat332

58868515887119CAluSxSINE/Alu2771

58871205888727CL1PB1LINE/L12392620

58887085888879CL1PBa1LINE/L144251

58889635889152CL1M5LINE/L132173024

58891685889310CMSTD-intLTR/MaLR1464

58893135889705CMSTDLTR/MaLR3941

58902515890387+L1PA3LINE/L160166152

58911585891390CMIRSINE/MIR25212

58914995891611CLTR67LTR/ERVL553440

58923005896254+L1HSLINE/L1133980 ( L1HS_11_4 )

58962615896347+LTR26LTR/ERV1516603

58963705896653+L1MEaLINE/L1188466

58966565896743+L1HSLINE/L1898

58967385897627+L1P1LINE/L16171491

58976265899662+L1PA4LINE/L141146153

58996465899668+AT_richLow_complexity123

58996695900208+L1MEaLINE/L1456993

59001985902757+L1M1LINE/L1272713

Ortholog in Chimp5758689-5762758PlusNscore 0.00

N positions

57499695753214CL1PB1LINE/L156862393

57532155753502CAluSxSINE/Alu2961

57535035755110CL1PB1LINE/L12392620

57550915755239CL1PB1LINE/L120051

57553475755539CL1M5LINE/L132173024

57555555755699CMSTD-intLTR/MaLR1462

57557085756092CMSTDLTR/MaLR3871

57566385756774+L1PA3LINE/L160166152

57567755756802+AT_richLow_complexity128

57575535757785CMIRSINE/MIR25212

57578915758004CLTR67LTR/ERVL553439

57586895762758+L1P1LINE/L1134103 (OCCUPIED)

57627655762851+LTR26LTR/ERV1516603

57628745763158+L1MEaLINE/L1188467

57631655763249+L1PtLINE/L11298

57632445764128+L1PtLINE/L14941368

57641275766166+L1PA4LINE/L141146153

57661735766712+L1MEaLINE/L1456993

57667025769257+L1M1LINE/L1272713

______

L1HS_11_17c24146892-24148613C_DISRUPTED_M_INTER_RMD

2414084424140914CMER94DNA/AcHobo12857

2414114124141393+L2LINE/L231253419

2414259724142726+CT-richLow_complexity4136

2414331124143332+AT_richLow_complexity122

2414361424143755CMIRSINE/MIR23693

2414450724144655CL1ME3ALINE/L161615991

2414465624144962+AluSxSINE/Alu1312

2414496324145546CL1ME3ALINE/L159905375

2414557324145610+AT_richLow_complexity138

2414573024145831CL1MDaLINE/L118182

2414622424146244+AT_richLow_complexity121

2414689224148613CL1HSLINE/L135831867 ( L1HS_11_17c ) (R12)

2414925924149636CMLT1BLTR/MaLR3904

2414967524149771CL2LINE/L233723274

2415044324151620CL1ME2LINE/L161624873

2415162124152038CMER61BLTR/ERV14271

2415203924152330CL1ME2LINE/L148724576

2415238124152982CL1ME2LINE/L140173350

2415311624153136+AT_richLow_complexity121

2415386324154177CAluYSINE/Alu3101

2415460124154652+AT_richLow_complexity152

Ortholog in Chimp24250587-24252910MinusNscore 6.45

N positions 24251211-24251360;

2424463024244880+L2LINE/L231253417

2424518124245222+AT_richLow_complexity142

2424608424246188+CT-richLow_complexity4108

2424709424247270CMIRSINE/MIR24971

2424818524248333CL1ME3ALINE/L161615995

2424833424248639+AluSxSINE/Alu1311

2424864024249240CL1ME3ALINE/L159945375

2424926724249304+AT_richLow_complexity138

2424942824249529CL1MDaLINE/L118182

2424979224249864+A-richLow_complexity174

2425058724251210CL1P1LINE/L137063086 (R2)

2425141024252910CL1PtLINE/L134061868 (R1)

2425355524253910CMLT1BLTR/MaLR39020

2425397124254067CL2LINE/L233723274

2425473624255907CL1ME2LINE/L161624873

2425590824256325CMER61BLTR/ERV14271

2425632624256617CL1ME2LINE/L148724576

2425666424257260CL1ME2LINE/L140153350

2425739424257418+AT_richLow_complexity125

2425814024258447CAluYSINE/Alu3001

2425886924258916+AT_richLow_complexity148

______

L1HS_11_25c34669416-34670953M_INTRA_RMD

3466282734663064CL1MLINE/L151934969

3466327834663356CL1MLINE/L146544572

3466386934663910+(CA)nSimple_repeat142

3466419134664816CL1ME3BLINE/L160035320

3466488134664940+MLT1ALTR/MaLR3493

3466496034665091CL1PB1LINE/L161506018

3466509234668951CL1PA2LINE/L161522289 (R12)

3466894734669335+L1P1LINE/L144484836 (D)

3466933634669421+L1P1LINE/L148374922 (D)

3466941634670953CL1HSLINE/L1155012 ( L1HS_11_25c ) (R12)

3467095134672365CL1MEcLINE/L153643855

3467238534674150CL1M2LINE/L149583150

3467415434674667CL1PA15LINE/L161505639

3467467634674906CL1M4cLINE/L11048806

3467515334675547+LTR16A1LTR/ERVL45457

3467583334675861+AT_richLow_complexity129

3467604234676332CAluSgSINE/Alu2901

3467638634676803CL1MEcLINE/L138903471

3467680934677086+L1PB1LINE/L158676146

Ortholog in Chimp34964438-34966583MinusNscore 0.00

N positions

3495778234958191CL1MLINE/L153604969

3495840134958502CL1MLINE/L146874572

3495901534959049+(CA)nSimple_repeat136

3495933034959972CL1ME3BLINE/L160765367

3495997634960220+(TA)nSimple_repeat1249

3496022734960308+(TTTA)nSimple_repeat281

3496027234960311+(T)nSimple_repeat140

3496032334960421+MLT1ALTR/MaLR193

3496044134960572CL1PB1LINE/L161506018

3496057334966583CL1PA2LINE/L1603012 (R1,R2)

3496658134967993CL1ME3BLINE/L153643855

3496801334969781CL1M2LINE/L149583150

3496978534970298CL1PA15LINE/L161505639

3497079734971180+LTR16A1LTR/ERVL61457

3497146634971494+AT_richLow_complexity129

3497167534971965CAluSgSINE/Alu2901

3497201934972142CL1ME3BLINE/L138903757

3497214334972162+(TTTTC)nSimple_repeat120

3497216334972441CL1ME3BLINE/L137563471

3497244734972724+L1PB1LINE/L158676146

______

L1HS_12_31c64235466-64235787C_INTER_RMD_M_DISRUPTED

6422788764227988+MIRmSINE/MIR3113

6422806164228375+AluSxSINE/Alu1307

6422861464228635+AT_richLow_complexity122

6422877764228812+(TG)nSimple_repeat237

6422921664229364+MIRSINE/MIR100248

6422937264229402+(CAT)nSimple_repeat333

6422946864235155CL1PA3LINE/L16018317 (R2)

6423515664235465CAluYa5SINE/Alu3101 (D)

6423546664235787CL1HSLINE/L13163 ( L1HS_12_31c ) (R1)

6423593364235981+GA-richLow_complexity351

6423620164236340CMIR3SINE/MIR1331

6423731764237937+MER41BLTR/ERV11634

6423810364238403CHAL1LINE/L1559249

6423840664238435+AT_richLow_complexity130

6423848764238622+LTR67LTR/ERVL64209

6423867964238865+LTR67LTR/ERVL353540

6423922164239253+(TTA)nSimple_repeat234

6424204764242673+MER41BLTR/ERV11626

6424301764243172+MIR3SINE/MIR4160

6424362264243759+GA-richLow_complexity3141

6424376064243798+(CAG)nSimple_repeat240

6424389564243997CMIRSINE/MIR20083

6424472964244892+MER45ADNA/Tip1002177

Ortholog in Chimp23900259-23900568PlusNscore 0.00 (23900259-23906508 Nscore - 0.32)

N positions

2389181123891929+MIRSINE/MIR83222

2389203223892119+(TTC)nSimple_repeat188

2389289923893054CMIR3SINE/MIR1604

2389337223894006CMER41BLTR/ERV16341

2389678923896821+(TAA)nSimple_repeat234

2389717723897363CLTR67LTR/ERVL540353

2389742023897555CLTR67LTR/ERVL20964

2389760723897635+AT_richLow_complexity129

2389763923897939+HAL1LINE/L1249559

2389810523898725CMER41BLTR/ERV16341

2389970223899843+MIR3SINE/MIR1135

2390006623900114+CT-richLow_complexity351

2390025923906227+L1PA3LINE/L135792 (R)

2390650923906536+(CA)nSimple_repeat229

2390667823906698+AT_richLow_complexity121

2390693723907251CAluSxSINE/Alu3071

2390732423907425CMIRmSINE/MIR1133

______

L1HS_13_1879624042-79625783M_INTRA_RMD

7961877979618898CL1MA8LINE/L162886166

7961889979619212CAluYSINE/Alu3111

7961921379619317CL1MA8LINE/L161656073

7961931879619705CTHE1DLTR/MaLR3811

7961970679619891CL1MA8LINE/L160725888

7961996279620074+L2LINE/L232813396

7962013679620769+Tigger1DNA/MER2_type28666

7962077079621004+MER46ADNA/MER2_type2236

7962100579621450+Tigger1DNA/MER2_type6671243

7962181479621839+(T)nSimple_repeat126

7962273979622824CTigger1DNA/MER2_type24182331

7962306279623135CL2LINE/L234193335

7962314779623175+(TTTTG)nSimple_repeat331

7962375579624041CMLT1JLTR/MaLR33723

7962404279625783+L1HSLINE/L151751 ( L1HS_13_18 ) (R12)

7962578279628554+L1PA2LINE/L133776153 (R12)

7962865279628751CL3LINE/CR134863382

7962898879629284+AluSqSINE/Alu1299

7963011279630171+(GGAA)nSimple_repeat362

7963031179630609+AluSxSINE/Alu1300

7963116579631273CL2LINE/L233733255

7963154279631832+AluJbSINE/Alu1298

7963289379633368+L1ME1LINE/L156686148

7963336979633772CMSTALTR/MaLR4281

7963377379633788+L1ME1LINE/L161496160

7963379779633944CMIRSINE/MIR21665

7963434279634652CAluSgSINE/Alu3081

Ortholog in Chimp80546735-80549984PlusNscore 0.00

N positions

8054240980542594CL1MA8LINE/L160725888

8054266580542777+L2LINE/L232813396

8054282780544150+Tigger1DNA/MER2_type11243

8054451480544537+(T)nSimple_repeat124

8054543780545522CTigger1DNA/MER2_type24182331

8054576080545833CL2LINE/L234193335

8054584580545873+(TTTTG)nSimple_repeat331

8054645280546730CMLT1JLTR/MaLR33733

8054673180552762+L1PA2LINE/L116031 (R1,R2)

8055284980552948CL3LINE/CR134863382

8055318580553482+AluSqSINE/Alu1300

8055431080554361+(GGAA)nSimple_repeat354

8055450180554801+AluSxSINE/Alu1301

8055535780555465CL2LINE/L233733255

8055573480556024+AluJbSINE/Alu1298

8055708580557560+L1ME1LINE/L156686148

8055756180557964CMSTALTR/MaLR4281

8055796580557980+L1ME1LINE/L161496160

8055798980558136CMIRSINE/MIR21665

8055852680558836CAluSgSINE/Alu3081

______

L1HS_13_34c104832362-104832716C_INTER_RMD_M_DISRUPTED

104822440104823711+L1MA8LINE/L150056288

104823756104824417+L1MB8LINE/L154906172

104825989104826019+AT_richLow_complexity131

104826083104826214+L1M5LINE/L155435680

104826885104827036+MLT1JLTR/MaLR246404

104828400104828421+AT_richLow_complexity122

104828422104828699CAluJbSINE/Alu2891

104829051104829546CL3LINE/CR143153792

104830124104830146+AT_richLow_complexity123

104830508104830875CMSTALTR/MaLR4282

104832362104832716CL1HSLINE/L1933589 ( L1HS_13_34c ) (R2)

104832717104833016CAluYg6SINE/Alu3011 (D)

104833017104833602CL1HSLINE/L15884 (R1)

104833603104838696+L1PA3LINE/L19266031 (3' end of twinprimed L1)

104838792104838836+AT_richLow_complexity145

104840075104840095+AT_richLow_complexity121

104840181104840344CMER5BDNA/MER1_type1624

Ortholog in Chimp106338811-106339167MinusNscore 0.00

N positions

106328893106330156+L1MA8LINE/L150226288

106330179106330211+(TA)nSimple_repeat133

106330213106330874+L1MB8LINE/L154906172

106331401106331514CMIRbSINE/MIR20284

106332447106332477+AT_richLow_complexity131

106332541106332669+L1M5LINE/L155435680

106333315106333483+MLT1JLTR/MaLR232404

106334847106334868+AT_richLow_complexity122

106334869106335146CAluJbSINE/Alu2891

106335498106335994CL3LINE/CR143153792

106336572106336594+AT_richLow_complexity123

106336956106337323CMSTALTR/MaLR4152

106338811106339738CL1PtLINE/L19334 (R)

106339739106344835+L1PA3LINE/L19276031

106344931106344975+AT_richLow_complexity145

106346211106346231+AT_richLow_complexity121

106346317106346480CMER5BDNA/MER1_type1624

______

L1HS_13_35c104833017-104833602C_INTER_RMD_M_DISRUPTED

104823756104824417+L1MB8LINE/L154906172

104825989104826019+AT_richLow_complexity131

104826083104826214+L1M5LINE/L155435680

104826885104827036+MLT1JLTR/MaLR246404

104828400104828421+AT_richLow_complexity122

104828422104828699CAluJbSINE/Alu2891

104829051104829546CL3LINE/CR143153792

104830124104830146+AT_richLow_complexity123

104830508104830875CMSTALTR/MaLR4282

104832362104832716CL1HSLINE/L1933589 (R2)

104832717104833016CAluYg6SINE/Alu3011 (D)

104833017104833602CL1HSLINE/L15884 ( L1HS_13_35c ) (R1)

104833603104838696+L1PA3LINE/L19266031 (3' end of twim primed L1)

104838792104838836+AT_richLow_complexity145

104840075104840095+AT_richLow_complexity121

104840181104840344CMER5BDNA/MER1_type1624

104842455104842643+ERVLLTR/ERVL17721965

Ortholog in Chimp106339171-106339738MinusNscore 0.00

N positions

106330179106330211+(TA)nSimple_repeat133

106330213106330874+L1MB8LINE/L154906172

106331401106331514CMIRbSINE/MIR20284

106332447106332477+AT_richLow_complexity131

106332541106332669+L1M5LINE/L155435680

106333315106333483+MLT1JLTR/MaLR232404

106334847106334868+AT_richLow_complexity122

106334869106335146CAluJbSINE/Alu2891

106335498106335994CL3LINE/CR143153792

106336572106336594+AT_richLow_complexity123

106336956106337323CMSTALTR/MaLR4152

106338811106339738CL1PtLINE/L19334 (R)

106339739106344835+L1PA3LINE/L19276031

106344931106344975+AT_richLow_complexity145

106346211106346231+AT_richLow_complexity121

106346317106346480CMER5BDNA/MER1_type1624

106348588106348776+ERVLLTR/ERVL17721965

______

L1HS_14_2043136854-43141041C_INTER_RMD_M_DISRUPTED

4312661043127935CL1M5LINE/L153873974

4312857143128591+AT_richLow_complexity121

4313127743131301+AT_richLow_complexity125

4313130243131673CL1PB1LINE/L161515776

4313167443131768+(TA)nSimple_repeat195

4313176943134088CL1PB1LINE/L158013567

4313617543136849CMER89-intLTR/ERV160735358

4313685443141041+L1HSLINE/L114202 ( L1HS_14_20 )

4314103843142354+L1PA2LINE/L148376153

4314235643143019CMER89-intLTR/ERV153634660

4314303043143404CMER89-intLTR/ERV145474170

4314344243143636+L1MCaLINE/L1292712

4314389743144419+L1MCaLINE/L15551091

4314442143144603+L1M2LINE/L12185

4314461943144704+L1M2LINE/L1587672

4314516543145209+(TCTA)nSimple_repeat450

4314524343145605+L1PA8LINE/L158056168

4314591543145985+AT_richLow_complexity171

4314664143146661+AT_richLow_complexity121

4314674143146810+AT_richLow_complexity170

4314688843147056CL1ME1LINE/L161495981

4314705743147263CMER30DNA/MER1_type2301

4314726443147577CL1ME1LINE/L159805657

4314757843147973CMLT1BLTR/MaLR3904

4314804243148234CL1PA16LINE/L161625955

4314823543150654CL1PA15-16LINE/L13398941

Ortholog in Chimp42672359-42676314PlusNscore 0.25

N positions 42676294-42676303;

4266215242663474CL1M5LINE/L153873974

4266411142664131+AT_richLow_complexity121

4266681642666837+AT_richLow_complexity122

4266683842667209CL1PB1LINE/L161515776

4266721042667290+(TA)nSimple_repeat181

4266729142669605CL1PB1LINE/L158013567

4267168042672354CMER89-intLTR/ERV160735358

4267235942676293+L1PtLINE/L113926

4267630942676814+L1PA2LINE/L156466153

4267681842677485CMER89-intLTR/ERV153654660

4267749642677871CMER89-intLTR/ERV145474170

4267790942678141+L1MCaLINE/L1286716

4267836342678890+L1MCaLINE/L15551091

4267889242679074+L1M2LINE/L12185

4267909042679175+L1M2LINE/L1587672

4267963642679688+(TCTA)nSimple_repeat458

4267972242680084+L1PA8LINE/L158056168

4268039442680464+AT_richLow_complexity171

4268112042681140+AT_richLow_complexity121

4268122042681289+AT_richLow_complexity170

4268135842681538CL1ME1LINE/L161585981

4268153942681744CMER30DNA/MER1_type2301

4268174542682058CL1ME1LINE/L159805657

4268205942682456CMLT1BLTR/MaLR3904

4268252542682717CL1PA16LINE/L161625955

4268271842685141CL1PA15-16LINE/L13398941

4268514242688585+HERV4_ILTR/ERV128346268

______

L1HS_14_3161822791-61825189C_INTRA_RMD

6181701961817224+MIRbSINE/MIR16248

6181719961817251+L2LINE/L233703419

6181801961818301CMLT1ALTR/MaLR3741

6181892961819322+MLT1BLTR/MaLR1390

6181948261819766+AluYSINE/Alu1280

6181976761819799+(CAA)nSimple_repeat133

6182041961820611+MLT1A0LTR/MaLR1186

6182060761820676+MLT1A0LTR/MaLR298371

6182092761822796CL1PA3LINE/L161954326

6182279161825189+L1HSLINE/L118094211 ( L1HS_14_31 ) (R1,R2)

6182521661825682CL2LINE/L234192875

6182575061825900+MER5A1DNA/MER1_type6159

6182611261826456+MLT1J2LTR/MaLR54444

6182646161826596CMER5ADNA/MER1_type18564

6182659761826707CL1PA5LINE/L161466036

6182670861826768CMER5ADNA/MER1_type633

6182796461828434CL2LINE/L234032893

6182869961829283CL1P4LINE/L147794193

6182927361829898CHAL1LINE/L124801818

6182992561829973CHAL1LINE/L117151666

6182997461830266CAluScSINE/Alu2951

6183026761830396CHAL1LINE/L116651536

6183054861831197CHAL1LINE/L11558849

Ortholog in Chimp61705520-61707613PlusNscore 0.48

N positions 61706143-61706152;

6169961761699901+AluYSINE/Alu1280

6169990261699955+(CAA)nSimple_repeat154

6170057561700767+MLT1A0LTR/MaLR1186

6170076361700832+MLT1A0LTR/MaLR298371

6170108361701778CL1PA3LINE/L162005506

6170289361704216+L1P1LINE/L121393473

6170425261705525CL1P2LINE/L155984326

6170552061707613+L1PtLINE/L118104211 (R12) (NOTE THAT THERE IS ~300 DIFFERENCE BETWEEN R1-R2 AND R12)

6170764061708107CL2LINE/L234192875

6170817561708325+MER5A1DNA/MER1_type6159

6170853761708881+MLT1J2LTR/MaLR54444

6170888661709010CMER5ADNA/MER1_type18564

6170901161709129CL1PA5LINE/L161546036

6170913061709190CMER5ADNA/MER1_type633

6171038661710818CL2LINE/L234032938

6171112161711708CL1P4LINE/L147794193

6171169861712323CHAL1LINE/L124801818

6171235061712398CHAL1LINE/L117151666

6171239961712686CAluScSINE/Alu2921

6171268761712816CHAL1LINE/L116651536

6171296861713641CHAL1LINE/L11558811

______

L1HS_14_3570011674-70013407C_DISRUPTED_M_INTER_RMD

7000824770008770+L1ME2LINE/L155856154

7000914170009161+AT_richLow_complexity121

7000944470010305CMER21ALTR/ERV192917

7001030670010336+(TG)nSimple_repeat232

7001033770010371+(TA)nSimple_repeat138

7001037270010387CMER21ALTR/ERV1161

7001051970010553+(TG)nSimple_repeat237

7001067270010853+L1MB4LINE/L17181

7001086270011597+L1MB4LINE/L19271662

7001160270011673CMLT-intLTR/MaLR572497

7001167470013407+L1HSLINE/L111734 ( L1HS_14_35 ) (R12)

7001341070014998+SVAOther31379

7001500570019358+L1PA2LINE/L117206069

7001936470019452CMLT-intLTR/MaLR505415

Ortholog in Chimp70116445-70119007PlusNscore 6.25

N positions 70117309-70117468;

7011299970113522+L1ME2LINE/L155856154

7011419570115054CMER21ALTR/ERV192924

7011505570115097+(TG)nSimple_repeat244

7011510670115144+AT_richLow_complexity139

7011528170115315+(TG)nSimple_repeat237

7011543470115615+L1MB4LINE/L17181

7011562470116368+L1MB4LINE/L19271662

7011637370116444CMLT-intLTR/MaLR572497

7011644670117252+L1PtLINE/L12809 (R1)

7011754470119008+L1PtLINE/L12131736 (R2)

7011901070119059+(TCTCCC)nSimple_repeat353

7011906970119431+SVA_BOther1362

7012111870123184+L1PtLINE/L122894338

7012453670125063+L1PA2LINE/L156616188

______

L1HS_15_2371612037-71615599C_INTRA_RMD

7160602271606374CL1MEcLINE/L1982619

7160637571606505CFLAM_CSINE/Alu1281

7160650671607078CL1MEcLINE/L161847

7160731771607933+L1MC5LINE/L168377427

7160793471608240+MER58BDNA/MER1_type1340

7160824171608520+L1MC5LINE/L174287713

7160852171608831CAluYSINE/Alu3101

7160883271609039+L1MC5LINE/L177147906

7160908771609291+L2LINE/L231213342

7160977671610055+AluJoSINE/Alu3296

7161116971611304+L2LINE/L220082147

7161136771611377+L1HSLINE/L114621472

7161137871612037CL1PA2LINE/L161555496

7161203771615599+L1HSLINE/L114715048 ( L1HS_15_23 ) (R1,R2)

7161590471615981CL2LINE/L231973113

7161627071616405CL1PA16LINE/L161576021

7161642771616633CL2LINE/L234193205

7161688171616955+L2LINE/L229583035

7161696171617054CL1MB1LINE/L161636062

7161731571617404CL1MC4aLINE/L159335843

7161740971617601+Charlie5DNA/MER1_type1200

7161760071617845+Charlie5DNA/MER1_type23522605

7161784671618148CAluYSINE/Alu3041

7161814971618176+Charlie5DNA/MER1_type26062624

7161819571618510CL1MC4aLINE/L158165497

7161867771618865CAluYSINE/Alu307119

7162032071620347+AT_richLow_complexity128

7162058471621039+Charlie4aDNA/MER1_type14508

7162121071621251+AT_richLow_complexity142

7162134371621434CMLT1JLTR/MaLR511415

7162144371621754+AluSxSINE/Alu1312

Ortholog in Chimp71326913-71329979PlusNscore 0.33

N positions 71329368-71329377;

7132089171321243CL1MEcLINE/L1982619

7132124471321376CFLAM_CSINE/Alu1331

7132137771321949CL1MEcLINE/L161847

7132218871322802+L1MC5LINE/L168377427

7132280371323109+MER58BDNA/MER1_type1340

7132311071323380+L1MC5LINE/L174287711

7132338171323718CAluYSINE/Alu3371

7132371971323926+L1MC5LINE/L177127906

7132397471324178+L2LINE/L231213342

7132465471324933+AluJoSINE/Alu3296

7132604871326183+L2LINE/L220082147

7132625671326913CL1PA2LINE/L161535496

7132691471329367+L1PtLINE/L114733929 (R12)

7132942871329979+L1PtLINE/L144675048 (R12)

7133028471330361CL2LINE/L231973113

7133064971330784CL1PA16LINE/L161576021

7133080671330993CL2LINE/L234193225

7133126171331331+L2LINE/L229643035

7133133771331476CL1MB1LINE/L161636010

7133169671331785CL1MC4aLINE/L159335843

7133179071331977+Charlie5DNA/MER1_type1200

7133197671332220+Charlie5DNA/MER1_type23522598

7133222171332525CAluYSINE/Alu3061

7133252671332553+Charlie5DNA/MER1_type25992624

7133257271332919CL1MC4aLINE/L158185469

7133305271333237CAluYSINE/Alu304119

7133468371334710+AT_richLow_complexity128

7133494371335398+Charlie4aDNA/MER1_type14508

7133557071335611+AT_richLow_complexity142

7133570371335794CMLT1JLTR/MaLR511415

7133580371336113+AluSxSINE/Alu1311

______

L1HS_16_11c34626287-34629551C_INTER_RMD_M_DISRUPTED

3461763934617663+(CAA)nSimple_repeat226

3461922834619531CAluSxSINE/Alu3001

3462139034622400+L1M4LINE/L133984478

3462558834625907CHSAT6Satellite3211

3462599634626251CMSTALTR/MaLR2851

3462628734629551CL1HSLINE/L142811018 ( L1HS_16_11c )

3462955234630187+L1PA3LINE/L155206155

3463020634630522+AluYSINE/Alu1311

3463196234632046CMER5BDNA/MER1_type17791

3463208834634039+L1PB4LINE/L141896156

3463410134634130+AT_richLow_complexity130

3463413134634369+(TA)nSimple_repeat1256

3463437534634655CAluSxSINE/Alu2781

3463499834635027+(TTTA)nSimple_repeat332

3463628234636491+L1MA9LINE/L142514446

3463649234636795+AluSgSINE/Alu1305

3463679634636843+L1MA9LINE/L144474485

3463684434637154+AluYSINE/Alu1311

3463715934637186+(CAAG)nSimple_repeat128

3463718734638315+L1MA9LINE/L144865671

3463837834638840+L1MA9LINE/L158056277

Ortholog in Chimp45014197-45017443PlusNscore 0.31

N positions 45014314-45014323;

4500506645005540CL1MA9LINE/L162885805

4500557845006791CL1MA9LINE/L156974477

4500679245007101CAluYSINE/Alu3101

4500710245007148CL1MA9LINE/L144764447

4500714945007442CAluSgSINE/Alu2961

4500744345007652CL1MA9LINE/L144464251

4500833445008393+GC_richLow_complexity160

4500890945008942+(TAAA)nSimple_repeat336

4500925245009529+AluSxSINE/Alu1278

4500953545009840+(TA)nSimple_repeat1327

4500985345009911+AT_richLow_complexity159

4500997345011923CL1PB4LINE/L161564189

4501349445013810CAluYSINE/Alu3111

4501383245014208CL1PA3LINE/L161555774

4501432445017443+L1P1LINE/L112814404 (OCCUPIED)

4501747945017734+MSTALTR/MaLR1285

4501782345018142CHSAT6Satellite3111

4502132945022337CL1M4LINE/L144783398

4502419745024496+AluSxSINE/Alu1297

4502605845026091+(TTG)nSimple_repeat235

______

L1HS_16_16c57585219-57585770C_INTER_RMD_M_DISRUPTED

5757493657577167+L1M3bLINE/L122594474

5757717357579399+L1MA7LINE/L1932232

5757940057579648CAluJoSINE/Alu2621

5757964957582010+L1MA7LINE/L122334502

5758201157582877+L1MA7LINE/L148495708

5758287757584761CL1P2LINE/L1192122

5758476257584806+(TTTA)nSimple_repeat248

5758480957585180CL1PA4LINE/L161475776 (R2)

5758518157585214+(TTTA)nSimple_repeat236

5758521957585770CL1HSLINE/L161545603 ( L1HS_16_16c ) (R1)

5758579457586649+L1MA7LINE/L156986596

5758665157587262+L1PB1LINE/L154706107

5758726657587284+(TAAAAA)nSimple_repeat220

5758728557587730+L1MA7LINE/L165807011

5758779057587910CMIRSINE/MIR14420

5758851957588716CMIRbSINE/MIR2118

5758910657589135+(T)nSimple_repeat130

5758942557589445+AT_richLow_complexity121

5758949557589675+MIRbSINE/MIR39265

5758977157590067CAluYSINE/Alu2971

5759038057590434+(TCTA)nSimple_repeat458

5759043557590724CAluSqSINE/Alu2821

5759155057591772CMIRbSINE/MIR2515

5759190957591932+(TC)nSimple_repeat124

5759193357591965+(CA)nSimple_repeat134

5759196757592046+L2LINE/L223772457

5759207857592366+L2LINE/L225302835

5759241757592605CAluYSINE/Alu298110

5759273257592865+L2LINE/L230413157

5759289257594098CL1PA4LINE/L161554944

5759420157594313+L2LINE/L232883412

5759432157594651CLTR16ALTR/ERVL41535

5759465957594818CMER63DNA/AcHobo1656

Ortholog in Chimp58497652-58497821MinusNscore 0.00

N positions

5848739358489624+L1M3bLINE/L122954474

5848963058491852+L1MA7LINE/L1932226

5849185358492101CAluJoSINE/Alu2621

5849210258494472+L1MA7LINE/L122274502

5849447358495338+L1MA7LINE/L148495708

5849533858497235CL1P2LINE/L1192119

5849723658497274+AT_richLow_complexity139

5849727758497821CL1PA4LINE/L161475603 (R12)

5849784558498699+L1MA7LINE/L156986596

5849870158499312+L1PB1LINE/L154706107

5849931658499334+(TAAAAA)nSimple_repeat220

5849933558499777+L1MA7LINE/L165807011

5849983858499972CMIRSINE/MIR14811

5850056658500763CMIRbSINE/MIR2118

5850146858501488+AT_richLow_complexity121

5850153858501718+MIRbSINE/MIR39265

5850181458502115CAluYSINE/Alu2981

5850242358502743CAluSqSINE/Alu3151

5850356958503791CMIRbSINE/MIR2515

5850392858503983+(TC)nSimple_repeat156

5850398458504010+(CA)nSimple_repeat128

5850401258504091+L2LINE/L223772457

5850412358504412+L2LINE/L225302835

5850446358504648CAluYSINE/Alu295110

5850477458504907+L2LINE/L230413157

5850493558506128CL1PA4LINE/L161554944

5850629758506342+L2LINE/L233703412

5850635058506680CLTR16ALTR/ERVL41535

5850668858506847CMER63DNA/AcHobo1656

______

L1HS_16_2379318488-79322115M_INTRA_RMD

7931501279315222+MER58ADNA/MER1_type6224

7931522579315351+GA-richLow_complexity1124

7931537579315739+GA-richLow_complexity1353

7931599479316133+MER112DNA/MER1_type110258

7931618579316565+L2LINE/L226903089

7931656679316619+(CA)nSimple_repeat255

7931662079316932+L2LINE/L230903378

7931750279317603+L1MC5LINE/L178097913

7931801479318164+L1MC3LINE/L167056857

7931820479318481+AluJbSINE/Alu1296

7931848879322115+L1HSLINE/L173631 ( L1HS_16_23 )

7932211379322525+L1ME1LINE/L157506161

7932251579323414+HAL1LINE/L19531881

7932358479323707+MER104DNA/Tc21125

7932389079324024+HAL1bLINE/L118521989

7932517079325373+L2LINE/L227002914

7932566979325726+L4LINE/RTE9461003

7932602879326103CL2LINE/L233783306

7932678579326926+MIRSINE/MIR108260

7932795179328007+MIRSINE/MIR158

Ortholog in Chimp80826702-80835146PlusNscore 8.85

N positions 80832198-80832353; 80833567-80834157;

8082320280823417+MER58ADNA/MER1_type3224

8082342080823551+GA-richLow_complexity1129

8082356680823935+GA-richLow_complexity1358

8082421180824350+MER112DNA/MER1_type110258

8082440280824781+L2LINE/L226903089

8082478280824826+(CA)nSimple_repeat246

8082482780825139+L2LINE/L230903378

8082568480825810+L1MC5LINE/L177767913

8082622080826365+L1MC3LINE/L167056851

8082636880826402+(CAA)nSimple_repeat136

8082641780826695+AluJoSINE/Alu1297

8082670280832197+L1PtLINE/L175505

8083238080833544+L1ME1LINE/L134434667

8083416580835555+L1ME1LINE/L147426161

8083556980836450+HAL1LINE/L19751881

8083662080836739+MER104DNA/Tc21125

8083821680838419+L2LINE/L227002914

8083908180839156CL2LINE/L233783306

8083976380839783+AT_richLow_complexity121

8083984280839981+MIRSINE/MIR108260

8084100680841062+MIRSINE/MIR158

8084108280841199+FLAM_CSINE/Alu1118

8084120880841329CCharlie2DNA/MER1_type19981862

8084136180841652CCharlie2DNA/MER1_type32416

______

L1HS_16_2480568460-80569573C_INTER_RMD_M_DISRUPTED

8055916780560594CL1MLINE/L156634202

8056059580560979+MSTBLTR/MaLR1426

8056098080563334CL1M1LINE/L142011175

8056343180563502+C-richLow_complexity270

8056350380563573CL1M3cLINE/L114531381

8056359180563642+(CA)nSimple_repeat253

8056365180563927CAluJoSINE/Alu28712

8056394380563971+AT_richLow_complexity129

8056409280564306+L1M5LINE/L137023970

8056431280564524+L1PA16LINE/L11218

8056450680565635+L1PA16LINE/L18451991

8056563680565937+AluYSINE/Alu1306

8056593880567839+L1PA16LINE/L119923903

8056784080568149CAluSgSINE/Alu3101

8056815080568459+L1PA16LINE/L139044210

8056846080569573+L1HSLINE/L111114 ( L1HS_16_24 ) (R1)

8056957480569891+AluYb8SINE/Alu1318 (D)

8056989280570964+L1HSLINE/L111152180 (R2)

8057096980573538+L1PA3LINE/L142836858

8057353680575974+L1PA16LINE/L141956752

8057597580576281CAluSxSINE/Alu3041

8057628280576404+L1PA16LINE/L167536869

8057642580576917+L1M5LINE/L139574461

8057691880577218+AluSxSINE/Alu1293

8057721980577426+L1M5LINE/L144624659

8057758480578212+L1M5LINE/L148785584

8057832780578587+MLT1JLTR/MaLR224615

Ortholog in Chimp82124509-82125613PlusNscore 0.00

N positions

8211540382117846CL1M4cLINE/L141971175

8211784982117940+CT-richLow_complexity396

8211801082118065+(CA)nSimple_repeat257

8211807482118360CAluJoSINE/Alu2872

8211858782118661+L1M5LINE/L137993873

8211874182118955+L1PA15-16LINE/L11218

8211893782120065+L1PA15-16LINE/L18451991

8212006682120368+AluYSINE/Alu1304

8212036982122292+L1PA15-16LINE/L119923904

8212230082122575CAluSgSINE/Alu30732

8212259082123887+L1PA16LINE/L126153905

8212388882124197CAluSgSINE/Alu3101

8212419882124506+L1PA16LINE/L139064209

8212450982130044+L1PtLINE/L115534

8213002982132203+L1PA3LINE/L139826155

8213220382134639+L1PA16LINE/L141986752

______

L1HS_17_23198430-3202087C_DISRUPTED_M_INTER_RMD

31873273193435CL1PA5LINE/L161465

31941743194196+MLT1KLTR/MaLR3860

31941973194706+LTR55LTR/ERV1548

31947073194915+MLT1KLTR/MaLR61301

31949753195056CMLT1KLTR/MaLR453372

31952263195983+HAL1LINE/L16371454

31960393196161+L1MEbLINE/L13126

31961813196291CL1MA7LINE/L158825771

31962923196393CL1MA2LINE/L163046202

31963963196471+MLT1KLTR/MaLR220297

31965413197229CL1MA2LINE/L161975509

31972323197287CL1MLINE/L168266771

31972883198430CL1PA3LINE/L161555013

31984303202087+L1HSLINE/L112204878 ( L1HS_17_2 ) (R12)

32020863203719CL1MLINE/L167835283

32037203203991CL1MA1LINE/L163026020

32039923204355CL1MLINE/L152824929

32043563204445CAluJbSINE/Alu301211

32044463205472CL1MLINE/L149283928

32054733205505+(TC)nSimple_repeat234

32055063206535CL1M1LINE/L139252889

32065363206640+L1M1LINE/L133563482

32074453207608+L1MC1LINE/L158375999

32074913207752+L1MB3LINE/L158816144

32077583207889CAluJoSINE/Alu1369

32078983207941+L1MB4LINE/L161366179

Ortholog in Chimp3387661-3395127PlusNscore 7.55

N positions 3389554-3390107; 3390945-3390954;

33774733382676CL1PA5LINE/L152284

33834143383436+MLT1KLTR/MaLR3860

33834373383947+LTR55LTR/ERV1548

33839483384156+MLT1KLTR/MaLR61301

33841683384297CMLT1KLTR/MaLR506372

33844673385214+HAL1LINE/L16371454

33853083385392+L1MEaLINE/L143126

33854123385522CL1MA7LINE/L158825771

33855233385624CL1MA2LINE/L163046202

33856273385702+MLT1KLTR/MaLR220297

33857723386463CL1MA2LINE/L161975509

33864663386521CL1MLINE/L154075352

33865193387661CL1PA3LINE/L161555013

33876613389553+L1P1LINE/L113433237

33901083390183+L1P1LINE/L141744249

33901743390457CL1P1LINE/L139813695

33904563390955+L1P1LINE/L139774480

33909623394302+L1PA2LINE/L127966155

33943593395127+L1P1LINE/L142335001

33951263396744CL1M1LINE/L153673835

33967643396976CL1M1LINE/L154575283

33969773397249CL1MA1LINE/L163026020

33972503399772CL1M1LINE/L152822889

33976143397703CAluJbSINE/Alu301211

33997753399877+L1M1LINE/L133553482

34007283400989+L1MB3LINE/L158816144

34009953401126CAluJoSINE/Alu1369

______

L1HS_18_22c39855243-39858789M_INTRA_RMD

3985078139851569CL1PA17LINE/L161655336

3985157139851797+L1P4LINE/L131113339

3985179839852115+AluSxSINE/Alu1308

3985211639852578+L1P4LINE/L133403801

3985262239852825CL1M5LINE/L140693848

3985290639853044CL1MDaLINE/L128472692

3985304539853366CAluSxSINE/Alu3031

3985336739854106CL1MDaLINE/L126911849

3985456239854582+AT_richLow_complexity121

3985465339855242CL1PA5LINE/L161545565

3985524339858789CL1HSLINE/L135711 ( L1HS_18_22c )

3986035439860477+MIRSINE/MIR123252

3986048939860579+L2LINE/L233283419

3986097439861064+MSTALTR/MaLR338428

3986112939861924CTHE1-intLTR/MaLR1514732

3986222039862976CMSTA-intLTR/MaLR7841

3986297739863354CMSTALTR/MaLR4281

3986375239863842+MIRSINE/MIR41137

3986400039864980+L1M1LINE/L125923618

Ortholog in Chimp40180532-40188625MinusNscore 9.80

N positions 40185686-40186468; 40184730-40184739;

4017607540176863CL1PA17LINE/L161655336

4017686540177091+L1P4LINE/L131113339

4017709240177410+AluSxSINE/Alu1309

4017741140177875+L1P4LINE/L133403801

4017791940178162CL1M5LINE/L140693808

4017820340178356CL1MDaLINE/L128472690

4017835740178664CAluSxSINE/Alu2891

4017866540179405CL1MDaLINE/L127741849

4017986140179881+AT_richLow_complexity121

4017995140184700CL1PA5LINE/L160311226

4018474040185685CL1PtLINE/L131542200

4018646940188625CL1PtLINE/L121611

4019007840190298+MIRbSINE/MIR21260

4019030640190396+L2LINE/L233283419

4019078240190880+MSTALTR/MaLR329428

4019094540191738CTHE1-intLTR/MaLR1514732

4019203340192789CMSTA-intLTR/MaLR7841

4019279040193169CMSTALTR/MaLR4281

4019356740193657+MIRSINE/MIR41137

4019381540194795+L1M1LINE/L125923620

______

L1HS_18_3863421851-63423817C_DISRUPTED_M_INTER_RMD

6341634763416713CMLT1ALTR/MaLR3744

6341680063416906+MIRmSINE/MIR14133

6341690763416927+AT_richLow_complexity121

6341692863417236CAluYSINE/Alu3081

6341723963417307+MIR3SINE/MIR119187

6341924863420412+Tigger1DNA/MER2_type11189

6342041063420603+Tigger1DNA/MER2_type21842380

6342067363420700+(TG)nSimple_repeat128

6342117063421205+(TTTTTA)nSimple_repeat236

6342130763421629+MLT1BLTR/MaLR1459

6342163163421667+(A)nSimple_repeat137

6342185163423817+L1HSLINE/L121972 ( L1HS_18_38 )

6342381863423938+L1PA4LINE/L160316152

6342393963424335+MLT2A1LTR/ERVL13503

6342433663424358+(CA)nSimple_repeat224

6342447663424524+(TA)nSimple_repeat248

6342497663425323CTHE1DLTR/MaLR3811

6342570263425912+MIRbSINE/MIR56268

6342737563427458+CT-richLow_complexity490

6342795063427978+(CAAAA)nSimple_repeat230

6342840563428546CL2LINE/L234143266

6342934063429370+AT_richLow_complexity131

Ortholog in Chimp64292213-64298265PlusNscore 8.11

N positions 64292393-64292863; 64294442-64294451; 64297798-64297807;

6428671264287078CMLT1ALTR/MaLR3744

6428716564287271+MIRmSINE/MIR14133

6428727264287298+AT_richLow_complexity127

6428729964287606CAluYSINE/Alu3071

6428960164290765+Tigger1DNA/MER2_type11189

6429076364290956+Tigger1DNA/MER2_type21842380

6429102664291057+(TG)nSimple_repeat132

6429152764291564+(T)nSimple_repeat138

6429166364291985+MLT1BLTR/MaLR1459

6429198764292030+A-richLow_complexity144

6429221264292392+L1PtLINE/L11181 (R1) (BROKEN BECAUSE OF Ns)

6429286464294441+L1PtLINE/L12781858 (R1)

6429445264295464+Tigger1DNA/MER2_type1741189

6429546264295655+Tigger1DNA/MER2_type21842380

6429572564295752+(TG)nSimple_repeat128

6429622164296244+(T)nSimple_repeat124

6429634364296665+MLT1BLTR/MaLR1459

6429666764296708+(A)nSimple_repeat142

6429689064297797+L1PtLINE/L11910

6429780864298265+L1PtLINE/L115151972 (R2)

6429826664298391+L1PA4LINE/L160316155

6429839264298776+MLT2A1LTR/ERVL13404

6429878564298805+(CA)nSimple_repeat222

6429892364298963+(TA)nSimple_repeat240

6429940664299753CTHE1DLTR/MaLR3811

6430009664300342+MIRbSINE/MIR19268

6430181464301896+CT-richLow_complexity280

6430239064302415+(CAAAA)nSimple_repeat227

6430287164303012CL2LINE/L234143266

6430380664303834+AT_richLow_complexity129

______

L1HS_19_12c59783480-59789179C_INTER_RMD_M_DISRUPTED

5977505259775087+AT_richLow_complexity136

5977627759776552CAluJoSINE/Alu28611

5977893159779002+GA-richLow_complexity272

5978141559783471CL1PA6LINE/L161484068 (R2)

5978348059789179CL1HSLINE/L161555 ( L1HS_19_12c ) (R1)

5979125959791364CMER63DNA/AcHobo1014909

5979160259791899+AluYSINE/Alu2296

5979195559792244CAluSpSINE/Alu2911

5979229059792580CMLT1CLTR/MaLR2691

5979262059792792+AluSg/xSINE/Alu123295

5979279359792913+L1M4LINE/L144214541

5979291559792951+MLT2A2LTR/ERVL525561

5979296159793151CL1P4cLINE/L17641

5979405959794343+LTR42LTR/ERVL3267

5979434759794490+MER65DLTR/ERV14147

5979454459794720+MER65DLTR/ERV1157341

5979473359795252CMER21ALTR/ERV1923376

5979525859795499CMER21ALTR/ERV12641

5979550059795586+MER65DLTR/ERV1342427

5979558759795825+MER8DNA/MER2_type1239

5979582659795862+MER65DLTR/ERV1428463

5979588559796104+LTR42LTR/ERVL265491

5979651159796623CMIRbSINE/MIR18168

Ortholog in Chimp60308686-60311189MinusNscore 0.00

N positions

6029990360299938+AT_richLow_complexity136

6030150860301783CAluJoSINE/Alu28611

6030662960310172CL1PA6LINE/L161482571 (R12- further undergone intra-element recombination)

6031016960311189CL1P2LINE/L110575 (R12- further undergone intra-element recombination)

6031326460313369CMER63DNA/AcHobo1014909

6031360760313907+AluYSINE/Alu2298

6031396560314040CAluSp/qSINE/Alu289213

6031468160314965CAluSxSINE/Alu2851

6031501160315302CMLT1CLTR/MaLR2691

6031534260315514+AluSg/xSINE/Alu123295

6031551560315644+L1M4LINE/L144214549

6031568160315873CL1P4cLINE/L17591

6031591660316241CL1M4LINE/L134883155

6031678260317067+LTR42LTR/ERVL3267

6031707160317214+MER65DLTR/ERV14147

6031726860317444+MER65DLTR/ERV1157341

6031745760317964CMER21ALTR/ERV1923389

6031794860318223CMER21ALTR/ERV12855

6031821860318307+MER65DLTR/ERV1337427

6031830860318546+MER8DNA/MER2_type1239

6031854760318583+MER65DLTR/ERV1428463

6031860660318819+LTR42LTR/ERVL265491

6031921860319338CMIRbSINE/MIR19468

______

L1HS_X_45c70935033-70938407C_INTRA_RMD

7092904270930266+L1MDLINE/L134754704

7093026770930577+AluScSINE/Alu6315

7093057870930600+L1MDLINE/L147054726

7093060170930893CAluJoSINE/Alu31138

7093089470931028+L1MDLINE/L147274860

7093103870931323CL1MB5LINE/L161655889

7093132470931633CAluJbSINE/Alu3051

7093163470932669CL1MB5LINE/L158884843

7093266970933786+L1M3eLINE/L112002352

7093378770934057CAluSqSINE/Alu2701

7093405870934286+L1M3eLINE/L123532590

7093432170934639CAluJbSINE/Alu3091

7093464070935039+L1M3eLINE/L130083429

7093503370938407CL1HSLINE/L14274895 ( L1HS_X_45c ) (R1,R2)

7093840770940163+L1PA4LINE/L143956151

7094015470940358+L1M3LINE/L135553770

7094041070941770+L1M1LINE/L12971678

7094176870942638+L1M3eLINE/L135864467

7094262770942856+L1M3eLINE/L149725193

7094289670942933+(TA)nSimple_repeat239

7094293470944190CL1PA6LINE/L161404884

7094419070945499+L1PA6LINE/L135504861

Ortholog in Chimp71122692-71125420MinusNscore 1.10

N positions 71124693-71124722;

7112178771121910+L1M3eLINE/L124122544

7112189671121941+L1M3eLINE/L129683014

7112199171122298CAluJbSINE/Alu2981

7112229971122698+L1M3eLINE/L130083429

7112269271124692CL1PtLINE/L142742270 (R12)

7112472371125420CL1PtLINE/L11593896 (R12)

7112542071127175+L1PA4LINE/L143956151

7112716671127383+L1M3LINE/L135553770

7112743571128795+L1M1LINE/L12971678

7112879371129663+L1M3eLINE/L135864467

7112965271129881+L1M3eLINE/L149725193

7112992171129963+(TA)nSimple_repeat244

7112996471130104CL1PA6LINE/L161355994

7113066171131588CL1PA6LINE/L158114884

______

L1HS_X_85108033780-108039316C_INTER_RMD_M_DISRUPTED

108023320108025407+L1M3eLINE/L1102517

108025454108025815+THE1BLTR/MaLR1362

108025818108027336+THE1B-intLTR/MaLR11580

108027337108027699+THE1BLTR/MaLR1364

108027700108028185+L1M1LINE/L126763168

108028188108030669+L1M1LINE/L133295742

108030670108030886+L1PB1LINE/L159346151

108030887108031875+L1M1LINE/L157436742

108031879108033770+L1PB1LINE/L161915

108033780108039316+L1HSLINE/L1115662 ( L1HS_X_85 )

108039318108039516+HERVHLTR/ERV156265824

108039511108039886+HERVHLTR/ERV173247713

108039887108040290+LTR7LTR/ERV11407

108040291108040318+(GAAAA)nSimple_repeat330

108040319108040691+L1PA5LINE/L157776149

108040699108044754+L1PB1LINE/L118986045

108044761108045244+L1PA10LINE/L156936177

108045264108045405+MLT1ALTR/MaLR185341

108045414108046264+L1PB1LINE/L160366867

108046260108046848+L1MA8LINE/L152965918

108046849108047099+L1MA8LINE/L160316290

108047100108047167+L1MA4LINE/L159196021

108047488108048343+L2LINE/L220252956

Ortholog in Chimp108418801-108424245PlusNscore 3.36

N positions 108421001-108421171; 108421231-108421231; 108421234-108421234; 108424224-108424233;

108408036108410111+L1M3eLINE/L1102517

108410158108410519+THE1BLTR/MaLR1362

108410522108412039+THE1B-intLTR/MaLR11580

108412040108412419+THE1BLTR/MaLR1364

108412420108412905+L1M1LINE/L126763168

108412908108416490+L1M1LINE/L133296749

108416490108416988+L1PB1LINE/L16542

108417499108418791+L1PB1LINE/L16211915

108418801108424208+L1PtLINE/L1115382 (OCCUPIED)

108424246108424396+HERVHLTR/ERV156745824

108424391108424766+HERVHLTR/ERV173247713

108424767108425129+LTR7LTR/ERV11380

108425244108426614+L1PA5LINE/L147436150

108426622108430671+L1PB1LINE/L118986045

108430678108431176+L1PA10LINE/L156936192

108431196108431336+MLT1ALTR/MaLR185341

108431347108432197+L1PB1LINE/L160366867

108432207108432587+L1MA8LINE/L153195725

108433078108433318+L1MA8LINE/L160316290

______

L1HS_Y_31c21393557-21398291C_DISRUPTED_M_INTER_RMD

2138697521388798+L1PA14LINE/L114974850

2138881621389753+L1P2LINE/L19975

2138975521391639+L1P2LINE/L111887

2139166221392937CL1PA4LINE/L161524879

2139292421393561CL1PA4LINE/L117151066

2139355721398291CL1HSLINE/L147544 ( L1HS_Y_31c ) (R12)

2139829221398427+L1PREC2LINE/L149525069

2139842821398760+L1PA3LINE/L158506183

2139876121399036+L1PREC2LINE/L150705386

2139903721399335CAluYSINE/Alu2991

2139933621399420+L1PA15LINE/L153875464

2139942121399716CAluSpSINE/Alu2991

2139971721399881+L1PA15LINE/L154655611

2139988221400184+AluYSINE/Alu1303

2140018521400253+L1PA15LINE/L156125680

2140025421400283+(CA)nSimple_repeat232

2140028421400366+L1PA15LINE/L156815768

2140036721400668CAluYSINE/Alu3011

2140066921401062+L1PA15LINE/L157696162

2140235821402558CL1PB4LINE/L159765774

2140257121402710+L1PB4LINE/L160176156

2140276821403059+AluSgSINE/Alu1294

2140307921403099+AT_richLow_complexity121

2140370321404725CL1PREC2LINE/L161595112

Ortholog in Chimp14906949-14923038PlusNscore 0.00

N positions

1490041914901831+L1PREC2LINE/L145516159

1490243514902455+AT_richLow_complexity121

1490247514902770CAluSgSINE/Alu2981

1490282814902967CL1PB4LINE/L161566017

1490298014903177+L1PB4LINE/L157745973

1490449414904887CL1PA15LINE/L161635770

1490488814905195+AluYSINE/Alu1308

1490519614905271CL1PA15LINE/L157695698

1490527214905305+(TG)nSimple_repeat236

1490530614905372CL1PA15LINE/L156975618

1490537314905675CAluYSINE/Alu3031

1490567614905840CL1PA15LINE/L156175466

1490584114906138+AluSpSINE/Alu1301

1490613914906511CL1PA15LINE/L154655070

1490651214906813CL1PA3LINE/L161555850

1490681414906948CL1PREC2LINE/L150694952

1490694914912983+L1PA2LINE/L146032 (R1)

1491298314913605CL1PREC2LINE/L149684328

1491361814914293CL1PA6LINE/L161545490

1491429414914599CAluYSINE/Alu3061

1491460014918220CL1PA6LINE/L154891874

1491822214923038+L1P1LINE/L114877 (R2)

1492303314923669+L1PA4LINE/L110651704

1492366814924945+L1PA4LINE/L148796152

1492496814926857CL1PA6LINE/L118871

1492685914927796CL1P2LINE/L19759

1492781414929402CL1PA14LINE/L148503245

______

Supplementary file 1 - Recombination mediated deletions – Truncated L1HS elements, Human Vs Celera comparison

L1HS_3_14c C_INTER_RMD ??

189 7.4 0.0 0.0 chr3 22060937 22060963 (177440864) + (CAAAAA)n Simple_repeat 4 30 (0) 37

450 32.2 11.7 0.8 chr3 22061065 22061330 (177440497) C L2 LINE/L2 (1667) 1752 1458 36

466 12.7 0.0 0.0 chr3 22061452 22061522 (177440305) + AluSp/q SINE/Alu 226 296 (17) 38

300 14.5 1.6 0.0 chr3 22061523 22061584 (177440243) C L1M2 LINE/L1 (1817) 4326 4264 39

728 20.1 7.7 1.6 chr3 22061616 22061797 (177440030) C L1M2 LINE/L1 (1010) 5133 4941 40

7282 15.7 6.0 3.6 chr3 22063602 22065510 (177436317) C L1MA8 LINE/L1 (2) 6289 4316 41

2028 12.4 0.3 0.0 chr3 22065511 22065836 (177435991) + AluSq SINE/Alu 1 327 (0) 42

7282 17.9 8.8 3.6 chr3 22065837 22066576 (177435251) C L1MA8 LINE/L1 (1828) 4315 3551 41

1379 22.6 1.4 0.0 chr3 22066580 22066854 (177434973) + AluJo SINE/Alu 1 279 (33) 43

231 6.1 0.0 0.0 chr3 22066855 22066887 (177434940) + (CAAA)n Simple_repeat 1 33 (0) 44

16108 0.3 0.0 0.0 chr3 22066888 22069693 (177432134) C L1HS LINE/L1 (2586) 3437 329 45 (R1)

20482 0.2 0.0 0.0 chr3 22069692 22072804 (177429023) + L1HS LINE/L1 3064 6176 (0) 46 (R2)

335 28.2 3.1 3.9 chr3 22073187 22073315 (177428512) C MLT1H LTR/MaLR (16) 533 406 47

245 33.3 0.0 0.0 chr3 22073404 22073481 (177428346) C MLT1H2 LTR/MaLR (323) 161 84 48

646 29.4 3.1 5.3 chr3 22073622 22073874 (177427953) + MIRb SINE/MIR 14 262 (0) 49

2103 12.5 0.0 1.3 chr3 22074010 22074309 (177427518) C AluSx SINE/Alu (16) 296 1 50

216 9.7 0.0 0.0 chr3 22074491 22074521 (177427306) + (TGAA)n Simple_repeat 3 33 (0) 51

23 0.0 0.0 0.0 chr3 22075113 22075135 (177426692) + AT_rich Low_complexity 1 23 (0) 52

22 0.0 0.0 0.0 chr3 22075176 22075197 (177426630) + AT_rich Low_complexity 1 22 (0) 53

274 23.2 2.9 1.4 chr3 22075816 22075885 (177425942) C MER5B DNA/MER1_type (104) 74 4 54

282 29.6 0.0 0.0 chr3 22075963 22076050 (177425777) C Charlie2 DNA/MER1_type (2598) 263 176 55

288 24.5 7.9 3.0 chr3 22076077 22076177 (177425650) C Charlie2 DNA/MER1_type (2751) 110 5 55

Ortholog in Celera

SW perc perc perc query position in query matching repeat position in repeat

score div. del. ins. sequence begin end (left) repeat class/family begin end (left) ID

5371 15.8 6.9 3.0 gi|89161204:22028483-22038898 1666 3574 (6842) C L1MA8 LINE/L1 (2) 6289 4316 1

2095 12.4 0.3 0.0 gi|89161204:22028483-22038898 3575 3900 (6516) + AluSq SINE/Alu 1 313 (0) 2

3013 18.1 7.7 5.1 gi|89161204:22028483-22038898 3901 4640 (5776) C L1MA8 LINE/L1 (1828) 4315 3551 1

1507 22.6 1.4 0.0 gi|89161204:22028483-22038898 4644 4918 (5498) + AluJo SINE/Alu 1 279 (33) 3

231 6.1 0.0 0.0 gi|89161204:22028483-22038898 4919 4951 (5465) + (CAAA)n Simple_repeat 1 33 (0) 4

871 16.3 6.2 0.5 gi|89161204:22028483-22038898 4992 5170 (5246) C L1MA8 LINE/L1 (2585) 3558 3370 1 (R12 ? )

23 53.3 0.0 0.0 gi|89161204:22028483-22038898 5320 5349 (5067) + AT_rich Low_complexity 1 30 (0) 5

337 26.9 0.8 2.6 gi|89161204:22028483-22038898 5803 5931 (4485) C MLT1H2 LTR/ERVL-MaLR (16) 533 382 6

230 31.2 3.0 0.0 gi|89161204:22028483-22038898 6020 6120 (4296) C MLT1J2 LTR/ERVL-MaLR (328) 161 65 7

654 29.4 3.1 5.4 gi|89161204:22028483-22038898 6238 6490 (3926) + MIRb SINE/MIR 14 262 (0) 8

2188 12.3 0.0 1.4 gi|89161204:22028483-22038898 6626 6925 (3491) C AluSx SINE/Alu (16) 296 1 9

216 9.7 0.0 0.0 gi|89161204:22028483-22038898 7107 7137 (3279) + (TGAA)n Simple_repeat 3 33 (0) 10

25 56.0 0.0 0.0 gi|89161204:22028483-22038898 7728 7752 (2664) + AT_rich Low_complexity 1 25 (0) 11

22 54.5 0.0 0.0 gi|89161204:22028483-22038898 7792 7813 (2603) + AT_rich Low_complexity 1 22 (0) 12

230 26.7 10.0 0.0 gi|89161204:22028483-22038898 7826 7915 (2501) + Tigger16a DNA/TcMar-Tigger 742 840 (93) 13

267 23.2 2.9 1.4 gi|89161204:22028483-22038898 8432 8501 (1915) C MER5B DNA/hAT-Charlie (104) 74 4 14

284 29.6 0.0 0.0 gi|89161204:22028483-22038898 8579 8666 (1750) C Charlie2a DNA/hAT-Charlie (2598) 263 176 15

284 24.4 7.9 2.8 gi|89161204:22028483-22038898 8693 8793 (1623) C Charlie2a DNA/hAT-Charlie (2751) 110 5 15

423 18.8 11.6 5.0 gi|89161204:22028483-22038898 8796 8875 (1541) + L2a LINE/L2 3308 3394 (32) 16

2509 18.0 1.4 12.2 gi|89161204:22028483-22038898 8876 9445 (971) + MLT2B2 LTR/ERVL 1 515 (0) 17

423 18.8 11.6 5.0 gi|89161204:22028483-22038898 9446 9476 (940) + L2a LINE/L2 3395 3426 (0) 16

21 60.0 0.0 0.0 gi|89161204:22028483-22038898 9811 9845 (571) + AT_rich Low_complexity 1 35 (0) 18

26 81.5 0.0 0.0 gi|89161204:22028483-22038898 10019 10072 (344) + AT_rich Low_complexity 1 54 (0) 19

207 0.0 0.0 0.0 gi|89161204:22028483-22038898 10229 10251 (165) + (TTAAA)n Simple_repeat 4 26 (0) 20

______

L1HS_4_8 (Reference Human) M_DISRUPTED

203 33.3 5.3 6.1 chr4 16547199 16547329 (174725734) C MIR3 SINE/MIR (31) 177 48 220

704 17.0 0.0 0.9 chr4 16547348 16547460 (174725603) + FLAM_A SINE/Alu 8 119 (23) 221

2055 14.4 0.0 0.6 chr4 16547480 16547793 (174725270) C AluSx SINE/Alu (0) 312 1 222

286 34.1 3.2 2.4 chr4 16547995 16548120 (174724943) + MIRb SINE/MIR 40 166 (102) 223

1723 13.4 1.0 3.1 chr4 16548440 16548732 (174724331) + AluJb SINE/Alu 23 309 (3) 224

295 20.8 8.3 0.0 chr4 16550074 16550145 (174722918) + L1ME4a LINE/L1 5715 5792 (329) 225

365 30.1 7.1 5.2 chr4 16550581 16550888 (174722175) + L1ME4a LINE/L1 5789 6102 (19) 225

253 33.0 5.5 0.0 chr4 16551405 16551495 (174721568) C MIR3 SINE/MIR (46) 162 67 226

225 34.2 2.5 5.8 chr4 16551517 16551637 (174721426) C L2 LINE/L2 (5) 3373 3257 227

196 25.6 0.0 0.0 chr4 16551805 16551847 (174721216) + L2 LINE/L2 3373 3415 (4) 228

27 6.2 0.0 0.0 chr4 16551854 16551901 (174721162) + AT_rich Low_complexity 1 48 (0) 229

27 8.7 0.0 0.0 chr4 16551944 16552012 (174721051) + AT_rich Low_complexity 1 69 (0) 230

207 33.8 8.4 0.0 chr4 16552058 16552128 (174720935) C MIRb SINE/MIR (29) 239 163 231

523 33.1 7.9 4.7 chr4 16552156 16552409 (174720654) C MIR SINE/MIR (0) 262 1 232

404 13.4 10.4 0.0 chr4 16553284 16553350 (174719713) C MLT1C LTR/MaLR (0) 467 394 233

19171 0.6 0.1 0.7 chr4 16553498 16555351 (174717712) + L1HS LINE/L1 3 1857 (4175) 234 (R1) (L1HS_4_8)

2782 0.7 0.0 0.0 chr4 16555352 16555647 (174717416) + AluYb8 SINE/Alu 23 318 (0) 235 (D)

29360 0.5 0.0 0.0 chr4 16555648 16559834 (174713229) + L1HS LINE/L1 1858 6031 (1) 236 (R2)

2548 15.3 2.2 0.0 chr4 16559835 16560240 (174712823) C MLT1C LTR/MaLR (52) 415 1 233

2433 8.3 0.0 0.0 chr4 16560272 16560572 (174712491) C AluY SINE/Alu (9) 302 2 237

1921 12.0 0.0 9.6 chr4 16560600 16560913 (174712150) + AluSx SINE/Alu 1 284 (28) 238

182 3.7 3.7 0.0 chr4 16560914 16560940 (174712123) + (TAA)n Simple_repeat 2 29 (0) 239

2195 9.0 1.4 0.0 chr4 16560960 16561248 (174711815) C L1PA10 LINE/L1 (248) 5920 5628 240

2605 16.2 1.0 5.6 chr4 16561719 16562221 (174710842) + MLT1D LTR/MaLR 26 505 (0) 241

189 13.9 0.0 2.7 chr4 16563100 16563136 (174709927) C MIRm SINE/MIR (11) 265 230 242

213 3.9 0.0 0.0 chr4 16564221 16564246 (174708817) + (A)n Simple_repeat 1 26 (0) 243

2192 16.9 5.8 6.2 chr4 16565149 16565582 (174707481) C MSTB1 LTR/MaLR (0) 432 1 244

1257 16.7 1.2 7.4 chr4 16565590 16565847 (174707216) C MSTB-int LTR/MaLR (7) 1644 1403 244

3213 22.0 1.7 0.3 chr4 16565845 16566505 (174706558) C MSTB-int LTR/MaLR (981) 670 1 244

523 17.2 2.1 0.0 chr4 16566510 16566602 (174706461) C MSTB1 LTR/MaLR (335) 97 3 245

2464 19.1 2.9 0.0 chr4 16566759 16567172 (174705891) C MSTB LTR/MaLR (0) 426 1 244

Celera ortholog (5 kb upstream and downstream of the identified ortholog)

1078 14.6 1.1 3.3 gi|89161206:17404459-17416251 2 186 (11607) + AluJb SINE/Alu 129 309 (3) 1

271 19.4 8.3 0.0 gi|89161206:17404459-17416251 1528 1599 (10194) + L1MC LINE/L1 5713 5790 (2092) 2

684 25.6 3.6 1.5 gi|89161206:17404459-17416251 1612 1805 (9988) + LTR79 LTR/ERVL 20 217 (310) 3

357 26.1 18.9 0.5 gi|89161206:17404459-17416251 1837 2032 (9761) + LTR79 LTR/ERVL 296 527 (0) 3

224 33.0 5.5 0.0 gi|89161206:17404459-17416251 2859 2949 (8844) C MIR3 SINE/MIR (46) 162 67 4

205 22.7 0.0 0.0 gi|89161206:17404459-17416251 3258 3301 (8492) + L2c LINE/L2 3340 3383 (4) 5

27 72.9 0.0 0.0 gi|89161206:17404459-17416251 3308 3355 (8438) + AT_rich Low_complexity 1 48 (0) 6

27 89.9 0.0 0.0 gi|89161206:17404459-17416251 3398 3466 (8327) + AT_rich Low_complexity 1 69 (0) 7

183 33.8 8.4 0.0 gi|89161206:17404459-17416251 3512 3582 (8211) C MIRb SINE/MIR (29) 239 163 8

454 33.6 4.8 4.8 gi|89161206:17404459-17416251 3633 3863 (7930) C MIR SINE/MIR (31) 231 1 9

394 13.4 10.4 0.0 gi|89161206:17404459-17416251 4738 4804 (6989) C MLT1C LTR/ERVL-MaLR (0) 467 394 10

29228 0.6 0.0 0.0 gi|89161206:17404459-17416251 4952 10979 (814) + L1HS LINE/L1 126 6154 (1) 11 (R)

2534 15.3 2.2 0.0 gi|89161206:17404459-17416251 10980 11385 (408) C MLT1C LTR/ERVL-MaLR (52) 415 1 10

2450 8.3 0.0 0.0 gi|89161206:17404459-17416251 11417 11717 (76) C AluY SINE/Alu (9) 302 2 12

359 14.3 0.0 0.0 gi|89161206:17404459-17416251 11745 11793 (0) + AluYk11 SINE/Alu 1 49 (263) 13

______

L1HS_4_9 (Reference Human) M_DISRUPTED

203 33.3 5.3 6.1 chr4 16547199 16547329 (174725734) C MIR3 SINE/MIR (31) 177 48 220

704 17.0 0.0 0.9 chr4 16547348 16547460 (174725603) + FLAM_A SINE/Alu 8 119 (23) 221

2055 14.4 0.0 0.6 chr4 16547480 16547793 (174725270) C AluSx SINE/Alu (0) 312 1 222

286 34.1 3.2 2.4 chr4 16547995 16548120 (174724943) + MIRb SINE/MIR 40 166 (102) 223

1723 13.4 1.0 3.1 chr4 16548440 16548732 (174724331) + AluJb SINE/Alu 23 309 (3) 224

295 20.8 8.3 0.0 chr4 16550074 16550145 (174722918) + L1ME4a LINE/L1 5715 5792 (329) 225

365 30.1 7.1 5.2 chr4 16550581 16550888 (174722175) + L1ME4a LINE/L1 5789 6102 (19) 225

253 33.0 5.5 0.0 chr4 16551405 16551495 (174721568) C MIR3 SINE/MIR (46) 162 67 226

225 34.2 2.5 5.8 chr4 16551517 16551637 (174721426) C L2 LINE/L2 (5) 3373 3257 227

196 25.6 0.0 0.0 chr4 16551805 16551847 (174721216) + L2 LINE/L2 3373 3415 (4) 228

27 6.2 0.0 0.0 chr4 16551854 16551901 (174721162) + AT_rich Low_complexity 1 48 (0) 229

27 8.7 0.0 0.0 chr4 16551944 16552012 (174721051) + AT_rich Low_complexity 1 69 (0) 230

207 33.8 8.4 0.0 chr4 16552058 16552128 (174720935) C MIRb SINE/MIR (29) 239 163 231

523 33.1 7.9 4.7 chr4 16552156 16552409 (174720654) C MIR SINE/MIR (0) 262 1 232

404 13.4 10.4 0.0 chr4 16553284 16553350 (174719713) C MLT1C LTR/MaLR (0) 467 394 233

19171 0.6 0.1 0.7 chr4 16553498 16555351 (174717712) + L1HS LINE/L1 3 1857 (4175) 234 (R1)

2782 0.7 0.0 0.0 chr4 16555352 16555647 (174717416) + AluYb8 SINE/Alu 23 318 (0) 235 (D)

29360 0.5 0.0 0.0 chr4 16555648 16559834 (174713229) + L1HS LINE/L1 1858 6031 (1) 236 (R2) (L1HS_4_9)

2548 15.3 2.2 0.0 chr4 16559835 16560240 (174712823) C MLT1C LTR/MaLR (52) 415 1 233

2433 8.3 0.0 0.0 chr4 16560272 16560572 (174712491) C AluY SINE/Alu (9) 302 2 237

1921 12.0 0.0 9.6 chr4 16560600 16560913 (174712150) + AluSx SINE/Alu 1 284 (28) 238

182 3.7 3.7 0.0 chr4 16560914 16560940 (174712123) + (TAA)n Simple_repeat 2 29 (0) 239

2195 9.0 1.4 0.0 chr4 16560960 16561248 (174711815) C L1PA10 LINE/L1 (248) 5920 5628 240

2605 16.2 1.0 5.6 chr4 16561719 16562221 (174710842) + MLT1D LTR/MaLR 26 505 (0) 241

189 13.9 0.0 2.7 chr4 16563100 16563136 (174709927) C MIRm SINE/MIR (11) 265 230 242

213 3.9 0.0 0.0 chr4 16564221 16564246 (174708817) + (A)n Simple_repeat 1 26 (0) 243

2192 16.9 5.8 6.2 chr4 16565149 16565582 (174707481) C MSTB1 LTR/MaLR (0) 432 1 244

1257 16.7 1.2 7.4 chr4 16565590 16565847 (174707216) C MSTB-int LTR/MaLR (7) 1644 1403 244

3213 22.0 1.7 0.3 chr4 16565845 16566505 (174706558) C MSTB-int LTR/MaLR (981) 670 1 244

523 17.2 2.1 0.0 chr4 16566510 16566602 (174706461) C MSTB1 LTR/MaLR (335) 97 3 245

2464 19.1 2.9 0.0 chr4 16566759 16567172 (174705891) C MSTB LTR/MaLR (0) 426 1 244

Celera ortholog (5 kb upstream and downstream of the identified ortholog)

1078 14.6 1.1 3.3 gi|89161206:17404459-17416251 2 186 (11607) + AluJb SINE/Alu 129 309 (3) 1

271 19.4 8.3 0.0 gi|89161206:17404459-17416251 1528 1599 (10194) + L1MC LINE/L1 5713 5790 (2092) 2

684 25.6 3.6 1.5 gi|89161206:17404459-17416251 1612 1805 (9988) + LTR79 LTR/ERVL 20 217 (310) 3

357 26.1 18.9 0.5 gi|89161206:17404459-17416251 1837 2032 (9761) + LTR79 LTR/ERVL 296 527 (0) 3

224 33.0 5.5 0.0 gi|89161206:17404459-17416251 2859 2949 (8844) C MIR3 SINE/MIR (46) 162 67 4

205 22.7 0.0 0.0 gi|89161206:17404459-17416251 3258 3301 (8492) + L2c LINE/L2 3340 3383 (4) 5

27 72.9 0.0 0.0 gi|89161206:17404459-17416251 3308 3355 (8438) + AT_rich Low_complexity 1 48 (0) 6

27 89.9 0.0 0.0 gi|89161206:17404459-17416251 3398 3466 (8327) + AT_rich Low_complexity 1 69 (0) 7

183 33.8 8.4 0.0 gi|89161206:17404459-17416251 3512 3582 (8211) C MIRb SINE/MIR (29) 239 163 8

454 33.6 4.8 4.8 gi|89161206:17404459-17416251 3633 3863 (7930) C MIR SINE/MIR (31) 231 1 9

394 13.4 10.4 0.0 gi|89161206:17404459-17416251 4738 4804 (6989) C MLT1C LTR/ERVL-MaLR (0) 467 394 10

29228 0.6 0.0 0.0 gi|89161206:17404459-17416251 4952 10979 (814) + L1HS LINE/L1 126 6154 (1) 11 (R)

2534 15.3 2.2 0.0 gi|89161206:17404459-17416251 10980 11385 (408) C MLT1C LTR/ERVL-MaLR (52) 415 1 10

2450 8.3 0.0 0.0 gi|89161206:17404459-17416251 11417 11717 (76) C AluY SINE/Alu (9) 302 2 12

359 14.3 0.0 0.0 gi|89161206:17404459-17416251 11745 11793 (0) + AluYk11 SINE/Alu 1 49 (263) 13

______

L1HS_4_23c (Reference human)

234 24.6 1.8 0.0 chr4 45746438 45746494 (145526569) + L2 LINE/L2 3362 3419 (0) 320

283 29.3 4.9 2.0 chr4 45747436 45747615 (145525448) + MIRb SINE/MIR 30 262 (0) 321

21 0.0 0.0 0.0 chr4 45748531 45748551 (145524512) + AT_rich Low_complexity 1 21 (0) 322

792 32.0 5.7 6.6 chr4 45748621 45749132 (145523931) + MLT1J LTR/MaLR 5 511 (0) 323

221 31.9 5.8 0.0 chr4 45749760 45749828 (145523235) + MIR SINE/MIR 49 121 (141) 324

617 27.6 16.2 1.7 chr4 45749923 45750268 (145522795) C L1M5 LINE/L1 (3282) 2864 2469 325

8995 0.1 0.0 0.0 chr4 45750761 45751768 (145521295) C L1HS LINE/L1 (1132) 5014 4007 326 (R2)

7982 0.3 0.0 0.1 chr4 45751763 45752952 (145520111) + L1HS LINE/L1 5028 6216 (0) 326 (R1)

680 37.3 5.6 2.6 chr4 45752953 45753508 (145519555) + L2 LINE/L2 2851 3416 (3) 327

354 15.2 0.0 0.0 chr4 45753769 45753827 (145519236) C L1M1 LINE/L1 (705) 5600 5542 328

1006 30.3 8.6 6.9 chr4 45755493 45756167 (145516896) C L1ME3B LINE/L1 (9) 6231 5552 329

1743 13.7 0.0 8.2 chr4 45756168 45756486 (145516577) C AluSx SINE/Alu (19) 293 1 330

1006 29.4 9.7 5.2 chr4 45756487 45756810 (145516253) C L1ME3B LINE/L1 (689) 5551 5205 329

240 3.5 0.0 0.0 chr4 45757028 45757056 (145516007) + (TG)n Simple_repeat 2 30 (0) 331

215 29.9 0.0 5.4 chr4 45757648 45757739 (145515324) + MIRb SINE/MIR 112 198 (70) 332

Ortholog in Celera

244 22.8 1.8 0.0 gi|89161206:46501288-46511292 625 681 (9324) + L2a LINE/L2 3369 3426 (0) 1

283 27.7 5.7 1.6 gi|89161206:46501288-46511292 1615 1802 (8203) + MIRb SINE/MIR 16 262 (0) 2

21 52.4 0.0 0.0 gi|89161206:46501288-46511292 2718 2738 (7267) + AT_rich Low_complexity 1 21 (0) 3

644 32.2 5.9 6.7 gi|89161206:46501288-46511292 2808 3319 (6686) + MLT1J LTR/ERVL-MaLR 5 512 (0) 4

218 31.9 5.8 0.0 gi|89161206:46501288-46511292 3947 4015 (5990) + MIR SINE/MIR 49 121 (141) 5

613 27.2 14.8 1.4 gi|89161206:46501288-46511292 4110 4459 (5546) C L1M5 LINE/L1 (3282) 2864 2469 6

454 4.2 1.2 0.0 gi|89161206:46501288-46511292 4940 5004 (5001) C L1P1 LINE/L1 (1116) 5030 4962 7 (R12)

659 37.6 5.4 1.9 gi|89161206:46501288-46511292 5006 5501 (4504) + L2a LINE/L2 2911 3423 (3) 8

354 15.2 0.0 0.0 gi|89161206:46501288-46511292 5762 5820 (4185) C L1M1 LINE/L1 (702) 5600 5542 9

967 29.9 8.2 5.6 gi|89161206:46501288-46511292 7486 8160 (1845) C L1ME3B LINE/L1 (11) 6231 5550 10

1880 12.5 0.0 8.9 gi|89161206:46501288-46511292 8161 8479 (1526) C AluSx1 SINE/Alu (19) 293 1 11

967 28.9 9.6 4.6 gi|89161206:46501288-46511292 8480 8803 (1202) C L1ME3B LINE/L1 (693) 5549 5205 10

240 3.5 0.0 0.0 gi|89161206:46501288-46511292 9021 9049 (956) + (TG)n Simple_repeat 2 30 (0) 12

215 30.0 0.0 5.8 gi|89161206:46501288-46511292 9641 9732 (273) + MIRb SINE/MIR 112 198 (70) 13

______

L1HS_7_15c (Reference Human genome)

667 17.7 7.1 0.0 chr7 31486660 31486800 (127334624) + ORSL DNA/Tip100 1 151 (124) 9

716 22.2 0.0 0.0 chr7 31486808 31486942 (127334482) C AluJb SINE/Alu (176) 136 2 10

785 13.6 6.8 0.0 chr7 31486946 31487077 (127334347) + ORSL DNA/Tip100 135 275 (0) 9

404 25.8 10.4 0.0 chr7 31487453 31487635 (127333789) + MIR SINE/MIR 20 239 (29) 11

25 0.0 0.0 0.0 chr7 31487681 31487705 (127333719) + AT_rich Low_complexity 1 25 (0) 12

1688 20.4 3.8 2.8 chr7 31488292 31488684 (127332740) + MER31A LTR/ERV1 89 485 (0) 13

227 34.5 15.7 2.0 chr7 31488790 31489088 (127332336) C L2 LINE/L2 (799) 2620 2281 14

221 22.6 0.0 1.9 chr7 31489665 31489718 (127331706) + MIRb SINE/MIR 116 168 (100) 15

214 34.8 0.0 0.0 chr7 31490140 31490208 (127331216) + L2 LINE/L2 3349 3417 (2) 16 (R1)

583 12.6 1.1 0.0 chr7 31490218 31490304 (127331120) + L1PB1 LINE/L1 5613 5700 (451) 17

8236 0.4 0.0 0.0 chr7 31490305 31491778 (127329646) C L1HS LINE/L1 (0) 6196 4723 18 (R2)

3182 9.7 1.1 1.3 chr7 31491779 31492240 (127329184) + L1PB1 LINE/L1 5687 6147 (4) 17

218 22.2 2.2 0.0 chr7 31492267 31492311 (127329113) + L2 LINE/L2 3316 3361 (17) 19

339 31.4 7.9 0.7 chr7 31492529 31492696 (127328728) C MIR SINE/MIR (80) 186 1 20

363 29.4 3.7 3.9 chr7 31492823 31493014 (127328410) + MIR SINE/MIR 20 210 (58) 21

21 3.6 0.0 0.0 chr7 31493078 31493105 (127328319) + AT_rich Low_complexity 1 28 (0) 22

262 26.8 5.3 3.0 chr7 31493785 31493915 (127327509) + L2 LINE/L2 2701 2834 (585) 23

226 31.5 16.1 0.0 chr7 31494113 31494242 (127327182) + MIRb SINE/MIR 3 153 (115) 24

797 17.1 2.9 2.3 chr7 31494262 31494435 (127326989) + MER96B DNA/MER1_type? 5 179 (238) 25

569 24.0 15.0 3.4 chr7 31494511 31494777 (127326647) + MER5C DNA/MER1_type 27 324 (0) 26

686 32.2 9.4 2.8 chr7 31495095 31495585 (127325839) C L2 LINE/L2 (0) 3419 2889 27

2211 12.5 0.0 0.0 chr7 31495714 31496018 (127325406) C AluSx SINE/Alu (7) 305 1 28

Ortholog in Celera

650 26.1 5.7 8.6 gi|89161211:31507470-31517763 714 1011 (9283) + MLT1B LTR/ERVL-MaLR 34 323 (67) 1

287 24.8 8.6 0.0 gi|89161211:31507470-31517763 1213 1329 (8965) + MIRc SINE/MIR 25 151 (117) 2

660 17.7 7.1 0.0 gi|89161211:31507470-31517763 1580 1720 (8574) + ORSL DNA/hAT-Tip100 1 151 (124) 3

734 22.1 0.0 0.0 gi|89161211:31507470-31517763 1728 1863 (8431) C AluJb SINE/Alu (176) 136 1 4

779 13.6 6.8 0.0 gi|89161211:31507470-31517763 1866 1997 (8297) + ORSL DNA/hAT-Tip100 135 275 (0) 5

395 25.1 9.0 0.0 gi|89161211:31507470-31517763 2373 2505 (7789) + MIR SINE/MIR 20 177 (91) 6

25 40.0 0.0 0.0 gi|89161211:31507470-31517763 2599 2623 (7671) + AT_rich Low_complexity 1 25 (0) 7

25 64.0 0.0 0.0 gi|89161211:31507470-31517763 2601 2625 (7669) + AT_rich Low_complexity 1 25 (0) 8

1729 20.8 3.3 2.3 gi|89161211:31507470-31517763 3212 3604 (6690) + MER31A LTR/ERV1 89 485 (0) 9

323 33.5 1.2 1.8 gi|89161211:31507470-31517763 3845 4008 (6286) C L2 LINE/L2 (976) 2443 2281 10

294 29.1 0.0 1.2 gi|89161211:31507470-31517763 4585 4671 (5623) + MIRc SINE/MIR 113 198 (70) 11

2907 0.3 0.0 0.0 gi|89161211:31507470-31517763 5022 5343 (4951) C L1P1 LINE/L1 (1102) 5044 4723 12 (R12)

3181 9.7 1.1 1.3 gi|89161211:31507470-31517763 5344 5805 (4489) + L1PB1 LINE/L1 5687 6147 (4) 13

222 20.0 2.2 0.0 gi|89161211:31507470-31517763 5832 5876 (4418) + L2b LINE/L2 3313 3358 (17) 14

333 31.4 7.9 0.6 gi|89161211:31507470-31517763 6094 6261 (4033) C MIR SINE/MIR (82) 186 1 15

547 32.0 1.1 0.0 gi|89161211:31507470-31517763 6406 6580 (3714) + MIRc SINE/MIR 41 217 (51) 16

21 78.6 0.0 0.0 gi|89161211:31507470-31517763 6643 6670 (3624) + AT_rich Low_complexity 1 28 (0) 17

260 26.8 5.3 3.0 gi|89161211:31507470-31517763 7350 7480 (2814) + L2 LINE/L2 2701 2834 (585) 18

254 28.1 16.4 0.0 gi|89161211:31507470-31517763 7680 7807 (2487) + MIRc SINE/MIR 2 150 (118) 19

800 17.1 2.9 2.3 gi|89161211:31507470-31517763 7827 8000 (2294) + MER96B DNA/hAT 5 179 (238) 20

614 25.1 9.0 1.4 gi|89161211:31507470-31517763 8076 8342 (1952) + MER5C DNA/hAT-Charlie 27 313 (0) 21

504 29.5 9.7 4.0 gi|89161211:31507470-31517763 8660 9150 (1144) C L2a LINE/L2 (0) 3426 2889 22

2226 12.5 0.0 0.0 gi|89161211:31507470-31517763 9279 9583 (711) C AluSx SINE/Alu (7) 305 1 23

231 23.5 0.0 0.0 gi|89161211:31507470-31517763 10055 10105 (189) + MLT1K LTR/ERVL-MaLR 528 578 (17) 24

______

L1HS_11_30c (Reference human genome) 0CCUPIED

679 33.5 10.4 5.3 chr11 41041361 41042133 (93410251) C L2 LINE/L2 (18) 3401 2562 525

306 20.6 0.0 1.4 chr11 41042697 41042765 (93409619) + MSTA LTR/MaLR 2 69 (359) 526

21581 14.9 2.1 5.8 chr11 41042766 41046236 (93406148) + L1PA8 LINE/L1 22 3376 (2955) 527

2085 12.9 0.6 2.5 chr11 41046237 41046553 (93405831) + AluSx SINE/Alu 1 311 (1) 528

21581 10.1 1.3 1.4 chr11 41046554 41049554 (93402830) + L1PA8 LINE/L1 3377 6356 (1) 527

5051 13.3 18.2 0.0 chr11 41049576 41050497 (93401887) + Tigger1 DNA/MER2_type 1149 2238 (180) 529

1190 18.9 8.1 6.2 chr11 41050507 41050827 (93401557) + THE1D LTR/MaLR 55 381 (0) 526

1845 19.8 5.4 4.4 chr11 41051235 41051662 (93400722) C MSTB1 LTR/MaLR (0) 432 1 530

243 6.1 0.0 0.0 chr11 41053136 41053168 (93399216) + (T)n Simple_repeat 1 33 (0) 531

742 0.0 0.0 0.0 chr11 41053176 41053262 (93399122) C L1HS LINE/L1 (0) 6155 6069 532 (L1HS_11_30c)

2148 31.8 8.4 5.8 chr11 41053605 41054440 (93397944) + L2 LINE/L2 1669 2529 (890) 533

1487 17.9 18.7 4.3 chr11 41054441 41054814 (93397570) C MSTA LTR/MaLR (0) 428 1 534

3201 31.6 7.0 3.7 chr11 41054815 41056492 (93395892) C MLT-int LTR/MaLR (0) 1735 2 535

1828 17.6 12.5 1.0 chr11 41056495 41056878 (93395506) C MSTA LTR/MaLR (0) 428 1 536

2148 31.9 7.6 4.5 chr11 41056879 41057288 (93395096) + L2 LINE/L2 2530 2955 (464) 533

1424 13.6 3.6 0.9 chr11 41057800 41058022 (93394362) + MER30 DNA/MER1_type 2 230 (0) 537

2356 9.7 0.0 0.3 chr11 41058469 41058778 (93393606) C AluSp SINE/Alu (4) 309 1 538

222 20.4 0.0 0.0 chr11 41059841 41059884 (93392500) + (CA)n Simple_repeat 2 45 (0) 539

23 0.0 0.0 0.0 chr11 41059899 41059921 (93392463) + AT_rich Low_complexity 1 23 (0) 540

189 0.0 0.0 0.0 chr11 41060554 41060574 (93391810) + (T)n Simple_repeat 1 21 (0) 541

519 24.0 11.7 6.1 chr11 41060604 41060834 (93391550) C MIR SINE/MIR (15) 247 4 542

21 0.0 0.0 0.0 chr11 41061793 41061813 (93390571) + AT_rich Low_complexity 1 21 (0) 543

666 27.5 2.0 3.0 chr11 41062345 41062543 (93389841) + MIRb SINE/MIR 14 210 (58) 544

21 0.0 0.0 0.0 chr11 41062672 41062692 (93389692) + AT_rich Low_complexity 1 21 (0) 545

2288 10.6 0.0 0.6 chr11 41062693 41063006 (93389378) + AluSx SINE/Alu 1 312 (0) 546

485 28.7 9.4 1.3 chr11 41063568 41063726 (93388658) + MIRb SINE/MIR 68 239 (29) 547

Orhtholog in Celera

6068 10.1 1.6 0.1 gi|89161188:41245026-41255090 1 1393 (8672) + L1PA8 LINE/L1 4759 6171 (1) 1

763 14.9 10.6 0.0 gi|89161188:41245026-41255090 1415 1555 (8510) + Tigger1 DNA/TcMar-Tigger 1149 1304 (1114) 2 *

4322 13.9 4.4 0.0 gi|89161188:41245026-41255090 1534 2244 (7821) + Tigger1 DNA/TcMar-Tigger 1317 2058 (360) 3

600 11.8 4.3 0.0 gi|89161188:41245026-41255090 2242 2334 (7731) + Tigger1 DNA/TcMar-Tigger 2140 2236 (182) 4 *

1171 19.6 8.1 6.1 gi|89161188:41245026-41255090 2346 2666 (7399) + THE1D LTR/ERVL-MaLR 55 381 (0) 5

511 28.3 0.6 2.9 gi|89161188:41245026-41255090 2884 3061 (7004) + Tigger9a DNA/TcMar-Tigger 558 731 (1) 6

1847 19.6 5.4 4.4 gi|89161188:41245026-41255090 3074 3501 (6564) C MSTB1 LTR/ERVL-MaLR (0) 432 1 7

294 8.7 0.0 0.0 gi|89161188:41245026-41255090 4975 5020 (5045) + (T)n Simple_repeat 1 46 (0) 8

722 1.1 0.0 0.0 gi|89161188:41245026-41255090 5028 5114 (4951) C L1HS LINE/L1 (0) 6155 6069 9 (OCCUPIED)

1136 31.4 6.5 4.7 gi|89161188:41245026-41255090 5457 6291 (3774) + L2 LINE/L2 1669 2523 (896) 10

1151 21.6 6.7 4.7 gi|89161188:41245026-41255090 6294 6667 (3398) C MSTA LTR/ERVL-MaLR (0) 381 1 11

7039 17.8 1.1 0.9 gi|89161188:41245026-41255090 6668 8194 (1871) C MSTA-int LTR/ERVL-MaLR (0) 1580 96 11

1055 13.0 0.0 0.0 gi|89161188:41245026-41255090 8192 8345 (1720) C MSTA-int LTR/ERVL-MaLR (1424) 156 3 11 *

1786 17.6 12.5 0.9 gi|89161188:41245026-41255090 8348 8731 (1334) C MSTA LTR/ERVL-MaLR (0) 428 1 11

912 33.1 4.7 1.9 gi|89161188:41245026-41255090 8739 9141 (924) + L2 LINE/L2 2545 2958 (461) 10

290 35.3 7.6 1.5 gi|89161188:41245026-41255090 9372 9621 (444) + LTR85a LTR/Gypsy? 289 553 (149) 12

1417 13.6 3.6 0.9 gi|89161188:41245026-41255090 9653 9875 (190) + MER30 DNA/hAT-Charlie 2 230 (0) 13

______

L1HS_12_41c (Reference human genome) C_INTER_RMD

7775 23.0 8.0 3.2 chr12 86656449 86657589 (45691945) + L1MC3 LINE/L1 6625 7777 (8) 134

1751 16.4 2.5 0.0 chr12 86660380 86660665 (45688869) C AluJb SINE/Alu (19) 293 1 138

1095 31.3 6.4 3.6 chr12 86662548 86663015 (45686519) + MLT1K LTR/MaLR 1 481 (110) 139

714 28.8 10.0 0.5 chr12 86663296 86663515 (45686019) + MIR SINE/MIR 10 250 (12) 140

37 5.2 0.0 0.0 chr12 86663528 86663585 (45685949) + AT_rich Low_complexity 1 58 (0) 141

201 37.9 2.9 1.0 chr12 86663736 86663839 (45685695) C L2 LINE/L2 (17) 3402 3297 142

184 30.4 3.6 0.0 chr12 86663922 86663977 (45685557) C L2 LINE/L2 (211) 3167 3110 142

27 4.9 0.0 0.0 chr12 86664583 86664623 (45684911) + AT_rich Low_complexity 1 41 (0) 143

21 0.0 0.0 0.0 chr12 86665451 86665471 (45684063) + AT_rich Low_complexity 1 21 (0) 144

9646 0.2 0.0 0.0 chr12 86665472 86667330 (45682204) C L1HS LINE/L1 (3) 6152 4294 1 (L1HS_12_41c) (R2)

6299 0.7 0.0 0.0 chr12 86667329 86668039 (45681495) + L1HS LINE/L1 3568 4278 (1868) 145

193 2.9 5.9 0.0 chr12 86668344 86668377 (45681157) + (TTA)n Simple_repeat 1 36 (0) 146

8849 2.9 0.0 0.0 chr12 86668379 86670176 (45679358) C L1PA3 LINE/L1 (18) 6137 4340 147 (R1)

3494 2.2 0.2 0.0 chr12 86670177 86670585 (45678949) + L1PA3 LINE/L1 3902 4311 (1835) 147

216 33.9 3.2 8.1 chr12 86671399 86671584 (45677950) C L2 LINE/L2 (740) 2679 2503 148

1565 27.5 9.1 3.2 chr12 86671741 86672682 (45676852) + L1MD LINE/L1 3033 4065 (2081) 149

429 33.9 10.4 0.0 chr12 86672689 86672918 (45676616) C L2 LINE/L2 (1074) 2345 2092 148

2030 13.4 0.3 1.9 chr12 86672923 86673233 (45676301) + AluSq SINE/Alu 3 308 (5) 150

709 15.0 1.6 0.8 chr12 86673684 86673811 (45675723) + L1MB3 LINE/L1 6054 6182 (1) 151

423 22.3 1.8 1.8 chr12 86673815 86673928 (45675606) + Charlie2 DNA/MER1_type 2707 2820 (42) 152

2348 7.0 0.0 2.9 chr12 86674354 86674663 (45674871) + AluY SINE/Alu 1 301 (10) 153

Ortholog in Celera

1005 13.2 0.0 0.0 gi|89161189:87807275-87819039 10 145 (11620) C AluJb SINE/Alu (176) 136 1 1

1075 31.5 6.4 3.1 gi|89161189:87807275-87819039 2028 2495 (9270) + MLT1K LTR/ERVL-MaLR 1 483 (112) 2

698 28.8 10.0 0.4 gi|89161189:87807275-87819039 2776 2995 (8770) + MIR SINE/MIR 10 250 (12) 3

37 79.3 0.0 0.0 gi|89161189:87807275-87819039 3008 3065 (8700) + AT_rich Low_complexity 1 58 (0) 4

304 38.4 7.4 3.2 gi|89161189:87807275-87819039 3216 3457 (8308) C L2b LINE/L2 (17) 3358 3107 5

180 0.0 0.0 0.0 gi|89161189:87807275-87819039 4065 4084 (7681) + (T)n Simple_repeat 1 20 (0) 6

8849 2.4 0.0 0.0 gi|89161189:87807275-87819039 4952 6764 (5001) C L1HS LINE/L1 (3) 6152 4340 7 (R12)

3494 2.2 0.2 0.0 gi|89161189:87807275-87819039 6765 7173 (4592) + L1HS LINE/L1 3902 4311 (1835) 7

213 34.1 3.2 8.5 gi|89161189:87807275-87819039 7987 8172 (3593) C L2b LINE/L2 (740) 2679 2503 5

982 26.3 8.4 5.0 gi|89161189:87807275-87819039 8329 9137 (2628) + L1M5 LINE/L1 3033 3883 (2263) 8

238 25.7 8.0 0.0 gi|89161189:87807275-87819039 9158 9270 (2495) + L1M5 LINE/L1 3944 4065 (2081) 8

301 34.4 9.6 0.0 gi|89161189:87807275-87819039 9277 9506 (2259) C L2b LINE/L2 (1074) 2345 2092 5

2168 12.5 0.3 2.0 gi|89161189:87807275-87819039 9511 9821 (1944) + AluSq2 SINE/Alu 3 308 (4) 9

708 15.0 1.6 0.8 gi|89161189:87807275-87819039 10272 10399 (1366) + L1MB3 LINE/L1 6054 6182 (1) 10

422 22.3 1.8 1.8 gi|89161189:87807275-87819039 10403 10516 (1249) + Charlie2b DNA/hAT-Charlie 2627 2740 (42) 11

2466 6.8 0.0 3.0 gi|89161189:87807275-87819039 10942 11251 (514) + AluY SINE/Alu 1 301 (10) 12

469 13.8 11.7 0.0 gi|89161189:87807275-87819039 11662 11755 (10) C ORSL DNA/hAT-Tip100 (13) 262 158 13

______

L1HS_18_2c (Reference human genome) M_DISRUPTED

5028 15.3 2.3 5.0 chr18 823890 824715 (75292438) C MER49 LTR/ERV1 (36) 887 79 603

2203 10.6 0.7 0.0 chr18 824716 825007 (75292146) + AluSq SINE/Alu 6 299 (14) 605

5028 15.3 2.3 5.0 chr18 825008 825051 (75292102) C MER49 LTR/ERV1 (845) 78 35 603

347 13.9 9.7 0.0 chr18 825053 825124 (75292029) C L1MB2 LINE/L1 (213) 5958 5880 606

1670 17.7 3.8 0.0 chr18 825140 825427 (75291726) C AluJb SINE/Alu (13) 299 1 607

194 27.9 0.0 0.0 chr18 825428 825470 (75291683) + MER5B DNA/MER1_type 136 178 (0) 608

1322 3.6 0.0 1.2 chr18 825474 825639 (75291514) + L1PA2 LINE/L1 5992 6155 (0) 609

2039 13.2 3.1 0.0 chr18 825655 825942 (75291211) + AluSx SINE/Alu 1 297 (15) 610

220 30.1 0.0 1.4 chr18 825944 826017 (75291136) C MER5B DNA/MER1_type (32) 146 74 611

2026 14.3 1.0 0.0 chr18 826409 826715 (75290438) C AluSq SINE/Alu (3) 310 1 612

4690 1.7 0.0 1.9 chr18 826734 827111 (75290042) C L1HS LINE/L1 (1) 6154 5785 613 (R1) (L1HS_18_2c)

2903 0.7 0.0 0.0 chr18 827112 827418 (75289735) C AluYb8 SINE/Alu (11) 307 1 614 (D)

4690 1.7 0.0 1.9 chr18 827419 827581 (75289572) C L1HS LINE/L1 (371) 5784 5623 613 (R2)

817 1.1 0.0 0.0 chr18 827582 827670 (75289483) + L1P2 LINE/L1 5523 5611 (544) 615

391 30.0 4.6 0.0 chr18 827787 827916 (75289237) + MIR SINE/MIR 110 245 (17) 616

1979 12.4 3.9 2.6 chr18 828425 828731 (75288422) C AluSx SINE/Alu (1) 311 1 617

2216 10.6 7.2 2.6 chr18 828988 829335 (75287818) C THE1B LTR/MaLR (0) 364 1 618

1088 20.0 0.4 6.0 chr18 830458 830691 (75286462) + AluJo SINE/Alu 1 221 (91) 619

506 19.8 0.0 0.0 chr18 830694 830779 (75286374) C AluJ/FLAM SINE/Alu (225) 87 2 620

444 29.7 8.7 0.9 chr18 830927 831157 (75285996) C MIR SINE/MIR (12) 250 2 621

460 29.4 3.2 6.4 chr18 831384 831441 (75285712) + L2 LINE/L2 2930 2979 (440) 622

3506 6.5 4.4 10.0 chr18 831442 831609 (75285544) + LTR2C LTR/ERV1 4 172 (329) 623

261 0.0 0.0 0.0 chr18 831610 831638 (75285515) + (TAA)n Simple_repeat 2 30 (0) 624

Ortholog in Celera

1381 16.9 1.1 3.9 gi|89161196:706482-716803 84 348 (9974) C MER44B DNA/TcMar-Tigger (0) 550 293 1

1169 19.8 2.2 2.2 gi|89161196:706482-716803 747 968 (9354) C MER44B DNA/TcMar-Tigger (250) 300 79 1

2343 9.4 0.0 0.7 gi|89161196:706482-716803 970 1268 (9054) C AluSx1 SINE/Alu (15) 297 1 2

299 21.7 0.0 0.0 gi|89161196:706482-716803 1269 1328 (8994) + L1MD3 LINE/L1 5894 5953 (2042) 3

423 29.9 11.1 2.8 gi|89161196:706482-716803 1373 1724 (8598) C L2c LINE/L2 (896) 2523 2173 4

5021 15.4 2.3 5.1 gi|89161196:706482-716803 1745 1784 (8538) C MER49 LTR/ERV1 (2) 921 882 5

1847 15.1 2.6 2.2 gi|89161196:706482-716803 1785 2095 (8227) + AluJo SINE/Alu 1 312 (0) 6

5021 15.4 2.3 5.1 gi|89161196:706482-716803 2096 2920 (7402) C MER49 LTR/ERV1 (42) 881 71 5

2210 10.6 0.7 0.0 gi|89161196:706482-716803 2921 3212 (7110) + AluSq2 SINE/Alu 6 299 (13) 7

5021 15.4 2.3 5.1 gi|89161196:706482-716803 3213 3256 (7066) C MER49 LTR/ERV1 (853) 70 35 5

342 13.9 9.7 0.0 gi|89161196:706482-716803 3258 3329 (6993) C L1MB2 LINE/L1 (213) 5958 5880 8

1760 17.2 3.8 0.0 gi|89161196:706482-716803 3345 3634 (6688) C AluJb SINE/Alu (11) 301 1 9

222 25.6 0.0 0.0 gi|89161196:706482-716803 3635 3677 (6645) C MER5B DNA/hAT-Charlie (135) 43 1 10

1320 3.6 0.0 1.2 gi|89161196:706482-716803 3681 3846 (6476) + L1PA2 LINE/L1 5992 6155 (0) 11

2037 13.2 3.1 0.0 gi|89161196:706482-716803 3862 4149 (6173) + AluSz SINE/Alu 1 297 (15) 12

228 30.1 0.0 1.4 gi|89161196:706482-716803 4151 4224 (6098) C MER5B DNA/hAT-Charlie (32) 146 74 13

199 33.1 4.5 4.5 gi|89161196:706482-716803 4335 4467 (5855) C L2 LINE/L2 (1327) 2092 1960 14

2185 13.6 0.0 0.0 gi|89161196:706482-716803 4616 4925 (5397) C AluSq2 SINE/Alu (2) 310 1 15

4770 1.5 0.0 0.0 gi|89161196:706482-716803 4951 5483 (4839) C L1HS LINE/L1 (0) 6155 5623 16 (R)

817 1.1 0.0 0.0 gi|89161196:706482-716803 5484 5572 (4750) + L1HS LINE/L1 5523 5611 (544) 16

189 37.5 0.0 1.8 gi|89161196:706482-716803 5620 5676 (4646) + MIR SINE/MIR 6 61 (201) 17

437 30.0 4.6 0.0 gi|89161196:706482-716803 5689 5818 (4504) + MIR SINE/MIR 110 245 (17) 17

2121 11.4 4.0 0.3 gi|89161196:706482-716803 6327 6625 (3697) C AluSz SINE/Alu (2) 310 1 18

2161 11.2 7.2 2.5 gi|89161196:706482-716803 6882 7229 (3093) C THE1B LTR/ERVL-MaLR (0) 364 1 19

191 31.6 5.1 0.8 gi|89161196:706482-716803 7237 7354 (2968) + MIR3 SINE/MIR 57 179 (29) 20

1078 18.0 0.4 11.3 gi|89161196:706482-716803 8352 8596 (1726) + AluJo SINE/Alu 1 221 (91) 21

554 19.5 0.0 0.0 gi|89161196:706482-716803 8599 8685 (1637) C AluJo SINE/Alu (225) 87 1 22

422 29.7 8.7 0.8 gi|89161196:706482-716803 8832 9062 (1260) C MIR SINE/MIR (12) 250 2 23

471 31.9 1.6 6.2 gi|89161196:706482-716803 9265 9346 (976) + L2b LINE/L2 2903 2979 (440) 24

3525 5.9 4.4 10.6 gi|89161196:706482-716803 9347 9514 (808) + LTR2C LTR/ERV1 4 172 (329) 25

207 0.0 0.0 0.0 gi|89161196:706482-716803 9515 9537 (785) + (TAA)n Simple_repeat 2 24 (0) 26

3525 5.9 4.4 10.6 gi|89161196:706482-716803 9538 9896 (426) + LTR2C LTR/ERV1 173 500 (1) 25

471 33.0 3.8 5.1 gi|89161196:706482-716803 9897 10174 (148) + L2b LINE/L2 2977 3276 (111) 24

373 21.3 2.7 0.0 gi|89161196:706482-716803 10228 10302 (20) + MER91A DNA/hAT-Tip100 19 95 (101) 27

______

L1HS_18_3c (Reference human genome) (M_DISRUPTED)

347 13.9 9.7 0.0 chr18 825053 825124 (75292029) C L1MB2 LINE/L1 (213) 5958 5880 606

1670 17.7 3.8 0.0 chr18 825140 825427 (75291726) C AluJb SINE/Alu (13) 299 1 607

194 27.9 0.0 0.0 chr18 825428 825470 (75291683) + MER5B DNA/MER1_type 136 178 (0) 608

1322 3.6 0.0 1.2 chr18 825474 825639 (75291514) + L1PA2 LINE/L1 5992 6155 (0) 609

2039 13.2 3.1 0.0 chr18 825655 825942 (75291211) + AluSx SINE/Alu 1 297 (15) 610

220 30.1 0.0 1.4 chr18 825944 826017 (75291136) C MER5B DNA/MER1_type (32) 146 74 611

2026 14.3 1.0 0.0 chr18 826409 826715 (75290438) C AluSq SINE/Alu (3) 310 1 612

4690 1.7 0.0 1.9 chr18 826734 827111 (75290042) C L1HS LINE/L1 (1) 6154 5785 613 (R1)

2903 0.7 0.0 0.0 chr18 827112 827418 (75289735) C AluYb8 SINE/Alu (11) 307 1 614 (D)

4690 1.7 0.0 1.9 chr18 827419 827581 (75289572) C L1HS LINE/L1 (371) 5784 5623 613 (R2) (L1HS_18_3c)

817 1.1 0.0 0.0 chr18 827582 827670 (75289483) + L1P2 LINE/L1 5523 5611 (544) 615

391 30.0 4.6 0.0 chr18 827787 827916 (75289237) + MIR SINE/MIR 110 245 (17) 616

1979 12.4 3.9 2.6 chr18 828425 828731 (75288422) C AluSx SINE/Alu (1) 311 1 617

2216 10.6 7.2 2.6 chr18 828988 829335 (75287818) C THE1B LTR/MaLR (0) 364 1 618

1088 20.0 0.4 6.0 chr18 830458 830691 (75286462) + AluJo SINE/Alu 1 221 (91) 619

506 19.8 0.0 0.0 chr18 830694 830779 (75286374) C AluJ/FLAM SINE/Alu (225) 87 2 620

444 29.7 8.7 0.9 chr18 830927 831157 (75285996) C MIR SINE/MIR (12) 250 2 621

Ortholog in Celera

342 13.9 9.7 0.0 gi|89161196:706482-716803 3258 3329 (6993) C L1MB2 LINE/L1 (213) 5958 5880 8

1760 17.2 3.8 0.0 gi|89161196:706482-716803 3345 3634 (6688) C AluJb SINE/Alu (11) 301 1 9

222 25.6 0.0 0.0 gi|89161196:706482-716803 3635 3677 (6645) C MER5B DNA/hAT-Charlie (135) 43 1 10

1320 3.6 0.0 1.2 gi|89161196:706482-716803 3681 3846 (6476) + L1PA2 LINE/L1 5992 6155 (0) 11

2037 13.2 3.1 0.0 gi|89161196:706482-716803 3862 4149 (6173) + AluSz SINE/Alu 1 297 (15) 12

228 30.1 0.0 1.4 gi|89161196:706482-716803 4151 4224 (6098) C MER5B DNA/hAT-Charlie (32) 146 74 13

199 33.1 4.5 4.5 gi|89161196:706482-716803 4335 4467 (5855) C L2 LINE/L2 (1327) 2092 1960 14

2185 13.6 0.0 0.0 gi|89161196:706482-716803 4616 4925 (5397) C AluSq2 SINE/Alu (2) 310 1 15

4770 1.5 0.0 0.0 gi|89161196:706482-716803 4951 5483 (4839) C L1HS LINE/L1 (0) 6155 5623 16 (R)

817 1.1 0.0 0.0 gi|89161196:706482-716803 5484 5572 (4750) + L1HS LINE/L1 5523 5611 (544) 16

189 37.5 0.0 1.8 gi|89161196:706482-716803 5620 5676 (4646) + MIR SINE/MIR 6 61 (201) 17

437 30.0 4.6 0.0 gi|89161196:706482-716803 5689 5818 (4504) + MIR SINE/MIR 110 245 (17) 17

2121 11.4 4.0 0.3 gi|89161196:706482-716803 6327 6625 (3697) C AluSz SINE/Alu (2) 310 1 18

2161 11.2 7.2 2.5 gi|89161196:706482-716803 6882 7229 (3093) C THE1B LTR/ERVL-MaLR (0) 364 1 19

191 31.6 5.1 0.8 gi|89161196:706482-716803 7237 7354 (2968) + MIR3 SINE/MIR 57 179 (29) 20

1078 18.0 0.4 11.3 gi|89161196:706482-716803 8352 8596 (1726) + AluJo SINE/Alu 1 221 (91) 21

554 19.5 0.0 0.0 gi|89161196:706482-716803 8599 8685 (1637) C AluJo SINE/Alu (225) 87 1 22

422 29.7 8.7 0.8 gi|89161196:706482-716803 8832 9062 (1260) C MIR SINE/MIR (12) 250 2 23

______

L1HS_4_117c (Reference human genome) M_INTER_RMD

41 4.8 0.0 0.0 chr4 157184766 157184827 (34088236) + AT_rich Low_complexity 1 62 (0) 24

1870 18.7 3.0 2.1 chr4 157185187 157185656 (34087407) C MLT2A2 LTR/ERVL (79) 482 1 25

354 26.0 0.0 4.9 chr4 157185770 157185850 (34087213) + LTR16D LTR/ERVL 575 651 (4) 26

1885 15.6 8.4 0.0 chr4 157186035 157186368 (34086695) + MER57A LTR/ERV1 42 403 (0) 27

267 20.0 0.0 0.0 chr4 157187075 157187119 (34085944) C LTR16A1 LTR/ERVL (2) 455 411 28

475 5.6 1.4 1.4 chr4 157187134 157187205 (34085858) + (TTCC)n Simple_repeat 1 72 (0) 29

272 13.7 0.0 1.9 chr4 157187198 157187249 (34085814) + (TTCCC)n Simple_repeat 4 54 (0) 30

465 30.5 16.0 3.1 chr4 157187277 157187601 (34085462) C LTR16A1 LTR/ERVL (90) 367 1 28

21 0.0 0.0 0.0 chr4 157188800 157188820 (34084243) + AT_rich Low_complexity 1 21 (0) 31

8016 0.4 0.0 0.0 chr4 157188972 157190069 (34082994) C L1HS LINE/L1 (576) 5579 4482 32 (L1HS_4_117c) (R12)

5179 0.9 0.0 0.0 chr4 157190070 157190650 (34082413) + L1HS LINE/L1 5575 6155 (0) 32

24 3.2 0.0 0.0 chr4 157190651 157190681 (34082382) + AT_rich Low_complexity 1 31 (0) 33

587 10.1 0.0 0.0 chr4 157190730 157190818 (34082245) + L1MA5 LINE/L1 6212 6300 (0) 34

30 2.7 0.0 0.0 chr4 157191792 157191828 (34081235) + AT_rich Low_complexity 1 37 (0) 35

24 5.3 0.0 0.0 chr4 157192119 157192156 (34080907) + AT_rich Low_complexity 1 38 (0) 36

2195 11.8 0.0 0.3 chr4 157192159 157192457 (34080606) + AluSg SINE/Alu 3 300 (10) 37

1332 15.8 6.2 2.2 chr4 157194262 157194533 (34078530) + L1MC3 LINE/L1 7337 7619 (166) 38

758 28.1 12.1 3.5 chr4 157194534 157194880 (34078183) + L2 LINE/L2 3043 3419 (0) 39

232 22.9 4.8 1.2 chr4 157195781 157195864 (34077199) + MER5A DNA/MER1_type 97 183 (6) 40

29 0.0 0.0 0.0 chr4 157196118 157196146 (34076917) + AT_rich Low_complexity 1 29 (0) 41

2030 8.7 6.0 0.0 chr4 157196182 157196447 (34076616) C AluSc SINE/Alu (27) 282 1 42

258 34.4 7.0 3.2 chr4 157196532 157196687 (34076376) C L3b LINE/CR1 (319) 4189 4028 43

L1HS_4_117c Ortholog in Celera

41 79.0 0.0 0.0 gi|89161206:154308367-154317552 760 821 (8365) + AT_rich Low_complexity 1 62 (0) 3

644 34.4 1.4 0.9 gi|89161206:154308367-154317552 932 1151 (8035) + LTR16D2 LTR/ERVL 138 358 (214) 4

1882 18.9 2.7 1.7 gi|89161206:154308367-154317552 1181 1650 (7536) C MLT2A2 LTR/ERVL (79) 482 1 5

462 30.0 9.1 2.4 gi|89161206:154308367-154317552 1651 1844 (7342) + LTR16D2 LTR/ERVL 465 671 (4) 4

1365 14.8 4.0 0.9 gi|89161206:154308367-154317552 2029 2362 (6824) + MER57B2 LTR/ERV1 42 385 (0) 6

275 20.0 0.0 0.0 gi|89161206:154308367-154317552 3069 3113 (6073) C LTR16A1 LTR/ERVL (2) 454 410 7

365 5.8 0.0 1.9 gi|89161206:154308367-154317552 3135 3187 (5999) + (TTCC)n Simple_repeat 1 52 (0) 8

276 17.0 0.0 0.0 gi|89161206:154308367-154317552 3178 3230 (5956) + C-rich Low_complexity 125 177 (0) 9 *

593 30.8 15.1 2.2 gi|89161206:154308367-154317552 3259 3583 (5603) C LTR16A1 LTR/ERVL (90) 366 1 7

22 54.5 0.0 0.0 gi|89161206:154308367-154317552 4780 4801 (4385) + AT_rich Low_complexity 1 22 (0) 10

1802 0.5 0.5 0.0 gi|89161206:154308367-154317552 4952 5157 (4029) C L1P1 LINE/L1 (576) 5579 5373 11 * (R2)

8059 0.3 0.0 0.0 gi|89161206:154308367-154317552 5155 6235 (2951) C L1HS LINE/L1 (593) 5562 4482 12 (R1)

5176 0.9 0.0 0.0 gi|89161206:154308367-154317552 6236 6816 (2370) + L1HS LINE/L1 5575 6155 (0) 12

25 56.2 0.0 0.0 gi|89161206:154308367-154317552 6817 6848 (2338) + AT_rich Low_complexity 1 32 (0) 13

587 10.1 0.0 0.0 gi|89161206:154308367-154317552 6897 6985 (2201) + L1MA5 LINE/L1 6212 6300 (0) 14

30 59.5 0.0 0.0 gi|89161206:154308367-154317552 7959 7995 (1191) + AT_rich Low_complexity 1 37 (0) 15

24 52.6 0.0 0.0 gi|89161206:154308367-154317552 8286 8323 (863) + AT_rich Low_complexity 1 38 (0) 16

2273 11.7 0.0 0.3 gi|89161206:154308367-154317552 8326 8625 (561) + AluSg SINE/Alu 3 301 (9) 17

______

L1HS_8_26 Reference human genome M_INTER_RMD

2015 18.3 5.0 0.1 chr8 66463716 66464149 (79810677) + MER21A LTR/ERV1 484 923 (8) 195

910 14.8 5.1 1.1 chr8 66464162 66464339 (79810487) C MER65D LTR/ERV1 (132) 341 157 196

475 22.7 2.1 1.4 chr8 66464393 66464535 (79810291) C MER65D LTR/ERV1 (326) 147 4 196

500 24.6 1.0 13.4 chr8 66464544 66464745 (79810081) C LTR42 LTR/ERVL (235) 260 84 197

2020 11.1 11.4 0.0 chr8 66465154 66465494 (79809332) C MSTA LTR/MaLR (48) 380 1 198

188 28.1 3.7 10.3 chr8 66465680 66465786 (79809040) C MIR SINE/MIR (10) 252 153 199

2113 10.6 2.6 3.2 chr8 66465809 66466119 (79808707) + AluSc SINE/Alu 1 309 (0) 200

1202 1.2 0.1 0.0 chr8 66466274 66466434 (79808392) C L1P2 LINE/L1 (390) 5764 5603 201

3682 0.2 0.0 0.5 chr8 66466435 66466886 (79807940) + L1HS LINE/L1 5740 6191 (0) 202 (R12)

1081 20.5 1.8 1.4 chr8 66466915 66467132 (79807694) + MER20 DNA/MER1_type 1 219 (0) 203

353 31.4 1.0 1.0 chr8 66467166 66467268 (79807558) + L2 LINE/L2 3256 3358 (20) 204

240 20.4 0.0 1.8 chr8 66468426 66468480 (79806346) C MLT2B2 LTR/ERVL (0) 556 503 205

264 15.2 1.5 2.9 chr8 66468481 66468548 (79806278) + (TA)n Simple_repeat 2 68 (0) 206

2432 17.6 1.2 7.0 chr8 66468549 66469050 (79805776) C MLT2B2 LTR/ERVL (40) 475 3 205

22 0.0 0.0 0.0 chr8 66469356 66469377 (79805449) + AT_rich Low_complexity 1 22 (0) 207

2045 26.3 12.4 2.4 chr8 66470393 66471369 (79803457) C L2 LINE/L2 (56) 3363 2282 208

1893 18.0 2.4 2.6 chr8 66471427 66471795 (79803031) + Charlie1b DNA/MER1_type 103 480 (43) 209

L1HS_8_26 Ortholog in Celera

2003 17.8 4.3 0.0 gi|89161214:62289528-62298770 2268 2666 (6577) + MER21A LTR/ERVL 508 923 (8) 6

903 15.9 5.1 1.1 gi|89161214:62289528-62298770 2679 2856 (6387) C MER65D LTR/ERV1 (132) 341 157 7

475 22.7 2.1 1.4 gi|89161214:62289528-62298770 2910 3052 (6191) C MER65D LTR/ERV1 (326) 147 4 7

432 23.1 2.8 0.9 gi|89161214:62289528-62298770 3154 3262 (5981) C LTR42 LTR/ERVL (301) 194 84 8

1359 11.8 9.6 1.4 gi|89161214:62289528-62298770 3671 4011 (5232) C MSTA LTR/ERVL-MaLR (48) 380 1 9

185 28.7 1.2 10.7 gi|89161214:62289528-62298770 4197 4278 (4965) C MIR SINE/MIR (10) 252 178 10

2163 10.3 2.6 3.6 gi|89161214:62289528-62298770 4326 4636 (4607) + AluSc SINE/Alu 1 308 (1) 11

1202 1.2 0.1 0.0 gi|89161214:62289528-62298770 4791 4951 (4292) C L1HS LINE/L1 (390) 5764 5603 12

3762 0.0 0.0 0.0 gi|89161214:62289528-62298770 4952 5367 (3876) + L1HS LINE/L1 5740 6155 (0) 12 (R1)

411 2.1 0.0 0.0 gi|89161214:62289528-62298770 5368 5415 (3828) + (A)n Simple_repeat 1 48 (0) 13

3572 0.2 0.0 0.5 gi|89161214:62289528-62298770 5852 6245 (2998) + L1HS LINE/L1 5751 6144 (11) 14 (R2)

350 2.1 2.1 0.0 gi|89161214:62289528-62298770 6246 6292 (2951) + (TAAA)n Simple_repeat 2 49 (0) 15

1080 20.5 1.8 1.4 gi|89161214:62289528-62298770 6321 6538 (2705) + MER20 DNA/hAT-Charlie 1 219 (0) 16

295 35.3 1.0 1.0 gi|89161214:62289528-62298770 6572 6674 (2569) + L2b LINE/L2 3253 3355 (20) 17

240 20.4 0.0 1.9 gi|89161214:62289528-62298770 7832 7886 (1357) C MLT2B3 LTR/ERVL (0) 556 503 18

242 16.0 0.0 2.0 gi|89161214:62289528-62298770 7904 7954 (1289) + (TA)n Simple_repeat 2 51 (0) 19

2255 20.4 3.9 0.7 gi|89161214:62289528-62298770 7955 8456 (787) C MLT2B3 LTR/ERVL (40) 522 3 18

23 34.8 0.0 0.0 gi|89161214:62289528-62298770 8761 8783 (460) + AT_rich Low_complexity 1 23 (0) 20

______

L1HS_11_41c (Reference human genome) M_INTER_RMD

2330 9.4 0.0 1.0 chr11 59565615 59565925 (74886459) + AluSx SINE/Alu 1 308 (4) 148

1238 8.9 26.0 3.7 chr11 59565942 59566187 (74886197) + AluYa5 SINE/Alu 1 301 (9) 149

2326 7.9 1.6 0.0 chr11 59566948 59567252 (74885132) C AluY SINE/Alu (1) 310 1 150

215 32.2 3.8 5.3 chr11 59568270 59568400 (74883984) C MIR SINE/MIR (121) 141 13 151

469 7.3 14.6 0.0 chr11 59569732 59569813 (74882571) C L1MB3 LINE/L1 (3) 6180 6087 152

410 14.2 0.7 5.3 chr11 59569961 59570109 (74882275) + (TCTCTG)n Simple_repeat 1 142 (0) 153

630 14.9 0.0 2.8 chr11 59570110 59570288 (74882096) + (TC)n Simple_repeat 1 174 (0) 154

22 0.0 0.0 0.0 chr11 59572046 59572067 (74880317) + AT_rich Low_complexity 1 22 (0) 155

429 27.8 9.3 8.8 chr11 59572238 59572430 (74879954) C MIR SINE/MIR (67) 195 2 156

12256 1.8 0.0 0.0 chr11 59572704 59575033 (74877351) C L1HS LINE/L1 (0) 6203 3873 157 (R12)

7211 1.5 0.6 0.0 chr11 59575038 59575901 (74876483) + L1PA3 LINE/L1 5284 6152 (3) 158

253 16.7 1.8 1.8 chr11 59576255 59576309 (74876075) C MER5B DNA/MER1_type (0) 178 124 159

2102 13.3 0.7 1.0 chr11 59576320 59576622 (74875762) + AluSx SINE/Alu 1 302 (10) 160

39 2.2 0.0 0.0 chr11 59577523 59577568 (74874816) + AT_rich Low_complexity 1 46 (0) 161

3118 8.8 5.6 0.2 chr11 59577569 59578035 (74874349) + L1MA1 LINE/L1 5806 6297 (5) 162

2351 8.6 0.3 0.0 chr11 59578049 59578350 (74874034) + AluSc SINE/Alu 1 303 (6) 163

828 19.3 4.1 4.1 chr11 59578407 59578649 (74873735) + L1MA9 LINE/L1 6046 6288 (24) 164

366 28.2 6.4 0.0 chr11 59578750 59578859 (74873525) C MIRb SINE/MIR (48) 220 104 165

2146 14.2 0.0 0.0 chr11 59579583 59579891 (74872493) + AluSx SINE/Alu 1 309 (3) 166

L1HS_11_41c Ortholog in Celera

212 32.3 3.8 5.4 gi|89161188:57173918-57185787 518 648 (11222) C MIR SINE/MIR (121) 141 13 1

467 7.3 14.6 0.0 gi|89161188:57173918-57185787 1980 2061 (9809) C L1MB3 LINE/L1 (3) 6180 6087 2

523 15.5 1.0 4.6 gi|89161188:57173918-57185787 2209 2475 (9395) + (TCTCTG)n Simple_repeat 1 257 (0) 3

456 17.1 0.0 0.0 gi|89161188:57173918-57185787 2451 2561 (9309) + CT-rich Low_complexity 70 180 (0) 4 *

23 39.1 0.0 0.0 gi|89161188:57173918-57185787 4294 4316 (7554) + AT_rich Low_complexity 1 23 (0) 5

423 28.3 9.8 7.5 gi|89161188:57173918-57185787 4427 4678 (7192) C MIR SINE/MIR (6) 262 2 6

315 8.5 0.0 0.0 gi|89161188:57173918-57185787 4952 4998 (6872) + (T)n Simple_repeat 1 47 (0) 7

8034 0.9 0.0 0.0 gi|89161188:57173918-57185787 5000 6276 (5594) C L1HS LINE/L1 (0) 6155 4879 8 (R2)

292 11.5 0.0 0.0 gi|89161188:57173918-57185787 6329 6380 (5490) + L1MB2 LINE/L1 6115 6166 (5) 9

501 33.9 8.1 0.0 gi|89161188:57173918-57185787 6395 6615 (5255) C MLT2F LTR/ERVL (236) 427 189 10

459 26.6 4.8 0.8 gi|89161188:57173918-57185787 6639 6763 (5107) C LTR33C LTR/ERVL (486) 143 14 11

708 27.5 3.8 1.6 gi|89161188:57173918-57185787 6767 7006 (4864) + L1M5 LINE/L1 5456 5700 (494) 12

2097 11.1 0.0 0.4 gi|89161188:57173918-57185787 7108 7378 (4492) + AluSz SINE/Alu 8 277 (35) 13

270 0.0 0.0 0.0 gi|89161188:57173918-57185787 7382 7411 (4459) + (CAAA)n Simple_repeat 1 30 (0) 14

11915 3.1 0.1 0.0 gi|89161188:57173918-57185787 7492 8919 (2951) C L1PA3 LINE/L1 (845) 5301 3873 15 (R1)

7545 1.5 0.6 0.0 gi|89161188:57173918-57185787 8924 9787 (2083) + L1PA3 LINE/L1 5284 6152 (3) 15

270 16.7 1.8 1.8 gi|89161188:57173918-57185787 10141 10195 (1675) C MER5B DNA/hAT-Charlie (0) 178 124 16

2148 13.0 0.7 1.0 gi|89161188:57173918-57185787 10206 10505 (1365) + AluSz6 SINE/Alu 1 299 (13) 17

39 73.9 0.0 0.0 gi|89161188:57173918-57185787 11411 11456 (414) + AT_rich Low_complexity 1 46 (0) 18

2817 8.0 5.3 0.2 gi|89161188:57173918-57185787 11457 11870 (0) + L1MA1 LINE/L1 5806 6240 (62) 19

Recombination mediated deletions – Truncated L1HS elements, Human Vs Celera comparison

L1HS_1_63 Reference human genome C_INTER_RMD

2310 8.3 1.0 0.0 chr1 113680004 113680303 (133569416) C AluSp SINE/Alu (9) 304 2 480

15442 12.6 1.7 1.3 chr1 113680304 113681904 (133567815) C Tigger1 DNA/MER2_type (830) 1588 1 479

2265 10.1 0.3 1.3 chr1 113682091 113682392 (133567327) C AluSp SINE/Alu (14) 299 1 481

444 3.7 0.0 0.0 chr1 113683352 113683405 (133566314) + (TG)n Simple_repeat 2 55 (0) 482

324 25.7 0.0 1.3 chr1 113683409 113683483 (133566236) + L2 LINE/L2 3301 3374 (4) 483

314 14.6 0.0 0.0 chr1 113683523 113683577 (133566142) + AluSx SINE/Alu 245 299 (3) 484

4399 17.2 5.0 1.4 chr1 113683579 113684447 (133565272) + L1MB2 LINE/L1 5230 6135 (36) 485

360 39.5 5.2 4.8 chr1 113685480 113685748 (133563971) C L2 LINE/L2 (26) 3352 3083 486

26479 3.4 0.1 0.2 chr1 113685753 113689935 (133559784) + L1HS LINE/L1 1995 6155 (0) 487 (R1)

7259 3.6 0.9 0.0 chr1 113689938 113690958 (133558761) + L1PA4 LINE/L1 5128 6155 (0) 488 (R2)

233 32.4 9.2 1.4 chr1 113690974 113691114 (133558605) C L2 LINE/L2 (317) 3061 2910 486

1989 10.5 6.2 0.0 chr1 113691263 113691538 (133558181) C AluSg SINE/Alu (7) 303 11 489

1703 16.4 1.0 3.9 chr1 113691591 113691900 (133557819) C AluJo SINE/Alu (11) 301 1 490

297 29.5 0.0 1.3 chr1 113692262 113692340 (133557379) + MIR SINE/MIR 1 78 (184) 491

450 0.0 0.0 0.0 chr1 113692671 113692720 (133556999) + (TGGA)n Simple_repeat 4 53 (0) 492

843 6.9 0.0 0.0 chr1 113693058 113693159 (133556560) + AluSg/x SINE/Alu 135 236 (76) 493

387 25.5 12.9 1.2 chr1 113693161 113693323 (133556396) + MIR SINE/MIR 50 231 (31) 491

214 37.2 5.9 5.9 chr1 113693398 113693651 (133556068) C L2 LINE/L2 (455) 2964 2711 494

2507 5.2 0.3 1.3 chr1 113693652 113693960 (133555759) C AluY SINE/Alu (5) 306 1 495

262 35.4 3.1 1.0 chr1 113695067 113695163 (133554556) C MIRm SINE/MIR (21) 255 157 496

1204 18.7 8.1 3.4 chr1 113696363 113696683 (133553036) + MER44A DNA/MER2_type 1 336 (3) 497

Orhtolog in HuRef

7602 11.3 1.2 1.5 gi|157704448:111737462-111750565 1 1114 (11990) C Tigger1 DNA/TcMar-Tigger (1308) 1110 1 1

2314 9.9 0.3 1.3 gi|157704448:111737462-111750565 1301 1602 (11502) C AluSp SINE/Alu (14) 299 1 2

189 28.0 1.8 15.5 gi|157704448:111737462-111750565 2532 2562 (10542) + L2b LINE/L2 3287 3316 (71) 3

345 4.7 0.0 0.0 gi|157704448:111737462-111750565 2563 2605 (10499) + (TG)n Simple_repeat 2 44 (0) 4

300 27.6 0.2 1.8 gi|157704448:111737462-111750565 2606 2683 (10421) + L2b LINE/L2 3303 3383 (4) 3

353 10.6 0.0 0.0 gi|157704448:111737462-111750565 2723 2769 (10335) + AluJo SINE/Alu 245 291 (21) 5

3677 17.6 4.6 1.6 gi|157704448:111737462-111750565 2779 3647 (9457) + L1MB2 LINE/L1 5230 6135 (36) 6

383 33.0 8.1 5.4 gi|157704448:111737462-111750565 4680 4951 (8153) C L2c LINE/L2 (26) 3361 3083 7

26405 4.1 0.3 0.2 gi|157704448:111737462-111750565 4952 9124 (3980) + L1PA4 LINE/L1 1995 6155 (0) 8 (R12)

211 33.0 9.6 2.6 gi|157704448:111737462-111750565 9135 9280 (3824) C L2c LINE/L2 (322) 3065 2910 7

2032 10.9 6.2 0.0 gi|157704448:111737462-111750565 9429 9702 (3402) C AluSg SINE/Alu (9) 301 11 9

1824 16.2 0.3 3.3 gi|157704448:111737462-111750565 9755 10063 (3041) C AluJo SINE/Alu (11) 301 2 10

297 29.5 0.0 1.3 gi|157704448:111737462-111750565 10426 10504 (2600) + MIR SINE/MIR 1 78 (184) 11

414 0.0 0.0 0.0 gi|157704448:111737462-111750565 10835 10880 (2224) + (TGGA)n Simple_repeat 4 49 (0) 12

895 6.9 0.0 0.0 gi|157704448:111737462-111750565 11218 11319 (1785) + AluSx SINE/Alu 135 236 (76) 13

397 24.8 12.9 1.1 gi|157704448:111737462-111750565 11321 11483 (1621) + MIR SINE/MIR 50 231 (31) 11

202 37.9 5.5 5.9 gi|157704448:111737462-111750565 11558 11812 (1292) C L2 LINE/L2 (455) 2964 2711 14

2592 4.9 0.3 1.3 gi|157704448:111737462-111750565 11813 12119 (985) C AluY SINE/Alu (7) 304 1 15

______

L1HS_2_41 Reference human genome M_INTER_RMD

2081 20.9 3.1 7.1 chr2 109287006 109287329 (133663820) C L1MB1 LINE/L1 (51) 6138 5804 665

355 22.7 11.6 1.6 chr2 109287500 109287620 (133663529) C Charlie5 DNA/MER1_type (2471) 141 9 666

9571 1.5 0.0 0.0 chr2 109290311 109292221 (133658928) C L1PA2 LINE/L1 (0) 6155 4244 667

17275 1.7 0.5 0.0 chr2 109292220 109294476 (133656673) + L1HS LINE/L1 1845 4112 (1911) 668 (L1HS_2_41) (R12)

2336 20.9 4.1 3.8 chr2 109295239 109295849 (133655300) C L1MB5 LINE/L1 (0) 6174 5562 669

287 26.1 0.0 0.0 chr2 109297925 109297993 (133653156) C MER3 DNA/MER1_type (140) 69 1 1

Ortholog in HuReF

511 6.5 0.0 0.0 gi|157724517:103517969-103531048 1 62 (13018) C L1MA7 LINE/L1 (426) 5865 5804 1

369 18.8 3.5 0.0 gi|157724517:103517969-103531048 242 326 (12754) C Charlie5 DNA/hAT-Charlie (2492) 132 45 2

10143 1.4 0.1 0.0 gi|157724517:103517969-103531048 3044 4953 (8127) C L1PA2 LINE/L1 (0) 6155 4244 3

2469 2.7 2.5 0.0 gi|157724517:103517969-103531048 4952 5398 (7682) + L1HS LINE/L1 1968 2425 (3721) 4 * (R1)

3759 1.5 2.4 0.0 gi|157724517:103517969-103531048 5419 5875 (7205) C L1P1 LINE/L1 (1435) 4711 4244 5 *

18297 1.7 0.5 0.0 gi|157724517:103517969-103531048 5874 8129 (4951) + L1P1 LINE/L1 1968 4235 (1911) 5 (R2)

2355 20.3 4.6 3.8 gi|157724517:103517969-103531048 8893 9500 (3580) C L1MB5 LINE/L1 (0) 6174 5562 6

294 26.1 0.0 0.0 gi|157724517:103517969-103531048 11576 11644 (1436) C MER3 DNA/hAT-Charlie (140) 69 1 7

______

L1HS_2_49c Reference human genome M_DISRUPTED

1290 25.2 14.7 6.5 chr2 129881918 129882899 (113068250) C L1M4b LINE/L1 (3935) 3252 2065 407

1474 22.9 2.3 5.0 chr2 129882900 129883295 (113067854) C MLT1B LTR/MaLR (3) 387 3 409

906 28.3 10.4 6.6 chr2 129883296 129883441 (113067708) C L1MEc LINE/L1 (4963) 1437 1294 410

456 30.4 4.5 2.4 chr2 129883441 129883686 (113067463) C L1M5 LINE/L1 (736) 5504 5254 411

648 29.4 10.0 4.1 chr2 129884022 129884650 (113066499) C L1MC4 LINE/L1 (4355) 1860 1196 412

3280 2.1 0.3 0.3 chr2 129884651 129885037 (113066112) C L1PA3 LINE/L1 (0) 6155 5769 413

648 29.4 10.0 4.1 chr2 129885038 129885094 (113066055) C L1MC4 LINE/L1 (5020) 1195 1133 412

28729 0.4 0.0 0.1 chr2 129885097 129889422 (113061727) C L1HS LINE/L1 (0) 6032 1715 414 (L1HS_2_49c) (R1)

2813 0.7 0.0 0.3 chr2 129889423 129889730 (113061419) + AluYa5 SINE/Al 1 307 (3) 415 (D)

18979 0.3 0.1 0.4 chr2 129889731 129891443 (113059706) C L1HS LINE/L1 (4318) 1714 2 416 (R2)

1482 20.7 6.8 0.3 chr2 129892380 129892733 (113058416) C L1MB7 LINE/L1 (203) 5981 5605 417

622 16.1 0.0 0.0 chr2 129892755 129892866 (113058283) C L1MB7 LINE/L1 (706) 5472 5361 417

460 24.1 22.9 3.6 chr2 129892877 129893212 (113057937) C L1M4c LINE/L1 (4223) 2423 2013 418

4565 23.8 5.6 2.7 chr2 129893209 129894517 (113056632) C L1M4c LINE/L1 (5200) 1342 3 418

303 26.3 3.1 1.0 chr2 129894678 129894773 (113056376) C L1MEe LINE/L1 (4645) 209 112 419

2406 9.1 0.0 0.0 chr2 129895079 129895376 (113055773) + AluSc SINE/Alu 6 303 (6) 420

923 33.5 8.8 1.9 chr2 129895379 129895904 (113055245) + L1MCc LINE/L1 49 610 (5813) 421

289 32.5 4.0 6.2 chr2 129896078 129896254 (113054895) + Kanga1 DNA/Tc2 534 706 (1192) 422

795 31.8 7.0 3.3 chr2 129896337 129896762 (113054387) + L2 LINE/L2 193 634 (2785) 423

Ortholog in HuRef

954 18.9 0.5 0.0 gi|157724517:122471407-122485672 5 194 (14072) C L1M4c LINE/L1 (2191) 4191 4001 1

28 64.3 0.0 0.0 gi|157724517:122471407-122485672 196 223 (14043) + AT_rich Low_complexity 1 28 (0) 2

26 50.0 0.0 0.0 gi|157724517:122471407-122485672 201 226 (14040) + AT_rich Low_complexity 1 26 (0) 3 *

26 87.0 0.0 0.0 gi|157724517:122471407-122485672 237 290 (13976) + AT_rich Low_complexity 1 54 (0) 4

1010 23.5 4.6 8.6 gi|157724517:122471407-122485672 291 700 (13566) C L1M4c LINE/L1 (2414) 3968 3574 1 *

2586 21.8 2.4 1.7 gi|157724517:122471407-122485672 689 1388 (12878) C L1M4c LINE/L1 (3142) 3240 2536 1

1127 21.1 7.0 9.9 gi|157724517:122471407-122485672 1391 1756 (12510) C MLT1A0 LTR/ERVL-MaLR (0) 396 1 5

1707 26.5 4.5 5.6 gi|157724517:122471407-122485672 1760 2741 (11525) C L1M4c LINE/L1 (3856) 2526 1439 1

1470 22.9 2.3 5.2 gi|157724517:122471407-122485672 2742 3137 (11129) C MLT1B LTR/ERVL-MaLR (3) 387 3 6

1707 24.0 2.8 5.3 gi|157724517:122471407-122485672 3138 3287 (10979) C L1M4c LINE/L1 (4946) 1438 1299 1

630 28.1 3.3 1.2 gi|157724517:122471407-122485672 3287 3531 (10735) C L1MC4 LINE/L1 (670) 5571 5322 7 *

661 30.4 7.8 3.6 gi|157724517:122471407-122485672 3867 4447 (9819) C L1MC4 LINE/L1 (4355) 1860 1257 7

3317 1.6 0.3 0.3 gi|157724517:122471407-122485672 4500 4886 (9380) C L1PA3 LINE/L1 (0) 6155 5769 8

297 10.9 0.0 0.0 gi|157724517:122471407-122485672 4896 4950 (9316) + (T)n Simple_repeat 1 55 (0) 9

28768 0.3 0.0 0.0 gi|157724517:122471407-122485672 4952 10981 (3285) C L1HS LINE/L1 (0) 6155 125 10 (R)

1473 19.4 5.3 0.3 gi|157724517:122471407-122485672 11918 12238 (2028) C L1MB7 LINE/L1 (203) 5981 5645 11

621 16.1 0.0 0.0 gi|157724517:122471407-122485672 12293 12404 (1862) C L1MB7 LINE/L1 (712) 5472 5361 11

435 26.1 6.7 3.1 gi|157724517:122471407-122485672 12415 12746 (1520) C L1M4 LINE/L1 (4223) 2785 2330 12

4420 25.2 5.3 2.9 gi|157724517:122471407-122485672 12747 14055 (211) C L1M4 LINE/L1 (5200) 1704 365 12

249 12.2 0.0 0.0 gi|157724517:122471407-122485672 14216 14256 (10) C L1MEg LINE/L1 (4733) 1351 1311 13

______

L1HS_2_50c Reference human genome M_DISRUPTED

1290 25.2 14.7 6.5 chr2 129881918 129882899 (113068250) C L1M4b LINE/L1 (3935) 3252 2065 407

1474 22.9 2.3 5.0 chr2 129882900 129883295 (113067854) C MLT1B LTR/MaLR (3) 387 3 409

906 28.3 10.4 6.6 chr2 129883296 129883441 (113067708) C L1MEc LINE/L1 (4963) 1437 1294 410

456 30.4 4.5 2.4 chr2 129883441 129883686 (113067463) C L1M5 LINE/L1 (736) 5504 5254 411

648 29.4 10.0 4.1 chr2 129884022 129884650 (113066499) C L1MC4 LINE/L1 (4355) 1860 1196 412

3280 2.1 0.3 0.3 chr2 129884651 129885037 (113066112) C L1PA3 LINE/L1 (0) 6155 5769 413

648 29.4 10.0 4.1 chr2 129885038 129885094 (113066055) C L1MC4 LINE/L1 (5020) 1195 1133 412

28729 0.4 0.0 0.1 chr2 129885097 129889422 (113061727) C L1HS LINE/L1 (0) 6032 1715 414 (R1)

2813 0.7 0.0 0.3 chr2 129889423 129889730 (113061419) + AluYa5 SINE/Alu 1 307 (3) 415 (D)

18979 0.3 0.1 0.4 chr2 129889731 129891443 (113059706) C L1HS LINE/L1 (4318) 1714 2 416 (R2) (L1HS_2_50C)

1482 20.7 6.8 0.3 chr2 129892380 129892733 (113058416) C L1MB7 LINE/L1 (203) 5981 5605 417

622 16.1 0.0 0.0 chr2 129892755 129892866 (113058283) C L1MB7 LINE/L1 (706) 5472 5361 417

460 24.1 22.9 3.6 chr2 129892877 129893212 (113057937) C L1M4c LINE/L1 (4223) 2423 2013 418

4565 23.8 5.6 2.7 chr2 129893209 129894517 (113056632) C L1M4c LINE/L1 (5200) 1342 3 418

303 26.3 3.1 1.0 chr2 129894678 129894773 (113056376) C L1MEe LINE/L1 (4645) 209 112 419

2406 9.1 0.0 0.0 chr2 129895079 129895376 (113055773) + AluSc SINE/Alu 6 303 (6) 420

923 33.5 8.8 1.9 chr2 129895379 129895904 (113055245) + L1MCc LINE/L1 49 610 (5813) 421

289 32.5 4.0 6.2 chr2 129896078 129896254 (113054895) + Kanga1 DNA/Tc2 534 706 (1192) 422

795 31.8 7.0 3.3 chr2 129896337 129896762 (113054387) + L2 LINE/L2 193 634 (2785) 423

Ortholog in HuRef

954 18.9 0.5 0.0 gi|157724517:122471407-122485672 5 194 (14072) C L1M4c LINE/L1 (2191) 4191 4001 1

28 64.3 0.0 0.0 gi|157724517:122471407-122485672 196 223 (14043) + AT_rich Low_complexity 1 28 (0) 2

26 50.0 0.0 0.0 gi|157724517:122471407-122485672 201 226 (14040) + AT_rich Low_complexity 1 26 (0) 3 *

26 87.0 0.0 0.0 gi|157724517:122471407-122485672 237 290 (13976) + AT_rich Low_complexity 1 54 (0) 4

1010 23.5 4.6 8.6 gi|157724517:122471407-122485672 291 700 (13566) C L1M4c LINE/L1 (2414) 3968 3574 1 *

2586 21.8 2.4 1.7 gi|157724517:122471407-122485672 689 1388 (12878) C L1M4c LINE/L1 (3142) 3240 2536 1

1127 21.1 7.0 9.9 gi|157724517:122471407-122485672 1391 1756 (12510) C MLT1A0 LTR/ERVL-MaLR (0) 396 1 5

1707 26.5 4.5 5.6 gi|157724517:122471407-122485672 1760 2741 (11525) C L1M4c LINE/L1 (3856) 2526 1439 1

1470 22.9 2.3 5.2 gi|157724517:122471407-122485672 2742 3137 (11129) C MLT1B LTR/ERVL-MaLR (3) 387 3 6

1707 24.0 2.8 5.3 gi|157724517:122471407-122485672 3138 3287 (10979) C L1M4c LINE/L1 (4946) 1438 1299 1

630 28.1 3.3 1.2 gi|157724517:122471407-122485672 3287 3531 (10735) C L1MC4 LINE/L1 (670) 5571 5322 7 *

661 30.4 7.8 3.6 gi|157724517:122471407-122485672 3867 4447 (9819) C L1MC4 LINE/L1 (4355) 1860 1257 7

3317 1.6 0.3 0.3 gi|157724517:122471407-122485672 4500 4886 (9380) C L1PA3 LINE/L1 (0) 6155 5769 8

297 10.9 0.0 0.0 gi|157724517:122471407-122485672 4896 4950 (9316) + (T)n Simple_repeat 1 55 (0) 9

28768 0.3 0.0 0.0 gi|157724517:122471407-122485672 4952 10981 (3285) C L1HS LINE/L1 (0) 6155 125 10 (R)

1473 19.4 5.3 0.3 gi|157724517:122471407-122485672 11918 12238 (2028) C L1MB7 LINE/L1 (203) 5981 5645 11

621 16.1 0.0 0.0 gi|157724517:122471407-122485672 12293 12404 (1862) C L1MB7 LINE/L1 (712) 5472 5361 11

435 26.1 6.7 3.1 gi|157724517:122471407-122485672 12415 12746 (1520) C L1M4 LINE/L1 (4223) 2785 2330 12

4420 25.2 5.3 2.9 gi|157724517:122471407-122485672 12747 14055 (211) C L1M4 LINE/L1 (5200) 1704 365 12

249 12.2 0.0 0.0 gi|157724517:122471407-122485672 14216 14256 (10) C L1MEg LINE/L1 (4733) 1351 1311 13

______

L1HS_3_14c Reference human genome C_INTER_RMD ??

189 7.4 0.0 0.0 chr3 22060937 22060963 (177440864) + (CAAAAA)n Simple_repeat 4 30 (0) 37

450 32.2 11.7 0.8 chr3 22061065 22061330 (177440497) C L2 LINE/L2 (1667) 1752 1458 36

466 12.7 0.0 0.0 chr3 22061452 22061522 (177440305) + AluSp/q SINE/Alu 226 296 (17) 38

300 14.5 1.6 0.0 chr3 22061523 22061584 (177440243) C L1M2 LINE/L1 (1817) 4326 4264 39

728 20.1 7.7 1.6 chr3 22061616 22061797 (177440030) C L1M2 LINE/L1 (1010) 5133 4941 40

7282 15.7 6.0 3.6 chr3 22063602 22065510 (177436317) C L1MA8 LINE/L1 (2) 6289 4316 41

2028 12.4 0.3 0.0 chr3 22065511 22065836 (177435991) + AluSq SINE/Alu 1 327 (0) 42

7282 17.9 8.8 3.6 chr3 22065837 22066576 (177435251) C L1MA8 LINE/L1 (1828) 4315 3551 41

1379 22.6 1.4 0.0 chr3 22066580 22066854 (177434973) + AluJo SINE/Alu 1 279 (33) 43

231 6.1 0.0 0.0 chr3 22066855 22066887 (177434940) + (CAAA)n Simple_repeat 1 33 (0) 44

16108 0.3 0.0 0.0 chr3 22066888 22069693 (177432134) C L1HS LINE/L1 (2586) 3437 329 45 (R1) (L1HS_3_14c)

20482 0.2 0.0 0.0 chr3 22069692 22072804 (177429023) + L1HS LINE/L1 3064 6176 (0) 46 (R2)

335 28.2 3.1 3.9 chr3 22073187 22073315 (177428512) C MLT1H LTR/MaLR (16) 533 406 47

245 33.3 0.0 0.0 chr3 22073404 22073481 (177428346) C MLT1H2 LTR/MaLR (323) 161 84 48

646 29.4 3.1 5.3 chr3 22073622 22073874 (177427953) + MIRb SINE/MIR 14 262 (0) 49

2103 12.5 0.0 1.3 chr3 22074010 22074309 (177427518) C AluSx SINE/Alu (16) 296 1 50

216 9.7 0.0 0.0 chr3 22074491 22074521 (177427306) + (TGAA)n Simple_repeat 3 33 (0) 51

23 0.0 0.0 0.0 chr3 22075113 22075135 (177426692) + AT_rich Low_complexity 1 23 (0) 52

22 0.0 0.0 0.0 chr3 22075176 22075197 (177426630) + AT_rich Low_complexity 1 22 (0) 53

274 23.2 2.9 1.4 chr3 22075816 22075885 (177425942) C MER5B DNA/MER1_type (104) 74 4 54

282 29.6 0.0 0.0 chr3 22075963 22076050 (177425777) C Charlie2 DNA/MER1_type (2598) 263 176 55

288 24.5 7.9 3.0 chr3 22076077 22076177 (177425650) C Charlie2 DNA/MER1_type (2751) 110 5 55

Ortholog in HuRef

5342 15.8 6.9 3.0 gi|157731950:22036680-22048120 1666 3574 (7867) C L1MA8 LINE/L1 (2) 6289 4316 1

2095 12.4 0.3 0.0 gi|157731950:22036680-22048120 3575 3900 (7541) + AluSq SINE/Alu 1 313 (0) 2

3013 18.1 7.7 5.1 gi|157731950:22036680-22048120 3901 4640 (6801) C L1MA8 LINE/L1 (1828) 4315 3551 1

1507 22.6 1.4 0.0 gi|157731950:22036680-22048120 4644 4918 (6523) + AluJo SINE/Alu 1 279 (33) 3

231 6.1 0.0 0.0 gi|157731950:22036680-22048120 4919 4951 (6490) + (CAAA)n Simple_repeat 1 33 (0) 4

871 16.3 6.2 0.5 gi|157731950:22036680-22048120 4992 5170 (6271) C L1MA8 LINE/L1 (2585) 3558 3370 1 (R12 ????)

23 53.3 0.0 0.0 gi|157731950:22036680-22048120 5320 5349 (6092) + AT_rich Low_complexity 1 30 (0) 5

337 26.9 0.8 2.6 gi|157731950:22036680-22048120 5803 5931 (5510) C MLT1H2 LTR/ERVL-MaLR (16) 533 382 6

230 31.2 3.0 0.0 gi|157731950:22036680-22048120 6020 6120 (5321) C MLT1J2 LTR/ERVL-MaLR (328) 161 65 7

654 29.4 3.1 5.4 gi|157731950:22036680-22048120 6238 6490 (4951) + MIRb SINE/MIR 14 262 (0) 8

2196 12.3 0.0 1.4 gi|157731950:22036680-22048120 6626 6926 (4515) C AluSx SINE/Alu (15) 297 1 9

216 9.7 0.0 0.0 gi|157731950:22036680-22048120 7108 7138 (4303) + (TGAA)n Simple_repeat 3 33 (0) 10

25 56.0 0.0 0.0 gi|157731950:22036680-22048120 7729 7753 (3688) + AT_rich Low_complexity 1 25 (0) 11

22 54.5 0.0 0.0 gi|157731950:22036680-22048120 7793 7814 (3627) + AT_rich Low_complexity 1 22 (0) 12

230 26.7 10.0 0.0 gi|157731950:22036680-22048120 7827 7916 (3525) + Tigger16a DNA/TcMar-Tigger 742 840 (93) 13

267 23.2 2.9 1.4 gi|157731950:22036680-22048120 8433 8502 (2939) C MER5B DNA/hAT-Charlie (104) 74 4 14

284 29.6 0.0 0.0 gi|157731950:22036680-22048120 8580 8667 (2774) C Charlie2a DNA/hAT-Charlie (2598) 263 176 15

______

L1HS_4_8 (Reference human genome) M_DISRUPTED

203 33.3 5.3 6.1 chr4 16547199 16547329 (174725734) C MIR3 SINE/MIR (31) 177 48 220

704 17.0 0.0 0.9 chr4 16547348 16547460 (174725603) + FLAM_A SINE/Alu 8 119 (23) 221

2055 14.4 0.0 0.6 chr4 16547480 16547793 (174725270) C AluSx SINE/Alu (0) 312 1 222

286 34.1 3.2 2.4 chr4 16547995 16548120 (174724943) + MIRb SINE/MIR 40 166 (102) 223

1723 13.4 1.0 3.1 chr4 16548440 16548732 (174724331) + AluJb SINE/Alu 23 309 (3) 224

295 20.8 8.3 0.0 chr4 16550074 16550145 (174722918) + L1ME4a LINE/L1 5715 5792 (329) 225

365 30.1 7.1 5.2 chr4 16550581 16550888 (174722175) + L1ME4a LINE/L1 5789 6102 (19) 225

253 33.0 5.5 0.0 chr4 16551405 16551495 (174721568) C MIR3 SINE/MIR (46) 162 67 226

225 34.2 2.5 5.8 chr4 16551517 16551637 (174721426) C L2 LINE/L2 (5) 3373 3257 227

196 25.6 0.0 0.0 chr4 16551805 16551847 (174721216) + L2 LINE/L2 3373 3415 (4) 228

27 6.2 0.0 0.0 chr4 16551854 16551901 (174721162) + AT_rich Low_complexity 1 48 (0) 229

27 8.7 0.0 0.0 chr4 16551944 16552012 (174721051) + AT_rich Low_complexity 1 69 (0) 230

207 33.8 8.4 0.0 chr4 16552058 16552128 (174720935) C MIRb SINE/MIR (29) 239 163 231

523 33.1 7.9 4.7 chr4 16552156 16552409 (174720654) C MIR SINE/MIR (0) 262 1 232

404 13.4 10.4 0.0 chr4 16553284 16553350 (174719713) C MLT1C LTR/MaLR (0) 467 394 233

19171 0.6 0.1 0.7 chr4 16553498 16555351 (174717712) + L1HS LINE/L1 3 1857 (4175) 234 (R1) (L1HS_4_8)

2782 0.7 0.0 0.0 chr4 16555352 16555647 (174717416) + AluYb8 SINE/Alu 23 318 (0) 235 (D)