Online Resource 1: Tables S1 through S6 and Figures S1 through S6.
Table S1. Primers used in this study for PCR, qPCR and/or sequencing.
Element / Name / Sequence / Element / Name / SequenceIvanaA / 1103 / AGTTGGTTAGTGCTAGCTCAGT / LINE / 1077 / TCTCTGCCACAACAAGGACC
IvanaA / 1104 / CATGTGCTTGCAGTGCTTGA / LINE / 1078 / TAGGTTCCAGCGAGCCTTTG
IvanaA / 1105 / CAGCTAAGGAGTGTTGGGACA / LINE / 1079 / CAAAGGCTCGCTGGAACCTA
IvanaA / 1106 / CCTCCATTACATTATTCTCCAGATGC / LINE / 1080 / GTTTGGAAGCTTCAAGGCGG
IvanaA / 1107 / TGCACACCTAGCTCAAGAGG / LINE / 1081 / CCGCCTTGAAGCTTCCAAAC
IvanaA / 1108 / TCCTATTCCTTCGCTCAGCC / LINE / 1082 / GACGCTTTGCTCGTGTTTGT
IvanaA / 1109 / ACTGATGTGTGTGGCCCTTT / LINE / 1083 / ACAAACACGAGCAAAGCGTC
IvanaA / 1110 / TGCATAGCCAGTCTCCACTC / LINE / 1084 / GTTTCCGTAATTTCCGCGGG
IvanaA / 1111 / TGAAGAGGATAAGAGTTGGAATTGG / LINE / 1085q / CATGGAGATTGGCTGACCGT
IvanaA / 1112 / TTCTGAGAAGTGCCTTTGACA / LINE / 1086 / ATGAACACATGGCCACGGAT
IvanaA / 1113 / TCCTTCAGAAGCCTGGCATT / LINE / 1087 / ATCCGTGGCCATGTGTTCAT
IvanaA / 1114 / AGCCTCACATGTAGACAAGGC / LINE / 1088 / AGCTGGTACGCGCTTTACTT
IvanaA / 1115 / AGCAGATGGTGGGAAGCTTG / LINE / 1089 / CAAGTAAAGCGCGTACCAGC
IvanaA / 1116 / GCCAAAAACCCCATTGCACA / LINE / 1090q / GGTGTTGCTAAGGTCCTCCC
IvanaA / 1117 / AGAGATGAATTTGAGAGAAAGGGA / LINE / 1091q / GTCCATGCAGCCTCAAAACG
IvanaA / 1180q / AGCAGATGGTGGGAAGCTTG / LINE / 1092 / CTCCAGGTGCTTTCAGAGGG
IvanaA / 1184q / GCTGCTTGTCAAGGCATATGG / LINE / 1093 / CCAGCTTCATTCCAGGTCGT
IvanaA / 1191q / CATAATCAACYGTGCCCTGC / LINE / 1094 / TCCCACCCCACTAGATGAGG
IvanaA / 1192q / TGTGCAATGGGGTTTTTGGC / LINE / 1095 / TCCAGCGCCTAAAGACACAG
IvanaA / 1228 / GGTTGTTGCAAACTGTTACTTGTG / LINE / 1096 / CCCAAGTACATGCCCCACAT
IvanaA / 1229 / CTTGAGGCTCTAGATACCAGTTTGT / LINE / 1097 / TGTATACGGCGCACCAAAGT
IvanaA / 1230 / TGTTGCAAACTGTTACTTGTGTAAC / LINE / 1098 / CTGGTGTGGCATTGATGTTCAA
IvanaA / 1231 / AGGCTCTAGATACCAGTTTGTTAGA / LINE / 1099 / AGTGGTATGGATGTGGGTGC
IvanaB / 1118 / AGGTATTGTTTGTGTTTGGGCC / LINE / 1147 / CTACAAACACGGATATTCCTAGGCA
IvanaB / 1119 / CAGTTAAGCCTGCACGTGTG / LINE / 1148 / TCTGCTGAAATGTGGGGCAT
IvanaB / 1120 / TCCCCCATTGCAAGAACCTC / LINE / 1149q / GTCTTGTTGGGCCCAATTGC
IvanaB / 1121 / AATCCAACGATGTCACGGCT / LINE / 1150 / GACCTGTTCCACATCAGCCA
IvanaB / 1122 / TCTTCCCCTACCTCTGCCTG / LINE / 1075 / GCCTCCCCCATGCGATAATT
IvanaB / 1123 / GTCAGCTGCAATCCAAAGGC / LINE / 1076 / GCTTAGAGCACCCACATCCA
IvanaB / 1124 / TCTGTGTTGCTTGCCAGTCA / LINE / 1151 / CCCTCTGAAAGCACCTGGAG
IvanaB / 1125 / TGACTGGCAAGCAACACAGA / LINE / 1152 / ATTTGAGGGCCATACCTGCC
IvanaB / 1126 / AAGGCTTGCTTCCACTCCAA / LINE / 1153 / CTGGCAGAGCTACTAGGGGA
IvanaB / 1127 / AGTGACAATGACCAGCTGCA / LINE / 1154 / GACGCTTTGCTCGTGTTTGT
IvanaB / 1128 / CCATCGAGCTACAGGTGCAT / LINE / 1157 / AACAGAAACCGTCCCTTCCG
IvanaB / 1129 / CCTACTTCACTGCTGCAGGA / LINE / 1158 / CGTTTTGAGGCTGCATGGAC
IvanaB / 1130q / TCAGGTCTTGTTGCCAGCAT / LINE / 1159 / ACGACCTGGAATGAAGCTGG
IvanaB / 1131 / TCTTGTGACCTGCAGTACCG / LINE / 1198 / ACAGGTTAGGTGGATGGAAGC
IvanaB / 1132 / TGTCCCTCTCTGGTTGTGTTG / LINE / 1199 / TGGATGGAAGCAACAATGTCTG
IvanaB / 1133 / ACAAGTCATATACACGGCCCA / LINE / 1200 / CTCCCTAAAAGCCTTTGTAACGA
IvanaB / 1146 / ACTGCCTATACTCCTCARCAG / LINE / 1201 / GGATTGGGCATTAACAGACCTC
IvanaB / 1160 / AGGCCAACAGAGATGCATGT / LINE / 1202 / CCAACCAATCGTGTCTTGCC
IvanaB / 1161q / TGTAGTCCAATTGTGCCTGGT / LINE / 1203 / GCCTTCCAATCTCCCTCAATG
IvanaB / 1162 / ACAAGTCATATACACGGCCCA / LINE / 1204 / TGAGCCGCCATCCACATAAAAG
IvanaB / 1176q / TATGCACCTGTAGCTCGATGGG / LINE / 1205 / GGACCCAAGAAGCCTCCTGAT
IvanaB / 1177q / GCTCTATGGGCCTGTTTTAGC / LINE / 1206 / GGTTTCGAAATTATGGACAATGACA
IvanaB / 1178q / TGGGTGAGAAGTATTTTGCAGC / LINE / 1207 / AAGCGTCCTTTCTCAACCT
IvanaB / 1179q / TCTTGTGACCTGCAGTACCG / LINE / 1208 / CGGGCGCATTAAAATTGTTG
IvanaB / 1193 / GCACCTGTAGCTCGATGGG / LINE / 1209 / TAAGCCAGATCTTTCCAACAAC
IvanaB / 1194 / TGGCTCATTCTGGATCTGTAGT / LINE / 1210 / CCTTTGCCAACTCGTATGAAAG
IvanaB / 1195 / TTGATTCACACATCCTCTCCG / LINE / 1232 / GCTTGCTTGGAGATATGGTTTC
IvanaB / 1196 / GGTGACAGTTACGGTGGCC / LINE / 1233 / TTTTTTTTATTTTTTTTTGGTTGAG
IvanaB / 1197 / GCCAGGCCACACGTGC / LINE / 1234 / CCAACTTCACGTGGAAAGCG
LINE / 1074 / AATTATCGCATGGGGGAGGC / LINE / 1236 / CTGGAACCTAGAAGTTTATCACGA
qPrimers used for qPCR
Table S2. Sources of sequences used in multiple sequence alignment.
Element / Organism / Source / ReferenceALE / Triticeae (consensus) / TREP3455 / (Wicker et al. 2002)
Angela / Triticum aestivum / EMBL HG670306.1 / (Choulet et al. 2014)
ATCopia78 / Arabidopsis thaliana / Repbase / (Kapitonov and Jurka 2001)
Copia Dm / Drosophila melanogaster / Genbank P04146.3 / (Mount and Rubin 1985)
Gmr2/SIRE1 / Glycine max / Genbank AAO73527 / (Laten et al. 2003)
Gmr7 / Glycine max / SoyTEdb / (Du et al. 2010)
Gmr8 / Glycine max / SoyTEdb / (Du et al. 2010)
Gmr15 / Glycine max / SoyTEdb / (Du et al. 2010)
Gmr16 / Glycine max / SoyTEdb / (Du et al. 2010)
Gmr22/SORE-1 / Glycine max / GenbankBAG72096.1 / (Kanazawa et al. 2009)
Gmr49 / Glycine max / SoyTEdb / (Du et al. 2010)
Gmr71 / Glycine max / SoyTEdb / (Du et al. 2010)
Gmr74 / Glycine max / SoyTEdb / (Du et al. 2010)
Ivana / Hordeum vulgare / TREP2289 / (Wicker et al. 2002)
Maximus / Triticeae (consensus) / TREP3153 / (Wicker et al. 2002)
TAR / Triticum monococcum / TREP1316 / (Wicker et al. 2002)
Table S3. List of Repbase sequences with scores of >1000 recovered from Censor searches of the Repbase database using T. repens clones (Hand et al. 2010) as queries.
Accession / From / To / Repbase Name / Species / Class / ScoreGU443959 / 106822 / 107916 / ALFARE1_LTR / Medicago sativa / LTR/Gypsy / 1616
GU443959 / 107933 / 108930 / ALFARE1_I / Medicago sativa / LTR/Gypsy / 2874
GU443959 / 110443 / 111543 / ALFARE1_LTR / Medicago sativa / LTR/Gypsy / 1533
GU443959 / 118779 / 119576 / COPIA3-LTR_MT / Medicago truncatula / LTR/Copia / 4781
GU443959 / 120744 / 122594 / SHAMUDRAV_MT / Medicago truncatula / DNA/MuDR / 3427
GU443960 / 28 / 1264 / Copia-49_GM-I / Glycine max / LTR/Copia / 3653
GU443960 / 33717 / 34030 / COPIA-LTR_MT / Medicago truncatula / LTR/Copia / 1014
GU443961 / 16217 / 17224 / SHAMUDRAV_MT / Medicago truncatula / DNA/MuDR / 2754
GU443962 / 39158 / 39484 / COPMET_I / Medicago truncatula / LTR/Copia / 1253
GU443962 / 46255 / 46462 / MTIS112A / Medicago truncatula / DNA/Harbinger / 1050
GU443963 / 14165 / 15135 / COPIA2-LTR_MT / Medicago truncatula / LTR/Copia / 4819
GU443964 / 1086 / 2685 / LINE1A2_MT / Medicago truncatula / NonLTR/L1 / 4076
GU443964 / 3830 / 4014 / HAT3_MT / Medicago truncatula / DNA/hAT / 1036
GU443964 / 5082 / 9085 / COPIA-91-GM-1 / Glycine max / LTR/Copia / 7855
GU443964 / 10554 / 12044 / L1-14_GM / Glycine max / NonLTR/L1 / 2733
GU443964 / 34058 / 34860 / MTIS112A / Medicago truncatula / DNA/Harbinger / 5392
GU443964 / 35851 / 38217 / HARB-1_ALy / Arabidopsis lyrata / DNA/Harbinger / 7570
GU443964 / 42207 / 42441 / Copia-18_BD-I / Brachypodiumistachyon / LTR/Copia / 1008
GU443964 / 72235 / 72480 / RTE1_MT / Medicago truncatula / NonLTR/RTE / 1322
GU443964 / 100070 / 100527 / ALFARE2_LTR / Medicago sativa / LTR/Copia / 1186
GU443965 / 88678 / 89181 / Gypsy-109_GM-LTR / Glycine max / LTR/Gypsy / 1058
GU443965 / 92447 / 92829 / MTIS112A / Medicago truncatula / DNA/Harbinger / 1090
GU443965 / 92933 / 93378 / MTIS112A / Medicago truncatula / DNA/Harbinger / 1481
GU443965 / 113062 / 113644 / SHALINE8_MT / Medicago truncatula / NonLTR/L1 / 1335
GU443965 / 140201 / 144393 / SHALINE5_MT / Medicago truncatula / NonLTR/L1 / 11994
GU443966 / 18279 / 18610 / RTE1_MT / Medicago truncatula / NonLTR/RTE / 1646
GU443966 / 27290 / 27550 / TRAMET1 / Medicago truncatula / DNA / 1038
GU443966 / 32123 / 35892 / COPIA-68 PT-1 / Populus trichocarpa / LTR/Copia / 6802
GU443966 / 52454 / 52753 / COP2_I_MT / Medicago truncatula / LTR/Copia / 1713
GU443966 / 54669 / 56584 / COP2_I_MT / Medicago truncatula / LTR/Copia / 5338
Table S4. Amino acid variations deduced from mixed peak sequence data.
AminoAcids / Scorea / Frequency
IvanaA / IvanaB / LINE ORF1 / LINE ORF2
A/C / 0 / 0 / 0 / 0 / 1
A/G / 0 / 0 / 2 / 0 / 0
A/S / 1 / 0 / 1 / 1 / 3
A/T / 0 / 1 / 3 / 2 / 1
A/V / 0 / 0 / 1 / 1 / 0
C/L / -1 / 0 / 0 / 0 / 1
C/Y / -2 / 0 / 0 / 0 / 1
D/E / 2 / 2 / 4 / 0 / 5
D/G / -1 / 0 / 0 / 0 / 1
D/N / 1 / 0 / 3 / 0 / 6
E/G / -2 / 0 / 2 / 0 / 0
E/V / -2 / 0 / 1 / 0 / 1
F/L / 2 / 0 / 0 / 0 / 3
F/S / -2 / 0 / 3 / 0 / 0
F/V / -1 / 0 / 0 / 0 / 1
F/Y / 3 / 0 / 1 / 0 / 2
G/N / 0 / 0 / 0 / 0 / 1
G/R / -2 / 1 / 0 / 0 / 2
G/S / 0 / 1 / 0 / 0 / 0
G/V / -3 / 0 / 1 / 0 / 0
H/K / -1 / 0 / 0 / 0 / 1
H/N / 1 / 0 / 1 / 0 / 1
H/P / -2 / 0 / 0 / 0 / 1
H/Q / 0 / 0 / 1 / 0 / 3
H/R / 0 / 0 / 1 / 1 / 1
H/Y / 2 / 0 / 0 / 0 / 0
I/L / 2 / 0 / 1 / 0 / 1
I/M / 1 / 0 / 0 / 0 / 1
I/S / -2 / 0 / 1 / 0 / 0
I/T / -1 / 0 / 1 / 0 / 6
I/V / 3 / 0 / 3 / 0 / 4
K/M / -1 / 0 / 0 / 0 / 1
K/N / 0 / 1 / 0 / 0 / 2
K/Q / 1 / 1 / 0 / 0 / 1
K/R / 2 / 2 / 2 / 0 / 0
K/V / -2 / 0 / 0 / 0 / 1
K/ / -4 / 0 / 1 / 0 / 0
L/P / -3 / 1 / 1 / 0 / 2
L/Q / -2 / 0 / 0 / 0 / 1
L/V / 1 / 0 / 1 / 0 / 2
M/R / -1 / 0 / 3 / 0 / 0
M/T / -1 / 0 / 1 / 0 / 1
N/S / 1 / 4 / 5 / 0 / 2
N/T / 0 / 0 / 0 / 0 / 5
P/R / -2 / 0 / 0 / 0 / 1
P/S / -1 / 1 / 2 / 0 / 1
Q/R / 1 / 0 / 2 / 0 / 1
R/S / -1 / 0 / 0 / 1 / 2
S/T / 1 / 1 / 1 / 0 / 7
S/Y / -2 / 0 / 0 / 0 / 1
W/ / -4 / 0 / 1 / 0 / 0
X / - / 1 / 4 / 0 / 14
Totalb / 8 / 5 / 0 / 21
aBLOSUM62; bScore x frequency
Table S5. Element copy number estimates based on qPCR results with different primer pairs
Element / Primers / Calculated copy numberaIvanaA / 1115/1191 / 272
IvanaA / 1184/1192 / 273
IvanaB / 1161/1130 / 34
IvanaB / 1170/1179 / 4
IvanaB / 1176/1177 / 17
IvanaB / 1178/1179 / 9
LINE / 1090/1091 / 136
LINE / 1085/1149 / 34
aPer haploid genome
Table S6. Results of tBLASTn search against using the ORF2 hypothetical polyprotein from LINE1-Con against whole genome shotgun assemblies from T. pratense.
Assembly number / ORF2 coverage (amino acid residue) / Percent identity / Percent similarityASHM01013295.1a / 1-1093 / 87 / 95
ASHM01008152.1a / 8-1177 / 72 / 86
CVOM01034110.1b / 4-1387 / 70 / 83
ASHM01007706.1a / 8-991 / 77 / 89
ASHM01020708.1a / 4-866 / 77 / 88
ASHM01031906.1a / 1-768 / 85 / 93
ASHM01005244.1a / 1-1260 / 85 / 93
CVOM01018080.1b / 711-1393 / 85 / 90
CVOM01016529.1b / 11-1387 / 42 / 61
ASHM01005267.1a / 3-1392 / 40 / 62
aGenbank; bEMBL
Figure S1. Sequence of IvanaA-Con. Polymorphisms in purple. LTR placed at 5’ end (underlined). Start and stop codons for gag-pol ORF in red. Met-tRNA primer binding site indicated with double underline. Polypurine tract indicated with squiggle underline.
1 TGTATTAGAT AAGTAATTCA AAGTRAGCAA AAATGATAGT TTTAAGGTTG TTGCAAACTG
61 TTACTTGTGT AACAAGTAAC AGAAGTTAGT TAGTGACTTA RGCTAGTTAG TTGAGTTAGT
121 TGWTTCATGTWTTRRTAACC ATAGTTGGTT AGTGCTAGCT CAGTAGTTTT TGGGCATAAA
181 TACTACACTA TGCCTTTGTA AACATTAACA CTTTGATCAT TAATAAAGAA TCTTCCCTTT
241 CTCTCAAATT CATCTCTTAA TCATCATTTC ATTTTCATAA GTTCATARTYMATRRTTCTA
301 ACAAACTGGT ATCTAGAGCC TCAAGGTTCG TGGAACACAA GAATTGATCA AGATTCATAG
361 MAGCTTGTTC AATTATCTCA GCAACATCATGACAAGTCAG TTAGAGACTC TTAGCAACAG
421 CTTTGGTGGC AAACTCCCAA TTCTTGATGC AAAAAATTGG GATCGTTGGA ACAAACARAT
481 GAAGGTGATC TTTGGATTCC AAGAAGTGCA AGAAGTAATT GAAACTGCAA TTGGTGATCT
541 TGCAGAGAAT GCAACAGAAG CTCAAAGGAA TGCACATCGT GCATTGAAGA AAAAAGATTT
601 TAAGGCAATG TTCTTCATAC ACCAATGTGT WGATTTGGTG AATTTCCAGA AGATTGAGAA
661 TGCAACCTCA GCTAAGGAGT GTTGGGACAT TCTTGAAAAG GCTCATTCTG GGAATGAGAA
721 GTTGAAGCAG GTGAGATTAC AAACTTGGAA GAGGAAGTTT GAACTGCTAC AAATGGAGGC
781 AAATGAAAGC ATTGCAGAAT ATTTCAACAA GATCACCAAC ATYACMAATC AAATGAGRAG
841 CTGTGGTGAA ACMTGTGAYA ATCAATCCAT TGTTGGTAAG GTTATGAGAA CTTTATCTCC
901 TAAGTTTGAT TATATCACTG TTGCTATMAT GGAAACMAAA GACTTGACAA CACTCACYCT
961 KGATGAATTA CAATGCACAT TGGAATCACA TGARCAAAGR ATCATGGAAA GRATCAARGA
1021 TAGAGCCACT GATCAAGCAY TGCARGCACA TGCAGTCAAG AAGGGTAATG GMAAATGGAA
1081 GGGTAAAGAA AAGTCAAARA ATCAGWCCAA CAACAAAGAY ARCTCAAAGA AAAGTAATGA
1141 TCAAGGTGAA TCTTCATCAC AARGCACTGG TTCAAATCAA GAAAAGAAAG GGAAGTTCAA
1201 TCTSAAGAGY ATYCAGTGYT ACAATTGCCA GAAGTTTGGC CACTTTGCAA AAGATTGTAG
1261 AGGCAAGAAG GTTCCAAGAT ACTCCAACAA ACAAGATTCT GATGCACACC TAGCTCAAGA
1321 RGATAGTGAA TCAGAAGTTG ATCCAATGYT GCTRATGGCC ACAGTCACTG ATGAAGAAGA
1381 RCATCATGAA GGTTGGTATC TTGACACTGG CTGTAGTAAY CATATGACAA GTCACAGAGA
1441 ATGGTTGGTG AATTTCAATG ATTCATCAAA AACAAAGATA AGATTTGCAG ACAACAGAAC
1501 CATTCYAGCT GARGGAGTRG GTGATGTAWT GATCAARGGC AAGAAAGGGA ATCAAGCACT
1561 GATTACAGGA GTTCTGTATG TACCAGAAAT GAAGACAAAT TTGCTTAGTA TGGGTCAATT
1621 GCTAGAAAAG GGTTTCATCA TGCATCTGGA GAATAATGTA ATGGAGGTAT TTGACTCACA
1681 CAAGAACACT ATTTTGAGAG CTCCAATTTC TCAAAATAGA ACATTTCAAG TTCAAATTTC
1741 TGCAAATCAA TGTCTGGCTA GCATGAAGAT TAGTGATGAA GCATGGTTAT GGCATATGAG
1801 GTATGGTCAT CTCAATTTCA AAAGTTTGAG TTATCTGAAA AGTAATGAAT TAGTGAAAGG
1861 CTTGCCAGCA ATCAAAACTC CAAAAGATAT CTGTCAGCAT TGTTTGTTAG GCAAGCAAGC
1921 TAGAAAGTCC TTTGTTAAAG AAGTAGCTAT GAGGGCAAAA CAGGTACTAG CTGTTGTCTA
1981 TACTGATGTG TGTGGCCCTT TTGACACTAT GTCATTAGGA GGAAGTAGAT ACTTTGTCTC
2041 ATTCATTGAT GAGTTCAGCA GAATGATGTG GATTCATCTA ATGAAGAGCA AAGATGAAGT
2101 GCTTCAAAAA TTCAAAATCT TCAARTTAGA AGTTGAGAAT CAGTCTAATA TGAAGATTAA
2161 GGTGTTAAGG AGTGATGGTG GTGGTGAATA CACATCACAT GAGTTTAGGT CATTYTGTGA
2221 ATCWARTGGC ATTAAACATG AAGTTGTARC ACCTTACACA CCTCAACATA ATGGAATGGC
2281 TGAMRGRAGG AAYAGAACAA TCATGAATAT GACAAGATGC ATGTTRAAAG AGAAGCAATT
2341 ACCACATAGC TTCTGGGGTG AAGCAGTAGT CACAGCCTGC TATGTTCTGA ATAGATGCCC
2401 CACAAAGMAA TTGAATCAAG TRCCAGAAGC TATATGGTCA GGATCTACAC CATCAGTCAA
2461 ACACTTRAGA GTMTTTGGTT GYCTATGCTA CAAACACATT CCTGATCAGA AAAGRAAAAA
2521 ACTKGATGAC AAGAGTGARC TGATGATCAT GATAGGTTAT CATACWGCAG GAGCTTATAA
2581 ACTCTACAAT CCCATYACTA AGAAAGTAAC AAGCAGYAGA GATGTTACTT TTGAAGAGGA
2641 TAAGAGTTGG AATTGGGAYA CTAATGCTGA RMYATCTCCA AAGYACATTC CATTTCAGTT
2701 ACTTGATGAA GAAGTTACTG AATTAGACAC CATGCCAACA YCTCCACCTC CACAACACAA
2761 TCAAGTTGCA GTAAGAAGAT CAGAAAGAAC AAGCATTCCT AGTAGAACAC TGCAAGACTA
2821 TGAAACAATA CCAGATAACA TGATCACACC AGATGGTGAC ATAGTGCACT TAGCCTTATT
2881 TGTTGACACT GAGCCTCTCA CATATGAACA AGCAGCTAAG TTTGAAGAGT GGAGACTGGC
2941 TATGCAAGAA GAAATAGCTT CCATTGAAAG AAATCATACA TGGGATCTRG TTGATCTACC
3001 TGCCAACAAA AGACCTATAG CAGTCAAGTG GATTTATAAG TTGAAGCATC TGCCTGATGG
3061 TACTATAGCC AAGTACAAAG CAAGATTGGT GGCAAAAGGG TTCCTTCAGA AGCCTGGCAT
3121 TGATTTTACT GAGGTATTTG CACCAGTAGC TAGACTTGAR ACAGTTAGAC TGGTTGTAGC
3181 TATTGCAAAT CAYTTTCAAT GGGASTTTGT TCAGTTAGAT GTCAAGTCTG CCTTTCTAAA
3241 TGGCAAACTT GAGGAGGAAG TRTATGTAGA GCAGCCTCAA GGMTTCATAA CTARAGGRAA
3301 AGAAGATCAA GTRYTGAAAC TGAAYAAAGC TTTRTATGGC CTAAGACAGG CACCAAGRGC
3361 ATGGAATATT AGAATGGATG AATTTCTCAG CAAAAATGGA TATACAAAAT GCACTGTTGA
3421 GCATGGTATA TATGTYAARG GYACTTCWCA GAATAGAATT TGTATGGTGT GTCTATATGT
3481 GGATGATCTA CTCATAACTG GCAGCARCAA AGATGAGATT GTCAAACTGA CAAAKCAGTT
3541 AAGTACAGAG TTTGATATGA CAAACYTAGG AGGATTGAGA TACTTCCTTG GATTAGAATT
3601 CACTAAGACA ARTAGTGGAT TGTTGATACA TCAGARAAAA TATGTCTCAG ACATATTGAA
3661 AAGGTTYAAC ATGATGAATT GTAACCCAGC CAGCACACCA ATGGAGACCA GCTCAAGCTT
3721 GAACAATGAT GATGAAGGTA AATCTGTGAA TAGYACTAAC TATAAGCAGA TGGTGGGAAG
3781 CTTGAGATAT GCATGTAACT CAAGGCCAGA TATATGTCAT AGTGTAGGGA TTGTTAGTAG
3841 ATTCATGCAG TCACCTAAAC TATCTCATAT GCAAGCTGTG AAGAGAATTT TGAGATACTT
3901 GCAGGGCACR GTTGATTATG GTGTTTTGTA CTCCAACACA GATGGAAATC AAAGAAGATT
3961 GGTGGGCTAT TGTGATTCTG ATTGGTCTGG TGATAAGGTT GARAGGAAGA GTACCATGGG
4021 CTATGTCTTC ACACTGTTCA ATTGCCCYAT ATCATGGTGT TCAAAAAAGC AAAATGTAGT
4081 TGCCTTGTCT ACATGTGAGG CTGAGTACAT TTCTGCCTGC AATGCTGCTT GTCAAGGCAT
4141 ATGGTTACAG TCATTACTGC AGGAAATGAA GATTGATGTA GATCATGAAG TTGAGCTGAT
4201 GATAGACAAC AAATCAGCTA TTAATCTGGC CAAAAACCCC ATTGCACATG GGAGAAGCAA
4261 ACATATAGAA ACTAAGTTTC ATTTTTTGAG AGATCAAGTT ACAAAGGGGA AGATCAAGCT
4321 ATCTTACTGC AACACAAATG TTCAAATGGC AGATGTGCTC ACTAAGCCAT TGAAGATTGA
4381 TAGATTCAAG GATTTGAGAA GAATGATGAA TGTACAAAGT CTTGAGACTT TGAATTAAAG
4441 GGG
Figure S2. IvanaA-Con hypothetical polyprotein. Polymorphisms in red. The dominant amino acid is listed first. =: equal peak heightsat polymorphic sites.
MTSQLETLSNSFGGKLPILDAKNWDRWNKQMKVIFGFQEVQEVIETAIGDLAENATEAQRNAHRALKKKDFKAMFFIHQCVDLVNFQKIENATSAKECWDILEKAHSGNEKLKQVRLQTWKRKFELLQMEANESIAEYFNKITNITNQMRSCGETCDNQSIVGKVMRTLSPKFDYITVAIMETKDLTTLTLDELQCTLESHEQRIMERIKDRATDQALQAHAVKKGNGKWKGKEKSKNQ(S=T)NNKD(N/S)SKKSNDQGESSSQ(G/S)TGSNQEKKGKFNLKSIQCYNCQKFGHFAKDCRGKKVPRYSNKQDSDAHLAQEDSESEVDPMLLMATVTDEEEHHEGWYLDTGCSNHMTSHREWLVNFNDSSKTKIRFADNRTI(P/L)AEGVGDVLIKGKKGNQALITGVLYVPEMKTNLLSMGQLLEKGFIMHLENNVMEVFDSHKNTILRAPISQNRTFQVQISANQCLASMKISDEAWLWHMRYGHLNFKSLSYLKSNELVKGLPAIKTPKDICQHCLLGKQARKSFVKEVAMRAKQVLAVVYTDVCGPFDTMSLGGSRYFVSFIDEFSRMMWIHLMKSKDEVLQKFKIFKLEVENQSNMKIKVLRSDGGGEYTSHEFRSFCES(N=S)GIKHEVV(A=T)PYTPQHNGMA(E/D)(G/R)RNRTIMNMTRCMLKEKQLPHSFWGEAVVTACYVLNRCPTK(K/Q)LNQVPEAIWSGSTPSVKHLRVFGCLCYKHIPDQKRKKLDDKSELMIMIGYHTAGAYKLYNPITKKVTSSRDVTFEEDKSWNWDTNAE(T/X)SPKYIPFQLLDEEVTELDTMPT(S/P)PPPQHNQVAVRRSERTSIPSRTLQDYETIPDNMITPDGDIVHLALFVDTEPLTYEQAAKFEEWRLAMQEEIASIERNHTWDLVDLPANKRPIAVKWIYKLKHLPDGTIAKYKARLVAKGFLQKPGIDFTEVFAPVARLETVRLVVAIANHFQW(E/D)FVQLDVKSAFLNGKLEEEVYVEQPQGFIT(R/K)GKEDQVLKLNKALYGLRQAPRAWNIRMDEFLSKNGYTKCTVEHGIYVKGTSQNRICMVCLYVDDLLITGS(N/S)KDEIVKLT(K/N)QLSTEFDMTNLGGLRYFLGLEFTKT(N/S)SGLLIHQ(R/K)KYVSDILKRFNMMNCNPASTPMETSSSLNNDDEGKSVNSTNYKQMVGSLRYACNSRPDICHSVGIVSRFMQSPKLSHMQAVKRILRYLQGTVDYGVLYSNTDGNQRRLVGYCDSDWSGDKVERKSTMGYVFTLFNCPISWCSKKQNVVALSTCEAEYISACNAACQGIWLQSLLQEMKIDVDHEVELMIDNKSAINLAKNPIAHGRSKHIETKFHFLRDQVTKGKIKLSYCNTNVQMADVLTKPLKIDRFKDLRRMMNVQSLETLN
Figure S3. Sequence of IvanaB-Con. Polymorphisms in purple. LTR placed at 5’ end (underlined). Start and stop codons for gag-pol ORF in red. Met-tRNA primer binding site indicated with double underline. Polypurine tract indicated with squiggle underline.
1 TGTTAGGTAT TGTTTGTGTT TGGGCCTATT GGGCCRTGTA YATGACTTGT AGCCTATATA
61 AGGCATATTG TGGAAGATGA ATAACATGAG ATAGCACTTA TCACRACAAG TGGTATCAGT
121 TAAGCCTGCA CGTGTGGCYT GGCGCGCGCG CATAACCGTT KTTCAAAACG TTTTCCCTTT
181 TGCCGGTGAC AGTTAYGGKG GCCGTTTCAA CGGTTACRMC GGCGTTCTTT CTTGATTCAC
241 ACATCCYCTC CGATCAWTTT TCTTCCTCTT CACAGTTCAA TCATGACAGA AAACTCCCAC
301 TTTGTTCAAC CCGCAATTCC CAAATTTRAT GGTTATTACG AGCATTGGTC AATGCTCAYG
361 GAGAATCTTC TCCGATCGAA GGAGTTYTGG AATCTCATCG AGGTWGGTGT AGTTACAGCT
421 CCGRCGAATG CAACCGCGGA ACAACRACGA CTMGCTGATG AAAGCAAATT GCGCGATTTG
481 AAAGTCAAGA ACTATCTTTT CCAATCCATC GATCGTTCAA TCTTGGRAAC GATCTTGGTT
541 CGTGACACGG CTAAAGACAT TTGGGATGCT ATGAARCGCA AGTATCAGGG TTCTACAAAG
601 GTGAAACGAG CTCAGTTACA GTCTTTGCGT CGGGAATTTG AGGTTCTTGC AATGGGGGAG
661 AGTGAAACAG TCAATGAATA CTTTGCAAGA ACTCTTGCGA TTGCAAATCG CATGACCTCA
721 CATGGTGAAA GAATTGAACA AGTTATGGTG GTGGAAAAGA TTCTGCGATC TATGCCTCAG
781 AAATTCAATT ATGTAGTTTG TTCAATTGAA GAATCCAACG ATGTCACGGC TCTATCAATT
841 GATGAATTGC ARAGTAGCCT TCTTGTTCAT GAGCAACGTA TGCAAGGCCA GAAAGATCAY
901 AGTGAAGAGC AAGCTCTCAA GGTTTCCAAT ACAGGCAGAG GTAGGGGAAG AAATYCTTCA
961 CGAGGTCRTG GAAGAGGTAG GCAGAGTAAG GCTTTAATTG AATGTTACAA GTGTCACAAG
1021 CTTGGTCATT ACAGGAATGA GTGCCCTGAA TGGGAAGAAA ATGCTAATTT TGYTGAATAT
1081 CAAGATGAAG AAGAAACTMT TCTTATGGCT CATTCTGGAT CTRTAGTGAA TTCCATAGAA
1141 RAARCATGRT ATCTTGATAG TGGTTGTAGC AATCACATGA TTGGTACTAA GGSATGGCTC
1201 TTTGATTTTG ATGACAGTTT TAGAGAATCA GTCAAACTGG GTAATGATTC AAAAATGGCA
1261 GTGATGGGTA AAGGWAATAT CAGATTGAAT ATAGAAGGAA AGGTGCATGT YATCACTGAT
1321 GTGTATTATC TTCCTGGTCT AAGCAATAAT TTGTTGAGTA TTGGTCAGCT GCAATCCAAA
1381 GGCCTCACCA TTGTGTTTAG AAACAATGTT TGTCAATTGT TTCATGATGA AAAGGGTTTG
1441 ATAATAACCA CTGAGATGAC CATGAATAGA ATGTATATTG TGAGAGCTAC AGTTCAAATC
1501 CCTCAGTGCC TGCAKATTAC AWAGATAGAA GAAACTGAGC TCTGGCACAA TAGATATGCY
1561 CATCTTAGCA TCAAGGGGTT AAAGSTTCTA AATAACAAAA GAATGGTCAA AGGTTTACCT
1621 GAGTTAAARG AAGTTGAGGG CAAATGCACA GATTGCTTGA CTGGCAAGCA ACACAGAGAA
1681 ATCATTCCTA AACTRGCAAA TTGGAGAGCA TCACAGAAGT TAGAGYTAGT TCACTYTGAC
1741 ATTTGTGGTY CCATCAATCC CAAGTYTAAT GCAGGCAACA KGTATTTCAT AACCTTCACT
1801 GATGATTACTYTAGGAAGAC ATGGACTTAT TTTYTGCAAG ACAAGTCTAG TGCTTTTGAA
1861 GTTTTTAAGA AATTCAAGTC ACTAGTTGAA AAAGAATCAG GTTGTGAAAT TAAGTGTCTT
1921 AGAACTGATA GAGGTGGTGA ATTTACCTCA ACCATGTTTA ATGATTTTTG TAGCTCACAA
1981 GGTGTGAAAA GACAGTTAAC TACTGCCTAT ACTCCTCARC AGAATGGAGT TTCAGAAAGA
2041 AAGAATAGAW CCCTCTTGAA CATGGTGAGA AGCATGATCT CTGCTATGGA AGTACCTAAG
2101 AGTTTTTGGC CTGAAGCTGT GAAATGGGCA ACATATGTGA TGAATAGAAG YCCCACYTTT
2161 GCTGTGAARG ATATGACACC AGAAGAAGCT TGGAGTGSAA GCAAGCCTTC TGTRCATCAY
2221 TTCAGGGTGT TTGGTTGTCT TGCACAYGTT CATGTGCCTG ATGCTCATAG AAARAAGYTG
2281 GATGGGAAGA GTATCAAGTG CATTCTTCTT GGTGTTAGTG AGAAATCCAA AGCATACAAG
2341 TTGTATGATC CAGTTGAGAA GAAAATAATT GTTAGCAGAG ATGTGGTGTT TGAAGAATCT
2401 AGAARCTGGA ATTGGRATAA GAGAAAAACA GTTGTCAAAT CAACAGAGCC AGTTAGTGAY
2461 AATGAAGAGA ATGACAAYAT TGARCTGGAA GARRMARWWG AAGAAGWAGA TMATGGTCAT
2521 GAGRRTGTGA ATRATGAWGT TGTCTCWGAY TCWACAGAAG AWCAAAGTRM TGAAGGAGAT
2581 GATGATGKGT CWCCCAGAAT CAGAAGACCA CCACMATATC TKARAGACTA TGTGACTGGT
2641 CTTGAAARYA GTGARARTGA SAATGATCAG CTGCAAAATC TGGCYATTGC CATGTTYAGY
2701 TCCAGTGAAG ATCCTRCTAC TTTTGAWGAR GCAGTNAARA GTACMARATG GAAAGAAGCW
2761 ATGGATTCTG AGATCAAATC YATTGARGCY AAYAACACAT GGAAACTTGT GACYCTACCW
2821 CATGGTGTGA AGCCTRTTGG TGTAAARTGG ATATACAAGA CAAAGTWTAA TGAGAARGGG
2881 AAAATTGARA AACACAAAGC AAGACTAGTT GCAAAGGGGT ATTCCCAGAA ATATGGAGTT
2941 GATTTCAGTG AAGTKTATGC ACCTGTAGCT CGATGGGATA CAATCAGAAC AATATTGTCA
3001 TTAGCTGCTC ATGAAAAATG GAATGTGTTC CAACTTGATG TCAAAAGTGC ATTCCTACAT
3061 GGTGAATTAA TTGAAGATGT ATATGTGGAA CAACCYTTAG GATATCAAAA GGGAAATAAC
3121 AGTCAAGTAT ACAAGCTCAA TAAAGCTTTA TATGGGCTAA AACAGGCCCC TAGAGCTTGG
3181 TATAGCAAGG TAGAATCCTA CTTCACTGCT GCAGGATTTA AGAAATGTTC TCATGAACAT
3241 ACCTTGTTTG TCAAGAAAGG AAGTAAGAAT CAGATTCTGA TAGTAAGCAT ATATGTGGAT
3301 GATCTYATTT ATACTGRAAA TGATGTAGGG TTGATGATTG AGTTCAAGGA ATCTATGAAA
3361 GAAAAATTTG CCATGACAGA TCTTGGAAAR ATGAAGTACT TTCTTGGGAT AGAAGTAACT
3421 CAGTGTGAAC AAGGCATTTT CATTCAGCAG CATAAATATG GCCTGGARGT GTTAAARAGA
3481 TTTGGTATGG AGGATTGTAA CAAAGTTTGT AGTCCAAYTG TGCCTGGTTG CAAACTTGTT
3541 AAAAATGAAG TTGGAAAAGC TGCTAATCCA ACTGAGTATA AGCAGATGAT AGGTTGCTTG
3601 ATGTATATGC TRGCAACAAG ACCTGATATG GTTTTCTCTG TGTGTCTAGC TGCTAGATAT
3661 ATGGAAAGRC CAACAGAGAT GCATGTGGCT GCAGTAAAAA GAATTTTGAG GTACTTGAAA
3721 GGGACACTGA ACTTGGGAAT ATTGTACAAA TGCAAAACAG ACAACAATTT GATTTTACAA
3781 GGGTGGAGTG ACTCAGATTA TGCTGGTGAT TATGATGACA KGAAGAGCAC TTCAGGGTAC
3841 ATATTTACAA TGGGAACTAG TGCAATATGT TGGTCTTCCA AGAAACAACC YATTGTTACA
3901 CTTTCCACCA CAGAGGCAGA ATTTGTGTCA GCAKCTTCAT GTGCCTGCCA RTGCATTTGG
3961 GTGAGAAGTA TTTTGCAGCA TTTGAATGTG AAGCAAGATG GAAGCACTTT CATCAACTGT
4021 GACAATAKCT CCTCCATCAA GCTATCTAAR AATCYAATTT TGCATGGCAK GTGTAAACAT
4081 ATTGATGTAA GGTTCCATTT CCTTAGAGAT CTCAATAAGG AAGGCACTAT TGAACTTMGG
4141 TACTGCAGGT CACAAGATCA GCTGGCAGAY ATGATGACTA AAGCTCTAAA ACTTGATACT
4201 TTCTGCAGAT TAAGGGAGGG CATTGGAATG TGTGATARCT CGTGCATTGG ATAAGTGATT
4261 GTCATAGTGA ATCTGTGTAC TTGAGTCTTG TATAAGCTTG CTTGCTCTGC AAGCTTTGTC
4321 TGTCTRTTTG TTTTACTTGC TTTCYTAWTA GTTTATCTTA ATAGTTTRTG TTAATGTTGT
4381 CCCTCTCTGGYTGTGTTGTA AATTGATCTC TCAAGTGAGA ATCAATTCAAGGGAGGGTT
Figure S4. IvanaB-Con hypothetical polyprotein. Polymorphisms in red. The dominant amino acid is listed first. =: equal peak heightsat polymorphic sites. : nonsense codon
MTENSHFVQPAIPKF(D/N)GYYEHWSML(M/T)ENLLRSKEFWNLIEVGVVTAP(A=T)NATAEQ(R/Q)RLADESKLRDLKVKNYLFQSIDRSIL(E/G)TILVRDTAKDIWDAMKRKYQGSTKVKRAQLQSLRREFEVLAMGESETVNEYFARTLAIANRMTSHGERIEQVMVVEKILRSMPQKFNYVVCSIEESNDVTALSIDELQSSLLVHEQRMQGQKDHSEEQALKVSNTGRGRGRN(P/S)SRG(R/H)GRGRQSKALIECYKCHKLGHYRNECPEWEENANF(A/V)EYQDEEET(L/I)LMAHSGS(I/V)VNSIE(E/K)(A=T)(W/)YLDSGCSNHMIGTK(G/A)WLFDFDDSFRESVKLGNDSKMAVMGKGNIRLNIEGKVHVITDVYYLPGLSNNLLSIGQLQSKGLTIVFRNNVCQLFHDEKGLIITTEMTMNRMYIVRATVQIPQCL(Q/H)IT(K/)IEETELWHNRYAHLSIKGLK(V/L)LNNKRMVKGLPELKEVEGKCTDCLTGKQHREIIPKLANWRASQKLELVH(F/S)DICG(P/S)INPK(F/S)NAGN(M=R)YFITFTDDY(F=S)RKTWTYFLQDKSSAFEVFKKFKSLVEKESGCEIKCLRTDRGGEFTSTMFNDFCSSQGVKRQLTTAYTPQQNGVSERKNR(T/S)LLNMVRSMISAMEVPKSFWPEAVKWATYVMNRSPTFAVKDMTPEEAWS(A=G)SKPSVHHFRVFGCLAHVHVPDAHRKKLDGKSIKCILLGVSEKSKAYKLYDPVEKKIIVSRDVVFEESR(S/N)WNW(N/D)KRKTVVKSTEPVSDNEENDNIELEE(A/X)(E/X)EE(E=V)D(H/N)GHEXVN(N/D)(E/D)VVSDSTE(D=E)QS(N/X)EGDDD(G=V)SPRIRRPP(P/X)YL(R/K)DYVTGLE(N/S)SE(N=S)(D/E)NDQLQNLAIAMFSSSEDP(T/A)TF(E/D)EAVKST(K/R)WKEAMDSEIKSIEANNTWKLVTLPHGVKP(I/V)GVKWIYKTK(F=Y)NEKGKIEKHKARLVAKGYSQKYGVDFSEVYAPVARWDTIRTILSLAAHEKWNVFQLDVKSAFLHGELIEDVYVEQPLGYQKGNNSQVYKLNKALYGLKQAPRAWYSKVESYFTAAGFKKCSHEHTLFVKKGSKNQILIVSIYVDDLIYT(G/E)NDVGLMIEFKESMKEKFAMTDLGKMKYFLGIEVTQCEQGIFIQQHKYGLEVLKRFGMEDCNKVCSP(I/T)VPGCKLVKNEVGKAANPTEYKQMIGCLMYMLATRPDMVFSVCLAARYMERPTEMHVAAVKRILRYLKGTLNLGILYKCKTDNNLILQGWSDSDYAGDYDD(R/M)KSTSGYIFTMGTSAICWSSKKQPIVTLSTTEAEFVSA(A/S)SCACQCIWVRSILQHLNVKQDGSTFINCDN(S/I)SSIKLSKN(P/L)ILHG(R/M)CKHIDVRFHFLRDLNKEGTIELRYCRSQDQLADMMTKALKLDTFCRLREGIGMCD(S/N)SCIG
Figure S5.Sequence of LINE-Con. Polymorphisms in purple. Start and stop codons in red.
1 TCTAAGCATG CTGGGGGTAG TTGAGCTGAA AAATAGAATG AACAAAGTTG AAAAATAATC
61 TCTACTAAAT TCTTCGCCAC TGCATCTTCT TCTTATCATA TGATTGTTMY TAATTTGTAG
121 ARGTAAACAA GGTGATATTA TTTGAATTTC TTATTGTGTT TGAAAAAAAT ATGTTTTTTT
181 TAGTAATTTT ATGGACTAAA TTGATTAATA AAAAACACAT TCGAAGACCA AAAGATTAAC
241 TGAATAGACA TTTAAATATG TGTTAGAGAC TAAAATCAAA CTAAAATAGG ATGGAGACTA
301 AAATATGCTT GCTATTAAGG ACTTATCAAG AGTTTCGGAG AAGATCCAAA TTCCTCATAA
361 TAGAAACAAA TTTTTTTACT CTCTCCCTAG AAAGTATGMG CAACCCCCCC TTTGTCTTTT
421 CCACTGAATC TCTGCCACAA CAAGGACCCA AGAAGCCTCC TGATATTCTC AACCCTTCTA
481 AGGTGTCTTT TCGTGATAAA CTTCTAGGTT CCAGCGAGCC TTTGCCAACT CGTATGAAAG
541 AGGATCTTAT AGCTTCAAAA CAAGTGAGAA TAGAGTATGA AAGTGGTAAC AGACTCTTTC
601 CTAAAGTGTA CCTTGACAAT AATGTTTTTC AAGGTATGTG TACTCCTTGG AAAGATGCTT
661 TGGTTGTTAC ACTTYTGGGA AAAAAATTGG GTTACCACAC AATGAAGGAA AGACTCCAAA
721 AGGTTTGGAA GCTTCAAGGC GGTTTCGAAA TTATGGACAA TGACAATGGT TTTTATATGG
781 TCAAGTTTGA TCAAGCTGCA GAAAAAGAAA GGGTTATTTC AGATGGCCCT TGGATGATAT
841 TTGATCACTA CCTTGCTGTT TCACATTGGA CGCCAGAATT TGCCTCACCG GATGCAAAAG
901 TGGATCGCAC GGTTGTCTGG ATCCGCTTCC CTGGTCTCAA TCTTGTCTAT TATGATGAAA
961 GCTTTCTGTT AGCCATGGCT TCTGCCATTG GTCGCCCAAT AAAAGTTGAT CATAACACGC
1021 TAAAGGTTGARAAAGGACGC TTTGCTCGTG TTTGTGTTGA GGTTGACCTC ACTTTACCTG
1081 TTGTTGGAAA GATCTGGCTT AATGGACATT GGTACAAAGT ACAATATGAA GGGCTTCATA
1141 TTATTTGCAC AAATTGTGGA TGTTATGGTC ATCTTGGTAG AAATTGCAAC AAAAATCCTA
1201 TTTCATCGAC AGAAAAGTCA ACAGCGCCGT CGRCATCTCC TAACAGCRCC GYCGCAATAK
1261 CCACCGCGCC GTCATCCAGC CACCGCGCCA CAACTGTTAA CGGTAATCAT CAAAAYCRTG
1321 CAACAAGTGG TGACAACAAC AATTTTAATG CGCCCGCGGA AATTACGGAA ACTGAAAACG
1381 GGAATAGTAA TTGTGCTGAT AATAATGAGG GAAACAAAAT TAATGCTGCT AATAATGAAG
1441 AGAACAATTC CCCTCATGGA GATTGGCTGA CCGTTACAAG AAAGAAAAAR TCAAATCCCA
1501 AGTTTAATGC TAACAATTTC AATGGACAGG CTGGGAATAG AAATGGGCAA CATTCCAAAA
1561 ATAATATCCG CAATATTGTA GAGAAAATTA ATAGACAATA TCCAACAAAT GAGAATGGTC
1621 CAACAAATGT TAGAAGCAAA AATCGGTACC AAAATAAAAG GTCCAGAAAT GAAGCAATTG
1681 GGCCCAACAA GACCCCTCCG GTAGATACTC AACTTGTCCA CAATTTAGAA CCGTGTGGGA
1741 TATATAAGGG GGGYTATACA GCAATTCTTC AAAAAGTCAA TACTGTGAAG GCACGTGTGG
1801 AGCAACCCAT TGCTAATGAG AATAAAGTTC AGCTTGAATC TAGACCCAAA ATGTTGGAAC
1861 AACATGACAT AAARGACTCA CTCCACAATC AACAAATCAT GGCCACTATG CATCAAGCTC
1921 ACGTTAACAA GGTTGAAGGA GTTCATCATG AAATTGAATC CAATGGCAAG GTCAATGTGG
1981 AAATTCAAAC AACACCATAT GGAAATGAAC ACATGGCCAC RGATAAAAAT AGTGGTGATA
2041 ATATCATGGG AATAACCCAT GACACCAGTA TGAGTCTTAA TTAATGTATC CTTTTTTTAG
2101 GATTATTTTA GCTTTTATTA CTTTTTGTTT TTTAATGATT GTTATTAATT GGAATTGTAG
2161 AGGAGCTCAA GGTTTAAATT TCCGACGAGC TCTTACTAAT TTTTGCAGGA AGAATAAAGT
2221 TGATATAGTA GCCTTACAAG AGCCGCGTTG TAGTGGRAGT ACAGCCAAAA AAACAATYAA
2281 GAAACTGGGT TTCAAAAATT ATGTTATGGC CGAAGCTAGA GGTTTTTCTG GGGGTATCTG
2341 GCTGATGTGG AACAGGTCAG ACATTAAAAT TCAGTTAATA AAAAATGATT TTCATTTTCT
2401 TCATGTGCAG GTGAGTGAAA ATGAGATGGA ACCTTGGCTT TTAACTGTGG TTTATGCTAG
2461 CCCGCGAGAG AATGAGAGAC ATGATACTTG GCAGTTACTR CGGCAACTTG CTTATTCTAT
2521 CAACAAACYG TGGCTCGTGA TGGGAGATTT TAATGAAATT GCTCATCCTG ATGAGAAGAA
2581 AGGAGGTGCA CCAGTAGACG TTAGAAAATG CCAAATTTTT AATAGCTGGA TCAATGATTG
2641 TAACCTTCTT GAAGTCACAA CAGCTGGTAC GCGCTTTACT TGGAGAGGTC CTAAGTGGAA
2701 TGGGAGGGAT AGAGTTTTCA AGAAACTTGA TCGTGTCCTC TGTAATATTG ACTGGAGAAT
2761 TAAGTTCCAT GAAGGTGTTG CTAAGGTCCT CCCAAGGGTT CAATCTGATC ATCATCCCAT
2821 TATCGTGTTA CTTGAGGGAG AGACTGCTAC AAACAGAAAC CGTCCCTTCC GTTTTGAGGC
2881 TGCATGGACT TCCCATGATG ATTTCGATAA CTTTATGAAT TCTAAGTGGG AGAAAGATAA
2941 AGATATTGTG CAAAGCCTCC ATGATCTAAC AACTCATCTC AAGAAGTGGA ATAAAGAGAC
3001 ATTTGGAGAC ATCTTTAAAA GAAAAAAAGA GATATTAGGC AGGCTTCATG GAATTCAAAA
3061 TAGCTCTAAC TATGGTTATA GTASCTTTCT TGAGAATTTG GAAAAAGAGC TTCAAGATCA
3121 ACTTGCAGTC ACCCTTTACC AAGAAGAGTG TCTTTGGTTT CAAAAATCTA GGAGTCAATG
3181 GATTACTGAT GGAGACCGCA ATACCAAGTA TTATCACTCT AAAACTATTG TCAGAAGGAG
3241 ACGCAATAAA ATTATTTCTC TTCGCAATGA GGAAAGGACT TGGGTTGAGG ATCCAGAAAT
3301 TCTCAAAGAC TTGGTACGAA ATTTCTATAT CAACCTTTTT AAAGAGGACA AAGAAGTTCG
3361 TGATCCAATT ATTTCATGGA CTACCTATCC AKCGAACATG GAAGCTCATC ATAATGCTTT
3421 AAGTGCTACG ATCCAGTTTT CTGAATGCAA GAAAGCCCTT TTCGATATGG GCCCTCTGAA
3481 AGCACCTGGA GAGGATGGCT ACCCTGCTCT CTTTTTTCAA CAATGTTGGG AAACTGTGGC
3541 TGACTCTCTA TTCCGGTATG TTAACCAGGT TTGGATGAAT CCTTCTCTCA TCTCTACAAT
3601 TAATAATACT CTACTTGTTT TAATTCCTAA AGTAGACAAA CCTGAATTTG TTTCTCAATT
3661 TCGTCCTATA GCTTTGTGTA ATGTCGTCTA TAAAATTATT ACCAAGGTTA TTGTGAATAG
3721 AATTAAGCCT ATGTTAGATG GAATCATATC TCCCTATCAA TCCAGCTTCA TTCCGGGTCG
3781 TACCATACAT CATAATATTA TAGTGGCGCA AGAAATGGTG CATAGTATGG CTAGGATGAA
3841 AGGTAATAAG ATGTTTATGT CTATTAAAAT TGATCTTGAG AAAGCCTACG ATCGGCTTAA
3901 TTGGAAATTT GTTGAAAATT GTCTGAATGA ATGTAAGTTT CCTCCTAACC TCATTAATAT
3961 TATTCAACAT TGTATTTCTT CTCCATCTTT CAAAATCTTA TGGAATGGCG AGAAAACAGA
4021 CATTTTTACT CCTTCGAGAG GCATTAGGCA AGGAGACCCT TTRTCTCCGT ATCTTTTTGT
4081 CATTTGTATG GAGCGGTTGT CTCATATTAT TGCAGATCAG GTGGATGCTC AGTATTGGAA
4141 ACCTATGCGT GCAGGCAGGT ATGGCCCTCA AATATCTCAT CTTCTTTTTG CTGATGATCT
4201 TCTTTTGTTT GCAGAGGCTT CTATCGAGCA AGCACATTGT ATTATGCATT GTCTTGATCT
4261 TTTTTGTCAA GCTTCTGGAC AAAAGATCAA TAATCAGAAA ACAGAGATCT ACKTCTCTAA
4321 GAATGTTGAT CAACAGGGCA GGGATGCTAT TTTACACCAC ACAGGTTTTA AACATGTCGA
4381 TAATATAGRC AGGTATTTGG GGGCAAACAT TAACCCTGGC AGAGCTACTA GGGGAAAGTT
4441 TAAGAACATC ATTGACAAAA TTCAAAACAG GTTAGGTGGA TGGAAGCAAC AATGTCTGAG
4501 TTTTGCTGGT AGACTCACTT TATGTAAATC AGTTTTGAGC TCTATACCGT ATTAYCATAT
4561 GCARTATGCT AAGCTCCCTA AAASCCTTTG YAAYGARATG GAAAAAATTC AAAGRAGCTT
4621 TTTATGGGGA GAYACTRAYSWAKCTCGCAG ACCTCATCTR GTKGGRTGGG AYRTTTGTTG
4681 TCTTCCAAAG AATGAGGGDG GMTTRGGCAT TAAGAGACCY CATCATATGA ATGAYGCTTT
4741 TCTTATGAAG ATGMTKTGGA ATCTSATCAC YAAACCARAY GACCTTTGGT GTAAGGTTCT
4801 TTATAGTAAR TATGGAAGGA AYAATGAYCT TAGGGTAACC ATAARMTCYC AAYCYTATGA
4861 YTCTCSTTTA TGGAAAGCTT TAWCAGGTAT TTGGRRMMAA TTYCARCARA ATATTGTGTG
4921 GCAGKTGGGM GATGGWAAMA ATATYAATTT YTGGCTGGAT AAATGGACYC CWARYGGAAC
4981 TTCTYTTYTC TCYRTYACTA ATCAAAMYAS TATYGACWCA ACTCTYTCTG TGAGGGATGT
5041 GSTWACCCCYKCAGGAGAKT GGGAYTWTRA TTTTCTWACW TCWAACTTAC CTTCKAMCTT
5101 TKSTTTWCAG GTWCTYGCWA TYCCWGCKCC TAWRGAYAYA GACGGGCWAG ACAMYATTGG
5161 YTGGRGAGGA ACSAACAMTA GRRACTTCAC AGTYAAAAGT GCYTATGATT CTCAKAMCAC
5221 TRGAWCTCAK CCHATYGWGG GAGAYTGGAA GGCCTTGTGG AGYTGGAAAG GCCCKCATAG
5281 AATTCAAACW TTTATGTGGA TGGCRGCTCA YGAGCGGCTR CTYACTAATT ATAGTAGGAG
5341 CAAATGGGGGRTTGGAATTT CACCCATATG YTCTGCTTGT GACAAAGACA ATGAAACAAC
5401 TATYCATGTT TTGMGAGATT GYCCCWYMGC AAYYCAAAYA TGGATAAGGT TAGTCCCTTC
5461 AAATCAAATA TCTAATTTTT TCTCTCTTCA TTGCAGKGAW TGGATCTTCA AGAAYATMAA
5521 YMAYCARMYR CMTGGTATTC AAAATAAGAA GTGGAAMACR ATTTTTATGG TRGCGTGTTG
5581 GCACATRTGG ATGTGGAGRA AYAAAACWAT TTTTGAAGAT GAMTTYCARC GTCCRAATGA
5641 CCCMAYWTWYRWGATTMTCA AGAYGGTTGA AGACATAGAM AARTRCAYCM AMCAWCCYYT
5701 GARTATTCRC CRWWRYRACA CYRTTTTCAT TGGMTGGAAA AGWCCTMRRR AWGGGTGGAT
5761 CAAGCTWAAC TGTGAYGGAG CMTACAARGA TTCTTTGGGK CTWGCTGGRT GYGGTGGMCT