Supplementary Table S1 Pathological Alu Insertions (N=30) That Are Informative with Respect

Supplementary Table S1 Pathological Alu Insertions (n=31) that Are Informative with Respect to the Starting Position of the Alu Insert*

Target gene Sub-family Starting position Annotation of the 5’ junction Reference

of the Alu inserta of the Alu insertb

Simple insertions

CFTR Ya5 1 5’-gatttttgtcatcttcttca-3’ Chen et al. submitted

5’-GGCCGGGCGC-3’

CLCN5 Ya5 1 5’-GCTCGAAAGAAACAGGATGG-3’ Claverie-Martin et al. Hum Genet 2003;113:480-5

5’-GGCCGGGCGC-3’

FGFR2 Ya5 1 5’-AAGGGAAGCAAAAGAAAAGG-3’ Oldridge et al. Am J Hum Genet 1999;64:446-61

5’-GGCCGGGCGC-3’ (Note that the Alu insert contains an additional G at the 5’ end)

HMBS Ya5 1 5’-ATCTTGTCCCCTGTGGTGGA-3’ Mustajoki et al. Hum Mutat 1999;13:431-438

5’-GGCCGGCGCG-3’

NF1 Ya5 1 5’-AAAAAAACATGGGACTCAAA-3’ Wallace et al. Nature 1991;353:864-6

5’-GGCCGGGCGC-3’

NT5C3 Ya5 1 5’-TGGCAGATGGAGTGGCCAAT-3’ Manco et al. Haematologica 2006;91:266-7

5’-GGCCGGGCGC-3’

TNFRSF6 Ya5 1 5’-TCTAAATGTGAACTTCTAAT-3’ Tighe et al. Genes Immun 2002;3:S66-70

5’-GGCCGGGCGC-3’

FGFR2 Yb8 1 5’-ACCCGCCAAGCACGTATATT-3’ Oldridge et al. Am J Hum Genet 1999;64:446-61

5’-GGCCGGGCGC-3’

F8 Yb8 1 5’-AAGGTTCTTCATGAAATTCT-3’ Sukarova et al. Acta Haematol 2001;106:126-9

5’-GGCCGGGCGC-3’ (Associated with the loss of 2 bp from the target sequence)

HESX1 Yb8 1 5’-GTCTTTAGAGTAAACTGCTA-3’ Sobrier et al. Hum Mutat 2005;25:503

5’-GGCCGGGCGC-3’

BCHE Yb9 1 5’-TATTTTTTCCAGGAGTGAAG-3’ Muratani et al. Proc Natl Acad Sci USA 1991;88:11315-9

5’-GGCCGGGCGC-3’

F8 Yb9 1 5’-AACCAACAGGAACAGAAATT-3’ Ganguly et al. Hum Genet 2003;113:348-52

5’-GGCCGGGCGC-3’

BRCA2 Y 1 5’-AATCACAGGCAAATGTTGAA-3’ Miki et al. Nat Genet 1996;13:245-7

5’-GGCCGGGCGC-3’

BTK Y 1 5’-ATGAGTAAGTATGTTTATGT-3’ Conley et al. Hum Mutat 2005;25:324-5

5’-GGCCGGGCGC-3’

CASR Ya5 2 5’-GCGTGAGCTGCGGTGCTGCA-3’ Janicic et al. Am J Hum Genet 1995;56:880-6

5’-GGCCGGGCGCG-3’ (Can be alternatively interpreted as a full-length insert)

POMT1 Ya5 2 5’-AGATGTACTGCCCATAATAT-3’ Bouchet et al. Mol Genet Metab in press

5’-GGCCGGGCGCG-3’ (Can be alternatively interpreted as a full-length insert)

ZFHX1B Ya5 2 5’-ATTAAAACAGAACCACTAGA-3’ Ishihara et al. J Med Genet 2004;41:387-93

5’-GGCCGGGCGCG-3’ (Can be alternatively interpreted as a full-length insert)

APC Yb8 2 5’-AGAATAATGCCTCCAGTTCA-3’ Halling et al. Hum Hered 1999;49:97-102

5’-GGCCGGGCGCG-3’

F9 Y 2 5’-AACTGGTCCCTTCCACTTCA-3’ Li et al. Hum Mutat 2001;17:511-9

5’-GGCCGGGCGCG-3’

SERPING1 Y 2 5’-CAAAAATTAGCCAGGCATGG-3’ Stoppa-Lyonnet et al. Proc Natl Acad Sci USA

5’-GGCCGGGCGCG-3’ 1990;87:1551-5

(Can be alternatively interpreted as a full-length insert)

BRCA2 Ya5 2 5’-ATCTGAACATAAAAACAACA-3’ Teugels et al. Hum Mutat 2005;26:284

5’-TGCCGGGCGC-3’ (That the first nucleotide diverged from the consensus sequence

made it impossible to investigate the ‘microhomology’ issue)

BRCA1 Sq 2 5’-AATCTGCTTTCAAAACGAAA-3’ Teugels et al. Hum Mutat 2005;26:284

5’-TGCCAGGCGC-3’ (That the first nucleotide diverged from the consensus sequence

made it impossible to investigate the ‘microhomology’ issue)

CD40LG Yb8 16 5’-AAAAATTTTCATGCTGATGG-3’ Apoil et al. Immunogenetics 2006 Advance Online Pub.

5’-GGCGCGGTGGCTCACGCCTG

F9 Ya5 39 5’-GCAGATGCGAGCAGTTTTGT-3’ Vidaud et al. Eur J Hum Genet 1993;1:30-6

5’-TCCCAGCACTTTGGGAGGCC-3’

CRB1 Y 39 5’-GTAAAGATGACATAACCAGT-3’ den Hollander et al. Nat Genet 1999;23:217-21

5’-TCCCAGCACTTTGGGAGGCC-3’

GK Y 41 5’-AAAAAATAAGAACTTACTGA-3’ Zhang et al. Hum Mutat 2000;15:316-23

5’-CCAGCACTTTGGGAGGCCGA-3’

F9 Ya5 47 5’-GGCAGATGCGAGCAGTTTTG-3’ Wulff et al. Hum Mutat 2000;15:299

5’-CTTTGGGAGGCCGAGGCGGG-3’

CFTR Y 236 5’-cacctataatATACAAGATG-3’ Chen et al. submitted

5’-GAGCCGAGATCGCGCCACTG-3’

Large genomic deletions created upon Alu insertions (see Fig. 7 for extended sequence features)

ABCD1 Yb9 189 5’-ggctgaggcacaagaatccc-3’ Kutsche et al. Hum Mutat 2002;19:526-35

5’-ggctgaggcaggagaatggc-3’

APC Yb9 196 5’-gcaggagaatcacttgggag-3’ Su et al. Hum Genet 2000;106:101-7

5’-gcaggagaatggcgtgaacc-3’

SERPINC1 ? -6 5’-agcgagactctgtcaaaaat-3’ Beauchamp et al. Thromb Haemost 2000;83-715-21

5’-agcgagactccgtctcaaaa-3’

*The entries are listed in accordance with their order in Fig. 1

aBy reference to the insert’s respective consensus sequence

bTop sequence indicates ±10 nucleotides flanking the top strand cleavage site (indicated by a vertical arrow). In the lower sequence, shaded nucleotides represent the 5’-most end of the Alu insert. In the case of 5’ truncated Alu inserts, sequence that lies immediately 5’ to the truncation position in the respective consensus sequence was shown (unshaded). Microhomology between the top strand’s 5’ overhang and the sequence lying 5’ to the truncation position in the respective Alu consensus sequence is highlighted in red

Supplementary Table S2 Full-Length Alu Insertion Polymorphisms in the dbRIP

ID

/ ±10 bp flanking the top strand cleavage site /

Comment (whenever there is a modification of the original annotation)

RIP_Alu_chr1_004_01 / TGGCAATCATtaaaaagtca
RIP_Alu_chr1_014_01 / GTCAAGACCCatcagtgtgc
RIP_Alu_chr1_027_01 / TAAATAAATCtaggatatta
RIP_Alu_chr1_027_02 / ttGAAATCAAacctttgggt
RIP_Alu_chr1_036_01 / AATCATGAACgataacttac
RIP_Alu_chr1_043_01 / AATGAAACAAatgaaataaa
RIP_Alu_chr1_045_01 / TTCGAGACCGtgaaaccctg / The 5’-most G in the Alu sequence was re-assigned to the upstream TSD
RIP_Alu_chr1_046_01 / ATCCAACATCactaatcatc
RIP_Alu_chr1_047_01 / ATGTCTTGTTtaatattcat
RIP_Alu_chr1_056_01 / GAAATATAGGacaaggtaca
RIP_Alu_chr1_058_02 / AAAATAAATCaattaggatt
RIP_Alu_chr1_058_01 / TTCAAATGATttgaaatgtc
RIP_Alu_chr1_062_02 / ACAGACAGGCaaacaagaag
RIP_Alu_chr1_062_01 / tGTTATTACTtgacatgtat
RIP_Alu_chr1_063_01 / GGGAGACATGaacaaacctc
RIP_Alu_chr1_065_01 / acATTCACCAatatgggctg
RIP_Alu_chr1_069_01 / AGGGGAGTTCccctgaacac
RIP_Alu_chr1_070_01 / AAATAGTATTaaaagggact
RIP_Alu_chr1_070_02 / ACATAACCATaataccacta
RIP_Alu_chr1_075_01 / TTTGAATTTGaacagtctta
RIP_Alu_chr1_078_01 / AGTGTATCACtttcttattt
RIP_Alu_chr1_079_02 / GGATATTCTGtatactgtac
RIP_Alu_chr1_079_01 / ATCCTTTTAGttcacactgt
RIP_Alu_chr1_082_01 / AAAAATATAAatacaagcta
RIP_Alu_chr1_085_01 / ACACTGGCCTtattatcaag
RIP_Alu_chr1_086_02 / GTGCCATAAGatatattcag
RIP_Alu_chr1_093_02 / AAAGGAATCTaattttgaag
RIP_Alu_chr1_093_01 / tAAAAGTGCCatgcatttct
RIP_Alu_chr1_095_01 / AAATATAATTataaaattat
RIP_Alu_chr1_098_01 / ATATTTTTGAataaatgaac
RIP_Alu_chr1_102_01 / TTCTTGTTTCagctctccat
RIP_Alu_chr1_102_02 / CATTATTACTgttctattag
RIP_Alu_chr1_105_01 / AAAATGGGCAaagtacatta
RIP_Alu_chr1_112_01 / AACGTGTCTGaagacagcat
RIP_Alu_chr1_114_01 / AAAACTAAACatagaattac
RIP_Alu_chr1_114_02 / AAGAATTTGGgagggacttg
RIP_Alu_chr1_116_01 / TTCAGCGGGGagctctggac
RIP_Alu_chr1_118_01 / AGCTGGTTGCtaatattaaa
RIP_Alu_chr1_141_01 / GAGCAATATCcttgtacccc
RIP_Alu_chr1_143_01 / ACATACAAAGcctgagctcc
RIP_Alu_chr1_154_01 / ATCTTGAGGCaaatgaaaat
RIP_Alu_chr1_155_02 / GCTAAGACTAttattttctt
RIP_Alu_chr1_155_01 / GTAGGGCAAGgacagcaaac
RIP_Alu_chr1_157_01 / TACAGTGAAAtaccacttca
RIP_Alu_chr1_158_01 / AAAAGGACACaaccaaggag
RIP_Alu_chr1_161_01 / ATTCAGTTTTaaaagggaag / The upstream TSD was re-annotated as AAGGCATTCAGTTTT whilst the downstream one was re-annotated as AAGGCATTCGGTTTT. The single nucleotide difference might have occurred post-retrotranspositionally.
RIP_Alu_chr1_165_01 / GTTCACTTGCttccttcctg
RIP_Alu_chr1_167_01 / AACCTTTTTGtgccactgtg
RIP_Alu_chr1_175_01 / AGCTAAAATCataaaacttc
RIP_Alu_chr1_177_02 / ACATAGAGTAactgagtgga
RIP_Alu_chr1_179_01 / GTGATTTACTgtttcaagtg
RIP_Alu_chr1_181_01 / CACAACTCACaaaatccttc
RIP_Alu_chr1_182_02 / CCCAAGATTCtagcaggcaa
RIP_Alu_chr1_182_01 / GACTTGTTTTatacttttat
RIP_Alu_chr1_187_01 / ACGTGGCATGtaacaccagc
RIP_Alu_chr1_188_01 / AATAAAAGTAaaatttatgc
RIP_Alu_chr1_205_01 / GTAAAATCTGtaagaccaca
RIP_Alu_chr1_206_01 / TCAGGATTTGttacttcaga
RIP_Alu_chr1_207_01 / AGAAGCTATAatatgaataa
RIP_Alu_chr1_213_01 / AGAGGCCAGAgagcgctctt
RIP_Alu_chr1_216_01 / TGAGTCCATAaaattgtgaa
RIP_Alu_chr1_219_01 / TTACCAACACaaaaattata
RIP_Alu_chr1_220_01 / AAGCCAAGTCatctcaaccc
RIP_Alu_chr1_221_01 / AGAATTTTAAgaggagttta
RIP_Alu_chr1_223_01 / GCTCTTTGTGgatgttctgt
RIP_Alu_chr1_224_01 / AAAAGCTTCCcttccataac
RIP_Alu_chr1_225_01 / aAACAGCCCTaaaatctgct
RIP_Alu_chr1_227_02 / AAAAAAAAAAaatttgcaac
RIP_Alu_chr1_227_01 / AAAAAAAGACattagagtga
RIP_Alu_chr1_228_01 / ATTACCCTTCatcgagtgtt
RIP_Alu_chr1_230_02 / CAGGGCTGGCtgggcgcggt
RIP_Alu_chr1_230_03 / ACAATGTTTCaatgaaaatc
RIP_Alu_chr1_230_01 / cTGATGAATGactggatcat
RIP_Alu_chr1_232_01 / ATGTTGGCAAactttctggc
RIP_Alu_chr1_232_02 / CCCCAGGCAGaccttataga
RIP_Alu_chr1_235_01 / AAGGAATTGGctgtcccatc
RIP_Alu_chr1_237_02 / GTGGTGTTTAaattacatgc
RIP_Alu_chr10_003_01 / CTGTGAACTTtactatttct
RIP_Alu_chr10_004_01 / AAGAAAAAGAataatttcat
RIP_Alu_chr10_004_02 / AAATTAACACtagccacatg
RIP_Alu_chr10_009_01 / AAATGCAGTCagcctctaga
RIP_Alu_chr10_010_01 / gtAAGAAAGAagatggttta
RIP_Alu_chr10_020_02 / ATTTACCGGAacaacgatct
RIP_Alu_chr10_020_01 / GATTAGTAAGttctggggat
RIP_Alu_chr10_025_02 / atAGAAAGCTaattatgttc
RIP_Alu_chr10_029_01 / GATGATTTAGattcaatgca
RIP_Alu_chr10_032_01 / TATTCTATTCaacatatttt
RIP_Alu_chr10_034_01 / AAACATCATCatggggaaga
RIP_Alu_chr10_049_02 / GCACACATCTgtctgtgtgg
RIP_Alu_chr10_049_01 / aagaaATATCtcattcatca
RIP_Alu_chr10_054_02 / AAGTAGTTGAgtgtgctctt
RIP_Alu_chr10_054_03 / GAAAATCGGGgtgcctccag
RIP_Alu_chr10_056_01 / AGGTAGAATTctgagcaagc
RIP_Alu_chr10_057_02 / AATTTTTTTTtaaatgaagc
RIP_Alu_chr10_057_01 / Agaataagtcaaggatcagt / The 5’-most GAATAAGTC in the Alu sequence was re-assigned to the upstream TSD
RIP_Alu_chr10_058_01 / tAAGAATGATacaatggact
RIP_Alu_chr10_061_01 / ACTTGGATGAcaggttgatc
RIP_Alu_chr10_065_01 / GTATAAAACGaaagtaggaa
RIP_Alu_chr10_066_01 / GTGGCACATAtacaccatgg
RIP_Alu_chr10_067_01 / TTATGATGTCtcagaagttg
RIP_Alu_chr10_068_01 / aaAAGTTAAGaaacaacaga
RIP_Alu_chr10_070_01 / ACCTGGTGTAttatacatgc
RIP_Alu_chr10_072_02 / AGCTGAGAGGgggtttcctg
RIP_Alu_chr10_074_01 / AGCAAATAAAaaccctaaga
RIP_Alu_chr10_085_01 / AATCAGCATCcaccttacct
RIP_Alu_chr10_085_03 / ACCCAATTAActgaattttc
RIP_Alu_chr10_091_01 / ACTTACTCATataaccaaac
RIP_Alu_chr10_092_01 / CAAGAATCTGtaaaagcaat
RIP_Alu_chr10_105_01 / CAAAATTAGCtgagcatggt
RIP_Alu_chr10_107_02 / GTGATTAATGgacctgagtt
RIP_Alu_chr10_111_01 / ACCTACATTAatgctgatct
RIP_Alu_chr10_115_01 / ACCTATGCTTgtgtttcata
RIP_Alu_chr10_115_02 / AAGAATGATTagttagataa
RIP_Alu_chr10_116_01 / TGAGAGAGATtcattatcca
RIP_Alu_chr10_118_01 / TGTCATGAGAatgtcaaaaa
RIP_Alu_chr10_118_02 / atcaccgtTAacaaagaatt
RIP_Alu_chr10_119_01 / cAAAAGATTCaccaatgagt
RIP_Alu_chr10_123_03 / acAAATCTTCacaggagaca
RIP_Alu_chr10_128_01 / AATGATTACTaacccccacc
RIP_Alu_chr10_129_01 / GGCCAGATGCtccccaagcc
RIP_Alu_chr10_129_02 / AAAAAAACTAatgactgcag
RIP_Alu_chr10_130_01 / TCAAGAAACAaagatgttgg
RIP_Alu_chr10_131_01 / ACTAGAGAAGgcaagagcaa
RIP_Alu_chr10_132_02 / TCTTTAACAGaagattctac
RIP_Alu_chr10_132_01 / GCGCGTGAGGgaggctccta
RIP_Alu_chr10_133_01 / TGTATTTATGggaaaaggtg
RIP_Alu_chr11_000_01 / TGGAACTGTGtagtcccagt
RIP_Alu_chr11_007_01 / GAATGGATGAagggaggctt
RIP_Alu_chr11_009_01 / GAAATACCTGacgtcaggtg
RIP_Alu_chr11_014_01 / ATATGATTTTgctattctgt
RIP_Alu_chr11_015_01 / TGGAGGAATAatttcctgaa
RIP_Alu_chr11_016_01 / ATACTTTGCAaataaggagc
RIP_Alu_chr11_016_02 / CCACAACTACacacacactc
RIP_Alu_chr11_024_01 / CACATGAATAgatacgatgc
RIP_Alu_chr11_025_01 / CCATGGATGTtaccaaatca
RIP_Alu_chr11_027_01 / AGAACACAATaaaaagaata
RIP_Alu_chr11_029_01 / CTCTTTTTTGttgcatatac
RIP_Alu_chr11_031_01 / AACAAAATTAatgaaaagaa
RIP_Alu_chr11_031_02 / AAAAGAAAGAaagaaagaac
RIP_Alu_chr11_033_01 / TCACCTCCAGgctgattggt
RIP_Alu_chr11_037_01 / ATGCTTATTAtattagaaac
RIP_Alu_chr11_038_01 / GTGGTTTATTtaacatggga
RIP_Alu_chr11_039_01 / ATTACAAATTgtacaaatcg
RIP_Alu_chr11_040_01 / ATGTTCTTTAtagctttctt
RIP_Alu_chr11_042_01 / ttGAGAAACCatagaagttg
RIP_Alu_chr11_043_01 / TAGCCAGGTGggtggcctgc
RIP_Alu_chr11_043_02 / TAGATCAGTGtaggcatgta
RIP_Alu_chr11_048_01 / TAGACTGAAGgcattctcgg
RIP_Alu_chr11_049_01 / TAATGGTGAAaacccctgaa
RIP_Alu_chr11_057_02 / CTACACTTTTatcccccccc
RIP_Alu_chr11_058_02 / CCAAGTGTTAtttcaaagga
RIP_Alu_chr11_060_01 / GAAGGCAGGGgatggctggg
RIP_Alu_chr11_060_02 / AGACTGAATGaaccctcctc
RIP_Alu_chr11_061_02 / TGGCTTCCCCaagtggggct
RIP_Alu_chr11_065_01 / GTGTTGTTTCacaaacacaa
RIP_Alu_chr11_071_01 / CAATTCAGTAaagtatactt
RIP_Alu_chr11_073_01 / GTGGAAACACcccagatgtc
RIP_Alu_chr11_081_01 / ATATGAACCTgtagtaaaca
RIP_Alu_chr11_082_01 / GAACTGGCTCagtatcagct
RIP_Alu_chr11_088_01 / TGGAAACAGAacaaatgaag / The 5’-most A in the Alu sequence was re-assigned to the upstream TSD
RIP_Alu_chr11_089_01 / gAGTTTACTTactgtgagta / The 5’-most T in the Alu sequence was re-assigned to the upstream TSD
RIP_Alu_chr11_091_01 / tAAGATTATCtccacccaca
RIP_Alu_chr11_092_02 / TCCTAGACAGttgctgctct
RIP_Alu_chr11_092_01 / ACAGATTTTCttagttaaaa
RIP_Alu_chr11_092_03 / ATGGATTTACtttttttttc
RIP_Alu_chr11_096_02 / TGAATAATTCtgggcaccca
RIP_Alu_chr11_096_01 / GTTTATTATTttacttaatt
RIP_Alu_chr11_101_01 / GAATAGCCGAcacttcgtgg
RIP_Alu_chr11_103_01 / AATAAATAACtgaacgagaa
RIP_Alu_chr11_105_01 / TGTAGCAATAatcctgcagt
RIP_Alu_chr11_105_02 / TAGCACGTGAacataaattt
RIP_Alu_chr11_111_01 / TGGAGGCATCacactacctg
RIP_Alu_chr11_115_01 / ATGTGTCCCAggcgattctg
RIP_Alu_chr11_121_01 / GAAGGGCCGGggccgggcgc
RIP_Alu_chr12_001_01 / AAGAAATCGAgagatgattt
RIP_Alu_chr12_005_01 / AGAACACGCCccatagcaaa
RIP_Alu_chr12_010_03 / ATTGAGCCTCatcacaatag
RIP_Alu_chr12_010_01 / gtGGCACATAtacaccatgg
RIP_Alu_chr12_012_01 / AATGAGACTGaatctatttt
RIP_Alu_chr12_015_01 / AAGAAGTGCCaagattttat
RIP_Alu_chr12_016_01 / gactgTTTGAgttttttttc
RIP_Alu_chr12_022_02 / ATGGAAGGGAacagagagac
RIP_Alu_chr12_022_01 / GTATATGCACtgtcaactaa
RIP_Alu_chr12_026_01 / AAAGTCGTTCttgttttccc
RIP_Alu_chr12_029_01 / AGCTGCTTTTtccttccagc / The 5’-most TTTT in the Alu sequence was re-assigned to the upstream TSD
RIP_Alu_chr12_031_01 / CTCCCACGACacataaacat
RIP_Alu_chr12_032_01 / TGTTTATTCTatgtactttc
RIP_Alu_chr12_039_01 / GAGATATTAAaatcaataag
RIP_Alu_chr12_043_01 / GAAAGATCTGaaagtgcact
RIP_Alu_chr12_045_01 / GTATCAGTCAatgtagctct
RIP_Alu_chr12_053_01 / CATAATATCAgtagggaatt
RIP_Alu_chr12_056_01 / TTCTAATGAGaataaaagct
RIP_Alu_chr12_059_01 / AAATTTTCTCaatgaaaaat
RIP_Alu_chr12_063_01 / TAACAGAATAaacttatgta
RIP_Alu_chr12_074_01 / AAAATAATCCtctgtgttag
RIP_Alu_chr12_076_01 / TATTAAATATataagtcctt
RIP_Alu_chr12_078_01 / atATTAGCGGtttttgttat
RIP_Alu_chr12_082_02 / ACTTGTACTCagcagggatt
RIP_Alu_chr12_082_01 / AAACAAATTTattttctcac
RIP_Alu_chr12_084_01 / TATGCTCTCTtactgttgac
RIP_Alu_chr12_086_02 / tAAGAAACAGtattgaacaa
RIP_Alu_chr12_086_01 / AAAGAAAATGtatccttttg
RIP_Alu_chr12_090_01 / GAGTTGGATCaatttcttgt
RIP_Alu_chr12_092_01 / AGGAGCTGGGtcaggctctg
RIP_Alu_chr12_093_01 / ACTGCTGTTTgagcactaag
RIP_Alu_chr12_093_02 / AATTGTTGCCaaatttggga
RIP_Alu_chr12_095_01 / TGCCATTAACctttatttaa
RIP_Alu_chr12_096_01 / CACCAAGCTCcttgtcccca
RIP_Alu_chr12_102_01 / GAAATGGGGGccacacatgg
RIP_Alu_chr12_105_01 / acgcTAACACaaatgatagc
RIP_Alu_chr12_121_01 / CTCTTCGTTGaccccagagg
RIP_Alu_chr12_125_02 / AGAGACATCCatattggcta
RIP_Alu_chr12_126_01 / TCATTGCTTCaggtcagtgg
RIP_Alu_chr12_128_01 / tAAAAATCCCttcagtttct
RIP_Alu_chr12_128_02 / TATCTATCTGcagacataat
RIP_Alu_chr12_129_01 / aCTAAAATAAaataactatc
RIP_Alu_chr13_020_01 / TCCACACGTGtaagtaataa
RIP_Alu_chr13_021_03 / TCAATAGGGGaagtttctct
RIP_Alu_chr13_021_02 / GTAAACCCAGaaacatagaa
RIP_Alu_chr13_021_01 / AAAAAAAAGAaatagctcac
RIP_Alu_chr13_022_03 / AATTACTTCAtccccatgtg
RIP_Alu_chr13_022_01 / CCTGCAAGCTgaagacagac
RIP_Alu_chr13_022_02 / TTGGAGTTCCataaaaagtc
RIP_Alu_chr13_023_01 / ATAAAGAACAtatttaatca
RIP_Alu_chr13_024_01 / GGGAGAGGGGctgtgtgagt
RIP_Alu_chr13_028_02 / GACATCAGCTttggctgctg
RIP_Alu_chr13_030_01 / TGAGGGTTGTaaggtaacta / The 5’-most TGT in the Alu sequence was re-assigned to the upstream TSD
RIP_Alu_chr13_035_01 / TTGGCTATCTaaatggaaat
RIP_Alu_chr13_038_02 / AGAGAGTTGAattgtaggta
RIP_Alu_chr13_041_01 / ACTCACTCTCccttgacaga
RIP_Alu_chr13_041_02 / AACCCATTGCctgttaacat
RIP_Alu_chr13_048_01 / AAATAAAAAAatcagtattt
RIP_Alu_chr13_053_01 / TATGAAAATAaaagggactc
RIP_Alu_chr13_054_01 / TCACCTTTTTatacatatgt
RIP_Alu_chr13_058_01 / TGTAACACTCactgcaaggt
RIP_Alu_chr13_059_01 / tAAGATCATCaacactcctc
RIP_Alu_chr13_060_01 / AATTATTTTTattatagagt
RIP_Alu_chr13_062_02 / AATCTTCCAAattttcgata
RIP_Alu_chr13_062_01 / AAGAACTAAAatgattgggg
RIP_Alu_chr13_063_02 / TTTAAAATCAagcatacagc
RIP_Alu_chr13_063_01 / GAAAATAACAtttatttgga
RIP_Alu_chr13_071_01 / AAAAGGGTTTaaaaaaaaaa
RIP_Alu_chr13_072_01 / AACAAGATAGaaaaaagcca
RIP_Alu_chr13_075_01 / AAAAAAACTTtttactttga
RIP_Alu_chr13_077_01 / AGATGCTGGAaaagcaaatg
RIP_Alu_chr13_077_02 / GGGAATTGTTaaacaagttt
RIP_Alu_chr13_078_02 / GTGATGTCATatacttttca
RIP_Alu_chr13_078_01 / CTCAATCAGAacaaaaaaca
RIP_Alu_chr13_079_01 / AGTACAGGTGcctacagatt
RIP_Alu_chr13_079_02 / AGGCAATGTGactcagaggc
RIP_Alu_chr13_080_02 / GTATATTCTGttgatttggg
RIP_Alu_chr13_080_01 / GGTGAGCTGAatctattccc
RIP_Alu_chr13_083_01 / GATTAGTGACattaaaatga
RIP_Alu_chr13_085_01 / tcAAAAAAGCaaagtgccaa
RIP_Alu_chr13_089_02 / GGAGACAGATctgagattaa
RIP_Alu_chr13_089_04 / TGAAACTGCAcctctgtcct
RIP_Alu_chr13_091_01 / TGATGAGTTCatgtcctttg
RIP_Alu_chr13_094_01 / AAAAAACTGCaaggattctt
RIP_Alu_chr13_095_01 / CACTTTTGTTttagtttagt
RIP_Alu_chr13_097_01 / TTTTGAATCCactgtgaggt
RIP_Alu_chr13_098_02 / TGGATGGATAaagaaaacgt
RIP_Alu_chr13_100_01 / AATGACATGTtaaaagctgc / The 5’-most ATGT in the Alu sequence was re-assigned to the upstream TSD
RIP_Alu_chr13_102_03 / tAGAAAACCTaatttcagta
RIP_Alu_chr13_102_01 / tAAGAAACTGaattcatgac
RIP_Alu_chr13_106_01 / AAAAATTCTAaggtctgctt
RIP_Alu_chr13_107_01 / TTCTAATCTGatcgttaggc
RIP_Alu_chr13_109_02 / TTAACTTATTtgggttcttt
RIP_Alu_chr13_112_03 / GTCACCCAGAaggggctgct
RIP_Alu_chr13_112_01 / TACAAGAATTagcctgccat
RIP_Alu_chr14_020_01 / AAGGGGAGCCactgaaagtt
RIP_Alu_chr14_025_03 / AAAGAAAGAAaagaaaatag
RIP_Alu_chr14_030_01 / TACATTTTGTaaggctttag
RIP_Alu_chr14_033_01 / AATTACAGTCttgcaaggct
RIP_Alu_chr14_034_02 / AAATTTGAAGaagtataaca
RIP_Alu_chr14_034_01 / ACTTTCTATAactgagacac
RIP_Alu_chr14_034_03 / AGAAATTTCAaagctgttat
RIP_Alu_chr14_037_01 / AAAATTCTTTtaatcatata
RIP_Alu_chr14_038_01 / GGGAAGGTTTtattatttcg
RIP_Alu_chr14_039_02 / GCTAAGAATCtcttttctag
RIP_Alu_chr14_041_01 / AGACCTGATCttacgcaaat
RIP_Alu_chr14_044_0 / ATTGAAATCTttttagaagc
RIP_Alu_chr14_045_01 / agCCACTTGTaactgctgtt
RIP_Alu_chr14_047_01 / GTACACACCTtttcaattct
RIP_Alu_chr14_051_01 / GGCAAATGCCaacctgcaat
RIP_Alu_chr14_051_02 / AGCCAGATAGtgagttgtat
RIP_Alu_chr14_053_01 / AACAGTAATCaggacagtgt
RIP_Alu_chr14_056_01 / GAAAAGAGAAaagcaccgag
RIP_Alu_chr14_056_02 / AGGCTATGTGcttggaccat
RIP_Alu_chr14_058_01 / ATACTTTTAGttttagatac
RIP_Alu_chr14_059_01 / AAATCAATATtacttctact
RIP_Alu_chr14_059_02 / GTTCACTCATttattgatct
RIP_Alu_chr14_062_01 / GTCAACCTGAaccatgaata
RIP_Alu_chr14_065_01 / ATGTCCCCAAacgtaaatct
RIP_Alu_chr14_070_01 / tAAAACTATAtaaagtagta
RIP_Alu_chr14_073_01 / AAGAATATCCtggcaatagt
RIP_Alu_chr14_077_01 / GAAGAAACTAtagtttctgc
RIP_Alu_chr14_078_01 / atAAGAATTGacccatttac
RIP_Alu_chr14_080_02 / ACACTGCTTGactgccgtca
RIP_Alu_chr14_085_01 / TACTAGTTCCcctggaggta
RIP_Alu_chr14_086_01 / ACTAATGGTCagccatataa
RIP_Alu_chr14_086_02 / atAAAATCGTaaagctgatt
RIP_Alu_chr14_090_01 / TGACCAAAATtcctgcccaa
RIP_Alu_chr14_094_01 / GCTGTCCTTGttttgaattt
RIP_Alu_chr14_100_01 / AAGGGACAGCaaacctcaat
RIP_Alu_chr14_106_01 / ATATATATATataatggtgt
RIP_Alu_chr15_020_01 / TTGTTACGTCaaaattatct
RIP_Alu_chr15_024_01 / ATAAAACTTGaaagtcagtt
RIP_Alu_chr15_025_01 / GTCATCACCAatccctaatc
RIP_Alu_chr15_032_01 / AATTCCTCCTctccagttgg
RIP_Alu_chr15_037_02 / TTAATTTATCaagaaagact
RIP_Alu_chr15_041_01 / AATGGATCTTctgggggaaa
RIP_Alu_chr15_056_01 / ACATATTCTTtagttactta
RIP_Alu_chr15_057_01 / GAGCCTTCCTtggcttcgtc
RIP_Alu_chr15_062_01 / GATAAAAATTagctggacgt
RIP_Alu_chr15_064_01 / GAATGTTGTGaatacatgct
RIP_Alu_chr15_065_01 / ATCATATCGGattcatactg
RIP_Alu_chr15_068_01 / AAAGAGCGTCatgaagtgta
RIP_Alu_chr15_076_01 / TAGGGCCTTTaaggagtgat
RIP_Alu_chr15_079_01 / AATAAGTATTtcttagttct
RIP_Alu_chr15_079_02 / aaaTAAGCTTaactttgaag
RIP_Alu_chr15_088_01 / TCAGGAAACAaacaggtgct / The 5’-most A in the Alu sequence was re-assigned to the upstream TSD
RIP_Alu_chr15_089_01 / GTCTTTCATAatgtaagaaa
RIP_Alu_chr15_098_02 / AGGGTTTTCTacatgtaata
RIP_Alu_chr15_099_01 / TACAGATGTCtgggccccac
RIP_Alu_chr15_100_01 / ATGCTTTACCtctatataga
RIP_Alu_chr16_002_01 / TGTCAATGAGacaaaggagg
RIP_Alu_chr16_016_01 / GTGAATTCAGcagtcaattc
RIP_Alu_chr16_019_01 / CACTGAAGTAttcatagtga
RIP_Alu_chr16_020_01 / CAGGGACCGGtagttccctc
RIP_Alu_chr16_022_01 / CCATTTTTTGatacaaatta
RIP_Alu_chr16_026_02 / TGTGAAGAGGaagatgcttc
RIP_Alu_chr16_031_02 / aGGCAGATTCaccatctcaa
RIP_Alu_chr16_031_01 / CAAAGCTACAaacgtgttgg
RIP_Alu_chr16_032_02 / ATGTTGTTTTtagtgtacat
RIP_Alu_chr16_032_01 / TCAATTGGTAaattcatgta
RIP_Alu_chr16_033_01 / AGACAGGCCCattacctgga
RIP_Alu_chr16_034_01 / TTGCCATGCTtagcactact
RIP_Alu_chr16_045_01 / ATAGACTGCTagcaagacta
RIP_Alu_chr16_056_01 / CATATATGCAtagaaaatta
RIP_Alu_chr16_060_01 / AACTACTTAAatcaagagca
RIP_Alu_chr16_064_01 / TTGTTTTCTGaaaatagggc
RIP_Alu_chr16_065_01 / AAAAAAATTCagggactata
RIP_Alu_chr16_069_02 / CATTCGGGGAtgcttttagt
RIP_Alu_chr16_069_01 / CCGGTATATAtggagttgcc
RIP_Alu_chr16_078_01 / GTCAAATTCAcagaagcaga
RIP_Alu_chr16_082_01 / AAGTAAAGGAataaaagaat
RIP_Alu_chr17_005_01 / AACCACATGGcatgcttttt
RIP_Alu_chr17_006_01 / aagatttgtAttagctgagc / TSD was annotated as a single A
RIP_Alu_chr17_006_02 / taaagaTTCAaaatggcata
RIP_Alu_chr17_010_01 / TCCTGATTCAatttcctttg
RIP_Alu_chr17_013_01 / CTTTACCCTTtcattatgcg
RIP_Alu_chr17_014_04 / TTCCATTTGCttgtgctgac
RIP_Alu_chr17_014_03 / TCCACAAATAttcagaaatt
RIP_Alu_chr17_015_01 / GTCCAGTGTCattctaccca
RIP_Alu_chr17_027_01 / TGCGAGGGAAaagtagtttg
RIP_Alu_chr17_027_03 / AGAAGCTTAAaagagaaaga
RIP_Alu_chr17_033_01 / AACAGTTCTCattttataga
RIP_Alu_chr17_041_01 / TTTAAATTTTatttttgctt / The upstream TSD was re-annotated as AAAACCTTTAAATTTT whilst the downstream one was re-annotated as AAAACCTTTACATTTT. The single nucleotide difference might have occurred post-retrotranspositionally.
RIP_Alu_chr17_058_02 / AGCAAACCCAactccacccg
RIP_Alu_chr17_062_02 / GAAAACCTTCatatatgttt
RIP_Alu_chr17_063_05 / gCTGTAAATTtctgaatgag
RIP_Alu_chr17_063_02 / TTTTGGAATTaaatagtggt
RIP_Alu_chr17_064_02 / TAAAGGTTTAcagggctcca
RIP_Alu_chr17_064_01 / GTCTATTTGGtcattttagc
RIP_Alu_chr17_064_03 / AACCACTAAAtaatttaccc
RIP_Alu_chr17_067_01 / TCAGAATGTGaacccagata
RIP_Alu_chr17_070_01 / AAACACCCTCtgtggtgatc
RIP_Alu_chr17_070_02 / CAAAAATTAGctgggtgtgg
RIP_Alu_chr17_071_01 / TAGAACTCCCctttccatat
RIP_Alu_chr17_072_01 / AAAAAACGCCttgagactgg
RIP_Alu_chr17_073_01 / AAGCAAAACCactgggaacg
RIP_Alu_chr17_078_01 / GAGTCCTGTAttcccagcta
RIP_Alu_chr18_001_01 / AATAATTACAtaaacaagta
RIP_Alu_chr18_009_01 / AGAAAGAACGaagtaaaaag
RIP_Alu_chr18_011_01 / AAAGAAATAAtacggatacg
RIP_Alu_chr18_012_01 / ATATTATATAaatctatttc
RIP_Alu_chr18_014_01 / AAAAAGAGCAagtagcctaa
RIP_Alu_chr18_021_01 / GTTGGAACCAactatagatg
RIP_Alu_chr18_024_02 / ACTTCATCTTtttttttttt
RIP_Alu_chr18_024_01 / ATCACATTTTtaatcttcaa
RIP_Alu_chr18_024_03 / AAAAGGCATTtaaaactgaa
RIP_Alu_chr18_025_01 / AAAAGTGAGAaaactatgcc
RIP_Alu_chr18_030_01 / GTAAAAAAAAatatatagta
RIP_Alu_chr18_030_02 / ATACGTTCTGaaaattagaa
RIP_Alu_chr18_034_01 / GCAAATTTGAaactcaagtc
RIP_Alu_chr18_035_01 / AATCAGATTCatagactgtt
RIP_Alu_chr18_037_01 / AATAAAATTAaaattaaata
RIP_Alu_chr18_043_01 / AGTAGCTGCAatctagcatg
RIP_Alu_chr18_045_01 / ACAGACAATGattctataag
RIP_Alu_chr18_049_01 / AATCAGAGGGcagtgcttgt
RIP_Alu_chr18_052_01 / ATGAACATTCactggaacat
RIP_Alu_chr18_053_01 / ATAATGTTTGtgcatttaaa
RIP_Alu_chr18_053_02 / ATGGAATTGCtttaactgat
RIP_Alu_chr18_055_01 / CTGCTAAGTAtgatcaagtt
RIP_Alu_chr18_055_02 / GTCAAGACCCatcaatgtgc
RIP_Alu_chr18_060_01 / AATCAATTTTaagactatct
RIP_Alu_chr18_063_01 / ACAGGATTCCtatacatata
RIP_Alu_chr18_064_01 / gtATAATTTCtattttttaa
RIP_Alu_chr18_068_01 / GTCAATTAGTacagttagtc
RIP_Alu_chr18_068_02 / TTTCCTTTTCactattctat
RIP_Alu_chr18_070_01 / ACATCATGGAatgagagtaa
RIP_Alu_chr18_071_01 / ATAACAGTTAtgggaaaggt
RIP_Alu_chr18_072_01 / TTAGCTTATGatttttgagg
RIP_Alu_chr19_000_01 / TAGAGCTGTGctgtggccgg
RIP_Alu_chr19_013_01 / TGTGGGTGCTaacagatgca
RIP_Alu_chr19_022_01 / AAATGTGGCCaaaagtgtca
RIP_Alu_chr19_023_01 / TGGCTTTCACtgggtaccag
RIP_Alu_chr19_041_01 / ACTTTATCGCtggaagtaat
RIP_Alu_chr19_056_01 / AGATGATCATagacaccacc
RIP_Alu_chr19_056_03 / ACCACAACTTtagcagcttt
RIP_Alu_chr19_056_02 / AGGGTCTTTGcaggctggcc
RIP_Alu_chr19_058_02 / GTTAAATAAGttgcaaggat
RIP_Alu_chr19_058_01 / AGTGAGGCAAtacagaaata
RIP_Alu_chr2_000_01 / ACATCTTTTAtaaaatgcat
RIP_Alu_chr2_005_02 / TGAAAATCTTtggctctgta
RIP_Alu_chr2_011_01 / CATCTGCTTAaggaactgag
RIP_Alu_chr2_020_01 / ATGCCATGTGagtccaagga
RIP_Alu_chr2_021_02 / TAGCATTCCTttccttagtc
RIP_Alu_chr2_028_01 / AAAAATAATAataataataa
RIP_Alu_chr2_033_01 / TATTAGAAGAaccatataaa
RIP_Alu_chr2_034_02 / CAAGAGAGTTaggagctctg
RIP_Alu_chr2_036_02 / TAAAGAGAAAaatcttaaag
RIP_Alu_chr2_036_01 / AAAAAATATTttttataaat / The 5’-most T in the Alu sequence was re-assigned to the upstream TSD
RIP_Alu_chr2_038_02 / GCCGAGACTAtgagactttt
RIP_Alu_chr2_038_01 / GAAATGATTAatttttaata
RIP_Alu_chr2_039_02 / AACCACTGATatgtgggatt
RIP_Alu_chr2_043_01 / ACAAAAAATTatccgggcgt
RIP_Alu_chr2_050_01 / ACAAAAGTTCagaatattga
RIP_Alu_chr2_055_01 / GAGTAGGAGTtaactacata
RIP_Alu_chr2_057_01 / AGCTACTAGCcccgggagag
RIP_Alu_chr2_063_01 / AAGCAGGGCCaagtgtggtg
RIP_Alu_chr2_065_02 / TAGCCAGGTGtagtgtcgca
RIP_Alu_chr2_065_01 / AAGTAACATGatattaggat
RIP_Alu_chr2_077_01 / CAAAATTCCTtccttctttt
RIP_Alu_chr2_078_01 / AGAAACTCATacactgacgc
RIP_Alu_chr2_085_02 / ACATATGACCagtaaactca
RIP_Alu_chr2_101_02 / CTTAAGCAGGtactgattgg
RIP_Alu_chr2_102_01 / AATGAGTTCCaatgagaaca
RIP_Alu_chr2_107_01 / AGAGGGTCTTaaaagcaatt
RIP_Alu_chr2_113_02 / ATTTAAACATaagacctaaa
RIP_Alu_chr2_113_01 / atATTAAGGGaaggggggaa
RIP_Alu_chr2_114_01 / AGCCCCAATCatcattcatt
RIP_Alu_chr2_115_01 / AAAGAAATGGagaaatatct
RIP_Alu_chr2_117_01 / AAATACATCCatcaaataca
RIP_Alu_chr2_121_01 / aggcaaGGCAactctaacta
RIP_Alu_chr2_128_01 / ACTCTGTGTAatatttagtc
RIP_Alu_chr2_134_02 / TGATGATTTAactaaagtat
RIP_Alu_chr2_145_01 / ATATTTACAAagagatgaag
RIP_Alu_chr2_150_03 / cAAACAAGCAaaaataaata
RIP_Alu_chr2_150_02 / AACTTACATTatttttagat
RIP_Alu_chr2_152_01 / AATAGAGTGCaacacaacta
RIP_Alu_chr2_158_01 / GGTAACTACTtttaaaatga
RIP_Alu_chr2_160_01 / AAATTACGTAatgtgcatgc
RIP_Alu_chr2_161_01 / AAGAATCTTCtacttgttct
RIP_Alu_chr2_169_01 / CAATATTTTCcacactccct
RIP_Alu_chr2_173_01 / AGTTAAAGAGaattcttcca
RIP_Alu_chr2_174_01 / TGAGCTTCTCaattctgatt
RIP_Alu_chr2_178_02 / ATACATATAGcccactttgc
RIP_Alu_chr2_181_01 / AGAAGTGGTCtgtgcaccta
RIP_Alu_chr2_184_01 / TCCATAAACAactgattcgt
RIP_Alu_chr2_189_01 / AAACATACCAtagtggttaa
RIP_Alu_chr2_192_02 / ACATGTAAGAcacccacata
RIP_Alu_chr2_194_01 / ATTTCTCATTatggtcatac
RIP_Alu_chr2_195_02 / AAAACTTTTCctttgctttt
RIP_Alu_chr2_202_02 / GTGGCACATAtacaccatgg
RIP_Alu_chr2_202_01 / ACTGGGTTCCaataaaacag
RIP_Alu_chr2_203_01 / ACTTAAATGTtagacctaaa
RIP_Alu_chr2_204_01 / ACCTCTATGCaaataaacta
RIP_Alu_chr2_207_01 / ACTATAGTCCaagtggacct
RIP_Alu_chr2_208_02 / AAAAATTCCTatcaatattc
RIP_Alu_chr2_209_01 / ATCAACAAACatgtttctaa
RIP_Alu_chr2_213_01 / AGCAAGGCCCagggcctcaa
RIP_Alu_chr2_214_01 / AAGAATTCTTacaaaagcaa
RIP_Alu_chr2_215_01 / tAAACCTTTTaaaggaaatc
RIP_Alu_chr2_216_01 / GAAAGAAAGAaagaaagaaa
RIP_Alu_chr2_218_01 / ATCAGCACCAaaaactaatt
RIP_Alu_chr2_223_01 / tAAAAGCATGtatttagcag
RIP_Alu_chr2_231_02 / ACAGATTACCaataccccag
RIP_Alu_chr2_235_01 / CCACATGATTatctcaatag
RIP_Alu_chr20_002_02 / GAAATGTGCAatggtagagc / While the upstream TSD is AAAGAAATGTGCA, the downstream one is AAAGAAATGCA; the indicated difference can be explained by replication slippage.
RIP_Alu_chr20_006_01 / GTGGACATCCtttctgtgga / The 5’-most ACATCC in the Alu sequence was re-assigned to the upstream TSD
RIP_Alu_chr20_007_01 / ATGTATTGTCattccttttt
RIP_Alu_chr20_009_01 / aAAATTAAGGttcatgtttt
RIP_Alu_chr20_011_01 / ATTCTGTCTTacgtgcaaac
RIP_Alu_chr20_014_01 / TACATTATCTtagttttttt / The 5’-most T in the Alu sequence was re-assigned to the upstream TSD
RIP_Alu_chr20_014_02 / AGGTAGAAACatggaaatgt
RIP_Alu_chr20_020_01 / AATACCAAAAaatgcaacaa
RIP_Alu_chr20_026_01 / TAAATCATTCatcgttggag
RIP_Alu_chr20_026_02 / TGACATAATAttctgcagta
RIP_Alu_chr20_031_01 / CAGTCATTTTtctcactgct
RIP_Alu_chr20_035_02 / CTCAAGAGTTtttaagtaac
RIP_Alu_chr20_035_01 / TCAATCATTTatgtttaatt
RIP_Alu_chr20_044_01 / CCATGTGAAGttatgctgcc
RIP_Alu_chr20_045_01 / AACAGGAGGCtatttgtgta / The upstream TSD was re-annotated as AAAAAAAAAACAGGAGGC whilst the downstream one was re-annotated as AAAAAAAAAACCGGAGGC. The single nucleotide difference might have occurred post-retrotranspositionally.
RIP_Alu_chr20_046_01 / AAAAGATTGCaacaccaatg
RIP_Alu_chr20_052_01 / TTAGGAATCAaaaaggttaa
RIP_Alu_chr20_053_02 / GAAAAATTTCcaagattgca
RIP_Alu_chr20_053_01 / AGAATGCCCAcatttatgtg
RIP_Alu_chr20_058_01 / AATGTGTTTGttcctctgtt
RIP_Alu_chr20_059_02 / AGTGGGTTTTtcctcctgaa
RIP_Alu_chr20_059_01 / AACCACTCACacggttaatc
RIP_Alu_chr21_013_01 / AAGAATTGTAtacttttcaa
RIP_Alu_chr21_016_01 / GAAGCATTTCcaggggaaga
RIP_Alu_chr21_023_01 / AAATTATCTGtagttttctc
RIP_Alu_chr21_031_02 / GAGCTGACGAaatgcacttt
RIP_Alu_chr21_032_01 / CATATTCTCAaacagctaat
RIP_Alu_chr21_038_01 / ATGTTTTCTCccattctgtg
RIP_Alu_chr21_040_02 / TTTCATTGTTaaattatgca
RIP_Alu_chr21_041_01 / AATACCTAGAaagctgtcat
RIP_Alu_chr21_046_01 / atGATCTTTAattatatgaa
RIP_Alu_chr22_016_02 / CAGGGTCCAGaaatgaaccc
RIP_Alu_chr22_016_01 / TCATACAAGAaactatcacc
RIP_Alu_chr22_016_03 / AAACTCAGGAtgccttgtga
RIP_Alu_chr22_031_01 / CAAGGAAGTCagatggtata
RIP_Alu_chr22_049_01 / TGCCCCAATCatcattcact
RIP_Alu_chr3_000_02 / ACTTAAACGTtagacctaaa
RIP_Alu_chr3_000_01 / ATGGAGATATattatatatc
RIP_Alu_chr3_001_02 / GTCAGGAAACaacaggtgct
RIP_Alu_chr3_001_01 / AGTGCCATAAaggcaacctg
RIP_Alu_chr3_002_02 / TAAATAAATAaataaataaa
RIP_Alu_chr3_002_01 / GTCACAAATCtactagttct
RIP_Alu_chr3_003_01 / ACTATGACACaaagctggag
RIP_Alu_chr3_004_01 / AGAAAATCTCtccaatgtat
RIP_Alu_chr3_006_01 / tAAAAATGTAaaaagtgaga
RIP_Alu_chr3_010_01 / TGTCCTTTCCtttgtgcgtg
RIP_Alu_chr3_015_01 / ACAGGTTACTtatgtaccca
RIP_Alu_chr3_017_02 / GCTATTTTTAtgcttcagtt
RIP_Alu_chr3_017_01 / GTATGGTGTCagcatctgct
RIP_Alu_chr3_023_02 / TTTGATACAAatatcaaatg
RIP_Alu_chr3_026_01 / AAGGGACCGGagcaggaagt
RIP_Alu_chr3_031_02 / ATGGGTTTCAataagctttc
RIP_Alu_chr3_035_01 / AATTTAAATAtaccttcttt
RIP_Alu_chr3_040_01 / AGAAAATGTAagaggcacaa
RIP_Alu_chr3_043_01 / GAAAGCAGGTaggattttcc
RIP_Alu_chr3_061_01 / CATGTAAGCTtaaacaacat
RIP_Alu_chr3_067_01 / AAAAATGGTGctgtgcactc
RIP_Alu_chr3_077_01 / AATTCATTTTattcacaaca
RIP_Alu_chr3_081_02 / CTGGTAAACCtagagaaaat
RIP_Alu_chr3_101_02 / CCCCAAAACAatctcctttg
RIP_Alu_chr3_101_01 / AAAGCCCATCaataaataaa
RIP_Alu_chr3_103_01 / AAGAGGAAATtagttctgga
RIP_Alu_chr3_104_01 / AATTTTACTCaaatttcaat
RIP_Alu_chr3_111_01 / CATTCCTATTtctccacatc
RIP_Alu_chr3_111_02 / AAATTATTTAaatttccaaa
RIP_Alu_chr3_113_01 / TTACCTTCCCtcctgggtgt
RIP_Alu_chr3_115_01 / GACAAATATCacatgttctc
RIP_Alu_chr3_115_02 / AAGATTGAGAagagcacagt
RIP_Alu_chr3_123_01 / tAGAAATGAAagtctcttat
RIP_Alu_chr3_124_01 / AAAATATTTGaatcagtttt
RIP_Alu_chr3_127_01 / CACAAGCAGCtttggtttat
RIP_Alu_chr3_131_01 / AAACTGTCCTacatcatgta
RIP_Alu_chr3_142_01 / CGCACTTGCCatctctggct
RIP_Alu_chr3_145_01 / ATTAAATGCCatagaagttg
RIP_Alu_chr3_149_01 / AGAACTTGAGaataatatct
RIP_Alu_chr3_150_01 / AAAGAGGTCTacactgagag
RIP_Alu_chr3_150_02 / TGCAAAAATAatggagccac
RIP_Alu_chr3_164_01 / atAAAAATGCtactgatttt
RIP_Alu_chr3_167_01 / acAGAATCAGaatcctctaa
RIP_Alu_chr3_176_01 / GAATGAGATCttatcatttg
RIP_Alu_chr3_182_01 / CATGCAGCTTacatgaatga
RIP_Alu_chr3_183_01 / AAGAAAGGCAccacagaaca
RIP_Alu_chr3_186_01 / AGAGAGAGAGagaaaacaga
RIP_Alu_chr3_187_01 / ACACAGAGTAtttgagcatt
RIP_Alu_chr3_189_01 / TTGGCGCTCTactgaagact
RIP_Alu_chr3_192_01 / aAAGAGTGTAaagaggaaga
RIP_Alu_chr3_193_02 / ATATAACATAaaattctaat
RIP_Alu_chr4_004_01 / GTTGAGTGTTtaagactgct
RIP_Alu_chr4_009_02 / ACTCCAAGTCaaagttcaaa
RIP_Alu_chr4_016_01 / cAAAAGGATAagacataaag
RIP_Alu_chr4_026_01 / AATGTTAGCAaagaggtcat
RIP_Alu_chr4_030_01 / GAAGCCTTCAatttcaggtt
RIP_Alu_chr4_036_02 / GATTCATCCAaaagtgaagt
RIP_Alu_chr4_041_01 / AAACAAGATTttattttgct
RIP_Alu_chr4_044_01 / ACATCAATATcaggaaagca
RIP_Alu_chr4_053_01 / TGTATCTTTAaaaaaggttc
RIP_Alu_chr4_055_02 / CTTATTTACCatgactgcta
RIP_Alu_chr4_055_01 / tctAAACCTCattttcccat / The 5’-most C in the Alu sequence was re-assigned to the upstream TSD
RIP_Alu_chr4_059_01 / GACAACACTGctgggcgcgg
RIP_Alu_chr4_061_01 / GTGTGCTGTAttactttaat
RIP_Alu_chr4_066_02 / TAAGATTTGCtcaggtgtcc
RIP_Alu_chr4_081_01 / AATGTATATGttaagagtaa
RIP_Alu_chr4_082_01 / ATAGCTTTACtctttaatct
RIP_Alu_chr4_082_02 / TCAGACTTCActactataca
RIP_Alu_chr4_089_02 / GATCAGCATCaggctacaag
RIP_Alu_chr4_089_01 / GTGATTTTTTttaatggctt
RIP_Alu_chr4_090_01 / AATGCCAAGTatatctggag
RIP_Alu_chr4_095_01 / aaGAAGAGTTttttatgaga
RIP_Alu_chr4_097_01 / ACAAAATTTCtaggacactt
RIP_Alu_chr4_098_04 / TTAAGTTCCTatggcatatt
RIP_Alu_chr4_098_01 / ATACCCTGCTaattcaaatt
RIP_Alu_chr4_098_05 / AGTTTATTGCatcaagtttc
RIP_Alu_chr4_100_02 / aaAAAAAACCaaaaaacgta
RIP_Alu_chr4_100_01 / GGGTCTTTTCaagatccaga
RIP_Alu_chr4_100_03 / AGTTGATTAAacatgtatta

RIP_Alu_chr4_102_01

/ GTAAATGTAAagtatttata
RIP_Alu_chr4_105_01 / AAATCACCTAtggtgctgtg
RIP_Alu_chr4_107_01 / agagcattttgccgggcgcg / No TSD (i.e. blunt insertion)
RIP_Alu_chr4_109_01 / TACAAACATTagccaggcat
RIP_Alu_chr4_110_01 / TCAAGTACCCattttaggct
RIP_Alu_chr4_120_02 / ACGTCAAACTttgttttttt
RIP_Alu_chr4_120_01 / GCTGCAATGAatttctttct
RIP_Alu_chr4_122_01 / ATAAAATGTCtaggctgtgg
RIP_Alu_chr4_129_01 / ATATACTTCTtaaatcttat
RIP_Alu_chr4_133_03 / TGGTAAACCTaaatgtaaaa
RIP_Alu_chr4_133_02 / TGCAAGTATCacactatttt
RIP_Alu_chr4_134_02 / GGCTGGAGGAaaagaataca
RIP_Alu_chr4_134_01 / ACAAATTTATtctcttaaaa
RIP_Alu_chr4_138_02 / AATGTTACCAaaatgccaag
RIP_Alu_chr4_142_01 / ATTTTAAAAGaatggaacta
RIP_Alu_chr4_144_01 / AAGGAAAAAGaccatttgaa
RIP_Alu_chr4_148_01 / AAATCATCCCttctttttgc
RIP_Alu_chr4_150_01 / GGCTGCTCTAactcaaaata
RIP_Alu_chr4_151_01 / AGTATTTTTAaatgttggtt
RIP_Alu_chr4_160_01 / AAAAATTAGTagaggtaagt
RIP_Alu_chr4_163_01 / tAGAAATCTTatatatattt
RIP_Alu_chr4_167_02 / GGTTGGAAGAtaaacatttg
RIP_Alu_chr4_167_04 / AAAAGAAAAAagtagaaaaa
RIP_Alu_chr4_175_02 / GTTCTTTCTGaagataatgg
RIP_Alu_chr4_178_03 / AACAGGATTAacagtgaagg
RIP_Alu_chr4_178_01 / AAGAATACTTatgtggtctt
RIP_Alu_chr4_178_02 / ACCTAAACAAatgattaatc
RIP_Alu_chr4_180_01 / ATTTGATTTAatggagtaaa
RIP_Alu_chr4_181_03 / AATAAGCATTttgctaataa
RIP_Alu_chr4_181_01 / GAAGACACAGaaggacaacc
RIP_Alu_chr4_184_01 / GTGCTATGTTaggccgggtg
RIP_Alu_chr4_190_01 / TACTGGATTAagtctaacgc
RIP_Alu_chr4_190_02 / TAGCATGCTCaagaacatat
RIP_Alu_chr4_190_03 / AATGACTCCGatgactgcgt
RIP_Alu_chr5_004_01 / GACAGAAATCcactgcacac
RIP_Alu_chr5_006_02 / GTTTGAATACataatttcaa
RIP_Alu_chr5_011_01 / GAAGGAACTGtgtactcagc
RIP_Alu_chr5_013_01 / AAAAGAAGACaaggactctc
RIP_Alu_chr5_017_01 / CATGGAAGGGaaactgaagg
RIP_Alu_chr5_018_02 / tAATAGTTTCacatggaagg
RIP_Alu_chr5_021_02 / tttAAAAATAataataattt
RIP_Alu_chr5_022_01 / AAAAAATCTGaacagaagtt
RIP_Alu_chr5_023_01 / ACAGAAACCGcttcttgaaa
RIP_Alu_chr5_024_01 / AACTGAGGCAtagggagatt
RIP_Alu_chr5_024_02 / AAAACAATAGaacttggaca
RIP_Alu_chr5_025_02 / TTAAGCTTCTtaatttctcc
RIP_Alu_chr5_025_01 / TCTGGGAAAAacacaagaaa
RIP_Alu_chr5_029_02 / atAAAAATATtatttattca
RIP_Alu_chr5_031_01 / AGGTATATCCatgtgatgga
RIP_Alu_chr5_032_01 / AAACTGATGAcatatgaaca
RIP_Alu_chr5_033_01 / AATGTGTTAAaaagatatta
RIP_Alu_chr5_037_01 / GATGATTCTTaatgtaatga
RIP_Alu_chr5_039_01 / TATTTTTTACtctataacat
RIP_Alu_chr5_045_01 / AAATTAAAGGatgtgaagct
RIP_Alu_chr5_053_01 / ACCAGCTCCCtccaccacca
RIP_Alu_chr5_055_01 / GATACAGAGAcacaaagctt

RIP_Alu_chr5_061_01

/ AACAATTTTCtatttcttca
RIP_Alu_chr5_061_02 / AGAGGAAGTCaaattgtccc
RIP_Alu_chr5_061_03 / TGTTTCTTTCaagcatcaaa
RIP_Alu_chr5_062_01 / ATATAAAATCatacaacttt
RIP_Alu_chr5_070_01 / CTCACATATAtgcatcatca
RIP_Alu_chr5_073_01 / AACAGAATAAaaagaaataa
RIP_Alu_chr5_077_01 / ATAAGCCGGAcatggtggca
RIP_Alu_chr5_078_02 / AGTCATATCTatgaacttgg
RIP_Alu_chr5_079_01 / tAAAATAGCTtaggttaaaa
RIP_Alu_chr5_080_01 / CCTCCTTCTAaccctaccct
RIP_Alu_chr5_081_01 / AGAAAAGCAGtactaaagct
RIP_Alu_chr5_082_02 / TTAGAGCTCTcaaatagaaa
RIP_Alu_chr5_088_02 / TCAGCAACTCtccatctggg
RIP_Alu_chr5_089_01 / ATTAAACGCCatggaaatgt
RIP_Alu_chr5_091_01 / AAAGTCTATTatcacaaaaa
RIP_Alu_chr5_095_02 / AAAAAAAGAGaagggggcta
RIP_Alu_chr5_097_01 / TGCAATACAAttgcaacttg
RIP_Alu_chr5_099_01 / ATGATAAAGAaattttcagg
RIP_Alu_chr5_099_03 / ACAGATAAACaacttgggca
RIP_Alu_chr5_099_02 / TGTTATTAGCacagaacaca
RIP_Alu_chr5_103_02 / AATCAATTGTaaaaaataaa
RIP_Alu_chr5_103_01 / TGTGTGTGTGtgtgtgtgtg
RIP_Alu_chr5_112_01 / ATGGAGATCAattatttttc
RIP_Alu_chr5_114_01 / TAGAATATGTtaatgtcatc
RIP_Alu_chr5_115_01 / AAGAATCCTTaaatgatggg
RIP_Alu_chr5_116_01 / TTGGAGTATGtcaccgaatg
RIP_Alu_chr5_119_01 / GAGACTTCTCacttttggct
RIP_Alu_chr5_122_01 / AGGCAATGAAatacaaataa
RIP_Alu_chr5_125_01 / AATGAAGCTCatagtacaat
RIP_Alu_chr5_126_01 / TGACTGTCCTttggtggcat
RIP_Alu_chr5_128_01 / AGTCACTTTTctcaggtctc
RIP_Alu_chr5_141_01 / CTTGTGATTTttgtacattg
RIP_Alu_chr5_142_02 / AGACAGACAGactaatagtt
RIP_Alu_chr5_142_01 / ATAAAAGTATaccaaactgt
RIP_Alu_chr5_144_01 / GACTGTTCCAtctcatttag
RIP_Alu_chr5_146_01 / CCATAAAACAttaatgaaag
RIP_Alu_chr5_148_01 / CTGGCAACTGttgaaaaggg
RIP_Alu_chr5_155_01 / AAGAAAATTCataccatcat
RIP_Alu_chr5_157_01 / AAATAAATACcagcactcaa
RIP_Alu_chr5_160_01 / aAAGAAATCTatgaaatgtc
RIP_Alu_chr5_166_01 / AGTAAACATCacaatgttct
RIP_Alu_chr5_170_02 / AAGTAGAATGatggttaaca
RIP_Alu_chr5_170_01 / GAAAAAAGAGtaatgattgt
RIP_Alu_chr5_173_01 / GAACTCGATGaaaacgtttt
RIP_Alu_chr5_177_02 / tTTTACTTTAagttctggga
RIP_Alu_chr6_008_01 / CTTCACAGTAaattaagtac
RIP_Alu_chr6_009_02 / TTAATAAACAtatataaagt
RIP_Alu_chr6_012_02 / CTTTAGAGTGaaaaggaaaa
RIP_Alu_chr6_012_03 / AACTCAGTGAcatttccctc
RIP_Alu_chr6_012_01 / GTCATGCTGGattagggcga
RIP_Alu_chr6_018_01 / TCTCAATAAAttaggtattg
RIP_Alu_chr6_020_01 / GAATGTAACCattacctttg
RIP_Alu_chr6_020_02 / aaGTAATCCTatgcacctca
RIP_Alu_chr6_023_01 / ATATTTTCTCaggtggtagt
RIP_Alu_chr6_023_02 / AAAAACAGGAatttatttcc
RIP_Alu_chr6_024_01 / ATGACAACCAtgcctacccc
RIP_Alu_chr6_026_01 / GTCTTTATAAaaatctgatt
RIP_Alu_chr6_028_01 / GATGATAATAatagcataaa
RIP_Alu_chr6_031_01 / GGAGACAGGAgatgggaaag
RIP_Alu_chr6_032_03 / aatagAAGCAaaaaagaaac
RIP_Alu_chr6_032_01 / GTTCATGGAGcccttcttcc
RIP_Alu_chr6_033_01 / CAAGGCTGGAaatctgtttt
RIP_Alu_chr6_037_01 / GTTGAGATAGaaatgatggt
RIP_Alu_chr6_037_01 / GTTGAGATAGaaatgatggt
RIP_Alu_chr6_041_01 / TTCAAGCATAtactaaagta
RIP_Alu_chr6_044_02 / GATTGTCTGGataactttcc
RIP_Alu_chr6_044_01 / AGACAGTTGCtccttgaggg
RIP_Alu_chr6_050_01 / GAATAATGAGaatgggtatc
RIP_Alu_chr6_050_02 / TAGGTTTAACaggaaatcca
RIP_Alu_chr6_051_02 / TTAAGGTGTCagcatagctg
RIP_Alu_chr6_051_01 / AAGAGAGATAaaaaatgctc
RIP_Alu_chr6_051_03 / GGCCATGCTGtaacaggtga
RIP_Alu_chr6_052_02 / AAAGAATTCAaacactttta
RIP_Alu_chr6_054_03 / TCACATTTCTaactcatcct
RIP_Alu_chr6_054_02 / AACACAAGTTatctaagcat
RIP_Alu_chr6_055_01 / AAAAAATGCCttaactgtat
RIP_Alu_chr6_065_01 / GAAAAGAAAAaataccaaat
RIP_Alu_chr6_067_01 / TCAAATTGAAaataaagcca
RIP_Alu_chr6_068_02 / TACCAAATCAaattctagaa
RIP_Alu_chr6_074_02 / tAAAAACTTAaagtacgatt
RIP_Alu_chr6_083_01 / AATTAAAGACatacatgcaa
RIP_Alu_chr6_086_01 / GGTGGGTCCCtcatggatgg
RIP_Alu_chr6_088_01 / TATATTAGTAaattagctgg
RIP_Alu_chr6_089_01 / AGTACTTTTActttcagctt
RIP_Alu_chr6_091_01 / GTCCTTATGAaacccatttt
RIP_Alu_chr6_092_01 / ATCCTGGCTAacaaagtgaa
RIP_Alu_chr6_097_01 / AGAAACTCACttcacctaaa
RIP_Alu_chr6_098_01 / atAATTATGAaatataatag
RIP_Alu_chr6_104_02 / AATCCAGATAaactcagtgg
RIP_Alu_chr6_105_01 / AAAAAAGAGAaaagatgata
RIP_Alu_chr6_107_01 / ACAGAGTCTCactctgtcac
RIP_Alu_chr6_107_03 / AAACTTTTTCcacttttgtt
RIP_Alu_chr6_108_01 / cAAAAATCTAaagcaaaaaa
RIP_Alu_chr6_119_02 / AAAGAAAAGGttaatgctaa
RIP_Alu_chr6_120_02 / ATTGAGAGTCaatacagggg
RIP_Alu_chr6_121_01 / ATGGGAAAGGtatttataat
RIP_Alu_chr6_121_02 / CTATAAACTCataaaatttc
RIP_Alu_chr6_129_02 / ACACTACATGattagctccc
RIP_Alu_chr6_129_01 / GTATAATTTCagcaaagaaa
RIP_Alu_chr6_131_01 / TACTTTTTGAatgcatgaat
RIP_Alu_chr6_132_01 / AGCTGTAGTTattgttacca
RIP_Alu_chr6_133_02 / ACTGTATTGAtttcctgagt
RIP_Alu_chr6_133_01 / AAAAATTGGCaatggagcaa
RIP_Alu_chr6_135_01 / GCTTACATCAataaaatttg
RIP_Alu_chr6_138_01 / AAAAATTGTAactaccacta
RIP_Alu_chr6_154_01 / ATGTCTAGCCttagtgggca
RIP_Alu_chr6_159_01 / TACAAATTGGttgctcgtca
RIP_Alu_chr6_163_04 / ACCTAACTTAtcctaatacc
RIP_Alu_chr6_163_02 / CTGAAACTGGatcccttcct
RIP_Alu_chr6_163_03 / AAGAATTTTCaacccagaat
RIP_Alu_chr6_163_01 / ATGAGGTCTCcaagttttag
RIP_Alu_chr6_167_01 / GAGTCATTCCtactgtagat
RIP_Alu_chr6_170_01 / TGCTAGACTTtcagttaatc
RIP_Alu_chr7_003_01 / AGAGGTACTAataaataaaa
RIP_Alu_chr7_004_01 / GAAGTCAGTGaaatgggtct
RIP_Alu_chr7_007_01 / TGAATAGATAaagaaaatgt / The 5’-most A in the Alu sequence was re-assigned to the upstream TSD
RIP_Alu_chr7_008_01 / AAAACGTAACagttgacatg
RIP_Alu_chr7_011_02 / GTAGTATAGAatcattattc
RIP_Alu_chr7_027_02 / AAAGATACTAaactaactgt
RIP_Alu_chr7_033_02 / ATATAGTGAAaagataatat
RIP_Alu_chr7_033_01 / GCCAGGCTCAatcctattct
RIP_Alu_chr7_037_03 / ATATACAATAtataattatt
RIP_Alu_chr7_037_01 / GAGGGGAGCAccagttctat
RIP_Alu_chr7_037_02 / tAAAAATGTTatgtgcaaaa
RIP_Alu_chr7_038_01 / ACATACAGACacagagtacc
RIP_Alu_chr7_039_01 / GAAAATTAAAatttggcctc
RIP_Alu_chr7_042_03 / GGCCATGTGAagactcagag / This entry had been illustrated in the antisense strand with respect to the Alu sequence; converted to the sense strand
RIP_Alu_chr7_042_04 / AGGAATGAGCtactgatata
RIP_Alu_chr7_042_02 / GATAATAATTaatcaaagca / The 5’-most T in the Alu sequence was re-assigned to the upstream TSD
RIP_Alu_chr7_044_01 / TATGTGGGTAaatctctgtt
RIP_Alu_chr7_045_01 / GAATATTTAGatgaatttat
RIP_Alu_chr7_051_01 / GTGAGGAGCTacaggagcag
RIP_Alu_chr7_052_01 / agAAAAATGAattaggctat
RIP_Alu_chr7_057_02 / ATGGATTCTCtgcaatacct
RIP_Alu_chr7_064_02 / AGCACAGGGAatgtaagaaa
RIP_Alu_chr7_067_01 / AAGAAACCCAaagccatcac
RIP_Alu_chr7_070_01 / ATTTGGAGGCtagggtttta
RIP_Alu_chr7_071_01 / AATCATTACGaaagcatggc
RIP_Alu_chr7_076_02 / AATATTTTCAaaagcctttg
RIP_Alu_chr7_077_01 / ATTCCTTCACttatttaatc
RIP_Alu_chr7_078_01 / AGAAAGATGGacataccaat
RIP_Alu_chr7_079_01 / ATTGGGATTGaaaataaatt
RIP_Alu_chr7_080_01 / ATGGGCTCCAattccatcta
RIP_Alu_chr7_082_02 / CTGAACAACCatggccatcc
RIP_Alu_chr7_082_01 / AAGAACTCTGtacaaaacac
RIP_Alu_chr7_083_01 / TATAAGCTGCaaattataaa
RIP_Alu_chr7_083_03 / ACTTGGAACCaacccaaata
RIP_Alu_chr7_086_01 / AATTAAGGTCttccttcact
RIP_Alu_chr7_086_02 / AGCAAAAGCCtggatggaca
RIP_Alu_chr7_089_01 / GAATAAGGTCcaggatgtgg
RIP_Alu_chr7_090_01 / AAAAAAAAAGaaaaaagttt
RIP_Alu_chr7_093_01 / AAGAAATACAaaagcaacat
RIP_Alu_chr7_095_02 / tAAGAATTCCagaagaaaac
RIP_Alu_chr7_096_02 / GACTAGCGCCagaggctcat
RIP_Alu_chr7_103_05 / AAGATATACGataacatgtg
RIP_Alu_chr7_103_01 / TAAAATTTAAatgggagtaa
RIP_Alu_chr7_103_04 / AGTAGCTCAAaatatgtata
RIP_Alu_chr7_104_01 / ATCAAATGTAactaatttcc
RIP_Alu_chr7_107_01 / AAAGAAAGAAattctgacac
RIP_Alu_chr7_110_01 / GTACAGACTCtattttgtag
RIP_Alu_chr7_112_01 / TTAGAATCTAacaacaagtg
RIP_Alu_chr7_113_01 / AAATATTGTCattatttgaa
RIP_Alu_chr7_117_01 / TGCAGTCTGGaactctacta
RIP_Alu_chr7_124_01 / AAAGGGACTTagaatgttaa
RIP_Alu_chr7_124_02 / AGTCAAGTTAaaggacaccc
RIP_Alu_chr7_127_01 / AAGAAAAAGAataaaataaa
RIP_Alu_chr7_127_03 / TGCTGTGCCCagtatatatt
RIP_Alu_chr7_132_01 / TAATGGAGCAatccaaaatg
RIP_Alu_chr7_134_01 / TAGCCGGATGtggtggcacg
RIP_Alu_chr7_136_03 / GTCCTTTGTCatcctttttg
RIP_Alu_chr7_136_02 / ACCCACTGAGtataatttat
RIP_Alu_chr7_139_01 / TATTTGACTTaacccaatag
RIP_Alu_chr7_142_01 / GAAACTCAAAaactgctcaa / The 5’-most AA in the Alu sequence was re-assigned to the upstream TSD
RIP_Alu_chr7_143_01 / CAGTCAGCACaatactaaaa
RIP_Alu_chr7_151_01 / GTAGTGATCCagttctccgt
RIP_Alu_chr7_153_01 / TTAAACTCCAtatcaaacaa
RIP_Alu_chr7_154_02 / CTTATGTTACtaggagtacc
RIP_Alu_chr7_154_01 / GTGGGTGCAAttgatggaca
RIP_Alu_chr8_004_01 / GATAATCAATataatacact
RIP_Alu_chr8_005_01 / AAAATGGAGAtaataatcct
RIP_Alu_chr8_011_01 / CCTGGGAAATttctaccttc
RIP_Alu_chr8_012_01 / ATTTGGCTCCaacttacctc
RIP_Alu_chr8_015_01 / GTAATAATAGattgaccaca
RIP_Alu_chr8_015_03 / ATCGAAGCCTaaggatgtat
RIP_Alu_chr8_015_02 / AAACTTTTTCacagaattac
RIP_Alu_chr8_017_01 / TCCAGATATCtggattgatt
RIP_Alu_chr8_020_01 / GAGGCTTACAcactagccag
RIP_Alu_chr8_039_01 / TAATATTTAAccttttcaaa
RIP_Alu_chr8_041_01 / ACCTTAAAAGccccttcagc
RIP_Alu_chr8_042_01 / GTAGTGTTCTaatctcatag
RIP_Alu_chr8_047_01 / AGCTAGAAAGaagctgtctg
RIP_Alu_chr8_054_01 / AAGCAAAATCagctaaaaca
RIP_Alu_chr8_056_01 / GACCAATGGTtgctggaggt
RIP_Alu_chr8_061_01 / GGACAGTGTCttccagagta
RIP_Alu_chr8_061_02 / TGCAGGGCTGagtttttttc
RIP_Alu_chr8_063_01 / acAAGAATATatggacatga
RIP_Alu_chr8_069_01 / GAGCAACATGactggctgag
RIP_Alu_chr8_072_02 / ATAAAAGCTAagccgtggta
RIP_Alu_chr8_072_03 / TCACTATATCttgatggata
RIP_Alu_chr8_075_01 / ATTGATCCTCagttgtgggc
RIP_Alu_chr8_076_02 / CACACAAACAaacaaacaac
RIP_Alu_chr8_076_01 / TATAGTTTGAatagacataa
RIP_Alu_chr8_087_01 / TGCCCCTTTCcgtttcatgt
RIP_Alu_chr8_092_01 / CACATATTGAagaatattca
RIP_Alu_chr8_095_01 / GGCCACAGTAtaaccagtct
RIP_Alu_chr8_097_02 / AGAGGTATTAttgcccccat
RIP_Alu_chr8_097_01 / AAAGAGAATAataaagcaaa
RIP_Alu_chr8_098_02 / TATTATTTTTtttgtagaaa
RIP_Alu_chr8_104_01 / ATTAGCCGGGcgtggtggcg
RIP_Alu_chr8_106_01 / ATATGATACCacaaaaaata
RIP_Alu_chr8_106_02 / aaaatGGGCTtgacttctac
RIP_Alu_chr8_106_03 / CAAAGCAGACtgcatcacta
RIP_Alu_chr8_108_01 / TGAACATTGGaaaagcacag
RIP_Alu_chr8_109_01 / CCTAAGTCAGatcatatcac
RIP_Alu_chr8_110_01 / AGAAAACATGataatgaata
RIP_Alu_chr8_112_01 / ATAAGATTCCaatatcacac
RIP_Alu_chr8_116_01 / ATATTTTCTGaacacctctt
RIP_Alu_chr8_121_02 / AAGCATTTTCattttgaata
RIP_Alu_chr8_121_01 / TATGTTTTCCcatggtaaaa
RIP_Alu_chr8_124_01 / GAACTCAGGTaagacaactg
RIP_Alu_chr8_130_01 / AGAAAAATGAttactgttta
RIP_Alu_chr8_134_01 / AGTTATTATGacagtaacaa
RIP_Alu_chr8_137_01 / GAATAATTCCttttttatta
RIP_Alu_chr8_138_02 / GAGAAGGATAttggggccgg
RIP_Alu_chr8_139_01 / TACAAGCTACaatgtgggaa
RIP_Alu_chr8_140_01 / AGAAAACCATaaggagaata
RIP_Alu_chr8_140_02 / ATTTAACCATtattacatgt
RIP_Alu_chr8_144_01 / CACTACTCACtgacaatgct
RIP_Alu_chr9_000_01 / AAATTATCTGtttgcttatt
RIP_Alu_chr9_002_01 / TATGATTTCTttctcttccc
RIP_Alu_chr9_010_01 / AGTCACTCAAaaccatgcaa
RIP_Alu_chr9_013_02 / aAACACTTGGtaattctggg
RIP_Alu_chr9_016_02 / AGTGACAGCCatctccaggt
RIP_Alu_chr9_016_01 / tcAAGAATTTaatacttgta
RIP_Alu_chr9_018_02 / tAGAAATAGAtatgttctgg
RIP_Alu_chr9_022_01 / TTTGAATGCCagatccagaa
RIP_Alu_chr9_025_01 / ttAAAAATGTaaatgaatta
RIP_Alu_chr9_026_01 / AAATGCTTGAatatatgttt
RIP_Alu_chr9_029_01 / ACCCAGGCTTatggattcag
RIP_Alu_chr9_040_02 / GCTTGGTGTCctccctgtgg
RIP_Alu_chr9_075_01 / tAAAAACCAAtacaagagat
RIP_Alu_chr9_076_01 / aaaAACTATGttagtatgag
RIP_Alu_chr9_082_01 / ATTTGTTCCAtgcaggaata
RIP_Alu_chr9_093_02 / CACCCACTAAaaaaaaagtt
RIP_Alu_chr9_094_02 / AGAGCTCAACactgcaggtt
RIP_Alu_chr9_095_01 / aacaaaaAAGataataatag
RIP_Alu_chr9_097_01 / CACCACTTTCtcaaccaatt
RIP_Alu_chr9_098_01 / CTTTTTTAGGttgaatctgg
RIP_Alu_chr9_100_01 / TGAAGAAATAaatacatgac
RIP_Alu_chr9_104_01 / AATCCTCCTTatgggactat
RIP_Alu_chr9_109_01 / AACCAAAGCCatcattttca
RIP_Alu_chr9_115_01 / TTTGATTGCCctgctggttt
RIP_Alu_chr9_119_01 / AGAAAATTGCaaggaaaagg
RIP_Alu_chrX_002_02 / AAAAATTGTAatcatctgtg
RIP_Alu_chrX_004_01 / GCCCCACCAAtagtacccat
RIP_Alu_chrX_010_01 / TCTAACTCATaccgttgtga
RIP_Alu_chrX_032_01 / AGAAAGATCAatattttttc
RIP_Alu_chrX_044_01 / AAATGGTGTTattacttctc
RIP_Alu_chrX_044_02 / AAATGGTGTTattacttctc
RIP_Alu_chrX_047_01 / GTAGCTTAAGagtgttggtc
RIP_Alu_chrX_070_01 / AATAAGTAGGattctattgg
RIP_Alu_chrX_078_01 / aaaaaaaaaAaaaacgaaag
RIP_Alu_chrX_088_01 / AGAATTATGCtaaatctact
RIP_Alu_chrX_089_02 / ATTTTTTCCTcctaggcctc
RIP_Alu_chrX_090_01 / TGTTGGGACTtaggcaatac
RIP_Alu_chrX_090_02 / ACTAGTCATCatagataaat
RIP_Alu_chrX_091_01 / AGAATAGTTTacacaccaaa
RIP_Alu_chrX_091_02 / TCAATGTTCTtggattaggg
RIP_Alu_chrX_106_01 / AAGCAGTGTTacttcacccc
RIP_Alu_chrX_116_01 / GCAAATTCTGaaaccccacc
RIP_Alu_chrX_119_01 / CCATATTAAGtaggatactt
RIP_Alu_chrX_119_02 / CTCTGGATTCtggattctgg
RIP_Alu_chrX_129_01 / AGGCAAAGCAaagtaataat
RIP_Alu_chrX_138_01 / GAAAGTGCTTaacaaaagaa
RIP_Alu_chrX_151_01 / GCACCTGGCCagtggcttct
RIP_Alu_chrY_003_01 / AAAGAAACAAatgtaaaaga
RIP_Alu_chrY_004_01 / AAAAAGTGTCaaggtgattg
RIP_Alu_chrY_005_01 / CTGGTAGACAagagatgcga
RIP_Alu_chrY_009_01 / GAGGAAATACttaagacaat
RIP_Alu_chrY_013_01 / TTAACAAGGAtatccaggaa
RIP_Alu_chrY_014_01 / tAAGAATCCAacagctacaa
RIP_Alu_chrY_025_01 / TAATTTTCTTaaccgtatct

Supplementary Table S3 Alu Insertion Polymorphisms in the dbRIP with Starting Position

at 2

ID

/ Microhomology (highlighted in red)a / Comment (whenever there is a modification of the original annotation
RIP_Alu_chr1_056_02 / GAAGGCCCAGagatatcaaa
GGCCGGGCGCG
RIP_Alu_chr1_066_01 / GATCGTGTGGtattggtctt
GGCCGGGCGCG
RIP_Alu_chr1_067_01 / CACAGACTGGcaaattggat
GGCCGGGCGCG
RIP_Alu_chr1_086_01 / TTCTTAGGGAaactggagag
GGCCGGGCGCG
RIP_Alu_chr1_147_01 / CTCAATTAATtcaaaatact
GGCCGGGCGCG
RIP_Alu_chr1_185_01 / AATAGAATTGagacaaattg
GGCCGGGCGCG
RIP_Alu_chr1_215_01 / AAAGCTTTTGcctttgcggt
GGCCGGGCGCG
RIP_Alu_chr1_224_02 / TAATTATTAGtttggttttc
GGCCGGGCGCG
RIP_Alu_chr1_225_02 / CTATACAAAGaaatatattc
GGCCGGGCGCG
RIP_Alu_chr1_237_01 / CTTTGATTAGtatttttatg
GGCCGGGCGCG
RIP_Alu_chr10_029_02 / GTAAAAATACctattttctt
GGCCGGGCGCG
RIP_Alu_chr10_035_01 / GAGAAAAAAGccttttcaag
GGCCGGGAGCG / 5’-most AAG re-assigned to upstream TSD
RIP_Alu_chr10_046_03 / ATATCTTTGCtttggttcca
GGCCAGGCGCG
RIP_Alu_chr10_060_01 / AAAATAGAGGaaaactcttc
GGCCGGGCGCG
RIP_Alu_chr11_058_01 / AAGTACAGAGcagtgtgtat
GGCCGGGCACG
RIP_Alu_chr11_087_01 / TGAGAGATTGagaacaaata
GGCCGGGCGCG
RIP_Alu_chr11_102_02 / AAGAATTACAtgtagtatag
GGCCGGGCGCG
RIP_Alu_chr12_010_02 / AAATTAATTTtgtgaagtca
GGCCGGGCGCG
RIP_Alu_chr12_023_01 / GTAATTATGGtcagactagg
GGCCGGGCGCG / 5’-most G re-assigned to upstream TSD
RIP_Alu_chr12_029_02 / ACATGTATTGtactgttgtt
GGCCGGGCGCG
RIP_Alu_chr12_085_01 / AAAGATTGTGtaagcaaaaa
GGCCGGGCGCG / 5’-most G re-assigned to upstream TSD
RIP_Alu_chr12_089_01 / ATAAAAAATGtactatgagt
GGCCGGGCGCG / 5’-most G re-assigned to upstream TSD
RIP_Alu_chr12_096_02 / GTATTGTTTAaactgagatt
GGCCGGGCGCG
RIP_Alu_chr12_125_01 / GTATTTTTATatgcttcaca
GGCCGGGTGCA
RIP_Alu_chr13_028_01 / AAAGAGAGAGagagagcgcg
GGCCGGGCGCG / 5’-most G re-assigned to upstream TSD
RIP_Alu_chr13_043_01 / GGGATAAATGaaaggaatca
GGCCGGGCGCG / 5’-most G re-assigned to upstream TSD
RIP_Alu_chr13_081_01 / TATCATTGGGatactttgaa
GGCCGGGCGCG / 5’-most G re-assigned to upstream TSD
RIP_Alu_chr13_087_01 / CTAGATTTAGatatcagaca
GGCCGGGCGCG / 5’-most ATTTAG re-assigned to upstream TSD
RIP_Alu_chr13_109_01 / TTCATAGGGGcagggatgat
GGCCGGGCGCG
RIP_Alu_chr14_059_03 / GTTAAGGTTGatctctgggt
GGCCGGGCGCG
RIP_Alu_chr14_070_02 / ATCCTCCTTGagcctttcaa
GGCCGGGCGCG / 5’-most G re-assigned to upstream TSD
RIP_Alu_chr14_099_01 / TTCCAGGCAGagagaaaaga
GGCCGGGCGCG / 5’-most G re-assigned to upstream TSD
RIP_Alu_chr15_037_01 / TAAATTTTTCttataggccc
GGCCGGGCGCG
RIP_Alu_chr15_043_01 / CTGAGTACTGagtccagggc
GGCCGGGCGCG / 5’-most G re-assigned to upstream TSD
RIP_Alu_chr15_051_01 / GGAACTGGTAccattccttc
GGCTGGGCGCA / The upstream TSD was re-assigned as AAAGAGGAACTGGTA whilst the downstream one was re-annotated as AAAGAGGCGCTGGTA; the indicated difference might have occurred post-retrotranspositionally
RIP_Alu_chr15_054_01 / AGAGAGTAAGaccacgaaga
GGCCGGGCGCG / 5’-most G re-assigned to upstream TSD
RIP_Alu_chr16_011_01 / CAAAAATTAGccaggcatgg
GGCCGGGCGCG
RIP_Alu_chr16_015_02 / TTAATAGCGGacagagttca
GGCCGGGCGCG / 5’-most G re-assigned to upstream TSD
RIP_Alu_chr16_023_01 / ATTAGCTGGGcatggtggca
GGCCGGGCGCG / 5’-most G re-assigned to upstream TSD
RIP_Alu_chr16_026_01 / TGTAGGTAGGaccaagtttt
GGCCGGGCGCG / 5’-most TAGG re-assigned to upstream TSD
RIP_Alu_chr16_029_01 / AATGGTATTGatagatggtc
GGCCGGGCGCG
RIP_Alu_chr16_050_01 / gcCAGCTCAGtcaggagctg
GGCCGGGCGCG
RIP_Alu_chr16_064_02 / AACTGAACTGttcatgtttc
GGCCGGGCGCG / 5’-most G re-assigned to upstream TSD
RIP_Alu_chr16_081_02 / AGAGTTAGGGaggtgtgcaa
GGCCGGGCGCG
RIP_Alu_chr17_014_02 / ACATTAAGAGaccagaatta
GGCCAGGCGCG / 5’-most G re-assigned to upstream TSD
RIP_Alu_chr17_040_01 / acaaaaAAGGcatcccattg
GGCCGGGCGCG / 5’-most G re-assigned to upstream TSD
RIP_Alu_chr17_040_02 / aCTGCAATCAaatggcccac
GGCCAGGTGCG
RIP_Alu_chr17_042_01 / ATAGACCCTCaaagagagga
GGCCGGGCGCG
RIP_Alu_chr17_062_01 / ATGACATCTGtgcaagatta
GGCCGGGCGCG / 5’-most G re-assigned to upstream TSD
RIP_Alu_chr17_063_03 / ACACTAATGGtggaaggtac
GGCCAGGCGCG
RIP_Alu_chr17_065_01 / ATCATTACAGtgttgttgac
GGCCGGGCGCG / 5’-most G re-assigned to upstream TSD
RIP_Alu_chr18_042_01 / CCTACCTGTGaccttgcaga
GGCCGGGCGCG / 5’-most G re-assigned to upstream TSD
RIP_Alu_chr18_066_01 / TAGCAAGGTGttgtagtgtg
GGCCGGGCGCG / 5’-most G re-assigned to upstream TSD
RIP_Alu_chr18_069_01 / TAATGTGTCAttttcgtcac
GGCCGGGCGCG
RIP_Alu_chr19_020_01 / AATAGATTGAaatagagata
GGCCGGGCGCG
RIP_Alu_chr19_020_02 / AAAGGAAACTtagagggtct
GGCCGGGCGCG
RIP_Alu_chr19_035_01 / GGGTTCAGGGcttgggaaaa
GGCCGGGCGCG / 5’-most G re-assigned to upstream TSD
RIP_Alu_chr2_031_01 / AGTAGAATGGtgattgccag
GGCCGGGCGCG
RIP_Alu_chr2_039_01 / ATTACTATGGcgtaacccaa
GGCCGGGCGCG / 5’-most G re-assigned to upstream TSD
RIP_Alu_chr2_041_01 / AGTCACCCAGtctcatttca
GGCCAGGTGCA
RIP_Alu_chr2_049_01 / AAAAATATTGtatattaaaa
GGCCGGGCGCG
RIP_Alu_chr2_085_01 / AGTTTGGCTCttccccactg
GGCCGGGCGCG
RIP_Alu_chr2_089_01 / CAGCTCCTTGttcttcttaa
GGCCGGGCGCG / 5’-most G re-assigned to upstream TSD
RIP_Alu_chr2_095_01 / AGAATCTTAGtttgagtctg
GGCCGGGCGCG
RIP_Alu_chr2_134_01 / AAGAGACGAGtgaggagaac
GGCCGGGCGCG
RIP_Alu_chr2_169_02 / GAAAGAACTGtacatttaga
GGCCGGGCGCG
RIP_Alu_chr2_182_01 / GAATTACATCaaccacttca
GGCCGGGCGCG
RIP_Alu_chr2_182_02 / TAGAAAGAAGcagtcttgtg
GGCCGGGCGCG
RIP_Alu_chr2_192_01 / TGAAAGTTTGaaaacacact
GGCCGGGCGCG / 5’-most G re-assigned to upstream TSD
RIP_Alu_chr2_206_01 / ACATTTCCTGagggccaagg
GGCCGGGCGCG
RIP_Alu_chr2_231_01 / TTTTGCCCTTttagagttgc
GGCCGGGCGCG
RIP_Alu_chr2_240_01 / GAACGTGGAGtaagcctgga
GGCCGGGCGCG
RIP_Alu_chr20_019_01 / GAGGCCCTGGagagctccct
GGCCGGGCGCG
RIP_Alu_chr20_057_02 / GAACAGAGCGtgagagcaag
GGCCGGGCGCG / 5’-most G re-assigned to upstream TSD
RIP_Alu_chr20_060_01 / AAAAATTTGAagaagtatta
GGCCGGGCGCG
RIP_Alu_chr21_013_02 / AGTATAAAAGtttattctct
GGCCAGGCAAA
RIP_Alu_chr21_029_02 / aacaCTATGGatttggggtc
GGCCGGGCGCG / 5’-most G re-assigned to upstream TSD
RIP_Alu_chr21_038_02 / AGCCCAGGTGaggttataaa
GGCCGGGCGCG
RIP_Alu_chr21_039_01 / AGAATTTGAGaaaggggccc
GGCCGGGCGCG / 5’-most G re-assigned to upstream TSD
RIP_Alu_chr3_018_01 / AAGGTGACAGcagagatcag
GGCCGGGCGCG / 5’-most G re-assigned to upstream TSD
RIP_Alu_chr3_021_01 / GAAGTTCATGcaggtcatga
GGCCGGGCGCG / 5’-most G re-assigned to upstream TSD
RIP_Alu_chr3_031_01 / CAGAGCAAAGatgttggtta
GGCCGGGCGCG
RIP_Alu_chr3_059_01 / AAGATCTTTGcctccagttg
GGCCGGGCGCG
RIP_Alu_chr3_081_01 / AGTACCTGTGtgcagggctc
GGCCGGGCGCG
RIP_Alu_chr3_096_01 / GTCAGGTTGGtggggttctt
GGCCGGGCGCG
RIP_Alu_chr3_126_02 / AAATTATGAAaaacaaatca
GGCCGGGCGCG
RIP_Alu_chr3_126_01 / ACAGTACATGaaaaatgctg
GGCCGGGCGCG / 5’-most TG re-assigned to upstream TSD
RIP_Alu_chr3_134_01 / TGGGTGTTAActtgtgggtg
GGCCGGGCGCG
RIP_Alu_chr3_149_02 / AGCACCAGAGctctctcttt
GGCCGGGCGCG
RIP_Alu_chr3_175_01 / GGTATGAGTGagattcaaca
GGCCGGGCGCG / 5’-most G re-assigned to upstream TSD
RIP_Alu_chr3_179_01 / aAAAAATGGGaagaagtaga
GGCCGGGCGCG / 5’-most G re-assigned to upstream TSD
RIP_Alu_chr3_191_02 / AAAACACAGGtgacaacagt
GGCCGGGCGCG
RIP_Alu_chr3_193_01 / AACCTTTGAGtaacttttcg
GGCCGGGCGCG / 5’-most G re-assigned to upstream TSD
RIP_Alu_chr3_196_01 / GAGCGCATAGtaagtaaatt
GGCCGGGCGCG / 5’-most G re-assigned to upstream TSD
RIP_Alu_chr4_002_01 / GAGTATGCTGATTGATATTT
GGCCGGGCGCG / 5’-most G re-assigned to upstream TSD
RIP_Alu_chr4_023_01 / CAGATTCCAGagttcttagg
GGCCGGGCGCG / 5’-most G re-assigned to upstream TSD
RIP_Alu_chr4_041_03 / AACAAGATTTtattttgcta
GGCCGGGCGCG
RIP_Alu_chr4_046_01 / CACTGACTGGcaaattggat
GGTCAGGCGCA
RIP_Alu_chr4_068_01 / CTTTTTCTGGattccaaaaa
GGCCGGGCGCG / 5’-most G re-assigned to upstream TSD
RIP_Alu_chr4_073_01 / CAAAAATAAGttacgatgaa
GGCCAGGCGCG / 5’-most G re-assigned to upstream TSD
RIP_Alu_chr4_080_01 / ATGATTGAGGtctttaagaa
GGCCGGGCGCG / 5’-most G re-assigned to upstream TSD
RIP_Alu_chr4_087_01 / TTGAACGTGGagttttcacg
GGCCGGGCGCG / 5’-most G re-assigned to upstream TSD
RIP_Alu_chr4_087_03 / CACCCTTTTTacatcactca
GGCTGGGTGCA
RIP_Alu_chr4_098_02 / GAGAGACTTGcgtgtacttt
GGCCGGGCGCG / 5’-most G re-assigned to upstream TSD
RIP_Alu_chr4_098_03 / GCTGTAGAGGaaaattgtca
GGCCGGGCGCG / 5’-most G re-assigned to upstream TSD
RIP_Alu_chr4_113_01 / TGTAAAGATGactaattcta
GGCCGGGCGCG / 5’-most G re-assigned to upstream TSD
RIP_Alu_chr4_126_01 / GTTGGTCCTGcccagtggat
GGCCGGGCGCG / 5’-most G re-assigned to upstream TSD
RIP_Alu_chr4_133_01 / AAAAGATGGGctgggcatgg
GGACGGGCGCG / 5’-most G re-assigned to upstream TSD
RIP_Alu_chr4_151_02 / aAATGTGGCAtatggaatat
GGCTGGGCATG / Upstream TSD was re-assigned as AATGTGGCA
RIP_Alu_chr4_171_01 / AAAATTTTGGttaaaataca
GGCCGGGCGCG / 5’-most G re-assigned to upstream TSD
RIP_Alu_chr4_172_01 / TGACGTGCAGagtatatctg
GGCCGGGCGCG / 5’-most G re-assigned to upstream TSD
RIP_Alu_chr4_185_01 / TGTGAGAAGGtgttgtcaca
GGCCGGGCGCG / 5’-most G re-assigned to upstream TSD
RIP_Alu_chr4_189_01 / AGAAGCAGGGtgagtgtgta
GGCCGGGCGCG / 5’-most G re-assigned to upstream TSD
RIP_Alu_chr5_009_02 / ATTAATCTTGtatccacaaa
GGCCGGGCGCG / 5’-most G re-assigned to upstream TSD
RIP_Alu_chr5_009_01 / CTGGCCTCCCaaaagctctg
GGCCGGGCGTG
RIP_Alu_chr5_018_01 / ATAGTGACTGtcctcaaaat
GGCCGGGCGCG
RIP_Alu_chr5_052_01 / CTGTGTTCTGtaattaccat
GGCCGGGCGCG / 5’-most G re-assigned to upstream TSD
RIP_Alu_chr5_065_01 / attcGATTTAGttactgacaa
GGCCGGGCGCG / 5’-most G re-assigned to upstream TSD
RIP_Alu_chr5_069_01 / TGCTCACATGaactatacaa
GGCCGGGCGCG
RIP_Alu_chr5_079_02 / ACAAGAGTAGaggtaatgtt
GGCTGGGCAGA / 5’-most G re-assigned to upstream TSD
RIP_Alu_chr5_109_01 / GCCTAACATGagtcgaagat
GGCCGGGCGCG / 5’-most G re-assigned to upstream TSD
RIP_Alu_chr5_164_01 / GACCTTAGAGagttagctag
GGCCGGGCGCG / 5’-most G re-assigned to upstream TSD
RIP_Alu_chr5_168_01 / TTTGAGATGGcagtgccaga
GGCCGGGCGCG
RIP_Alu_chr5_177_01 / GTGACCTTTGctccagttcc
GGCCAGGCGCG / 5’-most G re-assigned to upstream TSD
RIP_Alu_chr6_002_01 / TGCACTACTGttcaactcct
GGCCGGGCGCG / 5’-most G re-assigned to upstream TSD
RIP_Alu_chr6_007_01 / GGCTAAAGAGaattcttcat
GGCCGGGCGCG / 5’-most G re-assigned to upstream TSD
RIP_Alu_chr6_012_04 / aagagAAGAGaagaaggagg
GGCCGGGCGCG / 5’-most G re-assigned to upstream TSD
RIP_Alu_chr6_039_01 / TAAATTACAGcatctcatta
GGCCGGGCGCG / 5’-most G re-assigned to upstream TSD
RIP_Alu_chr6_042_01 / CTTAAACTGGccaggcatgg
GGCCGGGCGCG
RIP_Alu_chr6_046_01 / CACAAGGAAGagaaaataga
GGCCGGGCGCG
RIP_Alu_chr6_062_01 / ACATTTTGAGctgggtgcga
GGCCGGGTGCG / 5’-most G re-assigned to upstream TSD
RIP_Alu_chr6_076_01 / AAGGATGTGGagactaagtt
GGCCGGGCGCG / 5’-most G re-assigned to upstream TSD
RIP_Alu_chr6_095_01 / AGATATACAGatagtaaata
GGCCGGGCGCG
RIP_Alu_chr6_105_02 / ATGGATTTGGttggaagcca
GGCCGGGCGCG
RIP_Alu_chr6_116_01 / TGAGGAGTTGttattgtcaa
GGCCGGGCGCG / 5’-most G re-assigned to upstream TSD
RIP_Alu_chr6_119_01 / AAAAAATTAGctgggtatgg
GGCCGGGCGCG
RIP_Alu_chr6_134_01 / GCAGTGGAGGatgacccagc
GGCCGGGCGCG / 5’-most G re-assigned to upstream TSD
RIP_Alu_chr6_141_01 / AGTGGATTTTaagtttgccc
GGCCGGGCGCG
RIP_Alu_chr6_159_02 / CCATAATGACtaaactgata
GGCCGGGCACG
RIP_Alu_chr6_169_02 / AAAATCCTAGttcacacgag
GGCCGGGCGCG / 5’-most G re-assigned to upstream TSD
RIP_Alu_chr6_170_02 / TTATTGTTGGatgcaaatga
GGCCGGGCGCG / 5’-most G re-assigned to upstream TSD
RIP_Alu_chr7_024_01 / ACAGAAATTGaagggagaaa
GCCGGGCGCGG
RIP_Alu_chr7_024_02 / GAAACTTTGGtttagatact
GGCCGGGCGCG
RIP_Alu_chr7_030_01 / GTCAACGGTGcagaggttga
GGCCGGGCGCG
RIP_Alu_chr7_038_02 / CAGGGAATGGattttgctag
GGCCGGGTGCG
RIP_Alu_chr7_042_01 / AGACTTTTGGtgttgcagct
GGCCGGGCGCG
RIP_Alu_chr7_047_01 / AAAACTATTGaatggattta
GGCCGGGCGCG
RIP_Alu_chr7_051_02 / AAAATGACAGaaaatttact
GGCCGGGCGCG / 5’-most G re-assigned to upstream TSD
RIP_Alu_chr7_057_01 / AGAGATTGGGtttcgccatg
GGCCGGGCGCG
RIP_Alu_chr7_064_01 / GTGGAGGAGGatcacactag
GGCCGGGCGCG / 5’-most G re-assigned to upstream TSD
RIP_Alu_chr7_103_02 / AATTACTTTGcctaaatatt
GGCCGGGCGCG / 5’-most G re-assigned to upstream TSD
RIP_Alu_chr7_116_01 / TAGCTTCGAGcaaggaggga
GGCCGGGCGCG / 5’-most G re-assigned to upstream TSD
RIP_Alu_chr7_120_01 / TATAAAACAGaattggatgg
GGCCGGGCGCG / 5’-most G re-assigned to upstream TSD
RIP_Alu_chr7_136_01 / CTAACTTCTGctagcatata
GGCCGGGCGCG
RIP_Alu_chr7_140_02 / ATGTTTTTGGagaaattaag
GGCTGGGCGCG / 5’-most G re-assigned to upstream TSD
RIP_Alu_chr8_098_01 / TTCCTTAGTCataactttgc
GGCCGGGCGCA
RIP_Alu_chr8_107_01 / TTAGGAGATGtttaaatgtt
GGCCGGGCGCG / 5’-most G re-assigned to upstream TSD
RIP_Alu_chr8_113_01 / AATAACTGAGagggccccag
GGCCGGGCGCG
RIP_Alu_chr8_118_02 / AGTTCCATAGaatgggcatt
GGCCGGGCGCG
RIP_Alu_chr8_123_01 / ATCAAACCAGccacaacatc
GGCCGGGCGCG
RIP_Alu_chr9_004_01 / AATGGATGGAatttcaggca
GGCCGGGCGCG
RIP_Alu_chr9_013_01 / CCCTGTTTAGtgttttaatc
GGCCGGGCGCG / 5’-most G re-assigned to upstream TSD
RIP_Alu_chr9_021_01 / TGATTAATGGactttggggg
GGCCGGGCGCG
RIP_Alu_chr9_030_01 / ATTATTTTTGtctttttata
GGCCGGGCGCG / 5’-most G re-assigned to upstream TSD
RIP_Alu_chr9_035_01 / ATATGTTCAGagactccact
GGCCGGGCGCG
RIP_Alu_chr9_040_01 / CCTTTTTGGGaaaaaagtaa
GGCCGGGCGCG / 5’-most G re-assigned to upstream TSD
RIP_Alu_chr9_070_01 / AAATTACCTGtcagtctaga
GGCCGGGCGCG / 5’-most G re-assigned to upstream TSD
RIP_Alu_chr9_087_01 / TTTGAGACAGtgcctcaata
GGCCGGGCGCG / 5’-most G re-assigned to upstream TSD
RIP_Alu_chr9_116_01 / ATCATGTGAGatctaaatgt
GGCCGGGCGCG
RIP_Alu_chrX_005_01 / CACCGAAGAGaaattttaaa
GGCCGGGCGCG / 5’-most G re-assigned to upstream TSD
RIP_Alu_chrX_031_01 / CTTCTTGGCTctggttccag
GGCCGGGCGCG
RIP_Alu_chrX_093_01 / AATCCCATGGcccatctaac
GGCCGGGCGCG / 5’-most G re-assigned to upstream TSD
RIP_Alu_chrX_127_01 / ttagGAAAAGtagatgagag
GGCCGGGCGCG / 5’-most G re-assigned to upstream TSD
RIP_Alu_chrX_139_01 / AGAGATGGTGagtgggaaag
GGCCGGGCGCG / 5’-most G re-assigned to upstream TSD
RIP_Alu_chrX_148_01 / AAATGGGCAAaagccatttc
GGCCAGGCACG
RIP_Alu_chrY_016_01 / GAATTTTTAGtaaaaacaaa
GGCCGGGCGCG

aAll the entries with a microhomology (highlighted in red) can be alternatively interpreted as full-length insertions