TRAP (Tandem Repeats Analysis Program)

TRF Version 4.00

Sequence: arm_X assembled 2004-3-18 md5checksum:d304f6c7f10939bacf40e33958147342

Parameters: 2 5 7 80 10 25 1000

Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000

Length: 22224390
ACGTcount: A:0.29, C:0.21, G:0.21, T:0.29

Warning! 8514 characters in sequence are not A, C, G, or T




Found at i: i:15446450 original size:1 final size:1

Alignment explanation

Indices: 15446433--15446458 Score: 31 Period size: 1 Copynumber: 26.0 Consensus size: 1 15446423 AAATAGATTG * ** 15446433 AAAATAAAATTAAAAAAAAAAAAAAA 1 AAAAAAAAAAAAAAAAAAAAAAAAAA 15446459 TCAAATAAAA Statistics Matches: 21, Mismatches: 4, Indels: 0 0.84 0.16 0.00 Matches are distributed among these distances: 1 21 1.00 ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12 Consensus pattern (1 bp): A Left flanking sequence: Indices 15445933 -- 15446432 CATGCAACATGCAGCATGCAGCATGCAGCAGCAACTGGAATTCAGACAGCACTCGCCTGATTATG TGAAAAATGTCACAGTGAAAATAGCCACAGAGTTCGTCACATTGCCTCGAAATAAAAAAAAATAT AACCCATTTTGATTTTCAATTGAGGCGTTAAATTATCCAAAACACTGCGAACATAAATTATGCCG AGCACACTGCTCACAATCGAGCTGAAGAAAATGACGATAGAAAGCGATTGTTGTTCAATTTTTGA TTCTTTCGGTTTTTTTTTTTTTTAGTTTTCGACTTTATAACTTATCCCGGTAATTGGTCTATTAA GCCGTTGCGAATGCGGCACGTGCGCCCCCAATGGGACCCCTTCAAAGTGCTCGAATAAATACTTG AAATACATTGTACCGCCCGGCGGATTCGCCACGATAATATTATAAACCCAGAAACAAAAACAGCA ATAGCAACAACTTCAGGCGCCGTTCGGGCGATATAAAATAGATTG Right flanking sequence: Indices 15446459 -- 15446958 TCAAATAAAACAAAGCAAGCGAACTACACGAAAAAAGCATGGCACGCAAATAAATAAATGCAAAA GTCAACGAAATAAAAAAAAAAAAAAAATAATAAATAAATAAAAAGAACAAGAATGTGGCCATTAT CCGAAGTAGTGGACCAAGGAATAGGAATCCGATTTGGATTCGGAATAGGAATAGCAATGCGAATC ATCGGCGGCGACAGACATAAAAACGAAATATAAATTGCGTAGCGCTGACCTTCATTTCGGGCCAA GTAATTTTTCATAAACAATTTACGCGTTTCAGTCTATATATATATGTATATATATATATATATAT ATATATGCATATGTATGCATATATACGAGTATATATGGCGGCTATAGAGAGCGGTGTTTGGGGGC ATCACAACATCTTGTTCTGTGTGGCAGCTGCCATGGACGCTACGCATAATTATTCATGGGGCAAA CAGATATAGCGTCGATCTATATGGACGATCTAACTGGTCAGATGT Found at i:15447309 original size:4 final size:4 Alignment explanation

Indices: 15447300--15447316 Score: 34 Period size: 4 Copynumber: 4.2 Consensus size: 4 15447290 GAAACGAAAG 15447300 ATAA ATAA ATAA ATAA A 1 ATAA ATAA ATAA ATAA A 15447317 AAACATAATG Statistics Matches: 13, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 4 13 1.00 ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24 Consensus pattern (4 bp): ATAA Left flanking sequence: Indices 15446800 -- 15447299 GCATATATACGAGTATATATGGCGGCTATAGAGAGCGGTGTTTGGGGGCATCACAACATCTTGTT CTGTGTGGCAGCTGCCATGGACGCTACGCATAATTATTCATGGGGCAAACAGATATAGCGTCGAT CTATATGGACGATCTAACTGGTCAGATGTGAGCTAATCCCGATTTATGTTATCAAACAGAACGTT CGTTGTCGATGTCAAAATATTGAAACATTAGCTGCGAAATGGCGACAGCGGCACTTGGATACTGA AATATATCTAGTCAGATCTCGTAGGGATATGGATATATCTAGTGTGTGACAGCATTTGTTGGTAT CGATATGGAATGGTTATGCTATGGACTTACCGTTTCGATCGCCGGGACAGGTCTTGCAGCATTTT CCGGGCAACGAGATGGGATCATCGCATTTGGCCGGCGGGCACTCGTTTTTGATATTGCGACACTG GACGCGTGCAACGATGCGCCGCTTCTTGGGTATCTGAAACGAAAG Right flanking sequence: Indices 15447317 -- 15447816 AAACATAATGAGATGGGAGCGATATTAAAAAATAAAATGGCTAACATTATGATGCGTAAAACAAC TAATTGGCATTAGTGGTGCAGATTCCCAGGCCTGTCAGCTGCCACACTGATTTATGCCCCATTGG CCAGTGAATCTGGTCTAAATCGCAGACGTATCAAGCTAAGATCTCGACCAAAAATCGAAATTATC GTGGATATAGCAATTCGACGTGTTCGCCTTTTTTTTTATATAATTATATTTTTATGAATTCGCCA GAACACTTTGGTGGCTGCTGCTGTTTGTCTTTTTGATGTTCCCCCCATTGCTTTTCAGTTTTCTG TGTTTTTTGTGTTTTGTTTTTATTATTAATTTTTATTGGTCGCCAGTGCTGCTGCTGCTGATGAT GATGATGATGATGTAGCCGCCGTGCTTAAAGTTCAACAGCAGCAACATGTTTTAAATAATTTTAT GATGTGCTCATTTGCGACGCTTGCAGCCAACATAAATTATAATTA Found at i:15447696 original size:3 final size:3 Alignment explanation

Indices: 15447688--15447701 Score: 28 Period size: 3 Copynumber: 4.7 Consensus size: 3 15447678 TGGTCGCCAG 15447688 TGC TGC TGC TGC TG 1 TGC TGC TGC TGC TG 15447702 ATGATGATGA Statistics Matches: 11, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 3 11 1.00 ACGTcount: A:0.00, C:0.29, G:0.36, T:0.36 Consensus pattern (3 bp): TGC Left flanking sequence: Indices 15447188 -- 15447687 TTCCGGGCAACGAGATGGGATCATCGCATTTGGCCGGCGGGCACTCGTTTTTGATATTGCGACAC TGGACGCGTGCAACGATGCGCCGCTTCTTGGGTATCTGAAACGAAAGATAAATAAATAAATAAAA AACATAATGAGATGGGAGCGATATTAAAAAATAAAATGGCTAACATTATGATGCGTAAAACAACT AATTGGCATTAGTGGTGCAGATTCCCAGGCCTGTCAGCTGCCACACTGATTTATGCCCCATTGGC CAGTGAATCTGGTCTAAATCGCAGACGTATCAAGCTAAGATCTCGACCAAAAATCGAAATTATCG TGGATATAGCAATTCGACGTGTTCGCCTTTTTTTTTATATAATTATATTTTTATGAATTCGCCAG AACACTTTGGTGGCTGCTGCTGTTTGTCTTTTTGATGTTCCCCCCATTGCTTTTCAGTTTTCTGT GTTTTTTGTGTTTTGTTTTTATTATTAATTTTTATTGGTCGCCAG Right flanking sequence: Indices 15447702 -- 15448201 ATGATGATGATGATGATGTAGCCGCCGTGCTTAAAGTTCAACAGCAGCAACATGTTTTAAATAAT TTTATGATGTGCTCATTTGCGACGCTTGCAGCCAACATAAATTATAATTAATTAATTTCAAAGCT GACTTTTATGCAATGCACATTAAAAGTTAACCAAAGACGAAACAGCAGCATTCACACACATTTCG ATTGCCAGTATATGCGCACTGGAGAAATCGCAGCTTGCGAGCAGACCATTTATCCACATAGTACA TAAATGCATATATAATATAAATATATATATTTAGTAGTATATATATATATATATATATATATCTG GCCCGTCTGGTCCATCGCAGACTAGCAACAACAACTCACGCCCGCCCGGTGGCGTCAATTAATTT TCGTCTCCCGACCACGAATACGCATACGCATCTGTATCTGTATCTGTATCTGTAAATGTATCTGT ATCTGTATCTATATATCTATATCTATATGGGACCTCATGTTTTTT Found at i:15447706 original size:3 final size:3 Alignment explanation

Indices: 15447700--15447719 Score: 40 Period size: 3 Copynumber: 6.7 Consensus size: 3 15447690 CTGCTGCTGC 15447700 TGA TGA TGA TGA TGA TGA TG 1 TGA TGA TGA TGA TGA TGA TG 15447720 TAGCCGCCGT Statistics Matches: 17, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 3 17 1.00 ACGTcount: A:0.30, C:0.00, G:0.35, T:0.35 Consensus pattern (3 bp): TGA Left flanking sequence: Indices 15447200 -- 15447699 AGATGGGATCATCGCATTTGGCCGGCGGGCACTCGTTTTTGATATTGCGACACTGGACGCGTGCA ACGATGCGCCGCTTCTTGGGTATCTGAAACGAAAGATAAATAAATAAATAAAAAACATAATGAGA TGGGAGCGATATTAAAAAATAAAATGGCTAACATTATGATGCGTAAAACAACTAATTGGCATTAG TGGTGCAGATTCCCAGGCCTGTCAGCTGCCACACTGATTTATGCCCCATTGGCCAGTGAATCTGG TCTAAATCGCAGACGTATCAAGCTAAGATCTCGACCAAAAATCGAAATTATCGTGGATATAGCAA TTCGACGTGTTCGCCTTTTTTTTTATATAATTATATTTTTATGAATTCGCCAGAACACTTTGGTG GCTGCTGCTGTTTGTCTTTTTGATGTTCCCCCCATTGCTTTTCAGTTTTCTGTGTTTTTTGTGTT TTGTTTTTATTATTAATTTTTATTGGTCGCCAGTGCTGCTGCTGC Right flanking sequence: Indices 15447720 -- 15448219 TAGCCGCCGTGCTTAAAGTTCAACAGCAGCAACATGTTTTAAATAATTTTATGATGTGCTCATTT GCGACGCTTGCAGCCAACATAAATTATAATTAATTAATTTCAAAGCTGACTTTTATGCAATGCAC ATTAAAAGTTAACCAAAGACGAAACAGCAGCATTCACACACATTTCGATTGCCAGTATATGCGCA CTGGAGAAATCGCAGCTTGCGAGCAGACCATTTATCCACATAGTACATAAATGCATATATAATAT AAATATATATATTTAGTAGTATATATATATATATATATATATATCTGGCCCGTCTGGTCCATCGC AGACTAGCAACAACAACTCACGCCCGCCCGGTGGCGTCAATTAATTTTCGTCTCCCGACCACGAA TACGCATACGCATCTGTATCTGTATCTGTATCTGTAAATGTATCTGTATCTGTATCTATATATCT ATATCTATATGGGACCTCATGTTTTTTACCCGGCGAGGACACGAG Found at i:15447820 original size:4 final size:4 Alignment explanation

Indices: 15447811--15447823 Score: 26 Period size: 4 Copynumber: 3.2 Consensus size: 4 15447801 ACATAAATTA 15447811 TAAT TAAT TAAT T 1 TAAT TAAT TAAT T 15447824 TCAAAGCTGA Statistics Matches: 9, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 4 9 1.00 ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54 Consensus pattern (4 bp): TAAT Left flanking sequence: Indices 15447311 -- 15447810 AATAAAAAACATAATGAGATGGGAGCGATATTAAAAAATAAAATGGCTAACATTATGATGCGTAA AACAACTAATTGGCATTAGTGGTGCAGATTCCCAGGCCTGTCAGCTGCCACACTGATTTATGCCC CATTGGCCAGTGAATCTGGTCTAAATCGCAGACGTATCAAGCTAAGATCTCGACCAAAAATCGAA ATTATCGTGGATATAGCAATTCGACGTGTTCGCCTTTTTTTTTATATAATTATATTTTTATGAAT TCGCCAGAACACTTTGGTGGCTGCTGCTGTTTGTCTTTTTGATGTTCCCCCCATTGCTTTTCAGT TTTCTGTGTTTTTTGTGTTTTGTTTTTATTATTAATTTTTATTGGTCGCCAGTGCTGCTGCTGCT GATGATGATGATGATGATGTAGCCGCCGTGCTTAAAGTTCAACAGCAGCAACATGTTTTAAATAA TTTTATGATGTGCTCATTTGCGACGCTTGCAGCCAACATAAATTA Right flanking sequence: Indices 15447824 -- 15448323 TCAAAGCTGACTTTTATGCAATGCACATTAAAAGTTAACCAAAGACGAAACAGCAGCATTCACAC ACATTTCGATTGCCAGTATATGCGCACTGGAGAAATCGCAGCTTGCGAGCAGACCATTTATCCAC ATAGTACATAAATGCATATATAATATAAATATATATATTTAGTAGTATATATATATATATATATA TATATCTGGCCCGTCTGGTCCATCGCAGACTAGCAACAACAACTCACGCCCGCCCGGTGGCGTCA ATTAATTTTCGTCTCCCGACCACGAATACGCATACGCATCTGTATCTGTATCTGTATCTGTAAAT GTATCTGTATCTGTATCTATATATCTATATCTATATGGGACCTCATGTTTTTTACCCGGCGAGGA CACGAGTGTGACATTTTTATGTGTCGCTTGGGAAAATTGCCCAGTATTGCCCTCGTTCCCCCCTT TTCGTTATGTTTTTTTTTGCTTTTGCTGCTTTTTTTTTCTTGTTG Found at i:15447987 original size:2 final size:2 Alignment explanation

Indices: 15447969--15448023 Score: 71 Period size: 2 Copynumber: 27.0 Consensus size: 2 15447959 ACATAAATGC * * 15447969 AT AT AT A- AT AT AA AT AT AT AT AT TT AGT AGT AT AT AT AT AT AT 1 AT AT AT AT AT AT AT AT AT AT AT AT AT A-T A-T AT AT AT AT AT AT 15448012 AT AT AT AT AT AT 1 AT AT AT AT AT AT 15448024 CTGGCCCGTC Statistics Matches: 47, Mismatches: 4, Indels: 4 0.85 0.07 0.07 Matches are distributed among these distances: 1 1 0.02 2 41 0.87 3 5 0.11 ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47 Consensus pattern (2 bp): AT Left flanking sequence: Indices 15447469 -- 15447968 CAGACGTATCAAGCTAAGATCTCGACCAAAAATCGAAATTATCGTGGATATAGCAATTCGACGTG TTCGCCTTTTTTTTTATATAATTATATTTTTATGAATTCGCCAGAACACTTTGGTGGCTGCTGCT GTTTGTCTTTTTGATGTTCCCCCCATTGCTTTTCAGTTTTCTGTGTTTTTTGTGTTTTGTTTTTA TTATTAATTTTTATTGGTCGCCAGTGCTGCTGCTGCTGATGATGATGATGATGATGTAGCCGCCG TGCTTAAAGTTCAACAGCAGCAACATGTTTTAAATAATTTTATGATGTGCTCATTTGCGACGCTT GCAGCCAACATAAATTATAATTAATTAATTTCAAAGCTGACTTTTATGCAATGCACATTAAAAGT TAACCAAAGACGAAACAGCAGCATTCACACACATTTCGATTGCCAGTATATGCGCACTGGAGAAA TCGCAGCTTGCGAGCAGACCATTTATCCACATAGTACATAAATGC Right flanking sequence: Indices 15448024 -- 15448523 CTGGCCCGTCTGGTCCATCGCAGACTAGCAACAACAACTCACGCCCGCCCGGTGGCGTCAATTAA TTTTCGTCTCCCGACCACGAATACGCATACGCATCTGTATCTGTATCTGTATCTGTAAATGTATC TGTATCTGTATCTATATATCTATATCTATATGGGACCTCATGTTTTTTACCCGGCGAGGACACGA GTGTGACATTTTTATGTGTCGCTTGGGAAAATTGCCCAGTATTGCCCTCGTTCCCCCCTTTTCGT TATGTTTTTTTTTGCTTTTGCTGCTTTTTTTTTCTTGTTGGTAGTGCAACATTTTGTTCGGCATT TTTGCGTAATTCAATCGAACATCCACGAAAATGCTGAATTTGTTTTTCAATTTGGCAAGGTCCGT TGAATCCGTAGAATATTTGGCTGCGATTCGTAACAGATCGCGTAAAGAGCTCTAAAATCGATATT AATCATGCGTGGAAATGCCATAAATTAGGCGAGCAACCCAATCAT Found at i:15448120 original size:6 final size:6 Alignment explanation

Indices: 15448105--15448122 Score: 29 Period size: 6 Copynumber: 3.0 Consensus size: 6 15448095 TCTCCCGACC * 15448105 ACGAAT ACGCAT ACGCAT 1 ACGCAT ACGCAT ACGCAT 15448123 CTGTATCTGT Statistics Matches: 11, Mismatches: 1, Indels: 0 0.92 0.08 0.00 Matches are distributed among these distances: 6 11 1.00 ACGTcount: A:0.39, C:0.28, G:0.17, T:0.17 Consensus pattern (6 bp): ACGCAT Left flanking sequence: Indices 15447605 -- 15448104 CTTTTTGATGTTCCCCCCATTGCTTTTCAGTTTTCTGTGTTTTTTGTGTTTTGTTTTTATTATTA ATTTTTATTGGTCGCCAGTGCTGCTGCTGCTGATGATGATGATGATGATGTAGCCGCCGTGCTTA AAGTTCAACAGCAGCAACATGTTTTAAATAATTTTATGATGTGCTCATTTGCGACGCTTGCAGCC AACATAAATTATAATTAATTAATTTCAAAGCTGACTTTTATGCAATGCACATTAAAAGTTAACCA AAGACGAAACAGCAGCATTCACACACATTTCGATTGCCAGTATATGCGCACTGGAGAAATCGCAG CTTGCGAGCAGACCATTTATCCACATAGTACATAAATGCATATATAATATAAATATATATATTTA GTAGTATATATATATATATATATATATATCTGGCCCGTCTGGTCCATCGCAGACTAGCAACAACA ACTCACGCCCGCCCGGTGGCGTCAATTAATTTTCGTCTCCCGACC Right flanking sequence: Indices 15448123 -- 15448622 CTGTATCTGTATCTGTATCTGTAAATGTATCTGTATCTGTATCTATATATCTATATCTATATGGG ACCTCATGTTTTTTACCCGGCGAGGACACGAGTGTGACATTTTTATGTGTCGCTTGGGAAAATTG CCCAGTATTGCCCTCGTTCCCCCCTTTTCGTTATGTTTTTTTTTGCTTTTGCTGCTTTTTTTTTC TTGTTGGTAGTGCAACATTTTGTTCGGCATTTTTGCGTAATTCAATCGAACATCCACGAAAATGC TGAATTTGTTTTTCAATTTGGCAAGGTCCGTTGAATCCGTAGAATATTTGGCTGCGATTCGTAAC AGATCGCGTAAAGAGCTCTAAAATCGATATTAATCATGCGTGGAAATGCCATAAATTAGGCGAGC AACCCAATCATTTTCATTTCGCATTTTTAGTGCCACTTTTCCTTGCGATTTTCCGCAGCTTGTAG CGAATGTCGACGATCATTAGTCAATTTTCTCAGCAAGATCACACG i:15448184 original size:6 final size:6 Alignment explanation

Indices: 15448121--15448170 Score: 79 Period size: 6 Copynumber: 8.3 Consensus size: 6 15448111 ACGCATACGC ** * 15448121 ATCTGT ATCTGT ATCTGT ATCTGT AAATGT ATCTGT ATCTGT ATCTAT 1 ATCTGT ATCTGT ATCTGT ATCTGT ATCTGT ATCTGT ATCTGT ATCTGT 15448169 AT 1 AT 15448171 ATCTATATCT Statistics Matches: 39, Mismatches: 5, Indels: 0 0.89 0.11 0.00 Matches are distributed among these distances: 6 39 1.00 ACGTcount: A:0.24, C:0.14, G:0.14, T:0.48 Consensus pattern (6 bp): ATCTGT Left flanking sequence: Indices 15447621 -- 15448120 CCATTGCTTTTCAGTTTTCTGTGTTTTTTGTGTTTTGTTTTTATTATTAATTTTTATTGGTCGCC AGTGCTGCTGCTGCTGATGATGATGATGATGATGTAGCCGCCGTGCTTAAAGTTCAACAGCAGCA ACATGTTTTAAATAATTTTATGATGTGCTCATTTGCGACGCTTGCAGCCAACATAAATTATAATT AATTAATTTCAAAGCTGACTTTTATGCAATGCACATTAAAAGTTAACCAAAGACGAAACAGCAGC ATTCACACACATTTCGATTGCCAGTATATGCGCACTGGAGAAATCGCAGCTTGCGAGCAGACCAT TTATCCACATAGTACATAAATGCATATATAATATAAATATATATATTTAGTAGTATATATATATA TATATATATATATCTGGCCCGTCTGGTCCATCGCAGACTAGCAACAACAACTCACGCCCGCCCGG TGGCGTCAATTAATTTTCGTCTCCCGACCACGAATACGCATACGC Right flanking sequence: Indices 15448171 -- 15448670 ATCTATATCTATATGGGACCTCATGTTTTTTACCCGGCGAGGACACGAGTGTGACATTTTTATGT GTCGCTTGGGAAAATTGCCCAGTATTGCCCTCGTTCCCCCCTTTTCGTTATGTTTTTTTTTGCTT TTGCTGCTTTTTTTTTCTTGTTGGTAGTGCAACATTTTGTTCGGCATTTTTGCGTAATTCAATCG AACATCCACGAAAATGCTGAATTTGTTTTTCAATTTGGCAAGGTCCGTTGAATCCGTAGAATATT TGGCTGCGATTCGTAACAGATCGCGTAAAGAGCTCTAAAATCGATATTAATCATGCGTGGAAATG CCATAAATTAGGCGAGCAACCCAATCATTTTCATTTCGCATTTTTAGTGCCACTTTTCCTTGCGA TTTTCCGCAGCTTGTAGCGAATGTCGACGATCATTAGTCAATTTTCTCAGCAAGATCACACGGAA TTTCTTGGATTCGCGCATTTCAATTGGCATGTTTTAAGGATTACT Found at i:15448304 original size:6 final size:6 Alignment explanation

Indices: 15448293--15448305 Score: 26 Period size: 6 Copynumber: 2.2 Consensus size: 6 15448283 TTATGTTTTT 15448293 TTTTGC TTTTGC T 1 TTTTGC TTTTGC T 15448306 GCTTTTTTTT Statistics Matches: 7, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 6 7 1.00 ACGTcount: A:0.00, C:0.15, G:0.15, T:0.69 Consensus pattern (6 bp): TTTTGC Left flanking sequence: Indices 15447793 -- 15448292 TGCAGCCAACATAAATTATAATTAATTAATTTCAAAGCTGACTTTTATGCAATGCACATTAAAAG TTAACCAAAGACGAAACAGCAGCATTCACACACATTTCGATTGCCAGTATATGCGCACTGGAGAA ATCGCAGCTTGCGAGCAGACCATTTATCCACATAGTACATAAATGCATATATAATATAAATATAT ATATTTAGTAGTATATATATATATATATATATATATCTGGCCCGTCTGGTCCATCGCAGACTAGC AACAACAACTCACGCCCGCCCGGTGGCGTCAATTAATTTTCGTCTCCCGACCACGAATACGCATA CGCATCTGTATCTGTATCTGTATCTGTAAATGTATCTGTATCTGTATCTATATATCTATATCTAT ATGGGACCTCATGTTTTTTACCCGGCGAGGACACGAGTGTGACATTTTTATGTGTCGCTTGGGAA AATTGCCCAGTATTGCCCTCGTTCCCCCCTTTTCGTTATGTTTTT Right flanking sequence: Indices 15448306 -- 15448805 GCTTTTTTTTTCTTGTTGGTAGTGCAACATTTTGTTCGGCATTTTTGCGTAATTCAATCGAACAT CCACGAAAATGCTGAATTTGTTTTTCAATTTGGCAAGGTCCGTTGAATCCGTAGAATATTTGGCT GCGATTCGTAACAGATCGCGTAAAGAGCTCTAAAATCGATATTAATCATGCGTGGAAATGCCATA AATTAGGCGAGCAACCCAATCATTTTCATTTCGCATTTTTAGTGCCACTTTTCCTTGCGATTTTC CGCAGCTTGTAGCGAATGTCGACGATCATTAGTCAATTTTCTCAGCAAGATCACACGGAATTTCT TGGATTCGCGCATTTCAATTGGCATGTTTTAAGGATTACTTAATAGGCGCACTAAATATAAAGAA TATATGCTACAATAATATTTAAGAAAGTCTTCACTTACCGCCACACATTCACACTTGATGCAGTA CATAACTCCGAAGGGTGGACCCAAATCCGCATACCAGGTGGACCC Found at i:15448998 original size:6 final size:6 Alignment explanation

Indices: 15448987--15449006 Score: 40 Period size: 6 Copynumber: 3.3 Consensus size: 6 15448977 CTGGCGCCAG 15448987 TGCAAT TGCAAT TGCAAT TG 1 TGCAAT TGCAAT TGCAAT TG 15449007 ACTCTATATA Statistics Matches: 14, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 6 14 1.00 ACGTcount: A:0.30, C:0.15, G:0.20, T:0.35 Consensus pattern (6 bp): TGCAAT Left flanking sequence: Indices 15448487 -- 15448986 GTGGAAATGCCATAAATTAGGCGAGCAACCCAATCATTTTCATTTCGCATTTTTAGTGCCACTTT TCCTTGCGATTTTCCGCAGCTTGTAGCGAATGTCGACGATCATTAGTCAATTTTCTCAGCAAGAT CACACGGAATTTCTTGGATTCGCGCATTTCAATTGGCATGTTTTAAGGATTACTTAATAGGCGCA CTAAATATAAAGAATATATGCTACAATAATATTTAAGAAAGTCTTCACTTACCGCCACACATTCA CACTTGATGCAGTACATAACTCCGAAGGGTGGACCCAAATCCGCATACCAGGTGGACCCCAATTC GCGCAAAACTTTGCCAAACTGGCATTCGGTGACTGAAAGTAGATGGAAAAAACAAAGCAAAAAAT AAATATCTCATTCTGTTCGGTTTCCTCAATTGCCATTTAAGATCTATGGGATTGTACGTATCTAT ATGTTTACTATTATTTTTATTTTTTTTTCAGGTTGCTGGCGCCAG Right flanking sequence: Indices 15449007 -- 15449506 ACTCTATATAGATAGTATACATATATGTACATATATGAACAGCCGATGCCTATTTATCATCAGTC CGGCGATGATGCAAAGCGGGTCTAATAATTATAAAATTCTAATGACAGACGCCCACAAAGAAGAT GAAATCCAATGGGTGGATTGCCAATCGATCAGCAACTAATTAACTTCAATCGAGCTCCTCGCAGC TGGAAGCCCATCCTCGTACATACATTTGGTTTTCGGTTCAGGTTTTTCCATGCCGCTTCCTTGCG TTACCCAGATACTCAGATACTAAGATACTCAGATACAAAGATCCAATTCGGGTGGGCAGACCGAT GCAATCAGAATTGCAGAACGTTTTCAGCCAAAAGCGGCGAAACGTACGTACGAATTGAAAAACAA AAAAAAAAAACTGGCGCCACATTCGCTGAGAGGCGTTGAGTCGCTTCCGGCAGCGTTTTCAATTA CAAATGCAAGCGAATACACTGAGAAATATTTCGAGGAGTTTTCTA Found at i:15449399 original size:1 final size:1 Alignment explanation

Indices: 15449389--15449406 Score: 29 Period size: 1 Copynumber: 18.0 Consensus size: 1 15449379 GTACGAATTG * 15449389 AAAAACAAAAAAAAAAAA 1 AAAAAAAAAAAAAAAAAA 15449407 CTGGCGCCAC Statistics Matches: 15, Mismatches: 2, Indels: 0 0.88 0.12 0.00 Matches are distributed among these distances: 1 15 1.00 ACGTcount: A:0.94, C:0.06, G:0.00, T:0.00 Consensus pattern (1 bp): A Left flanking sequence: Indices 15448889 -- 15449388 CTGTTCGGTTTCCTCAATTGCCATTTAAGATCTATGGGATTGTACGTATCTATATGTTTACTATT ATTTTTATTTTTTTTTCAGGTTGCTGGCGCCAGTGCAATTGCAATTGCAATTGACTCTATATAGA TAGTATACATATATGTACATATATGAACAGCCGATGCCTATTTATCATCAGTCCGGCGATGATGC AAAGCGGGTCTAATAATTATAAAATTCTAATGACAGACGCCCACAAAGAAGATGAAATCCAATGG GTGGATTGCCAATCGATCAGCAACTAATTAACTTCAATCGAGCTCCTCGCAGCTGGAAGCCCATC CTCGTACATACATTTGGTTTTCGGTTCAGGTTTTTCCATGCCGCTTCCTTGCGTTACCCAGATAC TCAGATACTAAGATACTCAGATACAAAGATCCAATTCGGGTGGGCAGACCGATGCAATCAGAATT GCAGAACGTTTTCAGCCAAAAGCGGCGAAACGTACGTACGAATTG Right flanking sequence: Indices 15449407 -- 15449906 CTGGCGCCACATTCGCTGAGAGGCGTTGAGTCGCTTCCGGCAGCGTTTTCAATTACAAATGCAAG CGAATACACTGAGAAATATTTCGAGGAGTTTTCTATGGGAAAAAAAGCTAAGATATAACTAGCTA AGCTAAGAGATAACTAGTTTTATATACTATGCTTTCTTTCTTTAAGGAAATTATCATTTAAACCA GTTTAATTATAAAACTGACATCGAATTAATTGCCGTGTAGTTAAGTGGATTAAGAAGAAGCGACG TCTCTCTCTCTCTCTGGGGCGCCAACAAGTGTCAAATTGTGGGATTAGATCGAAGAAATAGTGAA ATATACGAACACGAGGAGCATCATCAGCATCCATCCACTTTGATAGTCTCAATTTCATTAGCAAC ATTTTTGGGATTACGTTTTTTTTTTTGTTATTTTTTGTTAATTGGCTGCGTGCGAGCGGCAAAAC TTTGCACAAAATGCCACAAATCGTATGCAAATCGAAAACGCGACG Found at i:15449674 original size:2 final size:2 Alignment explanation

Indices: 15449667--15449681 Score: 30 Period size: 2 Copynumber: 7.5 Consensus size: 2 15449657 AGAAGCGACG 15449667 TC TC TC TC TC TC TC T 1 TC TC TC TC TC TC TC T 15449682 GGGGCGCCAA Statistics Matches: 13, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 13 1.00 ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53 Consensus pattern (2 bp): TC Left flanking sequence: Indices 15449167 -- 15449666 AGCAACTAATTAACTTCAATCGAGCTCCTCGCAGCTGGAAGCCCATCCTCGTACATACATTTGGT TTTCGGTTCAGGTTTTTCCATGCCGCTTCCTTGCGTTACCCAGATACTCAGATACTAAGATACTC AGATACAAAGATCCAATTCGGGTGGGCAGACCGATGCAATCAGAATTGCAGAACGTTTTCAGCCA AAAGCGGCGAAACGTACGTACGAATTGAAAAACAAAAAAAAAAAACTGGCGCCACATTCGCTGAG AGGCGTTGAGTCGCTTCCGGCAGCGTTTTCAATTACAAATGCAAGCGAATACACTGAGAAATATT TCGAGGAGTTTTCTATGGGAAAAAAAGCTAAGATATAACTAGCTAAGCTAAGAGATAACTAGTTT TATATACTATGCTTTCTTTCTTTAAGGAAATTATCATTTAAACCAGTTTAATTATAAAACTGACA TCGAATTAATTGCCGTGTAGTTAAGTGGATTAAGAAGAAGCGACG Right flanking sequence: Indices 15449682 -- 15450181 GGGGCGCCAACAAGTGTCAAATTGTGGGATTAGATCGAAGAAATAGTGAAATATACGAACACGAG GAGCATCATCAGCATCCATCCACTTTGATAGTCTCAATTTCATTAGCAACATTTTTGGGATTACG TTTTTTTTTTTGTTATTTTTTGTTAATTGGCTGCGTGCGAGCGGCAAAACTTTGCACAAAATGCC ACAAATCGTATGCAAATCGAAAACGCGACGCGTTATTTTATTAATATATGTACCTTCGCCGGTGT CGCGGTAAAATTATGCTAAAACTTTTGGCGCCACTCATAAAAAATGTAAACGAAACAAAAGGAAA AAGCCGCCGATAAAAAAAAACACGGCACAAACGAATCAAAATCGCTAACTTTCGTAGACGACGCA TGGCAATGAGTTTTTGGTGTGTGGGGAAAATTAATTTGATTAAAACAAAAGGTCGCGACAGAAAC GCGCCAAAATCGCGCTGAAAACGCGCCGAAAACGCTGACATTTCA Found at i:15449816 original size:1 final size:1 Alignment explanation

Indices: 15449812--15449832 Score: 28 Period size: 1 Copynumber: 21.0 Consensus size: 1 15449802 TGGGATTACG * * 15449812 TTTTTTTTTTTGTTATTTTTT 1 TTTTTTTTTTTTTTTTTTTTT 15449833 GTTAATTGGC Statistics Matches: 16, Mismatches: 4, Indels: 0 0.80 0.20 0.00 Matches are distributed among these distances: 1 16 1.00 ACGTcount: A:0.05, C:0.00, G:0.05, T:0.90 Consensus pattern (1 bp): T Left flanking sequence: Indices 15449312 -- 15449811 ATTCGGGTGGGCAGACCGATGCAATCAGAATTGCAGAACGTTTTCAGCCAAAAGCGGCGAAACGT ACGTACGAATTGAAAAACAAAAAAAAAAAACTGGCGCCACATTCGCTGAGAGGCGTTGAGTCGCT TCCGGCAGCGTTTTCAATTACAAATGCAAGCGAATACACTGAGAAATATTTCGAGGAGTTTTCTA TGGGAAAAAAAGCTAAGATATAACTAGCTAAGCTAAGAGATAACTAGTTTTATATACTATGCTTT CTTTCTTTAAGGAAATTATCATTTAAACCAGTTTAATTATAAAACTGACATCGAATTAATTGCCG TGTAGTTAAGTGGATTAAGAAGAAGCGACGTCTCTCTCTCTCTCTGGGGCGCCAACAAGTGTCAA ATTGTGGGATTAGATCGAAGAAATAGTGAAATATACGAACACGAGGAGCATCATCAGCATCCATC CACTTTGATAGTCTCAATTTCATTAGCAACATTTTTGGGATTACG Right flanking sequence: Indices 15449833 -- 15450332 GTTAATTGGCTGCGTGCGAGCGGCAAAACTTTGCACAAAATGCCACAAATCGTATGCAAATCGAA AACGCGACGCGTTATTTTATTAATATATGTACCTTCGCCGGTGTCGCGGTAAAATTATGCTAAAA CTTTTGGCGCCACTCATAAAAAATGTAAACGAAACAAAAGGAAAAAGCCGCCGATAAAAAAAAAC ACGGCACAAACGAATCAAAATCGCTAACTTTCGTAGACGACGCATGGCAATGAGTTTTTGGTGTG TGGGGAAAATTAATTTGATTAAAACAAAAGGTCGCGACAGAAACGCGCCAAAATCGCGCTGAAAA CGCGCCGAAAACGCTGACATTTCAAAAATGTATGTTACAAACTTCGCAAGTTAATAGGTTCTTTT TTTATGTTTCGCAAGTGCGTAGCATACGAAATAGAACATTTTTAAAGTATATCTATATCAATCAA AGTAAGTAGCGAGTTGTTTTTTTTTTTTTTTTTTCAGTGTGTATC Found at i:15450310 original size:1 final size:1 Alignment explanation

Indices: 15450304--15450321 Score: 36 Period size: 1 Copynumber: 18.0 Consensus size: 1 15450294 TAGCGAGTTG 15450304 TTTTTTTTTTTTTTTTTT 1 TTTTTTTTTTTTTTTTTT 15450322 CAGTGTGTAT Statistics Matches: 17, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 1 17 1.00 ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00 Consensus pattern (1 bp): T Left flanking sequence: Indices 15449804 -- 15450303 GGATTACGTTTTTTTTTTTGTTATTTTTTGTTAATTGGCTGCGTGCGAGCGGCAAAACTTTGCAC AAAATGCCACAAATCGTATGCAAATCGAAAACGCGACGCGTTATTTTATTAATATATGTACCTTC GCCGGTGTCGCGGTAAAATTATGCTAAAACTTTTGGCGCCACTCATAAAAAATGTAAACGAAACA AAAGGAAAAAGCCGCCGATAAAAAAAAACACGGCACAAACGAATCAAAATCGCTAACTTTCGTAG ACGACGCATGGCAATGAGTTTTTGGTGTGTGGGGAAAATTAATTTGATTAAAACAAAAGGTCGCG ACAGAAACGCGCCAAAATCGCGCTGAAAACGCGCCGAAAACGCTGACATTTCAAAAATGTATGTT ACAAACTTCGCAAGTTAATAGGTTCTTTTTTTATGTTTCGCAAGTGCGTAGCATACGAAATAGAA CATTTTTAAAGTATATCTATATCAATCAAAGTAAGTAGCGAGTTG Right flanking sequence: Indices 15450322 -- 15450821 CAGTGTGTATCCATCCATCCATTCACCGCCGGTTGACACCTGTGGTTCCCCCGCGGTTATCGCGC ACATCATTCACAAACGATTCCATATCTCTGCCATATGCTGTTGCCCTGATAATCGGCCAGCTCCT TCGGCTTTTTCACATTTACTCGCCAAATGGCTGTGGCTCAAGAGTAGTAAAAACTAAATAGACAG CGAAAAAAAAGGGGGGAGCGACCATAAACTAATTAGCCATATTACACGTGATAGCTGGGGTATCT TTTTCACTTTTATTTTTGTTTTTGCTGCACCACCAGAACCGCCTGAACCGCCTGAACCACCAGAA CCGCCTGAACCGCCTGAACCACCTGAACCACTGAGAGTAGCCAAGAGAAGAAGCAAACCGAAACC GAAAAGCAGCGAATAACCACCGAATCTGGTGACGGCGCCATGGCGTATACGTGATAAGTGGCGCT AACGACGCGCGACGTTTATCAATTTTTTGTTGTTGCCCCCTTGTC Found at i:15450337 original size:4 final size:4 Alignment explanation

Indices: 15450330--15450343 Score: 28 Period size: 4 Copynumber: 3.5 Consensus size: 4 15450320 TTCAGTGTGT 15450330 ATCC ATCC ATCC AT 1 ATCC ATCC ATCC AT 15450344 TCACCGCCGG Statistics Matches: 10, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 4 10 1.00 ACGTcount: A:0.29, C:0.43, G:0.00, T:0.29 Consensus pattern (4 bp): ATCC Left flanking sequence: Indices 15449830 -- 15450329 TTTGTTAATTGGCTGCGTGCGAGCGGCAAAACTTTGCACAAAATGCCACAAATCGTATGCAAATC GAAAACGCGACGCGTTATTTTATTAATATATGTACCTTCGCCGGTGTCGCGGTAAAATTATGCTA AAACTTTTGGCGCCACTCATAAAAAATGTAAACGAAACAAAAGGAAAAAGCCGCCGATAAAAAAA AACACGGCACAAACGAATCAAAATCGCTAACTTTCGTAGACGACGCATGGCAATGAGTTTTTGGT GTGTGGGGAAAATTAATTTGATTAAAACAAAAGGTCGCGACAGAAACGCGCCAAAATCGCGCTGA AAACGCGCCGAAAACGCTGACATTTCAAAAATGTATGTTACAAACTTCGCAAGTTAATAGGTTCT TTTTTTATGTTTCGCAAGTGCGTAGCATACGAAATAGAACATTTTTAAAGTATATCTATATCAAT CAAAGTAAGTAGCGAGTTGTTTTTTTTTTTTTTTTTTCAGTGTGT Right flanking sequence: Indices 15450344 -- 15450843 TCACCGCCGGTTGACACCTGTGGTTCCCCCGCGGTTATCGCGCACATCATTCACAAACGATTCCA TATCTCTGCCATATGCTGTTGCCCTGATAATCGGCCAGCTCCTTCGGCTTTTTCACATTTACTCG CCAAATGGCTGTGGCTCAAGAGTAGTAAAAACTAAATAGACAGCGAAAAAAAAGGGGGGAGCGAC CATAAACTAATTAGCCATATTACACGTGATAGCTGGGGTATCTTTTTCACTTTTATTTTTGTTTT TGCTGCACCACCAGAACCGCCTGAACCGCCTGAACCACCAGAACCGCCTGAACCGCCTGAACCAC CTGAACCACTGAGAGTAGCCAAGAGAAGAAGCAAACCGAAACCGAAAAGCAGCGAATAACCACCG AATCTGGTGACGGCGCCATGGCGTATACGTGATAAGTGGCGCTAACGACGCGCGACGTTTATCAA TTTTTTGTTGTTGCCCCCTTGTCATTGGCGCCAGTTTTATTTGCG Found at i:15450603 original size:6 final size:6 Alignment explanation

Indices: 15450589--15450605 Score: 27 Period size: 6 Copynumber: 2.8 Consensus size: 6 15450579 TCTTTTTCAC * 15450589 TTTTAT TTTTGT TTTTG 1 TTTTGT TTTTGT TTTTG 15450606 CTGCACCACC Statistics Matches: 10, Mismatches: 1, Indels: 0 0.91 0.09 0.00 Matches are distributed among these distances: 6 10 1.00 ACGTcount: A:0.06, C:0.00, G:0.12, T:0.82 Consensus pattern (6 bp): TTTTGT Left flanking sequence: Indices 15450089 -- 15450588 TGTGTGGGGAAAATTAATTTGATTAAAACAAAAGGTCGCGACAGAAACGCGCCAAAATCGCGCTG AAAACGCGCCGAAAACGCTGACATTTCAAAAATGTATGTTACAAACTTCGCAAGTTAATAGGTTC TTTTTTTATGTTTCGCAAGTGCGTAGCATACGAAATAGAACATTTTTAAAGTATATCTATATCAA TCAAAGTAAGTAGCGAGTTGTTTTTTTTTTTTTTTTTTCAGTGTGTATCCATCCATCCATTCACC GCCGGTTGACACCTGTGGTTCCCCCGCGGTTATCGCGCACATCATTCACAAACGATTCCATATCT CTGCCATATGCTGTTGCCCTGATAATCGGCCAGCTCCTTCGGCTTTTTCACATTTACTCGCCAAA TGGCTGTGGCTCAAGAGTAGTAAAAACTAAATAGACAGCGAAAAAAAAGGGGGGAGCGACCATAA ACTAATTAGCCATATTACACGTGATAGCTGGGGTATCTTTTTCAC Right flanking sequence: Indices 15450606 -- 15451105 CTGCACCACCAGAACCGCCTGAACCGCCTGAACCACCAGAACCGCCTGAACCGCCTGAACCACCT GAACCACTGAGAGTAGCCAAGAGAAGAAGCAAACCGAAACCGAAAAGCAGCGAATAACCACCGAA TCTGGTGACGGCGCCATGGCGTATACGTGATAAGTGGCGCTAACGACGCGCGACGTTTATCAATT TTTTGTTGTTGCCCCCTTGTCATTGGCGCCAGTTTTATTTGCGTGCGAAACAATTTAAATACAAC AAGAACGCATCAGCGAAACAATGAATATAAGCAACGAGCGCAATAGATTTATAAGTATAAGTATA TAGAAGGCGATAATGCCCAGGCAAATTCATTAATCGAACTGCAAGTCTTGATCTCGCCCTGTCAC ACATTTCCCAGAAAGTGTCTCGCATAACAATCAAATTAATTAAATAGAAATTTCATTTAATTGTG GACAAACAAATTCGAATTTGAGCTACCCGCGATATGATAAGTTGC Found at i:15450712 original size:6 final size:6 Alignment explanation

Indices: 15450701--15450715 Score: 30 Period size: 6 Copynumber: 2.5 Consensus size: 6 15450691 GAGAAGAAGC 15450701 AAACCG AAACCG AAA 1 AAACCG AAACCG AAA 15450716 AGCAGCGAAT Statistics Matches: 9, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 6 9 1.00 ACGTcount: A:0.60, C:0.27, G:0.13, T:0.00 Consensus pattern (6 bp): AAACCG Left flanking sequence: Indices 15450201 -- 15450700 TCGCAAGTTAATAGGTTCTTTTTTTATGTTTCGCAAGTGCGTAGCATACGAAATAGAACATTTTT AAAGTATATCTATATCAATCAAAGTAAGTAGCGAGTTGTTTTTTTTTTTTTTTTTTCAGTGTGTA TCCATCCATCCATTCACCGCCGGTTGACACCTGTGGTTCCCCCGCGGTTATCGCGCACATCATTC ACAAACGATTCCATATCTCTGCCATATGCTGTTGCCCTGATAATCGGCCAGCTCCTTCGGCTTTT TCACATTTACTCGCCAAATGGCTGTGGCTCAAGAGTAGTAAAAACTAAATAGACAGCGAAAAAAA AGGGGGGAGCGACCATAAACTAATTAGCCATATTACACGTGATAGCTGGGGTATCTTTTTCACTT TTATTTTTGTTTTTGCTGCACCACCAGAACCGCCTGAACCGCCTGAACCACCAGAACCGCCTGAA CCGCCTGAACCACCTGAACCACTGAGAGTAGCCAAGAGAAGAAGC Right flanking sequence: Indices 15450716 -- 15451215 AGCAGCGAATAACCACCGAATCTGGTGACGGCGCCATGGCGTATACGTGATAAGTGGCGCTAACG ACGCGCGACGTTTATCAATTTTTTGTTGTTGCCCCCTTGTCATTGGCGCCAGTTTTATTTGCGTG CGAAACAATTTAAATACAACAAGAACGCATCAGCGAAACAATGAATATAAGCAACGAGCGCAATA GATTTATAAGTATAAGTATATAGAAGGCGATAATGCCCAGGCAAATTCATTAATCGAACTGCAAG TCTTGATCTCGCCCTGTCACACATTTCCCAGAAAGTGTCTCGCATAACAATCAAATTAATTAAAT AGAAATTTCATTTAATTGTGGACAAACAAATTCGAATTTGAGCTACCCGCGATATGATAAGTTGC TAGAACCGAAAACAAAAAAAGCCAGAGAACCAAACAAATAGAGCCCAAATGACAATTGGGCCTAA AGAAAGGTGTGATTACGACTATTTGTTGAGCAAACAGCGTAATTG Found at i:15450926 original size:6 final size:6 Alignment explanation

Indices: 15450915--15450930 Score: 32 Period size: 6 Copynumber: 2.7 Consensus size: 6 15450905 GCAATAGATT 15450915 TATAAG TATAAG TATA 1 TATAAG TATAAG TATA 15450931 TAGAAGGCGA Statistics Matches: 10, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 6 10 1.00 ACGTcount: A:0.50, C:0.00, G:0.12, T:0.38 Consensus pattern (6 bp): TATAAG Left flanking sequence: Indices 15450415 -- 15450914 TGCCATATGCTGTTGCCCTGATAATCGGCCAGCTCCTTCGGCTTTTTCACATTTACTCGCCAAAT GGCTGTGGCTCAAGAGTAGTAAAAACTAAATAGACAGCGAAAAAAAAGGGGGGAGCGACCATAAA CTAATTAGCCATATTACACGTGATAGCTGGGGTATCTTTTTCACTTTTATTTTTGTTTTTGCTGC ACCACCAGAACCGCCTGAACCGCCTGAACCACCAGAACCGCCTGAACCGCCTGAACCACCTGAAC CACTGAGAGTAGCCAAGAGAAGAAGCAAACCGAAACCGAAAAGCAGCGAATAACCACCGAATCTG GTGACGGCGCCATGGCGTATACGTGATAAGTGGCGCTAACGACGCGCGACGTTTATCAATTTTTT GTTGTTGCCCCCTTGTCATTGGCGCCAGTTTTATTTGCGTGCGAAACAATTTAAATACAACAAGA ACGCATCAGCGAAACAATGAATATAAGCAACGAGCGCAATAGATT Right flanking sequence: Indices 15450931 -- 15451430 TAGAAGGCGATAATGCCCAGGCAAATTCATTAATCGAACTGCAAGTCTTGATCTCGCCCTGTCAC ACATTTCCCAGAAAGTGTCTCGCATAACAATCAAATTAATTAAATAGAAATTTCATTTAATTGTG GACAAACAAATTCGAATTTGAGCTACCCGCGATATGATAAGTTGCTAGAACCGAAAACAAAAAAA GCCAGAGAACCAAACAAATAGAGCCCAAATGACAATTGGGCCTAAAGAAAGGTGTGATTACGACT ATTTGTTGAGCAAACAGCGTAATTGGGAAAAATGCCATAAAATGTTAATTATGTGGAAAAGGTGG AAAAAGTGGCCCAATCTTTTGTGGGGCCCATCTTTGGCGCTATCACGTTCTCCTGACTGACACTC CACTTCCTGTTTTGCCGCTCAGCTGTTGTGTGTGTGTGTGTTGCCACAATTTGTCTAGACATTTG ATGTATGACCGCGAAATAATAACAACAAAAAAAAAAAAAAATATA Found at i:15451354 original size:2 final size:2 Alignment explanation

Indices: 15451347--15451361 Score: 30 Period size: 2 Copynumber: 7.5 Consensus size: 2 15451337 GCTCAGCTGT 15451347 TG TG TG TG TG TG TG T 1 TG TG TG TG TG TG TG T 15451362 TGCCACAATT Statistics Matches: 13, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 13 1.00 ACGTcount: A:0.00, C:0.00, G:0.47, T:0.53 Consensus pattern (2 bp): TG Left flanking sequence: Indices 15450847 -- 15451346 GAAACAATTTAAATACAACAAGAACGCATCAGCGAAACAATGAATATAAGCAACGAGCGCAATAG ATTTATAAGTATAAGTATATAGAAGGCGATAATGCCCAGGCAAATTCATTAATCGAACTGCAAGT CTTGATCTCGCCCTGTCACACATTTCCCAGAAAGTGTCTCGCATAACAATCAAATTAATTAAATA GAAATTTCATTTAATTGTGGACAAACAAATTCGAATTTGAGCTACCCGCGATATGATAAGTTGCT AGAACCGAAAACAAAAAAAGCCAGAGAACCAAACAAATAGAGCCCAAATGACAATTGGGCCTAAA GAAAGGTGTGATTACGACTATTTGTTGAGCAAACAGCGTAATTGGGAAAAATGCCATAAAATGTT AATTATGTGGAAAAGGTGGAAAAAGTGGCCCAATCTTTTGTGGGGCCCATCTTTGGCGCTATCAC GTTCTCCTGACTGACACTCCACTTCCTGTTTTGCCGCTCAGCTGT Right flanking sequence: Indices 15451362 -- 15451861 TGCCACAATTTGTCTAGACATTTGATGTATGACCGCGAAATAATAACAACAAAAAAAAAAAAAAA TATACAAAAAATTAATAAAAATAATTGTGCAAAATTTCGCTACTTGTTTGTTTGCCCATGCACTT AACAGCGAACCGAATTCAATTTTCGGCTATGGGCGAATTAATTCCCGATCGTTTCCATTTGATTG ACAAGCTGATTGGGAATAACATCGAAATTTTCGTGCCATATACAATATATATATACATACATATA TATCATATATCCGTGTAAAATATTCTGTGCAAAAATGTTTGCGAAATTGCAGCGTGGGCGAAACA ACAACAGCAACACGAGCATTCCACAAGCTTTATTTTTAAGTTTGATTTAAGACGAAATGTCTAGA AATAAATTTGCCAACTTGTTCGCTCTTCGCCACGTCTCTTCATGCGGATTATTGACCATTTTCTC GCAGTGCAATGCACTCACAGCGAGATGTGCAACAAATTATGCTGC Found at i:15451608 original size:2 final size:2 Alignment explanation

Indices: 15451601--15451631 Score: 39 Period size: 2 Copynumber: 15.0 Consensus size: 2 15451591 GCCATATACA * * 15451601 AT AT AT AT AT AC AT AC AT AT AT AT CAT AT AT 1 AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT 15451632 CCGTGTAAAA Statistics Matches: 24, Mismatches: 4, Indels: 2 0.80 0.13 0.07 Matches are distributed among these distances: 2 22 0.92 3 2 0.08 ACGTcount: A:0.48, C:0.10, G:0.00, T:0.42 Consensus pattern (2 bp): AT Left flanking sequence: Indices 15451101 -- 15451600 GTTGCTAGAACCGAAAACAAAAAAAGCCAGAGAACCAAACAAATAGAGCCCAAATGACAATTGGG CCTAAAGAAAGGTGTGATTACGACTATTTGTTGAGCAAACAGCGTAATTGGGAAAAATGCCATAA AATGTTAATTATGTGGAAAAGGTGGAAAAAGTGGCCCAATCTTTTGTGGGGCCCATCTTTGGCGC TATCACGTTCTCCTGACTGACACTCCACTTCCTGTTTTGCCGCTCAGCTGTTGTGTGTGTGTGTG TTGCCACAATTTGTCTAGACATTTGATGTATGACCGCGAAATAATAACAACAAAAAAAAAAAAAA ATATACAAAAAATTAATAAAAATAATTGTGCAAAATTTCGCTACTTGTTTGTTTGCCCATGCACT TAACAGCGAACCGAATTCAATTTTCGGCTATGGGCGAATTAATTCCCGATCGTTTCCATTTGATT GACAAGCTGATTGGGAATAACATCGAAATTTTCGTGCCATATACA Right flanking sequence: Indices 15451632 -- 15452131 CCGTGTAAAATATTCTGTGCAAAAATGTTTGCGAAATTGCAGCGTGGGCGAAACAACAACAGCAA CACGAGCATTCCACAAGCTTTATTTTTAAGTTTGATTTAAGACGAAATGTCTAGAAATAAATTTG CCAACTTGTTCGCTCTTCGCCACGTCTCTTCATGCGGATTATTGACCATTTTCTCGCAGTGCAAT GCACTCACAGCGAGATGTGCAACAAATTATGCTGCATGAACGGCAAAAAGTCACAACATGAAAGT GTCTGGGCAAACATTTGTGGCATACGAGTCATTAGCAAACAAATGTTAAAAATACTAAAGACATT CTCGCTGGCAGCACTTGCAGTTGCCAGGCGACAATAAATTTGCCTAACTAATTGAAATTGGTAAG AAATTAAGAGTGGCAAATATTGCAGTTACTAACTAAGATCAGCTTAATTAATTAGTTTTAGGGCA GTTAAAAATATATATATATAATATAGTTAGAGCTTCCTTTTCGAC Found at i:15451691 original size:3 final size:3 Alignment explanation

Indices: 15451683--15451698 Score: 25 Period size: 3 Copynumber: 5.3 Consensus size: 3 15451673 GCGTGGGCGA * 15451683 AAC AAC AAC AGC AAC A 1 AAC AAC AAC AAC AAC A 15451699 CGAGCATTCC Statistics Matches: 11, Mismatches: 2, Indels: 0 0.85 0.15 0.00 Matches are distributed among these distances: 3 11 1.00 ACGTcount: A:0.62, C:0.31, G:0.06, T:0.00 Consensus pattern (3 bp): AAC Left flanking sequence: Indices 15451183 -- 15451682 TTACGACTATTTGTTGAGCAAACAGCGTAATTGGGAAAAATGCCATAAAATGTTAATTATGTGGA AAAGGTGGAAAAAGTGGCCCAATCTTTTGTGGGGCCCATCTTTGGCGCTATCACGTTCTCCTGAC TGACACTCCACTTCCTGTTTTGCCGCTCAGCTGTTGTGTGTGTGTGTGTTGCCACAATTTGTCTA GACATTTGATGTATGACCGCGAAATAATAACAACAAAAAAAAAAAAAAATATACAAAAAATTAAT AAAAATAATTGTGCAAAATTTCGCTACTTGTTTGTTTGCCCATGCACTTAACAGCGAACCGAATT CAATTTTCGGCTATGGGCGAATTAATTCCCGATCGTTTCCATTTGATTGACAAGCTGATTGGGAA TAACATCGAAATTTTCGTGCCATATACAATATATATATACATACATATATATCATATATCCGTGT AAAATATTCTGTGCAAAAATGTTTGCGAAATTGCAGCGTGGGCGA Right flanking sequence: Indices 15451699 -- 15452198 CGAGCATTCCACAAGCTTTATTTTTAAGTTTGATTTAAGACGAAATGTCTAGAAATAAATTTGCC AACTTGTTCGCTCTTCGCCACGTCTCTTCATGCGGATTATTGACCATTTTCTCGCAGTGCAATGC ACTCACAGCGAGATGTGCAACAAATTATGCTGCATGAACGGCAAAAAGTCACAACATGAAAGTGT CTGGGCAAACATTTGTGGCATACGAGTCATTAGCAAACAAATGTTAAAAATACTAAAGACATTCT CGCTGGCAGCACTTGCAGTTGCCAGGCGACAATAAATTTGCCTAACTAATTGAAATTGGTAAGAA ATTAAGAGTGGCAAATATTGCAGTTACTAACTAAGATCAGCTTAATTAATTAGTTTTAGGGCAGT TAAAAATATATATATATAATATAGTTAGAGCTTCCTTTTCGACCAATTTGTGTGGTGCGCCATTG CATCTTGCGGCATTAAGACAACAAACTAATGGTCTGCAATTCCTT Found at i:15452101 original size:2 final size:2 Alignment explanation

Indices: 15452094--15452111 Score: 29 Period size: 2 Copynumber: 9.5 Consensus size: 2 15452084 GCAGTTAAAA 15452094 AT AT AT AT AT AT A- AT AT A 1 AT AT AT AT AT AT AT AT AT A 15452112 GTTAGAGCTT Statistics Matches: 15, Mismatches: 0, Indels: 2 0.88 0.00 0.12 Matches are distributed among these distances: 1 1 0.07 2 14 0.93 ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44 Consensus pattern (2 bp): AT Left flanking sequence: Indices 15451594 -- 15452093 ATATACAATATATATATACATACATATATATCATATATCCGTGTAAAATATTCTGTGCAAAAATG TTTGCGAAATTGCAGCGTGGGCGAAACAACAACAGCAACACGAGCATTCCACAAGCTTTATTTTT AAGTTTGATTTAAGACGAAATGTCTAGAAATAAATTTGCCAACTTGTTCGCTCTTCGCCACGTCT CTTCATGCGGATTATTGACCATTTTCTCGCAGTGCAATGCACTCACAGCGAGATGTGCAACAAAT TATGCTGCATGAACGGCAAAAAGTCACAACATGAAAGTGTCTGGGCAAACATTTGTGGCATACGA GTCATTAGCAAACAAATGTTAAAAATACTAAAGACATTCTCGCTGGCAGCACTTGCAGTTGCCAG GCGACAATAAATTTGCCTAACTAATTGAAATTGGTAAGAAATTAAGAGTGGCAAATATTGCAGTT ACTAACTAAGATCAGCTTAATTAATTAGTTTTAGGGCAGTTAAAA Right flanking sequence: Indices 15452112 -- 15452611 GTTAGAGCTTCCTTTTCGACCAATTTGTGTGGTGCGCCATTGCATCTTGCGGCATTAAGACAACA AACTAATGGTCTGCAATTCCTTTTTTTTTTTTTGTGTGGTTCTGCAATGTGCTAATTACAGTCGA AAGAAAACAGGACCAACGAAAAAGGCCTAACAATGCATTTGGAAGGGGGGTGGTGGCGAGGGGCG TGGCTGTGAGTTGTGTAGTCGCTTTTTGGTGGCCAAAAAGGAAAATGGACCAAAAGATTTTCGCC TGTTGCCAAATGCGTTGCAGTCGACGCCGCTGACTCACATGACGCAGAACCAGCGGCGTCGAATT GTCGGCTATTTTTTGTAGACACACACACACACACACATCTGAATATATATACATATGTACATATG CCTTATGTACAATACATATAGCTGGGTATATGCAGGGACAGAGCGAAGTGCCTTTGAAAATTTTG GCGCTCGTACGCGCTTTTAATTGAGTTAAAAGATCAGCACAGATC Found at i:15452203 original size:1 final size:1 Alignment explanation

Indices: 15452197--15452209 Score: 26 Period size: 1 Copynumber: 13.0 Consensus size: 1 15452187 CTGCAATTCC 15452197 TTTTTTTTTTTTT 1 TTTTTTTTTTTTT 15452210 GTGTGGTTCT Statistics Matches: 12, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 1 12 1.00 ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00 Consensus pattern (1 bp): T Left flanking sequence: Indices 15451697 -- 15452196 CACGAGCATTCCACAAGCTTTATTTTTAAGTTTGATTTAAGACGAAATGTCTAGAAATAAATTTG CCAACTTGTTCGCTCTTCGCCACGTCTCTTCATGCGGATTATTGACCATTTTCTCGCAGTGCAAT GCACTCACAGCGAGATGTGCAACAAATTATGCTGCATGAACGGCAAAAAGTCACAACATGAAAGT GTCTGGGCAAACATTTGTGGCATACGAGTCATTAGCAAACAAATGTTAAAAATACTAAAGACATT CTCGCTGGCAGCACTTGCAGTTGCCAGGCGACAATAAATTTGCCTAACTAATTGAAATTGGTAAG AAATTAAGAGTGGCAAATATTGCAGTTACTAACTAAGATCAGCTTAATTAATTAGTTTTAGGGCA GTTAAAAATATATATATATAATATAGTTAGAGCTTCCTTTTCGACCAATTTGTGTGGTGCGCCAT TGCATCTTGCGGCATTAAGACAACAAACTAATGGTCTGCAATTCC Right flanking sequence: Indices 15452210 -- 15452709 GTGTGGTTCTGCAATGTGCTAATTACAGTCGAAAGAAAACAGGACCAACGAAAAAGGCCTAACAA TGCATTTGGAAGGGGGGTGGTGGCGAGGGGCGTGGCTGTGAGTTGTGTAGTCGCTTTTTGGTGGC CAAAAAGGAAAATGGACCAAAAGATTTTCGCCTGTTGCCAAATGCGTTGCAGTCGACGCCGCTGA CTCACATGACGCAGAACCAGCGGCGTCGAATTGTCGGCTATTTTTTGTAGACACACACACACACA CACATCTGAATATATATACATATGTACATATGCCTTATGTACAATACATATAGCTGGGTATATGC AGGGACAGAGCGAAGTGCCTTTGAAAATTTTGGCGCTCGTACGCGCTTTTAATTGAGTTAAAAGA TCAGCACAGATCGGTGCATATAGCTTTTGGCGCGATATATAGACCAGGCCGAATCTGTTTTCATT TATCTATAGCACGCATATGTACATACGTACACACATGCATACATA Found at i:15452460 original size:2 final size:2 Alignment explanation

Indices: 15452455--15452473 Score: 38 Period size: 2 Copynumber: 9.5 Consensus size: 2 15452445 TTTTTTGTAG 15452455 AC AC AC AC AC AC AC AC AC A 1 AC AC AC AC AC AC AC AC AC A 15452474 TCTGAATATA Statistics Matches: 17, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 17 1.00 ACGTcount: A:0.53, C:0.47, G:0.00, T:0.00 Consensus pattern (2 bp): AC Left flanking sequence: Indices 15451955 -- 15452454 TTCTCGCTGGCAGCACTTGCAGTTGCCAGGCGACAATAAATTTGCCTAACTAATTGAAATTGGTA AGAAATTAAGAGTGGCAAATATTGCAGTTACTAACTAAGATCAGCTTAATTAATTAGTTTTAGGG CAGTTAAAAATATATATATATAATATAGTTAGAGCTTCCTTTTCGACCAATTTGTGTGGTGCGCC ATTGCATCTTGCGGCATTAAGACAACAAACTAATGGTCTGCAATTCCTTTTTTTTTTTTTGTGTG GTTCTGCAATGTGCTAATTACAGTCGAAAGAAAACAGGACCAACGAAAAAGGCCTAACAATGCAT TTGGAAGGGGGGTGGTGGCGAGGGGCGTGGCTGTGAGTTGTGTAGTCGCTTTTTGGTGGCCAAAA AGGAAAATGGACCAAAAGATTTTCGCCTGTTGCCAAATGCGTTGCAGTCGACGCCGCTGACTCAC ATGACGCAGAACCAGCGGCGTCGAATTGTCGGCTATTTTTTGTAG Right flanking sequence: Indices 15452474 -- 15452973 TCTGAATATATATACATATGTACATATGCCTTATGTACAATACATATAGCTGGGTATATGCAGGG ACAGAGCGAAGTGCCTTTGAAAATTTTGGCGCTCGTACGCGCTTTTAATTGAGTTAAAAGATCAG CACAGATCGGTGCATATAGCTTTTGGCGCGATATATAGACCAGGCCGAATCTGTTTTCATTTATC TATAGCACGCATATGTACATACGTACACACATGCATACATACATATATGTATGTATGTTTGTTGC TTCATATACATATATATTTATTTATTTATTCCCCCCTCCATGCTATTTTCTGCTCTTGTTTAATG TTATTTTTATTTTGCGCCTTAATTAATTGTGGCAAAATAATTAGCGCAAATGTTAAAGCTCAACG CTGGCCATCATAAAATTCAATGAAAAGCGGCCAGCACATTAAGTAAATAAATGTTGATAAAATTT TCTCTTTCATTCATTTTTTTTTTTTTTTGGTTTTTTCTTTTGGGA Found at i:15452731 original size:4 final size:4 Alignment explanation

Indices: 15452714--15452730 Score: 27 Period size: 4 Copynumber: 4.2 Consensus size: 4 15452704 TACATACATA * 15452714 TATG TATG TATG TTTG T 1 TATG TATG TATG TATG T 15452731 TGCTTCATAT Statistics Matches: 12, Mismatches: 1, Indels: 0 0.92 0.08 0.00 Matches are distributed among these distances: 4 12 1.00 ACGTcount: A:0.18, C:0.00, G:0.24, T:0.59 Consensus pattern (4 bp): TATG Left flanking sequence: Indices 15452214 -- 15452713 GGTTCTGCAATGTGCTAATTACAGTCGAAAGAAAACAGGACCAACGAAAAAGGCCTAACAATGCA TTTGGAAGGGGGGTGGTGGCGAGGGGCGTGGCTGTGAGTTGTGTAGTCGCTTTTTGGTGGCCAAA AAGGAAAATGGACCAAAAGATTTTCGCCTGTTGCCAAATGCGTTGCAGTCGACGCCGCTGACTCA CATGACGCAGAACCAGCGGCGTCGAATTGTCGGCTATTTTTTGTAGACACACACACACACACACA TCTGAATATATATACATATGTACATATGCCTTATGTACAATACATATAGCTGGGTATATGCAGGG ACAGAGCGAAGTGCCTTTGAAAATTTTGGCGCTCGTACGCGCTTTTAATTGAGTTAAAAGATCAG CACAGATCGGTGCATATAGCTTTTGGCGCGATATATAGACCAGGCCGAATCTGTTTTCATTTATC TATAGCACGCATATGTACATACGTACACACATGCATACATACATA Right flanking sequence: Indices 15452731 -- 15453230 TGCTTCATATACATATATATTTATTTATTTATTCCCCCCTCCATGCTATTTTCTGCTCTTGTTTA ATGTTATTTTTATTTTGCGCCTTAATTAATTGTGGCAAAATAATTAGCGCAAATGTTAAAGCTCA ACGCTGGCCATCATAAAATTCAATGAAAAGCGGCCAGCACATTAAGTAAATAAATGTTGATAAAA TTTTCTCTTTCATTCATTTTTTTTTTTTTTTGGTTTTTTCTTTTGGGAGGGAAAAGGATGTGGTT TTTGGAAAACTTATGATTGCACTTTTCGAACTCTTCAAATTTGACAGCTACGAGTGTTGAACTGT CAATCAGTCCATTGGTCAATCAATCGATCAATCAATCGGTCGGTATGATTGAAATGAGTTAGAGG CGGCGAACAACAAAAAAACGGGGCGATAAAACTAAATGAAATATTTGTTTAAATGGTTCGCCAGC GCGACTTGTTTGTTTTATAAGCAATTAAATTATTTAAGTGCTAAG Found at