Tandem Repeats Finder Program written by:

                 Gary Benson
      Department of Biomathematical Sciences
          Mount Sinai School of Medicine

Version 4.00

Sequence: contig00000040

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: 1044
ACGTcount: A:0.24, C:0.26, G:0.31, T:0.19

Warning! 1 characters in sequence are not A, C, G, or T


Found at i:46 original size:6 final size:6

Alignment explanation

Indices: 31--46 Score: 25 Period size: 6 Copynumber: 2.7 Consensus size: 6 21 ATTCCAGCCA * 31 TTTCCT TTTTCT TTTT 1 TTTTCT TTTTCT TTTT 47 TTGCAAATTA Statistics Matches: 9, Mismatches: 1, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 6 9 1.00 ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81 Consensus pattern (6 bp): TTTTCT Left flanking sequence: Indices 1 -- 30 GGGGTGGATGTCAAGCCGGCATTCCAGCCA Right flanking sequence: Indices 47 -- 546 TTGCAAATTACCTTTTTGGCGTTTCAAATTTTTAATTTCAGCTCAAAAAAAGTTTTTAAAGCTCT TTTTAAGTGGTTTAAGAAGCTCGTTAGTTGCTGCGGATTCCACGTTGGGCGGAAAACCCGGAGCA AGAAGTTTGGTGCTGGCTCCTGTGCGCGCTTTGCAGCAGCAGAGCCTAAAGCCTCTGCTGCAATT CATTTTTTGCCGCCAATTTTGCACGCTGGGCTGCTAGTTCACCAGCCTTGCAGCAACAGTAGCAG CAGCAGCCAGCAGTGGCCGGCAGCAGCAGCAGCAGCAGCAGCGGCGGCAGCGACAGCAGCTGCTG CTGCATTGTCAGGAAGGACAGCGTTTACACCCAAGCTGCAGCGGATGGCGCTGCGCCTCTGATGC TCGAGTGACGCAGCTGCTGCACCTGCAGCCGACACAGCAGCAGCTGCAGCGCCACCAGCAACAGG AGCAGCAGCAACAGCAGCAGCAGCAGCAGCAGCTCACAGCGACAG Found at i:46 original size:7 final size:7 Alignment explanation

Indices: 31--47 Score: 27 Period size: 7 Copynumber: 2.4 Consensus size: 7 21 ATTCCAGCCA 31 TTTCCTT 1 TTTCCTT * 38 TTTCTTT 1 TTTCCTT 45 TTT 1 TTT 48 TGCAAATTAC Statistics Matches: 9, Mismatches: 1, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 7 9 1.00 ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82 Consensus pattern (7 bp): TTTCCTT Left flanking sequence: Indices 1 -- 30 GGGGTGGATGTCAAGCCGGCATTCCAGCCA Right flanking sequence: Indices 48 -- 547 TGCAAATTACCTTTTTGGCGTTTCAAATTTTTAATTTCAGCTCAAAAAAAGTTTTTAAAGCTCTT TTTAAGTGGTTTAAGAAGCTCGTTAGTTGCTGCGGATTCCACGTTGGGCGGAAAACCCGGAGCAA GAAGTTTGGTGCTGGCTCCTGTGCGCGCTTTGCAGCAGCAGAGCCTAAAGCCTCTGCTGCAATTC ATTTTTTGCCGCCAATTTTGCACGCTGGGCTGCTAGTTCACCAGCCTTGCAGCAACAGTAGCAGC AGCAGCCAGCAGTGGCCGGCAGCAGCAGCAGCAGCAGCAGCGGCGGCAGCGACAGCAGCTGCTGC TGCATTGTCAGGAAGGACAGCGTTTACACCCAAGCTGCAGCGGATGGCGCTGCGCCTCTGATGCT CGAGTGACGCAGCTGCTGCACCTGCAGCCGACACAGCAGCAGCTGCAGCGCCACCAGCAACAGGA GCAGCAGCAACAGCAGCAGCAGCAGCAGCAGCTCACAGCGACAGC Found at i:310 original size:3 final size:3 Alignment explanation

Indices: 291--366 Score: 71 Period size: 3 Copynumber: 24.7 Consensus size: 3 281 CACCAGCCTT * * ** * 291 GCA GCA ACA GTA GCA GCA GCA GCCA GCA GTG GCCG GCA GCA GCA GCA 1 GCA GCA GCA GCA GCA GCA GCA G-CA GCA GCA G-CA GCA GCA GCA GCA * * * * 338 GCA GCA GCA GCG GCG GCA GCG ACA GCA GC 1 GCA GCA GCA GCA GCA GCA GCA GCA GCA GC 367 TGCTGCTGCA Statistics Matches: 57, Mismatches: 14, Indels: 4 0.76 0.19 0.05 Matches are distributed among these distances: 3 52 0.91 4 5 0.09 ACGTcount: A:0.28, C:0.33, G:0.37, T:0.03 Consensus pattern (3 bp): GCA Left flanking sequence: Indices 1 -- 290 GGGGTGGATGTCAAGCCGGCATTCCAGCCATTTCCTTTTTCTTTTTTTGCAAATTACCTTTTTGG CGTTTCAAATTTTTAATTTCAGCTCAAAAAAAGTTTTTAAAGCTCTTTTTAAGTGGTTTAAGAAG CTCGTTAGTTGCTGCGGATTCCACGTTGGGCGGAAAACCCGGAGCAAGAAGTTTGGTGCTGGCTC CTGTGCGCGCTTTGCAGCAGCAGAGCCTAAAGCCTCTGCTGCAATTCATTTTTTGCCGCCAATTT TGCACGCTGGGCTGCTAGTTCACCAGCCTT Right flanking sequence: Indices 367 -- 866 TGCTGCTGCATTGTCAGGAAGGACAGCGTTTACACCCAAGCTGCAGCGGATGGCGCTGCGCCTCT GATGCTCGAGTGACGCAGCTGCTGCACCTGCAGCCGACACAGCAGCAGCTGCAGCGCCACCAGCA ACAGGAGCAGCAGCAACAGCAGCAGCAGCAGCAGCAGCTCACAGCGACAGCGAACTTATCTCCAG AGACCCCAAATGTTTTGTCTCCGCTGCCTTGGAAAGGAGGCCCTCCCTTACTTTTGCTGCAGCAT TGGGGCCCCCCGAGCATTTTGCTGCAGCTGCCCAGGGAGGTCTCCTGCTGCTGCTGCTGCTGCTG CTGCTTTAGTAGGAGGCGAAAGGTGTGGGCAGCAGCTGCTGGGGGGCCCCCAGNCTAAGGCCAGG GGGGCCCCCCAGGGCCAACTGGGGGGCCCCCTCAGCCCGGGACTTCAGCGGGGGAAAACAGAAAG GAGAATCTGCAAAAGAGAAAAAGATGAAAAGAATGTTAAAGAAAA Found at i:479 original size:3 final size:3 Alignment explanation

Indices: 471--534 Score: 79 Period size: 3 Copynumber: 21.3 Consensus size: 3 461 GCAGCCGACA * ** * * * * 471 CAG CAG CAG CTG CAG CGC CAC CAG CAA CAG GAG CAG CAG CAA CAG CAG 1 CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG 519 CAG CAG CAG CAG CAG C 1 CAG CAG CAG CAG CAG C 535 TCACAGCGAC Statistics Matches: 49, Mismatches: 12, Indels: 0 0.80 0.20 0.00 Matches are distributed among these distances: 3 49 1.00 ACGTcount: A:0.33, C:0.36, G:0.30, T:0.02 Consensus pattern (3 bp): CAG Left flanking sequence: Indices 1 -- 470 GGGGTGGATGTCAAGCCGGCATTCCAGCCATTTCCTTTTTCTTTTTTTGCAAATTACCTTTTTGG CGTTTCAAATTTTTAATTTCAGCTCAAAAAAAGTTTTTAAAGCTCTTTTTAAGTGGTTTAAGAAG CTCGTTAGTTGCTGCGGATTCCACGTTGGGCGGAAAACCCGGAGCAAGAAGTTTGGTGCTGGCTC CTGTGCGCGCTTTGCAGCAGCAGAGCCTAAAGCCTCTGCTGCAATTCATTTTTTGCCGCCAATTT TGCACGCTGGGCTGCTAGTTCACCAGCCTTGCAGCAACAGTAGCAGCAGCAGCCAGCAGTGGCCG GCAGCAGCAGCAGCAGCAGCAGCGGCGGCAGCGACAGCAGCTGCTGCTGCATTGTCAGGAAGGAC AGCGTTTACACCCAAGCTGCAGCGGATGGCGCTGCGCCTCTGATGCTCGAGTGACGCAGCTGCTG CACCTGCAGCCGACA Right flanking sequence: Indices 535 -- 1034 TCACAGCGACAGCGAACTTATCTCCAGAGACCCCAAATGTTTTGTCTCCGCTGCCTTGGAAAGGA GGCCCTCCCTTACTTTTGCTGCAGCATTGGGGCCCCCCGAGCATTTTGCTGCAGCTGCCCAGGGA GGTCTCCTGCTGCTGCTGCTGCTGCTGCTGCTTTAGTAGGAGGCGAAAGGTGTGGGCAGCAGCTG CTGGGGGGCCCCCAGNCTAAGGCCAGGGGGGCCCCCCAGGGCCAACTGGGGGGCCCCCTCAGCCC GGGACTTCAGCGGGGGAAAACAGAAAGGAGAATCTGCAAAAGAGAAAAAGATGAAAAGAATGTTA AAGAAAATAAATGTTGTGAGAGAAGAAGAAGCAGCAGAAGCAGGGAGTTGGAGGGAGCAGCAGCA GCAGCAGCAGCAGCAGCAGCACAGGCGAGGCGGCAAGGCCGCGGGGTGCTTCGATCTGCAGGCGG CCGAAGCTGCAGCAGAAGCAGCAGCAGCAGCAGGCAGCAGCAATG Found at i:483 original size:21 final size:21 Alignment explanation

Indices: 461--528 Score: 78 Period size: 21 Copynumber: 3.2 Consensus size: 21 451 TGCTGCACCT * * 461 GCAGCCGACACAGCAGCAGCT 1 GCAGCCGCCACAGCAGCAGCA * * 482 GCAG-CGCCACCAGCAACAGGA 1 GCAGCCGCCA-CAGCAGCAGCA * * 503 GCAGCAGCAACAGCAGCAGCA 1 GCAGCCGCCACAGCAGCAGCA 524 GCAGC 1 GCAGC 529 AGCAGCTCAC Statistics Matches: 37, Mismatches: 8, Indels: 4 0.76 0.16 0.08 Matches are distributed among these distances: 20 4 0.11 21 30 0.81 22 3 0.08 ACGTcount: A:0.32, C:0.37, G:0.29, T:0.01 Consensus pattern (21 bp): GCAGCCGCCACAGCAGCAGCA Left flanking sequence: Indices 1 -- 460 GGGGTGGATGTCAAGCCGGCATTCCAGCCATTTCCTTTTTCTTTTTTTGCAAATTACCTTTTTGG CGTTTCAAATTTTTAATTTCAGCTCAAAAAAAGTTTTTAAAGCTCTTTTTAAGTGGTTTAAGAAG CTCGTTAGTTGCTGCGGATTCCACGTTGGGCGGAAAACCCGGAGCAAGAAGTTTGGTGCTGGCTC CTGTGCGCGCTTTGCAGCAGCAGAGCCTAAAGCCTCTGCTGCAATTCATTTTTTGCCGCCAATTT TGCACGCTGGGCTGCTAGTTCACCAGCCTTGCAGCAACAGTAGCAGCAGCAGCCAGCAGTGGCCG GCAGCAGCAGCAGCAGCAGCAGCGGCGGCAGCGACAGCAGCTGCTGCTGCATTGTCAGGAAGGAC AGCGTTTACACCCAAGCTGCAGCGGATGGCGCTGCGCCTCTGATGCTCGAGTGACGCAGCTGCTG CACCT Right flanking sequence: Indices 529 -- 1028 AGCAGCTCACAGCGACAGCGAACTTATCTCCAGAGACCCCAAATGTTTTGTCTCCGCTGCCTTGG AAAGGAGGCCCTCCCTTACTTTTGCTGCAGCATTGGGGCCCCCCGAGCATTTTGCTGCAGCTGCC CAGGGAGGTCTCCTGCTGCTGCTGCTGCTGCTGCTGCTTTAGTAGGAGGCGAAAGGTGTGGGCAG CAGCTGCTGGGGGGCCCCCAGNCTAAGGCCAGGGGGGCCCCCCAGGGCCAACTGGGGGGCCCCCT CAGCCCGGGACTTCAGCGGGGGAAAACAGAAAGGAGAATCTGCAAAAGAGAAAAAGATGAAAAGA ATGTTAAAGAAAATAAATGTTGTGAGAGAAGAAGAAGCAGCAGAAGCAGGGAGTTGGAGGGAGCA GCAGCAGCAGCAGCAGCAGCAGCAGCACAGGCGAGGCGGCAAGGCCGCGGGGTGCTTCGATCTGC AGGCGGCCGAAGCTGCAGCAGAAGCAGCAGCAGCAGCAGGCAGCA Found at i:546 original size:6 final size:6 Alignment explanation

Indices: 537--549 Score: 26 Period size: 6 Copynumber: 2.2 Consensus size: 6 527 GCAGCAGCTC 537 ACAGCG ACAGCG A 1 ACAGCG ACAGCG A 550 ACTTATCTCC 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:0.38, C:0.31, G:0.31, T:0.00 Consensus pattern (6 bp): ACAGCG Left flanking sequence: Indices 37 -- 536 TTTTCTTTTTTTGCAAATTACCTTTTTGGCGTTTCAAATTTTTAATTTCAGCTCAAAAAAAGTTT TTAAAGCTCTTTTTAAGTGGTTTAAGAAGCTCGTTAGTTGCTGCGGATTCCACGTTGGGCGGAAA ACCCGGAGCAAGAAGTTTGGTGCTGGCTCCTGTGCGCGCTTTGCAGCAGCAGAGCCTAAAGCCTC TGCTGCAATTCATTTTTTGCCGCCAATTTTGCACGCTGGGCTGCTAGTTCACCAGCCTTGCAGCA ACAGTAGCAGCAGCAGCCAGCAGTGGCCGGCAGCAGCAGCAGCAGCAGCAGCGGCGGCAGCGACA GCAGCTGCTGCTGCATTGTCAGGAAGGACAGCGTTTACACCCAAGCTGCAGCGGATGGCGCTGCG CCTCTGATGCTCGAGTGACGCAGCTGCTGCACCTGCAGCCGACACAGCAGCAGCTGCAGCGCCAC CAGCAACAGGAGCAGCAGCAACAGCAGCAGCAGCAGCAGCAGCTC Right flanking sequence: Indices 550 -- 1044 ACTTATCTCCAGAGACCCCAAATGTTTTGTCTCCGCTGCCTTGGAAAGGAGGCCCTCCCTTACTT TTGCTGCAGCATTGGGGCCCCCCGAGCATTTTGCTGCAGCTGCCCAGGGAGGTCTCCTGCTGCTG CTGCTGCTGCTGCTGCTTTAGTAGGAGGCGAAAGGTGTGGGCAGCAGCTGCTGGGGGGCCCCCAG NCTAAGGCCAGGGGGGCCCCCCAGGGCCAACTGGGGGGCCCCCTCAGCCCGGGACTTCAGCGGGG GAAAACAGAAAGGAGAATCTGCAAAAGAGAAAAAGATGAAAAGAATGTTAAAGAAAATAAATGTT GTGAGAGAAGAAGAAGCAGCAGAAGCAGGGAGTTGGAGGGAGCAGCAGCAGCAGCAGCAGCAGCA GCAGCACAGGCGAGGCGGCAAGGCCGCGGGGTGCTTCGATCTGCAGGCGGCCGAAGCTGCAGCAG AAGCAGCAGCAGCAGCAGGCAGCAGCAATGGGCGCGTTTT Found at i:679 original size:3 final size:3 Alignment explanation

Indices: 671--696 Score: 52 Period size: 3 Copynumber: 8.7 Consensus size: 3 661 GGGAGGTCTC 671 CTG CTG CTG CTG CTG CTG CTG CTG CT 1 CTG CTG CTG CTG CTG CTG CTG CTG CT 697 TTAGTAGGAG Statistics Matches: 23, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 3 23 1.00 ACGTcount: A:0.00, C:0.35, G:0.31, T:0.35 Consensus pattern (3 bp): CTG Left flanking sequence: Indices 171 -- 670 GGAGCAAGAAGTTTGGTGCTGGCTCCTGTGCGCGCTTTGCAGCAGCAGAGCCTAAAGCCTCTGCT GCAATTCATTTTTTGCCGCCAATTTTGCACGCTGGGCTGCTAGTTCACCAGCCTTGCAGCAACAG TAGCAGCAGCAGCCAGCAGTGGCCGGCAGCAGCAGCAGCAGCAGCAGCGGCGGCAGCGACAGCAG CTGCTGCTGCATTGTCAGGAAGGACAGCGTTTACACCCAAGCTGCAGCGGATGGCGCTGCGCCTC TGATGCTCGAGTGACGCAGCTGCTGCACCTGCAGCCGACACAGCAGCAGCTGCAGCGCCACCAGC AACAGGAGCAGCAGCAACAGCAGCAGCAGCAGCAGCAGCTCACAGCGACAGCGAACTTATCTCCA GAGACCCCAAATGTTTTGTCTCCGCTGCCTTGGAAAGGAGGCCCTCCCTTACTTTTGCTGCAGCA TTGGGGCCCCCCGAGCATTTTGCTGCAGCTGCCCAGGGAGGTCTC Right flanking sequence: Indices 697 -- 1044 TTAGTAGGAGGCGAAAGGTGTGGGCAGCAGCTGCTGGGGGGCCCCCAGNCTAAGGCCAGGGGGGC CCCCCAGGGCCAACTGGGGGGCCCCCTCAGCCCGGGACTTCAGCGGGGGAAAACAGAAAGGAGAA TCTGCAAAAGAGAAAAAGATGAAAAGAATGTTAAAGAAAATAAATGTTGTGAGAGAAGAAGAAGC AGCAGAAGCAGGGAGTTGGAGGGAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCACAGGCGAGGCG GCAAGGCCGCGGGGTGCTTCGATCTGCAGGCGGCCGAAGCTGCAGCAGAAGCAGCAGCAGCAGCA GGCAGCAGCAATGGGCGCGTTTT Found at i:845 original size:8 final size:9 Alignment explanation

Indices: 832--851 Score: 33 Period size: 8 Copynumber: 2.3 Consensus size: 9 822 GAGAATCTGC 832 AAAAGA-GA 1 AAAAGATGA 840 AAAAGATGA 1 AAAAGATGA 849 AAA 1 AAA 852 GAATGTTAAA Statistics Matches: 11, Mismatches: 0, Indels: 1 0.92 0.00 0.08 Matches are distributed among these distances: 8 6 0.55 9 5 0.45 ACGTcount: A:0.75, C:0.00, G:0.20, T:0.05 Consensus pattern (9 bp): AAAAGATGA Left flanking sequence: Indices 332 -- 831 GCAGCAGCAGCAGCAGCGGCGGCAGCGACAGCAGCTGCTGCTGCATTGTCAGGAAGGACAGCGTT TACACCCAAGCTGCAGCGGATGGCGCTGCGCCTCTGATGCTCGAGTGACGCAGCTGCTGCACCTG CAGCCGACACAGCAGCAGCTGCAGCGCCACCAGCAACAGGAGCAGCAGCAACAGCAGCAGCAGCA GCAGCAGCTCACAGCGACAGCGAACTTATCTCCAGAGACCCCAAATGTTTTGTCTCCGCTGCCTT GGAAAGGAGGCCCTCCCTTACTTTTGCTGCAGCATTGGGGCCCCCCGAGCATTTTGCTGCAGCTG CCCAGGGAGGTCTCCTGCTGCTGCTGCTGCTGCTGCTGCTTTAGTAGGAGGCGAAAGGTGTGGGC AGCAGCTGCTGGGGGGCCCCCAGNCTAAGGCCAGGGGGGCCCCCCAGGGCCAACTGGGGGGCCCC CTCAGCCCGGGACTTCAGCGGGGGAAAACAGAAAGGAGAATCTGC Right flanking sequence: Indices 852 -- 1044 GAATGTTAAAGAAAATAAATGTTGTGAGAGAAGAAGAAGCAGCAGAAGCAGGGAGTTGGAGGGAG CAGCAGCAGCAGCAGCAGCAGCAGCAGCACAGGCGAGGCGGCAAGGCCGCGGGGTGCTTCGATCT GCAGGCGGCCGAAGCTGCAGCAGAAGCAGCAGCAGCAGCAGGCAGCAGCAATGGGCGCGTTTT Found at i:888 original size:3 final size:3 Alignment explanation

Indices: 880--899 Score: 26 Period size: 3 Copynumber: 6.7 Consensus size: 3 870 ATGTTGTGAG * * 880 AGA AGA AGA AGC AGC AGA AG 1 AGA AGA AGA AGA AGA AGA AG 900 CAGGGAGTTG Statistics Matches: 15, Mismatches: 2, Indels: 0 0.88 0.12 0.00 Matches are distributed among these distances: 3 15 1.00 ACGTcount: A:0.55, C:0.10, G:0.35, T:0.00 Consensus pattern (3 bp): AGA Left flanking sequence: Indices 380 -- 879 TCAGGAAGGACAGCGTTTACACCCAAGCTGCAGCGGATGGCGCTGCGCCTCTGATGCTCGAGTGA CGCAGCTGCTGCACCTGCAGCCGACACAGCAGCAGCTGCAGCGCCACCAGCAACAGGAGCAGCAG CAACAGCAGCAGCAGCAGCAGCAGCTCACAGCGACAGCGAACTTATCTCCAGAGACCCCAAATGT TTTGTCTCCGCTGCCTTGGAAAGGAGGCCCTCCCTTACTTTTGCTGCAGCATTGGGGCCCCCCGA GCATTTTGCTGCAGCTGCCCAGGGAGGTCTCCTGCTGCTGCTGCTGCTGCTGCTGCTTTAGTAGG AGGCGAAAGGTGTGGGCAGCAGCTGCTGGGGGGCCCCCAGNCTAAGGCCAGGGGGGCCCCCCAGG GCCAACTGGGGGGCCCCCTCAGCCCGGGACTTCAGCGGGGGAAAACAGAAAGGAGAATCTGCAAA AGAGAAAAAGATGAAAAGAATGTTAAAGAAAATAAATGTTGTGAG Right flanking sequence: Indices 900 -- 1044 CAGGGAGTTGGAGGGAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCACAGGCGAGGCGGCAAGGCC GCGGGGTGCTTCGATCTGCAGGCGGCCGAAGCTGCAGCAGAAGCAGCAGCAGCAGCAGGCAGCAG CAATGGGCGCGTTTT Found at i:901 original size:6 final size:6 Alignment explanation

Indices: 883--902 Score: 26 Period size: 6 Copynumber: 3.3 Consensus size: 6 873 TTGTGAGAGA * * 883 AGAAGA AGCAGC AGAAGC AG 1 AGAAGC AGAAGC AGAAGC AG 903 GGAGTTGGAG Statistics Matches: 11, Mismatches: 3, Indels: 0 0.79 0.21 0.00 Matches are distributed among these distances: 6 11 1.00 ACGTcount: A:0.50, C:0.15, G:0.35, T:0.00 Consensus pattern (6 bp): AGAAGC Left flanking sequence: Indices 383 -- 882 GGAAGGACAGCGTTTACACCCAAGCTGCAGCGGATGGCGCTGCGCCTCTGATGCTCGAGTGACGC AGCTGCTGCACCTGCAGCCGACACAGCAGCAGCTGCAGCGCCACCAGCAACAGGAGCAGCAGCAA CAGCAGCAGCAGCAGCAGCAGCTCACAGCGACAGCGAACTTATCTCCAGAGACCCCAAATGTTTT GTCTCCGCTGCCTTGGAAAGGAGGCCCTCCCTTACTTTTGCTGCAGCATTGGGGCCCCCCGAGCA TTTTGCTGCAGCTGCCCAGGGAGGTCTCCTGCTGCTGCTGCTGCTGCTGCTGCTTTAGTAGGAGG CGAAAGGTGTGGGCAGCAGCTGCTGGGGGGCCCCCAGNCTAAGGCCAGGGGGGCCCCCCAGGGCC AACTGGGGGGCCCCCTCAGCCCGGGACTTCAGCGGGGGAAAACAGAAAGGAGAATCTGCAAAAGA GAAAAAGATGAAAAGAATGTTAAAGAAAATAAATGTTGTGAGAGA Right flanking sequence: Indices 903 -- 1044 GGAGTTGGAGGGAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCACAGGCGAGGCGGCAAGGCCGCG GGGTGCTTCGATCTGCAGGCGGCCGAAGCTGCAGCAGAAGCAGCAGCAGCAGCAGGCAGCAGCAA TGGGCGCGTTTT Found at i:923 original size:3 final size:3 Alignment explanation

Indices: 915--945 Score: 62 Period size: 3 Copynumber: 10.3 Consensus size: 3 905 AGTTGGAGGG 915 AGC AGC AGC AGC AGC AGC AGC AGC AGC AGC A 1 AGC AGC AGC AGC AGC AGC AGC AGC AGC AGC A 946 CAGGCGAGGC Statistics Matches: 28, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 3 28 1.00 ACGTcount: A:0.35, C:0.32, G:0.32, T:0.00 Consensus pattern (3 bp): AGC Left flanking sequence: Indices 415 -- 914 GATGGCGCTGCGCCTCTGATGCTCGAGTGACGCAGCTGCTGCACCTGCAGCCGACACAGCAGCAG CTGCAGCGCCACCAGCAACAGGAGCAGCAGCAACAGCAGCAGCAGCAGCAGCAGCTCACAGCGAC AGCGAACTTATCTCCAGAGACCCCAAATGTTTTGTCTCCGCTGCCTTGGAAAGGAGGCCCTCCCT TACTTTTGCTGCAGCATTGGGGCCCCCCGAGCATTTTGCTGCAGCTGCCCAGGGAGGTCTCCTGC TGCTGCTGCTGCTGCTGCTGCTTTAGTAGGAGGCGAAAGGTGTGGGCAGCAGCTGCTGGGGGGCC CCCAGNCTAAGGCCAGGGGGGCCCCCCAGGGCCAACTGGGGGGCCCCCTCAGCCCGGGACTTCAG CGGGGGAAAACAGAAAGGAGAATCTGCAAAAGAGAAAAAGATGAAAAGAATGTTAAAGAAAATAA ATGTTGTGAGAGAAGAAGAAGCAGCAGAAGCAGGGAGTTGGAGGG Right flanking sequence: Indices 946 -- 1044 CAGGCGAGGCGGCAAGGCCGCGGGGTGCTTCGATCTGCAGGCGGCCGAAGCTGCAGCAGAAGCAG CAGCAGCAGCAGGCAGCAGCAATGGGCGCGTTTT Found at i:1012 original size:3 final size:3 Alignment explanation

Indices: 994--1031 Score: 53 Period size: 3 Copynumber: 12.3 Consensus size: 3 984 AGGCGGCCGA * * 994 AGC TGC AGC AGA AGC AGC AGC AGC AGC AGGC AGC AGC A 1 AGC AGC AGC AGC AGC AGC AGC AGC AGC A-GC AGC AGC A 1032 ATGGGCGCGT Statistics Matches: 30, Mismatches: 4, Indels: 2 0.83 0.11 0.06 Matches are distributed among these distances: 3 27 0.90 4 3 0.10 ACGTcount: A:0.34, C:0.29, G:0.34, T:0.03 Consensus pattern (3 bp): AGC Left flanking sequence: Indices 494 -- 993 GCAACAGGAGCAGCAGCAACAGCAGCAGCAGCAGCAGCAGCTCACAGCGACAGCGAACTTATCTC CAGAGACCCCAAATGTTTTGTCTCCGCTGCCTTGGAAAGGAGGCCCTCCCTTACTTTTGCTGCAG CATTGGGGCCCCCCGAGCATTTTGCTGCAGCTGCCCAGGGAGGTCTCCTGCTGCTGCTGCTGCTG CTGCTGCTTTAGTAGGAGGCGAAAGGTGTGGGCAGCAGCTGCTGGGGGGCCCCCAGNCTAAGGCC AGGGGGGCCCCCCAGGGCCAACTGGGGGGCCCCCTCAGCCCGGGACTTCAGCGGGGGAAAACAGA AAGGAGAATCTGCAAAAGAGAAAAAGATGAAAAGAATGTTAAAGAAAATAAATGTTGTGAGAGAA GAAGAAGCAGCAGAAGCAGGGAGTTGGAGGGAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCACAG GCGAGGCGGCAAGGCCGCGGGGTGCTTCGATCTGCAGGCGGCCGA Right flanking sequence: Indices 1032 -- 1044 ATGGGCGCGTTTT Done.