Tandem Repeats Finder Program written by:

                 Gary Benson
      Department of Biomathematical Sciences
          Mount Sinai School of Medicine

Version 4.00

Sequence: contig00000333

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: 5725
ACGTcount: A:0.23, C:0.26, G:0.23, T:0.27

Warning! 126 characters in sequence are not A, C, G, or T


Found at i:82 original size:3 final size:3

Alignment explanation

Indices: 74--322 Score: 98 Period size: 3 Copynumber: 84.3 Consensus size: 3 64 GGTCCCTGCA * * * * 74 AGC AGC AGC AGC AGC AGC AGC AGG AGC AGC AGG AGG AGC AGC AGC TG- 1 AGC AGC AGC AGC AGC AGC AGC AGC AGC AGC AGC AGC AGC AGC AGC AGC ** ** ** * * ** * * 121 AGC CCC CCC GCC CGC -CC NCC AGC AGC AGC AGC AGG AGC AGC AGC TG- 1 AGC AGC AGC AGC AGC AGC AGC AGC AGC AGC AGC AGC AGC AGC AGC AGC * ** * * ** * 167 AGC -CC CCC CGC -GC NGCC CCC AGC AGC AGC AGC AGG AGC AGC AGC 1 AGC AGC AGC AGC AGC AG-C AGC AGC AGC AGC AGC AGC AGC AGC AGC * * ** * ** ** 211 TG- AGC -CC CCC CGC GCC CCC NAGC AGC AGC AGC AGC AGC AGC AGC 1 AGC AGC AGC AGC AGC AGC AGC -AGC AGC AGC AGC AGC AGC AGC AGC * ** ** ** * ** 255 TG- AGC CCC CCC GCC CGCC CCC AGC AGC AGC AGC AGC AGC AGC AGC 1 AGC AGC AGC AGC AGC AG-C AGC AGC AGC AGC AGC AGC AGC AGC AGC * 300 AGG AGC AGC AGC ANGC AGC AGC A 1 AGC AGC AGC AGC A-GC AGC AGC A 323 CCGGTCTCGA Statistics Matches: 187, Mismatches: 47, Indels: 24 0.72 0.18 0.09 Matches are distributed among these distances: 2 9 0.05 3 171 0.91 4 7 0.04 ACGTcount: A:0.24, C:0.42, G:0.31, T:0.02 Consensus pattern (3 bp): AGC Left flanking sequence: Indices 1 -- 73 CCCAGCTAAGGTGTGGCAAAGCTGCGTCTTCCCCGTCCGAAACTCCCCAAACAGCTCCGTCAGGG TCCCTGCA Right flanking sequence: Indices 323 -- 822 CCGGTCTCGACGCCGCCGCCGAGGAGCGCGTCGAGGTGGGCGCTGCCAGTGGTGAAGCGGATGAG GTTGCGCCTGGCGGCGAAGACCTCGTGGGCGGANGCAAANAGCCGAANGCTGCANGAGCTGCCNT GGNCGGCGGCGGNCGACTTTGGCGGNCGCGCAGCTCGCCGAGGCCCTTCAGGGCGGCCAGGGCTT TCGGCGGCGCGAANGGCGACGCACTCCACCGTGTGGAGTCCGCCTGGCCAGACAACCAAACAGGG CCGACGCTCTTAAACGCTGTTTCGGGGTTTTTCTGCGGCAGACGCTCTTAAACGCTGTTTCGGGG TTTTTCTGCGGCAGACGCTCTTAAACGCTGTTTCGGGGTTTTTCTGCGGCAGACGCTCTTAAACG CTCTTAAGGGGTTTTTCTGCGGCAGACCCTCTTAAACGCTCTTAAGGGGTTTTTCTGCGGCAGAC GCTCTTAAACGCTCTTAAGGGGTTTTTCTGCGGCAGATGCTCTTA Found at i:136 original size:4 final size:4 Alignment explanation

Indices: 122--137 Score: 25 Period size: 4 Copynumber: 4.0 Consensus size: 4 112 CAGCAGCTGA * 122 GCCC CCCC GCCC GCCC 1 GCCC GCCC GCCC GCCC 138 NCCAGCAGCA Statistics Matches: 10, Mismatches: 2, Indels: 0 0.83 0.17 0.00 Matches are distributed among these distances: 4 10 1.00 ACGTcount: A:0.00, C:0.81, G:0.19, T:0.00 Consensus pattern (4 bp): GCCC Left flanking sequence: Indices 1 -- 121 CCCAGCTAAGGTGTGGCAAAGCTGCGTCTTCCCCGTCCGAAACTCCCCAAACAGCTCCGTCAGGG TCCCTGCAAGCAGCAGCAGCAGCAGCAGCAGGAGCAGCAGGAGGAGCAGCAGCTGA Right flanking sequence: Indices 138 -- 637 NCCAGCAGCAGCAGCAGGAGCAGCAGCTGAGCCCCCCCGCGCNGCCCCCAGCAGCAGCAGCAGGA GCAGCAGCTGAGCCCCCCCGCGCCCCCNAGCAGCAGCAGCAGCAGCAGCAGCTGAGCCCCCCCGC CCGCCCCCAGCAGCAGCAGCAGCAGCAGCAGCAGGAGCAGCAGCANGCAGCAGCACCGGTCTCGA CGCCGCCGCCGAGGAGCGCGTCGAGGTGGGCGCTGCCAGTGGTGAAGCGGATGAGGTTGCGCCTG GCGGCGAAGACCTCGTGGGCGGANGCAAANAGCCGAANGCTGCANGAGCTGCCNTGGNCGGCGGC GGNCGACTTTGGCGGNCGCGCAGCTCGCCGAGGCCCTTCAGGGCGGCCAGGGCTTTCGGCGGCGC GAANGGCGACGCACTCCACCGTGTGGAGTCCGCCTGGCCAGACAACCAAACAGGGCCGACGCTCT TAAACGCTGTTTCGGGGTTTTTCTGCGGCAGACGCTCTTAAACGC Found at i:161 original size:46 final size:45 Alignment explanation

Indices: 94--299 Score: 338 Period size: 46 Copynumber: 4.6 Consensus size: 45 84 GCAGCAGCAG * * 94 CAGGAGCAGCAGGAGGAGCAGCAGCTGAGCCCCCCCGCCCGCCCNC 1 CAGCAGCAGCAGCAGGAGCAGCAGCTGAGCCCCCCCGCCCGCCC-C * 140 CAGCAGCAGCAGCAGGAGCAGCAGCTGAGCCCCCCCGCGCNGCCCC 1 CAGCAGCAGCAGCAGGAGCAGCAGCTGAGCCCCCCCGC-CCGCCCC * 186 CAGCAGCAGCAGCAGGAGCAGCAGCTGAGCCCCCCCGCGC-CCCC 1 CAGCAGCAGCAGCAGGAGCAGCAGCTGAGCCCCCCCGCCCGCCCC * * 230 NAGCAGCAGCAGCAGCAGCAGCAGCTGAGCCCCCCCGCCCGCCCC 1 CAGCAGCAGCAGCAGGAGCAGCAGCTGAGCCCCCCCGCCCGCCCC * 275 CAGCAGCAGCAGCAGCAGCAGCAGC 1 CAGCAGCAGCAGCAGGAGCAGCAGC 300 AGGAGCAGCA Statistics Matches: 149, Mismatches: 9, Indels: 5 0.91 0.06 0.03 Matches are distributed among these distances: 44 41 0.28 45 28 0.19 46 75 0.50 47 5 0.03 ACGTcount: A:0.21, C:0.45, G:0.30, T:0.02 Consensus pattern (45 bp): CAGCAGCAGCAGCAGGAGCAGCAGCTGAGCCCCCCCGCCCGCCCC Left flanking sequence: Indices 1 -- 93 CCCAGCTAAGGTGTGGCAAAGCTGCGTCTTCCCCGTCCGAAACTCCCCAAACAGCTCCGTCAGGG TCCCTGCAAGCAGCAGCAGCAGCAGCAG Right flanking sequence: Indices 300 -- 799 AGGAGCAGCAGCANGCAGCAGCACCGGTCTCGACGCCGCCGCCGAGGAGCGCGTCGAGGTGGGCG CTGCCAGTGGTGAAGCGGATGAGGTTGCGCCTGGCGGCGAAGACCTCGTGGGCGGANGCAAANAG CCGAANGCTGCANGAGCTGCCNTGGNCGGCGGCGGNCGACTTTGGCGGNCGCGCAGCTCGCCGAG GCCCTTCAGGGCGGCCAGGGCTTTCGGCGGCGCGAANGGCGACGCACTCCACCGTGTGGAGTCCG CCTGGCCAGACAACCAAACAGGGCCGACGCTCTTAAACGCTGTTTCGGGGTTTTTCTGCGGCAGA CGCTCTTAAACGCTGTTTCGGGGTTTTTCTGCGGCAGACGCTCTTAAACGCTGTTTCGGGGTTTT TCTGCGGCAGACGCTCTTAAACGCTCTTAAGGGGTTTTTCTGCGGCAGACCCTCTTAAACGCTCT TAAGGGGTTTTTCTGCGGCAGACGCTCTTAAACGCTCTTAAGGGG Found at i:272 original size:4 final size:4 Alignment explanation

Indices: 258--273 Score: 25 Period size: 4 Copynumber: 4.0 Consensus size: 4 248 CAGCAGCTGA * 258 GCCC CCCC GCCC GCCC 1 GCCC GCCC GCCC GCCC 274 CCAGCAGCAG Statistics Matches: 10, Mismatches: 2, Indels: 0 0.83 0.17 0.00 Matches are distributed among these distances: 4 10 1.00 ACGTcount: A:0.00, C:0.81, G:0.19, T:0.00 Consensus pattern (4 bp): GCCC Left flanking sequence: Indices 1 -- 257 CCCAGCTAAGGTGTGGCAAAGCTGCGTCTTCCCCGTCCGAAACTCCCCAAACAGCTCCGTCAGGG TCCCTGCAAGCAGCAGCAGCAGCAGCAGCAGGAGCAGCAGGAGGAGCAGCAGCTGAGCCCCCCCG CCCGCCCNCCAGCAGCAGCAGCAGGAGCAGCAGCTGAGCCCCCCCGCGCNGCCCCCAGCAGCAGC AGCAGGAGCAGCAGCTGAGCCCCCCCGCGCCCCCNAGCAGCAGCAGCAGCAGCAGCAGCTGA Right flanking sequence: Indices 274 -- 773 CCAGCAGCAGCAGCAGCAGCAGCAGCAGGAGCAGCAGCANGCAGCAGCACCGGTCTCGACGCCGC CGCCGAGGAGCGCGTCGAGGTGGGCGCTGCCAGTGGTGAAGCGGATGAGGTTGCGCCTGGCGGCG AAGACCTCGTGGGCGGANGCAAANAGCCGAANGCTGCANGAGCTGCCNTGGNCGGCGGCGGNCGA CTTTGGCGGNCGCGCAGCTCGCCGAGGCCCTTCAGGGCGGCCAGGGCTTTCGGCGGCGCGAANGG CGACGCACTCCACCGTGTGGAGTCCGCCTGGCCAGACAACCAAACAGGGCCGACGCTCTTAAACG CTGTTTCGGGGTTTTTCTGCGGCAGACGCTCTTAAACGCTGTTTCGGGGTTTTTCTGCGGCAGAC GCTCTTAAACGCTGTTTCGGGGTTTTTCTGCGGCAGACGCTCTTAAACGCTCTTAAGGGGTTTTT CTGCGGCAGACCCTCTTAAACGCTCTTAAGGGGTTTTTCTGCGGC Found at i:636 original size:38 final size:38 Alignment explanation

Indices: 581--833 Score: 422 Period size: 38 Copynumber: 6.7 Consensus size: 38 571 AACCAAACAG * * ** 581 GGCCGACGCTCTTAAACGCTGTTTCGGGGTTTTTCTGC 1 GGCAGACGCTCTTAAACGCTCTTAAGGGGTTTTTCTGC * ** 619 GGCAGACGCTCTTAAACGCTGTTTCGGGGTTTTTCTGC 1 GGCAGACGCTCTTAAACGCTCTTAAGGGGTTTTTCTGC * ** 657 GGCAGACGCTCTTAAACGCTGTTTCGGGGTTTTTCTGC 1 GGCAGACGCTCTTAAACGCTCTTAAGGGGTTTTTCTGC 695 GGCAGACGCTCTTAAACGCTCTTAAGGGGTTTTTCTGC 1 GGCAGACGCTCTTAAACGCTCTTAAGGGGTTTTTCTGC * 733 GGCAGACCCTCTTAAACGCTCTTAAGGGGTTTTTCTGC 1 GGCAGACGCTCTTAAACGCTCTTAAGGGGTTTTTCTGC 771 GGCAGACGCTCTTAAACGCTCTTAAGGGGTTTTTCTGC 1 GGCAGACGCTCTTAAACGCTCTTAAGGGGTTTTTCTGC * 809 GGCAGATGCTCTTAAACGCTCTTAA 1 GGCAGACGCTCTTAAACGCTCTTAA 834 ACGCTCTTAA Statistics Matches: 208, Mismatches: 7, Indels: 0 0.97 0.03 0.00 Matches are distributed among these distances: 38 208 1.00 ACGTcount: A:0.17, C:0.25, G:0.26, T:0.32 Consensus pattern (38 bp): GGCAGACGCTCTTAAACGCTCTTAAGGGGTTTTTCTGC Left flanking sequence: Indices 81 -- 580 GCAGCAGCAGCAGCAGGAGCAGCAGGAGGAGCAGCAGCTGAGCCCCCCCGCCCGCCCNCCAGCAG CAGCAGCAGGAGCAGCAGCTGAGCCCCCCCGCGCNGCCCCCAGCAGCAGCAGCAGGAGCAGCAGC TGAGCCCCCCCGCGCCCCCNAGCAGCAGCAGCAGCAGCAGCAGCTGAGCCCCCCCGCCCGCCCCC AGCAGCAGCAGCAGCAGCAGCAGCAGGAGCAGCAGCANGCAGCAGCACCGGTCTCGACGCCGCCG CCGAGGAGCGCGTCGAGGTGGGCGCTGCCAGTGGTGAAGCGGATGAGGTTGCGCCTGGCGGCGAA GACCTCGTGGGCGGANGCAAANAGCCGAANGCTGCANGAGCTGCCNTGGNCGGCGGCGGNCGACT TTGGCGGNCGCGCAGCTCGCCGAGGCCCTTCAGGGCGGCCAGGGCTTTCGGCGGCGCGAANGGCG ACGCACTCCACCGTGTGGAGTCCGCCTGGCCAGACAACCAAACAG Right flanking sequence: Indices 834 -- 1333 ACGCTCTTAAGGGGTTTTTCTGTGGCAAACGCTGTTTGGGAGTGTTTGTGTGGCAAACGCTGTAT GGGAGTGTTTGTGTNGNGCAAACGCTGTTTGGGGGTTTTTCTGGGGCAAACGCTGTTTGGGGGTT TTTCTGGGGCAAACGCTGTTTGGGGGTTTTTCTGGGGCAAACGCTGTTTGGGAGTGTTTGGGGGC TGCTGGTTGGCGGGTTGCGCTGGCGCTTCGCTTACCCTCTCGCAGAGTCTCCAGGTCCTTTTTCG TCAGCCCTTTCGCCAGCAAGTGCTCCAGCTTCAGCGGCCCCGTCTGCAGCTCCTCGCCGCGCTGC GTCAACAACGCCGCCAAACAAACCGCCGCAAGTTCTGTCTCGGCNAGCTCATGCGGTGTCTCGGC AGCTCATGCGGTGTNCTCGGCAGCTCATGCGGTGTCTCGGCAGCTCATGCGGTGTCTCGGCAGCT CATGCGGTGTCTCGGCAGCTCATGCGGTGTCTCGGCAGCTCACGA Found at i:715 original size:10 final size:10 Alignment explanation

Indices: 700--719 Score: 40 Period size: 10 Copynumber: 2.0 Consensus size: 10 690 TCTGCGGCAG 700 ACGCTCTTAA 1 ACGCTCTTAA 710 ACGCTCTTAA 1 ACGCTCTTAA 720 GGGGTTTTTC Statistics Matches: 10, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 10 10 1.00 ACGTcount: A:0.30, C:0.30, G:0.10, T:0.30 Consensus pattern (10 bp): ACGCTCTTAA Left flanking sequence: Indices 200 -- 699 GGAGCAGCAGCTGAGCCCCCCCGCGCCCCCNAGCAGCAGCAGCAGCAGCAGCAGCTGAGCCCCCC CGCCCGCCCCCAGCAGCAGCAGCAGCAGCAGCAGCAGGAGCAGCAGCANGCAGCAGCACCGGTCT CGACGCCGCCGCCGAGGAGCGCGTCGAGGTGGGCGCTGCCAGTGGTGAAGCGGATGAGGTTGCGC CTGGCGGCGAAGACCTCGTGGGCGGANGCAAANAGCCGAANGCTGCANGAGCTGCCNTGGNCGGC GGCGGNCGACTTTGGCGGNCGCGCAGCTCGCCGAGGCCCTTCAGGGCGGCCAGGGCTTTCGGCGG CGCGAANGGCGACGCACTCCACCGTGTGGAGTCCGCCTGGCCAGACAACCAAACAGGGCCGACGC TCTTAAACGCTGTTTCGGGGTTTTTCTGCGGCAGACGCTCTTAAACGCTGTTTCGGGGTTTTTCT GCGGCAGACGCTCTTAAACGCTGTTTCGGGGTTTTTCTGCGGCAG Right flanking sequence: Indices 720 -- 1219 GGGGTTTTTCTGCGGCAGACCCTCTTAAACGCTCTTAAGGGGTTTTTCTGCGGCAGACGCTCTTA AACGCTCTTAAGGGGTTTTTCTGCGGCAGATGCTCTTAAACGCTCTTAAACGCTCTTAAGGGGTT TTTCTGTGGCAAACGCTGTTTGGGAGTGTTTGTGTGGCAAACGCTGTATGGGAGTGTTTGTGTNG NGCAAACGCTGTTTGGGGGTTTTTCTGGGGCAAACGCTGTTTGGGGGTTTTTCTGGGGCAAACGC TGTTTGGGGGTTTTTCTGGGGCAAACGCTGTTTGGGAGTGTTTGGGGGCTGCTGGTTGGCGGGTT GCGCTGGCGCTTCGCTTACCCTCTCGCAGAGTCTCCAGGTCCTTTTTCGTCAGCCCTTTCGCCAG CAAGTGCTCCAGCTTCAGCGGCCCCGTCTGCAGCTCCTCGCCGCGCTGCGTCAACAACGCCGCCA AACAAACCGCCGCAAGTTCTGTCTCGGCNAGCTCATGCGGTGTCT Found at i:791 original size:10 final size:10 Alignment explanation

Indices: 776--795 Score: 40 Period size: 10 Copynumber: 2.0 Consensus size: 10 766 TCTGCGGCAG 776 ACGCTCTTAA 1 ACGCTCTTAA 786 ACGCTCTTAA 1 ACGCTCTTAA 796 GGGGTTTTTC Statistics Matches: 10, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 10 10 1.00 ACGTcount: A:0.30, C:0.30, G:0.10, T:0.30 Consensus pattern (10 bp): ACGCTCTTAA Left flanking sequence: Indices 276 -- 775 AGCAGCAGCAGCAGCAGCAGCAGCAGGAGCAGCAGCANGCAGCAGCACCGGTCTCGACGCCGCCG CCGAGGAGCGCGTCGAGGTGGGCGCTGCCAGTGGTGAAGCGGATGAGGTTGCGCCTGGCGGCGAA GACCTCGTGGGCGGANGCAAANAGCCGAANGCTGCANGAGCTGCCNTGGNCGGCGGCGGNCGACT TTGGCGGNCGCGCAGCTCGCCGAGGCCCTTCAGGGCGGCCAGGGCTTTCGGCGGCGCGAANGGCG ACGCACTCCACCGTGTGGAGTCCGCCTGGCCAGACAACCAAACAGGGCCGACGCTCTTAAACGCT GTTTCGGGGTTTTTCTGCGGCAGACGCTCTTAAACGCTGTTTCGGGGTTTTTCTGCGGCAGACGC TCTTAAACGCTGTTTCGGGGTTTTTCTGCGGCAGACGCTCTTAAACGCTCTTAAGGGGTTTTTCT GCGGCAGACCCTCTTAAACGCTCTTAAGGGGTTTTTCTGCGGCAG Right flanking sequence: Indices 796 -- 1295 GGGGTTTTTCTGCGGCAGATGCTCTTAAACGCTCTTAAACGCTCTTAAGGGGTTTTTCTGTGGCA AACGCTGTTTGGGAGTGTTTGTGTGGCAAACGCTGTATGGGAGTGTTTGTGTNGNGCAAACGCTG TTTGGGGGTTTTTCTGGGGCAAACGCTGTTTGGGGGTTTTTCTGGGGCAAACGCTGTTTGGGGGT TTTTCTGGGGCAAACGCTGTTTGGGAGTGTTTGGGGGCTGCTGGTTGGCGGGTTGCGCTGGCGCT TCGCTTACCCTCTCGCAGAGTCTCCAGGTCCTTTTTCGTCAGCCCTTTCGCCAGCAAGTGCTCCA GCTTCAGCGGCCCCGTCTGCAGCTCCTCGCCGCGCTGCGTCAACAACGCCGCCAAACAAACCGCC GCAAGTTCTGTCTCGGCNAGCTCATGCGGTGTCTCGGCAGCTCATGCGGTGTNCTCGGCAGCTCA TGCGGTGTCTCGGCAGCTCATGCGGTGTCTCGGCAGCTCATGCGG Found at i:831 original size:10 final size:10 Alignment explanation

Indices: 816--843 Score: 56 Period size: 10 Copynumber: 2.8 Consensus size: 10 806 TGCGGCAGAT 816 GCTCTTAAAC 1 GCTCTTAAAC 826 GCTCTTAAAC 1 GCTCTTAAAC 836 GCTCTTAA 1 GCTCTTAA 844 GGGGTTTTTC Statistics Matches: 18, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 10 18 1.00 ACGTcount: A:0.29, C:0.29, G:0.11, T:0.32 Consensus pattern (10 bp): GCTCTTAAAC Left flanking sequence: Indices 316 -- 815 AGCAGCACCGGTCTCGACGCCGCCGCCGAGGAGCGCGTCGAGGTGGGCGCTGCCAGTGGTGAAGC GGATGAGGTTGCGCCTGGCGGCGAAGACCTCGTGGGCGGANGCAAANAGCCGAANGCTGCANGAG CTGCCNTGGNCGGCGGCGGNCGACTTTGGCGGNCGCGCAGCTCGCCGAGGCCCTTCAGGGCGGCC AGGGCTTTCGGCGGCGCGAANGGCGACGCACTCCACCGTGTGGAGTCCGCCTGGCCAGACAACCA AACAGGGCCGACGCTCTTAAACGCTGTTTCGGGGTTTTTCTGCGGCAGACGCTCTTAAACGCTGT TTCGGGGTTTTTCTGCGGCAGACGCTCTTAAACGCTGTTTCGGGGTTTTTCTGCGGCAGACGCTC TTAAACGCTCTTAAGGGGTTTTTCTGCGGCAGACCCTCTTAAACGCTCTTAAGGGGTTTTTCTGC GGCAGACGCTCTTAAACGCTCTTAAGGGGTTTTTCTGCGGCAGAT Right flanking sequence: Indices 844 -- 1343 GGGGTTTTTCTGTGGCAAACGCTGTTTGGGAGTGTTTGTGTGGCAAACGCTGTATGGGAGTGTTT GTGTNGNGCAAACGCTGTTTGGGGGTTTTTCTGGGGCAAACGCTGTTTGGGGGTTTTTCTGGGGC AAACGCTGTTTGGGGGTTTTTCTGGGGCAAACGCTGTTTGGGAGTGTTTGGGGGCTGCTGGTTGG CGGGTTGCGCTGGCGCTTCGCTTACCCTCTCGCAGAGTCTCCAGGTCCTTTTTCGTCAGCCCTTT CGCCAGCAAGTGCTCCAGCTTCAGCGGCCCCGTCTGCAGCTCCTCGCCGCGCTGCGTCAACAACG CCGCCAAACAAACCGCCGCAAGTTCTGTCTCGGCNAGCTCATGCGGTGTCTCGGCAGCTCATGCG GTGTNCTCGGCAGCTCATGCGGTGTCTCGGCAGCTCATGCGGTGTCTCGGCAGCTCATGCGGTGT CTCGGCAGCTCATGCGGTGTCTCGGCAGCTCACGACATCGTGGTG Found at i:885 original size:28 final size:28 Alignment explanation

Indices: 832--1022 Score: 259 Period size: 28 Copynumber: 6.8 Consensus size: 28 822 AAACGCTCTT * ** * 832 AAACGCTCTTAAGGGGTTTTTCTGTGGC 1 AAACGCTGTTTGGGGGTTTTTCTGGGGC * * * * 860 AAACGCTGTTTGGGAGTGTTTGTGTGGC 1 AAACGCTGTTTGGGGGTTTTTCTGGGGC * * * * * 888 AAACGCTGTATGGGAGTGTTTGTGTNGNGC 1 AAACGCTGTTTGGG-G-GTTTTTCTGGGGC 918 AAACGCTGTTTGGGGGTTTTTCTGGGGC 1 AAACGCTGTTTGGGGGTTTTTCTGGGGC 946 AAACGCTGTTTGGGGGTTTTTCTGGGGC 1 AAACGCTGTTTGGGGGTTTTTCTGGGGC 974 AAACGCTGTTTGGGGGTTTTTCTGGGGC 1 AAACGCTGTTTGGGGGTTTTTCTGGGGC * * 1002 AAACGCTGTTTGGGAGTGTTT 1 AAACGCTGTTTGGGGGTTTTT 1023 GGGGGCTGCT Statistics Matches: 141, Mismatches: 20, Indels: 4 0.85 0.12 0.02 Matches are distributed among these distances: 28 119 0.84 29 1 0.01 30 21 0.15 ACGTcount: A:0.14, C:0.13, G:0.37, T:0.35 Consensus pattern (28 bp): AAACGCTGTTTGGGGGTTTTTCTGGGGC Left flanking sequence: Indices 332 -- 831 ACGCCGCCGCCGAGGAGCGCGTCGAGGTGGGCGCTGCCAGTGGTGAAGCGGATGAGGTTGCGCCT GGCGGCGAAGACCTCGTGGGCGGANGCAAANAGCCGAANGCTGCANGAGCTGCCNTGGNCGGCGG CGGNCGACTTTGGCGGNCGCGCAGCTCGCCGAGGCCCTTCAGGGCGGCCAGGGCTTTCGGCGGCG CGAANGGCGACGCACTCCACCGTGTGGAGTCCGCCTGGCCAGACAACCAAACAGGGCCGACGCTC TTAAACGCTGTTTCGGGGTTTTTCTGCGGCAGACGCTCTTAAACGCTGTTTCGGGGTTTTTCTGC GGCAGACGCTCTTAAACGCTGTTTCGGGGTTTTTCTGCGGCAGACGCTCTTAAACGCTCTTAAGG GGTTTTTCTGCGGCAGACCCTCTTAAACGCTCTTAAGGGGTTTTTCTGCGGCAGACGCTCTTAAA CGCTCTTAAGGGGTTTTTCTGCGGCAGATGCTCTTAAACGCTCTT Right flanking sequence: Indices 1023 -- 1522 GGGGGCTGCTGGTTGGCGGGTTGCGCTGGCGCTTCGCTTACCCTCTCGCAGAGTCTCCAGGTCCT TTTTCGTCAGCCCTTTCGCCAGCAAGTGCTCCAGCTTCAGCGGCCCCGTCTGCAGCTCCTCGCCG CGCTGCGTCAACAACGCCGCCAAACAAACCGCCGCAAGTTCTGTCTCGGCNAGCTCATGCGGTGT CTCGGCAGCTCATGCGGTGTNCTCGGCAGCTCATGCGGTGTCTCGGCAGCTCATGCGGTGTCTCG GCAGCTCATGCGGTGTCTCGGCAGCTCATGCGGTGTCTCGGCAGCTCACGACATCGTGGTGTTGC TGCTCTGCTGCTTGTCGGGTTTCTTGAACTGTGGAGCTCATTGCGCACTGAGGGTCTTCGGTGTT GCAGCGACCTGCGGTTTGCTGCTGCGGCAGCGANGNAAGGGGGCCCCCTGNCTGCAGCNAAGCCG CAGCGNCCGGNAGGGGACNTAGCAGCAGANGCGCAGANGGGGCCC Found at i:922 original size:86 final size:84 Alignment explanation

Indices: 832--1008 Score: 245 Period size: 86 Copynumber: 2.1 Consensus size: 84 822 AAACGCTCTT * * * 832 AAACGCTCTTAAGGGGTTTTTCTGTGGCAAACGCTGTTTGGGAGTGTTTGTGTGGCAAACGCTGT 1 AAACGCTCTTAAGGGGTTTTTCTGGGGCAAACGCTGTTTGGGAGTGTTTCTGGGGCAAACGCTGT * * * 897 ATGGGAGTGTTTGTGTNGNGC 66 ATGGG-G-GTTTGTCTGGGGC * ** * * 918 AAACGCTGTTTGGGGGTTTTTCTGGGGCAAACGCTGTTTGGGGGTTTTTCTGGGGCAAACGCTGT 1 AAACGCTCTTAAGGGGTTTTTCTGGGGCAAACGCTGTTTGGGAGTGTTTCTGGGGCAAACGCTGT * * 983 TTGGGGGTTTTTCTGGGGC 66 ATGGGGGTTTGTCTGGGGC 1002 AAACGCT 1 AAACGCT 1009 GTTTGGGAGT Statistics Matches: 78, Mismatches: 13, Indels: 2 0.84 0.14 0.02 Matches are distributed among these distances: 84 16 0.21 85 1 0.01 86 61 0.78 ACGTcount: A:0.15, C:0.14, G:0.36, T:0.34 Consensus pattern (84 bp): AAACGCTCTTAAGGGGTTTTTCTGGGGCAAACGCTGTTTGGGAGTGTTTCTGGGGCAAACGCTGT ATGGGGGTTTGTCTGGGGC Left flanking sequence: Indices 332 -- 831 ACGCCGCCGCCGAGGAGCGCGTCGAGGTGGGCGCTGCCAGTGGTGAAGCGGATGAGGTTGCGCCT GGCGGCGAAGACCTCGTGGGCGGANGCAAANAGCCGAANGCTGCANGAGCTGCCNTGGNCGGCGG CGGNCGACTTTGGCGGNCGCGCAGCTCGCCGAGGCCCTTCAGGGCGGCCAGGGCTTTCGGCGGCG CGAANGGCGACGCACTCCACCGTGTGGAGTCCGCCTGGCCAGACAACCAAACAGGGCCGACGCTC TTAAACGCTGTTTCGGGGTTTTTCTGCGGCAGACGCTCTTAAACGCTGTTTCGGGGTTTTTCTGC GGCAGACGCTCTTAAACGCTGTTTCGGGGTTTTTCTGCGGCAGACGCTCTTAAACGCTCTTAAGG GGTTTTTCTGCGGCAGACCCTCTTAAACGCTCTTAAGGGGTTTTTCTGCGGCAGACGCTCTTAAA CGCTCTTAAGGGGTTTTTCTGCGGCAGATGCTCTTAAACGCTCTT Right flanking sequence: Indices 1009 -- 1508 GTTTGGGAGTGTTTGGGGGCTGCTGGTTGGCGGGTTGCGCTGGCGCTTCGCTTACCCTCTCGCAG AGTCTCCAGGTCCTTTTTCGTCAGCCCTTTCGCCAGCAAGTGCTCCAGCTTCAGCGGCCCCGTCT GCAGCTCCTCGCCGCGCTGCGTCAACAACGCCGCCAAACAAACCGCCGCAAGTTCTGTCTCGGCN AGCTCATGCGGTGTCTCGGCAGCTCATGCGGTGTNCTCGGCAGCTCATGCGGTGTCTCGGCAGCT CATGCGGTGTCTCGGCAGCTCATGCGGTGTCTCGGCAGCTCATGCGGTGTCTCGGCAGCTCACGA CATCGTGGTGTTGCTGCTCTGCTGCTTGTCGGGTTTCTTGAACTGTGGAGCTCATTGCGCACTGA GGGTCTTCGGTGTTGCAGCGACCTGCGGTTTGCTGCTGCGGCAGCGANGNAAGGGGGCCCCCTGN CTGCAGCNAAGCCGCAGCGNCCGGNAGGGGACNTAGCAGCAGANG Found at i:1229 original size:20 final size:20 Alignment explanation

Indices: 1194--1330 Score: 256 Period size: 20 Copynumber: 6.8 Consensus size: 20 1184 CCGCAAGTTC 1194 TGTCTCGGCNAGCTCATGCGG 1 TGTCTCGGC-AGCTCATGCGG 1215 TGTCTCGGCAGCTCATGCGG 1 TGTCTCGGCAGCTCATGCGG 1235 TGTNCTCGGCAGCTCATGCGG 1 TGT-CTCGGCAGCTCATGCGG 1256 TGTCTCGGCAGCTCATGCGG 1 TGTCTCGGCAGCTCATGCGG 1276 TGTCTCGGCAGCTCATGCGG 1 TGTCTCGGCAGCTCATGCGG 1296 TGTCTCGGCAGCTCATGCGG 1 TGTCTCGGCAGCTCATGCGG 1316 TGTCTCGGCAGCTCA 1 TGTCTCGGCAGCTCA 1331 CGACATCGTG Statistics Matches: 115, Mismatches: 0, Indels: 3 0.97 0.00 0.03 Matches are distributed among these distances: 20 86 0.75 21 29 0.25 ACGTcount: A:0.10, C:0.30, G:0.34, T:0.25 Consensus pattern (20 bp): TGTCTCGGCAGCTCATGCGG Left flanking sequence: Indices 694 -- 1193 CGGCAGACGCTCTTAAACGCTCTTAAGGGGTTTTTCTGCGGCAGACCCTCTTAAACGCTCTTAAG GGGTTTTTCTGCGGCAGACGCTCTTAAACGCTCTTAAGGGGTTTTTCTGCGGCAGATGCTCTTAA ACGCTCTTAAACGCTCTTAAGGGGTTTTTCTGTGGCAAACGCTGTTTGGGAGTGTTTGTGTGGCA AACGCTGTATGGGAGTGTTTGTGTNGNGCAAACGCTGTTTGGGGGTTTTTCTGGGGCAAACGCTG TTTGGGGGTTTTTCTGGGGCAAACGCTGTTTGGGGGTTTTTCTGGGGCAAACGCTGTTTGGGAGT GTTTGGGGGCTGCTGGTTGGCGGGTTGCGCTGGCGCTTCGCTTACCCTCTCGCAGAGTCTCCAGG TCCTTTTTCGTCAGCCCTTTCGCCAGCAAGTGCTCCAGCTTCAGCGGCCCCGTCTGCAGCTCCTC GCCGCGCTGCGTCAACAACGCCGCCAAACAAACCGCCGCAAGTTC Right flanking sequence: Indices 1331 -- 1830 CGACATCGTGGTGTTGCTGCTCTGCTGCTTGTCGGGTTTCTTGAACTGTGGAGCTCATTGCGCAC TGAGGGTCTTCGGTGTTGCAGCGACCTGCGGTTTGCTGCTGCGGCAGCGANGNAAGGGGGCCCCC TGNCTGCAGCNAAGCCGCAGCGNCCGGNAGGGGACNTAGCAGCAGANGCGCAGANGGGGCCCCCN AAGANGCTCCTAGAACTGCAACTNGCGAGGCCTNGCGGACTTCAAAATTGAATAAGTGGGAGGCA GGGGTTCTGCGCTGCGGGGGATACGCTGCTTTCTTCCTAGGGGGTCTGTACAGCTGAGCGGCCGC GCCGGNCGCCCAGCNGGAGAAAGGCAAATNCTTCAATTNCGAAAACGCTAAAAGTCAATCAAATG CTTTTTAGTTCTTCGCAAAAAATCAAAGAAAAGATTCGCTGCGGGTCTGTCAGTCGCTCGACTGC TCAAACCGCGGCGGCGCAACACCAACCCCNACCAACGGAAAAGCA Found at i:1934 original size:7 final size:7 Alignment explanation

Indices: 1924--1939 Score: 25 Period size: 7 Copynumber: 2.3 Consensus size: 7 1914 TCAAAAAATA 1924 AAGAAAG 1 AAGAAAG * 1931 AAGAAGG 1 AAGAAAG 1938 AA 1 AA 1940 TATTCGTCCA Statistics Matches: 8, Mismatches: 1, Indels: 0 0.89 0.11 0.00 Matches are distributed among these distances: 7 8 1.00 ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00 Consensus pattern (7 bp): AAGAAAG Left flanking sequence: Indices 1424 -- 1923 CGGTTTGCTGCTGCGGCAGCGANGNAAGGGGGCCCCCTGNCTGCAGCNAAGCCGCAGCGNCCGGN AGGGGACNTAGCAGCAGANGCGCAGANGGGGCCCCCNAAGANGCTCCTAGAACTGCAACTNGCGA GGCCTNGCGGACTTCAAAATTGAATAAGTGGGAGGCAGGGGTTCTGCGCTGCGGGGGATACGCTG CTTTCTTCCTAGGGGGTCTGTACAGCTGAGCGGCCGCGCCGGNCGCCCAGCNGGAGAAAGGCAAA TNCTTCAATTNCGAAAACGCTAAAAGTCAATCAAATGCTTTTTAGTTCTTCGCAAAAAATCAAAG AAAAGATTCGCTGCGGGTCTGTCAGTCGCTCGACTGCTCAAACCGCGGCGGCGCAACACCAACCC CNACCAACGGAAAAGCAGNGCTGATCCCCGCGAAATCTTCCACTAAATTCGCCCAACGATCTTTN TATTTCTAATTATTTAATTTAAATGNTCGTAAAAATCAAAAAATA Right flanking sequence: Indices 1940 -- 2439 TATTCGTCCACCTGTGACGCCTTCGTCCGCGGGCTGCGAGACCCGCGGGTTCCTTNNCCANGTGT NACAGACNACCTGGGGGNATGCNAGATGCAAAANCNTGGAACTNGGTTGCCGNCTAAATCATTTT ANAATTTGTCTTAAAATAAATTTAAAANCTTTTTTNTTTANATANNNNTTCAANNATGTTAATTT GTTTCTTTTCTGCGGACAATTCAGCTGCAGNCGCCGCTTCTGCAGGCTGCGGGGCTCTCCGTCCA ACTCGAAATCTACAAAACCCCATACAGCTGAACTCGAGAATAAAATTAAACAAGAGATAAATAAA TACCTTTAAATGCCACTTTCATTTTTTAATAAAAAAATTAAACTGTATTCCAAAAGAATGGAGGC ATGAGATCAATTTCAGATTGCAATTCAAGATAAACTCATTTTTATTAATTTGCTCAATTTGCTGT TGAGGAATTAAAAATTCAATCAAACTCTTACATTTAAACAATTTA Found at i:2440 original size:9 final size:9 Alignment explanation

Indices: 2426--2446 Score: 35 Period size: 9 Copynumber: 2.3 Consensus size: 9 2416 AAACTCTTAC * 2426 ATTTAAACA 1 ATTTAAAAA 2435 ATTTAAAAA 1 ATTTAAAAA 2444 ATT 1 ATT 2447 CAACTTTTAT Statistics Matches: 11, Mismatches: 1, Indels: 0 0.92 0.08 0.00 Matches are distributed among these distances: 9 11 1.00 ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38 Consensus pattern (9 bp): ATTTAAAAA Left flanking sequence: Indices 1926 -- 2425 GAAAGAAGAAGGAATATTCGTCCACCTGTGACGCCTTCGTCCGCGGGCTGCGAGACCCGCGGGTT CCTTNNCCANGTGTNACAGACNACCTGGGGGNATGCNAGATGCAAAANCNTGGAACTNGGTTGCC GNCTAAATCATTTTANAATTTGTCTTAAAATAAATTTAAAANCTTTTTTNTTTANATANNNNTTC AANNATGTTAATTTGTTTCTTTTCTGCGGACAATTCAGCTGCAGNCGCCGCTTCTGCAGGCTGCG GGGCTCTCCGTCCAACTCGAAATCTACAAAACCCCATACAGCTGAACTCGAGAATAAAATTAAAC AAGAGATAAATAAATACCTTTAAATGCCACTTTCATTTTTTAATAAAAAAATTAAACTGTATTCC AAAAGAATGGAGGCATGAGATCAATTTCAGATTGCAATTCAAGATAAACTCATTTTTATTAATTT GCTCAATTTGCTGTTGAGGAATTAAAAATTCAATCAAACTCTTAC Right flanking sequence: Indices 2447 -- 2946 CAACTTTTATAGTTTTGTAATTCACTTGTCTTTGTGTCCAAATNAGTTGAAATGAATAAATCAGA GGCAAGCAGCANGCAATTAAACACCAGCAAAGCTCAATAGTTAAACAGCAGCAGACAGCTGCAGC AGCAGCAGTAGTAGCAGCACCAGTAGCAGCATCAGCAGCAGTAGTAGTAGTAGTAGTAGCAGCAG CAGCAGTAGTAGCAGCAGCAGTAGCAGCAGGAGCAGCAGTAGCANGTAGCAGCAACTGTGTAAAA CGAATTCCGGAAGGGCCGACTCAATAGGCTGCTGCAGCAGCAAGTCCGATCTAATACATAAATAA TACAAGGCAAGATCTAGGGTTTAGGNGTTTAGGGTTTAGGGTTTAGGGTTTAGGGTTTGTTCTTT GCATTATCCAAAGTGAACAAGAAGAAATCAAAAAAAAAATTAAAACGAATTCAAATAAATCCATT CTTGCTGCAAACAAACCAGCACATTTGCTTTCTAATTAATGCTAA Found at i:2565 original size:3 final size:3 Alignment explanation

Indices: 2557--2695 Score: 134 Period size: 3 Copynumber: 45.7 Consensus size: 3 2547 AATAGTTAAA * * * * * 2557 CAG CAG CAG ACAG CTG CAG CAG CAG CAG TAG TAG CAG CAC CAG TAG 1 CAG CAG CAG -CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG * * * * * * * * 2603 CAG CAT CAG CAG CAG TAG TAG TAG TAG TAG TAG CAG CAG CAG CAG TAG 1 CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG * * * * * 2651 TAG CAG CAG CAG TAG CAG CAG GAG CAG CAG TAG CANG TAG CAG CA 1 CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CA-G CAG CAG CA 2696 ACTGTGTAAA Statistics Matches: 112, Mismatches: 22, Indels: 4 0.81 0.16 0.03 Matches are distributed among these distances: 3 107 0.96 4 5 0.04 ACGTcount: A:0.33, C:0.23, G:0.32, T:0.12 Consensus pattern (3 bp): CAG Left flanking sequence: Indices 2057 -- 2556 NCTAAATCATTTTANAATTTGTCTTAAAATAAATTTAAAANCTTTTTTNTTTANATANNNNTTCA ANNATGTTAATTTGTTTCTTTTCTGCGGACAATTCAGCTGCAGNCGCCGCTTCTGCAGGCTGCGG GGCTCTCCGTCCAACTCGAAATCTACAAAACCCCATACAGCTGAACTCGAGAATAAAATTAAACA AGAGATAAATAAATACCTTTAAATGCCACTTTCATTTTTTAATAAAAAAATTAAACTGTATTCCA AAAGAATGGAGGCATGAGATCAATTTCAGATTGCAATTCAAGATAAACTCATTTTTATTAATTTG CTCAATTTGCTGTTGAGGAATTAAAAATTCAATCAAACTCTTACATTTAAACAATTTAAAAAATT CAACTTTTATAGTTTTGTAATTCACTTGTCTTTGTGTCCAAATNAGTTGAAATGAATAAATCAGA GGCAAGCAGCANGCAATTAAACACCAGCAAAGCTCAATAGTTAAA Right flanking sequence: Indices 2696 -- 3195 ACTGTGTAAAACGAATTCCGGAAGGGCCGACTCAATAGGCTGCTGCAGCAGCAAGTCCGATCTAA TACATAAATAATACAAGGCAAGATCTAGGGTTTAGGNGTTTAGGGTTTAGGGTTTAGGGTTTAGG GTTTGTTCTTTGCATTATCCAAAGTGAACAAGAAGAAATCAAAAAAAAAATTAAAACGAATTCAA ATAAATCCATTCTTGCTGCAAACAAACCAGCACATTTGCTTTCTAATTAATGCTAAACCTAAACC CTAAACCATAAACCCTCAACCCTAAACTCTAAACGCTAAACCCTAAACCCTAATGCTAAACCCTT ATGTTAGCAAACNGGATGGCATCTTTATAGGATAAATANTGAAANTGCATCTGAAGTTGTTTGGT TTTCCATTTCGCACTTTGAGTGCAAACCCTAACCCGTAAACCCTAAACCCTAAACCCTAAACCCC GAACCCTAAACCCTAGCCTCCTAGCCCCTGTAACAGCTCTGCGTG Found at i:2613 original size:30 final size:30 Alignment explanation

Indices: 2558--2693 Score: 164 Period size: 30 Copynumber: 4.4 Consensus size: 30 2548 ATAGTTAAAC ** 2558 AGCAGCAGACAGCTGCAGCAGCAGCAGTAGT 1 AGCAGCAG-CAGTAGCAGCAGCAGCAGTAGT * 2589 AGCAGCACCAGTAGCAGCATCAGCAGCAGTAGT 1 AGCAGCAGCAGTAGCAG---CAGCAGCAGTAGT * * * 2622 AGTAGTAGTAGTAGCAGCAGCAGCAGTAGT 1 AGCAGCAGCAGTAGCAGCAGCAGCAGTAGT * * 2652 AGCAGCAGCAGTAGCAGCAGGAGCAGCAGT 1 AGCAGCAGCAGTAGCAGCAGCAGCAGTAGT * 2682 AGCANGTAGCAG 1 AGCA-GCAGCAG 2694 CAACTGTGTA Statistics Matches: 88, Mismatches: 13, Indels: 8 0.81 0.12 0.07 Matches are distributed among these distances: 30 49 0.56 31 13 0.15 33 26 0.30 ACGTcount: A:0.33, C:0.22, G:0.32, T:0.12 Consensus pattern (30 bp): AGCAGCAGCAGTAGCAGCAGCAGCAGTAGT Left flanking sequence: Indices 2058 -- 2557 CTAAATCATTTTANAATTTGTCTTAAAATAAATTTAAAANCTTTTTTNTTTANATANNNNTTCAA NNATGTTAATTTGTTTCTTTTCTGCGGACAATTCAGCTGCAGNCGCCGCTTCTGCAGGCTGCGGG GCTCTCCGTCCAACTCGAAATCTACAAAACCCCATACAGCTGAACTCGAGAATAAAATTAAACAA GAGATAAATAAATACCTTTAAATGCCACTTTCATTTTTTAATAAAAAAATTAAACTGTATTCCAA AAGAATGGAGGCATGAGATCAATTTCAGATTGCAATTCAAGATAAACTCATTTTTATTAATTTGC TCAATTTGCTGTTGAGGAATTAAAAATTCAATCAAACTCTTACATTTAAACAATTTAAAAAATTC AACTTTTATAGTTTTGTAATTCACTTGTCTTTGTGTCCAAATNAGTTGAAATGAATAAATCAGAG GCAAGCAGCANGCAATTAAACACCAGCAAAGCTCAATAGTTAAAC Right flanking sequence: Indices 2694 -- 3193 CAACTGTGTAAAACGAATTCCGGAAGGGCCGACTCAATAGGCTGCTGCAGCAGCAAGTCCGATCT AATACATAAATAATACAAGGCAAGATCTAGGGTTTAGGNGTTTAGGGTTTAGGGTTTAGGGTTTA GGGTTTGTTCTTTGCATTATCCAAAGTGAACAAGAAGAAATCAAAAAAAAAATTAAAACGAATTC AAATAAATCCATTCTTGCTGCAAACAAACCAGCACATTTGCTTTCTAATTAATGCTAAACCTAAA CCCTAAACCATAAACCCTCAACCCTAAACTCTAAACGCTAAACCCTAAACCCTAATGCTAAACCC TTATGTTAGCAAACNGGATGGCATCTTTATAGGATAAATANTGAAANTGCATCTGAAGTTGTTTG GTTTTCCATTTCGCACTTTGAGTGCAAACCCTAACCCGTAAACCCTAAACCCTAAACCCTAAACC CCGAACCCTAAACCCTAGCCTCCTAGCCCCTGTAACAGCTCTGCG Found at i:2618 original size:33 final size:32 Alignment explanation

Indices: 2568--2683 Score: 158 Period size: 33 Copynumber: 3.6 Consensus size: 32 2558 AGCAGCAGAC * 2568 AGCTGCAGCAGCAGCAGTAGTAGCAGCACCAGT 1 AGCAGCAGCAGCAGCAGTAGTAGCAGCA-CAGT * * * 2601 AGCAGCATCAGCAGCAGTAGTAGTAG--TAGT 1 AGCAGCAGCAGCAGCAGTAGTAGCAGCACAGT * 2631 AGTAGCAGCAGCAGCAGTAGTAGCAGCAGCAGT 1 AGCAGCAGCAGCAGCAGTAGTAGCAGCA-CAGT * 2664 AGCAGCAGGAGCAGCAGTAG 1 AGCAGCAGCAGCAGCAGTAG 2684 CANGTAGCAG Statistics Matches: 70, Mismatches: 10, Indels: 6 0.81 0.12 0.07 Matches are distributed among these distances: 30 26 0.37 33 44 0.63 ACGTcount: A:0.33, C:0.22, G:0.33, T:0.13 Consensus pattern (32 bp): AGCAGCAGCAGCAGCAGTAGTAGCAGCACAGT Left flanking sequence: Indices 2068 -- 2567 TTANAATTTGTCTTAAAATAAATTTAAAANCTTTTTTNTTTANATANNNNTTCAANNATGTTAAT TTGTTTCTTTTCTGCGGACAATTCAGCTGCAGNCGCCGCTTCTGCAGGCTGCGGGGCTCTCCGTC CAACTCGAAATCTACAAAACCCCATACAGCTGAACTCGAGAATAAAATTAAACAAGAGATAAATA AATACCTTTAAATGCCACTTTCATTTTTTAATAAAAAAATTAAACTGTATTCCAAAAGAATGGAG GCATGAGATCAATTTCAGATTGCAATTCAAGATAAACTCATTTTTATTAATTTGCTCAATTTGCT GTTGAGGAATTAAAAATTCAATCAAACTCTTACATTTAAACAATTTAAAAAATTCAACTTTTATA GTTTTGTAATTCACTTGTCTTTGTGTCCAAATNAGTTGAAATGAATAAATCAGAGGCAAGCAGCA NGCAATTAAACACCAGCAAAGCTCAATAGTTAAACAGCAGCAGAC Right flanking sequence: Indices 2684 -- 3183 CANGTAGCAGCAACTGTGTAAAACGAATTCCGGAAGGGCCGACTCAATAGGCTGCTGCAGCAGCA AGTCCGATCTAATACATAAATAATACAAGGCAAGATCTAGGGTTTAGGNGTTTAGGGTTTAGGGT TTAGGGTTTAGGGTTTGTTCTTTGCATTATCCAAAGTGAACAAGAAGAAATCAAAAAAAAAATTA AAACGAATTCAAATAAATCCATTCTTGCTGCAAACAAACCAGCACATTTGCTTTCTAATTAATGC TAAACCTAAACCCTAAACCATAAACCCTCAACCCTAAACTCTAAACGCTAAACCCTAAACCCTAA TGCTAAACCCTTATGTTAGCAAACNGGATGGCATCTTTATAGGATAAATANTGAAANTGCATCTG AAGTTGTTTGGTTTTCCATTTCGCACTTTGAGTGCAAACCCTAACCCGTAAACCCTAAACCCTAA ACCCTAAACCCCGAACCCTAAACCCTAGCCTCCTAGCCCCTGTAA Found at i:2808 original size:7 final size:7 Alignment explanation

Indices: 2786--2829 Score: 79 Period size: 7 Copynumber: 6.1 Consensus size: 7 2776 AGGCAAGATC 2786 TAGGGTT 1 TAGGGTT 2793 TAGGNGTT 1 TAGG-GTT 2801 TAGGGTT 1 TAGGGTT 2808 TAGGGTT 1 TAGGGTT 2815 TAGGGTT 1 TAGGGTT 2822 TAGGGTT 1 TAGGGTT 2829 T 1 T 2830 GTTCTTTGCA Statistics Matches: 36, Mismatches: 0, Indels: 2 0.95 0.00 0.05 Matches are distributed among these distances: 7 29 0.81 8 7 0.19 ACGTcount: A:0.14, C:0.00, G:0.41, T:0.43 Consensus pattern (7 bp): TAGGGTT Left flanking sequence: Indices 2286 -- 2785 TTTTTTAATAAAAAAATTAAACTGTATTCCAAAAGAATGGAGGCATGAGATCAATTTCAGATTGC AATTCAAGATAAACTCATTTTTATTAATTTGCTCAATTTGCTGTTGAGGAATTAAAAATTCAATC AAACTCTTACATTTAAACAATTTAAAAAATTCAACTTTTATAGTTTTGTAATTCACTTGTCTTTG TGTCCAAATNAGTTGAAATGAATAAATCAGAGGCAAGCAGCANGCAATTAAACACCAGCAAAGCT CAATAGTTAAACAGCAGCAGACAGCTGCAGCAGCAGCAGTAGTAGCAGCACCAGTAGCAGCATCA GCAGCAGTAGTAGTAGTAGTAGTAGCAGCAGCAGCAGTAGTAGCAGCAGCAGTAGCAGCAGGAGC AGCAGTAGCANGTAGCAGCAACTGTGTAAAACGAATTCCGGAAGGGCCGACTCAATAGGCTGCTG CAGCAGCAAGTCCGATCTAATACATAAATAATACAAGGCAAGATC Right flanking sequence: Indices 2830 -- 3329 GTTCTTTGCATTATCCAAAGTGAACAAGAAGAAATCAAAAAAAAAATTAAAACGAATTCAAATAA ATCCATTCTTGCTGCAAACAAACCAGCACATTTGCTTTCTAATTAATGCTAAACCTAAACCCTAA ACCATAAACCCTCAACCCTAAACTCTAAACGCTAAACCCTAAACCCTAATGCTAAACCCTTATGT TAGCAAACNGGATGGCATCTTTATAGGATAAATANTGAAANTGCATCTGAAGTTGTTTGGTTTTC CATTTCGCACTTTGAGTGCAAACCCTAACCCGTAAACCCTAAACCCTAAACCCTAAACCCCGAAC CCTAAACCCTAGCCTCCTAGCCCCTGTAACAGCTCTGCGTGTGTTTCCGAATTCATTCTTTGGCA CTTCTTTGATTTTGCAATTCAAATCATTTATAATTTCAATTTATTTCAAATATCTTTTATTTTAT TTATTTTAAAAGAAGTTAAAACCCCGCTGCGGCCGCTGGCTGCCG Found at i:2960 original size:7 final size:7 Alignment explanation

Indices: 2943--3019 Score: 98 Period size: 7 Copynumber: 11.3 Consensus size: 7 2933 CTAATTAATG 2943 CTAAA-C 1 CTAAACC 2949 CTAAACC 1 CTAAACC 2956 CTAAACC 1 CTAAACC * 2963 ATAAACC 1 CTAAACC * 2970 CTCAACC 1 CTAAACC * 2977 CTAAACT 1 CTAAACC * 2984 CTAAACG 1 CTAAACC 2991 CTAAACC 1 CTAAACC 2998 CTAAACC 1 CTAAACC ** 3005 CT-AATG 1 CTAAACC 3011 CTAAACC 1 CTAAACC 3018 CT 1 CT 3020 TATGTTAGCA Statistics Matches: 58, Mismatches: 11, Indels: 3 0.81 0.15 0.04 Matches are distributed among these distances: 6 9 0.16 7 49 0.84 ACGTcount: A:0.42, C:0.38, G:0.03, T:0.18 Consensus pattern (7 bp): CTAAACC Left flanking sequence: Indices 2443 -- 2942 AATTCAACTTTTATAGTTTTGTAATTCACTTGTCTTTGTGTCCAAATNAGTTGAAATGAATAAAT CAGAGGCAAGCAGCANGCAATTAAACACCAGCAAAGCTCAATAGTTAAACAGCAGCAGACAGCTG CAGCAGCAGCAGTAGTAGCAGCACCAGTAGCAGCATCAGCAGCAGTAGTAGTAGTAGTAGTAGCA GCAGCAGCAGTAGTAGCAGCAGCAGTAGCAGCAGGAGCAGCAGTAGCANGTAGCAGCAACTGTGT AAAACGAATTCCGGAAGGGCCGACTCAATAGGCTGCTGCAGCAGCAAGTCCGATCTAATACATAA ATAATACAAGGCAAGATCTAGGGTTTAGGNGTTTAGGGTTTAGGGTTTAGGGTTTAGGGTTTGTT CTTTGCATTATCCAAAGTGAACAAGAAGAAATCAAAAAAAAAATTAAAACGAATTCAAATAAATC CATTCTTGCTGCAAACAAACCAGCACATTTGCTTTCTAATTAATG Right flanking sequence: Indices 3020 -- 3519 TATGTTAGCAAACNGGATGGCATCTTTATAGGATAAATANTGAAANTGCATCTGAAGTTGTTTGG TTTTCCATTTCGCACTTTGAGTGCAAACCCTAACCCGTAAACCCTAAACCCTAAACCCTAAACCC CGAACCCTAAACCCTAGCCTCCTAGCCCCTGTAACAGCTCTGCGTGTGTTTCCGAATTCATTCTT TGGCACTTCTTTGATTTTGCAATTCAAATCATTTATAATTTCAATTTATTTCAAATATCTTTTAT TTTATTTATTTTAAAAGAAGTTAAAACCCCGCTGCGGCCGCTGGCTGCCGACTTTGGCGAACTTG AATTTCAAGTGTCTGCACGAGTTGAACTCAGAACTTGAACGAAGAGGGGAAACTGCGCATTTCTG GGGCTAAAAAGGCCGAAAGAGACAAAAATAAATGAATAAATTGAATAAAAGTGCAGATAAATGGA GAATTCGAGGAAGATATTCACAAAATCGAGATCTTTTCCTCGGAG Found at i:3134 original size:7 final size:7 Alignment explanation

Indices: 3109--3165 Score: 86 Period size: 7 Copynumber: 8.1 Consensus size: 7 3099 CTTTGAGTGC 3109 AAACCCT 1 AAACCCT * * 3116 AACCCGT 1 AAACCCT 3123 AAACCCT 1 AAACCCT 3130 AAACCCT 1 AAACCCT 3137 AAACCCT 1 AAACCCT * 3144 AAACCCC 1 AAACCCT * 3151 GAACCCT 1 AAACCCT 3158 AAACCCT 1 AAACCCT 3165 A 1 A 3166 GCCTCCTAGC Statistics Matches: 42, Mismatches: 8, Indels: 0 0.84 0.16 0.00 Matches are distributed among these distances: 7 42 1.00 ACGTcount: A:0.40, C:0.44, G:0.04, T:0.12 Consensus pattern (7 bp): AAACCCT Left flanking sequence: Indices 2609 -- 3108 CAGCAGCAGTAGTAGTAGTAGTAGTAGCAGCAGCAGCAGTAGTAGCAGCAGCAGTAGCAGCAGGA GCAGCAGTAGCANGTAGCAGCAACTGTGTAAAACGAATTCCGGAAGGGCCGACTCAATAGGCTGC TGCAGCAGCAAGTCCGATCTAATACATAAATAATACAAGGCAAGATCTAGGGTTTAGGNGTTTAG GGTTTAGGGTTTAGGGTTTAGGGTTTGTTCTTTGCATTATCCAAAGTGAACAAGAAGAAATCAAA AAAAAAATTAAAACGAATTCAAATAAATCCATTCTTGCTGCAAACAAACCAGCACATTTGCTTTC TAATTAATGCTAAACCTAAACCCTAAACCATAAACCCTCAACCCTAAACTCTAAACGCTAAACCC TAAACCCTAATGCTAAACCCTTATGTTAGCAAACNGGATGGCATCTTTATAGGATAAATANTGAA ANTGCATCTGAAGTTGTTTGGTTTTCCATTTCGCACTTTGAGTGC Right flanking sequence: Indices 3166 -- 3665 GCCTCCTAGCCCCTGTAACAGCTCTGCGTGTGTTTCCGAATTCATTCTTTGGCACTTCTTTGATT TTGCAATTCAAATCATTTATAATTTCAATTTATTTCAAATATCTTTTATTTTATTTATTTTAAAA GAAGTTAAAACCCCGCTGCGGCCGCTGGCTGCCGACTTTGGCGAACTTGAATTTCAAGTGTCTGC ACGAGTTGAACTCAGAACTTGAACGAAGAGGGGAAACTGCGCATTTCTGGGGCTAAAAAGGCCGA AAGAGACAAAAATAAATGAATAAATTGAATAAAAGTGCAGATAAATGGAGAATTCGAGGAAGATA TTCACAAAATCGAGATCTTTTCCTCGGAGTTTCTTCGGATGAGGCGTTGCTGTTTCCAAAACGAA CACAGCAACTCGCGGGCACTGCGGAGCCGATTCGGCGCCAAAATTAACGCTTTTTAGCGTCATCT GCGTCAAATTGAACGGCGAAACCGAATTAATTACNAAAAACTAAA Found at i:3284 original size:5 final size:5 Alignment explanation

Indices: 3274--3292 Score: 31 Period size: 5 Copynumber: 4.0 Consensus size: 5 3264 TTCAAATATC 3274 TTTTA TTTTA -TTTA TTTTA 1 TTTTA TTTTA TTTTA TTTTA 3293 AAAGAAGTTA Statistics Matches: 13, Mismatches: 0, Indels: 2 0.87 0.00 0.13 Matches are distributed among these distances: 4 4 0.31 5 9 0.69 ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79 Consensus pattern (5 bp): TTTTA Left flanking sequence: Indices 2774 -- 3273 CAAGGCAAGATCTAGGGTTTAGGNGTTTAGGGTTTAGGGTTTAGGGTTTAGGGTTTGTTCTTTGC ATTATCCAAAGTGAACAAGAAGAAATCAAAAAAAAAATTAAAACGAATTCAAATAAATCCATTCT TGCTGCAAACAAACCAGCACATTTGCTTTCTAATTAATGCTAAACCTAAACCCTAAACCATAAAC CCTCAACCCTAAACTCTAAACGCTAAACCCTAAACCCTAATGCTAAACCCTTATGTTAGCAAACN GGATGGCATCTTTATAGGATAAATANTGAAANTGCATCTGAAGTTGTTTGGTTTTCCATTTCGCA CTTTGAGTGCAAACCCTAACCCGTAAACCCTAAACCCTAAACCCTAAACCCCGAACCCTAAACCC TAGCCTCCTAGCCCCTGTAACAGCTCTGCGTGTGTTTCCGAATTCATTCTTTGGCACTTCTTTGA TTTTGCAATTCAAATCATTTATAATTTCAATTTATTTCAAATATC Right flanking sequence: Indices 3293 -- 3792 AAAGAAGTTAAAACCCCGCTGCGGCCGCTGGCTGCCGACTTTGGCGAACTTGAATTTCAAGTGTC TGCACGAGTTGAACTCAGAACTTGAACGAAGAGGGGAAACTGCGCATTTCTGGGGCTAAAAAGGC CGAAAGAGACAAAAATAAATGAATAAATTGAATAAAAGTGCAGATAAATGGAGAATTCGAGGAAG ATATTCACAAAATCGAGATCTTTTCCTCGGAGTTTCTTCGGATGAGGCGTTGCTGTTTCCAAAAC GAACACAGCAACTCGCGGGCACTGCGGAGCCGATTCGGCGCCAAAATTAACGCTTTTTAGCGTCA TCTGCGTCAAATTGAACGGCGAAACCGAATTAATTACNAAAAACTAAATTAATTTGCGCCTTTAA GTGTTAAAAACGGGCCAAGAGGCGCAAAAAGANGGGGAGCAGCCGTCCCTGTGCTCCGACAGCCC CAGCTGTACAGACAGCATGCGGCGCTGGCAGTGCGTGTGCCNGGT Found at i:3289 original size:9 final size:9 Alignment explanation

Indices: 3275--3292 Score: 36 Period size: 9 Copynumber: 2.0 Consensus size: 9 3265 TCAAATATCT 3275 TTTATTTTA 1 TTTATTTTA 3284 TTTATTTTA 1 TTTATTTTA 3293 AAAGAAGTTA Statistics Matches: 9, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 9 9 1.00 ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78 Consensus pattern (9 bp): TTTATTTTA Left flanking sequence: Indices 2775 -- 3274 AAGGCAAGATCTAGGGTTTAGGNGTTTAGGGTTTAGGGTTTAGGGTTTAGGGTTTGTTCTTTGCA TTATCCAAAGTGAACAAGAAGAAATCAAAAAAAAAATTAAAACGAATTCAAATAAATCCATTCTT GCTGCAAACAAACCAGCACATTTGCTTTCTAATTAATGCTAAACCTAAACCCTAAACCATAAACC CTCAACCCTAAACTCTAAACGCTAAACCCTAAACCCTAATGCTAAACCCTTATGTTAGCAAACNG GATGGCATCTTTATAGGATAAATANTGAAANTGCATCTGAAGTTGTTTGGTTTTCCATTTCGCAC TTTGAGTGCAAACCCTAACCCGTAAACCCTAAACCCTAAACCCTAAACCCCGAACCCTAAACCCT AGCCTCCTAGCCCCTGTAACAGCTCTGCGTGTGTTTCCGAATTCATTCTTTGGCACTTCTTTGAT TTTGCAATTCAAATCATTTATAATTTCAATTTATTTCAAATATCT Right flanking sequence: Indices 3293 -- 3792 AAAGAAGTTAAAACCCCGCTGCGGCCGCTGGCTGCCGACTTTGGCGAACTTGAATTTCAAGTGTC TGCACGAGTTGAACTCAGAACTTGAACGAAGAGGGGAAACTGCGCATTTCTGGGGCTAAAAAGGC CGAAAGAGACAAAAATAAATGAATAAATTGAATAAAAGTGCAGATAAATGGAGAATTCGAGGAAG ATATTCACAAAATCGAGATCTTTTCCTCGGAGTTTCTTCGGATGAGGCGTTGCTGTTTCCAAAAC GAACACAGCAACTCGCGGGCACTGCGGAGCCGATTCGGCGCCAAAATTAACGCTTTTTAGCGTCA TCTGCGTCAAATTGAACGGCGAAACCGAATTAATTACNAAAAACTAAATTAATTTGCGCCTTTAA GTGTTAAAAACGGGCCAAGAGGCGCAAAAAGANGGGGAGCAGCCGTCCCTGTGCTCCGACAGCCC CAGCTGTACAGACAGCATGCGGCGCTGGCAGTGCGTGTGCCNGGT Found at i:3447 original size:8 final size:9 Alignment explanation

Indices: 3436--3458 Score: 39 Period size: 9 Copynumber: 2.7 Consensus size: 9 3426 AAGAGACAAA 3436 AATAAA-TG 1 AATAAATTG 3444 AATAAATTG 1 AATAAATTG 3453 AATAAA 1 AATAAA 3459 AGTGCAGATA Statistics Matches: 14, Mismatches: 0, Indels: 1 0.93 0.00 0.07 Matches are distributed among these distances: 8 6 0.43 9 8 0.57 ACGTcount: A:0.65, C:0.00, G:0.09, T:0.26 Consensus pattern (9 bp): AATAAATTG Left flanking sequence: Indices 2936 -- 3435 ATTAATGCTAAACCTAAACCCTAAACCATAAACCCTCAACCCTAAACTCTAAACGCTAAACCCTA AACCCTAATGCTAAACCCTTATGTTAGCAAACNGGATGGCATCTTTATAGGATAAATANTGAAAN TGCATCTGAAGTTGTTTGGTTTTCCATTTCGCACTTTGAGTGCAAACCCTAACCCGTAAACCCTA AACCCTAAACCCTAAACCCCGAACCCTAAACCCTAGCCTCCTAGCCCCTGTAACAGCTCTGCGTG TGTTTCCGAATTCATTCTTTGGCACTTCTTTGATTTTGCAATTCAAATCATTTATAATTTCAATT TATTTCAAATATCTTTTATTTTATTTATTTTAAAAGAAGTTAAAACCCCGCTGCGGCCGCTGGCT GCCGACTTTGGCGAACTTGAATTTCAAGTGTCTGCACGAGTTGAACTCAGAACTTGAACGAAGAG GGGAAACTGCGCATTTCTGGGGCTAAAAAGGCCGAAAGAGACAAA Right flanking sequence: Indices 3459 -- 3958 AGTGCAGATAAATGGAGAATTCGAGGAAGATATTCACAAAATCGAGATCTTTTCCTCGGAGTTTC TTCGGATGAGGCGTTGCTGTTTCCAAAACGAACACAGCAACTCGCGGGCACTGCGGAGCCGATTC GGCGCCAAAATTAACGCTTTTTAGCGTCATCTGCGTCAAATTGAACGGCGAAACCGAATTAATTA CNAAAAACTAAATTAATTTGCGCCTTTAAGTGTTAAAAACGGGCCAAGAGGCGCAAAAAGANGGG GAGCAGCCGTCCCTGTGCTCCGACAGCCCCAGCTGTACAGACAGCATGCGGCGCTGGCAGTGCGT GTGCCNGGTTTAAAATTAAATTAAATTATTTATTTTAATAAATTTGANTAAATTTAATTTGTGGA TTCTTTGTTTTCACCCGAGCNTTCGCGCGGAACCACCTCCAANCCCCGCNGGCCCCCGNCTGTCT TTGATCGGATCGGACTTGTTCGGGGCTCTTTTTCTCTTCTTTTTC Found at i:3528 original size:11 final size:11 Alignment explanation

Indices: 3509--3529 Score: 35 Period size: 11 Copynumber: 1.9 Consensus size: 11 3499 ATCGAGATCT 3509 TTTCCTCGGAG 1 TTTCCTCGGAG * 3520 TTTCTTCGGA 1 TTTCCTCGGA 3530 TGAGGCGTTG Statistics Matches: 9, Mismatches: 1, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 11 9 1.00 ACGTcount: A:0.10, C:0.24, G:0.24, T:0.43 Consensus pattern (11 bp): TTTCCTCGGAG Left flanking sequence: Indices 3009 -- 3508 TGCTAAACCCTTATGTTAGCAAACNGGATGGCATCTTTATAGGATAAATANTGAAANTGCATCTG AAGTTGTTTGGTTTTCCATTTCGCACTTTGAGTGCAAACCCTAACCCGTAAACCCTAAACCCTAA ACCCTAAACCCCGAACCCTAAACCCTAGCCTCCTAGCCCCTGTAACAGCTCTGCGTGTGTTTCCG AATTCATTCTTTGGCACTTCTTTGATTTTGCAATTCAAATCATTTATAATTTCAATTTATTTCAA ATATCTTTTATTTTATTTATTTTAAAAGAAGTTAAAACCCCGCTGCGGCCGCTGGCTGCCGACTT TGGCGAACTTGAATTTCAAGTGTCTGCACGAGTTGAACTCAGAACTTGAACGAAGAGGGGAAACT GCGCATTTCTGGGGCTAAAAAGGCCGAAAGAGACAAAAATAAATGAATAAATTGAATAAAAGTGC AGATAAATGGAGAATTCGAGGAAGATATTCACAAAATCGAGATCT Right flanking sequence: Indices 3530 -- 4029 TGAGGCGTTGCTGTTTCCAAAACGAACACAGCAACTCGCGGGCACTGCGGAGCCGATTCGGCGCC AAAATTAACGCTTTTTAGCGTCATCTGCGTCAAATTGAACGGCGAAACCGAATTAATTACNAAAA ACTAAATTAATTTGCGCCTTTAAGTGTTAAAAACGGGCCAAGAGGCGCAAAAAGANGGGGAGCAG CCGTCCCTGTGCTCCGACAGCCCCAGCTGTACAGACAGCATGCGGCGCTGGCAGTGCGTGTGCCN GGTTTAAAATTAAATTAAATTATTTATTTTAATAAATTTGANTAAATTTAATTTGTGGATTCTTT GTTTTCACCCGAGCNTTCGCGCGGAACCACCTCCAANCCCCGCNGGCCCCCGNCTGTCTTTGATC GGATCGGACTTGTTCGGGGCTCTTTTTCTCTTCTTTTTCTCTCCTTTTGAATTCTTCTTTTNCCA AAATTAATTTTATTTTACTTTAAGAACTTCAAACTCTCCGGGACG Found at i:3802 original size:6 final size:6 Alignment explanation

Indices: 3793--3808 Score: 25 Period size: 5 Copynumber: 2.8 Consensus size: 6 3783 TGTGCCNGGT 3793 TTAAAA TT-AAA TTAAA 1 TTAAAA TTAAAA TTAAA 3809 TTATTTATTT Statistics Matches: 9, Mismatches: 0, Indels: 2 0.82 0.00 0.18 Matches are distributed among these distances: 5 5 0.56 6 4 0.44 ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38 Consensus pattern (6 bp): TTAAAA Left flanking sequence: Indices 3293 -- 3792 AAAGAAGTTAAAACCCCGCTGCGGCCGCTGGCTGCCGACTTTGGCGAACTTGAATTTCAAGTGTC TGCACGAGTTGAACTCAGAACTTGAACGAAGAGGGGAAACTGCGCATTTCTGGGGCTAAAAAGGC CGAAAGAGACAAAAATAAATGAATAAATTGAATAAAAGTGCAGATAAATGGAGAATTCGAGGAAG ATATTCACAAAATCGAGATCTTTTCCTCGGAGTTTCTTCGGATGAGGCGTTGCTGTTTCCAAAAC GAACACAGCAACTCGCGGGCACTGCGGAGCCGATTCGGCGCCAAAATTAACGCTTTTTAGCGTCA TCTGCGTCAAATTGAACGGCGAAACCGAATTAATTACNAAAAACTAAATTAATTTGCGCCTTTAA GTGTTAAAAACGGGCCAAGAGGCGCAAAAAGANGGGGAGCAGCCGTCCCTGTGCTCCGACAGCCC CAGCTGTACAGACAGCATGCGGCGCTGGCAGTGCGTGTGCCNGGT Right flanking sequence: Indices 3809 -- 4308 TTATTTATTTTAATAAATTTGANTAAATTTAATTTGTGGATTCTTTGTTTTCACCCGAGCNTTCG CGCGGAACCACCTCCAANCCCCGCNGGCCCCCGNCTGTCTTTGATCGGATCGGACTTGTTCGGGG CTCTTTTTCTCTTCTTTTTCTCTCCTTTTGAATTCTTCTTTTNCCAAAATTAATTTTATTTTACT TTAAGAACTTCAAACTCTCCGGGACGCCCCTTGTTGCTGCTTTTCTCNCCGAGGCNCACGGACCC CCCAGCGCCAAAANTGNCCTGCAGACTGCAAAGAAAATGCAGCAGCAGCAGACGCAGCAGCANGA TCCGCAGCAGCAGCAGCAGCAACAGCANGCAGCAACAGCAGCNAGCAGCAGNCAGCAAANAAACC CAGNACNAGCTCNGCCCAATGCCGGAGGGGATGCCCTCAGCGGCAGCTTTGACTCGAGCCATGAG AGGTAAATAAATTAATTTTAAAAGAATTTCTTTTTTTCCCTTTAA Found at i:3806 original size:5 final size:5 Alignment explanation

Indices: 3796--3811 Score: 32 Period size: 5 Copynumber: 3.2 Consensus size: 5 3786 GCCNGGTTTA 3796 AAATT AAATT AAATT A 1 AAATT AAATT AAATT A 3812 TTTATTTTAA Statistics Matches: 11, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 5 11 1.00 ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38 Consensus pattern (5 bp): AAATT Left flanking sequence: Indices 3296 -- 3795 GAAGTTAAAACCCCGCTGCGGCCGCTGGCTGCCGACTTTGGCGAACTTGAATTTCAAGTGTCTGC ACGAGTTGAACTCAGAACTTGAACGAAGAGGGGAAACTGCGCATTTCTGGGGCTAAAAAGGCCGA AAGAGACAAAAATAAATGAATAAATTGAATAAAAGTGCAGATAAATGGAGAATTCGAGGAAGATA TTCACAAAATCGAGATCTTTTCCTCGGAGTTTCTTCGGATGAGGCGTTGCTGTTTCCAAAACGAA CACAGCAACTCGCGGGCACTGCGGAGCCGATTCGGCGCCAAAATTAACGCTTTTTAGCGTCATCT GCGTCAAATTGAACGGCGAAACCGAATTAATTACNAAAAACTAAATTAATTTGCGCCTTTAAGTG TTAAAAACGGGCCAAGAGGCGCAAAAAGANGGGGAGCAGCCGTCCCTGTGCTCCGACAGCCCCAG CTGTACAGACAGCATGCGGCGCTGGCAGTGCGTGTGCCNGGTTTA Right flanking sequence: Indices 3812 -- 4311 TTTATTTTAATAAATTTGANTAAATTTAATTTGTGGATTCTTTGTTTTCACCCGAGCNTTCGCGC GGAACCACCTCCAANCCCCGCNGGCCCCCGNCTGTCTTTGATCGGATCGGACTTGTTCGGGGCTC TTTTTCTCTTCTTTTTCTCTCCTTTTGAATTCTTCTTTTNCCAAAATTAATTTTATTTTACTTTA AGAACTTCAAACTCTCCGGGACGCCCCTTGTTGCTGCTTTTCTCNCCGAGGCNCACGGACCCCCC AGCGCCAAAANTGNCCTGCAGACTGCAAAGAAAATGCAGCAGCAGCAGACGCAGCAGCANGATCC GCAGCAGCAGCAGCAGCAACAGCANGCAGCAACAGCAGCNAGCAGCAGNCAGCAAANAAACCCAG NACNAGCTCNGCCCAATGCCGGAGGGGATGCCCTCAGCGGCAGCTTTGACTCGAGCCATGAGAGG TAAATAAATTAATTTTAAAAGAATTTCTTTTTTTCCCTTTAAAAN Found at i:3828 original size:10 final size:10 Alignment explanation

Indices: 3815--3838 Score: 34 Period size: 10 Copynumber: 2.4 Consensus size: 10 3805 TAAATTATTT * 3815 ATTTTAATAA 1 ATTTGAATAA * 3825 ATTTGANTAA 1 ATTTGAATAA 3835 ATTT 1 ATTT 3839 AATTTGTGGA Statistics Matches: 12, Mismatches: 2, Indels: 0 0.86 0.14 0.00 Matches are distributed among these distances: 10 12 1.00 ACGTcount: A:0.42, C:0.00, G:0.04, T:0.50 Consensus pattern (10 bp): ATTTGAATAA Left flanking sequence: Indices 3315 -- 3814 GGCCGCTGGCTGCCGACTTTGGCGAACTTGAATTTCAAGTGTCTGCACGAGTTGAACTCAGAACT TGAACGAAGAGGGGAAACTGCGCATTTCTGGGGCTAAAAAGGCCGAAAGAGACAAAAATAAATGA ATAAATTGAATAAAAGTGCAGATAAATGGAGAATTCGAGGAAGATATTCACAAAATCGAGATCTT TTCCTCGGAGTTTCTTCGGATGAGGCGTTGCTGTTTCCAAAACGAACACAGCAACTCGCGGGCAC TGCGGAGCCGATTCGGCGCCAAAATTAACGCTTTTTAGCGTCATCTGCGTCAAATTGAACGGCGA AACCGAATTAATTACNAAAAACTAAATTAATTTGCGCCTTTAAGTGTTAAAAACGGGCCAAGAGG CGCAAAAAGANGGGGAGCAGCCGTCCCTGTGCTCCGACAGCCCCAGCTGTACAGACAGCATGCGG CGCTGGCAGTGCGTGTGCCNGGTTTAAAATTAAATTAAATTATTT Right flanking sequence: Indices 3839 -- 4338 AATTTGTGGATTCTTTGTTTTCACCCGAGCNTTCGCGCGGAACCACCTCCAANCCCCGCNGGCCC CCGNCTGTCTTTGATCGGATCGGACTTGTTCGGGGCTCTTTTTCTCTTCTTTTTCTCTCCTTTTG AATTCTTCTTTTNCCAAAATTAATTTTATTTTACTTTAAGAACTTCAAACTCTCCGGGACGCCCC TTGTTGCTGCTTTTCTCNCCGAGGCNCACGGACCCCCCAGCGCCAAAANTGNCCTGCAGACTGCA AAGAAAATGCAGCAGCAGCAGACGCAGCAGCANGATCCGCAGCAGCAGCAGCAGCAACAGCANGC AGCAACAGCAGCNAGCAGCAGNCAGCAAANAAACCCAGNACNAGCTCNGCCCAATGCCGGAGGGG ATGCCCTCAGCGGCAGCTTTGACTCGAGCCATGAGAGGTAAATAAATTAATTTTAAAAGAATTTC TTTTTTTCCCTTTAAAANTCTTCTAAAGCACTTTTCTCTCAACTC Found at i:3956 original size:11 final size:11 Alignment explanation

Indices: 3940--3967 Score: 49 Period size: 11 Copynumber: 2.5 Consensus size: 11 3930 TGTTCGGGGC 3940 TCTTTTTCTCT 1 TCTTTTTCTCT 3951 TCTTTTTCTCT 1 TCTTTTTCTCT * 3962 CCTTTT 1 TCTTTT 3968 GAATTCTTCT Statistics Matches: 16, Mismatches: 1, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 11 16 1.00 ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71 Consensus pattern (11 bp): TCTTTTTCTCT Left flanking sequence: Indices 3440 -- 3939 AATGAATAAATTGAATAAAAGTGCAGATAAATGGAGAATTCGAGGAAGATATTCACAAAATCGAG ATCTTTTCCTCGGAGTTTCTTCGGATGAGGCGTTGCTGTTTCCAAAACGAACACAGCAACTCGCG GGCACTGCGGAGCCGATTCGGCGCCAAAATTAACGCTTTTTAGCGTCATCTGCGTCAAATTGAAC GGCGAAACCGAATTAATTACNAAAAACTAAATTAATTTGCGCCTTTAAGTGTTAAAAACGGGCCA AGAGGCGCAAAAAGANGGGGAGCAGCCGTCCCTGTGCTCCGACAGCCCCAGCTGTACAGACAGCA TGCGGCGCTGGCAGTGCGTGTGCCNGGTTTAAAATTAAATTAAATTATTTATTTTAATAAATTTG ANTAAATTTAATTTGTGGATTCTTTGTTTTCACCCGAGCNTTCGCGCGGAACCACCTCCAANCCC CGCNGGCCCCCGNCTGTCTTTGATCGGATCGGACTTGTTCGGGGC Right flanking sequence: Indices 3968 -- 4467 GAATTCTTCTTTTNCCAAAATTAATTTTATTTTACTTTAAGAACTTCAAACTCTCCGGGACGCCC CTTGTTGCTGCTTTTCTCNCCGAGGCNCACGGACCCCCCAGCGCCAAAANTGNCCTGCAGACTGC AAAGAAAATGCAGCAGCAGCAGACGCAGCAGCANGATCCGCAGCAGCAGCAGCAGCAACAGCANG CAGCAACAGCAGCNAGCAGCAGNCAGCAAANAAACCCAGNACNAGCTCNGCCCAATGCCGGAGGG GATGCCCTCAGCGGCAGCTTTGACTCGAGCCATGAGAGGTAAATAAATTAATTTTAAAAGAATTT CTTTTTTTCCCTTTAAAANTCTTCTAAAGCACTTTTCTCTCAACTCCAGTCTTCACTTTTCNTTC ACTTTGTTTCCCNTCGCCAGCCCNGCAGCAAATAGCCCAGCAGCAGCAGNCAGCAGCAGCAGCAA CAGCAGCAGCAGCAGCAACTAAAATCATTTGCTTCAGCGCCTCGA Found at i:4001 original size:5 final size:5 Alignment explanation

Indices: 3991--4006 Score: 25 Period size: 5 Copynumber: 3.2 Consensus size: 5 3981 NCCAAAATTA * 3991 ATTTT ATTTT ACTTT A 1 ATTTT ATTTT ATTTT A 4007 AGAACTTCAA Statistics Matches: 10, Mismatches: 1, Indels: 0 0.91 0.09 0.00 Matches are distributed among these distances: 5 10 1.00 ACGTcount: A:0.25, C:0.06, G:0.00, T:0.69 Consensus pattern (5 bp): ATTTT Left flanking sequence: Indices 3491 -- 3990 TTCACAAAATCGAGATCTTTTCCTCGGAGTTTCTTCGGATGAGGCGTTGCTGTTTCCAAAACGAA CACAGCAACTCGCGGGCACTGCGGAGCCGATTCGGCGCCAAAATTAACGCTTTTTAGCGTCATCT GCGTCAAATTGAACGGCGAAACCGAATTAATTACNAAAAACTAAATTAATTTGCGCCTTTAAGTG TTAAAAACGGGCCAAGAGGCGCAAAAAGANGGGGAGCAGCCGTCCCTGTGCTCCGACAGCCCCAG CTGTACAGACAGCATGCGGCGCTGGCAGTGCGTGTGCCNGGTTTAAAATTAAATTAAATTATTTA TTTTAATAAATTTGANTAAATTTAATTTGTGGATTCTTTGTTTTCACCCGAGCNTTCGCGCGGAA CCACCTCCAANCCCCGCNGGCCCCCGNCTGTCTTTGATCGGATCGGACTTGTTCGGGGCTCTTTT TCTCTTCTTTTTCTCTCCTTTTGAATTCTTCTTTTNCCAAAATTA Right flanking sequence: Indices 4007 -- 4506 AGAACTTCAAACTCTCCGGGACGCCCCTTGTTGCTGCTTTTCTCNCCGAGGCNCACGGACCCCCC AGCGCCAAAANTGNCCTGCAGACTGCAAAGAAAATGCAGCAGCAGCAGACGCAGCAGCANGATCC GCAGCAGCAGCAGCAGCAACAGCANGCAGCAACAGCAGCNAGCAGCAGNCAGCAAANAAACCCAG NACNAGCTCNGCCCAATGCCGGAGGGGATGCCCTCAGCGGCAGCTTTGACTCGAGCCATGAGAGG TAAATAAATTAATTTTAAAAGAATTTCTTTTTTTCCCTTTAAAANTCTTCTAAAGCACTTTTCTC TCAACTCCAGTCTTCACTTTTCNTTCACTTTGTTTCCCNTCGCCAGCCCNGCAGCAAATAGCCCA GCAGCAGCAGNCAGCAGCAGCAGCAACAGCAGCAGCAGCAGCAACTAAAATCATTTGCTTCAGCG CCTCGAGGCGTTTTTGCTGCTACTCGATTTCTGTTTTTANTAATT Found at i:4115 original size:3 final size:3 Alignment explanation

Indices: 4107--4190 Score: 85 Period size: 3 Copynumber: 27.0 Consensus size: 3 4097 CAAAGAAAAT ** ** * * 4107 GCA GCA GCA GCA GAC GCA GCA GCA NGA TCC GCA GCA GCA GCA GCA GCA 1 GCA GCA GCA GCA GCA GCA GCA GCA GCA GCA GCA GCA GCA GCA GCA GCA * * 4155 ACA GCA NGCA GCA ACA GCA GCNA GCA GCA GNCA GCA 1 GCA GCA -GCA GCA GCA GCA GC-A GCA GCA G-CA GCA 4191 AANAAACCCA Statistics Matches: 63, Mismatches: 15, Indels: 6 0.75 0.18 0.07 Matches are distributed among these distances: 3 54 0.86 4 9 0.14 ACGTcount: A:0.33, C:0.32, G:0.29, T:0.01 Consensus pattern (3 bp): GCA Left flanking sequence: Indices 3607 -- 4106 TTTTAGCGTCATCTGCGTCAAATTGAACGGCGAAACCGAATTAATTACNAAAAACTAAATTAATT TGCGCCTTTAAGTGTTAAAAACGGGCCAAGAGGCGCAAAAAGANGGGGAGCAGCCGTCCCTGTGC TCCGACAGCCCCAGCTGTACAGACAGCATGCGGCGCTGGCAGTGCGTGTGCCNGGTTTAAAATTA AATTAAATTATTTATTTTAATAAATTTGANTAAATTTAATTTGTGGATTCTTTGTTTTCACCCGA GCNTTCGCGCGGAACCACCTCCAANCCCCGCNGGCCCCCGNCTGTCTTTGATCGGATCGGACTTG TTCGGGGCTCTTTTTCTCTTCTTTTTCTCTCCTTTTGAATTCTTCTTTTNCCAAAATTAATTTTA TTTTACTTTAAGAACTTCAAACTCTCCGGGACGCCCCTTGTTGCTGCTTTTCTCNCCGAGGCNCA CGGACCCCCCAGCGCCAAAANTGNCCTGCAGACTGCAAAGAAAAT Right flanking sequence: Indices 4191 -- 4690 AANAAACCCAGNACNAGCTCNGCCCAATGCCGGAGGGGATGCCCTCAGCGGCAGCTTTGACTCGA GCCATGAGAGGTAAATAAATTAATTTTAAAAGAATTTCTTTTTTTCCCTTTAAAANTCTTCTAAA GCACTTTTCTCTCAACTCCAGTCTTCACTTTTCNTTCACTTTGTTTCCCNTCGCCAGCCCNGCAG CAAATAGCCCAGCAGCAGCAGNCAGCAGCAGCAGCAACAGCAGCAGCAGCAGCAACTAAAATCAT TTGCTTCAGCGCCTCGAGGCGTTTTTGCTGCTACTCGATTTCTGTTTTTANTAATTTCTTTAATT CTTTTTANTTTTTTAATTTGGAATTTAATTCCATTTGCTTTCCACTCTTTTGCTGCTGCTCATTT CCTTAATTCTTTTTGCTGCTGCTCCTGCTTCCCTTTTTGCTGCTGCTGCTTCGTTTTTTGCGGCA GTTGATTCCCCTCTTGCTGCTGCTGCTTTGCCTTTTGCTGCTGCT Found at i:4403 original size:3 final size:3 Alignment explanation

Indices: 4395--4439 Score: 74 Period size: 3 Copynumber: 14.7 Consensus size: 3 4385 GCAAATAGCC * 4395 CAG CAG CAG CAG NCAG CAG CAG CAG CAA CAG CAG CAG CAG CAG CA 1 CAG CAG CAG CAG -CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CA 4440 ACTAAAATCA Statistics Matches: 39, Mismatches: 2, Indels: 2 0.91 0.05 0.05 Matches are distributed among these distances: 3 36 0.92 4 3 0.08 ACGTcount: A:0.36, C:0.33, G:0.29, T:0.00 Consensus pattern (3 bp): CAG Left flanking sequence: Indices 3895 -- 4394 CGCNGGCCCCCGNCTGTCTTTGATCGGATCGGACTTGTTCGGGGCTCTTTTTCTCTTCTTTTTCT CTCCTTTTGAATTCTTCTTTTNCCAAAATTAATTTTATTTTACTTTAAGAACTTCAAACTCTCCG GGACGCCCCTTGTTGCTGCTTTTCTCNCCGAGGCNCACGGACCCCCCAGCGCCAAAANTGNCCTG CAGACTGCAAAGAAAATGCAGCAGCAGCAGACGCAGCAGCANGATCCGCAGCAGCAGCAGCAGCA ACAGCANGCAGCAACAGCAGCNAGCAGCAGNCAGCAAANAAACCCAGNACNAGCTCNGCCCAATG CCGGAGGGGATGCCCTCAGCGGCAGCTTTGACTCGAGCCATGAGAGGTAAATAAATTAATTTTAA AAGAATTTCTTTTTTTCCCTTTAAAANTCTTCTAAAGCACTTTTCTCTCAACTCCAGTCTTCACT TTTCNTTCACTTTGTTTCCCNTCGCCAGCCCNGCAGCAAATAGCC Right flanking sequence: Indices 4440 -- 4939 ACTAAAATCATTTGCTTCAGCGCCTCGAGGCGTTTTTGCTGCTACTCGATTTCTGTTTTTANTAA TTTCTTTAATTCTTTTTANTTTTTTAATTTGGAATTTAATTCCATTTGCTTTCCACTCTTTTGCT GCTGCTCATTTCCTTAATTCTTTTTGCTGCTGCTCCTGCTTCCCTTTTTGCTGCTGCTGCTTCGT TTTTTGCGGCAGTTGATTCCCCTCTTGCTGCTGCTGCTTTGCCTTTTGCTGCTGCTGCTTCGCCT TTTGCTGCTGCTGATTCCCCTCTTGCTGCTGCTGTTTCTTTTGCTGCTGCTGATTCCCCTCTTGC TAATGCTGTTTCTTTTGCTGCTGCTGCTTCNTTCTCTTGCTGCCGCNTGCTGCTTTTGCGTTTGC TGCTGCTGNCTCCCCCNTNCTTGCTGCTGCTGCTTTTCCTTTTGTTGCTGNCTGCTTCTCCTCTT GCNTGCTGCTGCTGCTTTTCCTTTTGCTGCCGCTGCTCCCCCTCT Found at i:4405 original size:18 final size:17 Alignment explanation

Indices: 4382--4436 Score: 59 Period size: 15 Copynumber: 3.4 Consensus size: 17 4372 CGCCAGCCCN * 4382 GCAGCAAATAGCCCAGCA 1 GCAGCAAACAG-CCAGCA ** 4400 GCAGCAGNCAG-CAGCA 1 GCAGCAAACAGCCAGCA 4416 GCAGC-AACAG-CAGCA 1 GCAGCAAACAGCCAGCA 4431 GCAGCA 1 GCAGCA 4437 GCAACTAAAA Statistics Matches: 31, Mismatches: 5, Indels: 4 0.78 0.12 0.10 Matches are distributed among these distances: 15 13 0.42 16 10 0.32 18 8 0.26 ACGTcount: A:0.36, C:0.33, G:0.27, T:0.02 Consensus pattern (17 bp): GCAGCAAACAGCCAGCA Left flanking sequence: Indices 3882 -- 4381 CACCTCCAANCCCCGCNGGCCCCCGNCTGTCTTTGATCGGATCGGACTTGTTCGGGGCTCTTTTT CTCTTCTTTTTCTCTCCTTTTGAATTCTTCTTTTNCCAAAATTAATTTTATTTTACTTTAAGAAC TTCAAACTCTCCGGGACGCCCCTTGTTGCTGCTTTTCTCNCCGAGGCNCACGGACCCCCCAGCGC CAAAANTGNCCTGCAGACTGCAAAGAAAATGCAGCAGCAGCAGACGCAGCAGCANGATCCGCAGC AGCAGCAGCAGCAACAGCANGCAGCAACAGCAGCNAGCAGCAGNCAGCAAANAAACCCAGNACNA GCTCNGCCCAATGCCGGAGGGGATGCCCTCAGCGGCAGCTTTGACTCGAGCCATGAGAGGTAAAT AAATTAATTTTAAAAGAATTTCTTTTTTTCCCTTTAAAANTCTTCTAAAGCACTTTTCTCTCAAC TCCAGTCTTCACTTTTCNTTCACTTTGTTTCCCNTCGCCAGCCCN Right flanking sequence: Indices 4437 -- 4936 GCAACTAAAATCATTTGCTTCAGCGCCTCGAGGCGTTTTTGCTGCTACTCGATTTCTGTTTTTAN TAATTTCTTTAATTCTTTTTANTTTTTTAATTTGGAATTTAATTCCATTTGCTTTCCACTCTTTT GCTGCTGCTCATTTCCTTAATTCTTTTTGCTGCTGCTCCTGCTTCCCTTTTTGCTGCTGCTGCTT CGTTTTTTGCGGCAGTTGATTCCCCTCTTGCTGCTGCTGCTTTGCCTTTTGCTGCTGCTGCTTCG CCTTTTGCTGCTGCTGATTCCCCTCTTGCTGCTGCTGTTTCTTTTGCTGCTGCTGATTCCCCTCT TGCTAATGCTGTTTCTTTTGCTGCTGCTGCTTCNTTCTCTTGCTGCCGCNTGCTGCTTTTGCGTT TGCTGCTGCTGNCTCCCCCNTNCTTGCTGCTGCTGCTTTTCCTTTTGTTGCTGNCTGCTTCTCCT CTTGCNTGCTGCTGCTGCTTTTCCTTTTGCTGCCGCTGCTCCCCC Found at i:4528 original size:8 final size:8 Alignment explanation

Indices: 4502--4534 Score: 32 Period size: 8 Copynumber: 3.8 Consensus size: 8 4492 CTGTTTTTAN 4502 TAATTTCTT 1 TAATTT-TT 4511 TAATTCTTTT 1 TAA-T-TTTT * 4521 TANTTTTT 1 TAATTTTT 4529 TAATTT 1 TAATTT 4535 GGAATTTAAT Statistics Matches: 20, Mismatches: 2, Indels: 5 0.74 0.07 0.19 Matches are distributed among these distances: 8 9 0.45 9 4 0.20 10 5 0.25 11 2 0.10 ACGTcount: A:0.21, C:0.06, G:0.00, T:0.70 Consensus pattern (8 bp): TAATTTTT Left flanking sequence: Indices 4002 -- 4501 CTTTAAGAACTTCAAACTCTCCGGGACGCCCCTTGTTGCTGCTTTTCTCNCCGAGGCNCACGGAC CCCCCAGCGCCAAAANTGNCCTGCAGACTGCAAAGAAAATGCAGCAGCAGCAGACGCAGCAGCAN GATCCGCAGCAGCAGCAGCAGCAACAGCANGCAGCAACAGCAGCNAGCAGCAGNCAGCAAANAAA CCCAGNACNAGCTCNGCCCAATGCCGGAGGGGATGCCCTCAGCGGCAGCTTTGACTCGAGCCATG AGAGGTAAATAAATTAATTTTAAAAGAATTTCTTTTTTTCCCTTTAAAANTCTTCTAAAGCACTT TTCTCTCAACTCCAGTCTTCACTTTTCNTTCACTTTGTTTCCCNTCGCCAGCCCNGCAGCAAATA GCCCAGCAGCAGCAGNCAGCAGCAGCAGCAACAGCAGCAGCAGCAGCAACTAAAATCATTTGCTT CAGCGCCTCGAGGCGTTTTTGCTGCTACTCGATTTCTGTTTTTAN Right flanking sequence: Indices 4535 -- 5034 GGAATTTAATTCCATTTGCTTTCCACTCTTTTGCTGCTGCTCATTTCCTTAATTCTTTTTGCTGC TGCTCCTGCTTCCCTTTTTGCTGCTGCTGCTTCGTTTTTTGCGGCAGTTGATTCCCCTCTTGCTG CTGCTGCTTTGCCTTTTGCTGCTGCTGCTTCGCCTTTTGCTGCTGCTGATTCCCCTCTTGCTGCT GCTGTTTCTTTTGCTGCTGCTGATTCCCCTCTTGCTAATGCTGTTTCTTTTGCTGCTGCTGCTTC NTTCTCTTGCTGCCGCNTGCTGCTTTTGCGTTTGCTGCTGCTGNCTCCCCCNTNCTTGCTGCTGC TGCTTTTCCTTTTGTTGCTGNCTGCTTCTCCTCTTGCNTGCTGCTGCTGCTTTTCCTTTTGCTGC CGCTGCTCCCCCTCTTGCNTNGCNTGCTCCTTCCCTTCTTGCTGCTTCTGCTTCCCTTTTTGCTG TTGTTGCTTTCCGTCTTGCTGCNTGGTGTNTCCTTCTTTTGCTGC Found at i:4581 original size:24 final size:24 Alignment explanation

Indices: 4554--4627 Score: 66 Period size: 24 Copynumber: 2.9 Consensus size: 24 4544 TTCCATTTGC 4554 TTTCCACTCTTTTGCTGCTGCTCA 1 TTTCCACTCTTTTGCTGCTGCTCA * * 4578 TTTCCTTAATTCTTTTTGCTGCTGCTCC 1 TTTCC---ACTC-TTTTGCTGCTGCTCA 4606 TGCTTCC-CT-TTTTGCTGCTGCT 1 T--TTCCACTCTTTTGCTGCTGCT 4628 GCTTCGTTTT Statistics Matches: 41, Mismatches: 3, Indels: 12 0.73 0.05 0.21 Matches are distributed among these distances: 24 18 0.44 26 1 0.02 27 3 0.07 28 15 0.37 30 4 0.10 ACGTcount: A:0.05, C:0.31, G:0.14, T:0.50 Consensus pattern (24 bp): TTTCCACTCTTTTGCTGCTGCTCA Left flanking sequence: Indices 4054 -- 4553 GAGGCNCACGGACCCCCCAGCGCCAAAANTGNCCTGCAGACTGCAAAGAAAATGCAGCAGCAGCA GACGCAGCAGCANGATCCGCAGCAGCAGCAGCAGCAACAGCANGCAGCAACAGCAGCNAGCAGCA GNCAGCAAANAAACCCAGNACNAGCTCNGCCCAATGCCGGAGGGGATGCCCTCAGCGGCAGCTTT GACTCGAGCCATGAGAGGTAAATAAATTAATTTTAAAAGAATTTCTTTTTTTCCCTTTAAAANTC TTCTAAAGCACTTTTCTCTCAACTCCAGTCTTCACTTTTCNTTCACTTTGTTTCCCNTCGCCAGC CCNGCAGCAAATAGCCCAGCAGCAGCAGNCAGCAGCAGCAGCAACAGCAGCAGCAGCAGCAACTA AAATCATTTGCTTCAGCGCCTCGAGGCGTTTTTGCTGCTACTCGATTTCTGTTTTTANTAATTTC TTTAATTCTTTTTANTTTTTTAATTTGGAATTTAATTCCATTTGC Right flanking sequence: Indices 4628 -- 5127 GCTTCGTTTTTTGCGGCAGTTGATTCCCCTCTTGCTGCTGCTGCTTTGCCTTTTGCTGCTGCTGC TTCGCCTTTTGCTGCTGCTGATTCCCCTCTTGCTGCTGCTGTTTCTTTTGCTGCTGCTGATTCCC CTCTTGCTAATGCTGTTTCTTTTGCTGCTGCTGCTTCNTTCTCTTGCTGCCGCNTGCTGCTTTTG CGTTTGCTGCTGCTGNCTCCCCCNTNCTTGCTGCTGCTGCTTTTCCTTTTGTTGCTGNCTGCTTC TCCTCTTGCNTGCTGCTGCTGCTTTTCCTTTTGCTGCCGCTGCTCCCCCTCTTGCNTNGCNTGCT CCTTCCCTTCTTGCTGCTTCTGCTTCCCTTTTTGCTGTTGTTGCTTTCCGTCTTGCTGCNTGGTG TNTCCTTCTTTTGCTGCTGCTGCTTCCGCTCTTGCTGCTGCTGCTGTCCCTGCTGCTCCTTCCGC TCTTGCTGCTGCTGCTTCCTCTTTTGCTGCTGCTGCTCCCCGTTT Found at i:4602 original size:3 final size:3 Alignment explanation

Indices: 4594--4609 Score: 25 Period size: 3 Copynumber: 5.3 Consensus size: 3 4584 TAATTCTTTT * 4594 TGC TGC TGC TCC TGC T 1 TGC TGC TGC TGC TGC T 4610 TCCCTTTTTG 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:0.00, C:0.38, G:0.25, T:0.38 Consensus pattern (3 bp): TGC Left flanking sequence: Indices 4094 -- 4593 CTGCAAAGAAAATGCAGCAGCAGCAGACGCAGCAGCANGATCCGCAGCAGCAGCAGCAGCAACAG CANGCAGCAACAGCAGCNAGCAGCAGNCAGCAAANAAACCCAGNACNAGCTCNGCCCAATGCCGG AGGGGATGCCCTCAGCGGCAGCTTTGACTCGAGCCATGAGAGGTAAATAAATTAATTTTAAAAGA ATTTCTTTTTTTCCCTTTAAAANTCTTCTAAAGCACTTTTCTCTCAACTCCAGTCTTCACTTTTC NTTCACTTTGTTTCCCNTCGCCAGCCCNGCAGCAAATAGCCCAGCAGCAGCAGNCAGCAGCAGCA GCAACAGCAGCAGCAGCAGCAACTAAAATCATTTGCTTCAGCGCCTCGAGGCGTTTTTGCTGCTA CTCGATTTCTGTTTTTANTAATTTCTTTAATTCTTTTTANTTTTTTAATTTGGAATTTAATTCCA TTTGCTTTCCACTCTTTTGCTGCTGCTCATTTCCTTAATTCTTTT Right flanking sequence: Indices 4610 -- 5109 TCCCTTTTTGCTGCTGCTGCTTCGTTTTTTGCGGCAGTTGATTCCCCTCTTGCTGCTGCTGCTTT GCCTTTTGCTGCTGCTGCTTCGCCTTTTGCTGCTGCTGATTCCCCTCTTGCTGCTGCTGTTTCTT TTGCTGCTGCTGATTCCCCTCTTGCTAATGCTGTTTCTTTTGCTGCTGCTGCTTCNTTCTCTTGC TGCCGCNTGCTGCTTTTGCGTTTGCTGCTGCTGNCTCCCCCNTNCTTGCTGCTGCTGCTTTTCCT TTTGTTGCTGNCTGCTTCTCCTCTTGCNTGCTGCTGCTGCTTTTCCTTTTGCTGCCGCTGCTCCC CCTCTTGCNTNGCNTGCTCCTTCCCTTCTTGCTGCTTCTGCTTCCCTTTTTGCTGTTGTTGCTTT CCGTCTTGCTGCNTGGTGTNTCCTTCTTTTGCTGCTGCTGCTTCCGCTCTTGCTGCTGCTGCTGT CCCTGCTGCTCCTTCCGCTCTTGCTGCTGCTGCTTCCTCTTTTGC Found at i:4623 original size:21 final size:21 Alignment explanation

Indices: 4597--5223 Score: 483 Period size: 21 Copynumber: 29.6 Consensus size: 21 4587 TTCTTTTTGC * * 4597 TGCTGCTCCTGCTTCCCTTTT 1 TGCTGCTGCTGCTTCCCCTTT *** 4618 TGCTGCTGCTGCTTCGTTTTT 1 TGCTGCTGCTGCTTCCCCTTT * * * * * 4639 TGCGGCAGTTGATTCCCCTCT 1 TGCTGCTGCTGCTTCCCCTTT ** 4660 TGCTGCTGCTGCTTTGCCTTT 1 TGCTGCTGCTGCTTCCCCTTT * 4681 TGCTGCTGCTGCTTCGCCTTT 1 TGCTGCTGCTGCTTCCCCTTT * * 4702 TGCTGCTGCTGATTCCCCTCT 1 TGCTGCTGCTGCTTCCCCTTT * 4723 TGCTGCTGCTG-TT--TCTTT 1 TGCTGCTGCTGCTTCCCCTTT * * 4741 TGCTGCTGCTGATTCCCCTCT 1 TGCTGCTGCTGCTTCCCCTTT ** * 4762 TGCTAATGCTG-TT--TCTTT 1 TGCTGCTGCTGCTTCCCCTTT * * 4780 TGCTGCTGCTGCTTCNTTCTCTTGC 1 TGCTGCTGCTGCTTC---CCCTT-T * *** * 4805 TGCCGCNTGCTGCTTTTGCGTT 1 TGCTGC-TGCTGCTTCCCCTTT * * 4827 TGCTGCTGCTGNCTCCCCCNTNCT 1 TGCTGCTGCTG-CTTCCCC-T-TT ** 4851 TGCTGCTGCTGCTTTTCCTTT 1 TGCTGCTGCTGCTTCCCCTTT * * 4872 TGTTGCTGNCTGCTTCTCCTCTTGCN 1 TGCTGCTG-CTGCTTC-CC-CTT--T ** 4898 TGCTGCTGCTGCTTTTCCTTT 1 TGCTGCTGCTGCTTCCCCTTT * * * 4919 TGCTGCCGCTGCTCCCCCTCT 1 TGCTGCTGCTGCTTCCCCTTT * * * 4940 TGCNTNGCNTGCTCCTTCCCTTCT 1 TGC-T-GC-TGCTGCTTCCCCTTT * * 4964 TGCTGCTTCTGCTTCCCTTTT 1 TGCTGCTGCTGCTTCCCCTTT * * * * * 4985 TGCTGTTGTTGCTTTCCGTCT 1 TGCTGCTGCTGCTTCCCCTTT * ** * 5006 TGCTGCNTGGTGTNTCCTTCTTT 1 TGCTGC-TGCTGCTTCC-CCTTT * * 5029 TGCTGCTGCTGCTTCCGCTCT 1 TGCTGCTGCTGCTTCCCCTTT ** 5050 TGCTGCTGCTGCTGTCCC--- 1 TGCTGCTGCTGCTTCCCCTTT * * * 5068 TGCTGCT-C-C-TTCCGCTCT 1 TGCTGCTGCTGCTTCCCCTTT * 5086 TGCTGCTGCTGCTTCCTCTTT 1 TGCTGCTGCTGCTTCCCCTTT * * 5107 TGCTGCTGCTGCTCCCCGTTT 1 TGCTGCTGCTGCTTCCCCTTT * * * 5128 TCCTGCTGCTGCCTCACCTTT 1 TGCTGCTGCTGCTTCCCCTTT * *** 5149 TGCTGCTGCTGCTCCTTTTTT 1 TGCTGCTGCTGCTTCCCCTTT * * 5170 TGCTGCTGCTGCCTCGCCTTT 1 TGCTGCTGCTGCTTCCCCTTT * * 5191 TGCTGCTGCTGCGT-CCCGTT 1 TGCTGCTGCTGCTTCCCCTTT 5211 TGCTGCTGCTGCT 1 TGCTGCTGCTGCT 5224 GCTGCTGCAC Statistics Matches: 454, Mismatches: 122, Indels: 61 0.71 0.19 0.10 Matches are distributed among these distances: 15 3 0.01 17 1 0.00 18 40 0.09 19 5 0.01 20 20 0.04 21 273 0.60 22 31 0.07 23 21 0.05 24 34 0.07 25 11 0.02 26 15 0.03 ACGTcount: A:0.01, C:0.33, G:0.21, T:0.43 Consensus pattern (21 bp): TGCTGCTGCTGCTTCCCCTTT Left flanking sequence: Indices 4097 -- 4596 CAAAGAAAATGCAGCAGCAGCAGACGCAGCAGCANGATCCGCAGCAGCAGCAGCAGCAACAGCAN GCAGCAACAGCAGCNAGCAGCAGNCAGCAAANAAACCCAGNACNAGCTCNGCCCAATGCCGGAGG GGATGCCCTCAGCGGCAGCTTTGACTCGAGCCATGAGAGGTAAATAAATTAATTTTAAAAGAATT TCTTTTTTTCCCTTTAAAANTCTTCTAAAGCACTTTTCTCTCAACTCCAGTCTTCACTTTTCNTT CACTTTGTTTCCCNTCGCCAGCCCNGCAGCAAATAGCCCAGCAGCAGCAGNCAGCAGCAGCAGCA ACAGCAGCAGCAGCAGCAACTAAAATCATTTGCTTCAGCGCCTCGAGGCGTTTTTGCTGCTACTC GATTTCTGTTTTTANTAATTTCTTTAATTCTTTTTANTTTTTTAATTTGGAATTTAATTCCATTT GCTTTCCACTCTTTTGCTGCTGCTCATTTCCTTAATTCTTTTTGC Right flanking sequence: Indices 5224 -- 5723 GCTGCTGCACTTCGCGTTNTTTGCTGCAGCGCAGCCTCCACTCCCCTTCAAGTTGCAAAAAAATG ATTATCATTTATTATTAATTAATTAATTAATTTATTTATTTATTTANTNTTATTNNTAATTCAGG ATTGTCNTGTGGCCCCCCACCTGTTCTGGGACACACAGCCAGTGGTGAAGGCAGCGGAGCGGGCG GCGCTGGCCCCACAGGTGCAGCAAAGTGGAAATGAATTTNAAATTCTTTTTTCGATTTTGGAATT AAAAGAGAATAAATGAATAATTAATTTAAATCAAGCANATTTGGGAAATCCAGNCGGAGACGAAG ATGCANGCAAATCCNGGCAAAAAGATNCTTCNGGAATTCACNTTTACCNGCAGCAAAATAANCTC CCNAGNCAGCAAAACGNCTATTTGCTGCTGCAGCAAAACAAATTCCGTTTTCTGCTCCCCTTTGT CCCTTTATCCCGCCTTATCTTCCTAATGCAGCAGCAGCAGCAGCA Found at i:4626 original size:3 final size:3 Alignment explanation

Indices: 4618--4630 Score: 26 Period size: 3 Copynumber: 4.3 Consensus size: 3 4608 CTTCCCTTTT 4618 TGC TGC TGC TGC T 1 TGC TGC TGC TGC T 4631 TCGTTTTTTG Statistics Matches: 10, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 3 10 1.00 ACGTcount: A:0.00, C:0.31, G:0.31, T:0.38 Consensus pattern (3 bp): TGC Left flanking sequence: Indices 4118 -- 4617 AGACGCAGCAGCANGATCCGCAGCAGCAGCAGCAGCAACAGCANGCAGCAACAGCAGCNAGCAGC AGNCAGCAAANAAACCCAGNACNAGCTCNGCCCAATGCCGGAGGGGATGCCCTCAGCGGCAGCTT TGACTCGAGCCATGAGAGGTAAATAAATTAATTTTAAAAGAATTTCTTTTTTTCCCTTTAAAANT CTTCTAAAGCACTTTTCTCTCAACTCCAGTCTTCACTTTTCNTTCACTTTGTTTCCCNTCGCCAG CCCNGCAGCAAATAGCCCAGCAGCAGCAGNCAGCAGCAGCAGCAACAGCAGCAGCAGCAGCAACT AAAATCATTTGCTTCAGCGCCTCGAGGCGTTTTTGCTGCTACTCGATTTCTGTTTTTANTAATTT CTTTAATTCTTTTTANTTTTTTAATTTGGAATTTAATTCCATTTGCTTTCCACTCTTTTGCTGCT GCTCATTTCCTTAATTCTTTTTGCTGCTGCTCCTGCTTCCCTTTT Right flanking sequence: Indices 4631 -- 5130 TCGTTTTTTGCGGCAGTTGATTCCCCTCTTGCTGCTGCTGCTTTGCCTTTTGCTGCTGCTGCTTC GCCTTTTGCTGCTGCTGATTCCCCTCTTGCTGCTGCTGTTTCTTTTGCTGCTGCTGATTCCCCTC TTGCTAATGCTGTTTCTTTTGCTGCTGCTGCTTCNTTCTCTTGCTGCCGCNTGCTGCTTTTGCGT TTGCTGCTGCTGNCTCCCCCNTNCTTGCTGCTGCTGCTTTTCCTTTTGTTGCTGNCTGCTTCTCC TCTTGCNTGCTGCTGCTGCTTTTCCTTTTGCTGCCGCTGCTCCCCCTCTTGCNTNGCNTGCTCCT TCCCTTCTTGCTGCTTCTGCTTCCCTTTTTGCTGTTGTTGCTTTCCGTCTTGCTGCNTGGTGTNT CCTTCTTTTGCTGCTGCTGCTTCCGCTCTTGCTGCTGCTGCTGTCCCTGCTGCTCCTTCCGCTCT TGCTGCTGCTGCTTCCTCTTTTGCTGCTGCTGCTCCCCGTTTTCC Found at i:4668 original size:3 final size:3 Alignment explanation

Indices: 4660--4910 Score: 45 Period size: 3 Copynumber: 81.3 Consensus size: 3 4650 ATTCCCCTCT * ** * ** ** 4660 TGC TGC TGC TGC T-T TGCC TTT TGC TGC TGC TGC TTC GCC TTT TGC 1 TGC TGC TGC TGC TGC TG-C TGC TGC TGC TGC TGC TGC TGC TGC TGC * * ** ** * * ** * 4705 TGC TGC TGA TTC CCC TCT TGC TGC TGC TGT TTC TTT TGC TGC TGC TGA 1 TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC * ** ** ** * * ** * * 4753 TTC CCC TCT TGC TAA TGC TGT TTC TTT TGC TGC TGC TGC TTC NTTC 1 TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC -TGC ** * ** *** * ** 4799 TCT TGC TGC CGC NTGC TGC TTT TGC GTT TGC TGC TGC TGNC TCC CCC 1 TGC TGC TGC TGC -TGC TGC TGC TGC TGC TGC TGC TGC TG-C TGC TGC * ** * ** * * * ** 4846 NTNC TTGC TGC TGC TGC TTT TCC TTT TGT TGC TGNC TGC TTC TCC TCT 1 -TGC -TGC TGC TGC TGC TGC TGC TGC TGC TGC TG-C TGC TGC TGC TGC 4894 TGC NTGC TGC TGC TGC T 1 TGC -TGC TGC TGC TGC T 4911 TTTCCTTTTG Statistics Matches: 156, Mismatches: 84, Indels: 16 0.61 0.33 0.06 Matches are distributed among these distances: 2 1 0.01 3 138 0.88 4 17 0.11 ACGTcount: A:0.02, C:0.31, G:0.21, T:0.43 Consensus pattern (3 bp): TGC Left flanking sequence: Indices 4160 -- 4659 ANGCAGCAACAGCAGCNAGCAGCAGNCAGCAAANAAACCCAGNACNAGCTCNGCCCAATGCCGGA GGGGATGCCCTCAGCGGCAGCTTTGACTCGAGCCATGAGAGGTAAATAAATTAATTTTAAAAGAA TTTCTTTTTTTCCCTTTAAAANTCTTCTAAAGCACTTTTCTCTCAACTCCAGTCTTCACTTTTCN TTCACTTTGTTTCCCNTCGCCAGCCCNGCAGCAAATAGCCCAGCAGCAGCAGNCAGCAGCAGCAG CAACAGCAGCAGCAGCAGCAACTAAAATCATTTGCTTCAGCGCCTCGAGGCGTTTTTGCTGCTAC TCGATTTCTGTTTTTANTAATTTCTTTAATTCTTTTTANTTTTTTAATTTGGAATTTAATTCCAT TTGCTTTCCACTCTTTTGCTGCTGCTCATTTCCTTAATTCTTTTTGCTGCTGCTCCTGCTTCCCT TTTTGCTGCTGCTGCTTCGTTTTTTGCGGCAGTTGATTCCCCTCT Right flanking sequence: Indices 4911 -- 5410 TTTCCTTTTGCTGCCGCTGCTCCCCCTCTTGCNTNGCNTGCTCCTTCCCTTCTTGCTGCTTCTGC TTCCCTTTTTGCTGTTGTTGCTTTCCGTCTTGCTGCNTGGTGTNTCCTTCTTTTGCTGCTGCTGC TTCCGCTCTTGCTGCTGCTGCTGTCCCTGCTGCTCCTTCCGCTCTTGCTGCTGCTGCTTCCTCTT TTGCTGCTGCTGCTCCCCGTTTTCCTGCTGCTGCCTCACCTTTTGCTGCTGCTGCTCCTTTTTTT GCTGCTGCTGCCTCGCCTTTTGCTGCTGCTGCGTCCCGTTTGCTGCTGCTGCTGCTGCTGCACTT CGCGTTNTTTGCTGCAGCGCAGCCTCCACTCCCCTTCAAGTTGCAAAAAAATGATTATCATTTAT TATTAATTAATTAATTAATTTATTTATTTATTTANTNTTATTNNTAATTCAGGATTGTCNTGTGG CCCCCCACCTGTTCTGGGACACACAGCCAGTGGTGAAGGCAGCGG Found at i:4921 original size:92 final size:85 Alignment explanation

Indices: 4723--4942 Score: 261 Period size: 92 Copynumber: 2.5 Consensus size: 85 4713 ATTCCCCTCT * * * * 4723 TGCTGCTGCTGTTTCTTTTGCTGCTGCTGATTCCCCTCTTGCTAATGCTGTTTCTTTTGCTGCTG 1 TGCTGCTGCTTTTCCTTTTGCTGCTGCTGCTCCCCCTCTTGCTAATGCTGTTTCTTTTGCTGCTG * * 4788 CTGCTTCNTTCTCTTGCTGC 66 CTGCTTCATCCTCTTGCTGC * * * ** 4808 CGCNTGCTGCTTTTGCGTTTGCTGCTGCTGNCTCCCCCNTNCTTGCTGCTGCTGCTTTTCCTTTT 1 TGC-TGCTGCTTTTCCTTTTGCTGCTGCTG-CTCCCCC-T-CTTGCTAATGCTG--TTT-CTTTT * 4873 GTTGCTGNCTGCTTC-TCCTCTTGCNTGC 59 GCTGCTG-CTGCTTCATCCTCTTGC-TGC * 4901 TGCTGCTGCTTTTCCTTTTGCTGCCGCTGCTCCCCCTCTTGC 1 TGCTGCTGCTTTTCCTTTTGCTGCTGCTGCTCCCCCTCTTGC 4943 NTNGCNTGCT Statistics Matches: 112, Mismatches: 14, Indels: 14 0.80 0.10 0.10 Matches are distributed among these distances: 85 2 0.02 86 23 0.21 87 5 0.04 88 1 0.01 89 16 0.14 90 1 0.01 91 10 0.09 92 42 0.38 93 12 0.11 ACGTcount: A:0.01, C:0.32, G:0.20, T:0.43 Consensus pattern (85 bp): TGCTGCTGCTTTTCCTTTTGCTGCTGCTGCTCCCCCTCTTGCTAATGCTGTTTCTTTTGCTGCTG CTGCTTCATCCTCTTGCTGC Left flanking sequence: Indices 4223 -- 4722 GAGGGGATGCCCTCAGCGGCAGCTTTGACTCGAGCCATGAGAGGTAAATAAATTAATTTTAAAAG AATTTCTTTTTTTCCCTTTAAAANTCTTCTAAAGCACTTTTCTCTCAACTCCAGTCTTCACTTTT CNTTCACTTTGTTTCCCNTCGCCAGCCCNGCAGCAAATAGCCCAGCAGCAGCAGNCAGCAGCAGC AGCAACAGCAGCAGCAGCAGCAACTAAAATCATTTGCTTCAGCGCCTCGAGGCGTTTTTGCTGCT ACTCGATTTCTGTTTTTANTAATTTCTTTAATTCTTTTTANTTTTTTAATTTGGAATTTAATTCC ATTTGCTTTCCACTCTTTTGCTGCTGCTCATTTCCTTAATTCTTTTTGCTGCTGCTCCTGCTTCC CTTTTTGCTGCTGCTGCTTCGTTTTTTGCGGCAGTTGATTCCCCTCTTGCTGCTGCTGCTTTGCC TTTTGCTGCTGCTGCTTCGCCTTTTGCTGCTGCTGATTCCCCTCT Right flanking sequence: Indices 4943 -- 5442 NTNGCNTGCTCCTTCCCTTCTTGCTGCTTCTGCTTCCCTTTTTGCTGTTGTTGCTTTCCGTCTTG CTGCNTGGTGTNTCCTTCTTTTGCTGCTGCTGCTTCCGCTCTTGCTGCTGCTGCTGTCCCTGCTG CTCCTTCCGCTCTTGCTGCTGCTGCTTCCTCTTTTGCTGCTGCTGCTCCCCGTTTTCCTGCTGCT GCCTCACCTTTTGCTGCTGCTGCTCCTTTTTTTGCTGCTGCTGCCTCGCCTTTTGCTGCTGCTGC GTCCCGTTTGCTGCTGCTGCTGCTGCTGCACTTCGCGTTNTTTGCTGCAGCGCAGCCTCCACTCC CCTTCAAGTTGCAAAAAAATGATTATCATTTATTATTAATTAATTAATTAATTTATTTATTTATT TANTNTTATTNNTAATTCAGGATTGTCNTGTGGCCCCCCACCTGTTCTGGGACACACAGCCAGTG GTGAAGGCAGCGGAGCGGGCGGCGCTGGCCCCACAGGTGCAGCAA Found at i:4977 original size:6 final size:6 Alignment explanation

Indices: 4966--4978 Score: 26 Period size: 6 Copynumber: 2.2 Consensus size: 6 4956 TCCCTTCTTG 4966 CTGCTT CTGCTT C 1 CTGCTT CTGCTT C 4979 CCTTTTTGCT 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:0.38, G:0.15, T:0.46 Consensus pattern (6 bp): CTGCTT Left flanking sequence: Indices 4466 -- 4965 GAGGCGTTTTTGCTGCTACTCGATTTCTGTTTTTANTAATTTCTTTAATTCTTTTTANTTTTTTA ATTTGGAATTTAATTCCATTTGCTTTCCACTCTTTTGCTGCTGCTCATTTCCTTAATTCTTTTTG CTGCTGCTCCTGCTTCCCTTTTTGCTGCTGCTGCTTCGTTTTTTGCGGCAGTTGATTCCCCTCTT GCTGCTGCTGCTTTGCCTTTTGCTGCTGCTGCTTCGCCTTTTGCTGCTGCTGATTCCCCTCTTGC TGCTGCTGTTTCTTTTGCTGCTGCTGATTCCCCTCTTGCTAATGCTGTTTCTTTTGCTGCTGCTG CTTCNTTCTCTTGCTGCCGCNTGCTGCTTTTGCGTTTGCTGCTGCTGNCTCCCCCNTNCTTGCTG CTGCTGCTTTTCCTTTTGTTGCTGNCTGCTTCTCCTCTTGCNTGCTGCTGCTGCTTTTCCTTTTG CTGCCGCTGCTCCCCCTCTTGCNTNGCNTGCTCCTTCCCTTCTTG Right flanking sequence: Indices 4979 -- 5478 CCTTTTTGCTGTTGTTGCTTTCCGTCTTGCTGCNTGGTGTNTCCTTCTTTTGCTGCTGCTGCTTC CGCTCTTGCTGCTGCTGCTGTCCCTGCTGCTCCTTCCGCTCTTGCTGCTGCTGCTTCCTCTTTTG CTGCTGCTGCTCCCCGTTTTCCTGCTGCTGCCTCACCTTTTGCTGCTGCTGCTCCTTTTTTTGCT GCTGCTGCCTCGCCTTTTGCTGCTGCTGCGTCCCGTTTGCTGCTGCTGCTGCTGCTGCACTTCGC GTTNTTTGCTGCAGCGCAGCCTCCACTCCCCTTCAAGTTGCAAAAAAATGATTATCATTTATTAT TAATTAATTAATTAATTTATTTATTTATTTANTNTTATTNNTAATTCAGGATTGTCNTGTGGCCC CCCACCTGTTCTGGGACACACAGCCAGTGGTGAAGGCAGCGGAGCGGGCGGCGCTGGCCCCACAG GTGCAGCAAAGTGGAAATGAATTTNAAATTCTTTTTTCGATTTTG Found at i:5037 original size:3 final size:3 Alignment explanation

Indices: 5029--5231 Score: 81 Period size: 3 Copynumber: 66.0 Consensus size: 3 5019 NTCCTTCTTT * * ** * ** * 5029 TGC TGC TGC TGC TTC CGC TCT TGC TGC TGC TGC TGT CCC TGC TGC TCC 1 TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC * * ** * ** ** * *** 5077 TTC CGC TCT TGC TGC TGC TGC TTC CTC TTT TGC TGC TGC TGC TCC CCG 1 TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC ** * ** ** ** * ** ** 5125 TTT TCC TGC TGC TGC CTC ACC TTT TGC TGC TGC TGC TCC TTT TTT TGC 1 TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC ** * * * 5173 TGC TGC TGCC TCGCC TTT TGC TGC TGC TGC GTCC CGTT TGC TGC TGC 1 TGC TGC TG-C T-G-C TGC TGC TGC TGC TGC -TGC TG-C TGC TGC TGC 5220 TGC TGC TGC TGC 1 TGC TGC TGC TGC 5232 ACTTCGCGTT Statistics Matches: 134, Mismatches: 62, Indels: 8 0.66 0.30 0.04 Matches are distributed among these distances: 3 125 0.93 4 5 0.04 5 4 0.03 ACGTcount: A:0.00, C:0.37, G:0.23, T:0.39 Consensus pattern (3 bp): TGC Left flanking sequence: Indices 4529 -- 5028 TAATTTGGAATTTAATTCCATTTGCTTTCCACTCTTTTGCTGCTGCTCATTTCCTTAATTCTTTT TGCTGCTGCTCCTGCTTCCCTTTTTGCTGCTGCTGCTTCGTTTTTTGCGGCAGTTGATTCCCCTC TTGCTGCTGCTGCTTTGCCTTTTGCTGCTGCTGCTTCGCCTTTTGCTGCTGCTGATTCCCCTCTT GCTGCTGCTGTTTCTTTTGCTGCTGCTGATTCCCCTCTTGCTAATGCTGTTTCTTTTGCTGCTGC TGCTTCNTTCTCTTGCTGCCGCNTGCTGCTTTTGCGTTTGCTGCTGCTGNCTCCCCCNTNCTTGC TGCTGCTGCTTTTCCTTTTGTTGCTGNCTGCTTCTCCTCTTGCNTGCTGCTGCTGCTTTTCCTTT TGCTGCCGCTGCTCCCCCTCTTGCNTNGCNTGCTCCTTCCCTTCTTGCTGCTTCTGCTTCCCTTT TTGCTGTTGTTGCTTTCCGTCTTGCTGCNTGGTGTNTCCTTCTTT Right flanking sequence: Indices 5232 -- 5725 ACTTCGCGTTNTTTGCTGCAGCGCAGCCTCCACTCCCCTTCAAGTTGCAAAAAAATGATTATCAT TTATTATTAATTAATTAATTAATTTATTTATTTATTTANTNTTATTNNTAATTCAGGATTGTCNT GTGGCCCCCCACCTGTTCTGGGACACACAGCCAGTGGTGAAGGCAGCGGAGCGGGCGGCGCTGGC CCCACAGGTGCAGCAAAGTGGAAATGAATTTNAAATTCTTTTTTCGATTTTGGAATTAAAAGAGA ATAAATGAATAATTAATTTAAATCAAGCANATTTGGGAAATCCAGNCGGAGACGAAGATGCANGC AAATCCNGGCAAAAAGATNCTTCNGGAATTCACNTTTACCNGCAGCAAAATAANCTCCCNAGNCA GCAAAACGNCTATTTGCTGCTGCAGCAAAACAAATTCCGTTTTCTGCTCCCCTTTGTCCCTTTAT CCCGCCTTATCTTCCTAATGCAGCAGCAGCAGCAGCAGA Found at i:5333 original size:4 final size:4 Alignment explanation

Indices: 5295--5334 Score: 45 Period size: 4 Copynumber: 10.2 Consensus size: 4 5285 AATGATTATC * * * * 5295 ATTT A-TT ATTA ATTA ATTA ATTA ATTT ATTT ATTT ATTT A 1 ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT A 5335 NTNTTATTNN Statistics Matches: 33, Mismatches: 2, Indels: 2 0.89 0.05 0.05 Matches are distributed among these distances: 3 3 0.09 4 30 0.91 ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62 Consensus pattern (4 bp): ATTT Left flanking sequence: Indices 4795 -- 5294 NTTCTCTTGCTGCCGCNTGCTGCTTTTGCGTTTGCTGCTGCTGNCTCCCCCNTNCTTGCTGCTGC TGCTTTTCCTTTTGTTGCTGNCTGCTTCTCCTCTTGCNTGCTGCTGCTGCTTTTCCTTTTGCTGC CGCTGCTCCCCCTCTTGCNTNGCNTGCTCCTTCCCTTCTTGCTGCTTCTGCTTCCCTTTTTGCTG TTGTTGCTTTCCGTCTTGCTGCNTGGTGTNTCCTTCTTTTGCTGCTGCTGCTTCCGCTCTTGCTG CTGCTGCTGTCCCTGCTGCTCCTTCCGCTCTTGCTGCTGCTGCTTCCTCTTTTGCTGCTGCTGCT CCCCGTTTTCCTGCTGCTGCCTCACCTTTTGCTGCTGCTGCTCCTTTTTTTGCTGCTGCTGCCTC GCCTTTTGCTGCTGCTGCGTCCCGTTTGCTGCTGCTGCTGCTGCTGCACTTCGCGTTNTTTGCTG CAGCGCAGCCTCCACTCCCCTTCAAGTTGCAAAAAAATGATTATC Right flanking sequence: Indices 5335 -- 5725 NTNTTATTNNTAATTCAGGATTGTCNTGTGGCCCCCCACCTGTTCTGGGACACACAGCCAGTGGT GAAGGCAGCGGAGCGGGCGGCGCTGGCCCCACAGGTGCAGCAAAGTGGAAATGAATTTNAAATTC TTTTTTCGATTTTGGAATTAAAAGAGAATAAATGAATAATTAATTTAAATCAAGCANATTTGGGA AATCCAGNCGGAGACGAAGATGCANGCAAATCCNGGCAAAAAGATNCTTCNGGAATTCACNTTTA CCNGCAGCAAAATAANCTCCCNAGNCAGCAAAACGNCTATTTGCTGCTGCAGCAAAACAAATTCC GTTTTCTGCTCCCCTTTGTCCCTTTATCCCGCCTTATCTTCCTAATGCAGCAGCAGCAGCAGCAG A Found at i:5333 original size:12 final size:12 Alignment explanation

Indices: 5295--5334 Score: 52 Period size: 12 Copynumber: 3.4 Consensus size: 12 5285 AATGATTATC 5295 ATTTA-TTATTA 1 ATTTATTTATTA * * 5306 ATTAATTAATTA 1 ATTTATTTATTA * 5318 ATTTATTTATTT 1 ATTTATTTATTA 5330 ATTTA 1 ATTTA 5335 NTNTTATTNN Statistics Matches: 23, Mismatches: 5, Indels: 1 0.79 0.17 0.03 Matches are distributed among these distances: 11 4 0.17 12 19 0.83 ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62 Consensus pattern (12 bp): ATTTATTTATTA Left flanking sequence: Indices 4795 -- 5294 NTTCTCTTGCTGCCGCNTGCTGCTTTTGCGTTTGCTGCTGCTGNCTCCCCCNTNCTTGCTGCTGC TGCTTTTCCTTTTGTTGCTGNCTGCTTCTCCTCTTGCNTGCTGCTGCTGCTTTTCCTTTTGCTGC CGCTGCTCCCCCTCTTGCNTNGCNTGCTCCTTCCCTTCTTGCTGCTTCTGCTTCCCTTTTTGCTG TTGTTGCTTTCCGTCTTGCTGCNTGGTGTNTCCTTCTTTTGCTGCTGCTGCTTCCGCTCTTGCTG CTGCTGCTGTCCCTGCTGCTCCTTCCGCTCTTGCTGCTGCTGCTTCCTCTTTTGCTGCTGCTGCT CCCCGTTTTCCTGCTGCTGCCTCACCTTTTGCTGCTGCTGCTCCTTTTTTTGCTGCTGCTGCCTC GCCTTTTGCTGCTGCTGCGTCCCGTTTGCTGCTGCTGCTGCTGCTGCACTTCGCGTTNTTTGCTG CAGCGCAGCCTCCACTCCCCTTCAAGTTGCAAAAAAATGATTATC Right flanking sequence: Indices 5335 -- 5725 NTNTTATTNNTAATTCAGGATTGTCNTGTGGCCCCCCACCTGTTCTGGGACACACAGCCAGTGGT GAAGGCAGCGGAGCGGGCGGCGCTGGCCCCACAGGTGCAGCAAAGTGGAAATGAATTTNAAATTC TTTTTTCGATTTTGGAATTAAAAGAGAATAAATGAATAATTAATTTAAATCAAGCANATTTGGGA AATCCAGNCGGAGACGAAGATGCANGCAAATCCNGGCAAAAAGATNCTTCNGGAATTCACNTTTA CCNGCAGCAAAATAANCTCCCNAGNCAGCAAAACGNCTATTTGCTGCTGCAGCAAAACAAATTCC GTTTTCTGCTCCCCTTTGTCCCTTTATCCCGCCTTATCTTCCTAATGCAGCAGCAGCAGCAGCAG A Found at i:5684 original size:8 final size:8 Alignment explanation

Indices: 5671--5689 Score: 31 Period size: 8 Copynumber: 2.4 Consensus size: 8 5661 TTTTCTGCTC * 5671 CCCTTTGT 1 CCCTTTAT 5679 CCCTTTAT 1 CCCTTTAT 5687 CCC 1 CCC 5690 GCCTTATCTT Statistics Matches: 10, Mismatches: 1, Indels: 0 0.91 0.09 0.00 Matches are distributed among these distances: 8 10 1.00 ACGTcount: A:0.05, C:0.47, G:0.05, T:0.42 Consensus pattern (8 bp): CCCTTTAT Left flanking sequence: Indices 5171 -- 5670 GCTGCTGCTGCCTCGCCTTTTGCTGCTGCTGCGTCCCGTTTGCTGCTGCTGCTGCTGCTGCACTT CGCGTTNTTTGCTGCAGCGCAGCCTCCACTCCCCTTCAAGTTGCAAAAAAATGATTATCATTTAT TATTAATTAATTAATTAATTTATTTATTTATTTANTNTTATTNNTAATTCAGGATTGTCNTGTGG CCCCCCACCTGTTCTGGGACACACAGCCAGTGGTGAAGGCAGCGGAGCGGGCGGCGCTGGCCCCA CAGGTGCAGCAAAGTGGAAATGAATTTNAAATTCTTTTTTCGATTTTGGAATTAAAAGAGAATAA ATGAATAATTAATTTAAATCAAGCANATTTGGGAAATCCAGNCGGAGACGAAGATGCANGCAAAT CCNGGCAAAAAGATNCTTCNGGAATTCACNTTTACCNGCAGCAAAATAANCTCCCNAGNCAGCAA AACGNCTATTTGCTGCTGCAGCAAAACAAATTCCGTTTTCTGCTC Right flanking sequence: Indices 5690 -- 5725 GCCTTATCTTCCTAATGCAGCAGCAGCAGCAGCAGA Found at i:5714 original size:3 final size:3 Alignment explanation

Indices: 5706--5724 Score: 38 Period size: 3 Copynumber: 6.3 Consensus size: 3 5696 TCTTCCTAAT 5706 GCA GCA GCA GCA GCA GCA G 1 GCA GCA GCA GCA GCA GCA G 5725 A Statistics Matches: 16, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 3 16 1.00 ACGTcount: A:0.32, C:0.32, G:0.37, T:0.00 Consensus pattern (3 bp): GCA Left flanking sequence: Indices 5206 -- 5705 CCGTTTGCTGCTGCTGCTGCTGCTGCACTTCGCGTTNTTTGCTGCAGCGCAGCCTCCACTCCCCT TCAAGTTGCAAAAAAATGATTATCATTTATTATTAATTAATTAATTAATTTATTTATTTATTTAN TNTTATTNNTAATTCAGGATTGTCNTGTGGCCCCCCACCTGTTCTGGGACACACAGCCAGTGGTG AAGGCAGCGGAGCGGGCGGCGCTGGCCCCACAGGTGCAGCAAAGTGGAAATGAATTTNAAATTCT TTTTTCGATTTTGGAATTAAAAGAGAATAAATGAATAATTAATTTAAATCAAGCANATTTGGGAA ATCCAGNCGGAGACGAAGATGCANGCAAATCCNGGCAAAAAGATNCTTCNGGAATTCACNTTTAC CNGCAGCAAAATAANCTCCCNAGNCAGCAAAACGNCTATTTGCTGCTGCAGCAAAACAAATTCCG TTTTCTGCTCCCCTTTGTCCCTTTATCCCGCCTTATCTTCCTAAT Right flanking sequence: Indices 5725 -- 5725 A Done.