Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: At_chr10

Parameters: 2 7 7 80 10 50 1000

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

Length: 95480121
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.31

Warning! 2980117 characters in sequence are not A, C, G, or T


File 132 of 284

Found at i:44135513 original size:25 final size:25

Alignment explanation

Indices: 44135402--44135521 Score: 79 Period size: 25 Copynumber: 4.8 Consensus size: 25 44135392 TACAAGCTAT * 44135402 GAATTGGTATGCTCTCACGAGCTGTA 1 GAATTGGTAAGCTCTCACGAGCT-TA * * * 44135428 -AATTGGTAAGCACAT-ACGAGATGA 1 GAATTGGTAAGCTC-TCACGAGCTTA ** * 44135452 GAATCAGTAAGCTCTCATGAGC-T- 1 GAATTGGTAAGCTCTCACGAGCTTA * * 44135475 GCTATCGGTAAGCTCAT-ACGAGCTTA 1 G-AATTGGTAAGCTC-TCACGAGCTTA * 44135501 GAATTGGTAAGCTTTCACGAG 1 GAATTGGTAAGCTCTCACGAG 44135522 TTGCAATTAG Statistics Matches: 70, Mismatches: 16, Indels: 17 0.68 0.16 0.17 Matches are distributed among these distances: 23 1 0.01 24 19 0.27 25 48 0.69 26 2 0.03 ACGTcount: A:0.30, C:0.18, G:0.25, T:0.27 Consensus pattern (25 bp): GAATTGGTAAGCTCTCACGAGCTTA Found at i:44138927 original size:32 final size:32 Alignment explanation

Indices: 44138886--44138949 Score: 128 Period size: 32 Copynumber: 2.0 Consensus size: 32 44138876 AACTCTGATG 44138886 CCTTTAGGCGATATTATATGTCCCAAAAAACT 1 CCTTTAGGCGATATTATATGTCCCAAAAAACT 44138918 CCTTTAGGCGATATTATATGTCCCAAAAAACT 1 CCTTTAGGCGATATTATATGTCCCAAAAAACT 44138950 GACTTCTCGA Statistics Matches: 32, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 32 32 1.00 ACGTcount: A:0.34, C:0.22, G:0.12, T:0.31 Consensus pattern (32 bp): CCTTTAGGCGATATTATATGTCCCAAAAAACT Found at i:44146297 original size:27 final size:27 Alignment explanation

Indices: 44146264--44146407 Score: 144 Period size: 27 Copynumber: 5.3 Consensus size: 27 44146254 TACTGACATG ** * 44146264 CCCTCGATTTGTAGAATTACCATTTTA 1 CCCTCGATTTACAAAATTACCATTTTA * * * * * 44146291 CCTTCGATTTATAGAATTACCGTTTCA 1 CCCTCGATTTACAAAATTACCATTTTA * * *** 44146318 CCATCGATTTAAAAAATTAATGTTTTA 1 CCCTCGATTTACAAAATTACCATTTTA * 44146345 TCCTCGATTTACAAAATTACCATTTTA 1 CCCTCGATTTACAAAATTACCATTTTA * * 44146372 CCCTCAATTTACAAAATTACCTTTTTA 1 CCCTCGATTTACAAAATTACCATTTTA 44146399 CCCTCGATT 1 CCCTCGATT 44146408 GTGAAATTAC Statistics Matches: 97, Mismatches: 20, Indels: 0 0.83 0.17 0.00 Matches are distributed among these distances: 27 97 1.00 ACGTcount: A:0.31, C:0.22, G:0.07, T:0.40 Consensus pattern (27 bp): CCCTCGATTTACAAAATTACCATTTTA Found at i:44146429 original size:27 final size:27 Alignment explanation

Indices: 44146406--44146562 Score: 174 Period size: 27 Copynumber: 5.8 Consensus size: 27 44146396 TTACCCTCGA * * 44146406 TTGTGAAATTACTAAAATACCCCT-GT 1 TTGTAAAATTACCAAAATACCCCTAGT ** * 44146432 AGGATAGAATTACCAAAATACCCCTAGT 1 TTG-TAAAATTACCAAAATACCCCTAGT 44146460 TTGTAAAATTACCAAAATACCCCTAGT 1 TTGTAAAATTACCAAAATACCCCTAGT * ** * 44146487 TTGTAAAATTACCGAAATACCAATGGT 1 TTGTAAAATTACCAAAATACCCCTAGT * * * 44146514 TTGTGAAATTACCGAAATA-CCCTCAAT 1 TTGTAAAATTACCAAAATACCCCT-AGT 44146541 TTGTAAAATTACCAAAATACCC 1 TTGTAAAATTACCAAAATACCC 44146563 TTAATTTACA Statistics Matches: 108, Mismatches: 19, Indels: 6 0.81 0.14 0.05 Matches are distributed among these distances: 26 3 0.03 27 100 0.93 28 5 0.05 ACGTcount: A:0.40, C:0.20, G:0.11, T:0.29 Consensus pattern (27 bp): TTGTAAAATTACCAAAATACCCCTAGT Found at i:44146568 original size:27 final size:27 Alignment explanation

Indices: 44146439--44146674 Score: 179 Period size: 27 Copynumber: 8.7 Consensus size: 27 44146429 TGTAGGATAG * 44146439 AATTACCAAAATACCCCTAGTTTGTAA 1 AATTACCAAAATACCCTTAGTTTGTAA * 44146466 AATTACCAAAATACCCCTAGTTTGTAA 1 AATTACCAAAATACCCTTAGTTTGTAA * ** * * 44146493 AATTACCGAAATACCAATGGTTTGTGA 1 AATTACCAAAATACCCTTAGTTTGTAA * * * 44146520 AATTACCGAAATACCCTCAATTTGTAA 1 AATTACCAAAATACCCTTAGTTTGTAA * ** 44146547 AATTACCAAAATACCCTTAATTTACAA 1 AATTACCAAAATACCCTTAGTTTGTAA * * * 44146574 AATTA-TAGAAATACCCTTGACTTTCTAAA 1 AATTACCA-AAATACCCTT-AGTTTGT-AA ** * ** 44146603 AATTATAAAAATACCATT-GATTTACAA 1 AATTACCAAAATACCCTTAG-TTTGTAA ** * * 44146630 AATTACTGAAATACCCTTGGTTTGTAG 1 AATTACCAAAATACCCTTAGTTTGTAA * * 44146657 ATTTACCAAAACACCCTT 1 AATTACCAAAATACCCTT 44146675 GTAGGATGAA Statistics Matches: 168, Mismatches: 35, Indels: 12 0.78 0.16 0.06 Matches are distributed among these distances: 26 1 0.01 27 142 0.85 28 8 0.05 29 16 0.10 30 1 0.01 ACGTcount: A:0.41, C:0.19, G:0.08, T:0.31 Consensus pattern (27 bp): AATTACCAAAATACCCTTAGTTTGTAA Found at i:44146576 original size:81 final size:81 Alignment explanation

Indices: 44146439--44146588 Score: 212 Period size: 81 Copynumber: 1.9 Consensus size: 81 44146429 TGTAGGATAG * * ** * 44146439 AATTACCAAAATACCCCTAGTTTGTAAAATTACCAAAATACCCCTAGTTTGTAAAATTACCGAAA 1 AATTACCAAAATACCCCTAATTTGTAAAATTACCAAAATACCCCTAATTTACAAAATTACAGAAA 44146504 TACCAATGGTTTGTGA 66 TACCAATGGTTTGTGA * * * 44146520 AATTACCGAAATA-CCCTCAATTTGTAAAATTACCAAAATACCCTTAATTTACAAAATTATAGAA 1 AATTACCAAAATACCCCT-AATTTGTAAAATTACCAAAATACCCCTAATTTACAAAATTACAGAA 44146584 ATACC 65 ATACC 44146589 CTTGACTTTC Statistics Matches: 60, Mismatches: 8, Indels: 2 0.86 0.11 0.03 Matches are distributed among these distances: 80 4 0.07 81 56 0.93 ACGTcount: A:0.43, C:0.20, G:0.08, T:0.29 Consensus pattern (81 bp): AATTACCAAAATACCCCTAATTTGTAAAATTACCAAAATACCCCTAATTTACAAAATTACAGAAA TACCAATGGTTTGTGA Found at i:44147649 original size:24 final size:25 Alignment explanation

Indices: 44147567--44147660 Score: 145 Period size: 25 Copynumber: 3.8 Consensus size: 25 44147557 AGGAAGTGCT * * 44147567 AAAAGGGCTATGCCCTAGTTTACCG 1 AAAAGGGCTTTGCCCCAGTTTACCG * 44147592 AAAAGGGCTTTGCCCTAGTTTACCG 1 AAAAGGGCTTTGCCCCAGTTTACCG * 44147617 AAAAGGGCTTTGCCCCAGTTTATC- 1 AAAAGGGCTTTGCCCCAGTTTACCG 44147641 AAAAGGGCTTTGCCCCAGTT 1 AAAAGGGCTTTGCCCCAGTT 44147661 ATTAAAAGAG Statistics Matches: 66, Mismatches: 3, Indels: 1 0.94 0.04 0.01 Matches are distributed among these distances: 24 20 0.30 25 46 0.70 ACGTcount: A:0.26, C:0.24, G:0.23, T:0.27 Consensus pattern (25 bp): AAAAGGGCTTTGCCCCAGTTTACCG Found at i:44147673 original size:24 final size:24 Alignment explanation

Indices: 44147567--44147673 Score: 126 Period size: 25 Copynumber: 4.4 Consensus size: 24 44147557 AGGAAGTGCT * * * 44147567 AAAAGGGCTATGCCCTAGTTTACC 1 AAAAGGGCTTTGCCCCAGTTTATC * * 44147591 GAAAAGGGCTTTGCCCTAGTTTACC 1 -AAAAGGGCTTTGCCCCAGTTTATC 44147616 GAAAAGGGCTTTGCCCCAGTTTATC 1 -AAAAGGGCTTTGCCCCAGTTTATC * 44147641 AAAAGGGCTTTGCCCCAG-TTATT 1 AAAAGGGCTTTGCCCCAGTTTATC 44147664 AAAAGAGGCT 1 AAAAG-GGCT 44147674 AGGCCTCCAG Statistics Matches: 77, Mismatches: 4, Indels: 3 0.92 0.05 0.04 Matches are distributed among these distances: 23 9 0.12 24 22 0.29 25 46 0.60 ACGTcount: A:0.28, C:0.22, G:0.23, T:0.26 Consensus pattern (24 bp): AAAAGGGCTTTGCCCCAGTTTATC Found at i:44147913 original size:31 final size:31 Alignment explanation

Indices: 44147878--44147992 Score: 187 Period size: 31 Copynumber: 3.7 Consensus size: 31 44147868 CGTTTACAGT 44147878 AAAGGCTTCGGCCCAGTGATATGATTTATGA 1 AAAGGCTTCGGCCCAGTGATATGATTTATGA * * 44147909 AAAGGCTTTGGCCCAGAGATATGATTTATGA 1 AAAGGCTTCGGCCCAGTGATATGATTTATGA * 44147940 TAAGGCTTCGGCCCAGTGATATGATTTATGA 1 AAAGGCTTCGGCCCAGTGATATGATTTATGA * 44147971 TAAGGCTTCGGCCCAGT-ATATG 1 AAAGGCTTCGGCCCAGTGATATG 44147993 CCAAGACTAA Statistics Matches: 79, Mismatches: 5, Indels: 1 0.93 0.06 0.01 Matches are distributed among these distances: 30 5 0.06 31 74 0.94 ACGTcount: A:0.28, C:0.17, G:0.26, T:0.30 Consensus pattern (31 bp): AAAGGCTTCGGCCCAGTGATATGATTTATGA Found at i:44153520 original size:44 final size:47 Alignment explanation

Indices: 44153416--44153635 Score: 166 Period size: 49 Copynumber: 4.6 Consensus size: 47 44153406 GGTACGATGT * * * * 44153416 CGATGCCATGTTCCAAACATGGTCTTACACTGGCTCTCACATCTAAGT 1 CGATGCCATGTCCCAGACA-GGTCTTACACTGACTCTCACATCTAAGC 44153464 CGATGCCATGTCCCAGACAGGTCTTACACTGACATC-C-C-TC-AAGC 1 CGATGCCATGTCCCAGACAGGTCTTACACTGAC-TCTCACATCTAAGC * * * 44153508 CGATGCCATGTCCCAGATAGGTCTTACACT-AGCT-TGCATATCTGGAGGC 1 CGATGCCATGTCCCAGACAGGTCTTACACTGA-CTCT-CACATCT--AAGC * * * * * * ** 44153557 CGATGTCGTGTCCTAGATAGGTCTTACAGT-AGCTCTCATCTACCTGTGC 1 CGATGCCATGTCCCAGACAGGTCTTACACTGA-CTCTCA-C-ATCTAAGC * 44153606 CGATGCCATGTCCCAGACAGATCTTACACT 1 CGATGCCATGTCCCAGACAGGTCTTACACT 44153636 AGCATACACA Statistics Matches: 139, Mismatches: 21, Indels: 23 0.76 0.11 0.13 Matches are distributed among these distances: 43 2 0.01 44 34 0.24 45 2 0.01 46 3 0.02 47 14 0.10 48 19 0.14 49 61 0.44 50 1 0.01 51 3 0.02 ACGTcount: A:0.23, C:0.30, G:0.20, T:0.27 Consensus pattern (47 bp): CGATGCCATGTCCCAGACAGGTCTTACACTGACTCTCACATCTAAGC Found at i:44159481 original size:29 final size:29 Alignment explanation

Indices: 44159418--44159485 Score: 84 Period size: 29 Copynumber: 2.3 Consensus size: 29 44159408 TAATCAACCG * 44159418 CGCACACTTAGTGCCATGTACTTTAAACT 1 CGCACACTTAGTGCCATGCACTTTAAACT * ** 44159447 CACACACTTAGTGCCATGCA-TTTCAAGTT 1 CGCACACTTAGTGCCATGCACTTT-AAACT 44159476 CGCACACTTA 1 CGCACACTTA 44159486 CCTTTTCCGC Statistics Matches: 33, Mismatches: 5, Indels: 2 0.82 0.12 0.05 Matches are distributed among these distances: 28 3 0.09 29 30 0.91 ACGTcount: A:0.28, C:0.29, G:0.13, T:0.29 Consensus pattern (29 bp): CGCACACTTAGTGCCATGCACTTTAAACT Found at i:44159597 original size:174 final size:174 Alignment explanation

Indices: 44159307--44159634 Score: 629 Period size: 174 Copynumber: 1.9 Consensus size: 174 44159297 AACTCAAGGT * * 44159307 ACTTACCTTTTCCGCTGTCCAAAATTGACTCGGTAAAGTCGCACCCTTCATGTAAATAATTTATA 1 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA 44159372 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGT 66 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGT 44159437 ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC 131 ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC 44159481 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA 1 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA 44159546 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGT 66 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGT * 44159611 ACTTTAAACTCGCACACTTAGTGC 131 ACTTTAAACTCACACACTTAGTGC 44159635 TGTACAATTT Statistics Matches: 151, Mismatches: 3, Indels: 0 0.98 0.02 0.00 Matches are distributed among these distances: 174 151 1.00 ACGTcount: A:0.31, C:0.24, G:0.15, T:0.30 Consensus pattern (174 bp): ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGT ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC Found at i:44159626 original size:29 final size:30 Alignment explanation

Indices: 44159587--44159665 Score: 110 Period size: 29 Copynumber: 2.7 Consensus size: 30 44159577 CTTAATAATC 44159587 AACCGCGCACACTTAGTGCCATGTAC-TTTA 1 AACC-CGCACACTTAGTGCCATGTACATTTA * 44159617 AACTCGCACACTTAGTG-C-TGTACAATTTA 1 AACCCGCACACTTAGTGCCATGTAC-ATTTA 44159646 AACCCGCACACTTAGTGCCA 1 AACCCGCACACTTAGTGCCA 44159666 ATCTCATGAC Statistics Matches: 43, Mismatches: 2, Indels: 7 0.83 0.04 0.13 Matches are distributed among these distances: 27 5 0.12 28 1 0.02 29 33 0.77 30 4 0.09 ACGTcount: A:0.29, C:0.30, G:0.15, T:0.25 Consensus pattern (30 bp): AACCCGCACACTTAGTGCCATGTACATTTA Found at i:44169914 original size:28 final size:28 Alignment explanation

Indices: 44169851--44170003 Score: 263 Period size: 28 Copynumber: 5.5 Consensus size: 28 44169841 ATATTAAGTC * * 44169851 CGCACACTCAGTGCTATATAATC-AACT 1 CGCACACTTAGTGCTACATAATCAAACT * 44169878 CGCACACTTAGTGCTATATAATCAAACT 1 CGCACACTTAGTGCTACATAATCAAACT * 44169906 CGCACACTTAGTGCTACGTAATCAAACT 1 CGCACACTTAGTGCTACATAATCAAACT 44169934 CGCACACTTAGTGCTACATAATCAAACT 1 CGCACACTTAGTGCTACATAATCAAACT 44169962 CGCACACTTAGTGCTACATAATCAAACT 1 CGCACACTTAGTGCTACATAATCAAACT 44169990 CGCACACTTAGTGC 1 CGCACACTTAGTGC 44170004 CGTACAATTT Statistics Matches: 121, Mismatches: 4, Indels: 1 0.96 0.03 0.01 Matches are distributed among these distances: 27 22 0.18 28 99 0.82 ACGTcount: A:0.33, C:0.29, G:0.12, T:0.25 Consensus pattern (28 bp): CGCACACTTAGTGCTACATAATCAAACT Found at i:44174721 original size:49 final size:48 Alignment explanation

Indices: 44174668--44174888 Score: 186 Period size: 49 Copynumber: 4.6 Consensus size: 48 44174658 TATCGAGGCT * * * 44174668 GATGCCATGTCCCAGACGGGTCTTACACTAGCTCTCACTTATTTGTGTC 1 GATGCCATGTCCTAGACAGGTCTTACACTAGCTCTCA-TTATTTGTGCC * * * * * * 44174717 GATGCCATGTCCCAGACAGGTCTTACACT-GACACACCTCA----AGCC 1 GATGCCATGTCCTAGACAGGTCTTACACTAG-CTCTCATTATTTGTGCC * 44174761 GATGCCATGTCCTAGACAGGTCTTACACTAGCT-TGCA-TATCTTGAGGCC 1 GATGCCATGTCCTAGACAGGTCTTACACTAGCTCT-CATTAT-TTG-TGCC * * * ** * 44174810 GATGTCGTGTCCTAGACAGGTCTTACAATAGCTCTCATCTATCGGTGTC 1 GATGCCATGTCCTAGACAGGTCTTACACTAGCTCTCAT-TATTTGTGCC * 44174859 GATGACATGTCCTAGACAGGTCTTACACTA 1 GATGCCATGTCCTAGACAGGTCTTACACTA 44174889 ACATACACAT Statistics Matches: 137, Mismatches: 23, Indels: 24 0.74 0.12 0.13 Matches are distributed among these distances: 43 1 0.01 44 32 0.23 45 1 0.01 48 3 0.02 49 95 0.69 50 2 0.01 51 3 0.02 ACGTcount: A:0.23, C:0.28, G:0.21, T:0.28 Consensus pattern (48 bp): GATGCCATGTCCTAGACAGGTCTTACACTAGCTCTCATTATTTGTGCC Found at i:44174813 original size:93 final size:92 Alignment explanation

Indices: 44174668--44174836 Score: 225 Period size: 93 Copynumber: 1.8 Consensus size: 92 44174658 TATCGAGGCT * * * 44174668 GATGCCATGTCCCAGACGGGTCTTACACTAGCTCTCACTTATTTGTGTCGATGCCATGTCCCAGA 1 GATGCCATGTCCCAGACAGGTCTTACACTAGCTCTCAC-TATTTGGGCCGATGCCATGTCCCAGA 44174733 CAGGTCTTACACTGACACACCTCAAGCC 65 CAGGTCTTACACTGACACACCTCAAGCC * * * * 44174761 GATGCCATGTCCTAGACAGGTCTTACACTAGCT-TGCA-TATCTTGAGGCCGATGTCGTGTCCTA 1 GATGCCATGTCCCAGACAGGTCTTACACTAGCTCT-CACTAT-TTG-GGCCGATGCCATGTCCCA 44174824 GACAGGTCTTACA 63 GACAGGTCTTACA 44174837 ATAGCTCTCA Statistics Matches: 66, Mismatches: 7, Indels: 6 0.84 0.09 0.08 Matches are distributed among these distances: 91 3 0.05 92 4 0.06 93 59 0.89 ACGTcount: A:0.22, C:0.29, G:0.21, T:0.27 Consensus pattern (92 bp): GATGCCATGTCCCAGACAGGTCTTACACTAGCTCTCACTATTTGGGCCGATGCCATGTCCCAGAC AGGTCTTACACTGACACACCTCAAGCC Found at i:44174876 original size:142 final size:142 Alignment explanation

Indices: 44174618--44174887 Score: 357 Period size: 142 Copynumber: 1.9 Consensus size: 142 44174608 ACATCTAAGT * * * 44174618 CGATGCCATGTCTCTGACAGGCCTTACGCTGACTTTCATATATCGAGGCTGATGCCATGTCCCAG 1 CGATGCCATGTCTCTGACAGGCCTTACACTGACTTGCATATATCGAGGCCGATGCCATGTCCCAG * * ** * 44174683 ACGGGTCTTACACTAGCTCTCACTTATTTGTGTCGATGCCATGTCCCAGACAGGTCTTACACTGA 66 ACAGGTCTTACAATAGCTCTCACTTATCGGTGTCGATGACATGTCCCAGACAGGTCTTACACTGA 44174748 CACACCTCAAGC 131 CACACCTCAAGC * * * * * * 44174760 CGATGCCATGTC-CTAGACAGGTCTTACACT-AGCTTGCATATCTTGAGGCCGATGTCGTGTCCT 1 CGATGCCATGTCTCT-GACAGGCCTTACACTGA-CTTGCATATATCGAGGCCGATGCCATGTCCC * 44174823 AGACAGGTCTTACAATAGCTCTCA-TCTATCGGTGTCGATGACATGTCCTAGACAGGTCTTACAC 64 AGACAGGTCTTACAATAGCTCTCACT-TATCGGTGTCGATGACATGTCCCAGACAGGTCTTACAC 44174887 T 128 T 44174888 AACATACACA Statistics Matches: 110, Mismatches: 15, Indels: 6 0.84 0.11 0.05 Matches are distributed among these distances: 141 4 0.04 142 106 0.96 ACGTcount: A:0.22, C:0.28, G:0.21, T:0.29 Consensus pattern (142 bp): CGATGCCATGTCTCTGACAGGCCTTACACTGACTTGCATATATCGAGGCCGATGCCATGTCCCAG ACAGGTCTTACAATAGCTCTCACTTATCGGTGTCGATGACATGTCCCAGACAGGTCTTACACTGA CACACCTCAAGC Found at i:44182404 original size:10 final size:9 Alignment explanation

Indices: 44182389--44182451 Score: 56 Period size: 10 Copynumber: 6.8 Consensus size: 9 44182379 TCCACATGCT 44182389 ATTTTTCAAA 1 ATTTTT-AAA * 44182399 ATTTTTATGA 1 ATTTTTA-AA 44182409 ATTTTTATAA 1 ATTTTTA-AA * ** 44182419 TTTTTTTGA 1 ATTTTTAAA 44182428 A-TTTTAAA 1 ATTTTTAAA 44182436 ATTTTTAAA 1 ATTTTTAAA 44182445 ATTTTTA 1 ATTTTTA 44182452 TTACTTTTTA Statistics Matches: 43, Mismatches: 8, Indels: 5 0.77 0.14 0.09 Matches are distributed among these distances: 8 6 0.14 9 16 0.37 10 21 0.49 ACGTcount: A:0.35, C:0.02, G:0.03, T:0.60 Consensus pattern (9 bp): ATTTTTAAA Found at i:44182413 original size:9 final size:10 Alignment explanation

Indices: 44182398--44182452 Score: 55 Period size: 9 Copynumber: 5.9 Consensus size: 10 44182388 TATTTTTCAA 44182398 AATTTTTATG 1 AATTTTTATG 44182408 AATTTTTAT- 1 AATTTTTATG * 44182417 AATTTTTTTG 1 AATTTTTATG * 44182427 AA-TTTTA-A 1 AATTTTTATG * 44182435 AATTTTTA-A 1 AATTTTTATG 44182444 AATTTTTAT 1 AATTTTTAT 44182453 TACTTTTTAA Statistics Matches: 39, Mismatches: 3, Indels: 6 0.81 0.06 0.12 Matches are distributed among these distances: 8 2 0.05 9 26 0.67 10 11 0.28 ACGTcount: A:0.35, C:0.00, G:0.04, T:0.62 Consensus pattern (10 bp): AATTTTTATG Found at i:44182459 original size:27 final size:28 Alignment explanation

Indices: 44182398--44182464 Score: 75 Period size: 27 Copynumber: 2.4 Consensus size: 28 44182388 TATTTTTCAA * * 44182398 AATTTTTATGAATTTTTATAATTTTTTTG 1 AATTTTTA-AAATTTTTAAAATTTTTTTG 44182427 AA-TTTTAAAATTTTTAAAATTTTTATT- 1 AATTTTTAAAATTTTTAAAATTTTT-TTG * 44182454 ACTTTTTAAAA 1 AATTTTTAAAA 44182465 AGATTCAAAT Statistics Matches: 33, Mismatches: 3, Indels: 5 0.80 0.07 0.12 Matches are distributed among these distances: 27 16 0.48 28 15 0.45 29 2 0.06 ACGTcount: A:0.36, C:0.01, G:0.03, T:0.60 Consensus pattern (28 bp): AATTTTTAAAATTTTTAAAATTTTTTTG Found at i:44182589 original size:193 final size:193 Alignment explanation

Indices: 44182260--44182647 Score: 715 Period size: 193 Copynumber: 2.0 Consensus size: 193 44182250 TTCAACTCAC *** 44182260 TACTTTTTAAAAAGATTCAAATTTAACTATTAGCCTTTTAGAAAAAATTGAATTCCTTTTCTTTA 1 TACTTTTTAAAAAGATTCAAATTTAACTATTAGAAATTTAGAAAAAATTGAATTCCTTTTCTTTA 44182325 ACAAAAATACTTACTAAAATGTTAAATTTTTAAACATAACAACCCACATAACAATCCACATGCTA 66 ACAAAAATACTTACTAAAATGTTAAATTTTTAAACATAACAACCCACATAACAATCCACATGCTA 44182390 TTTTTCAAAATTTTTATGAATTTTTATAATTTTTTTGAATTTTAAAATTTTTAAAATTTTTAT 131 TTTTTCAAAATTTTTATGAATTTTTATAATTTTTTTGAATTTTAAAATTTTTAAAATTTTTAT * * 44182453 TACTTTTTAAAAAGATTCAAATTTAAATTTTTA-AAATTTAGAAAAAATTGAATTCCTTTTCTTT 1 TACTTTTTAAAAAGATTCAAATTT-AACTATTAGAAATTTAGAAAAAATTGAATTCCTTTTCTTT 44182517 AACAAAAATACTTACTAAAATGTTAAATTTTTAAACATAACAACCCACATAACAATCCACATGCT 65 AACAAAAATACTTACTAAAATGTTAAATTTTTAAACATAACAACCCACATAACAATCCACATGCT 44182582 ATTTTTCAAAATTTTTATGAATTTTTATAATTTTTTTGAATTTTAAAATTTTTAAAATTTTTAT 130 ATTTTTCAAAATTTTTATGAATTTTTATAATTTTTTTGAATTTTAAAATTTTTAAAATTTTTAT 44182646 TA 1 TA 44182648 AATTATATTT Statistics Matches: 189, Mismatches: 5, Indels: 2 0.96 0.03 0.01 Matches are distributed among these distances: 193 183 0.97 194 6 0.03 ACGTcount: A:0.41, C:0.11, G:0.04, T:0.44 Consensus pattern (193 bp): TACTTTTTAAAAAGATTCAAATTTAACTATTAGAAATTTAGAAAAAATTGAATTCCTTTTCTTTA ACAAAAATACTTACTAAAATGTTAAATTTTTAAACATAACAACCCACATAACAATCCACATGCTA TTTTTCAAAATTTTTATGAATTTTTATAATTTTTTTGAATTTTAAAATTTTTAAAATTTTTAT Found at i:44182597 original size:10 final size:9 Alignment explanation

Indices: 44182582--44182644 Score: 56 Period size: 10 Copynumber: 6.8 Consensus size: 9 44182572 TCCACATGCT 44182582 ATTTTTCAAA 1 ATTTTT-AAA * 44182592 ATTTTTATGA 1 ATTTTTA-AA 44182602 ATTTTTATAA 1 ATTTTTA-AA * ** 44182612 TTTTTTTGA 1 ATTTTTAAA 44182621 A-TTTTAAA 1 ATTTTTAAA 44182629 ATTTTTAAA 1 ATTTTTAAA 44182638 ATTTTTA 1 ATTTTTA 44182645 TTAAATTATA Statistics Matches: 43, Mismatches: 8, Indels: 5 0.77 0.14 0.09 Matches are distributed among these distances: 8 6 0.14 9 16 0.37 10 21 0.49 ACGTcount: A:0.35, C:0.02, G:0.03, T:0.60 Consensus pattern (9 bp): ATTTTTAAA Found at i:44182606 original size:9 final size:10 Alignment explanation

Indices: 44182591--44182645 Score: 55 Period size: 9 Copynumber: 5.9 Consensus size: 10 44182581 TATTTTTCAA 44182591 AATTTTTATG 1 AATTTTTATG 44182601 AATTTTTAT- 1 AATTTTTATG * 44182610 AATTTTTTTG 1 AATTTTTATG * 44182620 AA-TTTTA-A 1 AATTTTTATG * 44182628 AATTTTTA-A 1 AATTTTTATG 44182637 AATTTTTAT 1 AATTTTTAT 44182646 TAAATTATAT Statistics Matches: 39, Mismatches: 3, Indels: 6 0.81 0.06 0.12 Matches are distributed among these distances: 8 2 0.05 9 26 0.67 10 11 0.28 ACGTcount: A:0.35, C:0.00, G:0.04, T:0.62 Consensus pattern (10 bp): AATTTTTATG Found at i:44185719 original size:43 final size:44 Alignment explanation

Indices: 44185671--44185821 Score: 134 Period size: 43 Copynumber: 3.5 Consensus size: 44 44185661 AGCTCGTACA * 44185671 ATGCCAACATCCCAGACGTGGTCTTACATGTAAA-CAAATATCG 1 ATGCCAACGTCCCAGACGTGGTCTTACATGTAAATCAAATATCG * 44185714 ATGCC-ACTGTCCCAGACAG-GGTCTTGCATG-AAATCAAATA-CG 1 ATGCCAAC-GTCCCAGAC-GTGGTCTTACATGTAAATCAAATATCG **** * * * * 44185756 ATATTGATGTCCCAAACATGGTCTTACATGTAAATCATAA-GTCG 1 ATGCCAACGTCCCAGACGTGGTCTTACATGTAAATCA-AATATCG * 44185800 ATGCCAACGTACCAGACGTGGT 1 ATGCCAACGTCCCAGACGTGGT 44185822 GTAAATTATA Statistics Matches: 82, Mismatches: 18, Indels: 15 0.71 0.16 0.13 Matches are distributed among these distances: 42 27 0.33 43 36 0.44 44 19 0.23 ACGTcount: A:0.32, C:0.24, G:0.19, T:0.25 Consensus pattern (44 bp): ATGCCAACGTCCCAGACGTGGTCTTACATGTAAATCAAATATCG Found at i:44185834 original size:37 final size:37 Alignment explanation

Indices: 44185784--44185858 Score: 123 Period size: 37 Copynumber: 2.0 Consensus size: 37 44185774 TGGTCTTACA 44185784 TGTAAATCATAAGTCGATGCCAACGTACCAGACGTGG 1 TGTAAATCATAAGTCGATGCCAACGTACCAGACGTGG * * * 44185821 TGTAAATTATAAGTCGATGCCAACGTCCCAGATGTGG 1 TGTAAATCATAAGTCGATGCCAACGTACCAGACGTGG 44185858 T 1 T 44185859 CTTGCACAAA Statistics Matches: 35, Mismatches: 3, Indels: 0 0.92 0.08 0.00 Matches are distributed among these distances: 37 35 1.00 ACGTcount: A:0.31, C:0.20, G:0.24, T:0.25 Consensus pattern (37 bp): TGTAAATCATAAGTCGATGCCAACGTACCAGACGTGG Found at i:44190002 original size:16 final size:17 Alignment explanation

Indices: 44189973--44190012 Score: 73 Period size: 16 Copynumber: 2.4 Consensus size: 17 44189963 AAAGAAATAG 44189973 AGTAAGCTTTATAGCTT 1 AGTAAGCTTTATAGCTT 44189990 AGTAAGC-TTATAGCTT 1 AGTAAGCTTTATAGCTT 44190006 AGTAAGC 1 AGTAAGC 44190013 CCGTATAATT Statistics Matches: 23, Mismatches: 0, Indels: 1 0.96 0.00 0.04 Matches are distributed among these distances: 16 16 0.70 17 7 0.30 ACGTcount: A:0.33, C:0.12, G:0.20, T:0.35 Consensus pattern (17 bp): AGTAAGCTTTATAGCTT Found at i:44190444 original size:24 final size:24 Alignment explanation

Indices: 44190413--44190460 Score: 78 Period size: 24 Copynumber: 2.0 Consensus size: 24 44190403 CTGAGCTGAT 44190413 GAACAGTAAGCTCTGACGAGCTAA 1 GAACAGTAAGCTCTGACGAGCTAA * * 44190437 GAACAGTAAGCTCTTATGAGCTAA 1 GAACAGTAAGCTCTGACGAGCTAA 44190461 TATATCGGTA Statistics Matches: 22, Mismatches: 2, Indels: 0 0.92 0.08 0.00 Matches are distributed among these distances: 24 22 1.00 ACGTcount: A:0.38, C:0.19, G:0.23, T:0.21 Consensus pattern (24 bp): GAACAGTAAGCTCTGACGAGCTAA Found at i:44191917 original size:33 final size:33 Alignment explanation

Indices: 44191875--44191941 Score: 134 Period size: 33 Copynumber: 2.0 Consensus size: 33 44191865 TGATTTGGAG 44191875 CTTGAGCAGTTAGATGTGAAAACAACATTCTTA 1 CTTGAGCAGTTAGATGTGAAAACAACATTCTTA 44191908 CTTGAGCAGTTAGATGTGAAAACAACATTCTTA 1 CTTGAGCAGTTAGATGTGAAAACAACATTCTTA 44191941 C 1 C 44191942 ATGAAGAACT Statistics Matches: 34, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 33 34 1.00 ACGTcount: A:0.36, C:0.16, G:0.18, T:0.30 Consensus pattern (33 bp): CTTGAGCAGTTAGATGTGAAAACAACATTCTTA Found at i:44192371 original size:35 final size:35 Alignment explanation

Indices: 44192325--44192394 Score: 113 Period size: 35 Copynumber: 2.0 Consensus size: 35 44192315 GAAAAACATG ** 44192325 TAAATTGTACCTAAGTCAAAAATGGTACATTGAGA 1 TAAATTGTACCTAAGTCAAAAACAGTACATTGAGA * 44192360 TAAATTGTACCTAAGTCAGAAACAGTACATTGAGA 1 TAAATTGTACCTAAGTCAAAAACAGTACATTGAGA 44192395 AAGTTCTTTA Statistics Matches: 32, Mismatches: 3, Indels: 0 0.91 0.09 0.00 Matches are distributed among these distances: 35 32 1.00 ACGTcount: A:0.43, C:0.13, G:0.17, T:0.27 Consensus pattern (35 bp): TAAATTGTACCTAAGTCAAAAACAGTACATTGAGA Found at i:44193139 original size:113 final size:113 Alignment explanation

Indices: 44192941--44193160 Score: 325 Period size: 113 Copynumber: 1.9 Consensus size: 113 44192931 ATACAATGTT * * * 44192941 TTGTGATAGTGAGAGTGCCATCTTCCTTACGAATGATCAAATGTTTCACTAGAGAACAAATCACA 1 TTGTGATAGTCAGAATGCCATCTTCCTTACAAATGATCAAATGTTTCACTAGAGAACAAATCACA * * 44193006 TCAATGTTCAGTATCATTTTATACGTGATATTATTGCTCGTGATGATA 66 TCAATATTCAGTATCATTTTATACGTAATATTATTGCTCGTGATGATA * * * 44193054 TTGTGATAGTCATAATGTCATCTTCCTTACAAATGATCAAATGTTTCA-TAAGATAACAAATCAC 1 TTGTGATAGTCAGAATGCCATCTTCCTTACAAATGATCAAATGTTTCACT-AGAGAACAAATCAC * * * 44193118 ATCGATATTCAGTGTCATTTTATGCGTAATATTATTGCTCGTG 65 ATCAATATTCAGTATCATTTTATACGTAATATTATTGCTCGTG 44193161 GTGCTGTGAG Statistics Matches: 95, Mismatches: 11, Indels: 2 0.88 0.10 0.02 Matches are distributed among these distances: 112 1 0.01 113 94 0.99 ACGTcount: A:0.31, C:0.16, G:0.16, T:0.37 Consensus pattern (113 bp): TTGTGATAGTCAGAATGCCATCTTCCTTACAAATGATCAAATGTTTCACTAGAGAACAAATCACA TCAATATTCAGTATCATTTTATACGTAATATTATTGCTCGTGATGATA Found at i:44193394 original size:20 final size:20 Alignment explanation

Indices: 44193371--44193412 Score: 75 Period size: 20 Copynumber: 2.1 Consensus size: 20 44193361 ACCCTGTCAC 44193371 ATGTTAAAAAAATAAATACA 1 ATGTTAAAAAAATAAATACA * 44193391 ATGTTGAAAAAATAAATACA 1 ATGTTAAAAAAATAAATACA 44193411 AT 1 AT 44193413 AGCAAAATAA Statistics Matches: 21, Mismatches: 1, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 20 21 1.00 ACGTcount: A:0.62, C:0.05, G:0.07, T:0.26 Consensus pattern (20 bp): ATGTTAAAAAAATAAATACA Found at i:44193897 original size:23 final size:23 Alignment explanation

Indices: 44193870--44193914 Score: 90 Period size: 23 Copynumber: 2.0 Consensus size: 23 44193860 ATTCCAAGGT 44193870 AACTGCAAGAAAAATAATGCTCG 1 AACTGCAAGAAAAATAATGCTCG 44193893 AACTGCAAGAAAAATAATGCTC 1 AACTGCAAGAAAAATAATGCTC 44193915 TTAGGAAAAG Statistics Matches: 22, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 23 22 1.00 ACGTcount: A:0.49, C:0.18, G:0.16, T:0.18 Consensus pattern (23 bp): AACTGCAAGAAAAATAATGCTCG Found at i:44198569 original size:21 final size:21 Alignment explanation

Indices: 44198539--44198578 Score: 62 Period size: 21 Copynumber: 1.9 Consensus size: 21 44198529 TAACAGGATT * 44198539 GCTGACGTGGGAAGTTAACCA 1 GCTGACGTGGCAAGTTAACCA * 44198560 GCTGATGTGGCAAGTTAAC 1 GCTGACGTGGCAAGTTAAC 44198579 TTGCCATGTT Statistics Matches: 17, Mismatches: 2, Indels: 0 0.89 0.11 0.00 Matches are distributed among these distances: 21 17 1.00 ACGTcount: A:0.28, C:0.17, G:0.33, T:0.23 Consensus pattern (21 bp): GCTGACGTGGCAAGTTAACCA Found at i:44200373 original size:27 final size:26 Alignment explanation

Indices: 44200311--44200422 Score: 116 Period size: 27 Copynumber: 4.2 Consensus size: 26 44200301 AGCATGGCTG * * 44200311 CCAGAACAGATAATGTGACAGAGTCA 1 CCAGAACAGATAATGTGGCAGAGCCA * * 44200337 CTAGATACAGATAACCGTGGCAGAGCCA 1 CCAGA-ACAGATAA-TGTGGCAGAGCCA 44200365 CCAGAACAGATATATGTGGCAGAGCCA 1 CCAGAACAGATA-ATGTGGCAGAGCCA * * * * 44200392 CCAGATCAGATATTTGTGGTATAGCCA 1 CCAGAACAGATA-ATGTGGCAGAGCCA 44200419 CCAG 1 CCAG 44200423 GACGCTTCCT Statistics Matches: 73, Mismatches: 10, Indels: 5 0.83 0.11 0.06 Matches are distributed among these distances: 26 4 0.05 27 54 0.74 28 15 0.21 ACGTcount: A:0.36, C:0.22, G:0.24, T:0.18 Consensus pattern (26 bp): CCAGAACAGATAATGTGGCAGAGCCA Found at i:44203992 original size:27 final size:27 Alignment explanation

Indices: 44203962--44204055 Score: 102 Period size: 27 Copynumber: 3.4 Consensus size: 27 44203952 AGGAAGCGTC * * 44203962 CTGGTGGCTATACCACCGATATCTGAT 1 CTGGTGGCTCTGCCACCGATATCTGAT ** 44203989 CTGGTGGCTCTGCCACATATATCT-ATT 1 CTGGTGGCTCTGCCACCGATATCTGA-T 44204016 CTGGTGGCTCTGCCA-CGATTATCTGTAT 1 CTGGTGGCTCTGCCACCGA-TATCTG-AT * 44204044 CTGGTGACTCTG 1 CTGGTGGCTCTG 44204056 TCACATTATC Statistics Matches: 56, Mismatches: 7, Indels: 7 0.80 0.10 0.10 Matches are distributed among these distances: 26 2 0.04 27 41 0.73 28 12 0.21 29 1 0.02 ACGTcount: A:0.17, C:0.26, G:0.23, T:0.34 Consensus pattern (27 bp): CTGGTGGCTCTGCCACCGATATCTGAT Found at i:44204063 original size:27 final size:26 Alignment explanation

Indices: 44203981--44204074 Score: 125 Period size: 27 Copynumber: 3.5 Consensus size: 26 44203971 ATACCACCGA * 44203981 TATCTGATCTGGTGGCTCTGCCACAT 1 TATCTGTTCTGGTGGCTCTGCCACAT * 44204007 ATATCTATTCTGGTGGCTCTGCCACGAT 1 -TATCTGTTCTGGTGGCTCTGCCAC-AT * * 44204035 TATCTGTATCTGGTGACTCTGTCACAT 1 TATCTGT-TCTGGTGGCTCTGCCACAT 44204062 TATCTGTTCTGGT 1 TATCTGTTCTGGT 44204075 AGCTATGCTG Statistics Matches: 60, Mismatches: 5, Indels: 5 0.86 0.07 0.07 Matches are distributed among these distances: 26 6 0.10 27 37 0.62 28 17 0.28 ACGTcount: A:0.16, C:0.23, G:0.21, T:0.39 Consensus pattern (26 bp): TATCTGTTCTGGTGGCTCTGCCACAT Found at i:44204066 original size:54 final size:54 Alignment explanation

Indices: 44203962--44204080 Score: 152 Period size: 54 Copynumber: 2.2 Consensus size: 54 44203952 AGGAAGCGTC * 44203962 CTGGTGGCTATACCACCGATATCTGATCTGGTGGCTCTGCCACATATATCTATT 1 CTGGTGGCTATACCACCGATATCTGATCTGGTGACTCTGCCACATATATCTATT * * * * 44204016 CTGGTGGCTCTGCCA-CGATTATCTGTATCTGGTGACTCTGTCACAT-TATCTGTT 1 CTGGTGGCTATACCACCGA-TATCTG-ATCTGGTGACTCTGCCACATATATCTATT * 44204070 CTGGTAGCTAT 1 CTGGTGGCTAT 44204081 GCTGCAAATT Statistics Matches: 56, Mismatches: 7, Indels: 4 0.84 0.10 0.06 Matches are distributed among these distances: 53 3 0.05 54 35 0.62 55 18 0.32 ACGTcount: A:0.18, C:0.24, G:0.22, T:0.36 Consensus pattern (54 bp): CTGGTGGCTATACCACCGATATCTGATCTGGTGACTCTGCCACATATATCTATT Found at i:44206119 original size:19 final size:19 Alignment explanation

Indices: 44206095--44206133 Score: 78 Period size: 19 Copynumber: 2.1 Consensus size: 19 44206085 AATTTTAGAC 44206095 CCCGTCACCTGCCATGTCA 1 CCCGTCACCTGCCATGTCA 44206114 CCCGTCACCTGCCATGTCA 1 CCCGTCACCTGCCATGTCA 44206133 C 1 C 44206134 TTTGCCGTGA Statistics Matches: 20, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 19 20 1.00 ACGTcount: A:0.15, C:0.49, G:0.15, T:0.21 Consensus pattern (19 bp): CCCGTCACCTGCCATGTCA Found at i:44213840 original size:12 final size:12 Alignment explanation

Indices: 44213822--44213882 Score: 86 Period size: 12 Copynumber: 5.0 Consensus size: 12 44213812 CTGAGACACA 44213822 CGCCCGTGGCTC 1 CGCCCGTGGCTC * 44213834 TGCCCGTGGCTC 1 CGCCCGTGGCTC 44213846 CGCCCGTGGCTC 1 CGCCCGTGGCTC * 44213858 CACCCGTGGCTC 1 CGCCCGTGGCTC * 44213870 CACCCGTGTGCTC 1 CGCCCGTG-GCTC 44213883 AATTCTGAGC Statistics Matches: 45, Mismatches: 3, Indels: 1 0.92 0.06 0.02 Matches are distributed among these distances: 12 41 0.91 13 4 0.09 ACGTcount: A:0.03, C:0.48, G:0.30, T:0.20 Consensus pattern (12 bp): CGCCCGTGGCTC Found at i:44217168 original size:27 final size:27 Alignment explanation

Indices: 44217138--44217225 Score: 115 Period size: 27 Copynumber: 3.3 Consensus size: 27 44217128 TGGAGGAAGC 44217138 GTTCTGGTGGCTCTGCCACAAATATCT 1 GTTCTGGTGGCTCTGCCACAAATATCT * * 44217165 GTTCTGGTGGCACTGCCACAAATATCA 1 GTTCTGGTGGCTCTGCCACAAATATCT * * * 44217192 GTATCTGGTGACTCTGTCAC-ATTATCT 1 GT-TCTGGTGGCTCTGCCACAAATATCT 44217219 GTTCTGG 1 GTTCTGG 44217226 CAGCCATGCT Statistics Matches: 53, Mismatches: 7, Indels: 3 0.84 0.11 0.05 Matches are distributed among these distances: 26 5 0.09 27 34 0.64 28 14 0.26 ACGTcount: A:0.19, C:0.24, G:0.23, T:0.34 Consensus pattern (27 bp): GTTCTGGTGGCTCTGCCACAAATATCT Found at i:44219426 original size:11 final size:11 Alignment explanation

Indices: 44219410--44219441 Score: 64 Period size: 11 Copynumber: 2.9 Consensus size: 11 44219400 TTACAAGACA 44219410 TAAAATAAAAT 1 TAAAATAAAAT 44219421 TAAAATAAAAT 1 TAAAATAAAAT 44219432 TAAAATAAAA 1 TAAAATAAAA 44219442 CTTATTTTTT Statistics Matches: 21, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 11 21 1.00 ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25 Consensus pattern (11 bp): TAAAATAAAAT Found at i:44224568 original size:38 final size:38 Alignment explanation

Indices: 44224524--44224605 Score: 155 Period size: 38 Copynumber: 2.2 Consensus size: 38 44224514 GCATTCAATC * 44224524 AAACATGTTAGTCACCAAAATCTTCATAACAATCAAGT 1 AAACATGTTAGTCAACAAAATCTTCATAACAATCAAGT 44224562 AAACATGTTAGTCAACAAAATCTTCATAACAATCAAGT 1 AAACATGTTAGTCAACAAAATCTTCATAACAATCAAGT 44224600 AAACAT 1 AAACAT 44224606 AGATGAGCTC Statistics Matches: 43, Mismatches: 1, Indels: 0 0.98 0.02 0.00 Matches are distributed among these distances: 38 43 1.00 ACGTcount: A:0.48, C:0.20, G:0.07, T:0.26 Consensus pattern (38 bp): AAACATGTTAGTCAACAAAATCTTCATAACAATCAAGT Found at i:44236296 original size:31 final size:30 Alignment explanation

Indices: 44236250--44236332 Score: 141 Period size: 31 Copynumber: 2.7 Consensus size: 30 44236240 TTAGTCTCGA 44236250 CATAT-ACTGGGCCGAAGCCTTTTCATAAAT 1 CATATCACT-GGCCGAAGCCTTTTCATAAAT 44236280 CATATCACTAGGCCGAAGCCTTTTCATAAAT 1 CATATCACT-GGCCGAAGCCTTTTCATAAAT 44236311 CATATCACTGGCCGAAGCCTTT 1 CATATCACTGGCCGAAGCCTTT 44236333 ACTGTAAGCG Statistics Matches: 51, Mismatches: 1, Indels: 2 0.94 0.02 0.04 Matches are distributed among these distances: 30 18 0.35 31 33 0.65 ACGTcount: A:0.29, C:0.27, G:0.16, T:0.29 Consensus pattern (30 bp): CATATCACTGGCCGAAGCCTTTTCATAAAT Found at i:44236584 original size:25 final size:25 Alignment explanation

Indices: 44236552--44236621 Score: 104 Period size: 25 Copynumber: 2.8 Consensus size: 25 44236542 CTCTTTTAAT 44236552 AACTAGGGCAAAGCCCTTTTCGATA 1 AACTAGGGCAAAGCCCTTTTCGATA * * 44236577 AACTAGGGCAAAGCCTTTTTCGGTA 1 AACTAGGGCAAAGCCCTTTTCGATA * * 44236602 AACTGGGGCATAGCCCTTTT 1 AACTAGGGCAAAGCCCTTTT 44236622 AGCACTTCTT Statistics Matches: 40, Mismatches: 5, Indels: 0 0.89 0.11 0.00 Matches are distributed among these distances: 25 40 1.00 ACGTcount: A:0.27, C:0.23, G:0.23, T:0.27 Consensus pattern (25 bp): AACTAGGGCAAAGCCCTTTTCGATA Found at i:44238359 original size:217 final size:218 Alignment explanation

Indices: 44237983--44238418 Score: 786 Period size: 217 Copynumber: 2.0 Consensus size: 218 44237973 TGCTCAAAGA * * * 44237983 ATATATAAGCCATTTTCGCATGGCTATCCAAATTTATACAAAACCAAAGGGTCCATGACCAACAA 1 ATATATAAGCCATTTTCACAAGGCTATCCAAATTTATACAAAACCAAAGGGTACATGACCAACAA ** * 44238048 CAAAGCGGGTAGTCCTATACATGCCATTTCAAAGTTCAACCAAAAGTGTACCAAAAGGGGCTTTG 66 CAAAAAGGGTAGTCCTATACATGCCATTTCAAAGTTCAACCAAAAATGTACCAAAAGGGGCTTTG 44238113 ATAGTGTGGACGACTTCGACTTCGACAATCCCGAGTCCGATAGCTGACGAACCAAAATCTATAAA 131 ATAGTGTGGACGACTTCGACTTCGACAATCCCGAGTCCGATAGCTGACGAACCAAAATCTATAAA 44238178 ATAGAGAATCAAAGAAACGGAAT 196 ATAGAGAATCAAAGAAACGGAAT 44238201 ATATATAAGCCATTTTCACAAGGCTATCCAAATTTATACAAAACC-AAGGGTACATGACCAACAA 1 ATATATAAGCCATTTTCACAAGGCTATCCAAATTTATACAAAACCAAAGGGTACATGACCAACAA * 44238265 CAAAAAGGGTAGTCCTATACATGCCATTTTCAGAGTTCAACCAAAAATGTACCAAAA-GGGCTTT 66 CAAAAAGGGTAGTCCTATACATGCCA-TTTCAAAGTTCAACCAAAAATGTACCAAAAGGGGCTTT 44238329 GATAGTGTGGACGACTTCGACTTCGACAATCCCGAGTCCGATAGCTGACGAACCAAAATCTATAA 130 GATAGTGTGGACGACTTCGACTTCGACAATCCCGAGTCCGATAGCTGACGAACCAAAATCTATAA 44238394 AATAGAGAATCAAAGAAACGGAAT 195 AATAGAGAATCAAAGAAACGGAAT 44238418 A 1 A 44238419 AGCATTTAAT Statistics Matches: 210, Mismatches: 7, Indels: 3 0.95 0.03 0.01 Matches are distributed among these distances: 217 139 0.66 218 71 0.34 ACGTcount: A:0.39, C:0.21, G:0.18, T:0.22 Consensus pattern (218 bp): ATATATAAGCCATTTTCACAAGGCTATCCAAATTTATACAAAACCAAAGGGTACATGACCAACAA CAAAAAGGGTAGTCCTATACATGCCATTTCAAAGTTCAACCAAAAATGTACCAAAAGGGGCTTTG ATAGTGTGGACGACTTCGACTTCGACAATCCCGAGTCCGATAGCTGACGAACCAAAATCTATAAA ATAGAGAATCAAAGAAACGGAAT Found at i:44238789 original size:39 final size:39 Alignment explanation

Indices: 44238733--44238902 Score: 114 Period size: 40 Copynumber: 4.3 Consensus size: 39 44238723 ACCCAATTAT * * * 44238733 CTTCGAGATTTAGCCGGATATAACCACTCGCAC-AAGGC 1 CTTCGGGACTTAGCCGGATATAACCACTAGCACAAAGGC * *** * 44238771 CTTCGGGTCTTAGTCCGGATATGGTCACTAGCACAAATGC 1 CTTCGGGACTTAG-CCGGATATAACCACTAGCACAAAGGC * * 44238811 CTTCGGGACTTAGCCCGGAATTAGTAA-CTC-A-CACAAATGC 1 CTTCGGGACTTAG-CCGG-A-TA-TAACCACTAGCACAAAGGC * * * * * * 44238851 CTTCGAGACTTAGCCCGAAATTAATCACTAGCACAAACGT 1 CTTCGGGACTTAGCCGGATA-TAACCACTAGCACAAAGGC 44238891 CTTCGGGACTTA 1 CTTCGGGACTTA 44238903 ACCCCGTTAG Statistics Matches: 103, Mismatches: 21, Indels: 14 0.75 0.15 0.10 Matches are distributed among these distances: 37 4 0.04 38 13 0.13 39 20 0.19 40 59 0.57 41 2 0.02 42 4 0.04 43 1 0.01 ACGTcount: A:0.28, C:0.27, G:0.21, T:0.24 Consensus pattern (39 bp): CTTCGGGACTTAGCCGGATATAACCACTAGCACAAAGGC Found at i:44238823 original size:40 final size:39 Alignment explanation

Indices: 44238769--44238902 Score: 137 Period size: 40 Copynumber: 3.4 Consensus size: 39 44238759 CTCGCACAAG * * 44238769 GCCTTCGGGTCTTAGTCCGG-ATATGGTCACTAGCACAAAT 1 GCCTTCGGGACTTAG-CCGGAAT-TAGTCACTAGCACAAAT * 44238809 GCCTTCGGGACTTAGCCCGGAATTAGTAACTCA-CACAAAT 1 GCCTTCGGGACTTAG-CCGGAATTAGTCACT-AGCACAAAT * * * * 44238849 GCCTTCGAGACTTAGCCCGAAATTAATCACTAGCACAAAC 1 GCCTTCGGGACTTAG-CCGGAATTAGTCACTAGCACAAAT * 44238889 GTCTTCGGGACTTA 1 GCCTTCGGGACTTA 44238903 ACCCCGTTAG Statistics Matches: 80, Mismatches: 11, Indels: 6 0.82 0.11 0.06 Matches are distributed among these distances: 39 1 0.01 40 76 0.95 41 3 0.04 ACGTcount: A:0.28, C:0.27, G:0.21, T:0.25 Consensus pattern (39 bp): GCCTTCGGGACTTAGCCGGAATTAGTCACTAGCACAAAT Found at i:44246829 original size:39 final size:40 Alignment explanation

Indices: 44246757--44246966 Score: 221 Period size: 40 Copynumber: 5.3 Consensus size: 40 44246747 ACCCAATTAT * ** * 44246757 CTTCGGGATTTAG-CCGGATATAACCACTCGCAC-AAGGC 1 CTTCGGGACTTAGCCCGGATATAGTCACTCGCACAAATGC * * * * * 44246795 CTTCGGGTCTTAGTCCTGATATGGTCACTAGCACAAATGC 1 CTTCGGGACTTAGCCCGGATATAGTCACTCGCACAAATGC * 44246835 CTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATGC 1 CTTCGGGACTTAGCCCGGATATAGTCACTCGCACAAATGC * * 44246875 CTTCGGGGCTTAGCCCGGA-ATTAGTAACTCGCACAAATGC 1 CTTCGGGACTTAGCCCGGATA-TAGTCACTCGCACAAATGC * * * * 44246915 CTTCTGGACTTAGCCCGGA-ATTAATCACTAGCACAAATGT 1 CTTCGGGACTTAGCCCGGATA-TAGTCACTCGCACAAATGC * 44246955 CTTCAGGACTTA 1 CTTCGGGACTTA 44246967 ACCCCGTTAG Statistics Matches: 147, Mismatches: 22, Indels: 4 0.85 0.13 0.02 Matches are distributed among these distances: 38 11 0.07 39 16 0.11 40 120 0.82 ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25 Consensus pattern (40 bp): CTTCGGGACTTAGCCCGGATATAGTCACTCGCACAAATGC Found at i:44248997 original size:27 final size:27 Alignment explanation

Indices: 44248935--44249000 Score: 89 Period size: 27 Copynumber: 2.4 Consensus size: 27 44248925 GGGCATATTC * 44248935 GTCATTTTACCATACAGGGGTATTACG 1 GTCATTTTACCTTACAGGGGTATTACG * 44248962 GTCACTTTACCTTACAGGGGCT-TTACG 1 GTCATTTTACCTTACAGGGG-TATTACG * 44248989 GTCTTTTTACCT 1 GTCATTTTACCT 44249001 ATTAGAGGTA Statistics Matches: 34, Mismatches: 4, Indels: 2 0.85 0.10 0.05 Matches are distributed among these distances: 27 33 0.97 28 1 0.03 ACGTcount: A:0.20, C:0.23, G:0.20, T:0.38 Consensus pattern (27 bp): GTCATTTTACCTTACAGGGGTATTACG Found at i:44249083 original size:27 final size:27 Alignment explanation

Indices: 44249053--44249138 Score: 86 Period size: 27 Copynumber: 3.1 Consensus size: 27 44249043 GTAAATCTAC 44249053 AAACCAAGGGTATTTCAGTAATTTTGT 1 AAACCAAGGGTATTTCAGTAATTTTGT * 44249080 AAACCAATGGTATTTCTA-TAATTTT-T 1 AAACCAAGGGTATTTC-AGTAATTTTGT * * * 44249106 AGAAAGTCAAGGGTATTTCTGTAATTGTGT 1 --AAA-CCAAGGGTATTTCAGTAATTTTGT 44249136 AAA 1 AAA 44249139 TTAGGGGTAT Statistics Matches: 48, Mismatches: 5, Indels: 11 0.75 0.08 0.17 Matches are distributed among these distances: 26 1 0.02 27 22 0.46 28 7 0.15 29 17 0.35 30 1 0.02 ACGTcount: A:0.35, C:0.09, G:0.17, T:0.38 Consensus pattern (27 bp): AAACCAAGGGTATTTCAGTAATTTTGT Found at i:44249156 original size:27 final size:27 Alignment explanation

Indices: 44249140--44249239 Score: 130 Period size: 27 Copynumber: 3.7 Consensus size: 27 44249130 TTGTGTAAAT 44249140 TAGGGGTATTTTGGTAATTTTACAAA- 1 TAGGGGTATTTTGGTAATTTTACAAAC * * * 44249166 TTGAGGGTATTTCGGTAATTTCACAAAC 1 TAG-GGGTATTTTGGTAATTTTACAAAC * * 44249194 CAGTGGTATTTTGGTAATTTTACAAAC 1 TAGGGGTATTTTGGTAATTTTACAAAC * 44249221 TAGGGGTATTTGGGTAATT 1 TAGGGGTATTTTGGTAATT 44249240 CTACCCTATA Statistics Matches: 61, Mismatches: 11, Indels: 3 0.81 0.15 0.04 Matches are distributed among these distances: 26 2 0.03 27 58 0.95 28 1 0.02 ACGTcount: A:0.28, C:0.08, G:0.24, T:0.40 Consensus pattern (27 bp): TAGGGGTATTTTGGTAATTTTACAAAC Found at i:44249158 original size:56 final size:54 Alignment explanation

Indices: 44249050--44249185 Score: 130 Period size: 56 Copynumber: 2.5 Consensus size: 54 44249040 TTGGTAAATC * * * 44249050 TACAAACCAAGGGTATTTCAGTAATTTTGTAAACCAATGGTATTTCTATAATTTT 1 TACAAATCAAGGGTATTTCAGTAATTGTGTAAACCAAGGGTATTTCTATAA-TTT * * ** * * 44249105 TAGAAAGTCAAGGGTATTTCTGTAATTGTGTAAATTAGGGGTATTT-TGGTAATTT 1 TACAAA-TCAAGGGTATTTCAGTAATTGTGTAAACCAAGGGTATTTCT-ATAATTT ** * 44249160 TACAAATTGAGGGTATTTCGGTAATT 1 TACAAATCAAGGGTATTTCAGTAATT 44249186 TCACAAACCA Statistics Matches: 66, Mismatches: 13, Indels: 5 0.79 0.15 0.06 Matches are distributed among these distances: 54 17 0.26 55 14 0.21 56 35 0.53 ACGTcount: A:0.32, C:0.08, G:0.20, T:0.40 Consensus pattern (54 bp): TACAAATCAAGGGTATTTCAGTAATTGTGTAAACCAAGGGTATTTCTATAATTT Found at i:44249279 original size:27 final size:27 Alignment explanation

Indices: 44249141--44249279 Score: 95 Period size: 27 Copynumber: 5.1 Consensus size: 27 44249131 TGTGTAAATT * * * 44249141 AGGGGTATTTTGGTAATTTTACAAATTG 1 AGGGGTATTTCGGTAATTTAAC-AATCG * * * 44249169 A-GGGTATTTCGGTAATTTCACAAACC 1 AGGGGTATTTCGGTAATTTAACAATCG * * * * * 44249195 AGTGGTATTTTGGTAATTTTACAAACT 1 AGGGGTATTTCGGTAATTTAACAATCG * * * 44249222 AGGGGTATTTGGGTAATTCTACCCTAT-- 1 AGGGGTATTTCGGTAATT-TA-ACAATCG * 44249249 AGGGGTATTTCAGTAATTTAACAATCG 1 AGGGGTATTTCGGTAATTTAACAATCG 44249276 AGGG 1 AGGG 44249280 TAAAATAGTA Statistics Matches: 87, Mismatches: 19, Indels: 11 0.74 0.16 0.09 Matches are distributed among these distances: 25 3 0.03 26 5 0.06 27 75 0.86 28 2 0.02 29 2 0.02 ACGTcount: A:0.29, C:0.11, G:0.24, T:0.37 Consensus pattern (27 bp): AGGGGTATTTCGGTAATTTAACAATCG Found at i:44249301 original size:27 final size:27 Alignment explanation

Indices: 44249259--44249363 Score: 124 Period size: 27 Copynumber: 3.9 Consensus size: 27 44249249 AGGGGTATTT 44249259 CAGTAATT-TA-ACAATCGAGGGTAAAA 1 CAGTAATTCTATA-AATCGAGGGTAAAA * * * 44249285 TAGTAATTTTGTAAATCGAGGGTAAAA 1 CAGTAATTCTATAAATCGAGGGTAAAA * 44249312 CAGTAATTCTATAAATCAACGGGTAAAA 1 CAGTAATTCTATAAATCGA-GGGTAAAA * * 44249340 CAATAATTCTATAAATCGATGGTA 1 CAGTAATTCTATAAATCGAGGGTA 44249364 CTTTGGTAAT Statistics Matches: 67, Mismatches: 9, Indels: 5 0.83 0.11 0.06 Matches are distributed among these distances: 26 7 0.10 27 34 0.51 28 26 0.39 ACGTcount: A:0.44, C:0.10, G:0.17, T:0.29 Consensus pattern (27 bp): CAGTAATTCTATAAATCGAGGGTAAAA Found at i:44249373 original size:27 final size:27 Alignment explanation

Indices: 44249343--44249401 Score: 64 Period size: 27 Copynumber: 2.2 Consensus size: 27 44249333 GGTAAAACAA * * 44249343 TAATTCTATAAATCGATGGTACTTTGG 1 TAATTCTACAAATCGAGGGTACTTTGG * * * * 44249370 TAATTTTACAAGTCGAGGGTATTTTTG 1 TAATTCTACAAATCGAGGGTACTTTGG 44249397 TAATT 1 TAATT 44249402 GGTAAACTAA Statistics Matches: 26, Mismatches: 6, Indels: 0 0.81 0.19 0.00 Matches are distributed among these distances: 27 26 1.00 ACGTcount: A:0.29, C:0.08, G:0.19, T:0.44 Consensus pattern (27 bp): TAATTCTACAAATCGAGGGTACTTTGG Found at i:44251693 original size:56 final size:56 Alignment explanation

Indices: 44251599--44251762 Score: 217 Period size: 56 Copynumber: 2.9 Consensus size: 56 44251589 TGGATATATA * * * 44251599 AATGGCACTTAGTGTGCGAAGTATCGAGGA-AGGCACTTAGTGTGCGATACATCCAG 1 AATGACACTTAGTGTGCGAAGTATCGAGGATA-GAACTTAGTGTGCGAAACATCCAG * 44251655 AATGACACTTAGTGTGCGAAGTATCGAGGATAGAACTTAGTGTGCGAAACATCTAG 1 AATGACACTTAGTGTGCGAAGTATCGAGGATAGAACTTAGTGTGCGAAACATCCAG * * * 44251711 AATGACACTTAGTGTGC-AAGGTATC-AGGTATGGAACCTAGTGTGCGAGACAT 1 AATGACACTTAGTGTGCGAA-GTATCGAGG-ATAGAACTTAGTGTGCGAAACAT 44251763 TAAATATTCA Statistics Matches: 98, Mismatches: 7, Indels: 6 0.88 0.06 0.05 Matches are distributed among these distances: 55 5 0.05 56 92 0.94 57 1 0.01 ACGTcount: A:0.31, C:0.16, G:0.29, T:0.24 Consensus pattern (56 bp): AATGACACTTAGTGTGCGAAGTATCGAGGATAGAACTTAGTGTGCGAAACATCCAG Found at i:44251720 original size:28 final size:28 Alignment explanation

Indices: 44251599--44251727 Score: 136 Period size: 28 Copynumber: 4.6 Consensus size: 28 44251589 TGGATATATA * ** 44251599 AATGGCACTTAGTGTGCGAAGTATCGAGG 1 AATGACACTTAGTGTGCGAAACATCGA-G * * * 44251628 AA-GGCACTTAGTGTGCGATACATCCAG 1 AATGACACTTAGTGTGCGAAACATCGAG ** 44251655 AATGACACTTAGTGTGCGAAGTATCGAG 1 AATGACACTTAGTGTGCGAAACATCGAG * * 44251683 GATAGA-ACTTAGTGTGCGAAACATCTAG 1 AAT-GACACTTAGTGTGCGAAACATCGAG 44251711 AATGACACTTAGTGTGC 1 AATGACACTTAGTGTGC 44251728 AAGGTATCAG Statistics Matches: 83, Mismatches: 14, Indels: 7 0.80 0.13 0.07 Matches are distributed among these distances: 27 5 0.06 28 74 0.89 29 4 0.05 ACGTcount: A:0.31, C:0.16, G:0.28, T:0.25 Consensus pattern (28 bp): AATGACACTTAGTGTGCGAAACATCGAG Found at i:44251863 original size:32 final size:32 Alignment explanation

Indices: 44251813--44251936 Score: 140 Period size: 32 Copynumber: 3.9 Consensus size: 32 44251803 GATTGGTATG * * ** 44251813 AGATAGTATAGGTATGTACAAAAATTCACCCA 1 AGATGGTACAGGTATGTACAAAAATTCATACA * ** 44251845 AGATGGTACAGGTATGTACGAAAATTTGTACA 1 AGATGGTACAGGTATGTACAAAAATTCATACA * * ** * 44251877 AAATGGTGCAGGTATGTACGGAAATTCGTACA 1 AGATGGTACAGGTATGTACAAAAATTCATACA 44251909 AGATGGTACAGGTATGTACAAAAATTCA 1 AGATGGTACAGGTATGTACAAAAATTCA 44251937 ATTGAGTATT Statistics Matches: 76, Mismatches: 16, Indels: 0 0.83 0.17 0.00 Matches are distributed among these distances: 32 76 1.00 ACGTcount: A:0.40, C:0.12, G:0.23, T:0.26 Consensus pattern (32 bp): AGATGGTACAGGTATGTACAAAAATTCATACA Found at i:44261077 original size:28 final size:27 Alignment explanation

Indices: 44261035--44261132 Score: 108 Period size: 28 Copynumber: 3.5 Consensus size: 27 44261025 GATCATATAA * 44261035 ATGGCACTTAGTGTGCGTAGTACCGAGG 1 ATGGCACTTAGTGTGTG-AGTACCGAGG * * * 44261063 ATGGCACTTAATGTGTGA-TACATCCAGA 1 ATGGCACTTAGTGTGTGAGTAC--CGAGG * 44261091 ATGGCACTTAGTGTGTGAAGTATCGAGG 1 ATGGCACTTAGTGTGTG-AGTACCGAGG 44261119 ATGGCACTTAGTGT 1 ATGGCACTTAGTGT 44261133 CCAAAACATC Statistics Matches: 58, Mismatches: 8, Indels: 8 0.78 0.11 0.11 Matches are distributed among these distances: 26 3 0.05 27 1 0.02 28 51 0.88 29 1 0.02 30 2 0.03 ACGTcount: A:0.26, C:0.15, G:0.31, T:0.29 Consensus pattern (27 bp): ATGGCACTTAGTGTGTGAGTACCGAGG Found at i:44261120 original size:56 final size:56 Alignment explanation

Indices: 44261034--44261161 Score: 175 Period size: 56 Copynumber: 2.3 Consensus size: 56 44261024 CGATCATATA * *** * 44261034 AATGGCACTTAGTGTGCGTAGTACCGAGGATGGCACTTAATGTGTGATACATCCAG 1 AATGGCACTTAGTGTGCGAAGTACCGAGGATGGCACTTAATGTCCAAAACATCCAG * * * 44261090 AATGGCACTTAGTGTGTGAAGTATCGAGGATGGCACTTAGTGTCCAAAACATCCAG 1 AATGGCACTTAGTGTGCGAAGTACCGAGGATGGCACTTAATGTCCAAAACATCCAG * 44261146 AATGACACTTAGTGTG 1 AATGGCACTTAGTGTG 44261162 GGAGGTATTG Statistics Matches: 63, Mismatches: 9, Indels: 0 0.88 0.12 0.00 Matches are distributed among these distances: 56 63 1.00 ACGTcount: A:0.29, C:0.17, G:0.27, T:0.27 Consensus pattern (56 bp): AATGGCACTTAGTGTGCGAAGTACCGAGGATGGCACTTAATGTCCAAAACATCCAG Found at i:44261154 original size:28 final size:28 Alignment explanation

Indices: 44261082--44261160 Score: 86 Period size: 28 Copynumber: 2.8 Consensus size: 28 44261072 AATGTGTGAT *** 44261082 ACATCCAGAATGGCACTTAGTGTGTGAA 1 ACATCCAGAATGGCACTTAGTGTCCAAA ** * * 44261110 GTATCGAGGATGGCACTTAGTGTCCAAA 1 ACATCCAGAATGGCACTTAGTGTCCAAA * 44261138 ACATCCAGAATGACACTTAGTGT 1 ACATCCAGAATGGCACTTAGTGT 44261161 GGGAGGTATT Statistics Matches: 39, Mismatches: 12, Indels: 0 0.76 0.24 0.00 Matches are distributed among these distances: 28 39 1.00 ACGTcount: A:0.32, C:0.19, G:0.24, T:0.25 Consensus pattern (28 bp): ACATCCAGAATGGCACTTAGTGTCCAAA Found at i:44261179 original size:56 final size:56 Alignment explanation

Indices: 44261034--44261197 Score: 159 Period size: 56 Copynumber: 2.9 Consensus size: 56 44261024 CGATCATATA * * * * * * *** * 44261034 AATGGCACTTAGTGTGCGTAGTACCGAGGATGGCACTTAATGTGTGATACATCCAG 1 AATGACACTTAGTGTGGGAAGTATCGAGGATGGCACCTAGTGTCCAAAACATCCAG * * * 44261090 AATGGCACTTAGTGTGTGAAGTATCGAGGATGGCACTTAGTGTCCAAAACATCCAG 1 AATGACACTTAGTGTGGGAAGTATCGAGGATGGCACCTAGTGTCCAAAACATCCAG * * * * 44261146 AATGACACTTAGTGTGGGAGGTATTG-GGTATGGCACCTAGTGTGCAATACAT 1 AATGACACTTAGTGTGGGAAGTATCGAGG-ATGGCACCTAGTGTCCAAAACAT 44261198 TGAAAATTCA Statistics Matches: 92, Mismatches: 15, Indels: 2 0.84 0.14 0.02 Matches are distributed among these distances: 55 2 0.02 56 90 0.98 ACGTcount: A:0.28, C:0.16, G:0.29, T:0.27 Consensus pattern (56 bp): AATGACACTTAGTGTGGGAAGTATCGAGGATGGCACCTAGTGTCCAAAACATCCAG Found at i:44269940 original size:40 final size:40 Alignment explanation

Indices: 44269887--44270404 Score: 898 Period size: 40 Copynumber: 13.0 Consensus size: 40 44269877 GATGATAACC * * * 44269887 GGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTA-ATTCC 1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA-TCT * 44269927 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCC 1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCT * 44269967 GGGCTAGGTCCCGAAGGCATTTGTGCGAGTTACTATATCT 1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCT 44270007 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCT 1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCT 44270047 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCT 1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCT 44270087 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCT 1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCT 44270127 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCT 1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCT 44270167 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCT 1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCT 44270207 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCT 1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCT 44270247 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCT 1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCT * 44270287 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCC 1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCT * * * 44270327 GGGCTAAGTCCCGAAGGCATTGGTGCGAGTTACGATATCC 1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCT * * 44270367 GGGCTATGTCCCGAAGGCA-TTGAGCGAG-TAGCTATATC 1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATATC 44270405 CGGTTAAATG Statistics Matches: 464, Mismatches: 12, Indels: 5 0.96 0.02 0.01 Matches are distributed among these distances: 38 2 0.00 39 13 0.03 40 448 0.97 41 1 0.00 ACGTcount: A:0.22, C:0.21, G:0.28, T:0.28 Consensus pattern (40 bp): GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCT Found at i:44279469 original size:28 final size:28 Alignment explanation

Indices: 44279437--44279501 Score: 103 Period size: 28 Copynumber: 2.3 Consensus size: 28 44279427 ATTTACTAGA * 44279437 ATACCCCTATGTATGCAAAATTACCATT 1 ATACCCCTATGTATGCAAAATGACCATT * * 44279465 ATACCCCTATGTGTGCAAAATGACCTTT 1 ATACCCCTATGTATGCAAAATGACCATT 44279493 ATACCCCTA 1 ATACCCCTA 44279502 GGGTTAATTT Statistics Matches: 34, Mismatches: 3, Indels: 0 0.92 0.08 0.00 Matches are distributed among these distances: 28 34 1.00 ACGTcount: A:0.32, C:0.28, G:0.09, T:0.31 Consensus pattern (28 bp): ATACCCCTATGTATGCAAAATGACCATT Found at i:44279648 original size:28 final size:27 Alignment explanation

Indices: 44279607--44279696 Score: 119 Period size: 28 Copynumber: 3.2 Consensus size: 27 44279597 AGCAAGCGTC 44279607 CTGGTGGCTA-TGCCACAAATTATCTGTT 1 CTGGTGGC-ACTGCCACAAA-TATCTGTT * * 44279635 CTGGTGGCCCTGCCACATATATCTGTT 1 CTGGTGGCACTGCCACAAATATCTGTT 44279662 CTGGTGGCACTGCCACAAAATATCTGTAT 1 CTGGTGGCACTGCCAC-AAATATCTGT-T 44279691 CTGGTG 1 CTGGTG 44279697 ACTCTGTCAC Statistics Matches: 55, Mismatches: 4, Indels: 5 0.86 0.06 0.08 Matches are distributed among these distances: 27 23 0.42 28 25 0.45 29 7 0.13 ACGTcount: A:0.20, C:0.24, G:0.23, T:0.32 Consensus pattern (27 bp): CTGGTGGCACTGCCACAAATATCTGTT Found at i:44279665 original size:27 final size:28 Alignment explanation

Indices: 44279607--44279722 Score: 121 Period size: 27 Copynumber: 4.2 Consensus size: 28 44279597 AGCAAGCGTC * 44279607 CTGGTGGCTATGCCACAAATTATCTGT-T 1 CTGGTGGCTCTGCCACAAA-TATCTGTAT * * 44279635 CTGGTGGCCCTGCCACATATATCTGT-T 1 CTGGTGGCTCTGCCACAAATATCTGTAT * 44279662 CTGGTGGCACTGCCACAAAATATCTGTAT 1 CTGGTGGCTCTGCCAC-AAATATCTGTAT * * * * 44279691 CTGGTGACTCTGTCAC-ATTTTCTGTAT 1 CTGGTGGCTCTGCCACAAATATCTGTAT 44279718 CTGGT 1 CTGGT 44279723 AGCCATGCTG Statistics Matches: 76, Mismatches: 10, Indels: 5 0.84 0.11 0.05 Matches are distributed among these distances: 27 37 0.49 28 25 0.33 29 14 0.18 ACGTcount: A:0.19, C:0.24, G:0.22, T:0.35 Consensus pattern (28 bp): CTGGTGGCTCTGCCACAAATATCTGTAT Found at i:44279715 original size:55 final size:56 Alignment explanation

Indices: 44279607--44279722 Score: 148 Period size: 55 Copynumber: 2.1 Consensus size: 56 44279597 AGCAAGCGTC * * 44279607 CTGGTGGCTATGCCACAAATTATCTGTTCTGGTGGCCCTGCCACATATATCTGT-T 1 CTGGTGGCTATGCCACAAAATATCTGTTCTGGTGACCCTGCCACATATATCTGTAT * * * 44279662 CTGGTGGC-ACTGCCACAAAATATCTGTATCTGGTGACTCTGTCACAT-TTTCTGTAT 1 CTGGTGGCTA-TGCCACAAAATATCTGT-TCTGGTGACCCTGCCACATATATCTGTAT 44279718 CTGGT 1 CTGGT 44279723 AGCCATGCTG Statistics Matches: 53, Mismatches: 5, Indels: 5 0.84 0.08 0.08 Matches are distributed among these distances: 54 1 0.02 55 30 0.57 56 22 0.42 ACGTcount: A:0.19, C:0.24, G:0.22, T:0.35 Consensus pattern (56 bp): CTGGTGGCTATGCCACAAAATATCTGTTCTGGTGACCCTGCCACATATATCTGTAT Found at i:44280813 original size:11 final size:10 Alignment explanation

Indices: 44280785--44280818 Score: 50 Period size: 10 Copynumber: 3.3 Consensus size: 10 44280775 AGCTTGTAAG 44280785 TATTCTGAAT 1 TATTCTGAAT * 44280795 TTTTCTGAAT 1 TATTCTGAAT 44280805 ATATTCTGAAT 1 -TATTCTGAAT 44280816 TAT 1 TAT 44280819 CTGTCTGTAC Statistics Matches: 21, Mismatches: 2, Indels: 2 0.84 0.08 0.08 Matches are distributed among these distances: 10 12 0.57 11 9 0.43 ACGTcount: A:0.29, C:0.09, G:0.09, T:0.53 Consensus pattern (10 bp): TATTCTGAAT Found at i:44284853 original size:20 final size:20 Alignment explanation

Indices: 44284828--44284866 Score: 78 Period size: 20 Copynumber: 1.9 Consensus size: 20 44284818 TGGTCAGTTG 44284828 GAAAGAGTTATTCAGATTCT 1 GAAAGAGTTATTCAGATTCT 44284848 GAAAGAGTTATTCAGATTC 1 GAAAGAGTTATTCAGATTC 44284867 AGATTCAGTT Statistics Matches: 19, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 20 19 1.00 ACGTcount: A:0.36, C:0.10, G:0.21, T:0.33 Consensus pattern (20 bp): GAAAGAGTTATTCAGATTCT Found at i:44285860 original size:13 final size:12 Alignment explanation

Indices: 44285803--44285859 Score: 87 Period size: 12 Copynumber: 4.7 Consensus size: 12 44285793 ATTGTAGATT 44285803 AAAAAAATCGAA 1 AAAAAAATCGAA 44285815 AAAAAAATCGAA 1 AAAAAAATCGAA * 44285827 AAAAAAATTGAA 1 AAAAAAATCGAA * 44285839 AAAAAAATTTGAA 1 AAAAAAA-TCGAA 44285852 AAAAAAAT 1 AAAAAAAT 44285860 TGCATACGGT Statistics Matches: 43, Mismatches: 1, Indels: 2 0.93 0.02 0.04 Matches are distributed among these distances: 12 31 0.72 13 12 0.28 ACGTcount: A:0.75, C:0.04, G:0.07, T:0.14 Consensus pattern (12 bp): AAAAAAATCGAA Found at i:44287440 original size:24 final size:24 Alignment explanation

Indices: 44287408--44287457 Score: 91 Period size: 24 Copynumber: 2.1 Consensus size: 24 44287398 GGGGCCACAT 44287408 TGCAAGCCAATGCCCGAACCGAAA 1 TGCAAGCCAATGCCCGAACCGAAA * 44287432 TGCAAGCCAATGCCTGAACCGAAA 1 TGCAAGCCAATGCCCGAACCGAAA 44287456 TG 1 TG 44287458 TGATGTTTGT Statistics Matches: 25, Mismatches: 1, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 24 25 1.00 ACGTcount: A:0.36, C:0.30, G:0.22, T:0.12 Consensus pattern (24 bp): TGCAAGCCAATGCCCGAACCGAAA Found at i:44291206 original size:10 final size:10 Alignment explanation

Indices: 44291190--44291247 Score: 55 Period size: 10 Copynumber: 5.7 Consensus size: 10 44291180 CAACTCCGAC 44291190 CAGCTCAATT 1 CAGCTCAATT * * 44291200 GAGCTCATTT 1 CAGCTCAATT 44291210 CAGCTCAA-T 1 CAGCTCAATT * 44291219 CAAGCTTAATT 1 C-AGCTCAATT * 44291230 TAGCTACAATT 1 CAGCT-CAATT 44291241 CAGCTCA 1 CAGCTCA 44291248 TTTATTTTAT Statistics Matches: 37, Mismatches: 8, Indels: 6 0.73 0.16 0.12 Matches are distributed among these distances: 9 2 0.05 10 26 0.70 11 9 0.24 ACGTcount: A:0.31, C:0.26, G:0.12, T:0.31 Consensus pattern (10 bp): CAGCTCAATT Found at i:44291251 original size:20 final size:19 Alignment explanation

Indices: 44291191--44291251 Score: 61 Period size: 20 Copynumber: 3.1 Consensus size: 19 44291181 AACTCCGACC * 44291191 AGCTCAATTGAGCTCATTT 1 AGCTCAATTCAGCTCATTT * 44291210 CAGCTCAA-TCAAGCTTAATTT 1 -AGCTCAATTC-AGC-TCATTT 44291231 AGCTACAATTCAGCTCATTT 1 AGCT-CAATTCAGCTCATTT 44291251 A 1 A 44291252 TTTTATTGGT Statistics Matches: 34, Mismatches: 3, Indels: 8 0.76 0.07 0.18 Matches are distributed among these distances: 19 1 0.03 20 20 0.59 21 11 0.32 22 2 0.06 ACGTcount: A:0.31, C:0.23, G:0.11, T:0.34 Consensus pattern (19 bp): AGCTCAATTCAGCTCATTT Found at i:44292544 original size:35 final size:35 Alignment explanation

Indices: 44292498--44292569 Score: 135 Period size: 35 Copynumber: 2.1 Consensus size: 35 44292488 GAAGCCATTA 44292498 AGCTGCCCATTGGTCCAATAACACGAGCTAGAGCT 1 AGCTGCCCATTGGTCCAATAACACGAGCTAGAGCT * 44292533 AGCTGCCCATTGGTCCAATAACGCGAGCTAGAGCT 1 AGCTGCCCATTGGTCCAATAACACGAGCTAGAGCT 44292568 AG 1 AG 44292570 ACGATTCAAA Statistics Matches: 36, Mismatches: 1, Indels: 0 0.97 0.03 0.00 Matches are distributed among these distances: 35 36 1.00 ACGTcount: A:0.28, C:0.28, G:0.25, T:0.19 Consensus pattern (35 bp): AGCTGCCCATTGGTCCAATAACACGAGCTAGAGCT Found at i:44297660 original size:14 final size:13 Alignment explanation

Indices: 44297639--44297690 Score: 61 Period size: 12 Copynumber: 3.8 Consensus size: 13 44297629 ATAGGTACGT 44297639 AAAAAAAAAGAGTTCG 1 AAAAAAAAA-A-TT-G 44297655 AAAAAAAAAATTG 1 AAAAAAAAAATTG 44297668 -AAAAAAAAATTG 1 AAAAAAAAAATTG 44297680 AAAAGAAAAAA 1 AAAA-AAAAAA 44297691 AAATTGCATA Statistics Matches: 34, Mismatches: 0, Indels: 6 0.85 0.00 0.15 Matches are distributed among these distances: 12 12 0.35 13 4 0.12 14 8 0.24 15 1 0.03 16 9 0.26 ACGTcount: A:0.75, C:0.02, G:0.12, T:0.12 Consensus pattern (13 bp): AAAAAAAAAATTG Found at i:44299938 original size:17 final size:17 Alignment explanation

Indices: 44299906--44299955 Score: 50 Period size: 15 Copynumber: 2.9 Consensus size: 17 44299896 GCGAAAATAC 44299906 AAAAGAAAAGAAAAATGAT 1 AAAA-AAAAG-AAAATGAT 44299925 AAAAAAAAGAAAAT--T 1 AAAAAAAAGAAAATGAT * * 44299940 CAAAAAAAGAGAATGA 1 AAAAAAAAGAAAATGA 44299956 AAAGAGAGCG Statistics Matches: 27, Mismatches: 2, Indels: 6 0.77 0.06 0.17 Matches are distributed among these distances: 15 13 0.48 17 5 0.19 18 5 0.19 19 4 0.15 ACGTcount: A:0.74, C:0.02, G:0.14, T:0.10 Consensus pattern (17 bp): AAAAAAAAGAAAATGAT Found at i:44307422 original size:13 final size:13 Alignment explanation

Indices: 44307393--44307432 Score: 53 Period size: 14 Copynumber: 2.9 Consensus size: 13 44307383 AACCGACCAA * 44307393 TTTGTTCATATCCC 1 TTTGTTCCTA-CCC 44307407 TTTGTTCCTACCC 1 TTTGTTCCTACCC 44307420 TTTCGTTCCTACC 1 TTT-GTTCCTACC 44307433 ATTCCGTTCG Statistics Matches: 24, Mismatches: 1, Indels: 2 0.89 0.04 0.07 Matches are distributed among these distances: 13 6 0.25 14 18 0.75 ACGTcount: A:0.10, C:0.35, G:0.07, T:0.47 Consensus pattern (13 bp): TTTGTTCCTACCC Found at i:44318540 original size:20 final size:20 Alignment explanation

Indices: 44318515--44318569 Score: 74 Period size: 20 Copynumber: 2.8 Consensus size: 20 44318505 TGTGGTTCAA * 44318515 CTCATTCGAGCTCAAGTTAG 1 CTCATTCGAGCTCAAGTCAG * 44318535 CTCATTCGTGCTCAAGTCAG 1 CTCATTCGAGCTCAAGTCAG * * 44318555 GTCATTCAAGCTCAA 1 CTCATTCGAGCTCAA 44318570 TTTAACTCGT Statistics Matches: 30, Mismatches: 5, Indels: 0 0.86 0.14 0.00 Matches are distributed among these distances: 20 30 1.00 ACGTcount: A:0.25, C:0.27, G:0.18, T:0.29 Consensus pattern (20 bp): CTCATTCGAGCTCAAGTCAG Found at i:44320177 original size:10 final size:11 Alignment explanation

Indices: 44320162--44320212 Score: 52 Period size: 11 Copynumber: 4.7 Consensus size: 11 44320152 TCGATATTGT * 44320162 AAAAAAAA-GG 1 AAAAAAAATCG 44320172 AAAAAAAATCG 1 AAAAAAAATCG * * 44320183 AAAAAAATTCA 1 AAAAAAAATCG 44320194 AAAAAAAATTC- 1 AAAAAAAA-TCG 44320205 AAAAAAAA 1 AAAAAAAA 44320213 AAATTGTATT Statistics Matches: 35, Mismatches: 4, Indels: 3 0.83 0.10 0.07 Matches are distributed among these distances: 10 8 0.23 11 25 0.71 12 2 0.06 ACGTcount: A:0.78, C:0.06, G:0.06, T:0.10 Consensus pattern (11 bp): AAAAAAAATCG Found at i:44320197 original size:11 final size:11 Alignment explanation

Indices: 44320172--44320212 Score: 57 Period size: 11 Copynumber: 3.7 Consensus size: 11 44320162 AAAAAAAAGG 44320172 AAAAAAAA-TC 1 AAAAAAAATTC * 44320182 GAAAAAAATTC 1 AAAAAAAATTC 44320193 AAAAAAAAATTC 1 -AAAAAAAATTC 44320205 AAAAAAAA 1 AAAAAAAA 44320213 AAATTGTATT Statistics Matches: 27, Mismatches: 2, Indels: 3 0.84 0.06 0.09 Matches are distributed among these distances: 10 7 0.26 11 10 0.37 12 10 0.37 ACGTcount: A:0.78, C:0.07, G:0.02, T:0.12 Consensus pattern (11 bp): AAAAAAAATTC Found at i:44320217 original size:14 final size:12 Alignment explanation

Indices: 44320183--44320213 Score: 62 Period size: 12 Copynumber: 2.6 Consensus size: 12 44320173 AAAAAAATCG 44320183 AAAAAAATTCAA 1 AAAAAAATTCAA 44320195 AAAAAAATTCAA 1 AAAAAAATTCAA 44320207 AAAAAAA 1 AAAAAAA 44320214 AATTGTATTC Statistics Matches: 19, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 12 19 1.00 ACGTcount: A:0.81, C:0.06, G:0.00, T:0.13 Consensus pattern (12 bp): AAAAAAATTCAA Found at i:44322755 original size:20 final size:20 Alignment explanation

Indices: 44322730--44322784 Score: 74 Period size: 20 Copynumber: 2.8 Consensus size: 20 44322720 TGTGGTTCAA * * 44322730 CTCATTCGAGCTCAGGTTAG 1 CTCATTCGAGCTCAAGTCAG * 44322750 CTCATTCGTGCTCAAGTCAG 1 CTCATTCGAGCTCAAGTCAG * 44322770 CTCATTCAAGCTCAA 1 CTCATTCGAGCTCAA 44322785 TTTAACTCGT Statistics Matches: 30, Mismatches: 5, Indels: 0 0.86 0.14 0.00 Matches are distributed among these distances: 20 30 1.00 ACGTcount: A:0.24, C:0.29, G:0.18, T:0.29 Consensus pattern (20 bp): CTCATTCGAGCTCAAGTCAG Found at i:44324646 original size:14 final size:14 Alignment explanation

Indices: 44324624--44324659 Score: 63 Period size: 14 Copynumber: 2.6 Consensus size: 14 44324614 TAGAAAGAGG * 44324624 GGTACGAATGAAAT 1 GGTAGGAATGAAAT 44324638 GGTAGGAATGAAAT 1 GGTAGGAATGAAAT 44324652 GGTAGGAA 1 GGTAGGAA 44324660 CAAAGGGATA Statistics Matches: 21, Mismatches: 1, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 14 21 1.00 ACGTcount: A:0.42, C:0.03, G:0.36, T:0.19 Consensus pattern (14 bp): GGTAGGAATGAAAT Found at i:44325707 original size:20 final size:20 Alignment explanation

Indices: 44325684--44325737 Score: 63 Period size: 20 Copynumber: 2.7 Consensus size: 20 44325674 AGTTTTTCCC * 44325684 AGCTCGATTTAGCTCACATG 1 AGCTCAATTTAGCTCACATG * *** 44325704 AGCTTAATTTAGCTCGTTTG 1 AGCTCAATTTAGCTCACATG 44325724 AGCTCAATTTAGCT 1 AGCTCAATTTAGCT 44325738 TACTTTAGCT Statistics Matches: 28, Mismatches: 6, Indels: 0 0.82 0.18 0.00 Matches are distributed among these distances: 20 28 1.00 ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37 Consensus pattern (20 bp): AGCTCAATTTAGCTCACATG Found at i:44325719 original size:30 final size:30 Alignment explanation

Indices: 44325684--44325757 Score: 98 Period size: 30 Copynumber: 2.5 Consensus size: 30 44325674 AGTTTTTCCC 44325684 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT 1 AGCTCG-TTTGAGCTCA-ATTGAGCTTAATTT * * 44325714 AGCTCGTTTGAGCTCAATTTAGCTTACTTT 1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT 44325744 AGCTCGTTTGAGCT 1 AGCTCGTTTGAGCT 44325758 TGGCTTAAGT Statistics Matches: 40, Mismatches: 2, Indels: 4 0.87 0.04 0.09 Matches are distributed among these distances: 29 4 0.10 30 36 0.90 ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39 Consensus pattern (30 bp): AGCTCGTTTGAGCTCAATTGAGCTTAATTT Found at i:44325747 original size:20 final size:20 Alignment explanation

Indices: 44325684--44325748 Score: 53 Period size: 20 Copynumber: 3.2 Consensus size: 20 44325674 AGTTTTTCCC * * * * 44325684 AGCTCGATTTAGCTCACATG 1 AGCTCAATTTAGCTTACTTT * 44325704 AGCTTAATTTAGC-T-CGTTT 1 AGCTCAATTTAGCTTAC-TTT 44325723 GAGCTCAATTTAGCTTACTTT 1 -AGCTCAATTTAGCTTACTTT 44325744 AGCTC 1 AGCTC 44325749 GTTTGAGCTT Statistics Matches: 35, Mismatches: 6, Indels: 8 0.71 0.12 0.16 Matches are distributed among these distances: 18 1 0.03 19 1 0.03 20 28 0.80 21 4 0.11 22 1 0.03 ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38 Consensus pattern (20 bp): AGCTCAATTTAGCTTACTTT Found at i:44328464 original size:13 final size:13 Alignment explanation

Indices: 44328446--44328470 Score: 50 Period size: 13 Copynumber: 1.9 Consensus size: 13 44328436 TAACCTACAA 44328446 AATTAAATAACAT 1 AATTAAATAACAT 44328459 AATTAAATAACA 1 AATTAAATAACA 44328471 CACAACTATT Statistics Matches: 12, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 13 12 1.00 ACGTcount: A:0.64, C:0.08, G:0.00, T:0.28 Consensus pattern (13 bp): AATTAAATAACAT Found at i:44328740 original size:20 final size:21 Alignment explanation

Indices: 44328695--44328750 Score: 69 Period size: 21 Copynumber: 2.7 Consensus size: 21 44328685 AAAAAGGAAT * * * 44328695 GAGCTGAAACGAGCTAAATTC 1 GAGCTCAAATGAGCTAAATAC 44328716 GAGCTCAAATGAGCTAAA-AC 1 GAGCTCAAATGAGCTAAATAC * 44328736 GAGCTCAAGTGAGCT 1 GAGCTCAAATGAGCT 44328751 GATGGGAACT Statistics Matches: 31, Mismatches: 4, Indels: 1 0.86 0.11 0.03 Matches are distributed among these distances: 20 15 0.48 21 16 0.52 ACGTcount: A:0.38, C:0.20, G:0.25, T:0.18 Consensus pattern (21 bp): GAGCTCAAATGAGCTAAATAC Found at i:44330732 original size:23 final size:23 Alignment explanation

Indices: 44330706--44330761 Score: 73 Period size: 23 Copynumber: 2.5 Consensus size: 23 44330696 GTTATACAAG 44330706 TTTGAAAAAAAA-CCGAAAAAAAA 1 TTTGAAAAAAAATCC-AAAAAAAA * 44330729 TTTGAAAAAAAATTCAAAAAAAA 1 TTTGAAAAAAAATCCAAAAAAAA 44330752 --TGAAAAAAAA 1 TTTGAAAAAAAA 44330762 AGTGATTTAT Statistics Matches: 31, Mismatches: 1, Indels: 4 0.86 0.03 0.11 Matches are distributed among these distances: 21 10 0.32 23 20 0.65 24 1 0.03 ACGTcount: A:0.71, C:0.05, G:0.07, T:0.16 Consensus pattern (23 bp): TTTGAAAAAAAATCCAAAAAAAA Found at i:44331699 original size:6 final size:5 Alignment explanation

Indices: 44331679--44331735 Score: 55 Period size: 5 Copynumber: 11.0 Consensus size: 5 44331669 AAGAGAAAAC * 44331679 AAAGA AAAGA AAAGCA AAAGCA AAAGA AGA-A AAAGA AAACGA AATA-A 1 AAAGA AAAGA AAAG-A AAAG-A AAAGA AAAGA AAAGA AAA-GA AA-AGA 44331726 AAAGA AAAGA 1 AAAGA AAAGA 44331736 GAGGCAAGAG Statistics Matches: 45, Mismatches: 2, Indels: 10 0.79 0.04 0.18 Matches are distributed among these distances: 4 4 0.09 5 25 0.56 6 15 0.33 7 1 0.02 ACGTcount: A:0.75, C:0.05, G:0.18, T:0.02 Consensus pattern (5 bp): AAAGA Found at i:44331712 original size:15 final size:14 Alignment explanation

Indices: 44331679--44331735 Score: 51 Period size: 16 Copynumber: 3.7 Consensus size: 14 44331669 AAGAGAAAAC * 44331679 AAAGAAAAGAAAAGCA 1 AAAGAAAAG--AAGAA 44331695 AAAGCAAAAGAAGAA 1 AAAG-AAAAGAAGAA * 44331710 AAAGAAAACGAAATAA 1 AAAGAAAA-G-AAGAA 44331726 AAAGAAAAGA 1 AAAGAAAAGA 44331736 GAGGCAAGAG Statistics Matches: 36, Mismatches: 2, Indels: 8 0.78 0.04 0.17 Matches are distributed among these distances: 14 5 0.14 15 10 0.28 16 16 0.44 17 5 0.14 ACGTcount: A:0.75, C:0.05, G:0.18, T:0.02 Consensus pattern (14 bp): AAAGAAAAGAAGAA Found at i:44331815 original size:11 final size:12 Alignment explanation

Indices: 44331783--44331813 Score: 62 Period size: 12 Copynumber: 2.6 Consensus size: 12 44331773 TTGAGAGAAC 44331783 TTGAAAAAGCCT 1 TTGAAAAAGCCT 44331795 TTGAAAAAGCCT 1 TTGAAAAAGCCT 44331807 TTGAAAA 1 TTGAAAA 44331814 GCAAAAAGAA Statistics Matches: 19, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 12 19 1.00 ACGTcount: A:0.45, C:0.13, G:0.16, T:0.26 Consensus pattern (12 bp): TTGAAAAAGCCT Found at i:44340568 original size:14 final size:14 Alignment explanation

Indices: 44340546--44340590 Score: 65 Period size: 14 Copynumber: 3.3 Consensus size: 14 44340536 TTAAAGAAGC 44340546 AACTCATTAAATTA 1 AACTCATTAAATTA * 44340560 AATTCATTAAA-TA 1 AACTCATTAAATTA * 44340573 AACTCATTTAATTA 1 AACTCATTAAATTA 44340587 AACT 1 AACT 44340591 AAGATGAGTT Statistics Matches: 27, Mismatches: 3, Indels: 2 0.84 0.09 0.06 Matches are distributed among these distances: 13 11 0.41 14 16 0.59 ACGTcount: A:0.49, C:0.13, G:0.00, T:0.38 Consensus pattern (14 bp): AACTCATTAAATTA Found at i:44341880 original size:12 final size:12 Alignment explanation

Indices: 44341840--44341895 Score: 58 Period size: 12 Copynumber: 4.4 Consensus size: 12 44341830 ATTTCTTTTG 44341840 TTTCAATTTCTT 1 TTTCAATTTCTT * * 44341852 TCCCTTTAATCTCTT 1 T---TTCAATTTCTT 44341867 TTTCAATTTCTT 1 TTTCAATTTCTT * 44341879 TTTCAACTTCTT 1 TTTCAATTTCTT 44341891 TTTCA 1 TTTCA 44341896 CTCTCAAATT Statistics Matches: 36, Mismatches: 5, Indels: 6 0.77 0.11 0.13 Matches are distributed among these distances: 12 26 0.72 15 10 0.28 ACGTcount: A:0.16, C:0.23, G:0.00, T:0.61 Consensus pattern (12 bp): TTTCAATTTCTT Found at i:44341959 original size:12 final size:12 Alignment explanation

Indices: 44341942--44341974 Score: 59 Period size: 12 Copynumber: 2.8 Consensus size: 12 44341932 TTTTCTTTTT 44341942 GCTTTTT-AAAG 1 GCTTTTTCAAAG 44341953 GCTTTTTCAAAG 1 GCTTTTTCAAAG 44341965 GCTTTTTCAA 1 GCTTTTTCAA 44341975 GTTCTCTCAA Statistics Matches: 21, Mismatches: 0, Indels: 1 0.95 0.00 0.05 Matches are distributed among these distances: 11 7 0.33 12 14 0.67 ACGTcount: A:0.24, C:0.15, G:0.15, T:0.45 Consensus pattern (12 bp): GCTTTTTCAAAG Found at i:44342078 original size:21 final size:20 Alignment explanation

Indices: 44342045--44342088 Score: 54 Period size: 20 Copynumber: 2.1 Consensus size: 20 44342035 TTTCGTTTGT 44342045 TTTTCTTCTTTTGCTTTT-TC 1 TTTTCTTCTTTTG-TTTTCTC * 44342065 TTTTCTTTTCTTTGTTTTCTC 1 TTTTCTTCT-TTTGTTTTCTC 44342086 TTT 1 TTT 44342089 ACAAGAATGT Statistics Matches: 21, Mismatches: 1, Indels: 3 0.84 0.04 0.12 Matches are distributed among these distances: 20 12 0.57 21 9 0.43 ACGTcount: A:0.00, C:0.18, G:0.05, T:0.77 Consensus pattern (20 bp): TTTTCTTCTTTTGTTTTCTC Found at i:44343011 original size:11 final size:12 Alignment explanation

Indices: 44342986--44343026 Score: 50 Period size: 10 Copynumber: 3.5 Consensus size: 12 44342976 ATTAAACACA * 44342986 TTTTTTTCAGATT 1 TTTTTTTGA-ATT 44342999 TTTTTTT--ATT 1 TTTTTTTGAATT 44343009 TTTTTTTGAATT 1 TTTTTTTGAATT 44343021 TTTTTT 1 TTTTTT 44343027 AACTTGTATA Statistics Matches: 26, Mismatches: 0, Indels: 5 0.84 0.00 0.16 Matches are distributed among these distances: 10 10 0.38 12 9 0.35 13 7 0.27 ACGTcount: A:0.12, C:0.02, G:0.05, T:0.80 Consensus pattern (12 bp): TTTTTTTGAATT Found at i:44343011 original size:21 final size:21 Alignment explanation

Indices: 44342985--44343027 Score: 59 Period size: 21 Copynumber: 2.0 Consensus size: 21 44342975 CATTAAACAC * 44342985 ATTTTTTTCAGATTTTTTTTT 1 ATTTTTTTCAGAATTTTTTTT ** 44343006 ATTTTTTTTTGAATTTTTTTT 1 ATTTTTTTCAGAATTTTTTTT 44343027 A 1 A 44343028 ACTTGTATAA Statistics Matches: 19, Mismatches: 3, Indels: 0 0.86 0.14 0.00 Matches are distributed among these distances: 21 19 1.00 ACGTcount: A:0.16, C:0.02, G:0.05, T:0.77 Consensus pattern (21 bp): ATTTTTTTCAGAATTTTTTTT Found at i:44344329 original size:13 final size:13 Alignment explanation

Indices: 44344311--44344348 Score: 67 Period size: 13 Copynumber: 2.9 Consensus size: 13 44344301 TGGTCATCAT 44344311 GGTGTGAACACAA 1 GGTGTGAACACAA 44344324 GGTGTGAACACAA 1 GGTGTGAACACAA * 44344337 AGTGTGAACACA 1 GGTGTGAACACA 44344349 TGATCAGTAC Statistics Matches: 24, Mismatches: 1, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 13 24 1.00 ACGTcount: A:0.39, C:0.16, G:0.29, T:0.16 Consensus pattern (13 bp): GGTGTGAACACAA Found at i:44352004 original size:22 final size:22 Alignment explanation

Indices: 44351974--44352017 Score: 79 Period size: 22 Copynumber: 2.0 Consensus size: 22 44351964 TTTGGTATTT 44351974 GGGAATTGGTACGAAATGGTAA 1 GGGAATTGGTACGAAATGGTAA * 44351996 GGGATTTGGTACGAAATGGTAA 1 GGGAATTGGTACGAAATGGTAA 44352018 TGGTTCAAAA Statistics Matches: 21, Mismatches: 1, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 22 21 1.00 ACGTcount: A:0.34, C:0.05, G:0.36, T:0.25 Consensus pattern (22 bp): GGGAATTGGTACGAAATGGTAA Found at i:44352250 original size:51 final size:51 Alignment explanation

Indices: 44352193--44352289 Score: 185 Period size: 51 Copynumber: 1.9 Consensus size: 51 44352183 GATAAGTTTG * 44352193 AAAGAAAGACTCGGAAAGACGCCACTAGAAGCTAGATAAGTCTTACGGGTA 1 AAAGAAAGACTCGAAAAGACGCCACTAGAAGCTAGATAAGTCTTACGGGTA 44352244 AAAGAAAGACTCGAAAAGACGCCACTAGAAGCTAGATAAGTCTTAC 1 AAAGAAAGACTCGAAAAGACGCCACTAGAAGCTAGATAAGTCTTAC 44352290 TGATGTGATC Statistics Matches: 45, Mismatches: 1, Indels: 0 0.98 0.02 0.00 Matches are distributed among these distances: 51 45 1.00 ACGTcount: A:0.43, C:0.19, G:0.23, T:0.15 Consensus pattern (51 bp): AAAGAAAGACTCGAAAAGACGCCACTAGAAGCTAGATAAGTCTTACGGGTA Found at i:44353640 original size:20 final size:20 Alignment explanation

Indices: 44353617--44353673 Score: 69 Period size: 20 Copynumber: 2.8 Consensus size: 20 44353607 GGGTTAAGAT * 44353617 TGAGCTGAATTGAGCTTGAG 1 TGAGCTGAATTGAGCTCGAG * * 44353637 TGAGTTGACTTGAGCTCGAG 1 TGAGCTGAATTGAGCTCGAG * 44353657 TGAGCTGGAAATGAGCT 1 TGAGCT-GAATTGAGCT 44353674 AAACGGAGCT Statistics Matches: 30, Mismatches: 6, Indels: 1 0.81 0.16 0.03 Matches are distributed among these distances: 20 22 0.73 21 8 0.27 ACGTcount: A:0.25, C:0.12, G:0.35, T:0.28 Consensus pattern (20 bp): TGAGCTGAATTGAGCTCGAG Found at i:44355158 original size:226 final size:226 Alignment explanation

Indices: 44354760--44355168 Score: 782 Period size: 226 Copynumber: 1.8 Consensus size: 226 44354750 AAAACCTCTA * * 44354760 TACAAATGAAAGAAAACAAATATTTATAGGTACATAGATGACCATTCAAATTCGGCATTTAGGTG 1 TACAAATGAAAGAAAACAAATATTTATAGGCACATAGATGACCATTCAAATTCGGCATCTAGGTG 44354825 TTCACACAATAATAAAAACGTTCACACTAATGTATTAAAATAGTTCATAAATTCGGCAGATTCAT 66 TTCACACAATAATAAAAACGTTCACACTAATGTATTAAAATAGTTCATAAATTCGGCAGATTCAT 44354890 GCACTAGTTGAATGGACACTTTCTTCCCCCTAAGTGTGTGCATGAATGCTTAGAATTTGGTAGCA 131 GCACTAGTTGAATGGACACTTTCTTCCCCCTAAGTGTGTGCATGAATGCTTAGAATTTGGTAGCA 44354955 ATTCGCTAATTAAAAATGTCAAAAGGTCCTT 196 ATTCGCTAATTAAAAATGTCAAAAGGTCCTT 44354986 TACAAATGAAAGAAAACAAATATTTATAGGCACATAGATGACCATTCAAATTCGGCATCTAGGTG 1 TACAAATGAAAGAAAACAAATATTTATAGGCACATAGATGACCATTCAAATTCGGCATCTAGGTG 44355051 TTCACACAATAATAAAAACGTTCACACTAATGTATTAAAATAGTTCATAAATTCGGCAGATTCAT 66 TTCACACAATAATAAAAACGTTCACACTAATGTATTAAAATAGTTCATAAATTCGGCAGATTCAT * * 44355116 GCACTAGTTGAATGGACACTTTCTTCCCCCTTAGTTTGTGCATGAATGCTTAG 131 GCACTAGTTGAATGGACACTTTCTTCCCCCTAAGTGTGTGCATGAATGCTTAG 44355169 TCATAAAGAA Statistics Matches: 179, Mismatches: 4, Indels: 0 0.98 0.02 0.00 Matches are distributed among these distances: 226 179 1.00 ACGTcount: A:0.37, C:0.17, G:0.16, T:0.30 Consensus pattern (226 bp): TACAAATGAAAGAAAACAAATATTTATAGGCACATAGATGACCATTCAAATTCGGCATCTAGGTG TTCACACAATAATAAAAACGTTCACACTAATGTATTAAAATAGTTCATAAATTCGGCAGATTCAT GCACTAGTTGAATGGACACTTTCTTCCCCCTAAGTGTGTGCATGAATGCTTAGAATTTGGTAGCA ATTCGCTAATTAAAAATGTCAAAAGGTCCTT Found at i:44357576 original size:13 final size:12 Alignment explanation

Indices: 44357534--44357576 Score: 59 Period size: 12 Copynumber: 3.6 Consensus size: 12 44357524 GAACTCTTTT * 44357534 TCTTTTTCATTC 1 TCTTTTTCAATC 44357546 TCTTTTTCAATC 1 TCTTTTTCAATC * 44357558 TGTTTTTCAATC 1 TCTTTTTCAATC * 44357570 TCATTTT 1 TCTTTTT 44357577 GTTTCCTCTC Statistics Matches: 27, Mismatches: 4, Indels: 0 0.87 0.13 0.00 Matches are distributed among these distances: 12 27 1.00 ACGTcount: A:0.14, C:0.21, G:0.02, T:0.63 Consensus pattern (12 bp): TCTTTTTCAATC Found at i:44357690 original size:15 final size:15 Alignment explanation

Indices: 44357670--44357726 Score: 50 Period size: 17 Copynumber: 3.9 Consensus size: 15 44357660 TTTTCTTGCC 44357670 TCTCTTTTCTTTT-G 1 TCTCTTTTCTTTTCG 44357684 ATCTCTTTTTTCTTTTCG 1 -TCTC--TTTTCTTTTCG 44357702 TCT-TTTTCTTTTC- 1 TCTCTTTTCTTTTCG * 44357715 TC-ATTTTCTTTT 1 TCTCTTTTCTTTT 44357727 TACAAGAGGA Statistics Matches: 38, Mismatches: 0, Indels: 10 0.79 0.00 0.21 Matches are distributed among these distances: 13 11 0.29 14 10 0.26 15 4 0.11 17 12 0.32 18 1 0.03 ACGTcount: A:0.04, C:0.21, G:0.04, T:0.72 Consensus pattern (15 bp): TCTCTTTTCTTTTCG Found at i:44357709 original size:14 final size:13 Alignment explanation

Indices: 44357685--44357726 Score: 57 Period size: 14 Copynumber: 3.1 Consensus size: 13 44357675 TTTCTTTTGA 44357685 TCTCTTTTTTCTTT 1 TCTC-TTTTTCTTT 44357699 TCGTCTTTTTCTTT 1 TC-TCTTTTTCTTT * 44357713 TCTCATTTTCTTT 1 TCTCTTTTTCTTT 44357726 T 1 T 44357727 TACAAGAGGA Statistics Matches: 26, Mismatches: 1, Indels: 3 0.87 0.03 0.10 Matches are distributed among these distances: 13 11 0.42 14 13 0.50 15 2 0.08 ACGTcount: A:0.02, C:0.21, G:0.02, T:0.74 Consensus pattern (13 bp): TCTCTTTTTCTTT Found at i:44357727 original size:14 final size:14 Alignment explanation

Indices: 44357691--44357726 Score: 56 Period size: 13 Copynumber: 2.6 Consensus size: 14 44357681 TTGATCTCTT * 44357691 TTTTCTTTTCGTCT 1 TTTTCTTTTCGTCA 44357705 TTTTCTTTTC-TCA 1 TTTTCTTTTCGTCA 44357718 TTTTCTTTT 1 TTTTCTTTT 44357727 TACAAGAGGA Statistics Matches: 21, Mismatches: 1, Indels: 1 0.91 0.04 0.04 Matches are distributed among these distances: 13 11 0.52 14 10 0.48 ACGTcount: A:0.03, C:0.19, G:0.03, T:0.75 Consensus pattern (14 bp): TTTTCTTTTCGTCA Found at i:44360900 original size:48 final size:48 Alignment explanation

Indices: 44360838--44361118 Score: 512 Period size: 48 Copynumber: 5.9 Consensus size: 48 44360828 AATTCTAAAT 44360838 TGTG-ATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA 1 TGTGAATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA * 44360885 TGTGAATAGGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA 1 TGTGAATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA * 44360933 TGTGAATAGGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA 1 TGTGAATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA * 44360981 TGTGAATAGGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA 1 TGTGAATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA 44361029 TGTTG-ATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA 1 TG-TGAATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA 44361077 TGTGAATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG 1 TGTGAATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG 44361119 GTGAAACAGG Statistics Matches: 229, Mismatches: 2, Indels: 5 0.97 0.01 0.02 Matches are distributed among these distances: 47 6 0.03 48 221 0.97 49 2 0.01 ACGTcount: A:0.31, C:0.09, G:0.31, T:0.29 Consensus pattern (48 bp): TGTGAATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA Found at i:44361514 original size:47 final size:47 Alignment explanation

Indices: 44361391--44361684 Score: 417 Period size: 49 Copynumber: 6.1 Consensus size: 47 44361381 TTCTAAATTG * 44361391 TGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATG 1 TGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATA * 44361438 TGAATAGGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATA 1 TG-ATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATA 44361486 TGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATA 1 TGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATA 44361533 TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATA 1 --TGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATA * 44361582 TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATG 1 --TGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATA *** * * * * * * * * 44361631 TGACGGGGCCGAGTGGCCAACGTGATGGATGTGAAAGTGCATAAATG 1 TGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATA 44361678 TGATAAG 1 TGATAAG 44361685 TCCCGAAGGG Statistics Matches: 227, Mismatches: 17, Indels: 6 0.91 0.07 0.02 Matches are distributed among these distances: 47 87 0.38 48 45 0.20 49 95 0.42 ACGTcount: A:0.32, C:0.09, G:0.31, T:0.28 Consensus pattern (47 bp): TGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATA Found at i:44361550 original size:49 final size:49 Alignment explanation

Indices: 44361389--44361684 Score: 437 Period size: 47 Copynumber: 6.2 Consensus size: 49 44361379 AATTCTAAAT 44361389 TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATA 1 TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATA * 44361436 TGTGAATAGGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATA 1 TGTG-ATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATA 44361486 --TGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATA 1 TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATA 44361533 TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATA 1 TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATA 44361582 TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATA 1 TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATA *** * * * * * * 44361629 TGTGACGGGGCCGAGTGGCCAACGTGATGGATGTGAAAGTGCATA-A-A 1 TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATA 44361676 TGTGATAAG 1 TGTGATAAG 44361685 TCCCGAAGGG Statistics Matches: 229, Mismatches: 13, Indels: 14 0.89 0.05 0.05 Matches are distributed among these distances: 47 94 0.41 48 39 0.17 49 90 0.39 50 6 0.03 ACGTcount: A:0.32, C:0.09, G:0.31, T:0.28 Consensus pattern (49 bp): TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATA Found at i:44361627 original size:96 final size:96 Alignment explanation

Indices: 44361389--44361684 Score: 456 Period size: 96 Copynumber: 3.1 Consensus size: 96 44361379 AATTCTAAAT 44361389 TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGAATAGGGCCTAATG 1 TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTG-ATAGGGCCTAATG 44361454 GCCGATGTGATGAATGTGAAAGTGTATATATA 65 GCCGATGTGATGAATGTGAAAGTGTATATATA * 44361486 --TGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAAT 1 TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTGATAGGGCCTAAT 44361549 GGCCGATGTGATGAATGTGAAAGTGTATATATA 64 GGCCGATGTGATGAATGTGAAAGTGTATATATA ** * * 44361582 TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGACGGGGCCGAGTGG 1 TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAGGGCCTAATGG * * * * 44361647 CCAACGTGATGGATGTGAAAGTGCATA-A-A 66 CCGATGTGATGAATGTGAAAGTGTATATATA 44361676 TGTGATAAG 1 TGTGATAAG 44361685 TCCCGAAGGG Statistics Matches: 185, Mismatches: 10, Indels: 11 0.90 0.05 0.05 Matches are distributed among these distances: 94 10 0.05 95 40 0.22 96 86 0.46 97 10 0.05 98 39 0.21 ACGTcount: A:0.32, C:0.09, G:0.31, T:0.28 Consensus pattern (96 bp): TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAGGGCCTAATGG CCGATGTGATGAATGTGAAAGTGTATATATA Found at i:44361665 original size:551 final size:551 Alignment explanation

Indices: 44360568--44361669 Score: 2048 Period size: 551 Copynumber: 2.0 Consensus size: 551 44360558 TAGTCAAGCA 44360568 GTGAAACAGGGGAAACTTTAAGAAAAGTCTGGTATTGATTGGCCAAACCTAAAATTCTGGAAATT 1 GTGAAACAGGGGAAACTTTAAGAAAAGTCTGGTATTGATTGGCCAAACCTAAAATTCTGGAAATT 44360633 TTATGGATGGAAGACATACGAGTCTATATTCAGGAAAAATTTACGAAAAGTGATTTGGAGTTTTG 66 TTATGGATGGAAGACATACGAGTCTATATTCAGGAAAAATTTACGAAAAGTGATTTGGAGTTTTG 44360698 TAGCTCCAGTTATAAATAATTTAGTGACTATTGCTCAGGAAAAACAGCTTGTGCTGAATTTGAGA 131 TAGCTCCAGTTATAAATAATTTAGTGACTATTGCTCAGGAAAAACAGCTTGTGCTGAATTTGAGA 44360763 TTGTGTTGTAAACCTTGATAAACTTGTTTTAGTTGCTTATAAGCTATTGATTAAACCCATATGTG 196 TTGTGTTGTAAACCTTGATAAACTTGTTTTAGTTGCTTATAAGCTATTGATTAAACCCATATGTG 44360828 AATTCTAAATTGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGAATA 261 AATTCTAAATTGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGAATA * * 44360893 GGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGAATAGGGCCTAATGGCCGATG 326 GGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGAATAAGGCCTAATGGCCGATG * 44360958 TGATGAATGTGAAAGTGTATATATGTGAATAGGGCCTAATGGCCGATGTGATGAATGTGAAAGTG 391 TGATGAATGTGAAAGTGTATATATGTGAATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG * * 44361023 TATATATGTTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGAATAAGG 456 TATATATATTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGAACAAGG * * * 44361088 CCTAATGGCCGATGTGATGAATGTGAAAGTG 521 CCGAATGGCCAACGTGATGAATGTGAAAGTG 44361119 GTGAAACAGGGGAAACTTTAAGAAAAGTCTGGTATTGATTGGCCAAACCTAAAATTCTGGAAATT 1 GTGAAACAGGGGAAACTTTAAGAAAAGTCTGGTATTGATTGGCCAAACCTAAAATTCTGGAAATT 44361184 TTATGGATGGAAGACATACGAGTCTATATTCAGGAAAAATTTACGAAAAGTGATTTGGAGTTTTG 66 TTATGGATGGAAGACATACGAGTCTATATTCAGGAAAAATTTACGAAAAGTGATTTGGAGTTTTG 44361249 TAGCTCCAGTTATAAATAATTTAGTGACTATTGCTCAGGAAAAACAGCTTGTGCTGAATTTGAGA 131 TAGCTCCAGTTATAAATAATTTAGTGACTATTGCTCAGGAAAAACAGCTTGTGCTGAATTTGAGA 44361314 TTGTGTTGTAAACCTTGATAAACTTGTTTTAGTTGCTTATAAGCTATTGATTAAACCCATATGTG 196 TTGTGTTGTAAACCTTGATAAACTTGTTTTAGTTGCTTATAAGCTATTGATTAAACCCATATGTG 44361379 AATTCTAAATTGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGAATA 261 AATTCTAAATTGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGAATA 44361444 GGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATG-ATAAGGCCTAATGGCCGATG 326 GGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGAATAAGGCCTAATGGCCGATG 44361508 TGATGAATGTGAAAGTGTATATATATGTG-ATAAGGCCTAATGGCCGATGTGATGAATGTGAAAG 391 TGATGAATGTGAAAGTG--TATATATGTGAATAAGGCCTAATGGCCGATGTGATGAATGTGAAAG * 44361572 TGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTG-ACG 454 TGTATATATAT-TGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGAACA * * * 44361636 GGGCCGAGTGGCCAACGTGATGGATGTGAAAGTG 518 AGGCCGAATGGCCAACGTGATGAATGTGAAAGTG 44361670 CATAAATGTG Statistics Matches: 536, Mismatches: 12, Indels: 6 0.97 0.02 0.01 Matches are distributed among these distances: 550 36 0.07 551 441 0.82 552 59 0.11 ACGTcount: A:0.33, C:0.10, G:0.26, T:0.31 Consensus pattern (551 bp): GTGAAACAGGGGAAACTTTAAGAAAAGTCTGGTATTGATTGGCCAAACCTAAAATTCTGGAAATT TTATGGATGGAAGACATACGAGTCTATATTCAGGAAAAATTTACGAAAAGTGATTTGGAGTTTTG TAGCTCCAGTTATAAATAATTTAGTGACTATTGCTCAGGAAAAACAGCTTGTGCTGAATTTGAGA TTGTGTTGTAAACCTTGATAAACTTGTTTTAGTTGCTTATAAGCTATTGATTAAACCCATATGTG AATTCTAAATTGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGAATA GGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGAATAAGGCCTAATGGCCGATG TGATGAATGTGAAAGTGTATATATGTGAATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG TATATATATTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGAACAAGG CCGAATGGCCAACGTGATGAATGTGAAAGTG Found at i:44365476 original size:20 final size:21 Alignment explanation

Indices: 44365430--44365476 Score: 53 Period size: 20 Copynumber: 2.3 Consensus size: 21 44365420 GTAAGCTCGG 44365430 TTGAGCTCAAACGAGCTGAAA 1 TTGAGCTCAAACGAGCTGAAA ** * 44365451 -CAAGCTCAAATGAGCT-AAA 1 TTGAGCTCAAACGAGCTGAAA 44365470 TTGAGCT 1 TTGAGCT 44365477 GGACGGAGCT Statistics Matches: 20, Mismatches: 5, Indels: 3 0.71 0.18 0.11 Matches are distributed among these distances: 19 3 0.15 20 17 0.85 ACGTcount: A:0.38, C:0.19, G:0.21, T:0.21 Consensus pattern (21 bp): TTGAGCTCAAACGAGCTGAAA Found at i:44369633 original size:12 final size:12 Alignment explanation

Indices: 44369615--44369649 Score: 52 Period size: 12 Copynumber: 2.9 Consensus size: 12 44369605 TATTAAATTT 44369615 TTAATTAATAAG 1 TTAATTAATAAG * * 44369627 TTCATTAATTAG 1 TTAATTAATAAG 44369639 TTAATTAATAA 1 TTAATTAATAA 44369650 ACCACATATT Statistics Matches: 19, Mismatches: 4, Indels: 0 0.83 0.17 0.00 Matches are distributed among these distances: 12 19 1.00 ACGTcount: A:0.46, C:0.03, G:0.06, T:0.46 Consensus pattern (12 bp): TTAATTAATAAG Found at i:44373886 original size:30 final size:30 Alignment explanation

Indices: 44373852--44373949 Score: 90 Period size: 30 Copynumber: 3.3 Consensus size: 30 44373842 AGCTCACTCC 44373852 TAGCTCATATTCAGCTCACGAGCTAAACCT 1 TAGCTCATATTCAGCTCACGAGCTAAACCT ** * * * * * 44373882 TAGCTCAGCTTCAGCTTAGGAGTTTAATCT 1 TAGCTCATATTCAGCTCACGAGCTAAACCT * * * 44373912 CAGCTCA-ACTTTAGCTCACGAGCTAAAGCT 1 TAGCTCATA-TTCAGCTCACGAGCTAAACCT 44373942 TAGCTCAT 1 TAGCTCAT 44373950 TTTAGTTTAA Statistics Matches: 50, Mismatches: 16, Indels: 3 0.72 0.23 0.04 Matches are distributed among these distances: 30 50 1.00 ACGTcount: A:0.28, C:0.27, G:0.16, T:0.30 Consensus pattern (30 bp): TAGCTCATATTCAGCTCACGAGCTAAACCT Found at i:44377455 original size:11 final size:10 Alignment explanation

Indices: 44377419--44377464 Score: 56 Period size: 10 Copynumber: 4.5 Consensus size: 10 44377409 AGCTCCCTTG 44377419 AGCTCGTTTT 1 AGCTCGTTTT * * 44377429 AACTCGTTTG 1 AGCTCGTTTT 44377439 AGCTCGTATTT 1 AGCTCGT-TTT * 44377450 AGCTCGTTTC 1 AGCTCGTTTT 44377460 AGCTC 1 AGCTC 44377465 ATTCCTTTTC Statistics Matches: 30, Mismatches: 5, Indels: 2 0.81 0.14 0.05 Matches are distributed among these distances: 10 21 0.70 11 9 0.30 ACGTcount: A:0.15, C:0.24, G:0.20, T:0.41 Consensus pattern (10 bp): AGCTCGTTTT Found at i:44377455 original size:21 final size:20 Alignment explanation

Indices: 44377416--44377464 Score: 71 Period size: 21 Copynumber: 2.4 Consensus size: 20 44377406 ATCAGCTCCC 44377416 TTGAGCTCGTTTTAACTCGT 1 TTGAGCTCGTTTTAACTCGT * 44377436 TTGAGCTCGTATTTAGCTCGT 1 TTGAGCTCGT-TTTAACTCGT * 44377457 TTCAGCTC 1 TTGAGCTC 44377465 ATTCCTTTTC Statistics Matches: 26, Mismatches: 2, Indels: 1 0.90 0.07 0.03 Matches are distributed among these distances: 20 10 0.38 21 16 0.62 ACGTcount: A:0.14, C:0.22, G:0.20, T:0.43 Consensus pattern (20 bp): TTGAGCTCGTTTTAACTCGT Found at i:44377785 original size:30 final size:30 Alignment explanation

Indices: 44377726--44377822 Score: 97 Period size: 30 Copynumber: 3.2 Consensus size: 30 44377716 AGCTCACTCC * * 44377726 TAGCTC-ACTTTCAACTCACGAGCTAAACCT 1 TAGCTCAAC-TTCAGCTTACGAGCTAAACCT * * * 44377756 TAGCTCAACTTCAGCTTAGGAGTTTAACCT 1 TAGCTCAACTTCAGCTTACGAGCTAAACCT * * * * 44377786 CAGCACAACTTTAGCTTACGAGCTAAAGCT 1 TAGCTCAACTTCAGCTTACGAGCTAAACCT 44377816 TAGCTCA 1 TAGCTCA 44377823 TTTTAGTTTA Statistics Matches: 52, Mismatches: 14, Indels: 2 0.76 0.21 0.03 Matches are distributed among these distances: 30 50 0.96 31 2 0.04 ACGTcount: A:0.30, C:0.28, G:0.14, T:0.28 Consensus pattern (30 bp): TAGCTCAACTTCAGCTTACGAGCTAAACCT Found at i:44380493 original size:11 final size:12 Alignment explanation

Indices: 44380461--44380491 Score: 62 Period size: 12 Copynumber: 2.6 Consensus size: 12 44380451 TTGAGAGAAC 44380461 TTGAAAAAGCCT 1 TTGAAAAAGCCT 44380473 TTGAAAAAGCCT 1 TTGAAAAAGCCT 44380485 TTGAAAA 1 TTGAAAA 44380492 GCAAAATGAA Statistics Matches: 19, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 12 19 1.00 ACGTcount: A:0.45, C:0.13, G:0.16, T:0.26 Consensus pattern (12 bp): TTGAAAAAGCCT Found at i:44380515 original size:18 final size:18 Alignment explanation

Indices: 44380494--44380528 Score: 52 Period size: 18 Copynumber: 1.9 Consensus size: 18 44380484 TTTGAAAAGC 44380494 AAAATGAAAATGAAAAAT 1 AAAATGAAAATGAAAAAT * * 44380512 AAAATGAGATTGAAAAA 1 AAAATGAAAATGAAAAA 44380529 GAGAACGAAA Statistics Matches: 15, Mismatches: 2, Indels: 0 0.88 0.12 0.00 Matches are distributed among these distances: 18 15 1.00 ACGTcount: A:0.69, C:0.00, G:0.14, T:0.17 Consensus pattern (18 bp): AAAATGAAAATGAAAAAT Done.