Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr1
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: 37323695
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.32
Warning! 1370832 characters in sequence are not A, C, G, or T
File 64 of 93
Found at i:24418466 original size:34 final size:35
Alignment explanation
Indices: 24418411--24418488 Score: 115
Period size: 34 Copynumber: 2.3 Consensus size: 35
24418401 GGTGAGAGGA
*
24418411 GCAGATTTAGCTGCTGATTTTGGAGGCTGAAAAGT
1 GCAGATTTTGCTGCTGATTTTGGAGGCTGAAAAGT
*
24418446 GCAG-TTTTGCTGCT-AGTTTTGGAGGCTGAGAAGT
1 GCAGATTTTGCTGCTGA-TTTTGGAGGCTGAAAAGT
24418480 GCAGATTTT
1 GCAGATTTT
24418489 TTAAGCTGAT
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
33 1 0.03
34 30 0.77
35 8 0.21
ACGTcount: A:0.22, C:0.12, G:0.32, T:0.35
Consensus pattern (35 bp):
GCAGATTTTGCTGCTGATTTTGGAGGCTGAAAAGT
Found at i:24418825 original size:16 final size:15
Alignment explanation
Indices: 24418782--24418825 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 15
24418772 CGGACGGTGG
24418782 AAGAAAGAAAGAAAAA
1 AAGAAAGAAA-AAAAA
* *
24418798 AAGAAAAGAAAAGAAC
1 AAG-AAAGAAAAAAAA
24418814 AAGAAAGAAAAA
1 AAGAAAGAAAAA
24418826 TGGGCATGGC
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
15 8 0.33
16 9 0.38
17 7 0.29
ACGTcount: A:0.80, C:0.02, G:0.18, T:0.00
Consensus pattern (15 bp):
AAGAAAGAAAAAAAA
Found at i:24423963 original size:2 final size:2
Alignment explanation
Indices: 24423958--24423988 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
24423948 ATATATATAT
*
24423958 AC AC AC AC AC AC AC AC AC AC AC AC AG AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
24423989 TATATACACA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.45, G:0.03, T:0.00
Consensus pattern (2 bp):
AC
Found at i:24425488 original size:80 final size:80
Alignment explanation
Indices: 24425280--24425470 Score: 244
Period size: 80 Copynumber: 2.4 Consensus size: 80
24425270 GGTACAATGC
** * * * *
24425280 CCAA-CTTAACCTTGTCATATACTTACCTCCACACCATA-ACGATAGCCAACATACATAAAAGGA
1 CCAAGCTTAACCTTGTGGTATTCTTACCCCCACACCA-AGACTAGAGCCAACATACATAAAAGGA
*
24425343 AATGATGGCATGTTGG
65 AATGATGGCACGTTGG
* * *
24425359 CCAAGCTTAACCTTTTGGTATTCTTAGCCCCACACCAAGACTAGAGCCAACATACA-AAAGGGAA
1 CCAAGCTTAACCTTGTGGTATTCTTACCCCCACACCAAGACTAGAGCCAACATACATAAAAGGAA
24425423 ATAGATGGCACGTTGG
66 AT-GATGGCACGTTGG
*
24425439 CCAAGCTTAATCTTGTGGTATTCTTACCCCCA
1 CCAAGCTTAACCTTGTGGTATTCTTACCCCCA
24425471 TATTGGGATT
Statistics
Matches: 96, Mismatches: 13, Indels: 5
0.84 0.11 0.04
Matches are distributed among these distances:
79 14 0.15
80 82 0.85
ACGTcount: A:0.33, C:0.26, G:0.16, T:0.25
Consensus pattern (80 bp):
CCAAGCTTAACCTTGTGGTATTCTTACCCCCACACCAAGACTAGAGCCAACATACATAAAAGGAA
ATGATGGCACGTTGG
Found at i:24435872 original size:5 final size:5
Alignment explanation
Indices: 24435858--24435908 Score: 75
Period size: 5 Copynumber: 10.2 Consensus size: 5
24435848 CTATTCAACC
* * *
24435858 TAACC TAACT TAACT TATCT TAACT TGACT TAACT TAACT TAACT TAACT
1 TAACT TAACT TAACT TAACT TAACT TAACT TAACT TAACT TAACT TAACT
24435908 T
1 T
24435909 GGGCCACACT
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
5 41 1.00
ACGTcount: A:0.35, C:0.22, G:0.02, T:0.41
Consensus pattern (5 bp):
TAACT
Found at i:24447477 original size:11 final size:11
Alignment explanation
Indices: 24447437--24447475 Score: 60
Period size: 11 Copynumber: 3.5 Consensus size: 11
24447427 TACTGTAAAT
24447437 TTTAAAACAAC
1 TTTAAAACAAC
24447448 TTTAAAACAAC
1 TTTAAAACAAC
* *
24447459 TTTAAACCAGC
1 TTTAAAACAAC
24447470 TTTAAA
1 TTTAAA
24447476 CCCAAAAACT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
11 26 1.00
ACGTcount: A:0.49, C:0.18, G:0.03, T:0.31
Consensus pattern (11 bp):
TTTAAAACAAC
Found at i:24447494 original size:22 final size:22
Alignment explanation
Indices: 24447469--24447512 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
24447459 TTTAAACCAG
*
24447469 CTTTAAACCCAAAAACTCTGAT
1 CTTTAAAACCAAAAACTCTGAT
*
24447491 CTTTAAAACCAAAAGCTCTGAT
1 CTTTAAAACCAAAAACTCTGAT
24447513 ATCAACCAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.41, C:0.25, G:0.07, T:0.27
Consensus pattern (22 bp):
CTTTAAAACCAAAAACTCTGAT
Found at i:24447912 original size:12 final size:12
Alignment explanation
Indices: 24447895--24447926 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
24447885 AGATAAAACG
24447895 AAATATTCAATA
1 AAATATTCAATA
24447907 AAATATTCAATA
1 AAATATTCAATA
24447919 AAA-ATTCA
1 AAATATTCA
24447927 TTCATACTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 5 0.25
12 15 0.75
ACGTcount: A:0.59, C:0.09, G:0.00, T:0.31
Consensus pattern (12 bp):
AAATATTCAATA
Found at i:24459182 original size:54 final size:54
Alignment explanation
Indices: 24459124--24459343 Score: 354
Period size: 54 Copynumber: 4.1 Consensus size: 54
24459114 GAGGGAGATG
24459124 GATGGGATG-TCTGGCTATGTGCACGATGTGGTGGGATGCACATGAGCTGGGTGA
1 GATGGGATGTTC-GGCTATGTGCACGATGTGGTGGGATGCACATGAGCTGGGTGA
*
24459178 GATGGGATATTCGGCTATGTGCACGATGTGGTGGGATGCACATGAGCTGGGTGA
1 GATGGGATGTTCGGCTATGTGCACGATGTGGTGGGATGCACATGAGCTGGGTGA
* *
24459232 GATGGGATG-TCTGACTATGTGCACGATGTGGTGGGATGCACATGACCTGGGTGA
1 GATGGGATGTTC-GGCTATGTGCACGATGTGGTGGGATGCACATGAGCTGGGTGA
* * *
24459286 GAAGGGATGTTCGGCTATGTGCATGATGTGGTGGGATGCACATGAGTTGGGTGA
1 GATGGGATGTTCGGCTATGTGCACGATGTGGTGGGATGCACATGAGCTGGGTGA
24459340 GATG
1 GATG
24459344 CACATAATGA
Statistics
Matches: 153, Mismatches: 10, Indels: 6
0.91 0.06 0.04
Matches are distributed among these distances:
53 2 0.01
54 147 0.96
55 4 0.03
ACGTcount: A:0.20, C:0.12, G:0.41, T:0.26
Consensus pattern (54 bp):
GATGGGATGTTCGGCTATGTGCACGATGTGGTGGGATGCACATGAGCTGGGTGA
Found at i:24459842 original size:98 final size:98
Alignment explanation
Indices: 24459673--24459866 Score: 334
Period size: 98 Copynumber: 2.0 Consensus size: 98
24459663 GATTCGGAGG
**
24459673 CAGTTGGGACCTAGATTGAGTGTCCACGTATGCTCGTCTTCTTGGTAGGTACTATGGCATCTTAG
1 CAGTTGGGACCTAGATTGAGTGTCCACGTATGCTCGTCTTCTTGGTAGGTACTATGAAATCTTAG
* * *
24459738 TAGTGGTACTTTCACTTAAAGTCATTCTGCTCA
66 TAGTGGTACCTTAACTTAAAGTCACTCTGCTCA
*
24459771 CAGTTGGGACCTAGATTGAGTGTCCACGTATGCTTGTCTTCTTGGTAGGTACTATGAAATCTTAG
1 CAGTTGGGACCTAGATTGAGTGTCCACGTATGCTCGTCTTCTTGGTAGGTACTATGAAATCTTAG
24459836 TAGTGGTACCTTAACTTAAAGTCACTCTGCT
66 TAGTGGTACCTTAACTTAAAGTCACTCTGCT
24459867 GACAATTGAG
Statistics
Matches: 90, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
98 90 1.00
ACGTcount: A:0.22, C:0.20, G:0.23, T:0.36
Consensus pattern (98 bp):
CAGTTGGGACCTAGATTGAGTGTCCACGTATGCTCGTCTTCTTGGTAGGTACTATGAAATCTTAG
TAGTGGTACCTTAACTTAAAGTCACTCTGCTCA
Found at i:24461216 original size:43 final size:43
Alignment explanation
Indices: 24461149--24461263 Score: 144
Period size: 43 Copynumber: 2.7 Consensus size: 43
24461139 CTCCATACTT
* *
24461149 AGCTCATGTGCACTCCCTAC-TCGCACATGGCCGGGTTATCATA
1 AGCTCATGTGCACT-CCTACATCGCACATAGCCGGGTCATCATA
* * * *
24461192 AGCTCATGTGCACTTCTACATCGCATATAGCTGGGTCATCATC
1 AGCTCATGTGCACTCCTACATCGCACATAGCCGGGTCATCATA
*
24461235 AGCTCATGTGCACTCCCACA-CGCACATAG
1 AGCTCATGTGCACTCCTACATCGCACATAG
24461264 TTAGGTCATC
Statistics
Matches: 62, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
42 12 0.19
43 50 0.81
ACGTcount: A:0.23, C:0.32, G:0.19, T:0.25
Consensus pattern (43 bp):
AGCTCATGTGCACTCCTACATCGCACATAGCCGGGTCATCATA
Found at i:24468834 original size:43 final size:43
Alignment explanation
Indices: 24468765--24468868 Score: 138
Period size: 43 Copynumber: 2.4 Consensus size: 43
24468755 CCTCCATACT
* *
24468765 CAACTCATGTGCACTCCCTACTCACACATGGCCGGGTCATCAC
1 CAACTCATGTGCACTCCCTACCCACACATAGCCGGGTCATCAC
* * *
24468808 CAACTCATGTGCACT-TCTACACCACACATAGCTGGGTCATCAT
1 CAACTCATGTGCACTCCCTAC-CCACACATAGCCGGGTCATCAC
*
24468851 CAGCTCATGTGCACTCCC
1 CAACTCATGTGCACTCCC
24468869 ACACGTACAT
Statistics
Matches: 52, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
42 4 0.08
43 47 0.90
44 1 0.02
ACGTcount: A:0.24, C:0.38, G:0.15, T:0.23
Consensus pattern (43 bp):
CAACTCATGTGCACTCCCTACCCACACATAGCCGGGTCATCAC
Found at i:24471448 original size:20 final size:20
Alignment explanation
Indices: 24471419--24471461 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
24471409 ATTAGGTTAC
24471419 TTTTAAGTTAGTT-ATTTTAA
1 TTTTAAGTTA-TTCATTTTAA
* *
24471439 TTTTATGTTATTCCTTTTAA
1 TTTTAAGTTATTCATTTTAA
24471459 TTT
1 TTT
24471462 GGTTATGATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 2 0.10
20 18 0.90
ACGTcount: A:0.23, C:0.05, G:0.07, T:0.65
Consensus pattern (20 bp):
TTTTAAGTTATTCATTTTAA
Found at i:24472586 original size:14 final size:14
Alignment explanation
Indices: 24472567--24472593 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
24472557 TTGATTTTAA
24472567 TTTTAGTTAATTAG
1 TTTTAGTTAATTAG
24472581 TTTTAGTTAATTA
1 TTTTAGTTAATTA
24472594 ATTAATTTTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.00, G:0.11, T:0.59
Consensus pattern (14 bp):
TTTTAGTTAATTAG
Found at i:24474784 original size:19 final size:19
Alignment explanation
Indices: 24474760--24474801 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
24474750 TGTGGCAAGG
*
24474760 TGAAAATGGCATGGAAGCT
1 TGAAAATGGCATGGAAGCA
**
24474779 TGAAAATGGTGTGGAAGCA
1 TGAAAATGGCATGGAAGCA
24474798 TGAA
1 TGAA
24474802 GGTGAAGAAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.38, C:0.07, G:0.33, T:0.21
Consensus pattern (19 bp):
TGAAAATGGCATGGAAGCA
Found at i:24475227 original size:18 final size:19
Alignment explanation
Indices: 24475188--24475227 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
24475178 TTAATATTTT
24475188 AATATTATTTTATTCATAA
1 AATATTATTTTATTCATAA
24475207 AATATTATTTTATTC-TAA
1 AATATTATTTTATTCATAA
24475225 AAT
1 AAT
24475228 TTTCCACTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 6 0.29
19 15 0.71
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.53
Consensus pattern (19 bp):
AATATTATTTTATTCATAA
Found at i:24477836 original size:35 final size:35
Alignment explanation
Indices: 24477797--24477865 Score: 84
Period size: 35 Copynumber: 2.0 Consensus size: 35
24477787 TCTAGTTGCA
** * *
24477797 ATTTATCGGTAGATGGAGTCTTCTATCAATAGATC
1 ATTTATCAATAGATGGAGCCATCTATCAATAGATC
* *
24477832 ATTTATCAATAGATTGAGCCATCTATCGATAGAT
1 ATTTATCAATAGATGGAGCCATCTATCAATAGAT
24477866 TGGGCTATCT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
35 28 1.00
ACGTcount: A:0.32, C:0.14, G:0.17, T:0.36
Consensus pattern (35 bp):
ATTTATCAATAGATGGAGCCATCTATCAATAGATC
Found at i:24477863 original size:20 final size:20
Alignment explanation
Indices: 24477835--24477885 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
24477825 ATAGATCATT
*
24477835 TATCAATAGATTGAGCCATC
1 TATCGATAGATTGAGCCATC
* *
24477855 TATCGATAGATTGGGCTATC
1 TATCGATAGATTGAGCCATC
*
24477875 TATGGATAGAT
1 TATCGATAGAT
24477886 CTAGTCATTT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.31, C:0.14, G:0.22, T:0.33
Consensus pattern (20 bp):
TATCGATAGATTGAGCCATC
Found at i:24479589 original size:25 final size:25
Alignment explanation
Indices: 24479560--24479607 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
24479550 CACCACCATG
*
24479560 TATATCAACTCATGGCCTAGCCACA
1 TATATCAACCCATGGCCTAGCCACA
* *
24479585 TATATCAACCCGTGGCCTTGCCA
1 TATATCAACCCATGGCCTAGCCA
24479608 TGTATTTATA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.27, C:0.33, G:0.15, T:0.25
Consensus pattern (25 bp):
TATATCAACCCATGGCCTAGCCACA
Found at i:24482751 original size:2 final size:2
Alignment explanation
Indices: 24482739--24482775 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
24482729 ATTATGTTGG
*
24482739 TA TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
24482776 GTTGTGCATT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:24484290 original size:14 final size:14
Alignment explanation
Indices: 24484271--24484297 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
24484261 CTTTCTTCTT
24484271 TTTGCATGTAATAA
1 TTTGCATGTAATAA
24484285 TTTGCATGTAATA
1 TTTGCATGTAATA
24484298 GTGAATCCAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.33, C:0.07, G:0.15, T:0.44
Consensus pattern (14 bp):
TTTGCATGTAATAA
Found at i:24490662 original size:35 final size:35
Alignment explanation
Indices: 24490618--24490731 Score: 110
Period size: 35 Copynumber: 3.3 Consensus size: 35
24490608 GTTAGTTTTG
*
24490618 GGTTTTGGTTGATCCCGTGAAAAACCATTGTTAAA
1 GGTTGTGGTTGATCCCGTGAAAAACCATTGTTAAA
* ** * * *
24490653 GGTTGTGGTTGAGCCTTTGAAAAGCCACT-TT--G
1 GGTTGTGGTTGATCCCGTGAAAAACCATTGTTAAA
*
24490685 GGTTTTGGTTGATCCCAGT-AAAAACCATTGTTAAA
1 GGTTGTGGTTGATCCC-GTGAAAAACCATTGTTAAA
*
24490720 GGTTGCGGTTGA
1 GGTTGTGGTTGA
24490732 GCTTGTGAAA
Statistics
Matches: 59, Mismatches: 16, Indels: 8
0.71 0.19 0.10
Matches are distributed among these distances:
32 21 0.36
33 3 0.05
34 2 0.03
35 33 0.56
ACGTcount: A:0.25, C:0.14, G:0.27, T:0.34
Consensus pattern (35 bp):
GGTTGTGGTTGATCCCGTGAAAAACCATTGTTAAA
Found at i:24490697 original size:67 final size:67
Alignment explanation
Indices: 24490614--24490744 Score: 221
Period size: 67 Copynumber: 2.0 Consensus size: 67
24490604 AAAAGTTAGT
*
24490614 TTTGGGTTTTGGTTGATCCC-GTGAAAAACCATTGTTAAAGGTTGTGGTTGAGCCTT-TGAAAAG
1 TTTGGGTTTTGGTTGATCCCAGT-AAAAACCATTGTTAAAGGTTGCGGTTGAG-CTTGTGAAAAG
24490677 CCAC
64 CCAC
24490681 TTTGGGTTTTGGTTGATCCCAGTAAAAACCATTGTTAAAGGTTGCGGTTGAGCTTGTGAAAAGC
1 TTTGGGTTTTGGTTGATCCCAGTAAAAACCATTGTTAAAGGTTGCGGTTGAGCTTGTGAAAAGC
24490745 TATTGTAAAA
Statistics
Matches: 61, Mismatches: 1, Indels: 4
0.92 0.02 0.06
Matches are distributed among these distances:
66 3 0.05
67 56 0.92
68 2 0.03
ACGTcount: A:0.24, C:0.14, G:0.27, T:0.34
Consensus pattern (67 bp):
TTTGGGTTTTGGTTGATCCCAGTAAAAACCATTGTTAAAGGTTGCGGTTGAGCTTGTGAAAAGCC
AC
Found at i:24496041 original size:21 final size:22
Alignment explanation
Indices: 24496006--24496047 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
24495996 CTAGAAAAGC
24496006 ACCTAAAATACTAAA-ATCTAA
1 ACCTAAAATACTAAAGATCTAA
24496027 ACCTAAAAT-CTTAAAGATCTA
1 ACCTAAAATAC-TAAAGATCTA
24496048 GCTACTTAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 1 0.05
21 13 0.68
22 5 0.26
ACGTcount: A:0.52, C:0.19, G:0.02, T:0.26
Consensus pattern (22 bp):
ACCTAAAATACTAAAGATCTAA
Found at i:24509491 original size:60 final size:60
Alignment explanation
Indices: 24509427--24509586 Score: 175
Period size: 60 Copynumber: 2.7 Consensus size: 60
24509417 TTCTCGCTGT
*
24509427 AGCGAAATACATTCTCGCTGCAGTGAGAAACTTTCTGTTTCTGGG-TAGCAATTTCGCTTA-
1 AGCGAAATACATTCTCGCTGCAGCGAGAAACTTTCTGTTTCTGGGTTA-CAATTTCGC-TAC
* * *
24509487 AGCGAGATTGA-ATT-TCACTGCAGCGAGAAACTTTCCGTTTCTGGGTTACAATTTCGCTAC
1 AGCGA-AAT-ACATTCTCGCTGCAGCGAGAAACTTTCTGTTTCTGGGTTACAATTTCGCTAC
* * * * *
24509547 AGCGAGATTCAATCTCGCTGCAGCGAAAAACTTTTTGTTT
1 AGCGAAATACATTCTCGCTGCAGCGAGAAACTTTCTGTTT
24509587 TGGTCTCTTA
Statistics
Matches: 82, Mismatches: 12, Indels: 12
0.77 0.11 0.11
Matches are distributed among these distances:
59 5 0.06
60 69 0.84
61 7 0.09
62 1 0.01
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.33
Consensus pattern (60 bp):
AGCGAAATACATTCTCGCTGCAGCGAGAAACTTTCTGTTTCTGGGTTACAATTTCGCTAC
Found at i:24512096 original size:14 final size:14
Alignment explanation
Indices: 24512050--24512096 Score: 67
Period size: 14 Copynumber: 3.3 Consensus size: 14
24512040 AAGGCAATAC
*
24512050 TTTTCTTCTTTTCT
1 TTTTCTTCTTTTTT
*
24512064 TTTTCTTCTCTTTTG
1 TTTTCTTCT-TTTTT
24512079 TTTTCTTCTTTTTT
1 TTTTCTTCTTTTTT
24512093 TTTT
1 TTTT
24512097 TTAACTCCAG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
14 17 0.59
15 12 0.41
ACGTcount: A:0.00, C:0.17, G:0.02, T:0.81
Consensus pattern (14 bp):
TTTTCTTCTTTTTT
Found at i:24512097 original size:15 final size:15
Alignment explanation
Indices: 24512050--24512097 Score: 62
Period size: 15 Copynumber: 3.3 Consensus size: 15
24512040 AAGGCAATAC
*
24512050 TTTTCTTC-TTTTCT
1 TTTTCTTCTTTTTTT
* *
24512064 TTTTCTTCTCTTTTG
1 TTTTCTTCTTTTTTT
24512079 TTTTCTTCTTTTTTT
1 TTTTCTTCTTTTTTT
24512094 TTTT
1 TTTT
24512098 TAACTCCAGC
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
14 8 0.29
15 20 0.71
ACGTcount: A:0.00, C:0.17, G:0.02, T:0.81
Consensus pattern (15 bp):
TTTTCTTCTTTTTTT
Found at i:24514186 original size:12 final size:12
Alignment explanation
Indices: 24514169--24514193 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
24514159 AAATCTTTAC
24514169 TACTTACCTCTT
1 TACTTACCTCTT
24514181 TACTTACCTCTT
1 TACTTACCTCTT
24514193 T
1 T
24514194 TCCATTACGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.32, G:0.00, T:0.52
Consensus pattern (12 bp):
TACTTACCTCTT
Found at i:24514402 original size:21 final size:21
Alignment explanation
Indices: 24514360--24514427 Score: 75
Period size: 21 Copynumber: 3.2 Consensus size: 21
24514350 TTGAATTGAG
*
24514360 GCATCAGTCCTTT-TCATAAAT
1 GCATCAGT-CTTTGTCATGAAT
* *
24514381 GCATCGGTCTTTGTTATGAAT
1 GCATCAGTCTTTGTCATGAAT
*
24514402 GTATCAGTCTTTGTCATGAATT
1 GCATCAGTCTTTGTCATGAA-T
24514424 GCAT
1 GCAT
24514428 GAACATATCC
Statistics
Matches: 38, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
20 4 0.11
21 30 0.79
22 4 0.11
ACGTcount: A:0.24, C:0.18, G:0.18, T:0.41
Consensus pattern (21 bp):
GCATCAGTCTTTGTCATGAAT
Found at i:24520785 original size:3 final size:3
Alignment explanation
Indices: 24520777--24520803 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
24520767 AAAGAAGTTC
24520777 ATG ATG ATG ATG ATG ATG ATG ATG ATG
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG
24520804 TAGAAATCTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (3 bp):
ATG
Found at i:24523671 original size:32 final size:32
Alignment explanation
Indices: 24523630--24523695 Score: 132
Period size: 32 Copynumber: 2.1 Consensus size: 32
24523620 TGGAAGGAAA
24523630 GAAAAATATTCTTCTAAAAGCAATTCAGGTGT
1 GAAAAATATTCTTCTAAAAGCAATTCAGGTGT
24523662 GAAAAATATTCTTCTAAAAGCAATTCAGGTGT
1 GAAAAATATTCTTCTAAAAGCAATTCAGGTGT
24523694 GA
1 GA
24523696 TAATTAGTCC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.41, C:0.12, G:0.17, T:0.30
Consensus pattern (32 bp):
GAAAAATATTCTTCTAAAAGCAATTCAGGTGT
Found at i:24525152 original size:20 final size:20
Alignment explanation
Indices: 24525123--24525165 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
24525113 ATTAGGTTAC
24525123 TTTTAAGTTAGTT-ATTTTAA
1 TTTTAAGTTA-TTCATTTTAA
* *
24525143 TTTTATGTTATTCCTTTTAA
1 TTTTAAGTTATTCATTTTAA
24525163 TTT
1 TTT
24525166 GGTTATTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 2 0.10
20 18 0.90
ACGTcount: A:0.23, C:0.05, G:0.07, T:0.65
Consensus pattern (20 bp):
TTTTAAGTTATTCATTTTAA
Found at i:24526300 original size:14 final size:14
Alignment explanation
Indices: 24526265--24526300 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
24526255 CTTGTTGGTT
24526265 TTAATTTTAGTTAA
1 TTAATTTTAGTTAA
* *
24526279 TCAGTTTTAGTTAA
1 TTAATTTTAGTTAA
24526293 TTAATTTT
1 TTAATTTT
24526301 GATTATTTGG
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.31, C:0.03, G:0.08, T:0.58
Consensus pattern (14 bp):
TTAATTTTAGTTAA
Found at i:24529556 original size:22 final size:22
Alignment explanation
Indices: 24529526--24529569 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
24529516 CCATGTGTTC
24529526 TTATATTTTG-ATGATATATATT
1 TTATATTTTGAATGATA-ATATT
*
24529548 TTATGTTTTGAATGATAATATT
1 TTATATTTTGAATGATAATATT
24529570 ATGTGATAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 14 0.70
23 6 0.30
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.57
Consensus pattern (22 bp):
TTATATTTTGAATGATAATATT
Found at i:24530708 original size:22 final size:23
Alignment explanation
Indices: 24530683--24530729 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
24530673 ATATCTATGT
24530683 ATTACTA-CAAGAACTAAG-CTAA
1 ATTACTATCAA-AACTAAGCCTAA
*
24530705 ATTACTATCAAAATTAAGCCTAA
1 ATTACTATCAAAACTAAGCCTAA
24530728 AT
1 AT
24530730 AAGTTTATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 13 0.59
23 9 0.41
ACGTcount: A:0.49, C:0.17, G:0.06, T:0.28
Consensus pattern (23 bp):
ATTACTATCAAAACTAAGCCTAA
Found at i:24533150 original size:29 final size:30
Alignment explanation
Indices: 24533106--24533176 Score: 90
Period size: 29 Copynumber: 2.4 Consensus size: 30
24533096 GGCCCATTAA
24533106 GAGATTACTCCAAGCGATGCC-ACCGATGG
1 GAGATTACTCCAAGCGATGCCTACCGATGG
** *
24533135 GAGATTACTCTGAGCGATGCCTACCGTTGG
1 GAGATTACTCCAAGCGATGCCTACCGATGG
* *
24533165 GATAGTACTCCA
1 GAGATTACTCCA
24533177 GTTGATGATA
Statistics
Matches: 34, Mismatches: 7, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
29 19 0.56
30 15 0.44
ACGTcount: A:0.25, C:0.25, G:0.27, T:0.23
Consensus pattern (30 bp):
GAGATTACTCCAAGCGATGCCTACCGATGG
Found at i:24533174 original size:30 final size:29
Alignment explanation
Indices: 24533118--24533174 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 29
24533108 GATTACTCCA
*
24533118 AGCGATGCCACCGATGGGAGATTACTCTG
1 AGCGATGCCACCGATGGGAGAGTACTCTG
* *
24533147 AGCGATGCCTACCGTTGGGATAGTACTC
1 AGCGATGCC-ACCGATGGGAGAGTACTC
24533175 CAGTTGATGA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 9 0.38
30 15 0.62
ACGTcount: A:0.23, C:0.25, G:0.30, T:0.23
Consensus pattern (29 bp):
AGCGATGCCACCGATGGGAGAGTACTCTG
Found at i:24533551 original size:32 final size:32
Alignment explanation
Indices: 24533515--24533580 Score: 91
Period size: 32 Copynumber: 2.1 Consensus size: 32
24533505 GTGATGATCT
24533515 TTGGAGATCTT-GGAGAT-ATGATATGCCCCATA
1 TTGGAGA-CTTAGG-GATAATGATATGCCCCATA
*
24533547 TTGGAGACTTAGGGATAATGATATGCCCTATA
1 TTGGAGACTTAGGGATAATGATATGCCCCATA
24533579 TT
1 TT
24533581 TAGAGATGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
31 6 0.19
32 25 0.81
ACGTcount: A:0.29, C:0.14, G:0.24, T:0.33
Consensus pattern (32 bp):
TTGGAGACTTAGGGATAATGATATGCCCCATA
Found at i:24535665 original size:80 final size:81
Alignment explanation
Indices: 24535532--24535706 Score: 271
Period size: 80 Copynumber: 2.2 Consensus size: 81
24535522 ACAAGCAACA
* *
24535532 ATAAGGAAAGTTAGTGCATAATCCCCCTACCTAAAGAGCAAGGTTCGAATCCCCCCTCCCCCAAT
1 ATAAGGAAAGTTGGGGCATAATCCCCCTACCTAAAGAGCAAGGTTCGAATCCCCCCTCCCCCAAT
24535597 TAT-AAAAAAAAAACT
66 TATAAAAAAAAAAACT
* * * **
24535612 ATAAGGAAAGTTGGGGCATAATCCCCTTGCCTAAATAGCAAGGTTCGAATCCCCCCTCCCTTAAT
1 ATAAGGAAAGTTGGGGCATAATCCCCCTACCTAAAGAGCAAGGTTCGAATCCCCCCTCCCCCAAT
24535677 TATAAAAAAAAAAAACT
66 TAT-AAAAAAAAAAACT
24535694 ATAAGGAAAGTTG
1 ATAAGGAAAGTTG
24535707 ATAATCATGA
Statistics
Matches: 86, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
80 61 0.71
82 25 0.29
ACGTcount: A:0.40, C:0.23, G:0.15, T:0.22
Consensus pattern (81 bp):
ATAAGGAAAGTTGGGGCATAATCCCCCTACCTAAAGAGCAAGGTTCGAATCCCCCCTCCCCCAAT
TATAAAAAAAAAAACT
Found at i:24536100 original size:54 final size:54
Alignment explanation
Indices: 24536018--24536176 Score: 255
Period size: 54 Copynumber: 2.9 Consensus size: 54
24536008 ATTTGTATAC
*
24536018 CACCCTATCTCACCCAGCTCATGTGCATCCCCCCACATCGTGCACATAGCCAGA
1 CACCCCATCTCACCCAGCTCATGTGCATCCCCCCACATCGTGCACATAGCCAGA
* * * *
24536072 CACCCCATCTCAACCAGCTCATGTGCATCCCCTCACATCGTGCACATAGTCGGA
1 CACCCCATCTCACCCAGCTCATGTGCATCCCCCCACATCGTGCACATAGCCAGA
* *
24536126 CACCCCATCTCACCCAGTTCATGTGCATTCCCCCACATCGTGCACATAGCC
1 CACCCCATCTCACCCAGCTCATGTGCATCCCCCCACATCGTGCACATAGCC
24536177 GGAGTCATCG
Statistics
Matches: 95, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
54 95 1.00
ACGTcount: A:0.23, C:0.43, G:0.13, T:0.20
Consensus pattern (54 bp):
CACCCCATCTCACCCAGCTCATGTGCATCCCCCCACATCGTGCACATAGCCAGA
Found at i:24552788 original size:78 final size:79
Alignment explanation
Indices: 24552632--24552809 Score: 220
Period size: 78 Copynumber: 2.3 Consensus size: 79
24552622 TATTTTTCCT
* * *
24552632 CCACACCAGGACTAGAGCCAACATACATAAAGGGAAAAGATGGCACGTTAACCAAGCTTAACCTT
1 CCACACCAGGACTAGAGCCAACATACAAAAAGGG-AAAGATGGCACGTCAACCAAGCTTAACCCT
*
24552697 GTGGTATTCTTACCC
65 GTCGTATTCTTACCC
* * **
24552712 CCACACTAGGACTCA-AGCCAACATACAAAAAGGG-AAGATGGCATGTCGGCCAAGCTTAACCCT
1 CCACACCAGGACT-AGAGCCAACATACAAAAAGGGAAAGATGGCACGTCAACCAAGCTTAACCCT
24552775 GTCGTATTCTTA-CC
65 GTCGTATTCTTACCC
*
24552789 CAACACC-GAGACTAGAGCCAA
1 CCACACCAG-GACTAGAGCCAA
24552810 TCACAACACA
Statistics
Matches: 85, Mismatches: 10, Indels: 9
0.82 0.10 0.09
Matches are distributed among these distances:
76 2 0.02
77 17 0.20
78 35 0.41
80 30 0.35
81 1 0.01
ACGTcount: A:0.35, C:0.28, G:0.19, T:0.18
Consensus pattern (79 bp):
CCACACCAGGACTAGAGCCAACATACAAAAAGGGAAAGATGGCACGTCAACCAAGCTTAACCCTG
TCGTATTCTTACCC
Found at i:24554614 original size:35 final size:35
Alignment explanation
Indices: 24554575--24554728 Score: 231
Period size: 35 Copynumber: 4.4 Consensus size: 35
24554565 AAGTGTGGAT
24554575 AATGATGTTGATGTGTGCAAGTAGGGAGTGCACAC
1 AATGATGTTGATGTGTGCAAGTAGGGAGTGCACAC
24554610 AATGATGTTGATGTGTGCGAA-TAGGGAGTGCACAC
1 AATGATGTTGATGTGTGC-AAGTAGGGAGTGCACAC
* *
24554645 GACGATGTTGATGTGTGCAAGTAGGGAGTGCACA-
1 AATGATGTTGATGTGTGCAAGTAGGGAGTGCACAC
* *
24554679 AGATGATGTTGATGTGTGCGAGTAAGGAGTGCACAC
1 A-ATGATGTTGATGTGTGCAAGTAGGGAGTGCACAC
*
24554715 GATGATGTTGATGT
1 AATGATGTTGATGT
24554729 ACACGATGTG
Statistics
Matches: 108, Mismatches: 7, Indels: 8
0.88 0.06 0.07
Matches are distributed among these distances:
34 2 0.02
35 104 0.96
36 2 0.02
ACGTcount: A:0.27, C:0.10, G:0.36, T:0.27
Consensus pattern (35 bp):
AATGATGTTGATGTGTGCAAGTAGGGAGTGCACAC
Found at i:24554657 original size:70 final size:70
Alignment explanation
Indices: 24554578--24554728 Score: 259
Period size: 70 Copynumber: 2.2 Consensus size: 70
24554568 TGTGGATAAT
*
24554578 GATGTTGATGTGTGCAAGTAGGGAGTGCACACA-ATGATGTTGATGTGTGCGAATAGGGAGTGCA
1 GATGTTGATGTGTGCAAGTAGGGAGTGCACA-AGATGATGTTGATGTGTGCGAATAAGGAGTGCA
24554642 CACGAC
65 CACGAC
*
24554648 GATGTTGATGTGTGCAAGTAGGGAGTGCACAAGATGATGTTGATGTGTGCGAGTAAGGAGTGCAC
1 GATGTTGATGTGTGCAAGTAGGGAGTGCACAAGATGATGTTGATGTGTGCGAATAAGGAGTGCAC
*
24554713 ACGAT
66 ACGAC
24554718 GATGTTGATGT
1 GATGTTGATGT
24554729 ACACGATGTG
Statistics
Matches: 77, Mismatches: 3, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
69 1 0.01
70 76 0.99
ACGTcount: A:0.26, C:0.11, G:0.36, T:0.26
Consensus pattern (70 bp):
GATGTTGATGTGTGCAAGTAGGGAGTGCACAAGATGATGTTGATGTGTGCGAATAAGGAGTGCAC
ACGAC
Found at i:24554746 original size:35 final size:36
Alignment explanation
Indices: 24554576--24554754 Score: 215
Period size: 35 Copynumber: 5.1 Consensus size: 36
24554566 AGTGTGGATA
* *
24554576 ATGATGTTGATGTGTGC-AAGTAGGGAGTGCACACA
1 ATGATGTTGATGTGTGCGATGTAGGGAGTGCACACG
*
24554611 ATGATGTTGATGTGTGCGA-ATAGGGAGTGCACACG
1 ATGATGTTGATGTGTGCGATGTAGGGAGTGCACACG
* * *
24554646 ACGATGTTGATGTGTGC-AAGTAGGGAGTGCACAAG
1 ATGATGTTGATGTGTGCGATGTAGGGAGTGCACACG
*
24554681 ATGATGTTGATGTGTGCGA-GTAAGGAGTGCACACG
1 ATGATGTTGATGTGTGCGATGTAGGGAGTGCACACG
*** * *
24554716 ATGATGTTGATGTACACGATGT-GGGGGTGCACCCG
1 ATGATGTTGATGTGTGCGATGTAGGGAGTGCACACG
24554751 ATGA
1 ATGA
24554755 CTTCGGCTAT
Statistics
Matches: 126, Mismatches: 14, Indels: 8
0.85 0.09 0.05
Matches are distributed among these distances:
34 1 0.01
35 121 0.96
36 4 0.03
ACGTcount: A:0.26, C:0.12, G:0.36, T:0.25
Consensus pattern (36 bp):
ATGATGTTGATGTGTGCGATGTAGGGAGTGCACACG
Found at i:24554845 original size:21 final size:21
Alignment explanation
Indices: 24554821--24554868 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
24554811 CTTGCTTGTA
*
24554821 TATATATATATATATATATGC
1 TATAGATATATATATATATGC
* * *
24554842 TATAGATATGTTTTTATATGC
1 TATAGATATATATATATATGC
24554863 TATAGA
1 TATAGA
24554869 AAAGGGTATG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.38, C:0.04, G:0.10, T:0.48
Consensus pattern (21 bp):
TATAGATATATATATATATGC
Found at i:24558032 original size:2 final size:2
Alignment explanation
Indices: 24558020--24558050 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
24558010 TGCAACAAGG
24558020 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
24558051 GTTAGAGGCA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:24560846 original size:35 final size:35
Alignment explanation
Indices: 24560807--24560889 Score: 139
Period size: 35 Copynumber: 2.4 Consensus size: 35
24560797 AGTGTGGATA
*
24560807 ATGATGTTGATGTGTGCAAGTAGGGAGTGCACACG
1 ATGATGTTGATGTGTGCAAGTAAGGAGTGCACACG
*
24560842 ATGATGTTGATGTGTGCGAGTAAGGAGTGCACACG
1 ATGATGTTGATGTGTGCAAGTAAGGAGTGCACACG
*
24560877 ATAATGTTGATGT
1 ATGATGTTGATGT
24560890 ACGCGATGTG
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 45 1.00
ACGTcount: A:0.27, C:0.10, G:0.35, T:0.29
Consensus pattern (35 bp):
ATGATGTTGATGTGTGCAAGTAAGGAGTGCACACG
Found at i:24560987 original size:2 final size:2
Alignment explanation
Indices: 24560980--24561012 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
24560970 TACATGCTTG
24560980 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
24561013 GCTATAGATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:24564489 original size:32 final size:32
Alignment explanation
Indices: 24564453--24564565 Score: 102
Period size: 32 Copynumber: 3.4 Consensus size: 32
24564443 TTTACCAGGA
*
24564453 TCAATCAAAACCTAAAGTGGTTTTTCAAAGGC
1 TCAACCAAAACCTAAAGTGGTTTTTCAAAGGC
* * * * **
24564485 TCAATCACAACCTTTCACAA-TGGTATCTCATGGGC
1 TCAACCAAAACC--T-A-AAGTGGTTTTTCAAAGGC
*
24564520 TCAACCAAAACCCAAAGTGGTTTTTCAAAGGC
1 TCAACCAAAACCTAAAGTGGTTTTTCAAAGGC
*
24564552 TCAACCACAACCTA
1 TCAACCAAAACCTA
24564566 CAACAATGGT
Statistics
Matches: 62, Mismatches: 14, Indels: 10
0.72 0.16 0.12
Matches are distributed among these distances:
31 2 0.03
32 35 0.56
34 1 0.02
35 22 0.35
36 2 0.03
ACGTcount: A:0.35, C:0.27, G:0.13, T:0.25
Consensus pattern (32 bp):
TCAACCAAAACCTAAAGTGGTTTTTCAAAGGC
Found at i:24564537 original size:67 final size:68
Alignment explanation
Indices: 24564450--24564603 Score: 213
Period size: 67 Copynumber: 2.3 Consensus size: 68
24564440 GTTTTTACCA
* * * *
24564450 GGATCAATCAAAACCTAAAGTGGTTTTTCAAAGGCTCAATCACAACCTTTC-ACAATGG-TATCT
1 GGATCAACCAAAACCCAAAGTGGTTTTTCAAAGGCTCAACCACAACC-TACAACAATGGTTATCT
*
24564513 CATG
65 CACG
* *
24564517 GGCTCAACCAAAACCCAAAGTGGTTTTTCAAAGGCTCAACCACAACCTACAACAATGGTTTTTCT
1 GGATCAACCAAAACCCAAAGTGGTTTTTCAAAGGCTCAACCACAACCTACAACAATGG-TTATCT
24564582 CACG
65 CACG
24564586 GGATCAACCAAAACCCAA
1 GGATCAACCAAAACCCAA
24564604 CAACTAACTT
Statistics
Matches: 76, Mismatches: 8, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
66 2 0.03
67 50 0.66
69 24 0.32
ACGTcount: A:0.36, C:0.27, G:0.14, T:0.23
Consensus pattern (68 bp):
GGATCAACCAAAACCCAAAGTGGTTTTTCAAAGGCTCAACCACAACCTACAACAATGGTTATCTC
ACG
Found at i:24574152 original size:18 final size:18
Alignment explanation
Indices: 24574131--24574176 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 18
24574121 ATGTATATAT
24574131 GTGAATGTGATTGCCTAG
1 GTGAATGTGATTGCCTAG
*
24574149 GTGAATATGATTGCCTAG
1 GTGAATGTGATTGCCTAG
*
24574167 GTGGATGTGA
1 GTGAATGTGA
24574177 CGAAGCTAGT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.24, C:0.09, G:0.35, T:0.33
Consensus pattern (18 bp):
GTGAATGTGATTGCCTAG
Found at i:24574946 original size:36 final size:37
Alignment explanation
Indices: 24574857--24574946 Score: 103
Period size: 36 Copynumber: 2.5 Consensus size: 37
24574847 CTTCGATGCT
* * *
24574857 GGGCGTGATTTGATTCTCCACCAGTTGCTTCGGCATT
1 GGGCGTGATTTGATTCTCCACCAGTTACTTCAGCATC
* **
24574894 GGGTGTGATTTG-TTCTCCACTTGTTACTTCAGCA-C
1 GGGCGTGATTTGATTCTCCACCAGTTACTTCAGCATC
*
24574929 GTGCGTGATTTGATTCTC
1 GGGCGTGATTTGATTCTC
24574947 TATCGGTTGG
Statistics
Matches: 44, Mismatches: 8, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
35 10 0.23
36 23 0.52
37 11 0.25
ACGTcount: A:0.13, C:0.22, G:0.26, T:0.39
Consensus pattern (37 bp):
GGGCGTGATTTGATTCTCCACCAGTTACTTCAGCATC
Found at i:24586678 original size:13 final size:13
Alignment explanation
Indices: 24586660--24586684 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
24586650 GGAAAATGGG
24586660 ATTTTATAAAATA
1 ATTTTATAAAATA
24586673 ATTTTATAAAAT
1 ATTTTATAAAAT
24586685 TTTTGAAAAT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
ATTTTATAAAATA
Found at i:24594036 original size:41 final size:43
Alignment explanation
Indices: 24593949--24594070 Score: 185
Period size: 41 Copynumber: 2.9 Consensus size: 43
24593939 TTGTGTAATA
24593949 ATGATGACCTAGCTATGTGCGAGTAGGGAGTGCACATGAGCCG
1 ATGATGACCTAGCTATGTGCGAGTAGGGAGTGCACATGAGCCG
* **
24593992 ATGATGACCCAGCTATGTGCGA-T-GGGAGTGCACATGAGTTG
1 ATGATGACCTAGCTATGTGCGAGTAGGGAGTGCACATGAGCCG
* *
24594033 ATGATGACCTAGCTATGTTCGAGTAGAGAGTGCACATG
1 ATGATGACCTAGCTATGTGCGAGTAGGGAGTGCACATG
24594071 TGTCAAGCCC
Statistics
Matches: 71, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
41 36 0.51
42 2 0.03
43 33 0.46
ACGTcount: A:0.26, C:0.17, G:0.33, T:0.24
Consensus pattern (43 bp):
ATGATGACCTAGCTATGTGCGAGTAGGGAGTGCACATGAGCCG
Found at i:24597065 original size:11 final size:11
Alignment explanation
Indices: 24597049--24597076 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
24597039 AGCCTTTGGG
24597049 TTTAAAGTTGT
1 TTTAAAGTTGT
24597060 TTTAAAGTTGT
1 TTTAAAGTTGT
24597071 TTTAAA
1 TTTAAA
24597077 ATTTACAGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.32, C:0.00, G:0.14, T:0.54
Consensus pattern (11 bp):
TTTAAAGTTGT
Found at i:24597134 original size:5 final size:5
Alignment explanation
Indices: 24597100--24597130 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
24597090 GTGTGGCTCC
*
24597100 AAGTT AAGTT AAGTT AAGTT AAGTT AGGTT A
1 AAGTT AAGTT AAGTT AAGTT AAGTT AAGTT A
24597131 GGTTGAATAG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.39, C:0.00, G:0.23, T:0.39
Consensus pattern (5 bp):
AAGTT
Found at i:24603278 original size:13 final size:13
Alignment explanation
Indices: 24603255--24603287 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
24603245 ATCATTGCTT
24603255 CAAACCACCATTTC
1 CAAA-CACCATTTC
24603269 CAAACACCATTTC
1 CAAACACCATTTC
24603282 CAAACA
1 CAAACA
24603288 TCCTTATATG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 15 0.79
14 4 0.21
ACGTcount: A:0.42, C:0.39, G:0.00, T:0.18
Consensus pattern (13 bp):
CAAACACCATTTC
Found at i:24607359 original size:16 final size:16
Alignment explanation
Indices: 24607317--24607356 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
24607307 CCATGCCCAT
*
24607317 TTTTATTTTCTATTTC
1 TTTTCTTTTCTATTTC
*
24607333 TTTTCTTTTCTTTTTC
1 TTTTCTTTTCTATTTC
24607349 -TTTCTTTT
1 TTTTCTTTT
24607357 TCTCTCTTCC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 8 0.36
16 14 0.64
ACGTcount: A:0.05, C:0.15, G:0.00, T:0.80
Consensus pattern (16 bp):
TTTTCTTTTCTATTTC
Found at i:24607388 original size:31 final size:29
Alignment explanation
Indices: 24607339--24607396 Score: 73
Period size: 31 Copynumber: 1.9 Consensus size: 29
24607329 TTTCTTTTCT
*
24607339 TTTCTTTTTCTTTCTTTTTCTCTCTTCCATG
1 TTTCTTCTTCTTTCTTTTT-TCT-TTCCATG
24607370 TTTCTTCTTC-TTCTTTTTTTCTTTCCA
1 TTTCTTCTTCTTTC-TTTTTTCTTTCCA
24607397 ACCCGTCACT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
29 5 0.20
30 6 0.24
31 14 0.56
ACGTcount: A:0.03, C:0.26, G:0.02, T:0.69
Consensus pattern (29 bp):
TTTCTTCTTCTTTCTTTTTTCTTTCCATG
Found at i:24609450 original size:86 final size:84
Alignment explanation
Indices: 24609301--24609478 Score: 266
Period size: 86 Copynumber: 2.1 Consensus size: 84
24609291 GGTCGTGACA
* *
24609301 ACATAAGCCAATGATGACCCTGCTATGTGCGGTGGGAGTGCACATGAGCTGATGATGACCCGACT
1 ACATGAGCCAATGATGACCCAGCTATGTGCGGTGGGAGTGCACATGAGCTGATGATGACCCGACT
* *
24609366 ATGTGCAAATAGAGAGTGC
66 ATATACAAATAGAGAGTGC
*
24609385 ACATGAGCCAATGATGACCCAGCTATGTGCGGTGTGAGAGTGCACATGAGCTGATGATTACCCGA
1 ACATGAGCCAATGATGACCCAGCTATGTGCGGTG-G-GAGTGCACATGAGCTGATGATGACCCGA
* * *
24609450 CTATATACGAGTAGGGAGTGC
64 CTATATACAAATAGAGAGTGC
24609471 ACATGAGC
1 ACATGAGC
24609479 TGAGTGTGGC
Statistics
Matches: 84, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
84 32 0.38
85 1 0.01
86 51 0.61
ACGTcount: A:0.29, C:0.20, G:0.30, T:0.21
Consensus pattern (84 bp):
ACATGAGCCAATGATGACCCAGCTATGTGCGGTGGGAGTGCACATGAGCTGATGATGACCCGACT
ATATACAAATAGAGAGTGC
Found at i:24609479 original size:43 final size:43
Alignment explanation
Indices: 24609311--24609481 Score: 192
Period size: 43 Copynumber: 4.0 Consensus size: 43
24609301 ACATAAGCCA
24609311 ATGATGACCCTG-CTATGTGCG-GT-GGGAGTGCACATGAGCTG
1 ATGATGACCC-GACTATGTGCGAGTAGGGAGTGCACATGAGCTG
* * * **
24609352 ATGATGACCCGACTATGTGCAAATAGAGAGTGCACATGAGCCA
1 ATGATGACCCGACTATGTGCGAGTAGGGAGTGCACATGAGCTG
24609395 ATGATGACCC-AGCTATGTGCG-GT-GTGAGAGTGCACATGAGCTG
1 ATGATGACCCGA-CTATGTGCGAGTAG-G-GAGTGCACATGAGCTG
* * *
24609438 ATGATTACCCGACTATATACGAGTAGGGAGTGCACATGAGCTG
1 ATGATGACCCGACTATGTGCGAGTAGGGAGTGCACATGAGCTG
24609481 A
1 A
24609482 GTGTGGCGGC
Statistics
Matches: 108, Mismatches: 13, Indels: 16
0.79 0.09 0.12
Matches are distributed among these distances:
40 1 0.01
41 19 0.18
42 3 0.03
43 80 0.74
44 4 0.04
45 1 0.01
ACGTcount: A:0.27, C:0.19, G:0.31, T:0.22
Consensus pattern (43 bp):
ATGATGACCCGACTATGTGCGAGTAGGGAGTGCACATGAGCTG
Found at i:24611263 original size:21 final size:21
Alignment explanation
Indices: 24611233--24611272 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
24611223 TTGCTATTAT
*
24611233 ATATATATATATATACTTTTA
1 ATATAAATATATATACTTTTA
*
24611254 ATATAAATATATTTACTTT
1 ATATAAATATATATACTTT
24611273 CTATTTTGTG
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:0.42, C:0.05, G:0.00, T:0.53
Consensus pattern (21 bp):
ATATAAATATATATACTTTTA
Found at i:24611525 original size:15 final size:14
Alignment explanation
Indices: 24611500--24611528 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
24611490 TTGTAATGTC
24611500 TTTTAATATATATA
1 TTTTAATATATATA
24611514 TTTT-ATATATATA
1 TTTTAATATATATA
24611527 TT
1 TT
24611529 AGATTCATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (14 bp):
TTTTAATATATATA
Found at i:24613651 original size:33 final size:33
Alignment explanation
Indices: 24613609--24613675 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
24613599 TGAACTAAAG
24613609 TTACTAATTAGCACAATGATTTGAGTTTGGATT
1 TTACTAATTAGCACAATGATTTGAGTTTGGATT
24613642 TTACTAATTAGCACAATGATTTGAGTTTGGATT
1 TTACTAATTAGCACAATGATTTGAGTTTGGATT
24613675 T
1 T
24613676 CAATTTCTTG
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:0.30, C:0.09, G:0.18, T:0.43
Consensus pattern (33 bp):
TTACTAATTAGCACAATGATTTGAGTTTGGATT
Found at i:24613835 original size:21 final size:21
Alignment explanation
Indices: 24613811--24613851 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
24613801 ATTTTGAATG
24613811 AGGTATCGATACCTCATGAAC
1 AGGTATCGATACCTCATGAAC
*
24613832 AGGTATCGATACCTCTTGAA
1 AGGTATCGATACCTCATGAA
24613852 TAGAATGGTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.32, C:0.22, G:0.20, T:0.27
Consensus pattern (21 bp):
AGGTATCGATACCTCATGAAC
Found at i:24614991 original size:13 final size:12
Alignment explanation
Indices: 24614944--24614991 Score: 51
Period size: 13 Copynumber: 3.7 Consensus size: 12
24614934 TATTTAATTT
*
24614944 TAATTTTTAAAA
1 TAATATTTAAAA
24614956 TAATATATTAAAA
1 TAATAT-TTAAAA
24614969 TAATTAATTTAAAA
1 TAA-T-ATTTAAAA
24614983 TATATATTT
1 TA-ATATTT
24614992 TAATATTTTA
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
12 5 0.16
13 13 0.42
14 10 0.32
15 3 0.10
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (12 bp):
TAATATTTAAAA
Found at i:24614993 original size:14 final size:13
Alignment explanation
Indices: 24614944--24614994 Score: 59
Period size: 14 Copynumber: 3.8 Consensus size: 13
24614934 TATTTAATTT
24614944 TAAT-TTTTAAAA
1 TAATATTTTAAAA
*
24614956 TAATATATTAAAA
1 TAATATTTTAAAA
*
24614969 TAATTAATTTAAAA
1 TAA-TATTTTAAAA
24614983 TATATATTTTAA
1 TA-ATATTTTAA
24614995 TATTTTAATT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
12 4 0.12
13 10 0.31
14 17 0.53
15 1 0.03
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (13 bp):
TAATATTTTAAAA
Found at i:24615001 original size:22 final size:23
Alignment explanation
Indices: 24614940--24615002 Score: 58
Period size: 22 Copynumber: 2.7 Consensus size: 23
24614930 TTTTTATTTA
24614940 ATTTTAAT-TTTTAAAATAATAT
1 ATTTTAATATTTTAAAATAATAT
* *
24614962 ATTAAAATAATTAATTTAAAAT-ATAT
1 ATT---TTAA-TATTTTAAAATAATAT
24614988 ATTTTAATATTTTAA
1 ATTTTAATATTTTAA
24615003 TTAACCGAGT
Statistics
Matches: 32, Mismatches: 4, Indels: 10
0.70 0.09 0.22
Matches are distributed among these distances:
22 10 0.31
23 3 0.09
25 3 0.09
26 8 0.25
27 8 0.25
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (23 bp):
ATTTTAATATTTTAAAATAATAT
Found at i:24616109 original size:3 final size:3
Alignment explanation
Indices: 24616103--24616158 Score: 58
Period size: 3 Copynumber: 18.7 Consensus size: 3
24616093 GACGACGACG
* * * * * *
24616103 ACA ACA ACA AGA ACA GCA ACA ACA ACA ATA ACA GCA GCA GCA ACA ACA
1 ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA
24616151 ACA ACA AC
1 ACA ACA AC
24616159 GTCAACAGCA
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.59, C:0.30, G:0.09, T:0.02
Consensus pattern (3 bp):
ACA
Found at i:24616124 original size:12 final size:12
Alignment explanation
Indices: 24616107--24616168 Score: 52
Period size: 12 Copynumber: 5.2 Consensus size: 12
24616097 ACGACGACAA
*
24616107 CAACAAGAACAG
1 CAACAACAACAG
*
24616119 CAACAACAACAA
1 CAACAACAACAG
* * *
24616131 TAACAGCAGCAG
1 CAACAACAACAG
*
24616143 CAACAACAACAA
1 CAACAACAACAG
**
24616155 CAACGTCAACAG
1 CAACAACAACAG
24616167 CA
1 CA
24616169 CTGCTCTGAA
Statistics
Matches: 37, Mismatches: 13, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
12 37 1.00
ACGTcount: A:0.55, C:0.31, G:0.11, T:0.03
Consensus pattern (12 bp):
CAACAACAACAG
Found at i:24616124 original size:18 final size:18
Alignment explanation
Indices: 24616103--24616158 Score: 67
Period size: 18 Copynumber: 3.1 Consensus size: 18
24616093 GACGACGACG
*
24616103 ACAACAACAAGAACAGCA
1 ACAACAACAACAACAGCA
*
24616121 ACAACAACAATAACAGCA
1 ACAACAACAACAACAGCA
* * *
24616139 GCAGCAACAACAACAACA
1 ACAACAACAACAACAGCA
24616157 AC
1 AC
24616159 GTCAACAGCA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.59, C:0.30, G:0.09, T:0.02
Consensus pattern (18 bp):
ACAACAACAACAACAGCA
Found at i:24619388 original size:11 final size:11
Alignment explanation
Indices: 24619372--24619400 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
24619362 GAAATGCATG
24619372 TCTTTTTCTTT
1 TCTTTTTCTTT
24619383 TCTTTTTCTTT
1 TCTTTTTCTTT
24619394 T-TTTTTC
1 TCTTTTTC
24619401 GGGATAGAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 6 0.33
11 12 0.67
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (11 bp):
TCTTTTTCTTT
Found at i:24621441 original size:38 final size:37
Alignment explanation
Indices: 24621369--24621447 Score: 97
Period size: 38 Copynumber: 2.1 Consensus size: 37
24621359 TTTAAATAAG
24621369 TTTTTAAATTATATTAAAAAAATTAATTTGATTTTTAT
1 TTTTTAAATTATATTAAAAAAA-TAATTTGATTTTTAT
* **
24621407 TTTTTAAATTATATTTAAATAAA-GCTTTGAATTTTTAT
1 TTTTTAAATTATA-TTAAAAAAATAATTTG-ATTTTTAT
24621445 TTT
1 TTT
24621448 AAGACAAATA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
37 4 0.11
38 24 0.67
39 8 0.22
ACGTcount: A:0.38, C:0.01, G:0.04, T:0.57
Consensus pattern (37 bp):
TTTTTAAATTATATTAAAAAAATAATTTGATTTTTAT
Found at i:24621948 original size:19 final size:19
Alignment explanation
Indices: 24621924--24621977 Score: 67
Period size: 19 Copynumber: 2.9 Consensus size: 19
24621914 AAATATAAAT
*
24621924 TTAATATATTTATTTTTTA
1 TTAATATATTTATTTTATA
*
24621943 TTAATATAATT-TTTTATA
1 TTAATATATTTATTTTATA
24621961 TT-ATATATTTTATTTTA
1 TTAATATA-TTTATTTTA
24621978 ATTCCTATGA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
17 5 0.17
18 10 0.33
19 15 0.50
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (19 bp):
TTAATATATTTATTTTATA
Found at i:24621951 original size:30 final size:30
Alignment explanation
Indices: 24621915--24621974 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
24621905 TATGAATTAA
*
24621915 AATATAAATTTAATATATT-TATTTTTTATT
1 AATAT-AATTTAATATATTATATATTTTATT
**
24621945 AATATAATTTTTTATATTATATATTTTATT
1 AATATAATTTAATATATTATATATTTTATT
24621975 TTAATTCCTA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
29 11 0.42
30 15 0.58
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (30 bp):
AATATAATTTAATATATTATATATTTTATT
Found at i:24621965 original size:15 final size:17
Alignment explanation
Indices: 24621924--24621971 Score: 55
Period size: 16 Copynumber: 2.8 Consensus size: 17
24621914 AAATATAAAT
24621924 TTAATATATTTATTTTTTA
1 TTAATATA--TATTTTTTA
24621943 TTAATATA-ATTTTTTA
1 TTAATATATATTTTTTA
*
24621959 -TATTATATATTTT
1 TTAATATATATTTT
24621972 ATTTTAATTC
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
15 6 0.22
16 13 0.48
19 8 0.30
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (17 bp):
TTAATATATATTTTTTA
Found at i:24622097 original size:31 final size:30
Alignment explanation
Indices: 24622053--24622133 Score: 92
Period size: 31 Copynumber: 2.7 Consensus size: 30
24622043 TNTCTTGTAA
**
24622053 ATATAT-TTATTTTTATTTTTTGTTATAATT
1 ATATATATTATTTTT-TTTTTTAATATAATT
24622083 ATATATATTATTTTTGTTTTTTAATATAATT
1 ATATATATTATTTTT-TTTTTTAATATAATT
* * *
24622114 TTTTATATTATATTTTTTTT
1 ATATATATTATTTTTTTTTT
24622134 CTTTTAAAGA
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
30 11 0.25
31 33 0.75
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.70
Consensus pattern (30 bp):
ATATATATTATTTTTTTTTTTAATATAATT
Found at i:24625439 original size:3 final size:3
Alignment explanation
Indices: 24625431--24625489 Score: 52
Period size: 3 Copynumber: 20.7 Consensus size: 3
24625421 CGTATATACC
* * * * *
24625431 CAT CAT CAT CAT CAT C-T CAC CAA C-C CAT CAT CAT CAT CAC CAG C-T
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT
24625476 CAT CAT CAT CAT CA
1 CAT CAT CAT CAT CA
24625490 CCAGCTCATG
Statistics
Matches: 46, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
2 4 0.09
3 42 0.91
ACGTcount: A:0.32, C:0.41, G:0.02, T:0.25
Consensus pattern (3 bp):
CAT
Found at i:24625493 original size:20 final size:20
Alignment explanation
Indices: 24625436--24625498 Score: 101
Period size: 20 Copynumber: 3.2 Consensus size: 20
24625426 ATACCCATCA
*
24625436 TCATCATCATC-TCACCAAC
1 TCATCATCATCATCACCAGC
*
24625455 CCATCATCATCATCACCAGC
1 TCATCATCATCATCACCAGC
24625475 TCATCATCATCATCACCAGC
1 TCATCATCATCATCACCAGC
24625495 TCAT
1 TCAT
24625499 GCGCACTCCC
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
19 10 0.25
20 30 0.75
ACGTcount: A:0.30, C:0.41, G:0.03, T:0.25
Consensus pattern (20 bp):
TCATCATCATCATCACCAGC
Found at i:24625545 original size:43 final size:44
Alignment explanation
Indices: 24625484--24625606 Score: 146
Period size: 43 Copynumber: 2.9 Consensus size: 44
24625474 CTCATCATCA
* ** *
24625484 TCATCACC-AGCTCATGCGCACTCCCTACTCGCACATGGCTGGG
1 TCATCACCGAGCTTATGCGCACTCCCTACTCGCACATAACCGGG
*
24625527 TCATCACCGAG-TTATGCGCACTCCCTACTCTCACATAACCGGG
1 TCATCACCGAGCTTATGCGCACTCCCTACTCGCACATAACCGGG
* *
24625570 TCATC-CTCG-GCTTATGCGCACTCCGTACTTGCACATA
1 TCATCAC-CGAGCTTATGCGCACTCCCTACTCGCACATA
24625607 GCCCAGTCAA
Statistics
Matches: 69, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
42 2 0.03
43 65 0.94
44 2 0.03
ACGTcount: A:0.20, C:0.37, G:0.18, T:0.24
Consensus pattern (44 bp):
TCATCACCGAGCTTATGCGCACTCCCTACTCGCACATAACCGGG
Found at i:24626781 original size:173 final size:172
Alignment explanation
Indices: 24626491--24626836 Score: 683
Period size: 173 Copynumber: 2.0 Consensus size: 172
24626481 CAATATTCAA
24626491 CCATGAAAATAAGAACAAAAGCATGGGTAAGCTAGGTATCAAGGAGAATTAAAGAAATTTTAACT
1 CCATGAAAATAAGAACAAAAGCATGGGTAAGCTAGGTATCAAGGAGAATTAAAGAAATTTTAACT
24626556 TACCTAGCTTGTTTCCTTGATTTCTTCACTTTTTCTTTGAATTTCCACCTAGGTTTTCTTGTTTT
66 TACCTAGCTTGTTTCCTTGATTTCTTCACTTTTTCTTTGAATTTCCACCTAGGTTTTCTTGTTTT
24626621 TCCCTTTGTTCTTCCTTTTCTCTTGTTGCTGGTTGTCTAGGC
131 TCCCTTTGTTCTTCCTTTTCTCTTGTTGCTGGTTGTCTAGGC
24626663 CNCATGAAAATAAGAACAAAAGCATGGGTAAGCTAGGTATCAAGGAGAATTAAAGAAATTTTAAC
1 C-CATGAAAATAAGAACAAAAGCATGGGTAAGCTAGGTATCAAGGAGAATTAAAGAAATTTTAAC
24626728 TTACCTAGCTTGTTTCCTTGATTTCTTCACTTTTTCTTTGAATTTCCACCTAGGTTTTCTTGTTT
65 TTACCTAGCTTGTTTCCTTGATTTCTTCACTTTTTCTTTGAATTTCCACCTAGGTTTTCTTGTTT
24626793 TTCCCTTTGTTCTTCCTTTTCTCTTGTTGCTGGTTGTCTAGGC
130 TTCCCTTTGTTCTTCCTTTTCTCTTGTTGCTGGTTGTCTAGGC
24626836 C
1 C
24626837 GAATATGGTG
Statistics
Matches: 173, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
172 1 0.01
173 172 0.99
ACGTcount: A:0.23, C:0.19, G:0.16, T:0.42
Consensus pattern (172 bp):
CCATGAAAATAAGAACAAAAGCATGGGTAAGCTAGGTATCAAGGAGAATTAAAGAAATTTTAACT
TACCTAGCTTGTTTCCTTGATTTCTTCACTTTTTCTTTGAATTTCCACCTAGGTTTTCTTGTTTT
TCCCTTTGTTCTTCCTTTTCTCTTGTTGCTGGTTGTCTAGGC
Found at i:24634075 original size:8 final size:8
Alignment explanation
Indices: 24634045--24634083 Score: 51
Period size: 8 Copynumber: 4.9 Consensus size: 8
24634035 TTACTATATG
*
24634045 TATATATA
1 TATATACA
*
24634053 TATATATA
1 TATATACA
24634061 TATATACA
1 TATATACA
*
24634069 TATATACG
1 TATATACA
24634077 TATATAC
1 TATATAC
24634084 CCATCATCAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
8 29 1.00
ACGTcount: A:0.46, C:0.08, G:0.03, T:0.44
Consensus pattern (8 bp):
TATATACA
Found at i:24634082 original size:2 final size:2
Alignment explanation
Indices: 24634039--24634074 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
24634029 CACACATTAC
* *
24634039 TA TA TG TA TA TA TA TA TA TA TA TA TA TA CA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
24634075 CGTATATACC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (2 bp):
TA
Found at i:24640852 original size:19 final size:19
Alignment explanation
Indices: 24640828--24640865 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
24640818 ACTTCTAAAC
24640828 CTCAAATCATACTCAAATA
1 CTCAAATCATACTCAAATA
*
24640847 CTCAAATCATACTCCAATA
1 CTCAAATCATACTCAAATA
24640866 AGTTAAATGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.45, C:0.29, G:0.00, T:0.26
Consensus pattern (19 bp):
CTCAAATCATACTCAAATA
Found at i:24642279 original size:251 final size:251
Alignment explanation
Indices: 24641687--24644671 Score: 2693
Period size: 251 Copynumber: 12.0 Consensus size: 251
24641677 TACATGTAAC
* * * *
24641687 TATAATTATTTTT-TTCTTATTATTTTTTATTTTACAATTAAAATTTATATATCGTTAAATACTT
1 TATAATTATTTTTATCCTTATTATTCTTTATTTTAAAATTAAAATTTGTATATCGTTAAATACTT
* ** * *
24641751 TTAGTCTAAGAATATAAATTTAAATGTTTGTTTTTCCATTAAAATT-AATTTTTTTACTTAATTG
66 TTAGCCCGAGAATATAAATTTAAATATTTGATTTT-CATTAAAATTAAATTTTTTTACTTAATTG
* * * * * * * *
24641815 ACTTGTTACGATAACTCTCACATATTTACATTAGGATTTT-AACTTGCTTGTTCTACTTTTATAT
130 ACTTATTACGTTAACTCTCACACATTTACGTTAAGATTTTAAATTTGCTTGTTCCACTTTTATAA
* * * *
24641879 GTTTTTACGTCAATTCTTACAATTTTACGTCAAGA-TTTTACAATGATAACTCTTAAC
195 GTTTTTACGTCAATTCTTACAACTTTACGTCAAGACTTTT-CAATGGTAACTTTTAAT
* * *
24641936 TATATTTATTTTT-TTCTTATTATTCTTTATTTTAAAATTAAAATTTATATATCGTTAAATACTT
1 TATAATTATTTTTATCCTTATTATTCTTTATTTTAAAATTAAAATTTGTATATCGTTAAATACTT
** * *
24642000 TTAATCCGAGAATATTAATTTAAATATTTGATTTTCATTAAAATTAAAATTTTTTTATTTAATTG
66 TTAGCCCGAGAATATAAATTTAAATATTTGATTTTCATTAAAATT-AAATTTTTTTACTTAATTG
* * * ** * *
24642065 ACTTATCACGTTAACTCTGACAAATTTATATTAAGATTTTAAATTTGCTTGTTTCACTTTTATGA
130 ACTTATTACGTTAACTCTCACACATTTACGTTAAGATTTTAAATTTGCTTGTTCCACTTTTATAA
* * * * *
24642130 GTTTTTACCTCAACTCTTACAATTTTATGTCAAGACTTTTTAATGGTAACTTTTAAT
195 GTTTTTACGTCAATTCTTACAACTTTACGTCAAGACTTTTCAATGGTAACTTTTAAT
* *
24642187 TATAATTATTTTTATCCTTATTATTTTTTATTTTAAAATTAAAATTTGCATATCGTTAAATA-TT
1 TATAATTATTTTTATCCTTATTATTCTTTATTTTAAAATTAAAATTTGTATATCGTTAAATACTT
*** * * *
24642251 TTGAGTTTGAGAATATAAATTT-AATATTT-ATTTTTAATTAAAATTAGATTTTTTTACATAATT
66 TT-AGCCCGAGAATATAAATTTAAATATTTGA-TTTTCATTAAAATTAAATTTTTTTACTTAATT
* * * * *
24642314 TACTTATTATGTTAACTTTCACACATTTACGTTAAGATTTTAAATTTACTTGTTCCACCTTTATA
129 GACTTATTACGTTAACTCTCACACATTTACGTTAAGATTTTAAATTTGCTTGTTCCACTTTTATA
* * * * ** * * * * *
24642379 AGCTTTT-CGTTAATTTTTATAGTTTTACGTCAAGGCTTTTTAAAGGTAACTTGTAAC
194 AGTTTTTACGTCAATTCTTACAACTTTACGTCAAGACTTTTCAATGGTAACTTTTAAT
*
24642436 TATAATTATTTTTATCCTTATTATT-TTT-TATT----TTAAAA----T-TATCGTTAAATACTT
1 TATAATTATTTTTATCCTTATTATTCTTTATTTTAAAATTAAAATTTGTATATCGTTAAATACTT
* * * * * * * *
24642490 CTAGCCAGATAATAT-AATTTAAATGTTAGTTTTTTATTAAAATTAGATTTTTTTAC----TT-A
66 TTAGCCCGAGAATATAAATTTAAATATTTGATTTTCATTAAAATTAAATTTTTTTACTTAATTGA
* *
24642549 C-----A--TTAACTCTCACACATTTACGTTAAGATTTTAAATTTGTTTGTTCCACCTTTATAAG
131 CTTATTACGTTAACTCTCACACATTTACGTTAAGATTTTAAATTTGCTTGTTCCACTTTTATAAG
* * * **
24642607 -TTTTATGTCAATTCTTATAGCTTTACGTCAAGACTTTTCAATAATAACTTTTAAT
196 TTTTTACGTCAATTCTTACAACTTTACGTCAAGACTTTTCAATGGTAACTTTTAAT
* * * * * *
24642662 TATAACTATTGTTATCCTAAATATTCTTTATTTTAAAATTAAAATTTGTATA-CGTTAGATATTT
1 TATAATTATTTTTATCCTTATTATTCTTTATTTTAAAATTAAAATTTGTATATCGTTAAATACTT
**** * * * *
24642726 TTAATTTGAGAATAAAAATTTAAATGTTT-ATTTTTCATTAAAATTAGATTTTTTTACTTAATTA
66 TTAGCCCGAGAATATAAATTTAAATATTTGA-TTTTCATTAAAATTAAATTTTTTTACTTAATTG
* * ** * * *
24642790 ACTTATTAAGTCAACTCTCACACATTTATATTAAAATTTTAAATTTGCTTGTTCTATTTTTATAA
130 ACTTATTACGTTAACTCTCACACATTTACGTTAAGATTTTAAATTTGCTTGTTCCACTTTTATAA
** * * * * *
24642855 GTTTTTATATCAATTCTTACAGCTTTATGTCAAGTCTTTTCAATGGTTA-TTTGTAGCT
195 GTTTTTACGTCAATTCTTACAACTTTACGTCAAGACTTTTCAATGGTAACTTT-TA-AT
* * * * *
24642913 T-TAATTATTTTTATTCTTATTGTTCTTTATTTTAAAATTAAAATTTTTATACCGTTAAATATTT
1 TATAATTATTTTTATCCTTATTATTCTTTATTTTAAAATTAAAATTTGTATATCGTTAAATACTT
* * * *
24642977 TTTGCTCGAGAATATAAATTTAAATGTTT-ATTTTTCATTAAAATTAGATTTTTTGTACTTAATT
66 TTAGCCCGAGAATATAAATTTAAATATTTGA-TTTTCATTAAAATTAAATTTTTT-TACTTAATT
* * * * * * *
24643041 GACTTATTATGTTGACTCTTATACAATTACGTTAAGATTTTAAATTTACTTGTTTCACTTTTAT-
129 GACTTATTACGTTAACTCTCACACATTTACGTTAAGATTTTAAATTTGCTTGTTCCACTTTTATA
* *
24643105 A------A-G-------TT-----TTTACGTCAAGACTTTTCAATGGTAACTTCTAAC
194 AGTTTTTACGTCAATTCTTACAACTTTACGTCAAGACTTTTCAATGGTAACTTTTAAT
* * * *
24643144 TATAATTATTTTTATCTTTATTATTTTTTATTTTAAAATTAGAATTTGTATATAGTTAAATACTT
1 TATAATTATTTTTATCCTTATTATTCTTTATTTTAAAATTAAAATTTGTATATCGTTAAATACTT
* * * * * * * *
24643209 TTAGCTCGAGAATATAAATTTAAATTTTTGCTTTTCATTAAAATGAGAAATTTGTGACTGAATTG
66 TTAGCCCGAGAATATAAATTTAAATATTTGATTTTCATTAAAATTA-AATTTTTTTACTTAATTG
* * * *
24643274 ACTTGTTACGTTAACTCTCATATATTTACGTTAAGATTTTAAATTTTCTTGTTCCACTTTTATAA
130 ACTTATTACGTTAACTCTCACACATTTACGTTAAGATTTTAAATTTGCTTGTTCCACTTTTAT-A
* *
24643339 AG-TTTTACGTCAACTT-TTACAACTTTACATCAAGGCTTTTCAATGGTAACTTTTAAT
194 AGTTTTTACGTCAA-TTCTTACAACTTTACGTCAAGACTTTTCAATGGTAACTTTTAAT
* *
24643396 TATAATTATTTTTATCCTTATTATTCTTTATTTTGAAA-TAAAGATTTGTATATCATTAAATACT
1 TATAATTATTTTTATCCTTATTATTCTTTATTTTAAAATTAAA-ATTTGTATATCGTTAAATACT
** * * * * *
24643460 TTTAGCCAAAGAAAATAAATTTAATTATTT-ATTTTTCATTGAAATTAGATTTTTTTACGTAATT
65 TTTAGCCCGAGAATATAAATTTAAATATTTGA-TTTTCATTAAAATTAAATTTTTTTACTTAATT
* * * * * * *
24643524 GATTTGTTACGTTAATTCTCACATATTTACGTTAGGATGTTAAATTTGCTTGTTTCA-TCTTTAT
129 GACTTATTACGTTAACTCTCACACATTTACGTTAAGATTTTAAATTTGCTTGTTCCACT-TTTAT
* * * * * * *
24643588 ATGTTTTTATGTCAATTCTTAC-AGTTTCACATCAAGGCTTTTCAATGATAACTTTTAAC
193 AAGTTTTTACGTCAATTCTTACAACTTT-ACGTCAAGACTTTTCAATGGTAACTTTTAAT
* * *
24643647 TACAATTATCTTTATCCTTATTATTCTTTATTCTAAAATTAAAATTTGTATATCGTTAAATACTT
1 TATAATTATTTTTATCCTTATTATTCTTTATTTTAAAATTAAAATTTGTATATCGTTAAATACTT
*
24643712 TTAGCCCAAGAATATAAATTTAAATATTT-ATTTTTCATTAAAATTATAATTTTTTTAACTTAAT
66 TTAGCCCGAGAATATAAATTTAAATATTTGA-TTTTCATTAAAATTA-AATTTTTTT-ACTTAAT
* * ** * * *
24643776 TAACTTTTTATATTAACTTTCACACATTTACGTTAGGATTTTAAATTTACTTGTTCCA-TCTTTA
128 TGACTTATTACGTTAACTCTCACACATTTACGTTAAGATTTTAAATTTGCTTGTTCCACT-TTTA
*
24643840 TAAGTTTTTACGTCAATTCTTATAATTTTTTACGTCAATTCTTATAACTTTATGTCAAGGCTTTT
192 TAAGTTTTTACGTCAATTC----------TTA---CAA--CTT-T-AC-----GTCAAGACTTTT
*** *
24643905 CAATTACAACTTTTAAC
235 CAATGGTAACTTTTAAT
* * * * * *
24643922 TAGAATTA-TTTTATTCTTGTTATTTTTTA-TTTAAAATTAAAATTTATATATCATTAAATACTT
1 TATAATTATTTTTATCCTTATTATTCTTTATTTTAAAATTAAAATTTGTATATCGTTAAATACTT
** * *
24643985 TTAATCCGAGAATATAAATTTAAATGTTTGTTTTTCATTAAAATTAGAATTTTTGTTACTTAATT
66 TTAGCCCGAGAATATAAATTTAAATATTTGATTTTCATTAAAATTA-AATTTTT-TTACTTAATT
* * * **
24644050 GACTTATTACGTTAACTTTCACACATTTATGTTAAAATTTTAAACTTT-CTTGTTCCACCGTTAT
129 GACTTATTACGTTAACTCTCACACATTTACGTTAAGATTTTAAA-TTTGCTTGTTCCACTTTTAT
* * * * * *
24644114 AAGTTTTT-CATGCTAATTCTTACAAGTTTACGTCCAGACTTTTCAATAGTAACTTGTAAC
193 AAGTTTTTACGT-C-AATTCTTACAACTTTACGTCAAGACTTTTCAATGGTAACTTTTAAT
* *
24644174 TATAATTATTTTTATCCTTATTATTTTTTATTTTAAAATTAAAATTTGTATATTGTTAAATACTT
1 TATAATTATTTTTATCCTTATTATTCTTTATTTTAAAATTAAAATTTGTATATCGTTAAATACTT
** * * * * * *
24644239 TTAGTTCGAGAATATAAATTTAAATGTTTGCTTTGCATTAAAATTATAATTTTGTGACATAATTG
66 TTAGCCCGAGAATATAAATTTAAATATTTGATTTTCATTAAAATTA-AATTTTTTTACTTAATTG
* * * * * * *
24644304 AGTTGTTACGTTAACTCTCATACGTTTATGTTAAGATTTTAAATTTTCTTGTTCTACTTTTATAA
130 ACTTATTACGTTAACTCTCACACATTTACGTTAAGATTTTAAATTTGCTTGTTCCACTTTTATAA
** * * * * * * *
24644369 GTTTTTATATAAACTCTTACAGCTTTACATTAATG-TTTTTCAATGGTAACTCTTAAT
195 GTTTTTACGTCAATTCTTACAACTTTACGTCAA-GACTTTTCAATGGTAACTTTTAAT
* * * * **
24644426 TATAATTATTTATATCCTTATTATTCTTTATCTTAAAATTAAAA-TTATATATAGTTAAATGTTT
1 TATAATTATTTTTATCCTTATTATTCTTTATTTTAAAATTAAAATTTGTATATCGTTAAATACTT
* * * *
24644490 TTAGCCCAAGAATATAAATTGAAATATTT--TTTT-ATTAAAATTAAAATTTTTTATTTAATTGA
66 TTAGCCCGAGAATATAAATTTAAATATTTGATTTTCATTAAAATTAAATTTTTTTACTTAATTGA
* * * * * * * * * *
24644552 TTTGTTACATTAACTCTTACATATTTACGTTAATATTTTAAATTTACTTGTTCCACCTTTAAAAA
131 CTTATTACGTTAACTCTCACACATTTACGTTAAGATTTTAAATTTGCTTGTTCCACTTTTATAAG
* * * * *
24644617 TTTTTATGTTAATTTTTACAACTTTACATCAAGGCTTTTCAATGGTAACTTTTAA
196 TTTTTACGTCAATTCTTACAACTTTACGTCAAGACTTTTCAATGGTAACTTTTAA
24644672 CAACTTTAAA
Statistics
Matches: 2272, Mismatches: 356, Indels: 218
0.80 0.13 0.08
Matches are distributed among these distances:
225 4 0.00
226 113 0.05
227 3 0.00
228 4 0.00
231 1 0.00
232 189 0.08
233 9 0.00
234 3 0.00
236 19 0.01
237 46 0.02
238 51 0.02
239 4 0.00
240 1 0.00
241 2 0.00
242 2 0.00
243 6 0.00
245 1 0.00
246 1 0.00
247 117 0.05
248 23 0.01
249 208 0.09
250 219 0.10
251 412 0.18
252 362 0.16
253 163 0.07
254 81 0.04
257 2 0.00
258 1 0.00
259 2 0.00
261 3 0.00
263 3 0.00
264 3 0.00
266 1 0.00
267 1 0.00
269 2 0.00
270 3 0.00
272 2 0.00
273 145 0.06
274 27 0.01
275 33 0.01
ACGTcount: A:0.32, C:0.11, G:0.08, T:0.50
Consensus pattern (251 bp):
TATAATTATTTTTATCCTTATTATTCTTTATTTTAAAATTAAAATTTGTATATCGTTAAATACTT
TTAGCCCGAGAATATAAATTTAAATATTTGATTTTCATTAAAATTAAATTTTTTTACTTAATTGA
CTTATTACGTTAACTCTCACACATTTACGTTAAGATTTTAAATTTGCTTGTTCCACTTTTATAAG
TTTTTACGTCAATTCTTACAACTTTACGTCAAGACTTTTCAATGGTAACTTTTAAT
Found at i:24643863 original size:22 final size:22
Alignment explanation
Indices: 24643837--24643886 Score: 91
Period size: 22 Copynumber: 2.3 Consensus size: 22
24643827 TGTTCCATCT
24643837 TTATAAGTTTTTACGTCAATTC
1 TTATAAGTTTTTACGTCAATTC
*
24643859 TTATAATTTTTTACGTCAATTC
1 TTATAAGTTTTTACGTCAATTC
24643881 TTATAA
1 TTATAA
24643887 CTTTATGTCA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.30, C:0.12, G:0.06, T:0.52
Consensus pattern (22 bp):
TTATAAGTTTTTACGTCAATTC
Found at i:24643896 original size:20 final size:21
Alignment explanation
Indices: 24643837--24643897 Score: 70
Period size: 22 Copynumber: 2.9 Consensus size: 21
24643827 TGTTCCATCT
*
24643837 TTATAAGTTTTTACGTCAATTC
1 TTATAA-TCTTTACGTCAATTC
*
24643859 TTATAATTTTTTACGTCAATTC
1 TTATAA-TCTTTACGTCAATTC
*
24643881 TTATAA-CTTTATGTCAA
1 TTATAATCTTTACGTCAA
24643898 GGCTTTTCAA
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
20 9 0.25
22 27 0.75
ACGTcount: A:0.30, C:0.13, G:0.07, T:0.51
Consensus pattern (21 bp):
TTATAATCTTTACGTCAATTC
Found at i:24644593 original size:247 final size:244
Alignment explanation
Indices: 24643916--24644668 Score: 809
Period size: 247 Copynumber: 3.0 Consensus size: 244
24643906 AATTACAACT
* * *
24643916 TTTAACTAGAATTATTTTATTCTTGTTATTTTTTATTTAAAATTAAAATTTATATATCA-TTAAA
1 TTTAACTATAATTATTTTATCCTTATTATTTTTTATTTAAAATTAAAATTTATATAT-AGTTAAA
* * *
24643980 TACTTTTAATCCGAGAATATAAATTTAAATGTTTGTTTTTCATTAAAATTAGAATTTTTGTTACT
65 TACTTTTAGTCCGAGAATATAAATTTAAAT-ATT-TTTTT-ATTAAAATTA-AAATTTTGTTACT
* * *
24644045 TAATTGACTTATTACGTTAACT-TTCACACATTTATGTTAAAATTTTAAACTTTCTTGTTCCACC
126 TAATTGACTTGTTACGTTAACTCTT-ACATATTTATGTTAAAATTTTAAATTTTCTTGTTCCACC
* * * * *
24644109 GTTATAAGTTTTTCATGCTAATTCTTACAAG-TTTACGTCCAGACTTTTCAATAGTAAC
190 TTTATAAGTTTTT-AT-ATAATTCTTAC-AGCTTTACATCAAG-CTTTTCAATGGTAAC
* *
24644167 TTGTAACTATAATTATTTTTATCCTTATTATTTTTTATTTTAAAATTAAAATTTGTATATTGTTA
1 TT-TAACTATAATTA-TTTTATCCTTATTATTTTTTA-TTTAAAATTAAAATTTATATATAGTTA
* * * * *
24644232 AATACTTTTAGTTCGAGAATATAAATTTAAATGTTTGCTTTGCATTAAAATTATAATTTTGTGAC
63 AATACTTTTAGTCCGAGAATATAAATTTAAATATTT--TTT-TATTAAAATTAAAATTTTGTTAC
* * * *
24644297 ATAATTGAGTTGTTACGTTAACTC-T-CATACGTTTATGTTAAGATTTTAAATTTTCTTGTTCTA
125 TTAATTGACTTGTTACGTTAACTCTTACATA--TTTATGTTAAAATTTTAAATTTTCTTGTTCCA
* * * *
24644360 CTTTTATAAGTTTTTATATAAACTCTTACAGCTTTACATTAATGTTTTTCAATGGTAAC
188 CCTTTATAAGTTTTTATAT-AATTCTTACAGCTTTACATCAA-GCTTTTCAATGGTAAC
* *
24644419 TCTTAATTATAATTATTTATATCCTTATTATTCTTTATCTTAAAATTAAAA-TTATATATAGTTA
1 T-TTAACTATAATTATTT-TATCCTTATTATTTTTTAT-TTAAAATTAAAATTTATATATAGTTA
** * * * *
24644483 AATGTTTTTAGCCCAAGAATATAAATTGAAATATTTTTTTATTAAAATTAAAATTTT-TTATTTA
63 AATACTTTTAGTCCGAGAATATAAATTTAAATATTTTTTTATTAAAATTAAAATTTTGTTACTTA
* * * * *
24644547 ATTGATTTGTTACATTAACTCTTACATATTTACGTTAATATTTTAAATTTACTTGTTCCACCTTT
128 ATTGACTTGTTACGTTAACTCTTACATATTTATGTTAAAATTTTAAATTTTCTTGTTCCACCTTT
* * * * *
24644612 AAAAATTTTTATGTTAATTTTTACAACTTTACATCAAGGCTTTTCAATGGTAAC
193 ATAAGTTTTTAT-ATAATTCTTACAGCTTTACATCAA-GCTTTTCAATGGTAAC
24644666 TTT
1 TTT
24644669 TAACAACTTT
Statistics
Matches: 423, Mismatches: 60, Indels: 43
0.80 0.11 0.08
Matches are distributed among these distances:
246 2 0.00
247 99 0.23
248 18 0.04
249 7 0.02
251 52 0.12
252 83 0.20
253 95 0.22
254 67 0.16
ACGTcount: A:0.33, C:0.10, G:0.08, T:0.49
Consensus pattern (244 bp):
TTTAACTATAATTATTTTATCCTTATTATTTTTTATTTAAAATTAAAATTTATATATAGTTAAAT
ACTTTTAGTCCGAGAATATAAATTTAAATATTTTTTTATTAAAATTAAAATTTTGTTACTTAATT
GACTTGTTACGTTAACTCTTACATATTTATGTTAAAATTTTAAATTTTCTTGTTCCACCTTTATA
AGTTTTTATATAATTCTTACAGCTTTACATCAAGCTTTTCAATGGTAAC
Found at i:24644668 original size:778 final size:777
Alignment explanation
Indices: 24643110--24644648 Score: 1918
Period size: 778 Copynumber: 2.0 Consensus size: 777
24643100 TTTATAAGTT
** *
24643110 TTTACGTCAAGACTTTTCAATGGTAACTTCTAACTATAATTATTTTTATCTTTATTATTTTTTAT
1 TTTACGTCAAGACTTTTCAATGACAACTTCTAACTAGAATTATTTTTATCTTTATTATTTTTTAT
* * *
24643175 TTTAAAATTAGAATTTGTATATAGTTAAATACTTTTAGCTCGAGAATATAAATTTAAATTTTTGC
66 TTTAAAATTAAAATTTATATATAGTTAAATACTTTTAGCTCGAGAATATAAATTTAAATGTTTGC
* * *
24643240 TTTTCATTAAAATGAGAAATTTGTGACTGAATTGACTTGTTACGTTAACTCTCATATATTTACGT
131 TTTTCATTAAAATGAGAAATTTGTGACTGAATTGACTTATTACGTTAACTCTCACACATTTACGT
* * ** *
24643305 TAAGATTTTAAATTTTCTTGTTCCACTTTTATAAAGTTTTACGTCAACTTTTACAACTTTACATC
196 TAAAATTTTAAACTTTCTTGTTCCACCGTTATAAAGTTTTACATCAACTTTTACAACTTTACATC
* * * * *
24643370 AAGGCTTTTCAATGGTAACTTTTAATTATAATTATTTTTATCCTTATTATTCTTTATTTTGAAAT
261 AAGACTTTTCAATAGTAACTTGTAACTATAATTATTTTTATCCTTATTATTCTTTATTTTAAAAT
* * *
24643435 AAAGATTTGTATATCATTAAATACTTTTAGCCAAAGAAAATAAATTTAATTATTTATTTTTCATT
326 AAAGATTTGTATATCATTAAATACTTTTAGCCAAAGAAAATAAATTTAAATATTTACTTTGCATT
* * * * * * * * *
24643500 GAAATTAGATTTTTTTACGTAATTGATTTGTTACGTTAATTCTCACATATTTACGTTAGGATGTT
391 AAAATTAAATTTTGTGACATAATTGAGTTGTTACGTTAACTCTCACACATTTACGTTAAGATGTT
* * * *
24643565 AAATTTGCTTGTTTCATCTTTATATGTTTTTATGTCAATTCTTACAGTTTCACATCAAGGCTTTT
456 AAATTTGCTTGTTTCATCTTTATAAGTTTTTATATAAACTCTTACAGTTTCACATCAAGGCTTTT
* *
24643630 CAATGATAACTTTTAACTACAATTATCTTTATCCTTATTATTCTTTATTCTAAAATTAAAATTTG
521 CAATGATAACTCTTAACTACAATTATCTTTATCCTTATTATTCTTTATTCTAAAATTAAAATTTA
* *
24643695 TATATCGTTAAATACTTTTAGCCCAAGAATATAAATTTAAATATTTATTTTTCATTAAAATTATA
586 TATATAGTTAAATACTTTTAGCCCAAGAATATAAATTGAAATATTTATTTTTCATTAAAATTATA
* * *
24643760 ATTTTTTTAACTTAATTAACTTTTTATATTAACTTTCACACATTTACGTTAGGATTTTAAATTTA
651 AATTTTTTAACTTAATTAACTTTTTACATTAACTTTCACACATTTACGTTAAGATTTTAAATTTA
* * * * * *
24643825 CTTGTTCCATCTTTATAAGTTTTTACGTCAATTCTTATAATTTTTTACGTCAATTCTTATAAC
716 CTTGTTCCACCTTTAAAAATTTTTACGTCAATTCTTACAA-TCTTTACATCAATTCTTATAAC
* * * * *
24643888 TTTATGTCAAGGCTTTTCAATTACAACTTTTAACTAGAATTA-TTTTAT-TCTTGTTATTTTTTA
1 TTTACGTCAAGACTTTTCAATGACAACTTCTAACTAGAATTATTTTTATCT-TTATTATTTTTTA
*
24643951 -TTTAAAATTAAAATTTATATATCA-TTAAATACTTTTA-ATCCGAGAATATAAATTTAAATGTT
65 TTTTAAAATTAAAATTTATATAT-AGTTAAATACTTTTAGCT-CGAGAATATAAATTTAAATGTT
* * * * * *
24644013 TGTTTTTCATTAAAATTAGAATTTTTGTTACTTAATTGACTTATTACGTTAACTTTCACACATTT
128 TGCTTTTCATTAAAATGAGAA-ATTTGTGACTGAATTGACTTATTACGTTAACTCTCACACATTT
* * *
24644078 ATGTTAAAATTTTAAACTTTCTTGTTCCACCGTTAT-AAGTTTTTCATGCTAA-TTCTTACAAGT
192 ACGTTAAAATTTTAAACTTTCTTGTTCCACCGTTATAAAGTTTTACAT-C-AACTT-TTACAACT
* * *
24644141 TTACGTCCAGACTTTTCAATAGTAACTTGTAACTATAATTATTTTTATCCTTATTATTTTTTATT
254 TTACATCAAGACTTTTCAATAGTAACTTGTAACTATAATTATTTTTATCCTTATTATTCTTTATT
** * * * * *
24644206 TTAAAATTAAA-ATTTGTATATTGTTAAATACTTTTAGTTC-GAGAATATAAATTTAAATGTTTG
319 TTAAAA-TAAAGATTTGTATATCATTAAATACTTTTAG-CCAAAGAAAATAAATTTAAATATTTA
* * *
24644269 CTTTGCATTAAAATTATAATTTTGTGACATAATTGAGTTGTTACGTTAACTCTCATACGTTTATG
382 CTTTGCATTAAAATTA-AATTTTGTGACATAATTGAGTTGTTACGTTAACTCTCACACATTTACG
* *
24644334 TTAAGATTTTAAATTTTCTTG-TTC-TACTTTTATAAGTTTTTATATAAACTCTTACAGCTTT-A
446 TTAAGATGTTAAATTTGCTTGTTTCAT-C-TTTATAAGTTTTTATATAAACTCTTACAG-TTTCA
* * * * * *
24644396 CATTAATGTTTTTCAATGGTAACTCTTAATTATAATTAT-TTATATCCTTATTATTCTTTA-TCT
508 CATCAAGGCTTTTCAATGATAACTCTTAACTACAATTATCTT-TATCCTTATTATTCTTTATTC-
**
24644459 TAAAATTAAAA-TTATATATAGTTAAATGTTTTTAGCCCAAGAATATAAATTGAAATA-TT-TTT
571 TAAAATTAAAATTTATATATAGTTAAATACTTTTAGCCCAAGAATATAAATTGAAATATTTATTT
* * *
24644521 TT-ATTAAAATTA-AAATTTTTT-ATTTAATTGA-TTTGTTACATTAACTCTT-ACATATTTACG
636 TTCATTAAAATTATAAATTTTTTAACTTAATTAACTTT-TTACATTAACT-TTCACACATTTACG
* * * *
24644581 TTAATATTTTAAATTTACTTGTTCCACCTTTAAAAATTTTTATGTTAATTTTTACAA-CTTTACA
699 TTAAGATTTTAAATTTACTTGTTCCACCTTTAAAAATTTTTACGTCAATTCTTACAATCTTTACA
24644645 TCAA
764 TCAA
24644649 GGCTTTTCAA
Statistics
Matches: 651, Mismatches: 93, Indels: 41
0.83 0.12 0.05
Matches are distributed among these distances:
771 9 0.01
772 3 0.00
773 76 0.12
774 10 0.02
775 11 0.02
776 88 0.14
777 92 0.14
778 211 0.32
779 148 0.23
780 3 0.00
ACGTcount: A:0.32, C:0.11, G:0.08, T:0.49
Consensus pattern (777 bp):
TTTACGTCAAGACTTTTCAATGACAACTTCTAACTAGAATTATTTTTATCTTTATTATTTTTTAT
TTTAAAATTAAAATTTATATATAGTTAAATACTTTTAGCTCGAGAATATAAATTTAAATGTTTGC
TTTTCATTAAAATGAGAAATTTGTGACTGAATTGACTTATTACGTTAACTCTCACACATTTACGT
TAAAATTTTAAACTTTCTTGTTCCACCGTTATAAAGTTTTACATCAACTTTTACAACTTTACATC
AAGACTTTTCAATAGTAACTTGTAACTATAATTATTTTTATCCTTATTATTCTTTATTTTAAAAT
AAAGATTTGTATATCATTAAATACTTTTAGCCAAAGAAAATAAATTTAAATATTTACTTTGCATT
AAAATTAAATTTTGTGACATAATTGAGTTGTTACGTTAACTCTCACACATTTACGTTAAGATGTT
AAATTTGCTTGTTTCATCTTTATAAGTTTTTATATAAACTCTTACAGTTTCACATCAAGGCTTTT
CAATGATAACTCTTAACTACAATTATCTTTATCCTTATTATTCTTTATTCTAAAATTAAAATTTA
TATATAGTTAAATACTTTTAGCCCAAGAATATAAATTGAAATATTTATTTTTCATTAAAATTATA
AATTTTTTAACTTAATTAACTTTTTACATTAACTTTCACACATTTACGTTAAGATTTTAAATTTA
CTTGTTCCACCTTTAAAAATTTTTACGTCAATTCTTACAATCTTTACATCAATTCTTATAAC
Found at i:24645692 original size:26 final size:26
Alignment explanation
Indices: 24645625--24645695 Score: 90
Period size: 25 Copynumber: 2.8 Consensus size: 26
24645615 GGAGTACTAT
*
24645625 TCTTGGTGCTCCCCAAGAAGCATCGA
1 TCTTGGTGCTCCCCAAGGAGCATCGA
* ** *
24645651 T-GTGGTGCTCTTCAAGGAGCATCGG
1 TCTTGGTGCTCCCCAAGGAGCATCGA
24645676 TCTTGGTGCTCCCCAAGGAG
1 TCTTGGTGCTCCCCAAGGAG
24645696 TACTAAGGAG
Statistics
Matches: 36, Mismatches: 8, Indels: 2
0.78 0.17 0.04
Matches are distributed among these distances:
25 20 0.56
26 16 0.44
ACGTcount: A:0.18, C:0.27, G:0.30, T:0.25
Consensus pattern (26 bp):
TCTTGGTGCTCCCCAAGGAGCATCGA
Found at i:24653031 original size:22 final size:22
Alignment explanation
Indices: 24652994--24653077 Score: 69
Period size: 22 Copynumber: 3.8 Consensus size: 22
24652984 GCAAATTAAT
* * *
24652994 TAGTTATTAAGCATTGCGTTAC
1 TAGTTCTTAGGCATTGCGTCAC
* *
24653016 TAGTTCTTAGGTATTGTGTCAC
1 TAGTTCTTAGGCATTGCGTCAC
* * **
24653038 TAGTTTTTAGGCATTGTGAGAC
1 TAGTTCTTAGGCATTGCGTCAC
* *
24653060 TGGTTTTTAGGCATTGCG
1 TAGTTCTTAGGCATTGCG
24653078 AAATTGGCTT
Statistics
Matches: 51, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 51 1.00
ACGTcount: A:0.20, C:0.12, G:0.25, T:0.43
Consensus pattern (22 bp):
TAGTTCTTAGGCATTGCGTCAC
Found at i:24653089 original size:22 final size:22
Alignment explanation
Indices: 24653042--24653099 Score: 71
Period size: 22 Copynumber: 2.6 Consensus size: 22
24653032 TGTCACTAGT
* * *
24653042 TTTTAGGCATTGTGAGACTGGT
1 TTTTAGGCATTGCGAAACTGGC
*
24653064 TTTTAGGCATTGCGAAATTGGC
1 TTTTAGGCATTGCGAAACTGGC
*
24653086 TTTTAGACATTGCG
1 TTTTAGGCATTGCG
24653100 TGGCTTAATC
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.21, C:0.12, G:0.28, T:0.40
Consensus pattern (22 bp):
TTTTAGGCATTGCGAAACTGGC
Found at i:24653166 original size:19 final size:21
Alignment explanation
Indices: 24653122--24653167 Score: 60
Period size: 19 Copynumber: 2.3 Consensus size: 21
24653112 TGCGTTTTTG
*
24653122 GGTTTTAGGCATTCTGTGACT
1 GGTTTTAGGCATGCTGTGACT
*
24653143 GGTTTTAGGC-TGCT-TGATT
1 GGTTTTAGGCATGCTGTGACT
24653162 GGTTTT
1 GGTTTT
24653168 TAAAAATTGC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 10 0.43
20 3 0.13
21 10 0.43
ACGTcount: A:0.11, C:0.11, G:0.30, T:0.48
Consensus pattern (21 bp):
GGTTTTAGGCATGCTGTGACT
Found at i:24653356 original size:22 final size:22
Alignment explanation
Indices: 24653340--24653404 Score: 103
Period size: 22 Copynumber: 3.0 Consensus size: 22
24653330 GTTGCATAAC
24653340 TGGTTTTTAGGCATTGCGTGAT
1 TGGTTTTTAGGCATTGCGTGAT
* *
24653362 TGGGTTTTAAGCATTGCGTGAT
1 TGGTTTTTAGGCATTGCGTGAT
*
24653384 TGGTTTTTAGGTATTGCGTGA
1 TGGTTTTTAGGCATTGCGTGA
24653405 CACTTTTTTG
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 38 1.00
ACGTcount: A:0.15, C:0.08, G:0.32, T:0.45
Consensus pattern (22 bp):
TGGTTTTTAGGCATTGCGTGAT
Found at i:24657053 original size:29 final size:29
Alignment explanation
Indices: 24657007--24657066 Score: 93
Period size: 29 Copynumber: 2.1 Consensus size: 29
24656997 GGTTGTTGAA
** *
24657007 AAGCCTTAAATTGTAAGTAAATCATGTTC
1 AAGCCTTAAATTACAAGTAAATCACGTTC
24657036 AAGCCTTAAATTACAAGTAAATCACGTTC
1 AAGCCTTAAATTACAAGTAAATCACGTTC
24657065 AA
1 AA
24657067 TATAATGCAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.42, C:0.17, G:0.12, T:0.30
Consensus pattern (29 bp):
AAGCCTTAAATTACAAGTAAATCACGTTC
Found at i:24657232 original size:22 final size:22
Alignment explanation
Indices: 24657091--24657225 Score: 207
Period size: 22 Copynumber: 6.1 Consensus size: 22
24657081 GGATGTGCGA
*
24657091 TCACGTAATGCTTAAAAACTAG
1 TCACGTAATGCCTAAAAACTAG
*
24657113 TCACGTAATGCTTAAAAACTAG
1 TCACGTAATGCCTAAAAACTAG
*
24657135 TCACGTAATGCCTAAAAACCAG
1 TCACGTAATGCCTAAAAACTAG
*
24657157 TCACGTAATGCTTAAAAACTAG
1 TCACGTAATGCCTAAAAACTAG
*
24657179 TCACGTAATGCCTAAAAACCAG
1 TCACGTAATGCCTAAAAACTAG
* *
24657201 TTACGTAATGCCTAAAATCTAG
1 TCACGTAATGCCTAAAAACTAG
24657223 TCA
1 TCA
24657226 TGCAATGTAA
Statistics
Matches: 103, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 103 1.00
ACGTcount: A:0.40, C:0.21, G:0.13, T:0.25
Consensus pattern (22 bp):
TCACGTAATGCCTAAAAACTAG
Found at i:24657333 original size:38 final size:38
Alignment explanation
Indices: 24657282--24657372 Score: 173
Period size: 38 Copynumber: 2.4 Consensus size: 38
24657272 TCAAAACTAG
*
24657282 TCACGCAATGCCTAAGTCACGCAATACATAACAAATAA
1 TCACGCAATGCCTAAGTCACGCAATACATAACAAACAA
24657320 TCACGCAATGCCTAAGTCACGCAATACATAACAAACAA
1 TCACGCAATGCCTAAGTCACGCAATACATAACAAACAA
24657358 TCACGCAATGCCTAA
1 TCACGCAATGCCTAA
24657373 CATCTAGTCA
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 52 1.00
ACGTcount: A:0.43, C:0.29, G:0.11, T:0.18
Consensus pattern (38 bp):
TCACGCAATGCCTAAGTCACGCAATACATAACAAACAA
Found at i:24659916 original size:33 final size:33
Alignment explanation
Indices: 24659873--24659941 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 33
24659863 AATCTTCTAG
* * *
24659873 TGATTGCATCTTCCGTTGGATCT-TCAGCTGCAT
1 TGATTACATCTCCCGTTGGATCTCCCA-CTGCAT
24659906 TGATTACATCTCCCGTTGGATCTCCCACTGCAT
1 TGATTACATCTCCCGTTGGATCTCCCACTGCAT
24659939 TGA
1 TGA
24659942 CTGTAGGTCT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
33 30 0.94
34 2 0.06
ACGTcount: A:0.17, C:0.28, G:0.19, T:0.36
Consensus pattern (33 bp):
TGATTACATCTCCCGTTGGATCTCCCACTGCAT
Found at i:24663110 original size:42 final size:42
Alignment explanation
Indices: 24663046--24663142 Score: 158
Period size: 42 Copynumber: 2.3 Consensus size: 42
24663036 GAGGAATGTA
*
24663046 CAAAATGCTTAAAGGTTGTTCTTCGTGTATTAAAAACCACTC
1 CAAAATGCTCAAAGGTTGTTCTTCGTGTATTAAAAACCACTC
* *
24663088 CAAAATGCTCAAAGGTTTTTCTTTGTGTATTAAAAACCACTC
1 CAAAATGCTCAAAGGTTGTTCTTCGTGTATTAAAAACCACTC
*
24663130 CAAAATGCACAAA
1 CAAAATGCTCAAA
24663143 AAGCTCTAAG
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 51 1.00
ACGTcount: A:0.37, C:0.20, G:0.12, T:0.31
Consensus pattern (42 bp):
CAAAATGCTCAAAGGTTGTTCTTCGTGTATTAAAAACCACTC
Found at i:24664427 original size:156 final size:156
Alignment explanation
Indices: 24664138--24664435 Score: 440
Period size: 156 Copynumber: 1.9 Consensus size: 156
24664128 TAATTCATTT
* * * * * **
24664138 AATACTGGTTGAACTAGGATTATAGTTAATATTTATTGTCAACATGTTAAAAACCTATTGAGTCA
1 AATACTAGTTGAAATAGGATTACAATTAATATTTATTGTCAACATATTAAAAACCTAAAGAGTCA
* * *
24664203 CACGTATTAACAATGTCAATTGAGAATTTAAAAAAGGGTTAATTAAATTGAACTTAATTAAAATA
66 CACATATTAACAATGTCAACTAAGAATTTAAAAAAGGGTTAATTAAATTGAACTTAATTAAAATA
24664268 AGTTGAGAACTTCGAGGATTTAATCA
131 AGTTGAGAACTTCGAGGATTTAATCA
24664294 AATACTAGTTGAAATAGGATTACAATTAATATTTATT-TGCAACATATTAAAAACCTAAAGAGTC
1 AATACTAGTTGAAATAGGATTACAATTAATATTTATTGT-CAACATATTAAAAACCTAAAGAGTC
* *
24664358 ACACATATTAACAATGT-AGACTAAGAATTTAAAAAGGGGTTAATTAAATTGAACTTAGTT-AAA
65 ACACATATTAACAATGTCA-ACTAAGAATTTAAAAAAGGGTTAATTAAATTGAACTTAATTAAAA
24664421 TGAAGTTGAGAACTT
129 T-AAGTTGAGAACTT
24664436 TAGGGACTTG
Statistics
Matches: 127, Mismatches: 12, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
155 6 0.05
156 121 0.95
ACGTcount: A:0.43, C:0.09, G:0.15, T:0.33
Consensus pattern (156 bp):
AATACTAGTTGAAATAGGATTACAATTAATATTTATTGTCAACATATTAAAAACCTAAAGAGTCA
CACATATTAACAATGTCAACTAAGAATTTAAAAAAGGGTTAATTAAATTGAACTTAATTAAAATA
AGTTGAGAACTTCGAGGATTTAATCA
Found at i:24666221 original size:17 final size:18
Alignment explanation
Indices: 24666199--24666241 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
24666189 CAAGTCTAAG
24666199 AAAGTT-AAAGAAAAACA
1 AAAGTTGAAAGAAAAACA
* *
24666216 AAAGTTGAGAGAGAAACAA
1 AAAGTTGAAAGAAAAAC-A
24666235 AAAGTTG
1 AAAGTTG
24666242 TCAATTCTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 6 0.27
18 8 0.36
19 8 0.36
ACGTcount: A:0.60, C:0.05, G:0.21, T:0.14
Consensus pattern (18 bp):
AAAGTTGAAAGAAAAACA
Found at i:24672826 original size:68 final size:68
Alignment explanation
Indices: 24672717--24672852 Score: 236
Period size: 68 Copynumber: 2.0 Consensus size: 68
24672707 ATAATCAAGT
* *
24672717 TTCCAAGCATCTAAATGTTATGAAACTAGTTGAGTAAGACCCACCAGTAGCTCAAACATGCTCGT
1 TTCCAAGCATCTAAATGTTATGAAACTAGTTGAGTAAGACCCACCAATAGCTCAAACATACTCGT
24672782 GTA
66 GTA
* *
24672785 TTCCAAGCATCTAAATGTTATGAAACTAGTTGAGTAAGACCCACCAATAGCTTAAACATACTTGT
1 TTCCAAGCATCTAAATGTTATGAAACTAGTTGAGTAAGACCCACCAATAGCTCAAACATACTCGT
24672850 GTA
66 GTA
24672853 AAAGTGTGAC
Statistics
Matches: 64, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
68 64 1.00
ACGTcount: A:0.35, C:0.21, G:0.16, T:0.28
Consensus pattern (68 bp):
TTCCAAGCATCTAAATGTTATGAAACTAGTTGAGTAAGACCCACCAATAGCTCAAACATACTCGT
GTA
Found at i:24673081 original size:57 final size:58
Alignment explanation
Indices: 24673014--24673123 Score: 168
Period size: 58 Copynumber: 1.9 Consensus size: 58
24673004 TCTTTGCATG
* * *
24673014 CATAGTATTTATT-AATTGCATAAAATAAATCTATCTCATGCATACTACTTTGCAGCA
1 CATAGCATTTATTAAATGGCATAAAATAAATCTATCACATGCATACTACTTTGCAGCA
* *
24673071 CATAGCATTTATTAAATGGTATAAAATAAATCTATCACATGCATTCTACTTTG
1 CATAGCATTTATTAAATGGCATAAAATAAATCTATCACATGCATACTACTTTG
24673124 GATGATTATG
Statistics
Matches: 47, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
57 12 0.26
58 35 0.74
ACGTcount: A:0.37, C:0.16, G:0.09, T:0.37
Consensus pattern (58 bp):
CATAGCATTTATTAAATGGCATAAAATAAATCTATCACATGCATACTACTTTGCAGCA
Found at i:24680154 original size:2 final size:2
Alignment explanation
Indices: 24680147--24680178 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
24680137 NNNNNNNNNN
*
24680147 AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
24680179 GGTATATGGT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:24683933 original size:19 final size:19
Alignment explanation
Indices: 24683909--24683952 Score: 88
Period size: 19 Copynumber: 2.3 Consensus size: 19
24683899 ATTCTCTAAA
24683909 ACTTTGTGTAATATCACGT
1 ACTTTGTGTAATATCACGT
24683928 ACTTTGTGTAATATCACGT
1 ACTTTGTGTAATATCACGT
24683947 ACTTTG
1 ACTTTG
24683953 ATATGGTGGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.25, C:0.16, G:0.16, T:0.43
Consensus pattern (19 bp):
ACTTTGTGTAATATCACGT
Found at i:24685305 original size:39 final size:39
Alignment explanation
Indices: 24685256--24685470 Score: 190
Period size: 39 Copynumber: 5.6 Consensus size: 39
24685246 GTCCTAGTAG
* **
24685256 TGTGTGGTGTGGGAGAGCACATGCCGATGATATATGCCA
1 TGTGCGGTGTGGGAGAGCACATGATGATGATATATGCCA
* * *
24685295 TGTGTGGTGTGGGAGAGCACATGATAATGACATATGCCA
1 TGTGCGGTGTGGGAGAGCACATGATGATGATATATGCCA
**
24685334 TGTGCGGTGTGGGAGAGCATTTGATGATGATATATGCCA
1 TGTGCGGTGTGGGAGAGCACATGATGATGATATATGCCA
* * * **
24685373 TGTGCGATGTGGGA-ATGCACATGACGGTGAT-GGTG--A
1 TGTGCGGTGTGGGAGA-GCACATGATGATGATATATGCCA
* * * **
24685409 GGTGCAGTGTGGGA-ATGCACCTGATGATGATAT-TGTAA
1 TGTGCGGTGTGGGAGA-GCACATGATGATGATATATGCCA
* *
24685447 TGTGCGGTGTGGAAGTGCACATGA
1 TGTGCGGTGTGGGAGAGCACATGA
24685471 GTCGGGGGAG
Statistics
Matches: 143, Mismatches: 28, Indels: 11
0.79 0.15 0.06
Matches are distributed among these distances:
36 28 0.20
38 22 0.15
39 93 0.65
ACGTcount: A:0.24, C:0.12, G:0.37, T:0.27
Consensus pattern (39 bp):
TGTGCGGTGTGGGAGAGCACATGATGATGATATATGCCA
Found at i:24687578 original size:61 final size:61
Alignment explanation
Indices: 24687483--24687633 Score: 205
Period size: 61 Copynumber: 2.5 Consensus size: 61
24687473 ATAGGAGACC
* * * * *
24687483 AAAACAGAAGGTTTTTCGCTGCAGCGAGATTCAATCTTCGCTGCAGCGAAATTTCTACCTA-
1 AAAACAGAAAGTTTTTCGTTGCAGCGAGATTCAATCTT-GCTGCAGCGAAATTGCAACCCAG
* * *
24687544 AAAACAGAATGTTTCTCATTGCAGCGAGATTCAATCTTGCTGCAGCGAAATTGCAACCCAG
1 AAAACAGAAAGTTTTTCGTTGCAGCGAGATTCAATCTTGCTGCAGCGAAATTGCAACCCAG
*
24687605 AAAACATAAAGTTTTTCGTTGCAGCGAGA
1 AAAACAGAAAGTTTTTCGTTGCAGCGAGA
24687634 ATGCATTTAG
Statistics
Matches: 78, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
60 19 0.24
61 59 0.76
ACGTcount: A:0.32, C:0.21, G:0.20, T:0.26
Consensus pattern (61 bp):
AAAACAGAAAGTTTTTCGTTGCAGCGAGATTCAATCTTGCTGCAGCGAAATTGCAACCCAG
Found at i:24688044 original size:43 final size:43
Alignment explanation
Indices: 24687983--24688097 Score: 160
Period size: 43 Copynumber: 2.7 Consensus size: 43
24687973 CCCATCATCA
* * **
24687983 TCATCACCAGCTCATGCGCACTCCCTACTCGCATATGGCTGGG
1 TCATCACCAGCTTATGCGCACTCCCTACTCGCACATAACTGGG
*
24688026 TCATCACCAGGTTATGCGCACTCCCTACTCGCACATAACTGGG
1 TCATCACCAGCTTATGCGCACTCCCTACTCGCACATAACTGGG
*
24688069 TCATC-CTCAACTTATGCGCACTCCCTACT
1 TCATCAC-CAGCTTATGCGCACTCCCTACT
24688098 TGCAAATAGC
Statistics
Matches: 64, Mismatches: 7, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
42 1 0.02
43 63 0.98
ACGTcount: A:0.21, C:0.37, G:0.17, T:0.25
Consensus pattern (43 bp):
TCATCACCAGCTTATGCGCACTCCCTACTCGCACATAACTGGG
Found at i:24690335 original size:38 final size:38
Alignment explanation
Indices: 24690288--24690373 Score: 120
Period size: 38 Copynumber: 2.3 Consensus size: 38
24690278 TAGTCGGAGT
*
24690288 CATCATGTGCATCCCCCCACATCGTGCAC-AGCTAATAC
1 CATCGTGTGCATCCCCCCACATCGTGCACAAGC-AATAC
* * *
24690326 CATTGTGTGCATCCCCCCTCATCGTGCACAAGCAATAT
1 CATCGTGTGCATCCCCCCACATCGTGCACAAGCAATAC
24690364 CATCGTGTGC
1 CATCGTGTGC
24690374 GTATCATCAT
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
38 39 0.93
39 3 0.07
ACGTcount: A:0.23, C:0.36, G:0.16, T:0.24
Consensus pattern (38 bp):
CATCGTGTGCATCCCCCCACATCGTGCACAAGCAATAC
Found at i:24696272 original size:42 final size:42
Alignment explanation
Indices: 24696226--24696344 Score: 166
Period size: 42 Copynumber: 2.8 Consensus size: 42
24696216 GTTGGATCAT
24696226 CATCGGCTTATGCGCACTCCTACTCGCACATAGCCAAGTCAA
1 CATCGGCTTATGCGCACTCCTACTCGCACATAGCCAAGTCAA
* * **** *
24696268 CATCGGCTTATGCACACTCCCACTCGCACATAGTTGGGTCAG
1 CATCGGCTTATGCGCACTCCTACTCGCACATAGCCAAGTCAA
*
24696310 CATCAGCTTATGCGCACTCCTACTCGCACATAGCC
1 CATCGGCTTATGCGCACTCCTACTCGCACATAGCC
24696345 GGGTTAATAT
Statistics
Matches: 65, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 65 1.00
ACGTcount: A:0.24, C:0.36, G:0.18, T:0.23
Consensus pattern (42 bp):
CATCGGCTTATGCGCACTCCTACTCGCACATAGCCAAGTCAA
Found at i:24700455 original size:17 final size:17
Alignment explanation
Indices: 24700433--24700472 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
24700423 TGATTTTGAG
24700433 AAAAAGAAAGAAAAAGA
1 AAAAAGAAAGAAAAAGA
*
24700450 AAAAAGGAAGAAAAAGA
1 AAAAAGAAAGAAAAAGA
*
24700467 AGAAAG
1 AAAAAG
24700473 TGAATGAAGG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.78, C:0.00, G:0.23, T:0.00
Consensus pattern (17 bp):
AAAAAGAAAGAAAAAGA
Found at i:24700463 original size:9 final size:9
Alignment explanation
Indices: 24700431--24700471 Score: 57
Period size: 9 Copynumber: 4.6 Consensus size: 9
24700421 TGTGATTTTG
24700431 AGAAAAAGAA
1 AGAAAAAG-A
24700441 AGAAAAAGA
1 AGAAAAAGA
*
24700450 A-AAAAGGA
1 AGAAAAAGA
24700458 AGAAAAAGA
1 AGAAAAAGA
24700467 AGAAA
1 AGAAA
24700472 GTGAATGAAG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
8 7 0.25
9 13 0.46
10 8 0.29
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (9 bp):
AGAAAAAGA
Found at i:24700808 original size:52 final size:51
Alignment explanation
Indices: 24700730--24700832 Score: 197
Period size: 52 Copynumber: 2.0 Consensus size: 51
24700720 CTAATTTGAA
24700730 TTTTGCATACGTATAAACTTATCCAGATAGTATATTGTTCTTGGTAAAAAG
1 TTTTGCATACGTATAAACTTATCCAGATAGTATATTGTTCTTGGTAAAAAG
24700781 NTTTTGCATACGTATAAACTTATCCAGATAGTATATTGTTCTTGGTAAAAAG
1 -TTTTGCATACGTATAAACTTATCCAGATAGTATATTGTTCTTGGTAAAAAG
24700833 ATCCCACACA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 51 1.00
ACGTcount: A:0.33, C:0.12, G:0.16, T:0.39
Consensus pattern (51 bp):
TTTTGCATACGTATAAACTTATCCAGATAGTATATTGTTCTTGGTAAAAAG
Found at i:24703924 original size:22 final size:21
Alignment explanation
Indices: 24703887--24703928 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
24703877 ATTTGATTTT
24703887 AGTTTATTTTTGTTAAGTTTCA
1 AGTTTATTTTTGTTAA-TTTCA
24703909 AGTTTATTTCTT-TTAATTTC
1 AGTTTATTT-TTGTTAATTTC
24703929 CTTTGTTAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 4 0.21
22 13 0.68
23 2 0.11
ACGTcount: A:0.21, C:0.07, G:0.10, T:0.62
Consensus pattern (21 bp):
AGTTTATTTTTGTTAATTTCA
Found at i:24729650 original size:19 final size:19
Alignment explanation
Indices: 24729626--24729663 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
24729616 CTGCCAAACC
*
24729626 CTCAAATTATACTCCAATA
1 CTCAAATCATACTCCAATA
24729645 CTCAAATCATACTCCAATA
1 CTCAAATCATACTCCAATA
24729664 AGTTAAATGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.42, C:0.29, G:0.00, T:0.29
Consensus pattern (19 bp):
CTCAAATCATACTCCAATA
Found at i:24732109 original size:66 final size:67
Alignment explanation
Indices: 24732006--24732162 Score: 196
Period size: 66 Copynumber: 2.4 Consensus size: 67
24731996 CCATTATTGT
* * *
24732006 AGGTTGTGGTTGAGCCTTGGAAAAACCACTTTGGGTTTTAGTTTAGCCCGTGCAAAA-CTAGTG-
1 AGGTTGTGGTTGAGCCTTGGAAAAACCACTTTAGGTTTTAGTTGAGCCCGTGAAAAATC-AGTGC
24732069 TAAA
65 T-AA
* * * *
24732073 AGGTTGTGGTTGAGCCTT-GAAAAACCATTTTAGGTTTTGGTTGATCCCGTGAAAAATCATTGCT
1 AGGTTGTGGTTGAGCCTTGGAAAAACCACTTTAGGTTTTAGTTGAGCCCGTGAAAAATCAGTGCT
24732137 AA
66 AA
24732139 AGGTTGTGGTTGAG-CTTGCGAAAA
1 AGGTTGTGGTTGAGCCTTG-GAAAA
24732163 GCCATTGTAA
Statistics
Matches: 79, Mismatches: 7, Indels: 8
0.84 0.07 0.09
Matches are distributed among these distances:
65 3 0.04
66 51 0.65
67 25 0.32
ACGTcount: A:0.27, C:0.13, G:0.27, T:0.32
Consensus pattern (67 bp):
AGGTTGTGGTTGAGCCTTGGAAAAACCACTTTAGGTTTTAGTTGAGCCCGTGAAAAATCAGTGCT
AA
Found at i:24732149 original size:35 final size:32
Alignment explanation
Indices: 24732071--24732151 Score: 83
Period size: 32 Copynumber: 2.5 Consensus size: 32
24732061 AACTAGTGTA
* *
24732071 AAAGGTTGTGGTTGAGCCTTGAAAAACCATTT
1 AAAGGTTGTGGTTGACCCGTGAAAAACCATTT
* * *
24732103 -TAGGTTTTGGTTGATCCCGTGAAAAATCATTGCT
1 AAAGGTTGTGGTTGA-CCCGTGAAAAACCATT--T
24732137 AAAGGTTGTGGTTGA
1 AAAGGTTGTGGTTGA
24732152 GCTTGCGAAA
Statistics
Matches: 38, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
31 12 0.32
32 13 0.34
34 1 0.03
35 12 0.32
ACGTcount: A:0.27, C:0.11, G:0.27, T:0.35
Consensus pattern (32 bp):
AAAGGTTGTGGTTGACCCGTGAAAAACCATTT
Found at i:24732522 original size:71 final size:70
Alignment explanation
Indices: 24732397--24732532 Score: 182
Period size: 71 Copynumber: 1.9 Consensus size: 70
24732387 TTATCTGGAC
* * *
24732397 CAACATAGTCAACTAGAAAGAAAGCATAGTCAACCTTACTCTAAAAAGATCAAGAAAATCAAGTT
1 CAACATAGTCAACTAGAAAGAAAGCATAGTCAACCCTACTCCAAAAAGACCAAGAAAATCAAGTT
24732462 CAGAA
66 CAGAA
* * * * * *
24732467 CAACAATAGTCAACTATAAAGGAAGTATAGTCGACCCTGCTCCAGAAAGACCAAGAAAATCAAGT
1 CAAC-ATAGTCAACTAGAAAGAAAGCATAGTCAACCCTACTCCAAAAAGACCAAGAAAATCAAGT
24732532 T
65 T
24732533 GAAAAATAGC
Statistics
Matches: 56, Mismatches: 9, Indels: 1
0.85 0.14 0.02
Matches are distributed among these distances:
70 4 0.07
71 52 0.93
ACGTcount: A:0.47, C:0.20, G:0.15, T:0.18
Consensus pattern (70 bp):
CAACATAGTCAACTAGAAAGAAAGCATAGTCAACCCTACTCCAAAAAGACCAAGAAAATCAAGTT
CAGAA
Found at i:24732640 original size:21 final size:20
Alignment explanation
Indices: 24732606--24732652 Score: 69
Period size: 21 Copynumber: 2.4 Consensus size: 20
24732596 AGGTCAATTT
24732606 TAAGAAGCCATAGTCGACTA
1 TAAGAAGCCATAGTCGACTA
*
24732626 TAAGAAAGGCATAGTCGACTA
1 TAAG-AAGCCATAGTCGACTA
24732647 T-AGAAG
1 TAAGAAG
24732653 GCCAAATTTG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
19 3 0.12
20 6 0.24
21 16 0.64
ACGTcount: A:0.43, C:0.15, G:0.23, T:0.19
Consensus pattern (20 bp):
TAAGAAGCCATAGTCGACTA
Found at i:24739994 original size:19 final size:20
Alignment explanation
Indices: 24739970--24740008 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
24739960 AAATATCCTA
24739970 ATTGTTT-TAAACTAATTAC
1 ATTGTTTATAAACTAATTAC
*
24739989 ATTGTTTATTAACTAATTAC
1 ATTGTTTATAAACTAATTAC
24740009 CATCCATCCT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 7 0.39
20 11 0.61
ACGTcount: A:0.36, C:0.10, G:0.05, T:0.49
Consensus pattern (20 bp):
ATTGTTTATAAACTAATTAC
Done.