Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr11 124536837
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: 124536837
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 312 characters in sequence are not A, C, G, or T
File 191 of 427
Found at i:52914310 original size:55 final size:55
Alignment explanation
Indices: 52914226--52914330 Score: 147
Period size: 55 Copynumber: 1.9 Consensus size: 55
52914216 TTAGGTCAGT
* *
52914226 ATTGTACACGAGCAGGCCACATGAACGTGTGCCATGATCGTGTTTAAAAGCCAGC
1 ATTGTACACGAGCAGGCCACACGAACGTGTGCCATGACCGTGTTTAAAAGCCAGC
* * * * *
52914281 ATTGTACACGAGTAGGCCACACGAGCGTGTGGCATGGCCGTGTTTTAAAG
1 ATTGTACACGAGCAGGCCACACGAACGTGTGCCATGACCGTGTTTAAAAG
52914331 TCAGTGTTGC
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
55 43 1.00
ACGTcount: A:0.27, C:0.22, G:0.29, T:0.23
Consensus pattern (55 bp):
ATTGTACACGAGCAGGCCACACGAACGTGTGCCATGACCGTGTTTAAAAGCCAGC
Found at i:52914395 original size:270 final size:270
Alignment explanation
Indices: 52913914--52914443 Score: 873
Period size: 270 Copynumber: 2.0 Consensus size: 270
52913904 ACGGGTGTGT
52913914 GTTATAGCCGTGCGTCCCCTATACTTAAAATTTTAGGTCAGTATTGTACACAAGCAGGCCACAAG
1 GTTATAGCCGTGCGTCCCCTATACTTAAAATTTTAGGTCAGTATTGTACACAAGCAGGCCACAAG
** * * * *
52913979 GGCGTGTGCCATGAGCATGTTTAAAAGCCAGTATTGTACACGGGTAGGCCATACGGGCATATGCC
66 AACGTGTGCCATGAGCATGTTTAAAAGCCAGCATTGTACACGAGTAGGCCACACGAGCATATGCC
* **
52914044 ATGGCCATGTTTTAAAGTTAGTGTTGCACATGGACTAAGGGCACAGGCGTGTCCCAAGCCACACG
131 ATGGCCATGTTTTAAAGTCAGTGTTGCACACAGACTAAGGGCACAGGCGTGTCCCAAGCCACACG
52914109 GGCGTGTGCGACCACACGGTCTATACCCACACGGGCACGTGGAGCCTTAAAGCATGAATTTTCCA
196 GGCGTGTGCGACCACACGGTCTATACCCACACGGGCACGTGGAGCCTTAAAGCATGAATTTTCCA
52914174 GCAGGCGTGC
261 GCAGGCGTGC
* * *
52914184 GTTATAGCCGTGCGTCCCCTGTACTTAAAATTTTAGGTCAGTATTGTACACGAGCAGGCCACATG
1 GTTATAGCCGTGCGTCCCCTATACTTAAAATTTTAGGTCAGTATTGTACACAAGCAGGCCACAAG
* * * * *
52914249 AACGTGTGCCATGATCGTGTTTAAAAGCCAGCATTGTACACGAGTAGGCCACACGAGCGTGTGGC
66 AACGTGTGCCATGAGCATGTTTAAAAGCCAGCATTGTACACGAGTAGGCCACACGAGCATATGCC
*
52914314 ATGGCCGTGTTTTAAAGTCAGTGTTGCACACAGACTAAGGGCACAGGCGTG-CCCGAAGCCACAC
131 ATGGCCATGTTTTAAAGTCAGTGTTGCACACAGACTAAGGGCACAGGCGTGTCCC-AAGCCACAC
*
52914378 GGGCGTGTGCGACCACACGGTCTATACCCACACGGGCTCGTGGAGCCTTAAAGCATGAATTTTCC
195 GGGCGTGTGCGACCACACGGTCTATACCCACACGGGCACGTGGAGCCTTAAAGCATGAATTTTCC
52914443 A
260 A
52914444 AGTTTTTCTT
Statistics
Matches: 240, Mismatches: 19, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
269 3 0.01
270 237 0.99
ACGTcount: A:0.25, C:0.25, G:0.27, T:0.23
Consensus pattern (270 bp):
GTTATAGCCGTGCGTCCCCTATACTTAAAATTTTAGGTCAGTATTGTACACAAGCAGGCCACAAG
AACGTGTGCCATGAGCATGTTTAAAAGCCAGCATTGTACACGAGTAGGCCACACGAGCATATGCC
ATGGCCATGTTTTAAAGTCAGTGTTGCACACAGACTAAGGGCACAGGCGTGTCCCAAGCCACACG
GGCGTGTGCGACCACACGGTCTATACCCACACGGGCACGTGGAGCCTTAAAGCATGAATTTTCCA
GCAGGCGTGC
Found at i:52916720 original size:40 final size:40
Alignment explanation
Indices: 52916590--52916742 Score: 128
Period size: 40 Copynumber: 3.9 Consensus size: 40
52916580 ATGGTAACCC
* * * * * * *
52916590 GCACCAAGGCCTACGGGACTTAACCCGGATATCACGA-TT
1 GCACCAATGCCTTCGGGTCTTAGCCCGGATATAACCACTA
* * * ** *
52916629 GCACAAATGCCTTCGGGTCTTGGCCCGGATAGAATGACTC
1 GCACCAATGCCTTCGGGTCTTAGCCCGGATATAACCACTA
* *
52916669 GCACGAATGCCTTCGGGTCTTAGCCCGGATATAGCCACTA
1 GCACCAATGCCTTCGGGTCTTAGCCCGGATATAACCACTA
* * * *
52916709 GCACCATTGCCTTCGAGTCTTAACCCGGTTATAA
1 GCACCAATGCCTTCGGGTCTTAGCCCGGATATAA
52916743 TTTCAGCATA
Statistics
Matches: 90, Mismatches: 23, Indels: 1
0.79 0.20 0.01
Matches are distributed among these distances:
39 28 0.31
40 62 0.69
ACGTcount: A:0.24, C:0.29, G:0.24, T:0.23
Consensus pattern (40 bp):
GCACCAATGCCTTCGGGTCTTAGCCCGGATATAACCACTA
Found at i:52927439 original size:46 final size:45
Alignment explanation
Indices: 52927284--52927457 Score: 172
Period size: 46 Copynumber: 3.8 Consensus size: 45
52927274 GGTTGAGCAT
*
52927284 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG-
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGC-AACGC
* *** * * * *
52927329 TCGAACTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTA-ACTAGGC
1 CCGAACTCGTTGAGTTGAGTCCGAGTTC-ACTTATGGATGCAACGC
* * *
52927374 ATCCGAGCTCGTTGTGTTGAGTCTGAGTTCACTTATGGATGCGAACGC
1 --CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGC-AACGC
*
52927422 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
52927458 GCGGGTTACA
Statistics
Matches: 102, Mismatches: 21, Indels: 11
0.76 0.16 0.08
Matches are distributed among these distances:
44 2 0.02
45 28 0.27
46 44 0.43
47 25 0.25
48 3 0.03
ACGTcount: A:0.21, C:0.20, G:0.29, T:0.29
Consensus pattern (45 bp):
CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAACGC
Found at i:52940054 original size:39 final size:39
Alignment explanation
Indices: 52939956--52940058 Score: 118
Period size: 39 Copynumber: 2.6 Consensus size: 39
52939946 CTCGCACGAA
*
52939956 TGCCTTCGGGCCTTAGCCCGGATATACCACTAGCACAAT
1 TGCCTTCGGGCCTTAGCCCGGATATACCACCAGCACAAT
* * *** *
52939995 TGCCTTCGGGTCTTAACCCGGATATAATTTCCAGCATAAT
1 TGCCTTCGGGCCTTAGCCCGGATAT-ACCACCAGCACAAT
*
52940035 TGTCTTCGGG-CTTAGCCCGGATAT
1 TGCCTTCGGGCCTTAGCCCGGATAT
52940059 CATTCAATTT
Statistics
Matches: 54, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
39 36 0.67
40 18 0.33
ACGTcount: A:0.21, C:0.28, G:0.21, T:0.29
Consensus pattern (39 bp):
TGCCTTCGGGCCTTAGCCCGGATATACCACCAGCACAAT
Found at i:52947930 original size:40 final size:40
Alignment explanation
Indices: 52947885--52948051 Score: 185
Period size: 40 Copynumber: 4.2 Consensus size: 40
52947875 CGGAATATAA
52947885 CCGGATATAATCACGT-GCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCAC-TAGCACAAATGCCTTCGGGTCTTAGC
* * * * *
52947925 CCGGATAGAATAACTCGCACGAATGCCTTCGGGCCTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
* * *
52947965 CCGGATATAACCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * * * *
52948005 CCGGATATAATTTCCAGCATAATTGTCTTCGGG-CTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
52948044 CCGGATAT
1 CCGGATAT
52948052 CATTCAATTT
Statistics
Matches: 107, Mismatches: 19, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
39 14 0.13
40 93 0.87
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.26
Consensus pattern (40 bp):
CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:52948035 original size:80 final size:79
Alignment explanation
Indices: 52947885--52948051 Score: 205
Period size: 80 Copynumber: 2.1 Consensus size: 79
52947875 CGGAATATAA
* *
52947885 CCGGATATAATCACGTGCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATAACTCGCACGAATG
1 CCGGATATAACCACGTGCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACTCGCACGAATG
52947950 CCTTCGGGCCTTAGC
66 CCTTCGGG-CTTAGC
* * ** *
52947965 CCGGATATAACCAC-TAGCACAATTGCCTTCGGGTCTTAACCCGGATATAATTTC-CAGCA-TAA
1 CCGGATATAACCACGT-GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACTC-GCACGAA
*
52948027 TTGTCTTCGGGCTTAGC
64 -TGCCTTCGGGCTTAGC
52948044 CCGGATAT
1 CCGGATAT
52948052 CATTCAATTT
Statistics
Matches: 76, Mismatches: 8, Indels: 7
0.84 0.09 0.08
Matches are distributed among these distances:
79 18 0.24
80 58 0.76
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.26
Consensus pattern (79 bp):
CCGGATATAACCACGTGCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACTCGCACGAATG
CCTTCGGGCTTAGC
Found at i:52948899 original size:17 final size:19
Alignment explanation
Indices: 52948876--52948921 Score: 53
Period size: 17 Copynumber: 2.5 Consensus size: 19
52948866 AAGAAGCATG
52948876 AATCATGCTCAAGAATG-C
1 AATCATGCTCAAGAATGAC
*
52948894 -ATCATGGC-CAAGTATGAC
1 AATCAT-GCTCAAGAATGAC
52948912 AATCATGCTC
1 AATCATGCTC
52948922 CTTTTCAACT
Statistics
Matches: 23, Mismatches: 1, Indels: 7
0.74 0.03 0.23
Matches are distributed among these distances:
17 12 0.52
18 5 0.22
19 6 0.26
ACGTcount: A:0.35, C:0.24, G:0.17, T:0.24
Consensus pattern (19 bp):
AATCATGCTCAAGAATGAC
Found at i:52953736 original size:47 final size:48
Alignment explanation
Indices: 52953616--52953754 Score: 154
Period size: 48 Copynumber: 2.9 Consensus size: 48
52953606 TACCATGGTT
* * *
52953616 ATACGTGTAACGTAGTGCTAAGTGGATATACCACGATTACACATATTG
1 ATACATGTAACGTGGTGCTAAGTGGATATACCACGATTACACATATCG
* * * * * *
52953664 ATACATGTAACGTGGTGCTAAGTGGATATGCGATGGTTGCATATATCG
1 ATACATGTAACGTGGTGCTAAGTGGATATACCACGATTACACATATCG
* * * *
52953712 ATTCAT-TAATGTGGTGCTAAGTGGATATAACACGATTAAACAT
1 ATACATGTAACGTGGTGCTAAGTGGATATACCACGATTACACAT
52953755 GTAACGTGGT
Statistics
Matches: 72, Mismatches: 19, Indels: 1
0.78 0.21 0.01
Matches are distributed among these distances:
47 28 0.39
48 44 0.61
ACGTcount: A:0.32, C:0.14, G:0.23, T:0.31
Consensus pattern (48 bp):
ATACATGTAACGTGGTGCTAAGTGGATATACCACGATTACACATATCG
Found at i:52958636 original size:44 final size:44
Alignment explanation
Indices: 52958586--52958721 Score: 115
Period size: 44 Copynumber: 3.2 Consensus size: 44
52958576 CATGGCTAGG
52958586 GTTTTTAAAACTTCCAAGCTTGATTGTAAGTCCATCTTTGCCCC
1 GTTTTTAAAACTTCCAAGCTTGATTGTAAGTCCATCTTTGCCCC
** *** * * * *
52958630 GTTTTT-AATGTTCTTTGCATTGACTG-AAG-ACATGGC-TAG---G
1 GTTTTTAAAACTTCCAAGC-TTGATTGTAAGTCCAT--CTTTGCCCC
52958670 GTTTTTAAAACTTCCAAGCTTGATTGTAAGTCCATCTTTGCCCC
1 GTTTTTAAAACTTCCAAGCTTGATTGTAAGTCCATCTTTGCCCC
52958714 GTTTTTAA
1 GTTTTTAA
52958722 TGTTCTTTGC
Statistics
Matches: 64, Mismatches: 18, Indels: 20
0.63 0.18 0.20
Matches are distributed among these distances:
40 13 0.20
41 12 0.19
42 6 0.09
43 12 0.19
44 21 0.33
ACGTcount: A:0.23, C:0.20, G:0.17, T:0.40
Consensus pattern (44 bp):
GTTTTTAAAACTTCCAAGCTTGATTGTAAGTCCATCTTTGCCCC
Found at i:52958711 original size:84 final size:84
Alignment explanation
Indices: 52958570--52958734 Score: 330
Period size: 84 Copynumber: 2.0 Consensus size: 84
52958560 ATATGGAGAT
52958570 TGAAGACATGGCTAGGGTTTTTAAAACTTCCAAGCTTGATTGTAAGTCCATCTTTGCCCCGTTTT
1 TGAAGACATGGCTAGGGTTTTTAAAACTTCCAAGCTTGATTGTAAGTCCATCTTTGCCCCGTTTT
52958635 TAATGTTCTTTGCATTGAC
66 TAATGTTCTTTGCATTGAC
52958654 TGAAGACATGGCTAGGGTTTTTAAAACTTCCAAGCTTGATTGTAAGTCCATCTTTGCCCCGTTTT
1 TGAAGACATGGCTAGGGTTTTTAAAACTTCCAAGCTTGATTGTAAGTCCATCTTTGCCCCGTTTT
52958719 TAATGTTCTTTGCATT
66 TAATGTTCTTTGCATT
52958735 TTTGAAATCC
Statistics
Matches: 81, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
84 81 1.00
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.40
Consensus pattern (84 bp):
TGAAGACATGGCTAGGGTTTTTAAAACTTCCAAGCTTGATTGTAAGTCCATCTTTGCCCCGTTTT
TAATGTTCTTTGCATTGAC
Found at i:52959638 original size:47 final size:48
Alignment explanation
Indices: 52959520--52959653 Score: 153
Period size: 48 Copynumber: 2.8 Consensus size: 48
52959510 TAGTTATAAG
* * * *
52959520 TGTAATGTGATGCTAAGTGGATATACCACGATTACACATATTGATACA
1 TGTAACGTGGTGCTAAGTGGATATACCACGGTTACACATATCGATACA
* * * * *
52959568 TGTAACGTGGTGCTAACTGGATATGCCACGGTTATATATATCGATTCA
1 TGTAACGTGGTGCTAAGTGGATATACCACGGTTACACATATCGATACA
* * *
52959616 T-TAACGTGGTGCTAAGTAGATATACCACAGTTAAACAT
1 TGTAACGTGGTGCTAAGTGGATATACCACGGTTACACAT
52959654 GTAACGTGGT
Statistics
Matches: 71, Mismatches: 15, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
47 31 0.44
48 40 0.56
ACGTcount: A:0.33, C:0.16, G:0.20, T:0.31
Consensus pattern (48 bp):
TGTAACGTGGTGCTAAGTGGATATACCACGGTTACACATATCGATACA
Found at i:52959659 original size:38 final size:38
Alignment explanation
Indices: 52959617--52959693 Score: 111
Period size: 38 Copynumber: 2.0 Consensus size: 38
52959607 ATCGATTCAT
52959617 TAACGTGGTGCTAAGTAG-ATATACCACAGTTAAACATG
1 TAACGTGGTGCTAAGT-GTATATACCACAGTTAAACATG
* * *
52959655 TAACGTGGTGCTAAGTGTATATGCCACGGTTATACATG
1 TAACGTGGTGCTAAGTGTATATACCACAGTTAAACATG
52959693 T
1 T
52959694 TAATATGAGA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
37 1 0.03
38 34 0.97
ACGTcount: A:0.31, C:0.16, G:0.23, T:0.30
Consensus pattern (38 bp):
TAACGTGGTGCTAAGTGTATATACCACAGTTAAACATG
Found at i:52974561 original size:34 final size:34
Alignment explanation
Indices: 52974523--52974629 Score: 178
Period size: 34 Copynumber: 3.1 Consensus size: 34
52974513 TTACAGTGTT
* *
52974523 ATTTGGTGTGTTGGATGGATTAGCTCATACGACC
1 ATTTGGTGTGCTGGATGGATTAGCTCATACGAGC
52974557 ATTTGGTGTGCTGGATGGATTAGCTCATACGAGC
1 ATTTGGTGTGCTGGATGGATTAGCTCATACGAGC
* *
52974591 ATTTGGTGTGCTAGATGGATTAGGTCATACGAGC
1 ATTTGGTGTGCTGGATGGATTAGCTCATACGAGC
52974625 ATTTG
1 ATTTG
52974630 ATCATGTCTC
Statistics
Matches: 69, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
34 69 1.00
ACGTcount: A:0.21, C:0.13, G:0.31, T:0.35
Consensus pattern (34 bp):
ATTTGGTGTGCTGGATGGATTAGCTCATACGAGC
Found at i:52975594 original size:49 final size:50
Alignment explanation
Indices: 52975530--52975660 Score: 149
Period size: 50 Copynumber: 2.6 Consensus size: 50
52975520 AGTCGATGCA
* * *
52975530 ATGTCCTAGACATGGTCTTACACTGACTATCA-AAATCGAGGCCGACATC
1 ATGTCCCAGACATGGTCTTACACTGACTATCACAAATCCAGGCCGACACC
* * * * **
52975579 ATGTCCCAGAGATGGTCTTACACT-AGCTCTCACATATCCATGCCGATGCC
1 ATGTCCCAGACATGGTCTTACACTGA-CTATCACAAATCCAGGCCGACACC
52975629 ATGTCCCAGACATGGTCTTACACTGACATATC
1 ATGTCCCAGACATGGTCTTACACTGAC-TATC
52975661 TCGTAGCCGA
Statistics
Matches: 67, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
48 1 0.01
49 27 0.40
50 35 0.52
51 4 0.06
ACGTcount: A:0.27, C:0.29, G:0.18, T:0.26
Consensus pattern (50 bp):
ATGTCCCAGACATGGTCTTACACTGACTATCACAAATCCAGGCCGACACC
Found at i:52977668 original size:35 final size:35
Alignment explanation
Indices: 52977617--52977686 Score: 122
Period size: 35 Copynumber: 2.0 Consensus size: 35
52977607 TCAGGAACAC
* *
52977617 AACATCGTAACATGTCTTCTAATATCTAAATTATT
1 AACACCGTAACATGTCTTCTAATACCTAAATTATT
52977652 AACACCGTAACATGTCTTCTAATACCTAAATTATT
1 AACACCGTAACATGTCTTCTAATACCTAAATTATT
52977687 CTTTCCGACT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.37, C:0.20, G:0.06, T:0.37
Consensus pattern (35 bp):
AACACCGTAACATGTCTTCTAATACCTAAATTATT
Found at i:52981630 original size:16 final size:16
Alignment explanation
Indices: 52981609--52981640 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
52981599 AGGTGTTAAT
*
52981609 TGTAACACCCCGAACC
1 TGTAACACCCCAAACC
52981625 TGTAACACCCCAAACC
1 TGTAACACCCCAAACC
52981641 CGTGACCGTC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.34, C:0.44, G:0.09, T:0.12
Consensus pattern (16 bp):
TGTAACACCCCAAACC
Found at i:52983121 original size:31 final size:29
Alignment explanation
Indices: 52983085--52983159 Score: 78
Period size: 29 Copynumber: 2.5 Consensus size: 29
52983075 CTTCGAGCTC
* *
52983085 GCACACCCAGTGCCGTATTTTTTTCCAGCAT
1 GCACACCCAGTGCC--ATATATTTCCAGCAT
**
52983116 GCACACTTAGTGCCATATATTTCCAGCAT
1 GCACACCCAGTGCCATATATTTCCAGCAT
**
52983145 GCACACTTAGTGCCA
1 GCACACCCAGTGCCA
52983160 ATCTCGTCAC
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
29 28 0.70
31 12 0.30
ACGTcount: A:0.24, C:0.31, G:0.16, T:0.29
Consensus pattern (29 bp):
GCACACCCAGTGCCATATATTTCCAGCAT
Found at i:52988228 original size:30 final size:29
Alignment explanation
Indices: 52988193--52988266 Score: 85
Period size: 29 Copynumber: 2.5 Consensus size: 29
52988183 CTTCGAGCTC
* *
52988193 GCACACCCAGTGCCGTATTTTTTCCAGCAT
1 GCACACCCAGTGCCATA-TATTTCCAGCAT
**
52988223 GCACACTTAGTGCCATATATTTCCAGCAT
1 GCACACCCAGTGCCATATATTTCCAGCAT
**
52988252 GCACACTTAGTGCCA
1 GCACACCCAGTGCCA
52988267 ATCTCGTCAC
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
29 26 0.65
30 14 0.35
ACGTcount: A:0.24, C:0.31, G:0.16, T:0.28
Consensus pattern (29 bp):
GCACACCCAGTGCCATATATTTCCAGCAT
Found at i:52998221 original size:40 final size:39
Alignment explanation
Indices: 52998166--52998302 Score: 138
Period size: 39 Copynumber: 3.5 Consensus size: 39
52998156 GGATATAGCG
* *
52998166 ACTCGCTCAAA-GCCTTCGGGACATAGCCCGG-TTAT-AA
1 ACTCGCACAAATGCCTTCGGGACATAACCCGGATT-TGAA
* *
52998203 TAGCTCGCACAAATGCCTTCGGGACTTAACCCGGATTTGGA
1 -A-CTCGCACAAATGCCTTCGGGACATAACCCGGATTTGAA
* ** *
52998244 ACTCGCACAAATGCCTTC-GGATCTTAGTCCGGATTTGGA
1 ACTCGCACAAATGCCTTCGGGA-CATAACCCGGATTTGAA
52998283 ACTCGCACAAATGCCTTCGG
1 ACTCGCACAAATGCCTTCGG
52998303 ATCTTAGTCC
Statistics
Matches: 87, Mismatches: 6, Indels: 10
0.84 0.06 0.10
Matches are distributed among these distances:
38 4 0.05
39 59 0.68
40 21 0.24
41 3 0.03
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (39 bp):
ACTCGCACAAATGCCTTCGGGACATAACCCGGATTTGAA
Found at i:52998260 original size:39 final size:39
Alignment explanation
Indices: 52998206--52998353 Score: 187
Period size: 39 Copynumber: 3.8 Consensus size: 39
52998196 GTTATAATAG
*
52998206 CTCGCACAAATGCCTTCGGGA-CTTAACCCGGATTTGGAA
1 CTCGCACAAATGCCTTC-GGATCTTAGCCCGGATTTGGAA
*
52998245 CTCGCACAAATGCCTTCGGATCTTAGTCCGGATTTGGAA
1 CTCGCACAAATGCCTTCGGATCTTAGCCCGGATTTGGAA
* * *
52998284 CTCGCACAAATGCCTTCGGATCTTAGTCCGGATATGGTCA
1 CTCGCACAAATGCCTTCGGATCTTAGCCCGGATTTGG-AA
*
52998324 C-AGCACAAA-GCCTTCGGGA-CTTAGCCCGGA
1 CTCGCACAAATGCCTTC-GGATCTTAGCCCGGA
52998354 CATCATTCGA
Statistics
Matches: 100, Mismatches: 6, Indels: 7
0.88 0.05 0.06
Matches are distributed among these distances:
38 19 0.19
39 79 0.79
40 2 0.02
ACGTcount: A:0.24, C:0.28, G:0.24, T:0.24
Consensus pattern (39 bp):
CTCGCACAAATGCCTTCGGATCTTAGCCCGGATTTGGAA
Found at i:53006278 original size:40 final size:40
Alignment explanation
Indices: 53006222--53006360 Score: 122
Period size: 40 Copynumber: 3.5 Consensus size: 40
53006212 GGATATAGCG
* * * *
53006222 ACTCGCTCAAAAGCCTTCGGGACATAGCCCGG-TTATAATA
1 ACTCGCACAAATGCCTTCGGGACATAACCCGGATT-TAAGA
* * **
53006262 GCTCGCACAAATGCCTTCGGGACTTAACCCGGATTTGGGA
1 ACTCGCACAAATGCCTTCGGGACATAACCCGGATTTAAGA
* ** * *
53006302 ACTCGCACAAATGCCTTC-GGATCTTAGTCCGAATTT-GGA
1 ACTCGCACAAATGCCTTCGGGA-CATAACCCGGATTTAAGA
53006341 ACTCGCACAAATGCCTTCGG
1 ACTCGCACAAATGCCTTCGG
53006361 ATCTTAGTCC
Statistics
Matches: 84, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
39 24 0.29
40 58 0.69
41 2 0.02
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (40 bp):
ACTCGCACAAATGCCTTCGGGACATAACCCGGATTTAAGA
Found at i:53006353 original size:39 final size:38
Alignment explanation
Indices: 53006263--53006411 Score: 183
Period size: 39 Copynumber: 3.8 Consensus size: 38
53006253 GTTATAATAG
**
53006263 CTCGCACAAATGCCTTCGGGACTTAACCCGGATTTGGGAA
1 CTCGCACAAATGCCTTC-GGACTTAGTCCGGATTT-GGAA
*
53006303 CTCGCACAAATGCCTTCGGATCTTAGTCCGAATTTGGAA
1 CTCGCACAAATGCCTTCGGA-CTTAGTCCGGATTTGGAA
* *
53006342 CTCGCACAAATGCCTTCGGATCTTAGTCCGGATATGGTCA
1 CTCGCACAAATGCCTTCGGA-CTTAGTCCGGATTTGG-AA
* *
53006382 CTAGCACAAA-GCCTTCGGACTTAGCCCGGA
1 CTCGCACAAATGCCTTCGGACTTAGTCCGGA
53006412 CATCATTCGA
Statistics
Matches: 99, Mismatches: 8, Indels: 6
0.88 0.07 0.05
Matches are distributed among these distances:
38 10 0.10
39 51 0.52
40 38 0.38
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (38 bp):
CTCGCACAAATGCCTTCGGACTTAGTCCGGATTTGGAA
Found at i:53013383 original size:29 final size:29
Alignment explanation
Indices: 53013326--53013384 Score: 75
Period size: 28 Copynumber: 2.0 Consensus size: 29
53013316 CATATAATAG
* **
53013326 AAAATTATATAAAATGAAAATAATTTATA
1 AAAATTATATAAAATAAAAATAAAATATA
53013355 AAAATT-TATAAAATAAAAATAAAAATATA
1 AAAATTATATAAAATAAAAAT-AAAATATA
53013384 A
1 A
53013385 CTAATTCAGT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
28 13 0.50
29 13 0.50
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.31
Consensus pattern (29 bp):
AAAATTATATAAAATAAAAATAAAATATA
Found at i:53013655 original size:14 final size:14
Alignment explanation
Indices: 53013636--53013665 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
53013626 TAATAGGTGT
53013636 TGTATTGTTAACCA
1 TGTATTGTTAACCA
53013650 TGTATTGTTAACCA
1 TGTATTGTTAACCA
53013664 TG
1 TG
53013666 ATAAGTGTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.27, C:0.13, G:0.17, T:0.43
Consensus pattern (14 bp):
TGTATTGTTAACCA
Found at i:53013739 original size:10 final size:10
Alignment explanation
Indices: 53013706--53013814 Score: 57
Period size: 10 Copynumber: 11.2 Consensus size: 10
53013696 TATAATAGTC
53013706 TTTTATATATT
1 TTTTATA-ATT
53013717 TTTTAT--TT
1 TTTTATAATT
53013725 GTTTTATAATT
1 -TTTTATAATT
53013736 TTTTATAATT
1 TTTTATAATT
* *
53013746 TTCTA-CATT
1 TTTTATAATT
*** *
53013755 TTCCGTAATC
1 TTTTATAATT
*
53013765 TTATATAA-T
1 TTTTATAATT
53013774 TTTTA-AATT
1 TTTTATAATT
* * *
53013783 TTCTATTATG
1 TTTTATAATT
* *
53013793 TTTAATATTT
1 TTTTATAATT
53013803 TTTTATAATT
1 TTTTATAATT
53013813 TT
1 TT
53013815 ATGCAATTTT
Statistics
Matches: 71, Mismatches: 21, Indels: 13
0.68 0.20 0.12
Matches are distributed among these distances:
8 4 0.06
9 21 0.30
10 38 0.54
11 8 0.11
ACGTcount: A:0.27, C:0.06, G:0.03, T:0.65
Consensus pattern (10 bp):
TTTTATAATT
Found at i:53014828 original size:15 final size:15
Alignment explanation
Indices: 53014794--53014843 Score: 57
Period size: 15 Copynumber: 3.4 Consensus size: 15
53014784 CATAATGAAA
*
53014794 ATTTTAGTTTTTAAT
1 ATTTTAGTTTTTATT
*
53014809 A-TTTATTTTTTATT
1 ATTTTAGTTTTTATT
*
53014823 ATTTTAGTTTTAATT
1 ATTTTAGTTTTTATT
*
53014838 TTTTTA
1 ATTTTA
53014844 AAGATTATTT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
14 12 0.41
15 17 0.59
ACGTcount: A:0.24, C:0.00, G:0.04, T:0.72
Consensus pattern (15 bp):
ATTTTAGTTTTTATT
Found at i:53015320 original size:29 final size:29
Alignment explanation
Indices: 53015288--53015345 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
53015278 AATTTTCTTC
53015288 AAAATT-TAAAAAATAAATTTGGAAATAAA
1 AAAATTATAAAAAAT-AATTTGGAAATAAA
* * *
53015317 AAAATTATAATAACTTATTTGGAAATAAA
1 AAAATTATAAAAAATAATTTGGAAATAAA
53015346 TTTTTATCTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 19 0.76
30 6 0.24
ACGTcount: A:0.60, C:0.02, G:0.07, T:0.31
Consensus pattern (29 bp):
AAAATTATAAAAAATAATTTGGAAATAAA
Found at i:53015511 original size:11 final size:11
Alignment explanation
Indices: 53015495--53015519 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
53015485 GTTAAAATTT
53015495 AAAAATTATTA
1 AAAAATTATTA
53015506 AAAAATTATTA
1 AAAAATTATTA
53015517 AAA
1 AAA
53015520 TGTTTAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (11 bp):
AAAAATTATTA
Found at i:53018287 original size:15 final size:15
Alignment explanation
Indices: 53018264--53018296 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
53018254 GAGGAGATAG
53018264 AAAAAAAT-AGGGAA
1 AAAAAAATAAGGGAA
53018278 AAAAAGAATAAGGGAA
1 AAAAA-AATAAGGGAA
53018294 AAA
1 AAA
53018297 GAAAGAAGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 5 0.29
15 3 0.18
16 9 0.53
ACGTcount: A:0.73, C:0.00, G:0.21, T:0.06
Consensus pattern (15 bp):
AAAAAAATAAGGGAA
Found at i:53019683 original size:31 final size:31
Alignment explanation
Indices: 53019648--53019707 Score: 120
Period size: 31 Copynumber: 1.9 Consensus size: 31
53019638 AAAAAAAGTA
53019648 TAATTTGAGTCTTTTATTTACCTTAGGGGTG
1 TAATTTGAGTCTTTTATTTACCTTAGGGGTG
53019679 TAATTTGAGTCTTTTATTTACCTTAGGGG
1 TAATTTGAGTCTTTTATTTACCTTAGGGG
53019708 CTGAATAAGG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.20, C:0.10, G:0.22, T:0.48
Consensus pattern (31 bp):
TAATTTGAGTCTTTTATTTACCTTAGGGGTG
Found at i:53019821 original size:22 final size:22
Alignment explanation
Indices: 53019794--53019854 Score: 95
Period size: 22 Copynumber: 2.8 Consensus size: 22
53019784 CTGGTCGATG
**
53019794 TGTTGCAACACAGGGAGTTTGA
1 TGTTGCAACACAGGGAGTTCAA
53019816 TGTTGCAACACAGGGAGTTCAA
1 TGTTGCAACACAGGGAGTTCAA
*
53019838 TGTTGCAACATAGGGAG
1 TGTTGCAACACAGGGAG
53019855 AAGGGCACAA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 36 1.00
ACGTcount: A:0.30, C:0.15, G:0.31, T:0.25
Consensus pattern (22 bp):
TGTTGCAACACAGGGAGTTCAA
Found at i:53023691 original size:31 final size:31
Alignment explanation
Indices: 53023647--53023761 Score: 189
Period size: 31 Copynumber: 3.7 Consensus size: 31
53023637 TTAGTCTTGA
*
53023647 CATAT-ACTAGGCCGAAGCC-TTTCTATAAAT
1 CATATCACTGGGCCGAAGCCTTTTC-ATAAAT
53023677 CATATCACTGGGCCGAAGCCTTTTCATAAAT
1 CATATCACTGGGCCGAAGCCTTTTCATAAAT
53023708 CATATCACTGGGCCGAAGCCTTTTCATAAAT
1 CATATCACTGGGCCGAAGCCTTTTCATAAAT
*
53023739 CATATCACTGGGCTGAAGCCTTT
1 CATATCACTGGGCCGAAGCCTTT
53023762 ACTGTAAACA
Statistics
Matches: 81, Mismatches: 2, Indels: 3
0.94 0.02 0.03
Matches are distributed among these distances:
30 5 0.06
31 72 0.89
32 4 0.05
ACGTcount: A:0.29, C:0.25, G:0.17, T:0.30
Consensus pattern (31 bp):
CATATCACTGGGCCGAAGCCTTTTCATAAAT
Found at i:53024009 original size:25 final size:25
Alignment explanation
Indices: 53023981--53024050 Score: 113
Period size: 25 Copynumber: 2.8 Consensus size: 25
53023971 CTCTTTTAAT
*
53023981 AACTGGGGCAAAGCCCTTTTTGATA
1 AACTGGGGCAAAGCCCTTTTCGATA
*
53024006 AACTGGGGCAAAGCCCTTTTCGGTA
1 AACTGGGGCAAAGCCCTTTTCGATA
*
53024031 AACTGGGGCATAGCCCTTTT
1 AACTGGGGCAAAGCCCTTTT
53024051 AGCACTTCTT
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 42 1.00
ACGTcount: A:0.24, C:0.23, G:0.26, T:0.27
Consensus pattern (25 bp):
AACTGGGGCAAAGCCCTTTTCGATA
Found at i:53024530 original size:20 final size:22
Alignment explanation
Indices: 53024505--53024545 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 22
53024495 GGGCCCAAAA
*
53024505 GCCCATT-TGGCCCAA-TTACT
1 GCCCATTGAGGCCCAACTTACT
53024525 GCCCATTGAGGCCCAACTTAC
1 GCCCATTGAGGCCCAACTTAC
53024546 CATCGTGCAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 7 0.39
21 7 0.39
22 4 0.22
ACGTcount: A:0.22, C:0.37, G:0.17, T:0.24
Consensus pattern (22 bp):
GCCCATTGAGGCCCAACTTACT
Found at i:53025089 original size:27 final size:27
Alignment explanation
Indices: 53024953--53025162 Score: 145
Period size: 27 Copynumber: 7.7 Consensus size: 27
53024943 TTTCATCCTA
* * * *
53024953 CAAGGGTGTTTTGGTAAATCTACAAAC
1 CAAGGGTATTTTGGTAATTTTACAAAT
** ** *
53024980 CAAGGGTATTTCAGTAATTTTGTAAAC
1 CAAGGGTATTTTGGTAATTTTACAAAT
* ** *
53025007 CAATGGTATTTTTATAATTTTTAGAAAGT
1 CAAGGGTATTTTGGTAA-TTTTACAAA-T
* **
53025036 CAATGGTATTTCT-GTAATTTTGTAAAT
1 CAAGGGTATTT-TGGTAATTTTACAAAT
53025063 CAAGGGTATTTTGGTAATTTTACAAAT
1 CAAGGGTATTTTGGTAATTTTACAAAT
** * * *
53025090 TGAGGGTATTTCGATAATTTCACAAA-
1 CAAGGGTATTTTGGTAATTTTACAAAT
* *
53025116 CCAGTGGTATTTTGGTAATTTAACAAAT
1 CAAG-GGTATTTTGGTAATTTTACAAAT
* *
53025144 TAGGGGTATTTTGGTAATT
1 CAAGGGTATTTTGGTAATT
53025163 CTATCCTACA
Statistics
Matches: 144, Mismatches: 33, Indels: 12
0.76 0.17 0.06
Matches are distributed among these distances:
26 3 0.02
27 111 0.77
28 15 0.10
29 14 0.10
30 1 0.01
ACGTcount: A:0.32, C:0.09, G:0.19, T:0.40
Consensus pattern (27 bp):
CAAGGGTATTTTGGTAATTTTACAAAT
Found at i:53025261 original size:54 final size:54
Alignment explanation
Indices: 53025194--53025312 Score: 202
Period size: 54 Copynumber: 2.2 Consensus size: 54
53025184 GTAATTTCAC
* **
53025194 AATCGAGGGTAAAACGGTAATTTTGTAAATTGAAGGTAAAATGGTAATTTTGTA
1 AATCGAGGGTAAAACGGTAATTTTGTAAATTGAAGGTAAAATGGTAATTCTACA
*
53025248 AATCGAGGGTAAAACGGTAATTTTGTAAATTGAGGGTAAAATGGTAATTCTACA
1 AATCGAGGGTAAAACGGTAATTTTGTAAATTGAAGGTAAAATGGTAATTCTACA
53025302 AATCGAGGGTA
1 AATCGAGGGTA
53025313 TTTCAGTAAT
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
54 61 1.00
ACGTcount: A:0.39, C:0.06, G:0.25, T:0.30
Consensus pattern (54 bp):
AATCGAGGGTAAAACGGTAATTTTGTAAATTGAAGGTAAAATGGTAATTCTACA
Found at i:53025304 original size:27 final size:27
Alignment explanation
Indices: 53025194--53025312 Score: 166
Period size: 27 Copynumber: 4.4 Consensus size: 27
53025184 GTAATTTCAC
53025194 AATCGAGGGTAAAACGGTAATTTTGTA
1 AATCGAGGGTAAAACGGTAATTTTGTA
* * *
53025221 AATTGAAGGTAAAATGGTAATTTTGTA
1 AATCGAGGGTAAAACGGTAATTTTGTA
53025248 AATCGAGGGTAAAACGGTAATTTTGTA
1 AATCGAGGGTAAAACGGTAATTTTGTA
* * * **
53025275 AATTGAGGGTAAAATGGTAATTCTACA
1 AATCGAGGGTAAAACGGTAATTTTGTA
53025302 AATCGAGGGTA
1 AATCGAGGGTA
53025313 TTTCAGTAAT
Statistics
Matches: 80, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 80 1.00
ACGTcount: A:0.39, C:0.06, G:0.25, T:0.30
Consensus pattern (27 bp):
AATCGAGGGTAAAACGGTAATTTTGTA
Found at i:53025322 original size:54 final size:54
Alignment explanation
Indices: 53025194--53025330 Score: 184
Period size: 54 Copynumber: 2.5 Consensus size: 54
53025184 GTAATTTCAC
* * **
53025194 AATCGAGGGTAAAACGGTAATTTTGTAAATTGAAGGTAAAATGGTAATTTTGTA
1 AATCGAGGGTAAAACAGTAATTTTGTAAATTGAAGGTAAAATGGTAATTCTACA
* *
53025248 AATCGAGGGTAAAACGGTAATTTTGTAAATTGAGGGTAAAATGGTAATTCTACA
1 AATCGAGGGTAAAACAGTAATTTTGTAAATTGAAGGTAAAATGGTAATTCTACA
*** *
53025302 AATCGAGGGTATTTCAGTAATTTGGTAAA
1 AATCGAGGGTAAAACAGTAATTTTGTAAA
53025331 CTAAAGTATT
Statistics
Matches: 74, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
54 74 1.00
ACGTcount: A:0.38, C:0.06, G:0.24, T:0.32
Consensus pattern (54 bp):
AATCGAGGGTAAAACAGTAATTTTGTAAATTGAAGGTAAAATGGTAATTCTACA
Found at i:53030292 original size:39 final size:39
Alignment explanation
Indices: 53030249--53030376 Score: 202
Period size: 39 Copynumber: 3.3 Consensus size: 39
53030239 GGTCTTTAAC
* * *
53030249 CCGGATATTTTTCCAGCACATAGCCTGCTGACCTCAAGT
1 CCGGATATTTTTCCAGCATATAGCCTGCGGACCTCATGT
* *
53030288 CCGGATATATTTCTAGCATATAGCCTGCGGACCTCATGT
1 CCGGATATTTTTCCAGCATATAGCCTGCGGACCTCATGT
*
53030327 CCGGATATTTTTCCAGTATATAGCCTGCGGACCTCATGT
1 CCGGATATTTTTCCAGCATATAGCCTGCGGACCTCATGT
53030366 CCGGATATTTT
1 CCGGATATTTT
53030377 CAATCTCATA
Statistics
Matches: 81, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
39 81 1.00
ACGTcount: A:0.22, C:0.27, G:0.20, T:0.32
Consensus pattern (39 bp):
CCGGATATTTTTCCAGCATATAGCCTGCGGACCTCATGT
Found at i:53038138 original size:19 final size:19
Alignment explanation
Indices: 53038114--53038171 Score: 107
Period size: 19 Copynumber: 3.1 Consensus size: 19
53038104 TTTCTTTACT
53038114 ACCCAAGCCTAGATAATTC
1 ACCCAAGCCTAGATAATTC
53038133 ACCCAAGCCTAGATAATTC
1 ACCCAAGCCTAGATAATTC
*
53038152 ACCCAAGCCTAGCTAATTC
1 ACCCAAGCCTAGATAATTC
53038171 A
1 A
53038172 TATTCCTACT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 38 1.00
ACGTcount: A:0.36, C:0.33, G:0.10, T:0.21
Consensus pattern (19 bp):
ACCCAAGCCTAGATAATTC
Found at i:53047109 original size:30 final size:30
Alignment explanation
Indices: 53047053--53047111 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
53047043 TTTACGAGTA
*
53047053 TAGGGACCAAAATGCAAATATGTAAAAGTT
1 TAGGGACCAAAATGAAAATATGTAAAAGTT
* *
53047083 TAGGGATCAAAATGTAAAAT-TTTAAAAGT
1 TAGGGACCAAAATG-AAAATATGTAAAAGT
53047112 ATGATTTATG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.47, C:0.07, G:0.19, T:0.27
Consensus pattern (30 bp):
TAGGGACCAAAATGAAAATATGTAAAAGTT
Found at i:53047601 original size:43 final size:45
Alignment explanation
Indices: 53047548--53047681 Score: 155
Period size: 43 Copynumber: 2.9 Consensus size: 45
53047538 GAGATATGTG
53047548 GCATCCGAGCTCGTTGAGAGGTCCGAGTTCATTATGGATGCG-A-
1 GCATCCGAGCTCGTTGAGAGGTCCGAGTTCATTATGGATGCGCAT
* * * *
53047591 GCATCTGAGCTCGTTGAGAGGTCTGAGTTCATAATAGATGCGACTCAT
1 GCATCCGAGCTCGTTGAGAGGTCCGAGTTCATTATGGATGCG---CAT
*
53047639 GTAACATCCGAGCTTGTTGAGAGGTCCGAGTTCATTATGGATG
1 G---CATCCGAGCTCGTTGAGAGGTCCGAGTTCATTATGGATG
53047682 TGTTACATGT
Statistics
Matches: 74, Mismatches: 9, Indels: 8
0.81 0.10 0.09
Matches are distributed among these distances:
43 38 0.51
47 1 0.01
48 1 0.01
51 34 0.46
ACGTcount: A:0.23, C:0.19, G:0.30, T:0.28
Consensus pattern (45 bp):
GCATCCGAGCTCGTTGAGAGGTCCGAGTTCATTATGGATGCGCAT
Found at i:53061541 original size:19 final size:17
Alignment explanation
Indices: 53061499--53061541 Score: 50
Period size: 19 Copynumber: 2.4 Consensus size: 17
53061489 TTGGGTACAC
*
53061499 AATTATTTTGATATTAA
1 AATTATTTTAATATTAA
53061516 AATTTATTTTAAATATATAA
1 AA-TTATTTT-AATAT-TAA
53061536 AATTAT
1 AATTAT
53061542 ATATTTAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 2 0.09
18 7 0.32
19 8 0.36
20 5 0.23
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (17 bp):
AATTATTTTAATATTAA
Found at i:53061562 original size:23 final size:21
Alignment explanation
Indices: 53061509--53061571 Score: 76
Period size: 22 Copynumber: 3.0 Consensus size: 21
53061499 AATTATTTTG
53061509 ATAT-TAAAATT-TATTTTAA
1 ATATATAAAATTATATTTTAA
53061528 ATATATAAAATTATATATTTAA
1 ATATATAAAATTATAT-TTTAA
* *
53061550 ATTTGTAATAATTATATTTTAA
1 ATATATAA-AATTATATTTTAA
53061572 TTTACATATT
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
19 4 0.11
20 7 0.18
21 3 0.08
22 16 0.42
23 8 0.21
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.51
Consensus pattern (21 bp):
ATATATAAAATTATATTTTAA
Found at i:53061795 original size:7 final size:7
Alignment explanation
Indices: 53061783--53061810 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
53061773 ATGACAATAA
53061783 TTAAATT
1 TTAAATT
53061790 TTAAATT
1 TTAAATT
53061797 TTAAATT
1 TTAAATT
53061804 TTAAATT
1 TTAAATT
53061811 GAAATTTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (7 bp):
TTAAATT
Found at i:53061822 original size:14 final size:14
Alignment explanation
Indices: 53061785--53061818 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
53061775 GACAATAATT
*
53061785 AAATTTTAAATTTT
1 AAATTTTAAATTTG
53061799 AAATTTTAAA-TTG
1 AAATTTTAAATTTG
53061812 AAATTTT
1 AAATTTT
53061819 TAAAAATATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 9 0.47
14 10 0.53
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (14 bp):
AAATTTTAAATTTG
Found at i:53063354 original size:26 final size:26
Alignment explanation
Indices: 53063325--53063386 Score: 72
Period size: 26 Copynumber: 2.4 Consensus size: 26
53063315 TTTCCCCGAC
*
53063325 AAAATTTTGATGATTTTACCCCT-AGT
1 AAAATTTTGACGATTTTACCCCTGA-T
* * *
53063351 AAAAATTTAACGATTTTTCCCCTGAT
1 AAAATTTTGACGATTTTACCCCTGAT
53063377 AAAATTTTGA
1 AAAATTTTGA
53063387 GAAAATATGT
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
26 28 0.97
27 1 0.03
ACGTcount: A:0.35, C:0.15, G:0.10, T:0.40
Consensus pattern (26 bp):
AAAATTTTGACGATTTTACCCCTGAT
Found at i:53102329 original size:20 final size:20
Alignment explanation
Indices: 53102306--53102374 Score: 50
Period size: 20 Copynumber: 3.1 Consensus size: 20
53102296 AGTTCCGAAC
53102306 TCGTTGAGTTGAGTCCGAGT
1 TCGTTGAGTTGAGTCCGAGT
*
53102326 TCG-TGAGATGTAAGTAGGCATCCGAGC
1 TCGTTGAG-T-T--G-A-G--TCCGAGT
53102353 TCGTTGAGTTGAGTCCGAGT
1 TCGTTGAGTTGAGTCCGAGT
53102373 TC
1 TC
53102375 ACTTATGGAT
Statistics
Matches: 38, Mismatches: 2, Indels: 18
0.66 0.03 0.31
Matches are distributed among these distances:
19 4 0.11
20 12 0.32
21 1 0.03
22 1 0.03
23 2 0.05
24 2 0.05
25 1 0.03
26 1 0.03
27 10 0.26
28 4 0.11
ACGTcount: A:0.19, C:0.17, G:0.33, T:0.30
Consensus pattern (20 bp):
TCGTTGAGTTGAGTCCGAGT
Found at i:53104363 original size:41 final size:41
Alignment explanation
Indices: 53104317--53104400 Score: 150
Period size: 41 Copynumber: 2.0 Consensus size: 41
53104307 GTATCAAGAA
*
53104317 CTATTTTGAGTTTCTCACAGTTCAAGACAATTATCAGGTTT
1 CTATTTTGAGTTTCTCACAGCTCAAGACAATTATCAGGTTT
*
53104358 CTATTTTGAGTTTCTCACAGCTCAAGATAATTATCAGGTTT
1 CTATTTTGAGTTTCTCACAGCTCAAGACAATTATCAGGTTT
53104399 CT
1 CT
53104401 TTTCCATTCT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.26, C:0.18, G:0.14, T:0.42
Consensus pattern (41 bp):
CTATTTTGAGTTTCTCACAGCTCAAGACAATTATCAGGTTT
Found at i:53106804 original size:26 final size:26
Alignment explanation
Indices: 53106768--53106824 Score: 78
Period size: 26 Copynumber: 2.2 Consensus size: 26
53106758 TCTTATACCT
* *
53106768 ATTTTACCCCTAACAAAATTTTGACG
1 ATTTTACCCCTAACAAAATCTTAACG
**
53106794 ATTTTACCCCTAGTAAAATCTTAACG
1 ATTTTACCCCTAACAAAATCTTAACG
53106820 ATTTT
1 ATTTT
53106825 GCCATTGGTA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.33, C:0.21, G:0.07, T:0.39
Consensus pattern (26 bp):
ATTTTACCCCTAACAAAATCTTAACG
Found at i:53129000 original size:33 final size:34
Alignment explanation
Indices: 53128963--53129029 Score: 109
Period size: 33 Copynumber: 2.0 Consensus size: 34
53128953 TGTTTAATTA
53128963 GGATTTAGCCTAGACTGGTAATCC-TAATTGACT
1 GGATTTAGCCTAGACTGGTAATCCATAATTGACT
* *
53128996 GGATTTAGCCTGGACTGGTAATCCATATTTGACT
1 GGATTTAGCCTAGACTGGTAATCCATAATTGACT
53129030 CTATAAGGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
33 23 0.74
34 8 0.26
ACGTcount: A:0.25, C:0.18, G:0.22, T:0.34
Consensus pattern (34 bp):
GGATTTAGCCTAGACTGGTAATCCATAATTGACT
Found at i:53129993 original size:39 final size:39
Alignment explanation
Indices: 53129949--53130027 Score: 158
Period size: 39 Copynumber: 2.0 Consensus size: 39
53129939 GACACATGGT
53129949 CGTGTCTCTGCCTGTGTGGAATATACCTAGGCTATTTTC
1 CGTGTCTCTGCCTGTGTGGAATATACCTAGGCTATTTTC
53129988 CGTGTCTCTGCCTGTGTGGAATATACCTAGGCTATTTTC
1 CGTGTCTCTGCCTGTGTGGAATATACCTAGGCTATTTTC
53130027 C
1 C
53130028 AAGCTTTGGT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.15, C:0.24, G:0.23, T:0.38
Consensus pattern (39 bp):
CGTGTCTCTGCCTGTGTGGAATATACCTAGGCTATTTTC
Found at i:53132429 original size:30 final size:30
Alignment explanation
Indices: 53132395--53132455 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
53132385 TCCTTAACTC
53132395 AAACTTTGGAAAAATTACAATTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
* * * * *
53132425 AAACTTTTGCATATTTACACTTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
53132455 A
1 A
53132456 GGCTCGGGAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (30 bp):
AAACTTTGGAAAAATTACAATTTTGCCCCT
Found at i:53136708 original size:27 final size:27
Alignment explanation
Indices: 53136677--53136743 Score: 116
Period size: 27 Copynumber: 2.5 Consensus size: 27
53136667 TTGTCACATT
53136677 TCACTTTGCCATATTTGGCACACTTTA
1 TCACTTTGCCATATTTGGCACACTTTA
*
53136704 TCACTTTGCCATGTTTGGCACACTTTA
1 TCACTTTGCCATATTTGGCACACTTTA
*
53136731 TCATTTTGCCATA
1 TCACTTTGCCATA
53136744 GTTCAACTAT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.21, C:0.25, G:0.12, T:0.42
Consensus pattern (27 bp):
TCACTTTGCCATATTTGGCACACTTTA
Found at i:53145638 original size:91 final size:94
Alignment explanation
Indices: 53145536--53145753 Score: 257
Period size: 94 Copynumber: 2.4 Consensus size: 94
53145526 GTGTATACAT
* ** *
53145536 GCTGATGCATGTCCCAGACATGTCTTACGCTAGCACGAAACT-TA-GCTGATG-TATGTCCCAGA
1 GCTGATGCATGTCCCAGACATGTCTTACACTAGCACGAAACTCTACGCCAATGCCATGTCCCAGA
* *
53145598 C-ACGTCTTACACTGGCTAACATCATCGAG
66 CGACGTCTTACACGGGCTAACAGCAT-GAG
* ** *
53145627 GCTGATGCATGTCCCAGACATGTCTTACACTGGCACTCACCTCTACGCCAATGCCATGTCCCAGA
1 GCTGATGCATGTCCCAGACATGTCTTACACTAGCACGAAACTCTACGCCAATGCCATGTCCCAGA
** * *
53145692 CGTGGTCTTACACGGGCTATCAGGATGAG
66 CGACGTCTTACACGGGCTAACAGCATGAG
*
53145721 ACTGATGCATGTCCCAGACATGTCTTA-ACTAGC
1 GCTGATGCATGTCCCAGACATGTCTTACACTAGC
53145754 CCTCCTCTCA
Statistics
Matches: 107, Mismatches: 16, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
91 37 0.35
92 2 0.02
93 10 0.09
94 40 0.37
95 18 0.17
ACGTcount: A:0.25, C:0.29, G:0.22, T:0.25
Consensus pattern (94 bp):
GCTGATGCATGTCCCAGACATGTCTTACACTAGCACGAAACTCTACGCCAATGCCATGTCCCAGA
CGACGTCTTACACGGGCTAACAGCATGAG
Found at i:53145643 original size:47 final size:47
Alignment explanation
Indices: 53145580--53145802 Score: 170
Period size: 47 Copynumber: 4.7 Consensus size: 47
53145570 ACGAAACTTA
* *
53145580 GCTGATGTATGTCCCAGACACGTCTTACACTGGCTAACATCATCGAG
1 GCTGATGCATGTCCCAGACATGTCTTACACTGGCTAACATCATCGAG
* *
53145627 GCTGATGCATGTCCCAGACATGTCTTACACTGGC--AC-TCACCTCTAC
1 GCTGATGCATGTCCCAGACATGTCTTACACTGGCTAACATCA--TCGAG
** * * * **
53145673 GCCAATGCCATGTCCCAGACGTGGTCTTACACGGGCTATCAGGAT-GAG
1 GCTGATG-CATGTCCCAGACAT-GTCTTACACTGGCTAACATCATCGAG
* * *** * * *
53145721 ACTGATGCATGTCCCAGACATGTCTTA-ACTAGCCCTCCTC-TCAAT
1 GCTGATGCATGTCCCAGACATGTCTTACACTGGCTAACATCATCGAG
*
53145766 GCTGATGTCATGTCCCAGACATGGTCTTATACTGGCT
1 GCTGATG-CATGTCCCAGACAT-GTCTTACACTGGCT
53145803 CTCACATAAC
Statistics
Matches: 136, Mismatches: 29, Indels: 21
0.73 0.16 0.11
Matches are distributed among these distances:
44 4 0.03
45 15 0.11
46 28 0.21
47 64 0.47
48 22 0.16
49 1 0.01
50 1 0.01
51 1 0.01
ACGTcount: A:0.23, C:0.30, G:0.21, T:0.26
Consensus pattern (47 bp):
GCTGATGCATGTCCCAGACATGTCTTACACTGGCTAACATCATCGAG
Found at i:53146197 original size:30 final size:30
Alignment explanation
Indices: 53146140--53146197 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
53146130 AAATTTATAT
* *
53146140 CTTTGATAAAATGACCATTTTGCCCCTAGA
1 CTTTGACAAAATGACCATTTTACCCCTAGA
*
53146170 CTTTGACAAAATGACCATTTTATCCCTA
1 CTTTGACAAAATGACCATTTTACCCCTA
53146198 TGCTCGAAAG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.31, C:0.24, G:0.10, T:0.34
Consensus pattern (30 bp):
CTTTGACAAAATGACCATTTTACCCCTAGA
Found at i:53148907 original size:57 final size:57
Alignment explanation
Indices: 53148814--53148933 Score: 231
Period size: 57 Copynumber: 2.1 Consensus size: 57
53148804 AGCTTTCTCA
*
53148814 AGGCATAGGCTATAACCTTGCCTTTTTGCATTAGCACACTCCCTAAACCGTTTAGGG
1 AGGCGTAGGCTATAACCTTGCCTTTTTGCATTAGCACACTCCCTAAACCGTTTAGGG
53148871 AGGCGTAGGCTATAACCTTGCCTTTTTGCATTAGCACACTCCCTAAACCGTTTAGGG
1 AGGCGTAGGCTATAACCTTGCCTTTTTGCATTAGCACACTCCCTAAACCGTTTAGGG
53148928 AGGCGT
1 AGGCGT
53148934 CATTAAAAAC
Statistics
Matches: 62, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
57 62 1.00
ACGTcount: A:0.23, C:0.26, G:0.22, T:0.29
Consensus pattern (57 bp):
AGGCGTAGGCTATAACCTTGCCTTTTTGCATTAGCACACTCCCTAAACCGTTTAGGG
Found at i:53150679 original size:43 final size:43
Alignment explanation
Indices: 53150617--53150702 Score: 145
Period size: 43 Copynumber: 2.0 Consensus size: 43
53150607 ATTTATTTCG
*
53150617 GGACAATCTCAGATGAAGTGATCTAACGACCCACACTTGAAAC
1 GGACAATCTCAGATAAAGTGATCTAACGACCCACACTTGAAAC
**
53150660 GGACAATCTGGGATAAAGTGATCTAACGACCCACACTTGAAAC
1 GGACAATCTCAGATAAAGTGATCTAACGACCCACACTTGAAAC
53150703 AGCCCCTATC
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 40 1.00
ACGTcount: A:0.37, C:0.24, G:0.20, T:0.19
Consensus pattern (43 bp):
GGACAATCTCAGATAAAGTGATCTAACGACCCACACTTGAAAC
Found at i:53152232 original size:55 final size:54
Alignment explanation
Indices: 53152173--53152291 Score: 141
Period size: 55 Copynumber: 2.2 Consensus size: 54
53152163 CGTGTGCGAC
* * * * *
53152173 ACTGACTTTAGGGCACGGCCATGACACACGCCTGTGTGGCCTACCCGTGGGCAAT
1 ACTGACTTTA-GACACAGCCATGACACACGCCCGTGTGGCCTAACCGTGGACAAT
* * *
53152228 ACTGACTTATAGACACAGCTATGGCACACGCCCGTGTGGCCTAACCGTGTACAAT
1 ACTGACTT-TAGACACAGCCATGACACACGCCCGTGTGGCCTAACCGTGGACAAT
53152283 ACTGA-TTTA
1 ACTGACTTTA
53152292 AAAATTTAAG
Statistics
Matches: 55, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
53 2 0.04
54 2 0.04
55 49 0.89
56 2 0.04
ACGTcount: A:0.24, C:0.29, G:0.24, T:0.23
Consensus pattern (54 bp):
ACTGACTTTAGACACAGCCATGACACACGCCCGTGTGGCCTAACCGTGGACAAT
Found at i:53153124 original size:49 final size:46
Alignment explanation
Indices: 53153055--53153417 Score: 198
Period size: 47 Copynumber: 7.7 Consensus size: 46
53153045 TTACCGCTGC
*
53153055 CATGTCCCA-AGCATGGTCTTACGCTAGCTATCTCCAACTAGGCCGATG
1 CATGTCCCAGA-CATGGTCTTACACTAGCTA-CT-CAACTAGGCCGATG
* *
53153103 CCATGTCCCAGACATGGTCTTACACTAGCT-CTCGTGTA-TATGTGCTGATG
1 -CATGTCCCAGACATGGTCTTACACTAGCTACTC---AACTA-G-GCCGATG
**
53153153 CATGTCCCAGACAT-GTCTTACACTAGC-ACGAAACTCA-GCCGATG
1 CATGTCCCAGACATGGTCTTACACTAGCTACTCAACT-AGGCCGATG
* * * * *
53153197 CATGTCCCAGACA-CGTCTTACACTGGCTAACATCATCGAGGTCGATG
1 CATGTCCCAGACATGGTCTTACACTAGCT-AC-TCAACTAGGCCGATG
* * * *
53153244 CATGTCCTAGACAT-GTCTTACACTGGC-ACTCACCTCTACGCCGATG
1 CATGTCCCAGACATGGTCTTACACTAGCTACTCA--ACTAGGCCGATG
* ** *
53153290 CCATGTCCCAGACGTGGTCTTACACGGGCTA-TC-A-TGATGCAGCTGATG
1 -CATGTCCCAGACATGGTCTTACACTAGCTACTCAACT-A-G--GCCGATG
* * ** * *
53153338 CATGTCCCAGACAT-GTCTTACAGTAGC-CCTCGTCTTAATGTCGATG
1 CATGTCCCAGACATGGTCTTACACTAGCTACTCAAC-T-AGGCCGATG
*
53153384 CCATGTCCCAGACATGGTCTTATACTAGCT-CTCA
1 -CATGTCCCAGACATGGTCTTACACTAGCTACTCA
53153418 CATAACCCAA
Statistics
Matches: 247, Mismatches: 36, Indels: 63
0.71 0.10 0.18
Matches are distributed among these distances:
44 35 0.14
45 4 0.02
46 31 0.13
47 75 0.30
48 50 0.20
49 45 0.18
50 7 0.03
ACGTcount: A:0.23, C:0.30, G:0.20, T:0.26
Consensus pattern (46 bp):
CATGTCCCAGACATGGTCTTACACTAGCTACTCAACTAGGCCGATG
Found at i:53153341 original size:94 final size:93
Alignment explanation
Indices: 53153096--53153405 Score: 326
Period size: 94 Copynumber: 3.3 Consensus size: 93
53153086 CTCCAACTAG
* * * *
53153096 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCGTGTATATG-TGCTGATGCATGTCC
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTATCATG---ATGCAGCTGATGCATGTCC
**
53153160 CAGACATGTCTTACACTAGCACGAAACTC-A
63 CAGACATGTCTTACACTAGCACTCAACTCTA
* * * * *
53153190 GCCGATG-CATGTCCCAGACA-CGTCTTACACTGGCTAACATCAT-CGAGGTCGATGCATGTCCT
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTATCATGATGC-AGCT-GATGCATGTCCC
* *
53153252 AGACATGTCTTACACTGGCACTCACCTCTA
64 AGACATGTCTTACACTAGCACTCAACTCTA
* *
53153282 CGCCGATGCCATGTCCCAGACGTGGTCTTACACGGGCTATCATGATGCAGCTGATGCATGTCCCA
1 -GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTATCATGATGCAGCTGATGCATGTCCCA
* * **
53153347 GACATGTCTTACAGTAGCCCTCGTCT-TAA
65 GACATGTCTTACACTAGCACTCAACTCT-A
*
53153376 TGTCGATGCCATGTCCCAGACATGGTCTTA
1 -GCCGATGCCATGTCCCAGACATGGTCTTA
53153406 TACTAGCTCT
Statistics
Matches: 179, Mismatches: 28, Indels: 18
0.80 0.12 0.08
Matches are distributed among these distances:
89 2 0.01
90 2 0.01
91 35 0.20
92 16 0.09
93 21 0.12
94 80 0.45
95 22 0.12
96 1 0.01
ACGTcount: A:0.23, C:0.30, G:0.21, T:0.26
Consensus pattern (93 bp):
GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTATCATGATGCAGCTGATGCATGTCCCAG
ACATGTCTTACACTAGCACTCAACTCTA
Found at i:53156257 original size:46 final size:46
Alignment explanation
Indices: 53156204--53156379 Score: 207
Period size: 46 Copynumber: 3.8 Consensus size: 46
53156194 TGGTTGAGCA
53156204 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
53156250 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
* *
53156295 CATCCAAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
53156343 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
53156380 GCGGGTTACA
Statistics
Matches: 109, Mismatches: 12, Indels: 18
0.78 0.09 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 3 0.03
46 62 0.57
47 28 0.26
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.21, C:0.21, G:0.29, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:53156360 original size:93 final size:93
Alignment explanation
Indices: 53156201--53156372 Score: 308
Period size: 93 Copynumber: 1.8 Consensus size: 93
53156191 AGATGGTTGA
* * *
53156201 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCAAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
53156266 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
*
53156294 GCATCCAAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCAAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
53156359 TGAGTCCGAGTTCG
66 TGAGTCCGAGTTCG
53156373 CTTATGGGCG
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.22, C:0.22, G:0.29, T:0.28
Consensus pattern (93 bp):
GCATCCAAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:53158732 original size:39 final size:39
Alignment explanation
Indices: 53158678--53158840 Score: 263
Period size: 39 Copynumber: 4.2 Consensus size: 39
53158668 TGTGAATGAA
53158678 TGTGCGAATTGTGATATCCGGGCTAAGCCCGAAGGCAAT
1 TGTGCGAATTGTGATATCCGGGCTAAGCCCGAAGGCAAT
53158717 TGTGCGAATTGTGATATCCGGGCTAAGCCCGAAGGCAAT
1 TGTGCGAATTGTGATATCCGGGCTAAGCCCGAAGGCAAT
** *
53158756 TGTGCGAGCTATGATATCCGGGCTAAGCCCGAAGGCAAT
1 TGTGCGAATTGTGATATCCGGGCTAAGCCCGAAGGCAAT
* * *
53158795 TGTGCGAGTTGTGATATCCGGGTTAAGTCCCGAAGGCATT
1 TGTGCGAATTGTGATATCCGGGCTAAG-CCCGAAGGCAAT
53158835 TGTGCG
1 TGTGCG
53158841 GGTTACCATA
Statistics
Matches: 116, Mismatches: 7, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
39 99 0.85
40 17 0.15
ACGTcount: A:0.23, C:0.20, G:0.32, T:0.25
Consensus pattern (39 bp):
TGTGCGAATTGTGATATCCGGGCTAAGCCCGAAGGCAAT
Found at i:53158856 original size:40 final size:39
Alignment explanation
Indices: 53158678--53158870 Score: 251
Period size: 39 Copynumber: 4.9 Consensus size: 39
53158668 TGTGAATGAA
* *
53158678 TGTGCGAATTGTGATATCCGGGCTAAGCCCGAAGGCAAT
1 TGTGCGAGTTATGATATCCGGGCTAAGCCCGAAGGCAAT
* *
53158717 TGTGCGAATTGTGATATCCGGGCTAAGCCCGAAGGCAAT
1 TGTGCGAGTTATGATATCCGGGCTAAGCCCGAAGGCAAT
*
53158756 TGTGCGAGCTATGATATCCGGGCTAAGCCCGAAGGCAAT
1 TGTGCGAGTTATGATATCCGGGCTAAGCCCGAAGGCAAT
* * *
53158795 TGTGCGAGTTGTGATATCCGGGTTAAGTCCCGAAGGCATT
1 TGTGCGAGTTATGATATCCGGGCTAAG-CCCGAAGGCAAT
* ** * *
53158835 TGTGCGGGTTACCATAACCGGGCTATGTCCCGAAGG
1 TGTGCGAGTTATGATATCCGGGCTAAG-CCCGAAGG
53158871 TGTTTTGAAC
Statistics
Matches: 139, Mismatches: 14, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
39 99 0.71
40 40 0.29
ACGTcount: A:0.23, C:0.21, G:0.32, T:0.24
Consensus pattern (39 bp):
TGTGCGAGTTATGATATCCGGGCTAAGCCCGAAGGCAAT
Found at i:53166684 original size:39 final size:39
Alignment explanation
Indices: 53166630--53166792 Score: 263
Period size: 39 Copynumber: 4.2 Consensus size: 39
53166620 TGTGAATGAA
53166630 TGTGCGAATTGTGATATCCGGGCTAAGCCCGAAGGCAAT
1 TGTGCGAATTGTGATATCCGGGCTAAGCCCGAAGGCAAT
53166669 TGTGCGAATTGTGATATCCGGGCTAAGCCCGAAGGCAAT
1 TGTGCGAATTGTGATATCCGGGCTAAGCCCGAAGGCAAT
** *
53166708 TGTGCGAGCTATGATATCCGGGCTAAGCCCGAAGGCAAT
1 TGTGCGAATTGTGATATCCGGGCTAAGCCCGAAGGCAAT
* * *
53166747 TGTGCGAGTTGTGATATCCGGGTTAAGTCCCGAAGGCATT
1 TGTGCGAATTGTGATATCCGGGCTAAG-CCCGAAGGCAAT
53166787 TGTGCG
1 TGTGCG
53166793 GGTTACCATA
Statistics
Matches: 116, Mismatches: 7, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
39 99 0.85
40 17 0.15
ACGTcount: A:0.23, C:0.20, G:0.32, T:0.25
Consensus pattern (39 bp):
TGTGCGAATTGTGATATCCGGGCTAAGCCCGAAGGCAAT
Found at i:53170497 original size:21 final size:21
Alignment explanation
Indices: 53170467--53170520 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
53170457 GTTCCATTTG
* *
53170467 GTATCGGTAGAACCCGTTAAA
1 GTATCAGTAGAACCCGTCAAA
53170488 GTATCAGTAGAACCCGTCAAA
1 GTATCAGTAGAACCCGTCAAA
* *
53170509 TTATCAATAGAA
1 GTATCAGTAGAA
53170521 GTGCAGGAGA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.39, C:0.19, G:0.19, T:0.24
Consensus pattern (21 bp):
GTATCAGTAGAACCCGTCAAA
Found at i:53170592 original size:21 final size:21
Alignment explanation
Indices: 53170566--53170619 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
53170556 GTTCCATTTG
*
53170566 GTATCAGTAGAACCCGTTAAA
1 GTATCAGTAGAACCCGTCAAA
53170587 GTATCAGTAGAACCCGTCAAA
1 GTATCAGTAGAACCCGTCAAA
* *
53170608 TTATCAATAGAA
1 GTATCAGTAGAA
53170620 GTGCAGGAGA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.41, C:0.19, G:0.17, T:0.24
Consensus pattern (21 bp):
GTATCAGTAGAACCCGTCAAA
Found at i:53170626 original size:99 final size:99
Alignment explanation
Indices: 53170455--53170654 Score: 382
Period size: 99 Copynumber: 2.0 Consensus size: 99
53170445 AGAAATTTAA
*
53170455 GGGTTCCATTTGGTATCGGTAGAACCCGTTAAAGTATCAGTAGAACCCGTCAAATTATCAATAGA
1 GGGTTCCATTTGGTATCAGTAGAACCCGTTAAAGTATCAGTAGAACCCGTCAAATTATCAATAGA
*
53170520 AGTGCAGGAGATGCTGAACTTTGGCTACTATCTT
66 AGTGCAGGAGATGCTGAACTTGGGCTACTATCTT
53170554 GGGTTCCATTTGGTATCAGTAGAACCCGTTAAAGTATCAGTAGAACCCGTCAAATTATCAATAGA
1 GGGTTCCATTTGGTATCAGTAGAACCCGTTAAAGTATCAGTAGAACCCGTCAAATTATCAATAGA
53170619 AGTGCAGGAGATGCTGAACTTGGGCTACTATCTT
66 AGTGCAGGAGATGCTGAACTTGGGCTACTATCTT
53170653 GG
1 GG
53170655 CTTGTTTCTA
Statistics
Matches: 99, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
99 99 1.00
ACGTcount: A:0.29, C:0.18, G:0.24, T:0.28
Consensus pattern (99 bp):
GGGTTCCATTTGGTATCAGTAGAACCCGTTAAAGTATCAGTAGAACCCGTCAAATTATCAATAGA
AGTGCAGGAGATGCTGAACTTGGGCTACTATCTT
Found at i:53177632 original size:75 final size:75
Alignment explanation
Indices: 53177428--53177620 Score: 323
Period size: 75 Copynumber: 2.6 Consensus size: 75
53177418 TTGATCGCGT
* *
53177428 TCACTCTCGTGTCTCCTCAACCTACTACTGCTTCTCTCTCTCCTATCTCTCTCCCGCTCCCTCTC
1 TCACTCTCGTGCCTCCTCGACCTACTACTGCTTCTCTCTCTCCTATCTCTCTCCCGCTCCCTCTC
*
53177493 TAGCTCACGA
66 AAGCTCACGA
* *
53177503 TCACTCTCGTGCCTCCTCGACCTACTACTGCTCCTCTCTCTCCTATCTCTCTCCCGTTCCCTCTC
1 TCACTCTCGTGCCTCCTCGACCTACTACTGCTTCTCTCTCTCCTATCTCTCTCCCGCTCCCTCTC
*
53177568 AATCTCACGA
66 AAGCTCACGA
*
53177578 TCACTTTCGTGCCTCCTCGACCTACTACTGCTTCTCTCTCTCC
1 TCACTCTCGTGCCTCCTCGACCTACTACTGCTTCTCTCTCTCC
53177621 GGTCTACCTC
Statistics
Matches: 110, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
75 110 1.00
ACGTcount: A:0.11, C:0.46, G:0.08, T:0.35
Consensus pattern (75 bp):
TCACTCTCGTGCCTCCTCGACCTACTACTGCTTCTCTCTCTCCTATCTCTCTCCCGCTCCCTCTC
AAGCTCACGA
Found at i:53177657 original size:20 final size:20
Alignment explanation
Indices: 53177632--53177690 Score: 69
Period size: 20 Copynumber: 3.3 Consensus size: 20
53177622 GTCTACCTCC
53177632 CTCTCTTTCTCCTTTTCCTT
1 CTCTCTTTCTCCTTTTCCTT
53177652 CTCTCTTTC-CC---TCC-T
1 CTCTCTTTCTCCTTTTCCTT
53177667 CTCTC--TCTCCTTTTCCTT
1 CTCTCTTTCTCCTTTTCCTT
53177685 CTCTCT
1 CTCTCT
53177691 CCTATCCCTC
Statistics
Matches: 33, Mismatches: 0, Indels: 13
0.72 0.00 0.28
Matches are distributed among these distances:
13 2 0.06
14 2 0.06
15 6 0.18
16 3 0.09
17 3 0.09
18 6 0.18
19 2 0.06
20 9 0.27
ACGTcount: A:0.00, C:0.46, G:0.00, T:0.54
Consensus pattern (20 bp):
CTCTCTTTCTCCTTTTCCTT
Found at i:53177669 original size:33 final size:33
Alignment explanation
Indices: 53177629--53177711 Score: 118
Period size: 33 Copynumber: 2.5 Consensus size: 33
53177619 CCGGTCTACC
53177629 TCCCTCTCTTTCTCCTTTTCCTTCTCTCT--T-
1 TCCCTCTCTTTCTCCTTTTCCTTCTCTCTCCTA
53177659 TCCCTCCTCTCTCTCTCCTTTTCCTTCTCTCTCCTA
1 TCCCT-CTCT-T-TCTCCTTTTCCTTCTCTCTCCTA
53177695 TCCCTCTCTTTCTCCTT
1 TCCCTCTCTTTCTCCTT
53177712 ATCTTTTTCT
Statistics
Matches: 47, Mismatches: 0, Indels: 9
0.84 0.00 0.16
Matches are distributed among these distances:
30 5 0.11
31 4 0.09
32 1 0.02
33 26 0.55
34 1 0.02
35 5 0.11
36 5 0.11
ACGTcount: A:0.01, C:0.47, G:0.00, T:0.52
Consensus pattern (33 bp):
TCCCTCTCTTTCTCCTTTTCCTTCTCTCTCCTA
Found at i:53177735 original size:33 final size:33
Alignment explanation
Indices: 53177632--53177735 Score: 111
Period size: 33 Copynumber: 3.2 Consensus size: 33
53177622 GTCTACCTCC
**
53177632 CTCTCTTTCTCCTTTTCCTTCTCTCTT-TCCCT
1 CTCTCTTTCTCCTTTTCCTTCTCTCTTCTATCT
* * *
53177664 CCTCTCTCTCTCCTTTTCCTTCTCTCTCCTATCC
1 -CTCTCTTTCTCCTTTTCCTTCTCTCTTCTATCT
* * * *
53177698 CTCTCTTTCTCCTTATCTTTTTCTCTTCTTTCT
1 CTCTCTTTCTCCTTTTCCTTCTCTCTTCTATCT
53177731 CTCTC
1 CTCTC
53177736 CCTTTCCTTC
Statistics
Matches: 58, Mismatches: 12, Indels: 2
0.81 0.17 0.03
Matches are distributed among these distances:
33 56 0.97
34 2 0.03
ACGTcount: A:0.02, C:0.43, G:0.00, T:0.55
Consensus pattern (33 bp):
CTCTCTTTCTCCTTTTCCTTCTCTCTTCTATCT
Found at i:53177735 original size:66 final size:66
Alignment explanation
Indices: 53177629--53177766 Score: 161
Period size: 66 Copynumber: 2.1 Consensus size: 66
53177619 CCGGTCTACC
* * * *
53177629 TCCCTCTCTTTCTCCTTTTCCTTCTCTCTTTCCCTCCTCTCTCTCTCCTTTTCCTTCTCTCTCCT
1 TCCCTCTCTTTCTCCTTATCCTTCTCTCTTTCCCTCCTCTCCCTCTCCTTCTCCCTCTCTCTCCT
53177694 A
66 A
* * ** * *
53177695 TCCCTCTCTTTCTCCTTATCTTTTTCTC-TTCTTTCTCTCTCCCTTTCCTTCTCCCTCTCTCTGC
1 TCCCTCTCTTTCTCCTTATCCTTCTCTCTTTCCCTC-CTCTCCCTCTCCTTCTCCCTCTCTCTCC
53177759 TA
65 TA
*
53177761 CCCCTC
1 TCCCTC
53177767 CTCTCTAAAT
Statistics
Matches: 60, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
65 5 0.08
66 55 0.92
ACGTcount: A:0.02, C:0.46, G:0.01, T:0.51
Consensus pattern (66 bp):
TCCCTCTCTTTCTCCTTATCCTTCTCTCTTTCCCTCCTCTCCCTCTCCTTCTCCCTCTCTCTCCT
A
Found at i:53178674 original size:56 final size:56
Alignment explanation
Indices: 53178611--53178769 Score: 160
Period size: 56 Copynumber: 2.8 Consensus size: 56
53178601 GTTAAGCTTA
53178611 ATAATATTATATTGATAATAAATTTTATTTTTATTTTTAAAAATATTTAAAATTATT
1 ATAATATTATATTGATAATAAATTTTATTTTTATTTTTAAAAATATTT-AAATTATT
*** * * ** * * * **
53178668 A-AATATTAATAAAAATATTATATTTT-TTAATATTATTAAACATATATATTTTATT
1 ATAATATT-ATATTGATAATAAATTTTATTTTTATTTTTAAAAATATTTAAATTATT
**
53178723 ATTTTATTATATTGATAATAAATTTTATTTTTATTTTTAAAAATATT
1 ATAATATTATATTGATAATAAATTTTATTTTTATTTTTAAAAATATT
53178770 AATAAAAATA
Statistics
Matches: 75, Mismatches: 24, Indels: 7
0.71 0.23 0.07
Matches are distributed among these distances:
55 20 0.27
56 41 0.55
57 14 0.19
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.55
Consensus pattern (56 bp):
ATAATATTATATTGATAATAAATTTTATTTTTATTTTTAAAAATATTTAAATTATT
Found at i:53178712 original size:27 final size:26
Alignment explanation
Indices: 53178669--53178719 Score: 75
Period size: 27 Copynumber: 1.9 Consensus size: 26
53178659 AAAATTATTA
53178669 AATATTAATAAAAATATTATATTTTTT
1 AATATTAATAAAAATA-TATATTTTTT
* *
53178696 AATATTATTAAACATATATATTTT
1 AATATTAATAAAAATATATATTTT
53178720 ATTATTTTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 8 0.36
27 14 0.64
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (26 bp):
AATATTAATAAAAATATATATTTTTT
Found at i:53178752 original size:94 final size:96
Alignment explanation
Indices: 53178654--53178873 Score: 254
Period size: 94 Copynumber: 2.3 Consensus size: 96
53178644 TTTTTAAAAA
* * * *
53178654 TATTTAAAATTATTAAATATTAATAAAAATATTATATTTTTTAATATTATTAAACATATATATTT
1 TATTTATAATTATTAAATATTAATAAAAATA-TATATCTTTCAATATTATTAAACATACATATTT
*
53178719 TATTATTT-TATTATA-TT-GATAATAAATT-T
65 AATTATTTATATT-TAGTTAGATAATAAATTAT
* *
53178748 TATTT-TTATTTTTAAAAATATTAATAAAAATATATATCTTTCAATATTATTAAACATACATATT
1 TATTTATAATTATT--AAATATTAATAAAAATATATATCTTTCAATATTATTAAACATACATATT
*
53178812 TAATTATTTATATTTAGTTATATAATAAATTAT
64 TAATTATTTATATTTAGTTAGATAATAAATTAT
*
53178845 T-TTTATAATTAATATAATTTATTAATAAA
1 TATTTATAATT-AT-TAA-ATATTAATAAA
53178874 TTATTTAATA
Statistics
Matches: 105, Mismatches: 11, Indels: 16
0.80 0.08 0.12
Matches are distributed among these distances:
93 5 0.05
94 44 0.42
95 23 0.22
96 13 0.12
97 8 0.08
98 11 0.10
99 1 0.01
ACGTcount: A:0.45, C:0.02, G:0.01, T:0.52
Consensus pattern (96 bp):
TATTTATAATTATTAAATATTAATAAAAATATATATCTTTCAATATTATTAAACATACATATTTA
ATTATTTATATTTAGTTAGATAATAAATTAT
Found at i:53178853 original size:16 final size:16
Alignment explanation
Indices: 53178832--53178879 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
53178822 TATTTAGTTA
53178832 TATAATAAATTATTTT
1 TATAATAAATTATTTT
* *
53178848 TATAATTAA-TATAATT
1 TATAATAAATTAT-TTT
53178864 TATTAATAAATTATTT
1 TA-TAATAAATTATTT
53178880 AATATTTTAA
Statistics
Matches: 25, Mismatches: 4, Indels: 5
0.74 0.12 0.15
Matches are distributed among these distances:
15 3 0.12
16 12 0.48
17 7 0.28
18 3 0.12
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (16 bp):
TATAATAAATTATTTT
Found at i:53178890 original size:33 final size:34
Alignment explanation
Indices: 53178829--53178909 Score: 85
Period size: 34 Copynumber: 2.4 Consensus size: 34
53178819 TTATATTTAG
*
53178829 TTATATAATAAATTATTTTTATAATTAA-TATAAT
1 TTAT-TAATAAATTATTTATATAATTAATTATAAT
* * *
53178863 TTATTAATAAATTATTTA-ATATTTTAATTTTATT
1 TTATTAATAAATTATTTATATA-ATTAATTATAAT
*
53178897 TTAATAATAAATT
1 TTATTAATAAATT
53178910 TTAAAAATAA
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
32 3 0.08
33 17 0.43
34 20 0.50
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (34 bp):
TTATTAATAAATTATTTATATAATTAATTATAAT
Found at i:53178934 original size:16 final size:17
Alignment explanation
Indices: 53178898--53178934 Score: 60
Period size: 16 Copynumber: 2.3 Consensus size: 17
53178888 AATTTTATTT
53178898 TAATAATAAATTTTAAA
1 TAATAATAAATTTTAAA
53178915 -AATAATAAA-TTTAAA
1 TAATAATAAATTTTAAA
53178930 TAATA
1 TAATA
53178935 TCATTCAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 6 0.32
16 13 0.68
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
TAATAATAAATTTTAAA
Found at i:53179768 original size:16 final size:15
Alignment explanation
Indices: 53179737--53179773 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
53179727 AGCACTCAAA
53179737 TTTTCAACATTTATT
1 TTTTCAACATTTATT
* *
53179752 TTTTTAACATTTAAT
1 TTTTCAACATTTATT
53179767 TTTTCAA
1 TTTTCAA
53179774 TTTATCAAAC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.30, C:0.11, G:0.00, T:0.59
Consensus pattern (15 bp):
TTTTCAACATTTATT
Found at i:53180402 original size:20 final size:22
Alignment explanation
Indices: 53180366--53180412 Score: 80
Period size: 20 Copynumber: 2.2 Consensus size: 22
53180356 CTTTTAATAA
53180366 TAAATTTTAACAATAATATTTT
1 TAAATTTTAACAATAATATTTT
53180388 TAAATTTT-A-AATAATATTTT
1 TAAATTTTAACAATAATATTTT
53180408 TAAAT
1 TAAAT
53180413 ATTATTGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
20 16 0.64
21 1 0.04
22 8 0.32
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (22 bp):
TAAATTTTAACAATAATATTTT
Found at i:53180513 original size:22 final size:23
Alignment explanation
Indices: 53180466--53180523 Score: 66
Period size: 25 Copynumber: 2.4 Consensus size: 23
53180456 TATTACAGTT
53180466 TATAGATATTTAATAATAAATAAAA
1 TATA-ATATTTAATAAT-AATAAAA
53180491 TATTAATATTTAATAAT-AT-AAA
1 TA-TAATATTTAATAATAATAAAA
53180513 TATAAGTATTT
1 TATAA-TATTT
53180524 GTTTAAATCA
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
21 3 0.10
22 10 0.32
23 2 0.06
25 14 0.45
26 2 0.06
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.43
Consensus pattern (23 bp):
TATAATATTTAATAATAATAAAA
Found at i:53181481 original size:23 final size:23
Alignment explanation
Indices: 53181437--53181482 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
53181427 AAATATGTCG
*
53181437 TTTTTTTTAATTGGTTAAAAATAT
1 TTTTTTTTAATT-GTAAAAAATAT
53181461 TTTTTTTTAATT-TAAAGAAATA
1 TTTTTTTTAATTGTAAA-AAATA
53181483 GGTTGATTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 3 0.15
23 5 0.25
24 12 0.60
ACGTcount: A:0.37, C:0.00, G:0.07, T:0.57
Consensus pattern (23 bp):
TTTTTTTTAATTGTAAAAAATAT
Found at i:53187065 original size:14 final size:14
Alignment explanation
Indices: 53187042--53187074 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
53187032 ATGGAAATTC
*
53187042 GATTTCTACTAGTT
1 GATTTATACTAGTT
53187056 GATTTATACTAGTT
1 GATTTATACTAGTT
53187070 GATTT
1 GATTT
53187075 CCTAACATCT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.24, C:0.09, G:0.15, T:0.52
Consensus pattern (14 bp):
GATTTATACTAGTT
Found at i:53187687 original size:26 final size:26
Alignment explanation
Indices: 53187636--53187687 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
53187626 TTTTCTTCAT
*
53187636 GTTTTTAATAACATAAAGAGCTATGA
1 GTTTTTAATAACATAAAGAGCAATGA
*
53187662 GTTTTTGAATAACATAAA-ATCAATGA
1 GTTTTT-AATAACATAAAGAGCAATGA
53187688 TTATGGTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 12 0.52
27 11 0.48
ACGTcount: A:0.44, C:0.08, G:0.13, T:0.35
Consensus pattern (26 bp):
GTTTTTAATAACATAAAGAGCAATGA
Found at i:53188120 original size:34 final size:35
Alignment explanation
Indices: 53188076--53188150 Score: 95
Period size: 34 Copynumber: 2.2 Consensus size: 35
53188066 TTCTTAATAA
*
53188076 TAAT-ATTATATTAA-AATTGTTATTAAATAT-TA-T
1 TAATAATTATATTAAGAA-TATTATTAAAT-TGTATT
53188109 TAATAATTATATTAAGAATATTATTAAATTGTATT
1 TAATAATTATATTAAGAATATTATTAAATTGTATT
53188144 TAATAAT
1 TAATAAT
53188151 AATTATGTTA
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
33 5 0.14
34 22 0.59
35 10 0.27
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (35 bp):
TAATAATTATATTAAGAATATTATTAAATTGTATT
Found at i:53188230 original size:25 final size:26
Alignment explanation
Indices: 53188181--53188230 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
53188171 AAATTATTTT
*
53188181 TTATTAAAATATATTTAACAATAATC
1 TTATTAAAATATATATAACAATAATC
*
53188207 TTATTAAAATTTA-ATAACAATAAT
1 TTATTAAAATATATATAACAATAAT
53188231 TAACTATCTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 10 0.45
26 12 0.55
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.42
Consensus pattern (26 bp):
TTATTAAAATATATATAACAATAATC
Found at i:53189147 original size:26 final size:27
Alignment explanation
Indices: 53189120--53189209 Score: 92
Period size: 27 Copynumber: 3.2 Consensus size: 27
53189110 ATAAAAAATC
53189120 AAAACTCATAGTTCTTTATGTTATTCA
1 AAAACTCATAGTTCTTTATGTTATTCA
*
53189147 AAAAC-CATAATTCTTGATTTTATGTTATTCA
1 AAAACTCATAGTTC-----TTTATGTTATTCA
* * *
53189178 AAAACTTATAGTTCTTTATATTATTAA
1 AAAACTCATAGTTCTTTATGTTATTCA
53189205 AAAAC
1 AAAAC
53189210 ATGAAGAAAA
Statistics
Matches: 52, Mismatches: 5, Indels: 12
0.75 0.07 0.17
Matches are distributed among these distances:
26 7 0.13
27 21 0.40
31 18 0.35
32 6 0.12
ACGTcount: A:0.39, C:0.12, G:0.06, T:0.43
Consensus pattern (27 bp):
AAAACTCATAGTTCTTTATGTTATTCA
Found at i:53189830 original size:25 final size:25
Alignment explanation
Indices: 53189801--53189851 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
53189791 CAAAGGAAAA
**
53189801 TCCTAATCTAATTCCTAATTTAAAG
1 TCCTAATAGAATTCCTAATTTAAAG
53189826 TCCTAATAGAATTCCTAATTTAAAG
1 TCCTAATAGAATTCCTAATTTAAAG
53189851 T
1 T
53189852 TTATAAAGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.37, C:0.18, G:0.06, T:0.39
Consensus pattern (25 bp):
TCCTAATAGAATTCCTAATTTAAAG
Found at i:53194481 original size:25 final size:25
Alignment explanation
Indices: 53194452--53194502 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
53194442 CAAAGGAAAA
**
53194452 TCCTAATCTAATTCCTAATTTAAAG
1 TCCTAATAGAATTCCTAATTTAAAG
53194477 TCCTAATAGAATTCCTAATTTAAAG
1 TCCTAATAGAATTCCTAATTTAAAG
53194502 T
1 T
53194503 TTATAAGGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.37, C:0.18, G:0.06, T:0.39
Consensus pattern (25 bp):
TCCTAATAGAATTCCTAATTTAAAG
Found at i:53195679 original size:30 final size:30
Alignment explanation
Indices: 53195586--53195682 Score: 115
Period size: 30 Copynumber: 3.2 Consensus size: 30
53195576 GTTTAAATAC
53195586 ATAAACCTATA-CCTTTCCCAGCATATGCTCAT
1 ATAAACCTATACCCTTT-CCAGC--ATGCTCAT
* * * *
53195618 ACAAACTTATACCCTTCCCAACATGCTCAT
1 ATAAACCTATACCCTTTCCAGCATGCTCAT
*
53195648 ATAAACCTATACCCTTTCTAGCATGCTCAT
1 ATAAACCTATACCCTTTCCAGCATGCTCAT
53195678 ATAAA
1 ATAAA
53195683 ACTTCAAACC
Statistics
Matches: 55, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
30 38 0.69
32 13 0.24
33 4 0.07
ACGTcount: A:0.34, C:0.31, G:0.05, T:0.30
Consensus pattern (30 bp):
ATAAACCTATACCCTTTCCAGCATGCTCAT
Found at i:53196142 original size:133 final size:129
Alignment explanation
Indices: 53195990--53196229 Score: 354
Period size: 133 Copynumber: 1.8 Consensus size: 129
53195980 GTTTGCCAAT
*
53195990 AGCTAAGAACAGAAAAATCAACAAAAGGAGCAGTCAATAAGAATCAAACAGTATAAAAGAAAAAG
1 AGCTAAGAACAGAAAAATCAACAAAAGGAGCAATCAATAAGAATCAAACAG--T-AAAGAAAAAG
* *
53196055 TAAAAACAGACAAACCCATTTAAATTTGAACTGAAAGAACACAAAAACAAAGATTTTAATTTACA
63 TAAAAACAAACAAACCCATTTAAA-TTGAACTAAAAGAACACAAAAACAAAGATTTTAATTTACA
53196120 AAG
127 AAG
** * * *
53196123 AGCTAAGAACATCAAAATCAACAAAAGGGGCAATCAATAAGAATCAAATAGTACAGAAAAAGTAA
1 AGCTAAGAACAGAAAAATCAACAAAAGGAGCAATCAATAAGAATCAAACAGTAAAGAAAAAGTAA
* *
53196188 AAACAAACAAACCTATTTTAATTGAACTAAAAGAACACAAAA
66 AAACAAACAAACCCATTTAAATTGAACTAAAAGAACACAAAA
53196230 GCGAAGACCG
Statistics
Matches: 97, Mismatches: 10, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
129 20 0.21
130 30 0.31
131 1 0.01
133 46 0.47
ACGTcount: A:0.57, C:0.14, G:0.12, T:0.16
Consensus pattern (129 bp):
AGCTAAGAACAGAAAAATCAACAAAAGGAGCAATCAATAAGAATCAAACAGTAAAGAAAAAGTAA
AAACAAACAAACCCATTTAAATTGAACTAAAAGAACACAAAAACAAAGATTTTAATTTACAAAG
Found at i:53196270 original size:133 final size:131
Alignment explanation
Indices: 53195992--53196258 Score: 335
Period size: 133 Copynumber: 2.1 Consensus size: 131
53195982 TTGCCAATAG
** *
53195992 CTAAGAACAGAAAAATCAACAAAAGGAGCAGTCAATAAGAATCAAACAGTATAAAAGAAAAAGTA
1 CTAAGAACATCAAAATCAACAAAAGGAGCAATCAATAAGAATCAAACAG-ATAAAAGAAAAAGTA
* * ***
53196057 AAAACAGACAAACCCATTTAAATTTGAACTGAAAGAACACAAAAACAAAGATTTTAATTTACAAA
65 AAAACAAACAAACCCATTTAAATTTGAACTAAAAGAACACAAAAACAAAGACCGTAATTTA-AAA
*
53196122 GAG
129 GAA
* * *
53196125 CTAAGAACATCAAAATCAACAAAAGGGGCAATCAATAAGAATCAAATAG-T-ACAGAAAAAGTAA
1 CTAAGAACATCAAAATCAACAAAAGGAGCAATCAATAAGAATCAAACAGATAAAAGAAAAAGTAA
* * * * *
53196188 AAACAAACAAACCTATTTTAA-TTGAACTAAAAGAACACAAAAGCGAAGACCGTAGTTT-AAAGA
66 AAACAAACAAACCCATTTAAATTTGAACTAAAAGAACACAAAAACAAAGACCGTAATTTAAAAGA
53196251 A
131 A
53196252 CTAAGAA
1 CTAAGAA
53196259 TAGCTAAATC
Statistics
Matches: 117, Mismatches: 17, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
127 12 0.10
129 30 0.26
130 30 0.26
131 1 0.01
133 44 0.38
ACGTcount: A:0.56, C:0.14, G:0.13, T:0.16
Consensus pattern (131 bp):
CTAAGAACATCAAAATCAACAAAAGGAGCAATCAATAAGAATCAAACAGATAAAAGAAAAAGTAA
AAACAAACAAACCCATTTAAATTTGAACTAAAAGAACACAAAAACAAAGACCGTAATTTAAAAGA
A
Found at i:53196951 original size:16 final size:16
Alignment explanation
Indices: 53196930--53197000 Score: 115
Period size: 16 Copynumber: 4.4 Consensus size: 16
53196920 GTTTGGTTCA
*
53196930 CTGTAATGGAATAGGG
1 CTGTAATGGAATAGAG
*
53196946 CTGTAATTGAATAGAG
1 CTGTAATGGAATAGAG
53196962 CTGTAATGGAATAGAG
1 CTGTAATGGAATAGAG
*
53196978 CTGTAATAGAATAGAG
1 CTGTAATGGAATAGAG
53196994 CTGTAAT
1 CTGTAAT
53197001 CAGTAATTCA
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 51 1.00
ACGTcount: A:0.37, C:0.07, G:0.28, T:0.28
Consensus pattern (16 bp):
CTGTAATGGAATAGAG
Found at i:53197066 original size:44 final size:46
Alignment explanation
Indices: 53196986--53197075 Score: 141
Period size: 44 Copynumber: 2.0 Consensus size: 46
53196976 AGCTGTAATA
53196986 GAATAGAGCTGTAATCAGTAATTCAACTGTTTGGTTGAATGGAATG
1 GAATAGAGCTGTAATCAGTAATTCAACTGTTTGGTTGAATGGAATG
*
53197032 GAATAGAGCTGTAAT-AG-AATTCTTA-TGTTTGGTTGAATGGAATG
1 GAATAGAGCTGTAATCAGTAATTC-AACTGTTTGGTTGAATGGAATG
53197076 ATGTTGTAAT
Statistics
Matches: 42, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
44 24 0.57
45 3 0.07
46 15 0.36
ACGTcount: A:0.32, C:0.07, G:0.27, T:0.34
Consensus pattern (46 bp):
GAATAGAGCTGTAATCAGTAATTCAACTGTTTGGTTGAATGGAATG
Found at i:53197238 original size:61 final size:55
Alignment explanation
Indices: 53197156--53197304 Score: 140
Period size: 61 Copynumber: 2.5 Consensus size: 55
53197146 GATTATTGTT
*
53197156 ATTAAATTTTAATA-AGATTATTGATACATATATTTTAATAAAAATAAAAATAAATAATTTA
1 ATTAAATTTTAATATA-ATTATT-ATA-ATATAATTTAAT-AAAAT---AATAAATAATTTA
* * *
53197217 ATTATATTTTAATATAATTATTATTAAATATAATTTAATAAAATAATATATATTTTA
1 ATTAAATTTTAATATAATTATTA-T-AATATAATTTAATAAAATAATAAATAATTTA
53197274 A-TAACATTATTAATATAATTATTAATAATAT
1 ATTAA-ATT-TTAATATAATTATT-ATAATAT
53197305 TTAATAATAA
Statistics
Matches: 77, Mismatches: 5, Indels: 16
0.79 0.05 0.16
Matches are distributed among these distances:
56 2 0.03
57 20 0.26
58 15 0.19
59 1 0.01
60 6 0.08
61 31 0.40
62 2 0.03
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.46
Consensus pattern (55 bp):
ATTAAATTTTAATATAATTATTATAATATAATTTAATAAAATAATAAATAATTTA
Found at i:53197286 original size:12 final size:11
Alignment explanation
Indices: 53197225--53197322 Score: 51
Period size: 12 Copynumber: 8.5 Consensus size: 11
53197215 TAATTATATT
53197225 TTAATATAATTA
1 TTAATA-AATTA
*
53197237 TTATTAAATATAA
1 TTAATAAAT-T-A
*
53197250 TTTAATAAAATA
1 -TTAATAAATTA
* *
53197262 AT-ATATATT-
1 TTAATAAATTA
53197271 TTAATAACATTA
1 TTAATAA-ATTA
53197283 TTAATATAATTA
1 TTAATA-AATTA
53197295 TTAATAATATTTA
1 TTAATAA-A-TTA
*
53197308 ATAAT-AATT-
1 TTAATAAATTA
53197317 TTAATA
1 TTAATA
53197323 TAAAATTATT
Statistics
Matches: 66, Mismatches: 10, Indels: 22
0.67 0.10 0.22
Matches are distributed among these distances:
9 5 0.08
10 10 0.15
11 9 0.14
12 25 0.38
13 10 0.15
14 7 0.11
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (11 bp):
TTAATAAATTA
Found at i:53197310 original size:46 final size:47
Alignment explanation
Indices: 53197211--53197325 Score: 127
Period size: 46 Copynumber: 2.5 Consensus size: 47
53197201 AAAAATAAAT
*
53197211 AATTTAAT-TATATTTTAATATAATTATTATTAAATATAATTTAATA
1 AATTTAATATATATTTTAATATAATTATTAATAAATATAATTTAATA
*
53197257 AA-ATAATATATATTTTAATA-ACATTATTAATATAAT-T-A-TTAATA
1 AATTTAATATATATTTTAATATA-ATTATTAATA-AATATAATTTAATA
53197301 ATATTTAATA-ATAATTTTAATATAA
1 A-ATTTAATATAT-ATTTTAATATAA
53197326 AATTATTATT
Statistics
Matches: 59, Mismatches: 3, Indels: 14
0.78 0.04 0.18
Matches are distributed among these distances:
44 7 0.12
45 9 0.15
46 39 0.66
47 4 0.07
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (47 bp):
AATTTAATATATATTTTAATATAATTATTAATAAATATAATTTAATA
Found at i:53201011 original size:55 final size:50
Alignment explanation
Indices: 53200946--53201086 Score: 165
Period size: 50 Copynumber: 2.7 Consensus size: 50
53200936 GACAGTAATA
* *
53200946 ACATTTCACTTACAGATAGAAAGAAAGAATATATCAAAATAATATATATATATGC
1 ACATTTCACTTACAGAT-GAAAG-AA-AATATATCAAAAGAATATATACATA--C
* * *
53201001 ACATTTCACTTACAGATGCATGCAAATATATCAAAAGAATATATACATAC
1 ACATTTCACTTACAGATGAAAGAAAATATATCAAAAGAATATATACATAC
* * *
53201051 ACATTTCACTTACAGATGCATGCAAATATATCAAAA
1 ACATTTCACTTACAGATGAAAGAAAATATATCAAAA
53201087 ATTATTATTA
Statistics
Matches: 81, Mismatches: 5, Indels: 5
0.89 0.05 0.05
Matches are distributed among these distances:
50 37 0.46
52 23 0.28
53 1 0.01
54 3 0.04
55 17 0.21
ACGTcount: A:0.48, C:0.16, G:0.09, T:0.28
Consensus pattern (50 bp):
ACATTTCACTTACAGATGAAAGAAAATATATCAAAAGAATATATACATAC
Found at i:53201665 original size:50 final size:52
Alignment explanation
Indices: 53201559--53201685 Score: 159
Period size: 50 Copynumber: 2.5 Consensus size: 52
53201549 ATTTATGTGG
* * * * *
53201559 AAGATAGAATTATATCAAAATAATAAATACACAAATACACACATACAGATAGA
1 AAGAAAGAA-TATATCAAAAGAATAAATACACAAACACACACAAACAGATACA
* *
53201612 AAGAAAGAATATATCAAAAGAA-AAA-ACATATACACACACAAACAGATACA
1 AAGAAAGAATATATCAAAAGAATAAATACACAAACACACACAAACAGATACA
*
53201662 AAGAAAGAATATATCAAAATAATA
1 AAGAAAGAATATATCAAAAGAATA
53201686 TATATATATA
Statistics
Matches: 65, Mismatches: 8, Indels: 4
0.84 0.10 0.05
Matches are distributed among these distances:
50 41 0.63
51 4 0.06
52 12 0.18
53 8 0.12
ACGTcount: A:0.62, C:0.13, G:0.08, T:0.17
Consensus pattern (52 bp):
AAGAAAGAATATATCAAAAGAATAAATACACAAACACACACAAACAGATACA
Found at i:53201760 original size:50 final size:50
Alignment explanation
Indices: 53201687--53201873 Score: 216
Period size: 50 Copynumber: 3.7 Consensus size: 50
53201677 AAAATAATAT
* *
53201687 ATATATATATGCACATTTCACTTACAGATGCATGCAAATATATCAAAAGA
1 ATATATACATACACATTTCACTTACAGATGCATGCAAATATATCAAAAGA
* **
53201737 ATATATACATACACATTTCACTTACAGATGCATGCAGCGAA-AT-TTATATGGA
1 ATATATACATACACATTTCACTTACAGATGCATGCA---AATATATCA-AAAGA
** ** * *
53201789 AGGTGCCAAATAAACATTTCACTTACAGATGCATGCAAATATATCAAAAGA
1 ATAT-ATACATACACATTTCACTTACAGATGCATGCAAATATATCAAAAGA
53201840 ATATATACATACACATTTCACTTACAGATGCATG
1 ATATATACATACACATTTCACTTACAGATGCATG
53201874 AAGCAAAATT
Statistics
Matches: 110, Mismatches: 20, Indels: 14
0.76 0.14 0.10
Matches are distributed among these distances:
50 62 0.56
51 9 0.08
52 9 0.08
53 30 0.27
ACGTcount: A:0.42, C:0.18, G:0.12, T:0.29
Consensus pattern (50 bp):
ATATATACATACACATTTCACTTACAGATGCATGCAAATATATCAAAAGA
Found at i:53201822 original size:53 final size:50
Alignment explanation
Indices: 53201749--53201908 Score: 157
Period size: 50 Copynumber: 3.1 Consensus size: 50
53201739 ATATACATAC
53201749 ACATTTCACTTACAGATGCATGCAGCGAAATTTATATGGAAGGTGCCAAATAA
1 ACATTTCACTTACAGATGCATG-AGC-AAATTTATATGGAA-GTGCCAAATAA
* ** ** *
53201802 ACATTTCACTTACAGATGCAT--GCAAATATATCAAAAGAA-T-ATATACATAC
1 ACATTTCACTTACAGATGCATGAGCAAATTTAT--ATGGAAGTGCCA-A-ATAA
53201852 ACATTTCACTTACAGATGCATGAAGCAAAATTTATATGGAAGTGCCAAATAA
1 ACATTTCACTTACAGATGCATG-AGC-AAATTTATATGGAAGTGCCAAATAA
53201904 ACATT
1 ACATT
53201909 AACAGCCATG
Statistics
Matches: 85, Mismatches: 12, Indels: 21
0.72 0.10 0.18
Matches are distributed among these distances:
48 1 0.01
49 9 0.11
50 26 0.31
51 4 0.05
52 12 0.14
53 25 0.29
54 8 0.09
ACGTcount: A:0.42, C:0.17, G:0.14, T:0.28
Consensus pattern (50 bp):
ACATTTCACTTACAGATGCATGAGCAAATTTATATGGAAGTGCCAAATAA
Found at i:53201823 original size:103 final size:102
Alignment explanation
Indices: 53201699--53201908 Score: 393
Period size: 103 Copynumber: 2.0 Consensus size: 102
53201689 ATATATATGC
53201699 ACATTTCACTTACAGATGCATGCAAATATATCAAAAGAATATATACATACACATTTCACTTACAG
1 ACATTTCACTTACAGATGCATGCAAATATATCAAAAGAATATATACATACACATTTCACTTACAG
* *
53201764 ATGCATGCAGCGAAATTTATATGGAAGGTGCCAAATAA
66 ATGCATGAAGCAAAATTTATATGGAA-GTGCCAAATAA
53201802 ACATTTCACTTACAGATGCATGCAAATATATCAAAAGAATATATACATACACATTTCACTTACAG
1 ACATTTCACTTACAGATGCATGCAAATATATCAAAAGAATATATACATACACATTTCACTTACAG
53201867 ATGCATGAAGCAAAATTTATATGGAAGTGCCAAATAA
66 ATGCATGAAGCAAAATTTATATGGAAGTGCCAAATAA
53201904 ACATT
1 ACATT
53201909 AACAGCCATG
Statistics
Matches: 105, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
102 16 0.15
103 89 0.85
ACGTcount: A:0.43, C:0.17, G:0.12, T:0.28
Consensus pattern (102 bp):
ACATTTCACTTACAGATGCATGCAAATATATCAAAAGAATATATACATACACATTTCACTTACAG
ATGCATGAAGCAAAATTTATATGGAAGTGCCAAATAA
Found at i:53205223 original size:14 final size:14
Alignment explanation
Indices: 53205204--53205230 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
53205194 ACAAACACAA
53205204 AAAAATACAAAATG
1 AAAAATACAAAATG
53205218 AAAAATACAAAAT
1 AAAAATACAAAAT
53205231 AAATTCACTA
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:0.74, C:0.07, G:0.04, T:0.15
Consensus pattern (14 bp):
AAAAATACAAAATG
Found at i:53208930 original size:40 final size:40
Alignment explanation
Indices: 53208848--53209068 Score: 272
Period size: 40 Copynumber: 5.6 Consensus size: 40
53208838 TATTTGGATG
* *
53208848 ATATCCGGGCTAAGTCCCGAAGGCA-TGGTGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCAGTTGTGCTATTGACT
53208887 ATATCCGGGCTAAGTCCCGAAGGCAGTTGTGCTATTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCAGTTGTGCTATTGACT
* *
53208927 ATATCCGGGCTATGTCCCGAAGGC-GTTTGTGCGAGTTG-CT
1 ATATCCGGGCTAAGTCCCGAAGGCAG-TTGTGCTA-TTGACT
* ** *
53208967 ATATCCGGGCTAAATCCCGAAGGCTTTTGTGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCAGTTGTGCTATTGACT
* * *
53209007 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-CT
1 ATATCCGGGCTAAGTCCCGAAGGCAGTTGTGCTA-TTGACT
*
53209047 ATATCC-GGCTAAATCCCGAAGG
1 ATATCCGGGCTAAGTCCCGAAGG
53209069 TACTTGGGTT
Statistics
Matches: 160, Mismatches: 16, Indels: 12
0.85 0.09 0.06
Matches are distributed among these distances:
39 42 0.26
40 113 0.71
41 5 0.03
ACGTcount: A:0.22, C:0.23, G:0.29, T:0.26
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCAGTTGTGCTATTGACT
Found at i:53208988 original size:80 final size:79
Alignment explanation
Indices: 53208848--53209068 Score: 320
Period size: 80 Copynumber: 2.8 Consensus size: 79
53208838 TATTTGGATG
* * * *
53208848 ATATCCGGGCTAAGTCCCGAAGGCATGGTGCTAG-TGACTATATCCGGGCTAAGTCCCGAAGGCA
1 ATATCCGGGCTAAGTCCCGAAGGCTTTGTGCGAGTTG-CTATATCCGGGCTAAATCCCGAAGGCA
*
53208912 GTTGTGCTATTGACT
65 GTTGTGCTAGTGACT
* *
53208927 ATATCCGGGCTATGTCCCGAAGGCGTTTGTGCGAGTTGCTATATCCGGGCTAAATCCCGAAGGCT
1 ATATCCGGGCTAAGTCCCGAAGGC-TTTGTGCGAGTTGCTATATCCGGGCTAAATCCCGAAGGCA
*
53208992 TTTGTGCTAGTGACT
65 GTTGTGCTAGTGACT
*
53209007 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCTATATCC-GGCTAAATCCCGAAGG
1 ATATCCGGGCTAAGTCCCGAAGGC-TTTGTGCGAGTTGCTATATCCGGGCTAAATCCCGAAGG
53209069 TACTTGGGTT
Statistics
Matches: 129, Mismatches: 11, Indels: 4
0.90 0.08 0.03
Matches are distributed among these distances:
79 39 0.30
80 88 0.68
81 2 0.02
ACGTcount: A:0.22, C:0.23, G:0.29, T:0.26
Consensus pattern (79 bp):
ATATCCGGGCTAAGTCCCGAAGGCTTTGTGCGAGTTGCTATATCCGGGCTAAATCCCGAAGGCAG
TTGTGCTAGTGACT
Found at i:53211751 original size:3 final size:3
Alignment explanation
Indices: 53211743--53211774 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
53211733 AAAAGTGAAA
53211743 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
53211775 AAATGGTCAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:53216751 original size:44 final size:44
Alignment explanation
Indices: 53216703--53216792 Score: 180
Period size: 44 Copynumber: 2.0 Consensus size: 44
53216693 TTTTGAAGTT
53216703 AATTTTCAAGTTAGATAATTGGTCGAATGGGTAGATAAACTTGA
1 AATTTTCAAGTTAGATAATTGGTCGAATGGGTAGATAAACTTGA
53216747 AATTTTCAAGTTAGATAATTGGTCGAATGGGTAGATAAACTTGA
1 AATTTTCAAGTTAGATAATTGGTCGAATGGGTAGATAAACTTGA
53216791 AA
1 AA
53216793 ATTGGATCTG
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 46 1.00
ACGTcount: A:0.38, C:0.07, G:0.22, T:0.33
Consensus pattern (44 bp):
AATTTTCAAGTTAGATAATTGGTCGAATGGGTAGATAAACTTGA
Found at i:53217096 original size:19 final size:19
Alignment explanation
Indices: 53217072--53217136 Score: 116
Period size: 19 Copynumber: 3.5 Consensus size: 19
53217062 CTTTAAGGAC
53217072 ATGCAATCTTAGATATGAT
1 ATGCAATCTTAGATATGAT
53217091 ATGCAATCTTAGATATGAT
1 ATGCAATCTTAGATATGAT
53217110 A--CAATCTTAGATATGAT
1 ATGCAATCTTAGATATGAT
53217127 ATGCAATCTT
1 ATGCAATCTT
53217137 GAAGCTATGA
Statistics
Matches: 44, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
17 17 0.39
19 27 0.61
ACGTcount: A:0.37, C:0.12, G:0.14, T:0.37
Consensus pattern (19 bp):
ATGCAATCTTAGATATGAT
Found at i:53217099 original size:36 final size:35
Alignment explanation
Indices: 53217059--53217136 Score: 97
Period size: 36 Copynumber: 2.2 Consensus size: 35
53217049 ATGGAAATAT
53217059 AATCTTTAAGGACATG-CAATCTTAGATATGATATGC
1 AATCTTT-A-GACATGACAATCTTAGATATGATATGC
*
53217095 AATC-TTAGATATGATACAATCTTAGATATGATATGC
1 AATCTTTAGACATG--ACAATCTTAGATATGATATGC
53217131 AATCTT
1 AATCTT
53217137 GAAGCTATGA
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
33 5 0.14
34 1 0.03
35 2 0.05
36 28 0.76
37 1 0.03
ACGTcount: A:0.37, C:0.13, G:0.14, T:0.36
Consensus pattern (35 bp):
AATCTTTAGACATGACAATCTTAGATATGATATGC
Found at i:53217107 original size:14 final size:15
Alignment explanation
Indices: 53217088--53217125 Score: 51
Period size: 17 Copynumber: 2.5 Consensus size: 15
53217078 TCTTAGATAT
53217088 GATATG-CAATCTTA
1 GATATGACAATCTTA
53217102 GATATGATACAATCTTA
1 GATATG--ACAATCTTA
53217119 GATATGA
1 GATATGA
53217126 TATGCAATCT
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
14 6 0.29
15 1 0.05
17 14 0.67
ACGTcount: A:0.39, C:0.11, G:0.16, T:0.34
Consensus pattern (15 bp):
GATATGACAATCTTA
Found at i:53217346 original size:29 final size:29
Alignment explanation
Indices: 53217313--53217374 Score: 124
Period size: 29 Copynumber: 2.1 Consensus size: 29
53217303 GAAAGTATTC
53217313 ACTCAAATTTCTCTCCCTCTTGCATTCTT
1 ACTCAAATTTCTCTCCCTCTTGCATTCTT
53217342 ACTCAAATTTCTCTCCCTCTTGCATTCTT
1 ACTCAAATTTCTCTCCCTCTTGCATTCTT
53217371 ACTC
1 ACTC
53217375 TCTGTGGTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.18, C:0.35, G:0.03, T:0.44
Consensus pattern (29 bp):
ACTCAAATTTCTCTCCCTCTTGCATTCTT
Found at i:53218944 original size:24 final size:24
Alignment explanation
Indices: 53218917--53218964 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
53218907 TGTAATTTTA
53218917 AATCTTGAAAAATTTTTAATCATT
1 AATCTTGAAAAATTTTTAATCATT
53218941 AATCTTGAAAAATTTTTAATCATT
1 AATCTTGAAAAATTTTTAATCATT
53218965 CTTTTTTGGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.42, C:0.08, G:0.04, T:0.46
Consensus pattern (24 bp):
AATCTTGAAAAATTTTTAATCATT
Found at i:53221588 original size:20 final size:20
Alignment explanation
Indices: 53221528--53221594 Score: 73
Period size: 20 Copynumber: 3.3 Consensus size: 20
53221518 AGTGTTTCTA
*
53221528 TTTGCACTTGGGTGCCTCTG
1 TTTGCACTTCGGTGCCTCTG
* *
53221548 ATTGCACAATC-GTGCCTCTG
1 TTTGCAC-TTCGGTGCCTCTG
*
53221568 TTTTCACTTCGGTGCCTCTG
1 TTTGCACTTCGGTGCCTCTG
53221588 TTATGCA
1 TT-TGCA
53221595 TCAATTATGC
Statistics
Matches: 37, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
19 2 0.05
20 31 0.84
21 4 0.11
ACGTcount: A:0.12, C:0.27, G:0.22, T:0.39
Consensus pattern (20 bp):
TTTGCACTTCGGTGCCTCTG
Found at i:53225324 original size:210 final size:208
Alignment explanation
Indices: 53224962--53225382 Score: 643
Period size: 210 Copynumber: 2.0 Consensus size: 208
53224952 ACTGTTTTGC
* * *
53224962 AAATTTTCAAGTTTTTCTAAAACTTTCTGATTTGATTCAATTTGATCCTGGATCATCCTCAAATT
1 AAATTTTCAAGATTTTCTAAAACTTTCTGATTTGATGCAATTTGATCCTAGATCATCCTCAAATT
*
53225027 GTTTTTTAGGGCTCCGTAAGTTCGATTTAAGGTCCATAAGTGATTTATTCTATAAATTGATTTCG
66 GTTTTTTAGGGCTCCGTAAGTTCGATTTAAGGTCCATAAGTGATTTATTCTATAAATTGATTTCA
* *
53225092 TTTGTTATATGTTTGTT-A-ATT-ATTTGTTTAATTGGTCTGAAATGAAATGAAATGTTCTATAT
131 TTTGTTACATGTTTGTTAATATTAATTTGGTTAATTGGTC-----TGAAATGAAATGTTCTATAT
*
53225154 TGCTTAGTAACACTCTGT
191 TGCTCAGTAACACTCTGT
*
53225172 AAATTTTCAAGATTTTCTAAAACTTTCTGATTTGATGCAATTTGATCCTAGATCGTCCTCAAATT
1 AAATTTTCAAGATTTTCTAAAACTTTCTGATTTGATGCAATTTGATCCTAGATCATCCTCAAATT
* * *
53225237 GTTTTTTAGGGCTCCGT-ATTTCGATTTAAGGTGCATAAGTGTATTTATTCTATAATTTGATTTC
66 GTTTTTTAGGGCTCCGTAAGTTCGATTTAAGGTCCATAAGTG-ATTTATTCTATAAATTGATTTC
53225301 ATTTGTTACATGTTTGTTAATTATTAATTTGGTTAATTGGTCTGAAATGAAATGTTCTATATTGC
130 ATTTGTTACATGTTTGTTAA-TATTAATTTGGTTAATTGGTCTGAAATGAAATGTTCTATATTGC
*
53225366 TCGGTAACACTCTGT
194 TCAGTAACACTCTGT
53225381 AA
1 AA
53225383 CCTTAATCCA
Statistics
Matches: 194, Mismatches: 12, Indels: 11
0.89 0.06 0.05
Matches are distributed among these distances:
209 60 0.31
210 115 0.59
211 1 0.01
213 3 0.02
214 15 0.08
ACGTcount: A:0.27, C:0.12, G:0.15, T:0.45
Consensus pattern (208 bp):
AAATTTTCAAGATTTTCTAAAACTTTCTGATTTGATGCAATTTGATCCTAGATCATCCTCAAATT
GTTTTTTAGGGCTCCGTAAGTTCGATTTAAGGTCCATAAGTGATTTATTCTATAAATTGATTTCA
TTTGTTACATGTTTGTTAATATTAATTTGGTTAATTGGTCTGAAATGAAATGTTCTATATTGCTC
AGTAACACTCTGT
Found at i:53236726 original size:9 final size:9
Alignment explanation
Indices: 53236709--53236738 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
53236699 GTTCATAGAT
*
53236709 TGAATTGAA
1 TGAAATGAA
53236718 TGAAATGAA
1 TGAAATGAA
53236727 TGAAATGAA
1 TGAAATGAA
53236736 TGA
1 TGA
53236739 TTGAATGGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.23, T:0.27
Consensus pattern (9 bp):
TGAAATGAA
Found at i:53253583 original size:30 final size:30
Alignment explanation
Indices: 53253549--53253609 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
53253539 TCCTTAACTC
53253549 AAACTTTGGAAAAATTACAATTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
* * * * *
53253579 AAACTTTTGCATATTTACACTTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
53253609 A
1 A
53253610 GGCTCGGGAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (30 bp):
AAACTTTGGAAAAATTACAATTTTGCCCCT
Done.