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 194 of 427
Found at i:53948705 original size:21 final size:20
Alignment explanation
Indices: 53948668--53948706 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
53948658 CCCATGTTGA
* *
53948668 CCCATTTTCTCTGTTTTTGG
1 CCCATTTTCACTCTTTTTGG
53948688 CCCATTTTTCACTCTTTTT
1 CCCA-TTTTCACTCTTTTT
53948707 ACTCTCTTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.08, C:0.28, G:0.08, T:0.56
Consensus pattern (20 bp):
CCCATTTTCACTCTTTTTGG
Found at i:53950600 original size:26 final size:25
Alignment explanation
Indices: 53950571--53950628 Score: 66
Period size: 25 Copynumber: 2.3 Consensus size: 25
53950561 ATAAAACCTA
*
53950571 AAAATGAAATAGTA-TTAAAGGAAAAT
1 AAAAT-AAAAAGTACTTAAA-GAAAAT
*
53950597 AAAATAAAAAGTACTTAAAGAAGAT
1 AAAATAAAAAGTACTTAAAGAAAAT
53950622 -AAATAAA
1 AAAATAAA
53950629 GATAAAAGTG
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
24 7 0.24
25 12 0.41
26 10 0.34
ACGTcount: A:0.66, C:0.02, G:0.12, T:0.21
Consensus pattern (25 bp):
AAAATAAAAAGTACTTAAAGAAAAT
Found at i:53950623 original size:25 final size:25
Alignment explanation
Indices: 53950571--53950635 Score: 67
Period size: 26 Copynumber: 2.4 Consensus size: 25
53950561 ATAAAACCTA
*
53950571 AAAATGAAATAGTATTAAAGGAAAAT
1 AAAAT-AAAAAGTATTAAAGGAAAAT
53950597 AAAATAAAAAGTACTTAAAGAAGATAAAT
1 AAAATAAAAAGTA-TTAAAG--GA-AAAT
53950626 AAAGATAAAA
1 AAA-ATAAAA
53950636 GTGAAAATAA
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
25 7 0.21
26 11 0.33
28 2 0.06
29 7 0.21
30 6 0.18
ACGTcount: A:0.66, C:0.02, G:0.12, T:0.20
Consensus pattern (25 bp):
AAAATAAAAAGTATTAAAGGAAAAT
Found at i:53964155 original size:79 final size:82
Alignment explanation
Indices: 53964015--53964199 Score: 229
Period size: 79 Copynumber: 2.3 Consensus size: 82
53964005 TCGAATGATG
* * *
53964015 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACTATATCCGGACTAGGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACTAAACCCGGACTAAGATCCGAAGGCATT
*
53964079 CGTGCGAGTTAATA-AA
66 CGTGCGAGTCAATATAA
* **
53964095 TCCGGGCTAAG-CCCGAAGGCATTTGTGC-AAGTTACTAAACCCGGGTTAAG-TCCCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACTAAACCCGGACTAAGAT-CCGAAGGCAT
*
53964157 TCGTGCGAGTCACTATAA
65 TCGTGCGAGTCAATATAA
**
53964175 -CCGGGCTTCGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
53964200 AGCGAGTCGT
Statistics
Matches: 91, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
78 1 0.01
79 56 0.62
80 34 0.37
ACGTcount: A:0.24, C:0.24, G:0.28, T:0.24
Consensus pattern (82 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACTAAACCCGGACTAAGATCCGAAGGCATT
CGTGCGAGTCAATATAA
Found at i:53964207 original size:40 final size:40
Alignment explanation
Indices: 53964016--53964207 Score: 151
Period size: 40 Copynumber: 4.8 Consensus size: 40
53964006 CGAATGATGT
* * * * *
53964016 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACTATAT
1 CCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTCACTAAAC
** * * * * *
53964056 CCGGACTAGGAT-CCGAAGGCATTCGTGCGAGTTAATAAAT
1 CCGGGTTAAG-TCCCGAAGGCATTTGTGCGAGTCACTAAAC
* * *
53964096 CCGGGCTAAG-CCCGAAGGCATTTGTGCAAGTTACTAAAC
1 CCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTCACTAAAC
*
53964135 CCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTCACTATAA-
1 CCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTCACTA-AAC
* *
53964175 CCGGGCTT-CGTCCCGAAGGCATTTGAGCGAGTC
1 CCGGG-TTAAGTCCCGAAGGCATTTGTGCGAGTC
53964208 GTTATATCCG
Statistics
Matches: 126, Mismatches: 20, Indels: 12
0.80 0.13 0.08
Matches are distributed among these distances:
39 33 0.26
40 82 0.65
41 11 0.09
ACGTcount: A:0.24, C:0.24, G:0.28, T:0.23
Consensus pattern (40 bp):
CCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTCACTAAAC
Found at i:53964230 original size:79 final size:79
Alignment explanation
Indices: 53964015--53964232 Score: 183
Period size: 79 Copynumber: 2.7 Consensus size: 79
53964005 TCGAATGATG
* * * * ** *
53964015 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACTATATCCGGACTAGGA-TCCGAAGGCAT
1 TCCGGGCTAAG-CCCGAAGGCATTTGAGC-AAGTCACTAAACCCGGGTTA-AATTCCGAAGGCAT
*
53964078 TCGTGCGAGTTAATAAA
63 TCGTGCGAGTCAATAAA
* * * *
53964095 TCCGGGCTAAGCCCGAAGGCATTTGTGCAAGTTACTAAACCCGGGTTAAGTCCCGAAGGCATTCG
1 TCCGGGCTAAGCCCGAAGGCATTTGAGCAAGTCACTAAACCCGGGTTAAATTCCGAAGGCATTCG
*
53964160 TGCGAGTCACTATAA
66 TGCGAGTCAATA-AA
** * ** * *
53964175 -CCGGGCTTCGTCCCGAAGGCATTTGAGCGAGTCGTTATATCC-GGTTAAATTCCGAAGG
1 TCCGGGCTAAG-CCCGAAGGCATTTGAGCAAGTCACTAAACCCGGGTTAAATTCCGAAGG
53964233 TACGTGATTC
Statistics
Matches: 113, Mismatches: 21, Indels: 9
0.79 0.15 0.06
Matches are distributed among these distances:
79 69 0.61
80 44 0.39
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.24
Consensus pattern (79 bp):
TCCGGGCTAAGCCCGAAGGCATTTGAGCAAGTCACTAAACCCGGGTTAAATTCCGAAGGCATTCG
TGCGAGTCAATAAA
Found at i:53968520 original size:43 final size:42
Alignment explanation
Indices: 53968355--53968521 Score: 167
Period size: 43 Copynumber: 3.9 Consensus size: 42
53968345 CATAAGCTCG
* * *
53968355 TACAATGCC-ATATCCCAGATATGGTCTTAAATGTAA-ATACA
1 TACAATGCCAATATCCCAGACATGGTCTTACATGTAATCTA-A
* * * * * *
53968396 TATCGATGCCACTATCCCAGACAAGGTCTTACACGAAATTATAA
1 TA-CAATGCCAATATCCCAGACATGGTCTTACATGTAA-TCTAA
** *
53968440 TATGATGCCAATGTCCCAGACATGGTCTTACATGTAATCTCAA
1 TACAATGCCAATATCCCAGACATGGTCTTACATGTAATCT-AA
*
53968483 TACAATGCCAATGTCCCAGACATGGTCTTACATGTAATC
1 TACAATGCCAATATCCCAGACATGGTCTTACATGTAATC
53968522 ACATCTCAAT
Statistics
Matches: 105, Mismatches: 16, Indels: 8
0.81 0.12 0.06
Matches are distributed among these distances:
41 2 0.02
42 8 0.08
43 89 0.85
44 3 0.03
45 3 0.03
ACGTcount: A:0.34, C:0.23, G:0.14, T:0.28
Consensus pattern (42 bp):
TACAATGCCAATATCCCAGACATGGTCTTACATGTAATCTAA
Found at i:53971206 original size:40 final size:40
Alignment explanation
Indices: 53971161--53971347 Score: 252
Period size: 40 Copynumber: 4.7 Consensus size: 40
53971151 TAAACCACAA
* * *
53971161 GCACAATTGCCTTCGGGTCTTAACCCGGGTATAGCAACTC
1 GCACAAATGCCTTCGGGTCTTAACCCGGATATAACAACTC
*
53971201 GCACAAATGCCTTCGGGTCTTAGCCCGGATATAACAACTC
1 GCACAAATGCCTTCGGGTCTTAACCCGGATATAACAACTC
*
53971241 ACACAAATGCCTTCGGGTCTTAACCCGGATATAACAACTC
1 GCACAAATGCCTTCGGGTCTTAACCCGGATATAACAACTC
* * *
53971281 GCAAAAATGCCTTCAGGTCTTAACCCGGATATAATC-ACTA
1 GCACAAATGCCTTCGGGTCTTAACCCGGATATAA-CAACTC
* * *
53971321 GCATAAATGCCTTTGGG-CTTAGCCCGG
1 GCACAAATGCCTTCGGGTCTTAACCCGG
53971348 GTATCATTCA
Statistics
Matches: 132, Mismatches: 14, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
39 9 0.07
40 122 0.92
41 1 0.01
ACGTcount: A:0.28, C:0.28, G:0.20, T:0.24
Consensus pattern (40 bp):
GCACAAATGCCTTCGGGTCTTAACCCGGATATAACAACTC
Found at i:53980735 original size:39 final size:39
Alignment explanation
Indices: 53980559--53980741 Score: 168
Period size: 39 Copynumber: 4.8 Consensus size: 39
53980549 GGATATAGCG
* * * *
53980559 ACTCGCTCAAA-GCCTTC-GGACATAGCCCGGTTATAATA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATAT-GTA
* * * *
53980597 GCTCGCACAAATGCCTTCGGGACTTAACCCGGATTTGGA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATGTA
*
53980636 ACTCGCACAAATGCCTTCGGGACTTA-ACCGG--AT-TA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATGTA
* *
53980671 ACTCGCACAAATGCCTTC--GATCTTAGTCCGGATATGTC
1 ACTCGCACAAATGCCTTCGGGA-CTTAGCCCGGATATGTA
*
53980709 ACTTAGCACAAA-GCCTTCGGGACTTAGCCCGGA
1 AC-TCGCACAAATGCCTTCGGGACTTAGCCCGGA
53980742 CATCATTCGA
Statistics
Matches: 119, Mismatches: 16, Indels: 19
0.77 0.10 0.12
Matches are distributed among these distances:
33 2 0.02
34 4 0.03
35 23 0.19
36 1 0.01
37 2 0.02
38 22 0.18
39 50 0.42
40 15 0.13
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.23
Consensus pattern (39 bp):
ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATGTA
Found at i:53980741 original size:74 final size:74
Alignment explanation
Indices: 53980566--53980741 Score: 180
Period size: 74 Copynumber: 2.3 Consensus size: 74
53980556 GCGACTCGCT
* *
53980566 CAAAGCCTTC-GGACATAGCCCGGTTATAATAGCTCGCACAAATGCCTTCGGGACTTAACCCGGA
1 CAAAGCCTTCGGGACTTAGCCCGG--AT-ATAACTCGCACAAATGCCTTC-GGACTTAACCCGGA
* *
53980630 TTTGGAACTCGCA
62 TATGGAACTAGCA
* **
53980643 CAAATGCCTTCGGGACTTA-ACCGGAT-TAACTCGCACAAATGCCTTC-GATCTTAGTCCGGATA
1 CAAA-GCCTTCGGGACTTAGCCCGGATATAACTCGCACAAATGCCTTCGGA-CTTAACCCGGATA
**
53980705 TGTCACTTAGCA
64 TGGAAC-TAGCA
53980717 CAAAGCCTTCGGGACTTAGCCCGGA
1 CAAAGCCTTCGGGACTTAGCCCGGA
53980742 CATCATTCGA
Statistics
Matches: 84, Mismatches: 10, Indels: 13
0.79 0.09 0.12
Matches are distributed among these distances:
72 2 0.02
73 28 0.33
74 32 0.38
76 2 0.02
77 4 0.05
78 10 0.12
79 6 0.07
ACGTcount: A:0.27, C:0.28, G:0.22, T:0.23
Consensus pattern (74 bp):
CAAAGCCTTCGGGACTTAGCCCGGATATAACTCGCACAAATGCCTTCGGACTTAACCCGGATATG
GAACTAGCA
Found at i:53989427 original size:40 final size:40
Alignment explanation
Indices: 53989361--53989527 Score: 160
Period size: 40 Copynumber: 4.2 Consensus size: 40
53989351 AAATTGAATG
* * *
53989361 ATATCCGGGCTAAG-CCCGAAGACAATTATGCTGGAAATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
* * ***
53989400 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
* *
53989440 ATATCCGGGCTAAGGCCCGAAGGC-ATTCGTGC-GAGTTATT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCTG-GTAATT
* * ** *
53989480 CTATCCGGGCTAAGACCCGAAGGCATTTGTGCACGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
53989520 ATATCCGG
1 ATATCCGG
53989528 TTATATTCCG
Statistics
Matches: 103, Mismatches: 20, Indels: 9
0.78 0.15 0.07
Matches are distributed among these distances:
39 16 0.16
40 85 0.83
41 2 0.02
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
Found at i:53993003 original size:18 final size:20
Alignment explanation
Indices: 53992967--53993013 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
53992957 AGTTGTAAGT
53992967 ATATATATGTGAATAATTTG
1 ATATATATGTGAATAATTTG
* *
53992987 ATAT-TATGTGATTATTTTG
1 ATATATATGTGAATAATTTG
53993006 ATGATATA
1 AT-ATATA
53993014 ACATGTTCTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
19 15 0.65
20 6 0.26
21 2 0.09
ACGTcount: A:0.36, C:0.00, G:0.15, T:0.49
Consensus pattern (20 bp):
ATATATATGTGAATAATTTG
Found at i:53993537 original size:51 final size:50
Alignment explanation
Indices: 53993472--53993649 Score: 182
Period size: 51 Copynumber: 3.5 Consensus size: 50
53993462 TTAGGTCGCA
53993472 TGTGTAGTACTAAGTGCAGGCTACTATGCATACCCGATAGTTTCAATCACG
1 TGTGTAGTACTAAGTGCAGGCTACTATGCATACCCGATAG-TTCAATCACG
** * * * * *
53993523 TGTGTAGTACTAAGTGCAGGCTACTA--CATGTACTGGATTGAT-AGGTCGCA
1 TGTGTAGTACTAAGTGCAGGCTACTATGCA--TACCCGATAGTTCA-ATCACG
** * * *
53993573 TGTGTAGTACTAAGTGCAGGCTACTATGCGCACCCGTTAACTTCGATCACG
1 TGTGTAGTACTAAGTGCAGGCTACTATGCATACCCGAT-AGTTCAATCACG
53993624 TGTGTAGTACTAAGTGCAGGCTACTA
1 TGTGTAGTACTAAGTGCAGGCTACTA
53993650 CGTGTATCAG
Statistics
Matches: 101, Mismatches: 19, Indels: 14
0.75 0.14 0.10
Matches are distributed among these distances:
49 3 0.03
50 34 0.34
51 63 0.62
52 1 0.01
ACGTcount: A:0.26, C:0.20, G:0.25, T:0.29
Consensus pattern (50 bp):
TGTGTAGTACTAAGTGCAGGCTACTATGCATACCCGATAGTTCAATCACG
Found at i:53993568 original size:101 final size:101
Alignment explanation
Indices: 53993417--53993655 Score: 354
Period size: 101 Copynumber: 2.4 Consensus size: 101
53993407 CAGTTTTAGG
* * * *
53993417 TCACGTGTGAAGTGCTAAGTGTAGGCTACTACGTGTACCAGGTTGTTAGGTCGCATGTGTAGTAC
1 TCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGGTTGATAGGTCGCATGTGTAGTAC
* **
53993482 TAAGTGCAGGCTACTATGCATACCCGATAGTTTCAA
66 TAAGTGCAGGCTACTATGCACACCCGATAACTTCAA
* *
53993518 TCACGTGTGTAGTACTAAGTGCAGGCTACTACATGTA-CTGGATTGATAGGTCGCATGTGTAGTA
1 TCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGG-TTGATAGGTCGCATGTGTAGTA
* * *
53993582 CTAAGTGCAGGCTACTATGCGCACCCGTTAACTTCGA
65 CTAAGTGCAGGCTACTATGCACACCCGATAACTTCAA
53993619 TCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTA
1 TCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTA
53993656 TCAGATGGAT
Statistics
Matches: 124, Mismatches: 13, Indels: 2
0.89 0.09 0.01
Matches are distributed among these distances:
100 3 0.02
101 121 0.98
ACGTcount: A:0.25, C:0.20, G:0.26, T:0.29
Consensus pattern (101 bp):
TCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGGTTGATAGGTCGCATGTGTAGTAC
TAAGTGCAGGCTACTATGCACACCCGATAACTTCAA
Found at i:53993677 original size:151 final size:152
Alignment explanation
Indices: 53993472--53993753 Score: 381
Period size: 151 Copynumber: 1.9 Consensus size: 152
53993462 TTAGGTCGCA
* * ** *
53993472 TGTGTAGTACTAAGTGCAGGCTACTATGCATACCCGATAGTTTCAATCACGTGTGTAGTACTAAG
1 TGTGTAGTACTAAGTGCAGGCTACTACGCATACCAGATAGGATCAATCACGTGTGTAGTAATAAG
* * ** * *
53993537 TGCAGGCTACTACATGTACTGGATTGATAGGTCGCATGTGTAGTACT-AAGTGCAGGCTACTATG
66 TACAGACTACTACATGTACCAGATTGATAGGTCACATGTGTAGTACTAAAG-CCAGGCTACTATG
53993601 CGCACCCGTTAACTTCGATCACG
130 CGCACCCGTTAACTTCGATCACG
** * *
53993624 TGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGAT-GGAT-AAGTCATGTGTGTAGTAATAA
1 TGTGTAGTACTAAGTGCAGGCTACTACGCATACCAGATAGGATCAA-TCACGTGTGTAGTAATAA
*
53993687 GTACAGACTACTACGTGTACCAGATTGATAGGTCACATGTGTAGTACTAAAGCCAGGCTACTATG
65 GTACAGACTACTACATGTACCAGATTGATAGGTCACATGTGTAGTACTAAAGCCAGGCTACTATG
53993752 CG
130 CG
53993754 TACCAGAGAG
Statistics
Matches: 112, Mismatches: 16, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
150 2 0.02
151 74 0.66
152 36 0.32
ACGTcount: A:0.28, C:0.19, G:0.25, T:0.29
Consensus pattern (152 bp):
TGTGTAGTACTAAGTGCAGGCTACTACGCATACCAGATAGGATCAATCACGTGTGTAGTAATAAG
TACAGACTACTACATGTACCAGATTGATAGGTCACATGTGTAGTACTAAAGCCAGGCTACTATGC
GCACCCGTTAACTTCGATCACG
Found at i:53993678 original size:101 final size:100
Alignment explanation
Indices: 53993417--53993699 Score: 350
Period size: 101 Copynumber: 2.8 Consensus size: 100
53993407 CAGTTTTAGG
* * * * *
53993417 TCACGTGTGAAGTGCTAAGTGTAGGCTACTACGTGTACCAGGTTGTTAGGTCGCATGTGTAGTAC
1 TCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTA-CAGATTGATAGGTCGCATGTGTAGTAC
* **
53993482 TAAGTGCAGGCTACTATGCATACCCGATAGTTTCAA
65 TAAGTGCAGGCTACTATGCACACCCGATAACTTCAA
* *
53993518 TCACGTGTGTAGTACTAAGTGCAGGCTACTACATGTACTGGATTGATAGGTCGCATGTGTAGTAC
1 TCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTAC-AGATTGATAGGTCGCATGTGTAGTAC
* * *
53993583 TAAGTGCAGGCTACTATGCGCACCCGTTAACTTCGA
65 TAAGTGCAGGCTACTATGCACACCCGATAACTTCAA
* * *** *
53993619 TCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGATGGATAAGTCATGTGTGTAGTAA
1 TCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTA-CAGATTGATAGGTCGCATGTGTAGTAC
* *
53993684 TAAGTACAGACTACTA
65 TAAGTGCAGGCTACTA
53993700 CGTGTACCAG
Statistics
Matches: 157, Mismatches: 23, Indels: 4
0.85 0.12 0.02
Matches are distributed among these distances:
100 1 0.01
101 155 0.99
102 1 0.01
ACGTcount: A:0.27, C:0.18, G:0.26, T:0.29
Consensus pattern (100 bp):
TCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACAGATTGATAGGTCGCATGTGTAGTACT
AAGTGCAGGCTACTATGCACACCCGATAACTTCAA
Found at i:53993760 original size:50 final size:50
Alignment explanation
Indices: 53993366--53993760 Score: 296
Period size: 50 Copynumber: 7.8 Consensus size: 50
53993356 GTTGTGAGAA
* * * *
53993366 CACATGTGTAGTACTATGTGCAGGCTACTATGTGTTTAAGACAG-TT-TTAGGT
1 CACATGTGTAGTACTAAGTGCAGGCTACTACGTG--T-A-CCAGATTGATAGGT
* * * * * *
53993418 CACGTGTGAAGTGCTAAGTGTAGGCTACTACGTGTACCAGGTTGTTAGGT
1 CACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTGATAGGT
* * ** * * * *
53993468 CGCATGTGTAGTACTAAGTGCAGGCTACTATGCATACCCGATAGTTTCA-AT
1 CACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTG-AT-AGGT
* * **
53993519 CACGTGTGTAGTACTAAGTGCAGGCTACTACATGTACTGGATTGATAGGT
1 CACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTGATAGGT
* * * * * * * *
53993569 CGCATGTGTAGTACTAAGTGCAGGCTACTATGCGCACCCG-TTAACTTCGAT
1 CACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTGA--TAGGT
* * * *
53993620 CACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGATGGATAAGT
1 CACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTGATAGGT
** * * *
53993670 CATGTGTGTAGTAATAAGTACAGACTACTACGTGTACCAGATTGATAGGT
1 CACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTGATAGGT
* * *
53993720 CACATGTGTAGTACTAAAG-CCAGGCTACTATGCGTACCAGA
1 CACATGTGTAGTACT-AAGTGCAGGCTACTACGTGTACCAGA
53993761 GAGCTTCGGT
Statistics
Matches: 267, Mismatches: 67, Indels: 20
0.75 0.19 0.06
Matches are distributed among these distances:
48 3 0.01
49 7 0.03
50 149 0.56
51 77 0.29
52 31 0.12
ACGTcount: A:0.27, C:0.18, G:0.26, T:0.29
Consensus pattern (50 bp):
CACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTGATAGGT
Found at i:53993981 original size:16 final size:16
Alignment explanation
Indices: 53993960--53993991 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
53993950 AGAATGGAGT
53993960 AAGTGAAATTATGTAA
1 AAGTGAAATTATGTAA
*
53993976 AAGTGAAATTTTGTAA
1 AAGTGAAATTATGTAA
53993992 TAAAACAATT
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:0.47, C:0.00, G:0.19, T:0.34
Consensus pattern (16 bp):
AAGTGAAATTATGTAA
Found at i:53995904 original size:28 final size:29
Alignment explanation
Indices: 53995837--53995937 Score: 125
Period size: 28 Copynumber: 3.5 Consensus size: 29
53995827 ATAGTGAATC
*
53995837 CGCACACTTAGTGCTATATACATTC-AGCT
1 CGCACACTTAGTGCTATATA-ATTCAAACT
53995866 CGCACACTTAGTGCTATATAA-TCAAACT
1 CGCACACTTAGTGCTATATAATTCAAACT
* * * *
53995894 CGCACACTTAGTGCTGTACAATTTTAAACC
1 CGCACACTTAGTGCTATATAA-TTCAAACT
53995924 CGCACACTTAGTGC
1 CGCACACTTAGTGC
53995938 CAATCTTGTC
Statistics
Matches: 64, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
27 2 0.03
28 23 0.36
29 20 0.31
30 19 0.30
ACGTcount: A:0.30, C:0.28, G:0.14, T:0.29
Consensus pattern (29 bp):
CGCACACTTAGTGCTATATAATTCAAACT
Found at i:54004125 original size:40 final size:40
Alignment explanation
Indices: 54004019--54004160 Score: 133
Period size: 40 Copynumber: 3.5 Consensus size: 40
54004009 CGAATGGTGT
* * * * * *
54004019 CCGGGCTAAGTCCCGAAGGCTTTTGTGCTAAGTGACTAAAT
1 CCGGGCTAAGTCCCGAAGGCATTCGTGC-GAGTTACCAAAA
* *
54004060 CTGGG-TCAATTCCCGAAGGCATTCGTGCGAGTTACCAAAA
1 CCGGGCT-AAGTCCCGAAGGCATTCGTGCGAGTTACCAAAA
* * * *
54004100 CCGGGTTAAGTCCCGAAGGTATTCGTGCGAGTTACTAAAT
1 CCGGGCTAAGTCCCGAAGGCATTCGTGCGAGTTACCAAAA
* *
54004140 CGGGGCTAATTCCCGAAGGCA
1 CCGGGCTAAGTCCCGAAGGCA
54004161 ATTGTGCAAA
Statistics
Matches: 82, Mismatches: 17, Indels: 5
0.79 0.16 0.05
Matches are distributed among these distances:
40 59 0.72
41 23 0.28
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.24
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTCGTGCGAGTTACCAAAA
Found at i:54004182 original size:80 final size:81
Alignment explanation
Indices: 54004019--54004197 Score: 195
Period size: 80 Copynumber: 2.2 Consensus size: 81
54004009 CGAATGGTGT
* *
54004019 CCGGGCTAAGTCCCGAAGGCTTTTGTGCTAAGTGACTAAATCTGGGTCAATTCCCGAAGGCATTC
1 CCGGGCTAAGTCCCGAAGGCTTTCGTGCTAAGTGACTAAATCGGGGTCAATTCCCGAAGGCATTC
* * *
54004084 GTGCGAGTTACCAAAA
66 GTGCAAATCACCAAAA
* * *
54004100 CCGGGTTAAGTCCCGAAGG-TATTCGTGC-GAGTTACTAAATCGGGG-CTAATTCCCGAAGGCAA
1 CCGGGCTAAGTCCCGAAGGCT-TTCGTGCTAAGTGACTAAATCGGGGTC-AATTCCCGAAGGC-A
* *
54004162 TT-GTGCAAATCACTATAA
63 TTCGTGCAAATCACCAAAA
* *
54004180 CCGAGCTATGTCCCGAAG
1 CCGGGCTAAGTCCCGAAG
54004198 ACAATCGAGT
Statistics
Matches: 82, Mismatches: 13, Indels: 7
0.80 0.13 0.07
Matches are distributed among these distances:
79 1 0.01
80 54 0.66
81 27 0.33
ACGTcount: A:0.27, C:0.23, G:0.26, T:0.24
Consensus pattern (81 bp):
CCGGGCTAAGTCCCGAAGGCTTTCGTGCTAAGTGACTAAATCGGGGTCAATTCCCGAAGGCATTC
GTGCAAATCACCAAAA
Found at i:54006216 original size:40 final size:40
Alignment explanation
Indices: 54006146--54006367 Score: 288
Period size: 40 Copynumber: 5.6 Consensus size: 40
54006136 AAACCAAGTA
** * *
54006146 CCTTCGGGGTTTAGCCGGA-TATAGCT-ACTCGCTCAAATG
1 CCTTCGGGACTTAGCCCGATTATAG-TAACTCGCACAAATG
* * * *
54006185 CCTTCGAGACTTTGCCCAATTATAGTAACTCGCACAATTG
1 CCTTCGGGACTTAGCCCGATTATAGTAACTCGCACAAATG
* *
54006225 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAATTG
1 CCTTCGGGACTTAGCCCGATTATAGTAACTCGCACAAATG
* *
54006265 CCTTCGGGACTTGGCCCGGTTATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGATTATAGTAACTCGCACAAATG
54006305 CCTTCGGGACTTAGCCCGGA-TATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCC-GATTATAGTAACTCGCACAAATG
*
54006345 CCTTCGGGACTTAGCCCGGTTAT
1 CCTTCGGGACTTAGCCCGATTAT
54006368 CAATCCGAAT
Statistics
Matches: 162, Mismatches: 17, Indels: 7
0.87 0.09 0.04
Matches are distributed among these distances:
39 15 0.09
40 146 0.90
41 1 0.01
ACGTcount: A:0.23, C:0.27, G:0.23, T:0.27
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGATTATAGTAACTCGCACAAATG
Found at i:54006288 original size:80 final size:80
Alignment explanation
Indices: 54006146--54006367 Score: 322
Period size: 80 Copynumber: 2.8 Consensus size: 80
54006136 AAACCAAGTA
** * * * **
54006146 CCTTCGGGGTTTAG-CCGGATATAGCT-ACTCGCTCAAATGCCTTCGAGACTTTGCCCAATTATA
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTATA
*
54006209 GTAACTCGCACAATTG
65 GTAACTCGCACAAATG
* * *
54006225 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAATTGCCTTCGGGACTTGGCCCGGTTATAG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTATAG
54006290 TAACTCGCACAAATG
66 TAACTCGCACAAATG
54006305 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTAT
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTAT
54006368 CAATCCGAAT
Statistics
Matches: 128, Mismatches: 13, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
79 13 0.10
80 115 0.90
ACGTcount: A:0.23, C:0.27, G:0.23, T:0.27
Consensus pattern (80 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTATAG
TAACTCGCACAAATG
Found at i:54014234 original size:40 final size:40
Alignment explanation
Indices: 54014165--54014385 Score: 340
Period size: 40 Copynumber: 5.6 Consensus size: 40
54014155 AAACCAAGTA
* * *
54014165 CCTTCGGG-TTTAG-CCGGATATAGCT-ACTCGCTCAAATG
1 CCTTCGGGACTTAGCCCGGTTATAG-TAACTCGCACAAATG
*
54014203 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAATTG
1 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
*
54014243 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAATTG
1 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
*
54014283 CCTTCGGGACTTAGCCCGGTTATAGTAACTCACACAAATG
1 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
* *
54014323 CCTTCGGGACTTAGCCCGGATATAGTAACTCACACAAATG
1 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
54014363 CCTTCGGGACTTAGCCCGGTTAT
1 CCTTCGGGACTTAGCCCGGTTAT
54014386 CAATCCGAAT
Statistics
Matches: 172, Mismatches: 8, Indels: 4
0.93 0.04 0.02
Matches are distributed among these distances:
38 8 0.05
39 5 0.03
40 159 0.92
ACGTcount: A:0.24, C:0.28, G:0.22, T:0.27
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
Found at i:54017231 original size:47 final size:47
Alignment explanation
Indices: 54017162--54017336 Score: 196
Period size: 47 Copynumber: 3.7 Consensus size: 47
54017152 TAAGGTGCCA
* *
54017162 ATGCCATGTCCCAGACACGGTCTTACACTAGCTCATATCTTAAGTCG
1 ATGCCATGTCCCAGACATGGTCTTACACTAGCTCATATCTCAAGTCG
* *
54017209 ATGCCATGTCCCAGACATGGTCTTACACT-GACT-ATCATCCCATAGCCG
1 ATGCCATGTCCCAGACATGGTCTTACACTAG-CTCAT-ATCTCA-AGTCG
* *
54017257 ATG-CATGTCCCAGACAT-GTCTTACACTAGCTCTTGTCTCAATGTCG
1 ATGCCATGTCCCAGACATGGTCTTACACTAGCTCATATCTCAA-GTCG
* * * *
54017303 ATGCCATATCCTAGACATGGTCTTATATTAGCTC
1 ATGCCATGTCCCAGACATGGTCTTACACTAGCTC
54017337 TCGTAATGTG
Statistics
Matches: 108, Mismatches: 12, Indels: 15
0.80 0.09 0.11
Matches are distributed among these distances:
45 1 0.01
46 25 0.23
47 62 0.57
48 20 0.19
ACGTcount: A:0.25, C:0.29, G:0.17, T:0.30
Consensus pattern (47 bp):
ATGCCATGTCCCAGACATGGTCTTACACTAGCTCATATCTCAAGTCG
Found at i:54017351 original size:94 final size:93
Alignment explanation
Indices: 54017166--54017383 Score: 240
Period size: 94 Copynumber: 2.3 Consensus size: 93
54017156 GTGCCAATGC
* * *
54017166 CATGTCCCAGACACGGTCTTACACTAGCTCATATCTTAAGTCGATGCCATGTCCCAGACATGGTC
1 CATGTCCCAGACA-TGTCTTACACTAGCTCATATCTCAAGTCGATGCCATATCCCAGACATGGTC
** *
54017231 TTACACTGACTATCATCCCATAGCCGATG
65 TTACACTGACTATCATAACATAGCCGATA
* * *
54017260 CATGTCCCAGACATGTCTTACACTAGCTCTTGTCTCAATGTCGATGCCATATCCTAGACATGGTC
1 CATGTCCCAGACATGTCTTACACTAGCTCATATCTCAA-GTCGATGCCATATCCCAGACATGGTC
* * * * ** *
54017325 TTATA-TTAGCTCTCGTAATGTGGCCGATA
65 TTACACTGA-CTATCATAACATAGCCGATA
* *
54017354 CATGCCCCAGACATGTCTTACACTGGCTCA
1 CATGTCCCAGACATGTCTTACACTAGCTCA
54017384 CGCAAGTGAC
Statistics
Matches: 103, Mismatches: 19, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
93 23 0.22
94 80 0.78
ACGTcount: A:0.24, C:0.29, G:0.17, T:0.29
Consensus pattern (93 bp):
CATGTCCCAGACATGTCTTACACTAGCTCATATCTCAAGTCGATGCCATATCCCAGACATGGTCT
TACACTGACTATCATAACATAGCCGATA
Found at i:54024847 original size:47 final size:49
Alignment explanation
Indices: 54024773--54024997 Score: 206
Period size: 47 Copynumber: 4.8 Consensus size: 49
54024763 TAAGGTGCCA
* **
54024773 ATGCTATGTCCCAGACATGGTCTTACACTAGCTCAT-ATCTCAA-ATTG
1 ATGCCATGTCCCAGACATGGTCTTACACTAGCTCATCATCTCAAGACCG
54024820 ATGCCATGTCCCAGACATGGTCTTACACT-GACT-ATCATCTCATAG-CCG
1 ATGCCATGTCCCAGACATGGTCTTACACTAG-CTCATCATCTCA-AGACCG
* * * * *
54024868 ATG-CATGTCCTAGACAT-GTCTTACACT-G-GCATACGTCTCAAGGCTG
1 ATGCCATGTCCCAGACATGGTCTTACACTAGCTCAT-CATCTCAAGACCG
* * *
54024914 ATG-CATGTCCCAGACAT-GTCTTACACTAGCTC-TCGTCTCAATATCG
1 ATGCCATGTCCCAGACATGGTCTTACACTAGCTCATCATCTCAAGACCG
* * *
54024960 ATGCCATATCCCAAACATGGTCTTATACTAGCTC-TCAT
1 ATGCCATGTCCCAGACATGGTCTTACACTAGCTCATCAT
54024998 AATGTGGTCG
Statistics
Matches: 150, Mismatches: 17, Indels: 21
0.80 0.09 0.11
Matches are distributed among these distances:
45 4 0.03
46 60 0.40
47 63 0.42
48 23 0.15
ACGTcount: A:0.26, C:0.28, G:0.16, T:0.30
Consensus pattern (49 bp):
ATGCCATGTCCCAGACATGGTCTTACACTAGCTCATCATCTCAAGACCG
Found at i:54024951 original size:46 final size:46
Alignment explanation
Indices: 54024773--54024997 Score: 208
Period size: 46 Copynumber: 4.8 Consensus size: 46
54024763 TAAGGTGCCA
**
54024773 ATGCTATGTCCCAGACATGGTCTTACACTAGCTCAT-ATCTCAAATTG
1 ATGC-ATGTCCCAGACATGGTCTTACACTAGCTC-TCATCTCAAGCTG
* *
54024820 ATGCCATGTCCCAGACATGGTCTTACACT-GACTATCATCTCATAGCCG
1 ATG-CATGTCCCAGACATGGTCTTACACTAG-CTCTCATCTCA-AGCTG
* * * *
54024868 ATGCATGTCCTAGACAT-GTCTTACACTGGCAT-ACGTCTCAAGGCTG
1 ATGCATGTCCCAGACATGGTCTTACACTAGC-TCTCATCTCAA-GCTG
* **
54024914 ATGCATGTCCCAGACAT-GTCTTACACTAGCTCTCGTCTCAATATCG
1 ATGCATGTCCCAGACATGGTCTTACACTAGCTCTCATCTCAAGCT-G
* * *
54024960 ATGCCATATCCCAAACATGGTCTTATACTAGCTCTCAT
1 ATG-CATGTCCCAGACATGGTCTTACACTAGCTCTCAT
54024998 AATGTGGTCG
Statistics
Matches: 150, Mismatches: 17, Indels: 21
0.80 0.09 0.11
Matches are distributed among these distances:
45 3 0.02
46 62 0.41
47 62 0.41
48 23 0.15
ACGTcount: A:0.26, C:0.28, G:0.16, T:0.30
Consensus pattern (46 bp):
ATGCATGTCCCAGACATGGTCTTACACTAGCTCTCATCTCAAGCTG
Found at i:54025030 original size:140 final size:141
Alignment explanation
Indices: 54024773--54025033 Score: 334
Period size: 140 Copynumber: 1.9 Consensus size: 141
54024763 TAAGGTGCCA
* * *
54024773 ATGCTATGTCCCAGACATGGTCTTACACTAGCTCATATCTCAAATTGATGCCATGTCCCAGACAT
1 ATGCTATGTCCCAGACATGGTCTTACACTAGCTCATATCTCAAATCGATGCCATATCCCAAACAT
* * *
54024838 GGTCTTACACTGACTATCATCTCATAGCCGATGCATGTCCTAGACATGTCTTACACTGGCATACG
66 GGTCTTACACTGACTATCATATCATAGCCGATGCATATCCCAGACATGTCTTACACTGGCATACG
54024903 TCTCAAGGCTG
131 TCTCAAGGCTG
*
54024914 ATGC-ATGTCCCAGACAT-GTCTTACACTAGCTC-TCGTCTCAATATCGATGCCATATCCCAAAC
1 ATGCTATGTCCCAGACATGGTCTTACACTAGCTCAT-ATCTCAA-ATCGATGCCATATCCCAAAC
* * * * * *
54024976 ATGGTCTTATACT-AGCTCTCATAAT-GTGGTCGATGCATATCCCAGGCATGTCTTACAC
64 ATGGTCTTACACTGA-CTATCAT-ATCATAGCCGATGCATATCCCAGACATGTCTTACAC
54025034 ATGCTCACGC
Statistics
Matches: 103, Mismatches: 13, Indels: 9
0.82 0.10 0.07
Matches are distributed among these distances:
138 1 0.01
139 22 0.21
140 75 0.73
141 5 0.05
ACGTcount: A:0.26, C:0.28, G:0.17, T:0.30
Consensus pattern (141 bp):
ATGCTATGTCCCAGACATGGTCTTACACTAGCTCATATCTCAAATCGATGCCATATCCCAAACAT
GGTCTTACACTGACTATCATATCATAGCCGATGCATATCCCAGACATGTCTTACACTGGCATACG
TCTCAAGGCTG
Found at i:54025395 original size:27 final size:27
Alignment explanation
Indices: 54025341--54025396 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 27
54025331 AGACAAATTG
*
54025341 TTGCAACTAGCTGTCATCTTTCTGAGC
1 TTGCAACTAGCTGTCATCTTTCTAAGC
*
54025368 TTGCAACTCA-CTGTCATCTTTTTAAGC
1 TTGCAACT-AGCTGTCATCTTTCTAAGC
54025395 TT
1 TT
54025397 CACAGATTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
27 25 0.96
28 1 0.04
ACGTcount: A:0.20, C:0.25, G:0.14, T:0.41
Consensus pattern (27 bp):
TTGCAACTAGCTGTCATCTTTCTAAGC
Found at i:54028445 original size:32 final size:32
Alignment explanation
Indices: 54028409--54028473 Score: 112
Period size: 32 Copynumber: 2.0 Consensus size: 32
54028399 ACTTGGTAAG
* *
54028409 TTTACTTTCTGATTATTTGAGCTTACTAAGCA
1 TTTACTTTCCGATTATTCGAGCTTACTAAGCA
54028441 TTTACTTTCCGATTATTCGAGCTTACTAAGCA
1 TTTACTTTCCGATTATTCGAGCTTACTAAGCA
54028473 T
1 T
54028474 ATAAATGCTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.25, C:0.18, G:0.12, T:0.45
Consensus pattern (32 bp):
TTTACTTTCCGATTATTCGAGCTTACTAAGCA
Found at i:54032940 original size:23 final size:22
Alignment explanation
Indices: 54032880--54032956 Score: 77
Period size: 23 Copynumber: 3.5 Consensus size: 22
54032870 GAGCTATGAT
*
54032880 CGGTAAGCTCCG-AGAGCTAAA
1 CGGTAAGCTCTGAAGAGCTAAA
*
54032901 CGGTAAGCTCTGTAGAGCTAAA
1 CGGTAAGCTCTGAAGAGCTAAA
*
54032923 GTGGTAAGC-CTCGAAGAGCTAAAA
1 -CGGTAAGCTCT-GAAGAGCT-AAA
*
54032947 CGGTACGCTC
1 CGGTAAGCTC
54032957 ATACGAGCTA
Statistics
Matches: 46, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
21 11 0.24
22 11 0.24
23 20 0.43
24 4 0.09
ACGTcount: A:0.31, C:0.22, G:0.29, T:0.18
Consensus pattern (22 bp):
CGGTAAGCTCTGAAGAGCTAAA
Found at i:54035049 original size:2 final size:2
Alignment explanation
Indices: 54035042--54035067 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
54035032 GCACTTATGA
54035042 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
54035068 GGTATTTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:54035771 original size:40 final size:40
Alignment explanation
Indices: 54035662--54035882 Score: 288
Period size: 40 Copynumber: 5.6 Consensus size: 40
54035652 TATTCAGATG
* * *
54035662 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
1 ATAACCGGGCTAAGTCCCGAAGGCAATTGTGCGAGTTACT
* * *
54035702 A-ATTCTGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACT
1 ATA-ACCGGGCTAAGTCCCGAAGGCAATTGTGCGAGTTACT
54035741 ATAACCGGGCTAAGTCCCGAAGGCAATTGTGCGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCAATTGTGCGAGTTACT
*
54035781 ATAATCGGGCTAAGTCCCGAAGGCAATTGTGCGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCAATTGTGCGAGTTACT
* *
54035821 ATAACCGGGCTAAGTCCCAAAGGCAATTGAGCGAG-TAGCT
1 ATAACCGGGCTAAGTCCCGAAGGCAATTGTGCGAGTTA-CT
* **
54035861 ATATCC-GGCTAAACCCCGAAGG
1 ATAACCGGGCTAAGTCCCGAAGG
54035883 TACTTGGCTT
Statistics
Matches: 162, Mismatches: 15, Indels: 9
0.87 0.08 0.05
Matches are distributed among these distances:
39 49 0.30
40 113 0.70
ACGTcount: A:0.28, C:0.23, G:0.27, T:0.23
Consensus pattern (40 bp):
ATAACCGGGCTAAGTCCCGAAGGCAATTGTGCGAGTTACT
Found at i:54041714 original size:80 final size:80
Alignment explanation
Indices: 54041630--54041778 Score: 183
Period size: 80 Copynumber: 1.9 Consensus size: 80
54041620 TATGGTAACC
* * * *
54041630 CGCACCAAGGCCTACGGGACTTAACCCGGATATCA-CGATTTGCACAAATGCCTTCGGGTCTTAG
1 CGCACCAAGGCCTACGGGACTTAACCCGGATAT-AGCCACTAGCACAAATGCCTTCGGGTCTTAA
54041694 CCCGGATAGAATGACT
65 CCCGGATAGAATGACT
* * * * * * *
54041710 CGCACGAATGCCTTCGGGTCTTAGCCCGGATGTAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CGCACCAAGGCCTACGGGACTTAACCCGGATATAGCCACTAGCACAAATGCCTTCGGGTCTTAAC
54041775 CCGG
66 CCGG
54041779 TTATAATTTC
Statistics
Matches: 57, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
79 1 0.02
80 56 0.98
ACGTcount: A:0.23, C:0.30, G:0.25, T:0.22
Consensus pattern (80 bp):
CGCACCAAGGCCTACGGGACTTAACCCGGATATAGCCACTAGCACAAATGCCTTCGGGTCTTAAC
CCGGATAGAATGACT
Found at i:54041720 original size:40 final size:38
Alignment explanation
Indices: 54041671--54041778 Score: 128
Period size: 40 Copynumber: 2.7 Consensus size: 38
54041661 ATCACGATTT
*
54041671 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATG-ACTC
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGAT-GAA-GCACTA
*
54041711 GCACGAATGCCTTCGGGTCTTAGCCCGGATGTAGCCACTA
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGATGAAG-CACTA
*
54041751 GCACAATTGCCTTCGGGTCTTAACCCGG
1 GCACAA-TGCCTTCGGGTCTTAGCCCGG
54041779 TTATAATTTC
Statistics
Matches: 61, Mismatches: 4, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
38 1 0.02
39 4 0.07
40 56 0.92
ACGTcount: A:0.21, C:0.30, G:0.26, T:0.23
Consensus pattern (38 bp):
GCACAATGCCTTCGGGTCTTAGCCCGGATGAAGCACTA
Found at i:54045390 original size:27 final size:26
Alignment explanation
Indices: 54045356--54045481 Score: 153
Period size: 27 Copynumber: 4.7 Consensus size: 26
54045346 TGGATAAGTT
54045356 GTAGAATTACCGAAATACCCCTGTAAG
1 GTAGAATTACCGAAATACCCCTGT-AG
* *
54045383 GTAGAATTACTGAAATACCCCTATAG
1 GTAGAATTACCGAAATACCCCTGTAG
**
54045409 AGTAGAATTATTGAAATACCCCTGTAGG
1 -GTAGAATTACCGAAATACCCCTGTA-G
* *
54045437 GTAGAATTACAGAGATACCCCTGTAG
1 GTAGAATTACCGAAATACCCCTGTAG
*
54045463 GAGAGAATTACCGAAATAC
1 G-TAGAATTACCGAAATAC
54045482 TGTTGTAAGG
Statistics
Matches: 86, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
26 4 0.05
27 81 0.94
28 1 0.01
ACGTcount: A:0.38, C:0.18, G:0.20, T:0.24
Consensus pattern (26 bp):
GTAGAATTACCGAAATACCCCTGTAG
Found at i:54045440 original size:54 final size:55
Alignment explanation
Indices: 54045356--54045481 Score: 184
Period size: 54 Copynumber: 2.3 Consensus size: 55
54045346 TGGATAAGTT
*
54045356 GTAGAATTACCGAAATACCCCTGTAAGGTAGAATTACTGAAATACCCCTATA-GA
1 GTAGAATTACCGAAATACCCCTGTAAGGTAGAATTACAGAAATACCCCTATAGGA
** * * *
54045410 GTAGAATTATTGAAATACCCCTGTAGGGTAGAATTACAGAGATACCCCTGTAGGA
1 GTAGAATTACCGAAATACCCCTGTAAGGTAGAATTACAGAAATACCCCTATAGGA
54045465 G-AGAATTACCGAAATAC
1 GTAGAATTACCGAAATAC
54045482 TGTTGTAAGG
Statistics
Matches: 63, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
54 60 0.95
55 3 0.05
ACGTcount: A:0.38, C:0.18, G:0.20, T:0.24
Consensus pattern (55 bp):
GTAGAATTACCGAAATACCCCTGTAAGGTAGAATTACAGAAATACCCCTATAGGA
Found at i:54051194 original size:40 final size:40
Alignment explanation
Indices: 54051149--54051316 Score: 185
Period size: 40 Copynumber: 4.2 Consensus size: 40
54051139 CGGAATATAA
54051149 CCGGATATAATCACGT-GCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCAC-TAGCACAAATGCCTTCGGGTCTTAGC
* * * *
54051189 CCGGATAGAATAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * *
54051229 CCGGATATAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * * * * *
54051269 CCGGATATAATTTCCAGCATAATTGTCTTCGGGGCTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
54051309 CCGGATAT
1 CCGGATAT
54051317 CATTCAATTT
Statistics
Matches: 107, Mismatches: 20, Indels: 2
0.83 0.16 0.02
Matches are distributed among these distances:
39 1 0.01
40 106 0.99
ACGTcount: A:0.24, C:0.27, G:0.23, T:0.26
Consensus pattern (40 bp):
CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:54054854 original size:41 final size:39
Alignment explanation
Indices: 54054746--54054896 Score: 128
Period size: 40 Copynumber: 3.8 Consensus size: 39
54054736 ATCACGATTT
*
54054746 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATGACTC
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGATAGAATGACTA
*
54054786 GCACGAATGCCTTCGGGTCTTAGCCCGGAT-GTA-GCCACTA
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGATAGAATG--ACTA
* * * ** *
54054826 GCCACAATTGCCTTCGGGTCTTAACCCGGTTATAATTTCCA
1 G-CACAA-TGCCTTCGGGTCTTAGCCCGGATAGAATGACTA
* *
54054867 GCATAATTGTCTTCGGG-CTTAGCCCGGATA
1 GCACAA-TGCCTTCGGGTCTTAGCCCGGATA
54054897 TCATTCAATT
Statistics
Matches: 91, Mismatches: 14, Indels: 13
0.77 0.12 0.11
Matches are distributed among these distances:
38 1 0.01
39 13 0.14
40 49 0.54
41 27 0.30
42 1 0.01
ACGTcount: A:0.22, C:0.28, G:0.24, T:0.26
Consensus pattern (39 bp):
GCACAATGCCTTCGGGTCTTAGCCCGGATAGAATGACTA
Found at i:54068030 original size:43 final size:42
Alignment explanation
Indices: 54067983--54068079 Score: 133
Period size: 42 Copynumber: 2.3 Consensus size: 42
54067973 CCAAACGTGC
54067983 TCTTACATGTAATCAAATATCAATGCC-ACTATCCCAGACAGGG
1 TCTTACATGTAATCAAATA-CAATGCCGA-TATCCCAGACAGGG
* * * *
54068026 TCTTACACGAAATCAAATACAATGCCGATGTCCCAGACATGG
1 TCTTACATGTAATCAAATACAATGCCGATATCCCAGACAGGG
54068068 TCTTACATGTAA
1 TCTTACATGTAA
54068080 ATCATAAGTC
Statistics
Matches: 47, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
42 29 0.62
43 18 0.38
ACGTcount: A:0.35, C:0.25, G:0.14, T:0.26
Consensus pattern (42 bp):
TCTTACATGTAATCAAATACAATGCCGATATCCCAGACAGGG
Found at i:54068082 original size:43 final size:43
Alignment explanation
Indices: 54067958--54068118 Score: 168
Period size: 43 Copynumber: 3.7 Consensus size: 43
54067948 GGAAAGCTCG
* *
54067958 TACAATGCCAACGTCCCAAACGTGCTCTTACATGT-AATCAAA
1 TACAATGCCAACGTCCCAAACATGGTCTTACATGTAAATCAAA
* * * *
54068000 TATCAATGCC-ACTATCCCAGACAGGGTCTTACACG-AAATCAAA
1 TA-CAATGCCAAC-GTCCCAAACATGGTCTTACATGTAAATCAAA
* * *
54068043 TACAATGCCGATGTCCCAGACATGGTCTTACATGTAAATCATAA
1 TACAATGCCAACGTCCCAAACATGGTCTTACATGTAAATCA-AA
*
54068087 GT-CGATGCCAACGTCCCAAACATGGTCTTACA
1 -TACAATGCCAACGTCCCAAACATGGTCTTACA
54068119 CGAAAACACA
Statistics
Matches: 98, Mismatches: 14, Indels: 12
0.79 0.11 0.10
Matches are distributed among these distances:
42 30 0.31
43 39 0.40
44 28 0.29
45 1 0.01
ACGTcount: A:0.34, C:0.27, G:0.15, T:0.24
Consensus pattern (43 bp):
TACAATGCCAACGTCCCAAACATGGTCTTACATGTAAATCAAA
Found at i:54068120 original size:86 final size:85
Alignment explanation
Indices: 54067958--54068123 Score: 201
Period size: 86 Copynumber: 1.9 Consensus size: 85
54067948 GGAAAGCTCG
* *
54067958 TACAATGCCAACGTCCCAAACGTGCTCTTACATGTAATCAAATATCAATGCCACTATCCCAGACA
1 TACAATGCCAACGTCCCAAACATGCTCTTACATGTAATCAAATATCAATGCCACTATCCCAAACA
54068023 GGGTCTTACACGAAATCAAA
66 GGGTCTTACACGAAATCAAA
* * * * * * *
54068043 TACAATGCCGATGTCCCAGACATGGTCTTACATGTAAATCATAA-GTCGATGCCAAC-GTCCCAA
1 TACAATGCCAACGTCCCAAACATGCTCTTACATGT-AATCA-AATATCAATGCC-ACTATCCCAA
*
54068106 ACATGGTCTTACACGAAA
63 ACAGGGTCTTACACGAAA
54068124 ACACATATCA
Statistics
Matches: 68, Mismatches: 10, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
85 30 0.44
86 34 0.50
87 4 0.06
ACGTcount: A:0.35, C:0.27, G:0.15, T:0.23
Consensus pattern (85 bp):
TACAATGCCAACGTCCCAAACATGCTCTTACATGTAATCAAATATCAATGCCACTATCCCAAACA
GGGTCTTACACGAAATCAAA
Found at i:54072090 original size:45 final size:45
Alignment explanation
Indices: 54072010--54072098 Score: 135
Period size: 45 Copynumber: 2.0 Consensus size: 45
54072000 GCCAAAACAT
*
54072010 ATGTCACATATATCACGATGATCAGACCACAACTCATTGAGTTCGG
1 ATGTCACATATATCACGA-GATCAGACCACAACTCAATGAGTTCGG
*
54072056 ATGTCACATATATCATGA-ACTCAGACCACAACTCAATGAGTTC
1 ATGTCACATATATCACGAGA-TCAGACCACAACTCAATGAGTTC
54072099 AAATTACATA
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
44 1 0.03
45 22 0.55
46 17 0.43
ACGTcount: A:0.35, C:0.25, G:0.15, T:0.26
Consensus pattern (45 bp):
ATGTCACATATATCACGAGATCAGACCACAACTCAATGAGTTCGG
Found at i:54076337 original size:24 final size:24
Alignment explanation
Indices: 54076310--54076360 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
54076300 ATGAATCGAC
* *
54076310 AAAAGCCGAAATGCTGAAATGTCG
1 AAAAGCCGAAAAGCTGAAAAGTCG
*
54076334 AAAAGCTGAAAAGCTGAAAAGTCG
1 AAAAGCCGAAAAGCTGAAAAGTCG
54076358 AAA
1 AAA
54076361 GTTTGGCTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.49, C:0.14, G:0.24, T:0.14
Consensus pattern (24 bp):
AAAAGCCGAAAAGCTGAAAAGTCG
Found at i:54076360 original size:16 final size:16
Alignment explanation
Indices: 54076310--54076354 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
54076300 ATGAATCGAC
*
54076310 AAAAGCCGAAATGCTG
1 AAAAGCCGAAAAGCTG
* *
54076326 AAATGTCGAAAAGCTG
1 AAAAGCCGAAAAGCTG
*
54076342 AAAAGCTGAAAAG
1 AAAAGCCGAAAAG
54076355 TCGAAAGTTT
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.49, C:0.13, G:0.24, T:0.13
Consensus pattern (16 bp):
AAAAGCCGAAAAGCTG
Found at i:54077895 original size:40 final size:40
Alignment explanation
Indices: 54077810--54077962 Score: 139
Period size: 40 Copynumber: 3.8 Consensus size: 40
54077800 GGATATAGCG
* * * * * ***
54077810 ACTCGCTCAAAAGCCTTTGGGACATAGCCCGGTTATAATA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATGGGA
* * *
54077850 GCTCGCACAAATGCCTTCGGGACTTAACCCGGATTTGGGA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATGGGA
* **
54077890 ACTCGCACAAATGCCTTC-GGATCTTAGTCCGGATATGGTC
1 ACTCGCACAAATGCCTTCGGGA-CTTAGCCCGGATATGGGA
*
54077930 ACTTAGCACAAA-GCCTTCGGGACTTAGCCCGGA
1 AC-TCGCACAAATGCCTTCGGGACTTAGCCCGGA
54077963 CATCATTCGA
Statistics
Matches: 91, Mismatches: 19, Indels: 6
0.78 0.16 0.05
Matches are distributed among these distances:
39 3 0.03
40 77 0.85
41 11 0.12
ACGTcount: A:0.25, C:0.27, G:0.24, T:0.24
Consensus pattern (40 bp):
ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATGGGA
Found at i:54079846 original size:29 final size:28
Alignment explanation
Indices: 54079791--54079906 Score: 124
Period size: 29 Copynumber: 4.0 Consensus size: 28
54079781 GTGAGAATGA
* * *
54079791 ATATGAATGTGACTGGGCCTAACGGGCC
1 ATATAAATGTGATTGGGCCTAATGGGCC
54079819 ATATAAATGTGATTTGGGCCTAATGGGCC
1 ATATAAATGTGA-TTGGGCCTAATGGGCC
* * *
54079848 ATATACAGGTGATTTGGGCCTAAAGGGGCC
1 ATATAAATGTGA-TTGGGCCT-AATGGGCC
* * *
54079878 ATATGAATATGATTGGGCATAATGGGCC
1 ATATAAATGTGATTGGGCCTAATGGGCC
54079906 A
1 A
54079907 GATACAAGTA
Statistics
Matches: 74, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
28 19 0.26
29 40 0.54
30 15 0.20
ACGTcount: A:0.28, C:0.16, G:0.30, T:0.26
Consensus pattern (28 bp):
ATATAAATGTGATTGGGCCTAATGGGCC
Found at i:54083296 original size:42 final size:42
Alignment explanation
Indices: 54083165--54083329 Score: 134
Period size: 42 Copynumber: 3.9 Consensus size: 42
54083155 TAAGATGCCA
* * * * *
54083165 ATGCCATATCCCAGATATGGTCTTATATGAGATCACATATATCG
1 ATGCCATATCCCAGAAACGGTCTTACACGAAATCAC--ATATCG
* * ** * ** * *
54083209 ATGCCGATAGCCTAGCTATGGTCTTACACGATGTC-CGTATTG
1 ATGCC-ATATCCCAGAAACGGTCTTACACGAAATCACATATCG
*
54083251 ATGCCATGTCCCAGAAACGGTCTTACACGAAATCACATATCG
1 ATGCCATATCCCAGAAACGGTCTTACACGAAATCACATATCG
* * *
54083293 ATGCCATATCCCAGATATGGTCTTACATGAAATCACA
1 ATGCCATATCCCAGAAACGGTCTTACACGAAATCACA
54083330 CATAACCCTA
Statistics
Matches: 96, Mismatches: 23, Indels: 6
0.77 0.18 0.05
Matches are distributed among these distances:
41 21 0.22
42 47 0.49
44 6 0.06
45 22 0.23
ACGTcount: A:0.30, C:0.24, G:0.18, T:0.28
Consensus pattern (42 bp):
ATGCCATATCCCAGAAACGGTCTTACACGAAATCACATATCG
Found at i:54089631 original size:26 final size:24
Alignment explanation
Indices: 54089588--54089639 Score: 59
Period size: 26 Copynumber: 2.1 Consensus size: 24
54089578 TTATCTCATT
* *
54089588 ATATTTCTATTTTATAATTGTTTATA
1 ATATTTATATTATATAA-TG-TTATA
*
54089614 ATATTTATATTATGTAATGTTATA
1 ATATTTATATTATATAATGTTATA
54089638 AT
1 AT
54089640 TGTGATGATC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
24 7 0.30
25 2 0.09
26 14 0.61
ACGTcount: A:0.35, C:0.02, G:0.06, T:0.58
Consensus pattern (24 bp):
ATATTTATATTATATAATGTTATA
Found at i:54089776 original size:37 final size:37
Alignment explanation
Indices: 54089726--54089799 Score: 148
Period size: 37 Copynumber: 2.0 Consensus size: 37
54089716 GAAAAGAGTT
54089726 ATATTTCATGCCTTTAGACCTAGTTAAATGTTTGTAC
1 ATATTTCATGCCTTTAGACCTAGTTAAATGTTTGTAC
54089763 ATATTTCATGCCTTTAGACCTAGTTAAATGTTTGTAC
1 ATATTTCATGCCTTTAGACCTAGTTAAATGTTTGTAC
54089800 TTAGGTACAC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.27, C:0.16, G:0.14, T:0.43
Consensus pattern (37 bp):
ATATTTCATGCCTTTAGACCTAGTTAAATGTTTGTAC
Found at i:54094422 original size:29 final size:29
Alignment explanation
Indices: 54094389--54094548 Score: 180
Period size: 29 Copynumber: 5.5 Consensus size: 29
54094379 GTGACGAGAT
54094389 TGGCACTAAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCATGCTGGAAATATA
54094418 TGGCACTAAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCATGCTGGAAATATA
54094447 TGGCACTAAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCATGCTGGAAATATA
* ** * ***
54094476 CGGCACTGGGTGTGCGA-GCTCGAAGGGTA
1 TGGCACTAAGTGTGC-ATGCTGGAAATATA
* ** * *
54094505 TGGCACTATGTGTGCGGGCT-TAAATCACA
1 TGGCACTAAGTGTGCATGCTGGAAAT-ATA
54094534 TGGCACTAAGTGTGC
1 TGGCACTAAGTGTGC
54094549 GAAATCGAGT
Statistics
Matches: 111, Mismatches: 17, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
28 2 0.02
29 108 0.97
30 1 0.01
ACGTcount: A:0.26, C:0.17, G:0.31, T:0.26
Consensus pattern (29 bp):
TGGCACTAAGTGTGCATGCTGGAAATATA
Found at i:54103824 original size:40 final size:40
Alignment explanation
Indices: 54103716--54103885 Score: 225
Period size: 40 Copynumber: 4.2 Consensus size: 40
54103706 CGGGATTTAA
* * * * *
54103716 CCGGATATAGCGACTCGCACGATTGCCTTCGGGTCATAAC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
* * * * * *
54103756 CCGGATTTGGT-GACTTGCACAAAGGCCTTCGGGTCTTAGC
1 CCGGATAT-ATCAACTCGCACGAATGCCTTCGGGTCTTAGC
54103796 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
54103836 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
54103876 CCGGATATAT
1 CCGGATATAT
54103886 TTCCAATGTT
Statistics
Matches: 113, Mismatches: 15, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
39 1 0.01
40 112 0.99
ACGTcount: A:0.22, C:0.28, G:0.25, T:0.25
Consensus pattern (40 bp):
CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
Found at i:54111919 original size:40 final size:40
Alignment explanation
Indices: 54111811--54111980 Score: 225
Period size: 40 Copynumber: 4.2 Consensus size: 40
54111801 CGGGATTTAA
* * * * *
54111811 CCGGATATAGCGACTCGCACGATTGCCTTCGGGTCATAAC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
* * * * * *
54111851 CCGGATTTGGT-GACTTGCACAAAGGCCTTCGGGTCTTAGC
1 CCGGATAT-ATCAACTCGCACGAATGCCTTCGGGTCTTAGC
54111891 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
54111931 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
54111971 CCGGATATAT
1 CCGGATATAT
54111981 TTCCAATGTT
Statistics
Matches: 113, Mismatches: 15, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
39 1 0.01
40 112 0.99
ACGTcount: A:0.22, C:0.28, G:0.25, T:0.25
Consensus pattern (40 bp):
CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
Found at i:54113965 original size:29 final size:29
Alignment explanation
Indices: 54113932--54114091 Score: 180
Period size: 29 Copynumber: 5.5 Consensus size: 29
54113922 GTGACTAGAT
54113932 TGGCACTAAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCATGCTGGAAATATA
54113961 TGGCACTAAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCATGCTGGAAATATA
54113990 TGGCACTAAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCATGCTGGAAATATA
* ** * ***
54114019 CGGCACTGGGTGTGCGA-GCTCGAAGGGTA
1 TGGCACTAAGTGTGC-ATGCTGGAAATATA
* ** * *
54114048 TGGCACTATGTGTGCGGGCT-TAAATCACA
1 TGGCACTAAGTGTGCATGCTGGAAAT-ATA
54114077 TGGCACTAAGTGTGC
1 TGGCACTAAGTGTGC
54114092 GAAATCGAGT
Statistics
Matches: 111, Mismatches: 17, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
28 2 0.02
29 108 0.97
30 1 0.01
ACGTcount: A:0.26, C:0.17, G:0.31, T:0.26
Consensus pattern (29 bp):
TGGCACTAAGTGTGCATGCTGGAAATATA
Found at i:54120800 original size:80 final size:80
Alignment explanation
Indices: 54120716--54120864 Score: 183
Period size: 80 Copynumber: 1.9 Consensus size: 80
54120706 TATGGTAACC
* * * *
54120716 CGCACCAAGGCCTACGGGACTTAACCCGGATATCA-CGATTTGCACAAATGCCTTCGGGTCTTAG
1 CGCACCAAGGCCTACGGGACTTAACCCGGATAT-AGCCACTAGCACAAATGCCTTCGGGTCTTAA
54120780 CCCGGATAGAATGACT
65 CCCGGATAGAATGACT
* * * * * * *
54120796 CGCACGAATGCCTTCGGGTCTTAGCCCGGATGTAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CGCACCAAGGCCTACGGGACTTAACCCGGATATAGCCACTAGCACAAATGCCTTCGGGTCTTAAC
54120861 CCGG
66 CCGG
54120865 TTATAATTTC
Statistics
Matches: 57, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
79 1 0.02
80 56 0.98
ACGTcount: A:0.23, C:0.30, G:0.25, T:0.22
Consensus pattern (80 bp):
CGCACCAAGGCCTACGGGACTTAACCCGGATATAGCCACTAGCACAAATGCCTTCGGGTCTTAAC
CCGGATAGAATGACT
Found at i:54120806 original size:40 final size:38
Alignment explanation
Indices: 54120757--54120864 Score: 128
Period size: 40 Copynumber: 2.7 Consensus size: 38
54120747 ATCACGATTT
*
54120757 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATG-ACTC
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGAT-GAA-GCACTA
*
54120797 GCACGAATGCCTTCGGGTCTTAGCCCGGATGTAGCCACTA
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGATGAAG-CACTA
*
54120837 GCACAATTGCCTTCGGGTCTTAACCCGG
1 GCACAA-TGCCTTCGGGTCTTAGCCCGG
54120865 TTATAATTTC
Statistics
Matches: 61, Mismatches: 4, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
38 1 0.02
39 4 0.07
40 56 0.92
ACGTcount: A:0.21, C:0.30, G:0.26, T:0.23
Consensus pattern (38 bp):
GCACAATGCCTTCGGGTCTTAGCCCGGATGAAGCACTA
Found at i:54131902 original size:25 final size:24
Alignment explanation
Indices: 54131868--54131920 Score: 70
Period size: 25 Copynumber: 2.2 Consensus size: 24
54131858 AAGTTAAAGC
54131868 GAGCCATATCAAGAAGCTCACAAA
1 GAGCCATATCAAGAAGCTCACAAA
* * *
54131892 GAGCCTATATCAGGACGCTCATAAA
1 GAGCC-ATATCAAGAAGCTCACAAA
54131917 GAGC
1 GAGC
54131921 TTCGTTTGTG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
24 5 0.20
25 20 0.80
ACGTcount: A:0.40, C:0.25, G:0.21, T:0.15
Consensus pattern (24 bp):
GAGCCATATCAAGAAGCTCACAAA
Found at i:54132574 original size:20 final size:20
Alignment explanation
Indices: 54132549--54132589 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
54132539 GTTAAGAAAT
* *
54132549 TATCCAAATATTTTAGTCTA
1 TATCCAAACATTCTAGTCTA
54132569 TATCCAAACATTCTAGTCTA
1 TATCCAAACATTCTAGTCTA
54132589 T
1 T
54132590 CATATAGCCC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.34, C:0.20, G:0.05, T:0.41
Consensus pattern (20 bp):
TATCCAAACATTCTAGTCTA
Found at i:54135003 original size:15 final size:15
Alignment explanation
Indices: 54134983--54135011 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
54134973 ATCTTAAACA
54134983 TGCACTTCTCATTAT
1 TGCACTTCTCATTAT
54134998 TGCACTTCTCATTA
1 TGCACTTCTCATTA
54135012 CCACATTTCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.21, C:0.28, G:0.07, T:0.45
Consensus pattern (15 bp):
TGCACTTCTCATTAT
Found at i:54140492 original size:20 final size:20
Alignment explanation
Indices: 54140467--54140525 Score: 109
Period size: 20 Copynumber: 3.0 Consensus size: 20
54140457 TAAATATGGT
54140467 ATGTATGATATGCACATGAA
1 ATGTATGATATGCACATGAA
*
54140487 ATGTATGATATGCACATGAT
1 ATGTATGATATGCACATGAA
54140507 ATGTATGATATGCACATGA
1 ATGTATGATATGCACATGA
54140526 GGTAATCATA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.37, C:0.10, G:0.20, T:0.32
Consensus pattern (20 bp):
ATGTATGATATGCACATGAA
Found at i:54140507 original size:11 final size:11
Alignment explanation
Indices: 54140471--54140525 Score: 55
Period size: 11 Copynumber: 5.4 Consensus size: 11
54140461 TATGGTATGT
54140471 ATGATATGCAC
1 ATGATATGCAC
* *
54140482 ATGAAATG--T
1 ATGATATGCAC
54140491 ATGATATGCAC
1 ATGATATGCAC
*
54140502 ATGATATG--T
1 ATGATATGCAC
54140511 ATGATATGCAC
1 ATGATATGCAC
54140522 ATGA
1 ATGA
54140526 GGTAATCATA
Statistics
Matches: 34, Mismatches: 6, Indels: 8
0.71 0.12 0.17
Matches are distributed among these distances:
9 15 0.44
11 19 0.56
ACGTcount: A:0.38, C:0.11, G:0.20, T:0.31
Consensus pattern (11 bp):
ATGATATGCAC
Found at i:54140603 original size:24 final size:24
Alignment explanation
Indices: 54140576--54140718 Score: 200
Period size: 24 Copynumber: 6.0 Consensus size: 24
54140566 GAGGAAGTGA
*
54140576 AAAAGGGTTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATC
54140600 AAAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATC
54140624 AAAAGGGCTTATGCCCCAGTTAT-
1 AAAAGGGCTTATGCCCCAGTTATC
*
54140647 AAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATC
* * *
54140671 GAAAGGGCTTTTGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATC
*
54140695 AAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAG-GGCTTATGCC-CCAGTTAT
54140719 ATGATAAAGC
Statistics
Matches: 110, Mismatches: 6, Indels: 5
0.91 0.05 0.04
Matches are distributed among these distances:
23 23 0.21
24 76 0.69
25 11 0.10
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.27
Consensus pattern (24 bp):
AAAAGGGCTTATGCCCCAGTTATC
Found at i:54140668 original size:47 final size:47
Alignment explanation
Indices: 54140576--54140718 Score: 198
Period size: 47 Copynumber: 3.0 Consensus size: 47
54140566 GAGGAAGTGA
*
54140576 AAAAGGGTTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTAT-AAAAGGGCTTATGCCCCAGTTATC
*
54140624 AAAAGGGCTTATGCCCCAGTTATAAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATAAAAGGGCTTATGCCCCAGTTATC
* * *
54140671 GAAAGGGCTTTTGCCCCAGTTATTAAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAGGGCTTATGCCCCAGTTA-TAAAAG-GGCTTATGCC-CCAGTTAT
54140719 ATGATAAAGC
Statistics
Matches: 87, Mismatches: 5, Indels: 5
0.90 0.05 0.05
Matches are distributed among these distances:
47 43 0.49
48 33 0.38
49 11 0.13
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.27
Consensus pattern (47 bp):
AAAAGGGCTTATGCCCCAGTTATAAAAGGGCTTATGCCCCAGTTATC
Found at i:54140692 original size:71 final size:72
Alignment explanation
Indices: 54140576--54140719 Score: 211
Period size: 71 Copynumber: 2.0 Consensus size: 72
54140566 GAGGAAGTGA
* *
54140576 AAAAGGGTTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATCAAAAG-GGCTTATGCC-
1 AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATCAAAAGAGGC-TAGGCCT
54140639 CCAGTTAT
65 CCAGTTAT
** * *
54140647 AAAAGGGCTTATGCCCCAGTTATTGAAAGGGCTTTTGCCCCAGTTATTAAAAGAGGCTAGGCCTC
1 AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATCAAAAGAGGCTAGGCCTC
54140712 CAGTTAT
66 CAGTTAT
54140719 A
1 A
54140720 TGATAAAGCA
Statistics
Matches: 65, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
71 53 0.82
72 12 0.18
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.27
Consensus pattern (72 bp):
AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATCAAAAGAGGCTAGGCCTC
CAGTTAT
Found at i:54140945 original size:31 final size:31
Alignment explanation
Indices: 54140910--54141004 Score: 172
Period size: 31 Copynumber: 3.1 Consensus size: 31
54140900 CGTTTACAGT
54140910 AAAGGCTTCGGCCCAGTAATATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
54140941 AAAGGCTTCGGCCCAGTAATATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
* *
54140972 AAAGGCTTCGGCCCAGTATTATAAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
54141003 AA
1 AA
54141005 TATGAAAAGG
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 62 1.00
ACGTcount: A:0.40, C:0.16, G:0.21, T:0.23
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTAATATGAAATATGA
Found at i:54141744 original size:17 final size:17
Alignment explanation
Indices: 54141704--54141737 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
54141694 GGCCGGGTTT
54141704 GGGGTGTTACATTACTA
1 GGGGTGTTACATTACTA
54141721 GGGGTGTTACATTACTA
1 GGGGTGTTACATTACTA
54141738 TTGGTGTGGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.24, C:0.12, G:0.29, T:0.35
Consensus pattern (17 bp):
GGGGTGTTACATTACTA
Found at i:54142491 original size:39 final size:35
Alignment explanation
Indices: 54142424--54142531 Score: 103
Period size: 34 Copynumber: 3.0 Consensus size: 35
54142414 AATAGGCAAA
* * *
54142424 TACAGTTTGGGCCTAAGCCCGTTTCAGTAACAGTCCAG
1 TACAG-TTGGGCCTTAGCCCATTACAGTAACAGT--AG
* *
54142462 TAACAGTTAGGGCCTTAGCCCAATACAGTATCAGTAG
1 T-ACAGTT-GGGCCTTAGCCCATTACAGTAACAGTAG
54142499 T--AGTGTGGGCCTTAGCCCATTACAGTAACAGTA
1 TACAGT-TGGGCCTTAGCCCATTACAGTAACAGTA
54142532 ACAGAAATGC
Statistics
Matches: 60, Mismatches: 7, Indels: 10
0.78 0.09 0.13
Matches are distributed among these distances:
34 28 0.47
35 1 0.02
37 3 0.05
38 3 0.05
39 25 0.42
ACGTcount: A:0.28, C:0.23, G:0.23, T:0.26
Consensus pattern (35 bp):
TACAGTTGGGCCTTAGCCCATTACAGTAACAGTAG
Found at i:54150995 original size:14 final size:15
Alignment explanation
Indices: 54150968--54150996 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
54150958 ATTATCATAA
54150968 AATGTGACTATATGC
1 AATGTGACTATATGC
54150983 AATGTGA-TATATGC
1 AATGTGACTATATGC
54150997 TTAAATGAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.34, C:0.10, G:0.21, T:0.34
Consensus pattern (15 bp):
AATGTGACTATATGC
Found at i:54153057 original size:27 final size:26
Alignment explanation
Indices: 54153017--54153224 Score: 192
Period size: 27 Copynumber: 7.9 Consensus size: 26
54153007 AGGAAGCGTC
*
54153017 CTGGTGGCTATGCCACAATTATCTGAT
1 CTGGTGGCTCTGCCAC-ATTATCTGAT
* *
54153044 CTGGTGGCTTTGCCACATATATCTGTT
1 CTGGTGGCTCTGCCACAT-TATCTGAT
* * * *
54153071 CCGGTGGCTCTTCCATGATTATCTTTAT
1 CTGGTGGCTCTGCCA-CATTATC-TGAT
*
54153099 CTGGT-G-ACT--CA-ATTATCTGAT
1 CTGGTGGCTCTGCCACATTATCTGAT
* *
54153120 CTAGTGTCTCTGCCACAATTATCTGAT
1 CTGGTGGCTCTGCCAC-ATTATCTGAT
*
54153147 CTGGTGGCTCTGCCACATATATCTGTT
1 CTGGTGGCTCTGCCACAT-TATCTGAT
54153174 CTGGTGGCTCTGCCACGATTATCTGTAT
1 CTGGTGGCTCTGCCAC-ATTATCTG-AT
* *
54153202 CTGGTGACTCTGTCACATTATCT
1 CTGGTGGCTCTGCCACATTATCT
54153225 ATTCTGGAAG
Statistics
Matches: 149, Mismatches: 20, Indels: 24
0.77 0.10 0.12
Matches are distributed among these distances:
21 7 0.05
22 6 0.04
23 2 0.01
24 2 0.01
25 2 0.01
26 6 0.04
27 99 0.66
28 25 0.17
ACGTcount: A:0.18, C:0.24, G:0.20, T:0.38
Consensus pattern (26 bp):
CTGGTGGCTCTGCCACATTATCTGAT
Found at i:54153170 original size:76 final size:75
Alignment explanation
Indices: 54153032--54153179 Score: 183
Period size: 76 Copynumber: 2.0 Consensus size: 75
54153022 GGCTATGCCA
* * * * * *
54153032 CAATTATCTGATCTGGTGGCTTTGCCACATATATCTGTTCCGGTGGCTCTTCCATGATTATCTTT
1 CAATTATCTGATCTAGTGGCTCTGCCACATATATCTGATCCGGTGGCTCTGCCATCATTATCTGT
54153097 ATCTGGTGACT
66 -TCTGGTGACT
* *
54153108 CAATTATCTGATCTAGTGTCTCTGCCACA-ATTATCTGATCTGGTGGCTCTGCCA-CATATATCT
1 CAATTATCTGATCTAGTGGCTCTGCCACATA-TATCTGATCCGGTGGCTCTGCCATCAT-TATCT
54153171 GTTCTGGTG
64 GTTCTGGTG
54153180 GCTCTGCCAC
Statistics
Matches: 62, Mismatches: 8, Indels: 5
0.83 0.11 0.07
Matches are distributed among these distances:
75 10 0.16
76 52 0.84
ACGTcount: A:0.18, C:0.23, G:0.20, T:0.39
Consensus pattern (75 bp):
CAATTATCTGATCTAGTGGCTCTGCCACATATATCTGATCCGGTGGCTCTGCCATCATTATCTGT
TCTGGTGACT
Found at i:54153185 original size:54 final size:53
Alignment explanation
Indices: 54153017--54153231 Score: 224
Period size: 54 Copynumber: 4.1 Consensus size: 53
54153007 AGGAAGCGTC
* *
54153017 CTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTTTGCCACATATATCTGTT
1 CTGGTGGCTCTGCCACAATTATCTGATCTGGTGGCTCTGCCACAT-TATCTGTT
* * ** * * *
54153071 CCGGTGGCTCTTCCATGATTATCTTTATCTGGT-G-ACT--CA-ATTATCTGAT
1 CTGGTGGCTCTGCCACAATTATC-TGATCTGGTGGCTCTGCCACATTATCTGTT
* *
54153120 CTAGTGTCTCTGCCACAATTATCTGATCTGGTGGCTCTGCCACATATATCTGTT
1 CTGGTGGCTCTGCCACAATTATCTGATCTGGTGGCTCTGCCACAT-TATCTGTT
* * * *
54153174 CTGGTGGCTCTGCCACGATTATCTGTATCTGGTGACTCTGTCACATTATCTATT
1 CTGGTGGCTCTGCCACAATTATCTG-ATCTGGTGGCTCTGCCACATTATCTGTT
54153228 CTGG
1 CTGG
54153232 AAGCCATGCT
Statistics
Matches: 129, Mismatches: 24, Indels: 16
0.76 0.14 0.09
Matches are distributed among these distances:
48 8 0.06
49 25 0.19
50 4 0.03
51 2 0.02
52 2 0.02
53 3 0.02
54 59 0.46
55 26 0.20
ACGTcount: A:0.18, C:0.24, G:0.20, T:0.38
Consensus pattern (53 bp):
CTGGTGGCTCTGCCACAATTATCTGATCTGGTGGCTCTGCCACATTATCTGTT
Found at i:54161038 original size:27 final size:26
Alignment explanation
Indices: 54160998--54161102 Score: 104
Period size: 27 Copynumber: 3.9 Consensus size: 26
54160988 AGGAAGCGTC
*
54160998 CTGGTGGCTATGCCACAATTATCTGAT
1 CTGGTGGCTCTGCCAC-ATTATCTGAT
*
54161025 CTGGTGGCTCTGCCACATATATATG-T
1 CTGGTGGCTCTGCCACAT-TATCTGAT
54161051 GCTGGTGGCTCTGCCACGATTATCTGTAT
1 -CTGGTGGCTCTGCCAC-ATTATCTG-AT
* ** *
54161080 CTAGTCACTCTGTCACATTATCT
1 CTGGTGGCTCTGCCACATTATCT
54161103 TTTCTGGCAG
Statistics
Matches: 66, Mismatches: 7, Indels: 10
0.80 0.08 0.12
Matches are distributed among these distances:
26 3 0.05
27 48 0.73
28 14 0.21
29 1 0.02
ACGTcount: A:0.19, C:0.25, G:0.21, T:0.35
Consensus pattern (26 bp):
CTGGTGGCTCTGCCACATTATCTGAT
Found at i:54164634 original size:95 final size:95
Alignment explanation
Indices: 54164528--54164719 Score: 366
Period size: 95 Copynumber: 2.0 Consensus size: 95
54164518 TCTTCCTTTC
54164528 TTCTCTTAATTGACTTTCCCTTTGAACGATTACACCTTCTTCCCTCTCTTCTCATTTGGATATTT
1 TTCTCTTAATTGACTTTCCCTTTGAACGATTACACCTTCTTCCCTCTCTTCTCATTTGGATATTT
54164593 GGGCCGATTTCTACCTAGCTCTCTCTCCAT
66 GGGCCGATTTCTACCTAGCTCTCTCTCCAT
*
54164623 TTCTCTTAATTGACTTTCCCTTTGAACGATTACAGCTTCTTCCCTCTCTTCTCATTTGGATATTT
1 TTCTCTTAATTGACTTTCCCTTTGAACGATTACACCTTCTTCCCTCTCTTCTCATTTGGATATTT
*
54164688 GGGCCGATTTCTACCTAGCTCTCTCTCTAT
66 GGGCCGATTTCTACCTAGCTCTCTCTCCAT
54164718 TT
1 TT
54164720 GTTTTAGTTT
Statistics
Matches: 95, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
95 95 1.00
ACGTcount: A:0.16, C:0.29, G:0.11, T:0.44
Consensus pattern (95 bp):
TTCTCTTAATTGACTTTCCCTTTGAACGATTACACCTTCTTCCCTCTCTTCTCATTTGGATATTT
GGGCCGATTTCTACCTAGCTCTCTCTCCAT
Found at i:54166042 original size:34 final size:33
Alignment explanation
Indices: 54165977--54166047 Score: 83
Period size: 34 Copynumber: 2.1 Consensus size: 33
54165967 TTGTACTGCC
*
54165977 ACTGTCACTGAACTGGGTAAGGCCCACACTGAT
1 ACTGTCACTGAACTGGGTAAGGCCCACACTGAA
*
54166010 ACTGTTACTGTAA-TGGGCTAAGGCCCTA-ACTGAA
1 ACTGTCACTG-AACTGGG-TAAGGCCC-ACACTGAA
54166044 ACTG
1 ACTG
54166048 AACTGTTACT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
33 13 0.39
34 19 0.58
35 1 0.03
ACGTcount: A:0.28, C:0.24, G:0.24, T:0.24
Consensus pattern (33 bp):
ACTGTCACTGAACTGGGTAAGGCCCACACTGAA
Found at i:54168546 original size:21 final size:22
Alignment explanation
Indices: 54168506--54168546 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
54168496 TTCGAAATAA
* *
54168506 AACATTATATCATTTCTAATTC
1 AACATTATATCAATTATAATTC
54168528 AACATT-TATCAATTATAAT
1 AACATTATATCAATTATAAT
54168547 CGGGCATGTG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 11 0.65
22 6 0.35
ACGTcount: A:0.41, C:0.15, G:0.00, T:0.44
Consensus pattern (22 bp):
AACATTATATCAATTATAATTC
Found at i:54173509 original size:40 final size:40
Alignment explanation
Indices: 54173450--54173650 Score: 291
Period size: 40 Copynumber: 5.0 Consensus size: 40
54173440 AAGTAGCTTT
* * *
54173450 GGGATTTAG-CCGAATATAG-CAACTCGCACAAATGCCTTC
1 GGGAATTAGCCCGGATATAGTC-ACTAGCACAAATGCCTTC
* * *
54173489 GGGACTTAGCCCGGATATAG-CAACTCGCACAAATGGCTTC
1 GGGAATTAGCCCGGATATAGTC-ACTAGCACAAATGCCTTC
*
54173529 GGGACTTAGCCCGGATATAGTCACTAGCACAAATGCCTTC
1 GGGAATTAGCCCGGATATAGTCACTAGCACAAATGCCTTC
*
54173569 GGGAATTAGCCCGGATATAGTCACTAGCACAAATGCCTTT
1 GGGAATTAGCCCGGATATAGTCACTAGCACAAATGCCTTC
54173609 GGGAATTAGCCCGGATATAGTCACTAGCACAAATGCCTTC
1 GGGAATTAGCCCGGATATAGTCACTAGCACAAATGCCTTC
54173649 GG
1 GG
54173651 ATCTTAGTCC
Statistics
Matches: 152, Mismatches: 8, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
39 8 0.05
40 143 0.94
41 1 0.01
ACGTcount: A:0.29, C:0.25, G:0.23, T:0.22
Consensus pattern (40 bp):
GGGAATTAGCCCGGATATAGTCACTAGCACAAATGCCTTC
Found at i:54178519 original size:79 final size:80
Alignment explanation
Indices: 54178381--54178583 Score: 187
Period size: 79 Copynumber: 2.5 Consensus size: 80
54178371 CGGAGCTTCA
* * ** * * * *
54178381 CCGGATATAGCTACTCGTTCAAACGCCTTCGGGACATAGCCCGGATATGGTAACCCGCACCAAGG
1 CCGGATATAGCCACTAGCACAAATGCCTTCGGGTCTTAGCCCGGATATGATAACCCGCACCAAGG
54178446 CCTACGGGACTTAAC
66 CCTACGGGACTTAAC
* * * * *
54178461 CCGGATATCA-CGA-TTGCACAAATGCCTTCGGGTCTTAGCCCGGATA-GAATGACTCGCACGAA
1 CCGGATAT-AGCCACTAGCACAAATGCCTTCGGGTCTTAGCCCGGATATG-ATAACCCGCACCAA
* * * *
54178523 TGCCTTCGGGTCTTAGC
64 GGCCTACGGGACTTAAC
* * *
54178540 CCGGATATAGCCACTAGCACCATTGCCTTCGGGTCTTAACCCGG
1 CCGGATATAGCCACTAGCACAAATGCCTTCGGGTCTTAGCCCGG
54178584 TTATAATTTC
Statistics
Matches: 99, Mismatches: 20, Indels: 8
0.78 0.16 0.06
Matches are distributed among these distances:
78 2 0.02
79 60 0.61
80 36 0.36
81 1 0.01
ACGTcount: A:0.24, C:0.31, G:0.24, T:0.22
Consensus pattern (80 bp):
CCGGATATAGCCACTAGCACAAATGCCTTCGGGTCTTAGCCCGGATATGATAACCCGCACCAAGG
CCTACGGGACTTAAC
Found at i:54178528 original size:40 final size:40
Alignment explanation
Indices: 54178476--54178583 Score: 135
Period size: 40 Copynumber: 2.7 Consensus size: 40
54178466 TATCACGATT
** *
54178476 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATGACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAACCACTA
* * *
54178516 GCACGAATGCCTTCGGGTCTTAGCCCGGATATAGCCACTA
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAACCACTA
* * *
54178556 GCACCATTGCCTTCGGGTCTTAACCCGG
1 GCACAAATGCCTTCGGGTCTTAGCCCGG
54178584 TTATAATTTC
Statistics
Matches: 59, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 59 1.00
ACGTcount: A:0.21, C:0.31, G:0.25, T:0.23
Consensus pattern (40 bp):
GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAACCACTA
Found at i:54186184 original size:79 final size:80
Alignment explanation
Indices: 54186041--54186247 Score: 188
Period size: 79 Copynumber: 2.6 Consensus size: 80
54186031 TCCTTCGGAG
* * ** * * * *
54186041 CTTAA-CCGGATATAGCTACTCGTTCAAACGCCTTCGGGACATAGCCCGGATATGGTAACCCGCA
1 CTTAACCCGGATATAGCCACTAGCACAAATGCCTTCGGGTCTTAGCCCGGATATGATAACCCGCA
54186105 CCAAGGCCTACGGGA
66 CCAAGGCCTACGGGA
* * * *
54186120 CTTAACCCGGATATCA-CGA-TTGCACAAATGCCTTCGGGTCTTAGCCCGGATA-GAATGACTCG
1 CTTAACCCGGATAT-AGCCACTAGCACAAATGCCTTCGGGTCTTAGCCCGGATATG-ATAACCCG
* * * *
54186182 CACGAATGCCTTCGGGT
64 CACCAAGGCCTACGGGA
* * * *
54186199 CTTAGCCCGGATATAGCCACTAGCACCATTGCCTTCGGGTCTTAACCCG
1 CTTAACCCGGATATAGCCACTAGCACAAATGCCTTCGGGTCTTAGCCCG
54186248 ATTATAATTT
Statistics
Matches: 103, Mismatches: 20, Indels: 9
0.78 0.15 0.07
Matches are distributed among these distances:
78 2 0.02
79 65 0.63
80 35 0.34
81 1 0.01
ACGTcount: A:0.24, C:0.30, G:0.23, T:0.22
Consensus pattern (80 bp):
CTTAACCCGGATATAGCCACTAGCACAAATGCCTTCGGGTCTTAGCCCGGATATGATAACCCGCA
CCAAGGCCTACGGGA
Found at i:54186193 original size:40 final size:40
Alignment explanation
Indices: 54186141--54186247 Score: 133
Period size: 40 Copynumber: 2.7 Consensus size: 40
54186131 TATCACGATT
** *
54186141 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATGACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAACCACTA
* * *
54186181 GCACGAATGCCTTCGGGTCTTAGCCCGGATATAGCCACTA
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAACCACTA
* * *
54186221 GCACCATTGCCTTCGGGTCTTAACCCG
1 GCACAAATGCCTTCGGGTCTTAGCCCG
54186248 ATTATAATTT
Statistics
Matches: 58, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 58 1.00
ACGTcount: A:0.21, C:0.31, G:0.24, T:0.23
Consensus pattern (40 bp):
GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAACCACTA
Found at i:54192552 original size:40 final size:40
Alignment explanation
Indices: 54192484--54192687 Score: 324
Period size: 40 Copynumber: 5.1 Consensus size: 40
54192474 AACCCAAGTA
* *
54192484 CCTTCGGGATTTAG-CCGGATATAG-CAACTCGCACAAATG
1 CCTTCGGGAATTAGCCCGGATATAGTC-ACTAGCACAAATG
* *
54192523 CCTTCGGGACTTAGCCCGGATATAG-CAACTCGCACAAATG
1 CCTTCGGGAATTAGCCCGGATATAGTC-ACTAGCACAAATG
*
54192563 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
1 CCTTCGGGAATTAGCCCGGATATAGTCACTAGCACAAATG
54192603 CCTTCGGGAATTAGCCCGGATATAGTCACTAGCACAAATG
1 CCTTCGGGAATTAGCCCGGATATAGTCACTAGCACAAATG
54192643 CCTTCGGGAATTAGCCCGGATATAGTCACTAGCACAAATG
1 CCTTCGGGAATTAGCCCGGATATAGTCACTAGCACAAATG
54192683 CCTTC
1 CCTTC
54192688 AGATCTTAGT
Statistics
Matches: 160, Mismatches: 3, Indels: 3
0.96 0.02 0.02
Matches are distributed among these distances:
39 13 0.08
40 146 0.91
41 1 0.01
ACGTcount: A:0.28, C:0.27, G:0.22, T:0.23
Consensus pattern (40 bp):
CCTTCGGGAATTAGCCCGGATATAGTCACTAGCACAAATG
Found at i:54203607 original size:47 final size:47
Alignment explanation
Indices: 54203409--54203609 Score: 176
Period size: 47 Copynumber: 4.3 Consensus size: 47
54203399 GGGTTATGTA
* * * * *
54203409 AGAGCCAGTATAAGACCATGTCTGGGACATGCATCGGCATTGATACG
1 AGAGCCAGTGTAAGACCATGTCTGGGACATGCATCAGCCTCGATATG
* * * *
54203456 AGGGCTAGT-TAAAGA-CATGTCTGAGACATGCATCAGCCAC-ATTATG
1 AGAGCCAGTGT-AAGACCATGTCTGGGACATGCATCAGCCTCGA-TATG
* * * * *
54203502 ATAGCCAGTGTAAGACCATGTCTGGGACATGGCATCAGCGTAGAAAGG
1 AGAGCCAGTGTAAGACCATGTCTGGGACAT-GCATCAGCCTCGATATG
**
54203550 AGAGCCAGTGTAAGA-CATGTCTGGGACATGCATTGGCCTCGATGATG
1 AGAGCCAGTGTAAGACCATGTCTGGGACATGCATCAGCCTCGAT-ATG
* *
54203597 ATAGCTAGTGTAA
1 AGAGCCAGTGTAA
54203610 TACGTGTTTA
Statistics
Matches: 121, Mismatches: 26, Indels: 14
0.75 0.16 0.09
Matches are distributed among these distances:
45 1 0.01
46 43 0.36
47 52 0.43
48 24 0.20
49 1 0.01
ACGTcount: A:0.30, C:0.19, G:0.28, T:0.22
Consensus pattern (47 bp):
AGAGCCAGTGTAAGACCATGTCTGGGACATGCATCAGCCTCGATATG
Found at i:54207487 original size:40 final size:40
Alignment explanation
Indices: 54207432--54207681 Score: 385
Period size: 40 Copynumber: 6.2 Consensus size: 40
54207422 AACATTGGAA
54207432 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
54207472 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
54207512 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
54207552 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
* * * *
54207592 ATATATCCGGGCTAAGACCCGAAGGCCTTTGTGCAAG-TC
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
* * * * * *
54207631 ACCAAATCCGGGTTATGACCCGAAGGCAATCGTGCGAGTCG
1 A-TATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
*
54207672 CTATATCCGG
1 ATATATCCGG
54207682 TTAAATCCCG
Statistics
Matches: 191, Mismatches: 17, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
39 2 0.01
40 189 0.99
ACGTcount: A:0.25, C:0.24, G:0.29, T:0.22
Consensus pattern (40 bp):
ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
Found at i:54214784 original size:40 final size:40
Alignment explanation
Indices: 54214729--54214978 Score: 385
Period size: 40 Copynumber: 6.2 Consensus size: 40
54214719 AACATTGGAA
54214729 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
54214769 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
54214809 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
54214849 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
* * * *
54214889 ATATATCCGGGCTAAGACCCGAAGGCCTTTGTGCAAG-TC
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
* * * * * *
54214928 ACCAAATCCGGGTTATGACCCGAAGGCAATCGTGCGAGTCG
1 A-TATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
*
54214969 CTATATCCGG
1 ATATATCCGG
54214979 TTAAATCCCG
Statistics
Matches: 191, Mismatches: 17, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
39 2 0.01
40 189 0.99
ACGTcount: A:0.25, C:0.24, G:0.29, T:0.22
Consensus pattern (40 bp):
ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
Found at i:54227649 original size:2 final size:2
Alignment explanation
Indices: 54227644--54227684 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
54227634 ATGAAATGTC
54227644 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
54227685 CCAATTGCAC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:54227925 original size:25 final size:25
Alignment explanation
Indices: 54227891--54227959 Score: 95
Period size: 25 Copynumber: 2.8 Consensus size: 25
54227881 GACCCACAGA
*
54227891 TCATGTGAGCATACCGATTTATAGG
1 TCATGTGAGCATACCGATTTATAGC
* *
54227916 TCATGAGAGCATACCGATCTATAGC
1 TCATGTGAGCATACCGATTTATAGC
54227941 TCGA-GTGAGCATACCGATT
1 TC-ATGTGAGCATACCGATT
54227960 CACAACTTGT
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
25 37 0.97
26 1 0.03
ACGTcount: A:0.29, C:0.20, G:0.23, T:0.28
Consensus pattern (25 bp):
TCATGTGAGCATACCGATTTATAGC
Found at i:54228563 original size:23 final size:24
Alignment explanation
Indices: 54228525--54228570 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
54228515 CATGTATAGG
54228525 TATTTTGGTTAATTTT-GGCCATA
1 TATTTTGGTTAATTTTAGGCCATA
**
54228548 TATTTTGGTTTTTTTTAGGCCAT
1 TATTTTGGTTAATTTTAGGCCAT
54228571 TTAACTTGGC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 14 0.70
24 6 0.30
ACGTcount: A:0.17, C:0.09, G:0.17, T:0.57
Consensus pattern (24 bp):
TATTTTGGTTAATTTTAGGCCATA
Found at i:54233821 original size:16 final size:16
Alignment explanation
Indices: 54233800--54233834 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
54233790 GTGAAACTGC
*
54233800 AAAGGCTGAAAAGTCG
1 AAAGGCTAAAAAGTCG
54233816 AAAGGCTAAAAAGTCG
1 AAAGGCTAAAAAGTCG
54233832 AAA
1 AAA
54233835 AGTGGGTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.51, C:0.11, G:0.26, T:0.11
Consensus pattern (16 bp):
AAAGGCTAAAAAGTCG
Found at i:54234262 original size:52 final size:54
Alignment explanation
Indices: 54234219--54234375 Score: 151
Period size: 54 Copynumber: 2.9 Consensus size: 54
54234209 CCATGTATGG
* *
54234219 TAAAATGACGATTTTTCTC-T-TGTGGTAAAATGACTATTTTACCCTTATGTGT
1 TAAAATGACGATTTTGCCCTTATGTGGTAAAATGACTATTTTACCCTTATGTGT
* * * * *
54234271 TAAATTGACGGTTTTGCCCTTATGTGGCAAAATGACTATTTTGCCCTTATGCGT
1 TAAAATGACGATTTTGCCCTTATGTGGTAAAATGACTATTTTACCCTTATGTGT
* * * * * *
54234325 TAAATTGAC-AGTTTTACCTTTATGT-GTCAAAATGACTGTTTTGCCCCTATG
1 TAAAATGACGA-TTTTGCCCTTATGTGGT-AAAATGACTATTTTACCCTTATG
54234376 CGATGTATGT
Statistics
Matches: 88, Mismatches: 13, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
52 15 0.17
53 2 0.02
54 71 0.81
ACGTcount: A:0.25, C:0.17, G:0.17, T:0.41
Consensus pattern (54 bp):
TAAAATGACGATTTTGCCCTTATGTGGTAAAATGACTATTTTACCCTTATGTGT
Found at i:54234279 original size:27 final size:27
Alignment explanation
Indices: 54234239--54234375 Score: 132
Period size: 27 Copynumber: 5.1 Consensus size: 27
54234229 ATTTTTCTCT
* *
54234239 TGTGGTAAAATGACTATTTTACCCTTA
1 TGTGTTAAAATGACTATTTTGCCCTTA
* **
54234266 TGTGTTAAATTGACGGTTTTGCCCTTA
1 TGTGTTAAAATGACTATTTTGCCCTTA
**
54234293 TGTGGCAAAATGACTATTTTGCCCTTA
1 TGTGTTAAAATGACTATTTTGCCCTTA
* * * *
54234320 TGCGTTAAATTGAC-AGTTTTACCTTTA
1 TGTGTTAAAATGACTA-TTTTGCCCTTA
* * *
54234347 TGTGTCAAAATGACTGTTTTGCCCCTA
1 TGTGTTAAAATGACTATTTTGCCCTTA
54234374 TG
1 TG
54234376 CGATGTATGT
Statistics
Matches: 85, Mismatches: 23, Indels: 4
0.76 0.21 0.04
Matches are distributed among these distances:
26 1 0.01
27 84 0.99
ACGTcount: A:0.24, C:0.17, G:0.18, T:0.41
Consensus pattern (27 bp):
TGTGTTAAAATGACTATTTTGCCCTTA
Found at i:54234305 original size:54 final size:54
Alignment explanation
Indices: 54234239--54234377 Score: 197
Period size: 54 Copynumber: 2.6 Consensus size: 54
54234229 ATTTTTCTCT
* * * * *
54234239 TGTGGTAAAATGACTATTTTACCCTTATGTGTTAAATTGACGGTTTTGCCCTTA
1 TGTGGCAAAATGACTATTTTGCCCTTATGCGTTAAATTGACAGTTTTACCCTTA
*
54234293 TGTGGCAAAATGACTATTTTGCCCTTATGCGTTAAATTGACAGTTTTACCTTTA
1 TGTGGCAAAATGACTATTTTGCCCTTATGCGTTAAATTGACAGTTTTACCCTTA
* * *
54234347 TGTGTCAAAATGACTGTTTTGCCCCTATGCG
1 TGTGGCAAAATGACTATTTTGCCCTTATGCG
54234378 ATGTATGTTT
Statistics
Matches: 76, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
54 76 1.00
ACGTcount: A:0.24, C:0.17, G:0.19, T:0.40
Consensus pattern (54 bp):
TGTGGCAAAATGACTATTTTGCCCTTATGCGTTAAATTGACAGTTTTACCCTTA
Found at i:54234733 original size:27 final size:26
Alignment explanation
Indices: 54234703--54234856 Score: 101
Period size: 27 Copynumber: 5.7 Consensus size: 26
54234693 CGTGTAGGTT
* *
54234703 AAAATGATGGTTTTACCCTTATGTGGAA
1 AAAATGAT-GTTTTGCCCTTATGT-GTA
* * *
54234731 AAAATGAATATTTTGTCCTTATGTGTT
1 AAAATG-ATGTTTTGCCCTTATGTGTA
* * * *
54234758 AAATTGACGGTTTCGCCCTTATGTGGA
1 AAAATGA-TGTTTTGCCCTTATGTGTA
* * *
54234785 AAAATGACTATTTTGCCCTTATGCGTT
1 AAAATGA-TGTTTTGCCCTTATGTGTA
* * * *
54234812 AAATTGACAGTTTTACCCTTATGTGTC
1 AAAATGA-TGTTTTGCCCTTATGTGTA
54234839 AAAATGATTGTTTTGCCC
1 AAAATGA-TGTTTTGCCC
54234857 CGATGTGATG
Statistics
Matches: 95, Mismatches: 29, Indels: 5
0.74 0.22 0.04
Matches are distributed among these distances:
26 1 0.01
27 74 0.78
28 18 0.19
29 2 0.02
ACGTcount: A:0.27, C:0.15, G:0.18, T:0.40
Consensus pattern (26 bp):
AAAATGATGTTTTGCCCTTATGTGTA
Found at i:54234813 original size:54 final size:54
Alignment explanation
Indices: 54234700--54234856 Score: 197
Period size: 54 Copynumber: 2.9 Consensus size: 54
54234690 ACCCGTGTAG
* * * *
54234700 GTTAAAATGATGGTTTTACCCTTATGTGGAAAAAATGAATATTTTGTCCTTATGT
1 GTTAAATTGACGGTTTTACCCTTATGTGG-AAAAATGAATATTTTGCCCTTATGC
** *
54234755 GTTAAATTGACGGTTTCGCCCTTATGTGGAAAAATGACTATTTTGCCCTTATGC
1 GTTAAATTGACGGTTTTACCCTTATGTGGAAAAATGAATATTTTGCCCTTATGC
* ** * *
54234809 GTTAAATTGACAGTTTTACCCTTATGTGTCAAAATGATTGTTTTGCCC
1 GTTAAATTGACGGTTTTACCCTTATGTGGAAAAATGAATATTTTGCCC
54234857 CGATGTGATG
Statistics
Matches: 88, Mismatches: 14, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
54 63 0.72
55 25 0.28
ACGTcount: A:0.27, C:0.15, G:0.18, T:0.40
Consensus pattern (54 bp):
GTTAAATTGACGGTTTTACCCTTATGTGGAAAAATGAATATTTTGCCCTTATGC
Found at i:54235155 original size:485 final size:485
Alignment explanation
Indices: 54234203--54235663 Score: 2317
Period size: 485 Copynumber: 3.0 Consensus size: 485
54234193 AAAATGACTG
* * * * * *
54234203 TAATACCCATGTATGGTAAAATGAC-GATTTTTCTC-T-TGTGGTAAAATGACTATTTTACCCTT
1 TAATACCCGTGTAGGGTAAAATGACAG-TTTTACCCTTATGTGGAAAAATGACTATTTTGCCCTT
* *
54234265 ATGTGTTAAATTGACGGTTTTGCCCTTATGTGGCAAAATGACTATTTTGCCCTTATGCGTTAAAT
65 ATGTGTTAAATTGACGGTTTCGCCCTTATGTGGAAAAATGACTATTTTGCCCTTATGCGTTAAAT
* *
54234330 TGACAGTTTTACCTTTATGTGTCAAAATGACTGTTTTGCCCCTATGCGATGTATGTTTATATTTT
130 TGACAGTTTTACCTTTATGTGTCAAAATGATTGTTTTGCCCCTATGTGATGTATGTTTATATTTT
* * *
54234395 AGCATGCTATGTGTAACTCTATTGAGTACATGTTTAATATTATGATATGACATGGCATGTTACAT
195 AGCATGCTATGTGTAACTGTATTGAGTACATGTTTAATATTATGATATGACATGACATGTTGCAT
54234460 GATGCATTGCATGGGGATGGGCTTATTGGAGGAAGTGTACTGTACTGGCAGCTCTGCTGCAAATC
260 GATGCATTGCATGGGGATGGGCTTATTGGAGGAAGTGTACTGTACTGGCAGCTCTGCTGCAAATC
* *
54234525 ACTGATGGCTCTAAGCCTATTATACTGGCAGCTCTATTGTAATTACTGATTAATGCTGCAACCGG
325 ACTGATGGCTCTAAGCCTATTATACTGGCAGCTCTGTTGTAATTACTGATTAGTGCTGCAACCGG
* * *
54234590 TGCTATATTTGGAGTGTAGGGATGGGTGGGTCGATTTTATCCCCACAAGGAGTGTAGGGCTGGAC
390 TGCTATATTTGAAGTGTAGGGATGGGTGGGTCGATTTTATCCCTACATGGAGTGTAGGGCTGGAC
54234655 GGAGTGGAGTGTAGAGGATGGATGGGTAGGA
455 GGAGTGGAGTGTAGAGGATGGATGGGTAGGA
* ** * *
54234686 TAATACCCGTGTAGGTTAAAATGATGGTTTTACCCTTATGTGGAAAAAATGAATATTTTGTCCTT
1 TAATACCCGTGTAGGGTAAAATGACAGTTTTACCCTTATGTGG-AAAAATGACTATTTTGCCCTT
54234751 ATGTGTTAAATTGACGGTTTCGCCCTTATGTGGAAAAATGACTATTTTGCCCTTATGCGTTAAAT
65 ATGTGTTAAATTGACGGTTTCGCCCTTATGTGGAAAAATGACTATTTTGCCCTTATGCGTTAAAT
* *
54234816 TGACAGTTTTACCCTTATGTGTCAAAATGATTGTTTTGCCCCGATGTGATGTATGTTTATA-TTT
130 TGACAGTTTTACCTTTATGTGTCAAAATGATTGTTTTGCCCCTATGTGATGTATGTTTATATTTT
54234880 AGCATGCTATGTGTAACTGTATTGAGTACATGTTTAATATTATGATATGACATGACATGTTGCAT
195 AGCATGCTATGTGTAACTGTATTGAGTACATGTTTAATATTATGATATGACATGACATGTTGCAT
* * * *
54234945 GGTGGATTGCATGGGGATGGGCTTATTGGAGGAAGTGTATTGTATTGGCAGCTCTGCTGCAAATC
260 GATGCATTGCATGGGGATGGGCTTATTGGAGGAAGTGTACTGTACTGGCAGCTCTGCTGCAAATC
* **
54235010 ACTGATGGCTCTAAGCCTATTATACTGGCAGCTCTGTTGCAATTACTGATTAGTG-TCGCAACTA
325 ACTGATGGCTCTAAGCCTATTATACTGGCAGCTCTGTTGTAATTACTGATTAGTGCT-GCAACCG
*
54235074 GTGCTATATTTGAAGTGTAGGGATGAGTGGGTCGATTTTATCCCTACATGGAGTGTAGGGCTGGA
389 GTGCTATATTTGAAGTGTAGGGATGGGTGGGTCGATTTTATCCCTACATGGAGTGTAGGGCTGGA
*
54235139 CGAAGTGGAGTGTAGAGGATGGATGGGTAGGA
454 CGGAGTGGAGTGTAGAGGATGGATGGGTAGGA
*
54235171 TAATACCCGTGTAGGGTAAAATGACAGTTTTGCCCTTATGTGGAAAAATGACTATTTTGCCCTTA
1 TAATACCCGTGTAGGGTAAAATGACAGTTTTACCCTTATGTGGAAAAATGACTATTTTGCCCTTA
* * * * *
54235236 TGTGTTAAATTGACGGTTTCACTCC-TATGTGGAAAAATGTCTATTTTTCCCTTGTACGTTAAAT
66 TGTGTTAAATTGACGGTTTCGC-CCTTATGTGGAAAAATGACTATTTTGCCCTTATGCGTTAAAT
*
54235300 TGACAGTTTTACCTTTATGTGTCAAAATGATTGTTTTGCCCTTATGTGATGTATGTTTATATTTT
130 TGACAGTTTTACCTTTATGTGTCAAAATGATTGTTTTGCCCCTATGTGATGTATGTTTATATTTT
54235365 AGCATGCTATGTGTAACTGTATTGAGTACATGTTTAATATTATGATATGACATGACATGTTGCAT
195 AGCATGCTATGTGTAACTGTATTGAGTACATGTTTAATATTATGATATGACATGACATGTTGCAT
* *
54235430 GATGCATTGCATGGGGATGAGGTTATATATGATTGAAGGAAGTGTACTATACTGGCAGCTCTGCT
260 GATGCATTGCATGGGGATG-GGCT-TAT-TG---G-AGGAAGTGTACTGTACTGGCAGCTCTGCT
* *
54235495 GCAAATCACTGATGGCTCTAAGCCTATCATACTGGCAGCCCTGTTGTAATTACTGATTAGTGCTG
318 GCAAATCACTGATGGCTCTAAGCCTATTATACTGGCAGCTCTGTTGTAATTACTGATTAGTGCTG
*
54235560 CAACCGGTGCTATATTT-AGAGTGTAGGGATGGGTGGGTCGATTTTAT-CCTCATATGGAGTGTA
383 CAACCGGTGCTATATTTGA-AGTGTAGGGATGGGTGGGTCGATTTTATCCCT-ACATGGAGTGTA
* *
54235623 GGGCTGGATGGAGTGGAGTGTAGAAGATGGATGGGTAGGA
446 GGGCTGGACGGAGTGGAGTGTAGAGGATGGATGGGTAGGA
54235663 T
1 T
54235664 TTTCTGTTCG
Statistics
Matches: 898, Mismatches: 63, Indels: 25
0.91 0.06 0.03
Matches are distributed among these distances:
483 27 0.03
484 137 0.15
485 406 0.45
486 140 0.16
487 3 0.00
488 2 0.00
491 5 0.01
492 177 0.20
493 1 0.00
ACGTcount: A:0.25, C:0.14, G:0.25, T:0.36
Consensus pattern (485 bp):
TAATACCCGTGTAGGGTAAAATGACAGTTTTACCCTTATGTGGAAAAATGACTATTTTGCCCTTA
TGTGTTAAATTGACGGTTTCGCCCTTATGTGGAAAAATGACTATTTTGCCCTTATGCGTTAAATT
GACAGTTTTACCTTTATGTGTCAAAATGATTGTTTTGCCCCTATGTGATGTATGTTTATATTTTA
GCATGCTATGTGTAACTGTATTGAGTACATGTTTAATATTATGATATGACATGACATGTTGCATG
ATGCATTGCATGGGGATGGGCTTATTGGAGGAAGTGTACTGTACTGGCAGCTCTGCTGCAAATCA
CTGATGGCTCTAAGCCTATTATACTGGCAGCTCTGTTGTAATTACTGATTAGTGCTGCAACCGGT
GCTATATTTGAAGTGTAGGGATGGGTGGGTCGATTTTATCCCTACATGGAGTGTAGGGCTGGACG
GAGTGGAGTGTAGAGGATGGATGGGTAGGA
Found at i:54235228 original size:27 final size:27
Alignment explanation
Indices: 54235188--54235288 Score: 89
Period size: 27 Copynumber: 3.7 Consensus size: 27
54235178 CGTGTAGGGT
54235188 AAAATGAC-AGTTTTGCCCTTATGTGGA
1 AAAATGACTA-TTTTGCCCTTATGTGGA
**
54235215 AAAATGACTATTTTGCCCTTATGTGTT
1 AAAATGACTATTTTGCCCTTATGTGGA
* ** **
54235242 AAATTGACGGTTTCACTCC-TATGTGGA
1 AAAATGACTATTTTGC-CCTTATGTGGA
* *
54235269 AAAATGTCTATTTTTCCCTT
1 AAAATGACTATTTTGCCCTT
54235289 GTACGTTAAA
Statistics
Matches: 56, Mismatches: 15, Indels: 6
0.73 0.19 0.08
Matches are distributed among these distances:
26 2 0.04
27 51 0.91
28 3 0.05
ACGTcount: A:0.27, C:0.17, G:0.17, T:0.40
Consensus pattern (27 bp):
AAAATGACTATTTTGCCCTTATGTGGA
Found at i:54235319 original size:54 final size:54
Alignment explanation
Indices: 54235187--54235344 Score: 165
Period size: 54 Copynumber: 2.9 Consensus size: 54
54235177 CCGTGTAGGG
* * * **
54235187 TAAAATGACAGTTTTGCCCTTATGTGGAAAAATGACTATTTTGCCCTTATGTGT
1 TAAATTGACAGTTTTACCTTTATGTGGAAAAATGACTATTTTGCCCTTATACGT
* * * * * *
54235241 TAAATTGACGGTTTCA-CTCCTATGTGGAAAAATGTCTATTTTTCCCTTGTACGT
1 TAAATTGACAGTTTTACCT-TTATGTGGAAAAATGACTATTTTGCCCTTATACGT
** * *
54235295 TAAATTGACAGTTTTACCTTTATGTGTCAAAATGATTGTTTTGCCCTTAT
1 TAAATTGACAGTTTTACCTTTATGTGGAAAAATGACTATTTTGCCCTTAT
54235345 GTGATGTATG
Statistics
Matches: 81, Mismatches: 21, Indels: 4
0.76 0.20 0.04
Matches are distributed among these distances:
53 1 0.01
54 78 0.96
55 2 0.02
ACGTcount: A:0.26, C:0.16, G:0.16, T:0.42
Consensus pattern (54 bp):
TAAATTGACAGTTTTACCTTTATGTGGAAAAATGACTATTTTGCCCTTATACGT
Found at i:54240155 original size:47 final size:47
Alignment explanation
Indices: 54240101--54240340 Score: 324
Period size: 47 Copynumber: 5.1 Consensus size: 47
54240091 TTAGGATTTT
** * *
54240101 ATGTGATGAATGTGAATGTGTATATATGAGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
*
54240148 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCTGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* *
54240195 ATGTGATGAATGTGAGCATGCATATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
*
54240242 ATGTGATGAATGTGAGCATGCATATATGTGATAAGGCC-AATTGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAA-TGGCCA
* * * * *
54240289 ATGTGATGAATATGAGATATGC--ATATGTGGTAAAGCCGAATGGTCA
1 ATGTGATGAATGTGA-ACATGCATATATGTGATAAGGCCGAATGGCCA
54240335 ATGTGA
1 ATGTGA
54240341 AATATATATA
Statistics
Matches: 175, Mismatches: 15, Indels: 7
0.89 0.08 0.04
Matches are distributed among these distances:
46 26 0.15
47 145 0.83
48 4 0.02
ACGTcount: A:0.33, C:0.10, G:0.29, T:0.28
Consensus pattern (47 bp):
ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
Found at i:54240201 original size:22 final size:22
Alignment explanation
Indices: 54240130--54240248 Score: 59
Period size: 22 Copynumber: 5.1 Consensus size: 22
54240120 GTATATATGA
*
54240130 GATAAGGCCGAATGGCCAATGT
1 GATAAGGCTGAATGGCCAATGT
* *
54240152 GATGAATG-TGAACAT-GCATATATGT
1 GAT-AAGGCTG-A-ATGGC-CA-ATGT
54240177 GATAAGGCTGAATGGCCAATGT
1 GATAAGGCTGAATGGCCAATGT
*
54240199 GATGAATG-TGAGCAT-G-CATATGTGT
1 GAT-AAGGCTGA--ATGGCCA-A--TGT
*
54240224 GATAAGGCCGAATGGCCAATGT
1 GATAAGGCTGAATGGCCAATGT
54240246 GAT
1 GAT
54240249 GAATGTGAGC
Statistics
Matches: 73, Mismatches: 8, Indels: 32
0.65 0.07 0.28
Matches are distributed among these distances:
22 22 0.30
23 16 0.22
24 16 0.22
25 19 0.26
ACGTcount: A:0.32, C:0.13, G:0.30, T:0.25
Consensus pattern (22 bp):
GATAAGGCTGAATGGCCAATGT
Found at i:54240365 original size:50 final size:50
Alignment explanation
Indices: 54240298--54240394 Score: 160
Period size: 50 Copynumber: 1.9 Consensus size: 50
54240288 AATGTGATGA
54240298 ATATGAGATATGCATATGTGGTAAAGCCGAATGG-TCAATGTGAAATATAT
1 ATATGAGATATGCATATGTGGTAAAGCCGAATGGCT-AATGTGAAATATAT
* *
54240348 ATATGAGATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATA
1 ATATGAGATATGCATATGTGGTAAAGCCGAATGGCTAATGTGAAATA
54240395 CGTAGGCGAT
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
50 43 0.98
51 1 0.02
ACGTcount: A:0.37, C:0.07, G:0.26, T:0.30
Consensus pattern (50 bp):
ATATGAGATATGCATATGTGGTAAAGCCGAATGGCTAATGTGAAATATAT
Found at i:54240653 original size:37 final size:37
Alignment explanation
Indices: 54240545--54240653 Score: 182
Period size: 37 Copynumber: 2.9 Consensus size: 37
54240535 GGAAATATAT
* *
54240545 TCCGGGTAAAACCCGATGACTACGTGTGGAGATTATG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
54240582 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
* *
54240619 TCCGGGTAAGACCCGATAACTACGTATGGAGATTT
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTT
54240654 CGTCTGAGCT
Statistics
Matches: 68, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 68 1.00
ACGTcount: A:0.26, C:0.19, G:0.29, T:0.26
Consensus pattern (37 bp):
TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
Found at i:54247188 original size:6 final size:6
Alignment explanation
Indices: 54247158--54247276 Score: 75
Period size: 6 Copynumber: 19.3 Consensus size: 6
54247148 AAGAAACATT
* * *
54247158 ATCAGA A-CTAGA ATCAAA ATGAGA ATCAGA ATCAGA ATCAG- GTGACAGA
1 ATCAGA ATC-AGA ATCAGA ATCAGA ATCAGA ATCAGA ATCAGA AT--CAGA
* * * *
54247207 ATCAGA ATCAGA ATTAG- GTGACAGA ATTAGA ATCAGA ATCAGT ATCAGGTA
1 ATCAGA ATCAGA ATCAGA AT--CAGA ATCAGA ATCAGA ATCAGA ATCA-G-A
*
54247258 A-CAGA ATCAAA ATCAGA AT
1 ATCAGA ATCAGA ATCAGA AT
54247277 GTGAATGCAA
Statistics
Matches: 86, Mismatches: 16, Indels: 22
0.69 0.13 0.18
Matches are distributed among these distances:
5 5 0.06
6 69 0.80
7 9 0.10
8 3 0.03
ACGTcount: A:0.48, C:0.13, G:0.19, T:0.19
Consensus pattern (6 bp):
ATCAGA
Found at i:54247212 original size:25 final size:25
Alignment explanation
Indices: 54247179--54247248 Score: 122
Period size: 25 Copynumber: 2.8 Consensus size: 25
54247169 AATCAAAATG
54247179 AGAATCAGAATCAGAATCAGGTGAC
1 AGAATCAGAATCAGAATCAGGTGAC
*
54247204 AGAATCAGAATCAGAATTAGGTGAC
1 AGAATCAGAATCAGAATCAGGTGAC
*
54247229 AGAATTAGAATCAGAATCAG
1 AGAATCAGAATCAGAATCAG
54247249 TATCAGGTAA
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:0.46, C:0.13, G:0.23, T:0.19
Consensus pattern (25 bp):
AGAATCAGAATCAGAATCAGGTGAC
Found at i:54247216 original size:31 final size:30
Alignment explanation
Indices: 54247179--54247276 Score: 116
Period size: 31 Copynumber: 3.4 Consensus size: 30
54247169 AATCAAAATG
54247179 AGAATCAGAATCAGAATCAGGTGACAGAATC
1 AGAATCAGAATCAG-ATCAGGTGACAGAATC
*
54247210 AGAATCAGAAT----T-AGGTGACAGAATT
1 AGAATCAGAATCAGATCAGGTGACAGAATC
*
54247235 AGAATCAGAATCAGTATCAGGTAACAGAATC
1 AGAATCAGAATCAG-ATCAGGTGACAGAATC
*
54247266 AAAATCAGAAT
1 AGAATCAGAAT
54247277 GTGAATGCAA
Statistics
Matches: 57, Mismatches: 4, Indels: 12
0.78 0.05 0.16
Matches are distributed among these distances:
25 23 0.40
26 1 0.02
30 1 0.02
31 32 0.56
ACGTcount: A:0.47, C:0.13, G:0.20, T:0.19
Consensus pattern (30 bp):
AGAATCAGAATCAGATCAGGTGACAGAATC
Found at i:54247263 original size:25 final size:25
Alignment explanation
Indices: 54247179--54247273 Score: 104
Period size: 25 Copynumber: 3.8 Consensus size: 25
54247169 AATCAAAATG
*
54247179 AGAATCAGAATCAGAATCAGGTGAC
1 AGAATCAGAATCAGAATCAGGTAAC
* *
54247204 AGAATCAGAATCAGAATTAGGTGAC
1 AGAATCAGAATCAGAATCAGGTAAC
* *
54247229 AGAATTAGAATCAGAATCA-GTATC
1 AGAATCAGAATCAGAATCAGGTAAC
*
54247253 AGGTAA-CAGAATCAAAATCAG
1 A-G-AATCAGAATCAGAATCAG
54247274 AATGTGAATG
Statistics
Matches: 60, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
24 4 0.07
25 54 0.90
26 2 0.03
ACGTcount: A:0.46, C:0.14, G:0.21, T:0.19
Consensus pattern (25 bp):
AGAATCAGAATCAGAATCAGGTAAC
Found at i:54247818 original size:27 final size:27
Alignment explanation
Indices: 54247788--54247981 Score: 262
Period size: 27 Copynumber: 7.2 Consensus size: 27
54247778 AACACCCTAG
* *
54247788 GGGTAAAATGGTAATTTTATAAATCGA
1 GGGTAAAACGGTAATTCTATAAATCGA
*
54247815 GGGTAAAACGGTAATTCTGTAAATCGA
1 GGGTAAAACGGTAATTCTATAAATCGA
* * *
54247842 GGGTAAAACGATAATTTTGTAAATCGA
1 GGGTAAAACGGTAATTCTATAAATCGA
**
54247869 GGGTAAAACAATAATTCTATAAATCGA
1 GGGTAAAACGGTAATTCTATAAATCGA
** *
54247896 GGGTAAAATAGTAATTTTATAAATCGA
1 GGGTAAAACGGTAATTCTATAAATCGA
** *
54247923 GGGTAAAATAGTAATTCTATAAAACGA
1 GGGTAAAACGGTAATTCTATAAATCGA
54247950 GGGTAAAACGGTAATTCTATAAATCGA
1 GGGTAAAACGGTAATTCTATAAATCGA
54247977 GGGTA
1 GGGTA
54247982 CTTTGGTAAT
Statistics
Matches: 151, Mismatches: 16, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 151 1.00
ACGTcount: A:0.42, C:0.08, G:0.22, T:0.28
Consensus pattern (27 bp):
GGGTAAAACGGTAATTCTATAAATCGA
Found at i:54248008 original size:54 final size:54
Alignment explanation
Indices: 54247788--54247981 Score: 289
Period size: 54 Copynumber: 3.6 Consensus size: 54
54247778 AACACCCTAG
* * *
54247788 GGGTAAAATGGTAATTTTATAAATCGAGGGTAAAACGGTAATTCTGTAAATCGA
1 GGGTAAAACGGTAATTTTATAAATCGAGGGTAAAACAGTAATTCTATAAATCGA
* * *
54247842 GGGTAAAACGATAATTTTGTAAATCGAGGGTAAAACAATAATTCTATAAATCGA
1 GGGTAAAACGGTAATTTTATAAATCGAGGGTAAAACAGTAATTCTATAAATCGA
** * *
54247896 GGGTAAAATAGTAATTTTATAAATCGAGGGTAAAATAGTAATTCTATAAAACGA
1 GGGTAAAACGGTAATTTTATAAATCGAGGGTAAAACAGTAATTCTATAAATCGA
*
54247950 GGGTAAAACGGTAATTCTATAAATCGAGGGTA
1 GGGTAAAACGGTAATTTTATAAATCGAGGGTA
54247982 CTTTGGTAAT
Statistics
Matches: 124, Mismatches: 16, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
54 124 1.00
ACGTcount: A:0.42, C:0.08, G:0.22, T:0.28
Consensus pattern (54 bp):
GGGTAAAACGGTAATTTTATAAATCGAGGGTAAAACAGTAATTCTATAAATCGA
Found at i:54248019 original size:81 final size:81
Alignment explanation
Indices: 54247799--54248008 Score: 233
Period size: 81 Copynumber: 2.6 Consensus size: 81
54247789 GGTAAAATGG
* ** * ** * * *
54247799 TAATTTTATAAATCGAGGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAA-CGATAATTTTGTA
1 TAATTCTATAAATCGAGGGTAAAATAGTAATTTTACAAATCGAGGGTAAAATAG-TAATTCTATA
*
54247863 AATCGAGGGTAAAACAA
65 AAACGAGGGTAAAACAA
*
54247880 TAATTCTATAAATCGAGGGTAAAATAGTAATTTTATAAATCGAGGGTAAAATAGTAATTCTATAA
1 TAATTCTATAAATCGAGGGTAAAATAGTAATTTTACAAATCGAGGGTAAAATAGTAATTCTATAA
**
54247945 AACGAGGGTAAAACGG
66 AACGAGGGTAAAACAA
*** * * *
54247961 TAATTCTATAAATCGAGGGTACTTTGGTAATTTTACAAGTTGAGGGTA
1 TAATTCTATAAATCGAGGGTAAAATAGTAATTTTACAAATCGAGGGTA
54248009 TTTCAGTAAT
Statistics
Matches: 110, Mismatches: 18, Indels: 2
0.85 0.14 0.02
Matches are distributed among these distances:
81 109 0.99
82 1 0.01
ACGTcount: A:0.40, C:0.08, G:0.21, T:0.30
Consensus pattern (81 bp):
TAATTCTATAAATCGAGGGTAAAATAGTAATTTTACAAATCGAGGGTAAAATAGTAATTCTATAA
AACGAGGGTAAAACAA
Found at i:54256147 original size:21 final size:20
Alignment explanation
Indices: 54256116--54256155 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 20
54256106 CCTGAACTGT
54256116 TGAAAAATTTC-AATGTTTTC
1 TGAAAAATTTCTAA-GTTTTC
54256136 TGAAAAATTTTCTAAGTTTT
1 TGAAAAA-TTTCTAAGTTTT
54256156 TTATTTAGTC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 7 0.39
21 9 0.50
22 2 0.11
ACGTcount: A:0.35, C:0.07, G:0.10, T:0.47
Consensus pattern (20 bp):
TGAAAAATTTCTAAGTTTTC
Found at i:54260987 original size:43 final size:43
Alignment explanation
Indices: 54260939--54261093 Score: 229
Period size: 43 Copynumber: 3.6 Consensus size: 43
54260929 CCAGCATTAC
*
54260939 GCCTGCTAGGCACGAAGGCCCGATTACACATCACCGGCACGAA
1 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAA
* * *
54260982 GCCTGCTAGGCATGAAGGCCCGAATACATATCACCGGCATGAA
1 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAA
* **
54261025 GCCTGTTAGGCACGAAGGCCCGAATACACATCACTAGCACGAA
1 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAA
* *
54261068 GCCTGATAGGCACGAAGGCCCAAATA
1 GCCTGCTAGGCACGAAGGCCCGAATA
54261094 TAATACCAGC
Statistics
Matches: 100, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
43 100 1.00
ACGTcount: A:0.31, C:0.30, G:0.25, T:0.14
Consensus pattern (43 bp):
GCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAA
Found at i:54261169 original size:38 final size:37
Alignment explanation
Indices: 54261091--54261209 Score: 112
Period size: 38 Copynumber: 3.1 Consensus size: 37
54261081 GAAGGCCCAA
* * * **
54261091 ATATAATACCAGCACTAGTCCTACGGGATTTATCTAGG
1 ATATAATACCAGCACAAG-CCTGCGGGATTTAACCCGG
54261129 ATATAATACCAGCACGAAGCCTGCGGGATTTAACCCGG
1 ATATAATACCAGCAC-AAGCCTGCGGGATTTAACCCGG
** **
54261167 ATATTTTACCAGCACAAAGCCTGCGAGTCTTTAAGCCCGG
1 ATATAATACCAGCAC-AAGCCTGCG-GGATTTAA-CCCGG
54261207 ATA
1 ATA
54261210 CACATCAAAT
Statistics
Matches: 68, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
38 52 0.76
39 8 0.12
40 8 0.12
ACGTcount: A:0.31, C:0.24, G:0.20, T:0.24
Consensus pattern (37 bp):
ATATAATACCAGCACAAGCCTGCGGGATTTAACCCGG
Found at i:54264842 original size:48 final size:48
Alignment explanation
Indices: 54264782--54264894 Score: 122
Period size: 48 Copynumber: 2.3 Consensus size: 48
54264772 AGTCCATTAT
* * * * *
54264782 GGTCTTATACTAGCTCTGCTCT-GCCCGTGCTGATGCCTATTCTC-GATA
1 GGTCTTACACTAGCACT-CACTGGCCCGTGCCGATGCCTA-TCCCAGATA
* *
54264830 GGTCTTACACTAGCACTCACTGGGCTGTGCCGATGCCTATCCCAGATA
1 GGTCTTACACTAGCACTCACTGGCCCGTGCCGATGCCTATCCCAGATA
54264878 GGTCTTACACTTAGCAC
1 GGTCTTACAC-TAGCAC
54264895 AAGTCGAGCT
Statistics
Matches: 55, Mismatches: 7, Indels: 5
0.82 0.10 0.07
Matches are distributed among these distances:
47 6 0.11
48 43 0.78
49 6 0.11
ACGTcount: A:0.19, C:0.30, G:0.21, T:0.30
Consensus pattern (48 bp):
GGTCTTACACTAGCACTCACTGGCCCGTGCCGATGCCTATCCCAGATA
Found at i:54266547 original size:85 final size:83
Alignment explanation
Indices: 54266403--54266563 Score: 286
Period size: 85 Copynumber: 1.9 Consensus size: 83
54266393 ATCATTTCAC
* *
54266403 CGGCATTACGCCTGCTAGGCACGAAGGCCCGATACACATCACCGGCACGAAGCCTGCTAGGCACG
1 CGGCATGAAGCCTGCTAGGCACGAAGGCCCGATACACATCACCGGCACGAAGCCTGCTAGGCACG
54266468 AAGGCCCGAATACACAACA
66 AAGG-CCGAATACACAACA
54266487 CGGCATGAAGCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAAGCCTGCTAGGCAC
1 CGGCATGAAGCCTGCTAGGCACGAAGGCCCG-ATACACATCACCGGCACGAAGCCTGCTAGGCAC
54266552 GAAGGCCGAATA
65 GAAGGCCGAATA
54266564 TAATACCAGC
Statistics
Matches: 74, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
84 36 0.49
85 38 0.51
ACGTcount: A:0.30, C:0.33, G:0.27, T:0.11
Consensus pattern (83 bp):
CGGCATGAAGCCTGCTAGGCACGAAGGCCCGATACACATCACCGGCACGAAGCCTGCTAGGCACG
AAGGCCGAATACACAACA
Found at i:54266548 original size:43 final size:43
Alignment explanation
Indices: 54266412--54266563 Score: 265
Period size: 42 Copynumber: 3.6 Consensus size: 43
54266402 CCGGCATTAC
54266412 GCCTGCTAGGCACGAAGGCCCG-ATACACATCACCGGCACGAA
1 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAA
* *
54266454 GCCTGCTAGGCACGAAGGCCCGAATACACAACA-CGGCATGAA
1 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAA
54266496 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAA
1 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAA
54266539 GCCTGCTAGGCACGAAGG-CCGAATA
1 GCCTGCTAGGCACGAAGGCCCGAATA
54266564 TAATACCAGC
Statistics
Matches: 104, Mismatches: 4, Indels: 4
0.93 0.04 0.04
Matches are distributed among these distances:
42 69 0.66
43 35 0.34
ACGTcount: A:0.30, C:0.33, G:0.27, T:0.10
Consensus pattern (43 bp):
GCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAA
Found at i:54266602 original size:37 final size:38
Alignment explanation
Indices: 54266561--54266676 Score: 155
Period size: 37 Copynumber: 3.1 Consensus size: 38
54266551 CGAAGGCCGA
* * *
54266561 ATATAATACCAGCACTAGGCCTG-GGGATTTATCCCGG
1 ATATAATACCAGCACGAAGCCTGCGGGATTTAACCCGG
54266598 ATATAATACCAGCACGAAGCCTGCGGGATTTAACCC-G
1 ATATAATACCAGCACGAAGCCTGCGGGATTTAACCCGG
** *
54266635 ATATTTTACCAGCACGAAGCCTGCGGGTTTTAAGCCCGG
1 ATATAATACCAGCACGAAGCCTGCGGGATTTAA-CCCGG
54266674 ATA
1 ATA
54266677 CACATCAAAT
Statistics
Matches: 70, Mismatches: 6, Indels: 4
0.88 0.08 0.05
Matches are distributed among these distances:
37 52 0.74
38 14 0.20
39 4 0.06
ACGTcount: A:0.28, C:0.25, G:0.23, T:0.23
Consensus pattern (38 bp):
ATATAATACCAGCACGAAGCCTGCGGGATTTAACCCGG
Found at i:54275039 original size:23 final size:23
Alignment explanation
Indices: 54275013--54275121 Score: 146
Period size: 23 Copynumber: 4.7 Consensus size: 23
54275003 GCTACATCTC
54275013 AGTGGTAGCTTCGGCTACAATAT
1 AGTGGTAGCTTCGGCTACAATAT
* * *
54275036 AGTGGTAGCTTTGGCTATAATAC
1 AGTGGTAGCTTCGGCTACAATAT
*
54275059 AGTGGTAGCTTTGGCTACAATAT
1 AGTGGTAGCTTCGGCTACAATAT
** *
54275082 AGTGGTAGCTTCGGCTACGTTAA
1 AGTGGTAGCTTCGGCTACAATAT
*
54275105 AGTGATAGCTTCGGCTA
1 AGTGGTAGCTTCGGCTA
54275122 TATTACAGTG
Statistics
Matches: 76, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 76 1.00
ACGTcount: A:0.25, C:0.16, G:0.28, T:0.32
Consensus pattern (23 bp):
AGTGGTAGCTTCGGCTACAATAT
Found at i:54278803 original size:39 final size:39
Alignment explanation
Indices: 54278719--54278871 Score: 216
Period size: 39 Copynumber: 3.9 Consensus size: 39
54278709 TATGGTAACC
** * *
54278719 CGCACAAAGGCCTTCGGGACTTAACCCGGATATCACAATT
1 CGCACAATTGCCTTCGGG-CTTAGCCCGGATATCACAACT
* *
54278759 TGCACAATTGCCTTCGGGCTTAGCCCGGATATCATAACT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT
*
54278798 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAATT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT
* *
54278837 TGCACAATTGCCTTCAGGCTTAGCCCGGATATCAC
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCAC
54278872 TCGAACATTC
Statistics
Matches: 102, Mismatches: 11, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
39 87 0.85
40 15 0.15
ACGTcount: A:0.25, C:0.30, G:0.20, T:0.25
Consensus pattern (39 bp):
CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT
Found at i:54278844 original size:78 final size:79
Alignment explanation
Indices: 54278688--54278870 Score: 269
Period size: 78 Copynumber: 2.3 Consensus size: 79
54278678 TCATTCAAAC
* * **
54278688 GCCTTCGGGACATAGCCCGGTTATGGTAACCCGCACAAAGGCCTTCGGGACTTAACCCGGATATC
1 GCCTTCGGG-CTTAGCCCGGATATCATAACCCGCACAAAGGCCTTCGGGACTTAACCCGGATATC
54278753 ACAATTTGCACAATT
65 ACAATTTGCACAATT
* ** *
54278768 GCCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATTGCCTTCGGG-CTTAGCCCGGATATCA
1 GCCTTCGGGCTTAGCCCGGATATCATAACCCGCACAAAGGCCTTCGGGACTTAACCCGGATATCA
54278832 CAATTTGCACAATT
66 CAATTTGCACAATT
*
54278846 GCCTTCAGGCTTAGCCCGGATATCA
1 GCCTTCGGGCTTAGCCCGGATATCA
54278871 CTCGAACATT
Statistics
Matches: 94, Mismatches: 9, Indels: 2
0.90 0.09 0.02
Matches are distributed among these distances:
78 53 0.56
79 32 0.34
80 9 0.10
ACGTcount: A:0.24, C:0.30, G:0.22, T:0.25
Consensus pattern (79 bp):
GCCTTCGGGCTTAGCCCGGATATCATAACCCGCACAAAGGCCTTCGGGACTTAACCCGGATATCA
CAATTTGCACAATT
Found at i:54286795 original size:39 final size:39
Alignment explanation
Indices: 54286711--54286863 Score: 225
Period size: 39 Copynumber: 3.9 Consensus size: 39
54286701 TATGGTAACC
** * *
54286711 CGCACAAAGGCCTTCGGGACTTAACCCGGATATCACAATT
1 CGCACAATTGCCTTCGGG-CTTAGCCCGGATATCACAACT
* *
54286751 TGCACAATTGCCTTCGGGCTTAGCCCGGATATCATAACT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT
*
54286790 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAATT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT
*
54286829 TGCACAATTGCCTTCGGGCTTAGCCCGGATATCAC
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCAC
54286864 TCGAACATTC
Statistics
Matches: 103, Mismatches: 10, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
39 88 0.85
40 15 0.15
ACGTcount: A:0.24, C:0.30, G:0.21, T:0.25
Consensus pattern (39 bp):
CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT
Found at i:54286832 original size:78 final size:79
Alignment explanation
Indices: 54286706--54286862 Score: 271
Period size: 78 Copynumber: 2.0 Consensus size: 79
54286696 CCGGTTATGG
54286706 TAACCCGCACAAAGGCCTTCGGGACTTAACCCGGATATCACAATTTGCACAATTGCCTTCGGGCT
1 TAACCCGCACAAAGGCCTTCGGGACTTAACCCGGATATCACAATTTGCACAATTGCCTTCGGGCT
54286771 TAGCCCGGATATCA
66 TAGCCCGGATATCA
* ** *
54286785 TAACTCGCACAATTGCCTTCGGG-CTTAGCCCGGATATCACAATTTGCACAATTGCCTTCGGGCT
1 TAACCCGCACAAAGGCCTTCGGGACTTAACCCGGATATCACAATTTGCACAATTGCCTTCGGGCT
54286849 TAGCCCGGATATCA
66 TAGCCCGGATATCA
54286863 CTCGAACATT
Statistics
Matches: 74, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
78 54 0.73
79 20 0.27
ACGTcount: A:0.25, C:0.30, G:0.20, T:0.25
Consensus pattern (79 bp):
TAACCCGCACAAAGGCCTTCGGGACTTAACCCGGATATCACAATTTGCACAATTGCCTTCGGGCT
TAGCCCGGATATCA
Done.