Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A08
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: 119882356
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2655529 characters in sequence are not A, C, G, or T
File 130 of 362
Found at i:43108598 original size:40 final size:40
Alignment explanation
Indices: 43108514--43108696 Score: 187
Period size: 40 Copynumber: 4.6 Consensus size: 40
43108504 TTGAATGCTG
* * * *
43108514 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACT-AT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTATTAAT
** *
43108553 ATCCGGACTAAGAT-CCGAAGGTATTTGTGCGAGTTATTAAT
1 -TCCGGGTTAAG-TCCCGAAGGCATTTGTGCGAGTTATTAAT
* * *
43108594 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGATA-CAAT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATTAAT
* *
43108633 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTT-TTAAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATT-AAT
43108673 TCCGGGTTAAGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
43108697 GAATGAGTTA
Statistics
Matches: 121, Mismatches: 16, Indels: 12
0.81 0.11 0.08
Matches are distributed among these distances:
39 35 0.29
40 76 0.63
41 10 0.08
ACGTcount: A:0.24, C:0.21, G:0.27, T:0.28
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATTAAT
Found at i:43108665 original size:79 final size:81
Alignment explanation
Indices: 43108514--43108693 Score: 219
Period size: 79 Copynumber: 2.3 Consensus size: 81
43108504 TTGAATGCTG
* * * *
43108514 TCCGGGCTAAGTCCCGAAGG-CTTTGTGCTAAGTGACTATATCCGGACTAAGATCCGAAGGTATT
1 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAGTGACAATATCCGGACTAAGATCCGAAGGCATT
* *
43108578 TGTGCGAGTTATT-AAT
66 CGTGCGAGTT-TTAAAA
**
43108594 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCG-AGAT-ACAAT-TCCGGGTTAAG-TCCCGAAGGCA
1 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAG-TGACAATATCCGGACTAAGAT-CCGAAGGCA
43108655 TTCGTGCGAGTTTTAAAA
64 TTCGTGCGAGTTTTAAAA
43108673 TCCGGGTTAAGTCCCGAAGGC
1 TCCGGGTTAAGTCCCGAAGGC
43108694 ATTGAATGAG
Statistics
Matches: 88, Mismatches: 8, Indels: 9
0.84 0.08 0.09
Matches are distributed among these distances:
78 3 0.03
79 51 0.58
80 25 0.28
81 9 0.10
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.27
Consensus pattern (81 bp):
TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAGTGACAATATCCGGACTAAGATCCGAAGGCATT
CGTGCGAGTTTTAAAA
Found at i:43108717 original size:39 final size:39
Alignment explanation
Indices: 43108594--43108743 Score: 117
Period size: 39 Copynumber: 3.8 Consensus size: 39
43108584 AGTTATTAAT
* ** * *
43108594 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAG--ATACAAT
1 TCCGGGTTAAGTCCCGAAGG-CATTGAACGAGTTCTA-AAA
** *
43108633 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTTTAAAA
1 TCCGGGTTAAGTCCCGAAGGCATT-GAACGAGTTCTAAAA
* **
43108673 TCCGGGTTAAGTCCCGAAGGCATTGAATGAGTTACTATGA
1 TCCGGGTTAAGTCCCGAAGGCATTGAACGAGTT-CTAAAA
* *
43108713 -CCGGGCTATGTCCCGAAGGCACTTGAACGAG
1 TCCGGGTTAAGTCCCGAAGGCA-TTGAACGAG
43108744 GAGCTATATC
Statistics
Matches: 94, Mismatches: 12, Indels: 9
0.82 0.10 0.08
Matches are distributed among these distances:
38 3 0.03
39 52 0.55
40 37 0.39
41 2 0.02
ACGTcount: A:0.25, C:0.22, G:0.29, T:0.25
Consensus pattern (39 bp):
TCCGGGTTAAGTCCCGAAGGCATTGAACGAGTTCTAAAA
Found at i:43108717 original size:79 final size:79
Alignment explanation
Indices: 43108567--43108733 Score: 194
Period size: 79 Copynumber: 2.1 Consensus size: 79
43108557 GGACTAAGAT
* * * * **
43108567 CCGAAGGTATTTGTGCGAGTTATTAATTCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGATACAA
1 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGGCCATTGAACGAGATACAA
* *
43108632 TTCCGGGTTAAGTC
66 TACCGGGCTAAGTC
* * *
43108646 CCGAAGGCATTCGTGCGAGTT-TTAAAATCCGGGTTAAGTCCCGAAGG-CATTGAATGAGTTACT
1 CCGAAGGCATTCGTGCGAGTTATT-AAATCCGGGTTAAGTCCCGAAGGCCATTGAACGAGATACA
*
43108709 ATGACCGGGCTATGTC
65 AT-ACCGGGCTAAGTC
43108725 CCGAAGGCA
1 CCGAAGGCA
43108734 CTTGAACGAG
Statistics
Matches: 74, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
78 14 0.19
79 60 0.81
ACGTcount: A:0.25, C:0.20, G:0.28, T:0.27
Consensus pattern (79 bp):
CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGGCCATTGAACGAGATACAA
TACCGGGCTAAGTC
Found at i:43116480 original size:40 final size:40
Alignment explanation
Indices: 43116396--43116579 Score: 196
Period size: 40 Copynumber: 4.6 Consensus size: 40
43116386 TTGAATGCTG
* * * *
43116396 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACT-AT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTATTAAT
** *
43116435 ATCCGGACTAAGAT-CCGAAGGTATTTGTGCGAGTTATTAAT
1 -TCCGGGTTAAG-TCCCGAAGGCATTTGTGCGAGTTATTAAT
* * *
43116476 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGATACTAAT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATTAAT
* *
43116516 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTT-TTAAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATT-AAT
43116556 TCCGGGTTAAGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
43116580 GAATGAGTTA
Statistics
Matches: 123, Mismatches: 16, Indels: 10
0.83 0.11 0.07
Matches are distributed among these distances:
39 2 0.02
40 111 0.90
41 10 0.08
ACGTcount: A:0.24, C:0.21, G:0.27, T:0.28
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATTAAT
Found at i:43116533 original size:80 final size:81
Alignment explanation
Indices: 43116396--43116576 Score: 221
Period size: 80 Copynumber: 2.3 Consensus size: 81
43116386 TTGAATGCTG
* * *
43116396 TCCGGGCTAAGTCCCGAAGG-CTTTGTGCTAAGTGACTATATCCGGACTAAGATCCGAAGGTATT
1 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAGTGACTATATCCGGACTAAGATCCGAAGGCATT
* *
43116460 TGTGCGAGTTATT-AAT
66 CGTGCGAGTT-TTAAAA
**
43116476 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCG-AGAT-ACTA-ATTCCGGGTTAAG-TCCCGAAGGC
1 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAG-TGACTATA-TCCGGACTAAGAT-CCGAAGGC
43116537 ATTCGTGCGAGTTTTAAAA
63 ATTCGTGCGAGTTTTAAAA
43116556 TCCGGGTTAAGTCCCGAAGGC
1 TCCGGGTTAAGTCCCGAAGGC
43116577 ATTGAATGAG
Statistics
Matches: 89, Mismatches: 7, Indels: 10
0.84 0.07 0.09
Matches are distributed among these distances:
79 4 0.04
80 76 0.85
81 9 0.10
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.28
Consensus pattern (81 bp):
TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAGTGACTATATCCGGACTAAGATCCGAAGGCATT
CGTGCGAGTTTTAAAA
Found at i:43116600 original size:39 final size:39
Alignment explanation
Indices: 43116464--43116626 Score: 134
Period size: 40 Copynumber: 4.1 Consensus size: 39
43116454 GGTATTTGTG
* * **
43116464 CGAGTTA-TTAATTCCGGGTTAAGTCCCGAAGGCCTTTGTG
1 CGAGTTACTT-ATACCGGGTTAAGTCCCGAAGG-CATTGAA
* * * **
43116504 CGAGATACTAATTCCGGGTTAAGTCCCGAAGGCATTCGTG
1 CGAGTTACTTATACCGGGTTAAGTCCCGAAGGCATT-GAA
*
43116544 CGAGTT--TTAAAATCCGGGTTAAGTCCCGAAGGCATTGAA
1 CGAGTTACTT-ATA-CCGGGTTAAGTCCCGAAGGCATTGAA
* * *
43116583 TGAGTTACTTATACCGGGCTATGTCCCGAAGGCACTTGAA
1 CGAGTTACTTATACCGGGTTAAGTCCCGAAGGCA-TTGAA
43116623 CGAG
1 CGAG
43116627 GAGCTATATC
Statistics
Matches: 102, Mismatches: 14, Indels: 14
0.78 0.11 0.11
Matches are distributed among these distances:
38 1 0.01
39 29 0.28
40 69 0.68
41 3 0.03
ACGTcount: A:0.25, C:0.21, G:0.27, T:0.27
Consensus pattern (39 bp):
CGAGTTACTTATACCGGGTTAAGTCCCGAAGGCATTGAA
Found at i:43118657 original size:49 final size:49
Alignment explanation
Indices: 43118552--43118824 Score: 219
Period size: 49 Copynumber: 5.7 Consensus size: 49
43118542 AGATGCCGAC
* * * *
43118552 GCCATGTCCCAGACATGGTCTTACACT-G-GTT-AGTACATTAAAGTCGAT
1 GCCATGTCCCAGACA-GGTCTTACACTAGCTTTCA-TATATCAAGGTCGAT
* *
43118600 GCCGTGTCCCAGACAGGTCTTACACTAGCTTTCATATATCGAGGTCGAT
1 GCCATGTCCCAGACAGGTCTTACACTAGCTTTCATATATCAAGGTCGAT
* * *
43118649 GCCATGTCCCAGACAGGTCTTACACTAGCTCTCATCTATCAATGTCGAT
1 GCCATGTCCCAGACAGGTCTTACACTAGCTTTCATATATCAAGGTCGAT
* * * *
43118698 GCCATGTCCCAGATAGGTCTTACACT-GAC--ACATA-A-CAAGCT-GAC
1 GCCATGTCCCAGACAGGTCTTACACTAG-CTTTCATATATCAAGGTCGAT
* * * ** * *
43118742 GCCATGTCCTAGATAGGTCTTACACTACCTTGT-ATATCCCGAGG-CTAAT
1 GCCATGTCCCAGACAGGTCTTACACTAGCTT-TCATATATCAAGGTC-GAT
* *
43118791 G-CATGTCCCAGACATGTCTTACACTAGCTCTCAT
1 GCCATGTCCCAGACAGGTCTTACACTAGCTTTCAT
43118825 CTCAATGCCG
Statistics
Matches: 182, Mismatches: 30, Indels: 26
0.76 0.13 0.11
Matches are distributed among these distances:
44 28 0.15
45 4 0.02
46 4 0.02
47 15 0.08
48 45 0.25
49 85 0.47
50 1 0.01
ACGTcount: A:0.26, C:0.28, G:0.19, T:0.28
Consensus pattern (49 bp):
GCCATGTCCCAGACAGGTCTTACACTAGCTTTCATATATCAAGGTCGAT
Found at i:43125044 original size:21 final size:20
Alignment explanation
Indices: 43125010--43125049 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
43125000 CACTTGGAAC
*
43125010 AGGGCACACGCCCGTGTGGA
1 AGGGCACACACCCGTGTGGA
43125030 AGGGCAACACACCCGTGTGG
1 AGGGC-ACACACCCGTGTGG
43125050 TCCTGTTGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.23, C:0.30, G:0.38, T:0.10
Consensus pattern (20 bp):
AGGGCACACACCCGTGTGGA
Found at i:43127250 original size:21 final size:22
Alignment explanation
Indices: 43127212--43127252 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
43127202 AATACCTAAA
*
43127212 AATGTGTTTGTGGATTAAATTG
1 AATGTGTTGGTGGATTAAATTG
43127234 AATGTGTTGGT-GATTAAAT
1 AATGTGTTGGTGGATTAAAT
43127253 AAGTTAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.29, C:0.00, G:0.27, T:0.44
Consensus pattern (22 bp):
AATGTGTTGGTGGATTAAATTG
Found at i:43129730 original size:29 final size:29
Alignment explanation
Indices: 43129688--43129746 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
43129678 ATGCCATCTC
43129688 TTAATCTTTTCTTTTACACATCTTGGCAT
1 TTAATCTTTTCTTTTACACATCTTGGCAT
43129717 TTAATCTTTTCTTTTACACATCTTGGCAT
1 TTAATCTTTTCTTTTACACATCTTGGCAT
43129746 T
1 T
43129747 CTCGTATGGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.20, C:0.20, G:0.07, T:0.53
Consensus pattern (29 bp):
TTAATCTTTTCTTTTACACATCTTGGCAT
Found at i:43143393 original size:20 final size:20
Alignment explanation
Indices: 43143368--43143406 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
43143358 AGAGACTAAA
* *
43143368 ATGAAAAGTTGTAAAATTTG
1 ATGAAAAATTCTAAAATTTG
43143388 ATGAAAAATTCTAAAATTT
1 ATGAAAAATTCTAAAATTT
43143407 TGTGTAACAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.49, C:0.03, G:0.13, T:0.36
Consensus pattern (20 bp):
ATGAAAAATTCTAAAATTTG
Found at i:43150876 original size:5 final size:5
Alignment explanation
Indices: 43150843--43150875 Score: 50
Period size: 5 Copynumber: 6.6 Consensus size: 5
43150833 TTTTGTGTTC
43150843 TTTATT TTTAT TTTAT TTTAT TTTAT TTT-T TTT
1 TTTA-T TTTAT TTTAT TTTAT TTTAT TTTAT TTT
43150876 TCAAATTGGT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.15
5 19 0.70
6 4 0.15
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (5 bp):
TTTAT
Found at i:43151126 original size:33 final size:33
Alignment explanation
Indices: 43151084--43151149 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
43151074 GAAGAAGCGT
43151084 AAGGATCGAAAGGCGTTAACACAATTACATCTG
1 AAGGATCGAAAGGCGTTAACACAATTACATCTG
43151117 AAGGATCGAAAGGCGTTAACACAATTACATCTG
1 AAGGATCGAAAGGCGTTAACACAATTACATCTG
43151150 CATTTGTCCA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.39, C:0.18, G:0.21, T:0.21
Consensus pattern (33 bp):
AAGGATCGAAAGGCGTTAACACAATTACATCTG
Found at i:43155796 original size:32 final size:32
Alignment explanation
Indices: 43155747--43155808 Score: 99
Period size: 32 Copynumber: 1.9 Consensus size: 32
43155737 TAATAGGCCA
*
43155747 CATTTTTCAGGCTCTTCTTTTGTTTTACTAGC
1 CATTTTTCAGGCTCTTCTTTTATTTTACTAGC
43155779 CATTGTTT-AGGCTCTTCTTTTATTTTACTA
1 CATT-TTTCAGGCTCTTCTTTTATTTTACTA
43155809 CTTCTCTAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
32 25 0.89
33 3 0.11
ACGTcount: A:0.15, C:0.19, G:0.11, T:0.55
Consensus pattern (32 bp):
CATTTTTCAGGCTCTTCTTTTATTTTACTAGC
Found at i:43157460 original size:41 final size:42
Alignment explanation
Indices: 43157402--43157537 Score: 127
Period size: 41 Copynumber: 3.3 Consensus size: 42
43157392 CGTTTGCAAT
* *
43157402 AAAACGCCG-TAAAAAACTGAGCAATAGCGGCTTTTTTAGTCC
1 AAAACGCCGCT-AAAAACTGAGCAATAGCGGCGTTTTTAGACC
** * *
43157444 -AAACGCCGCTAAAAACTGAGCAATAATGACGTTTTTGGACC
1 AAAACGCCGCTAAAAACTGAGCAATAGCGGCGTTTTTAGACC
* * * * *
43157485 AAAAACCCCGCTAAAAACTGAACAATAGCGGTGCTTTTGGA--
1 -AAAACGCCGCTAAAAACTGAGCAATAGCGGCGTTTTTAGACC
43157526 AAAACGCCGCTA
1 AAAACGCCGCTA
43157538 TAGATCAAGG
Statistics
Matches: 77, Mismatches: 14, Indels: 8
0.78 0.14 0.08
Matches are distributed among these distances:
40 11 0.14
41 33 0.43
42 1 0.01
43 32 0.42
ACGTcount: A:0.38, C:0.23, G:0.19, T:0.21
Consensus pattern (42 bp):
AAAACGCCGCTAAAAACTGAGCAATAGCGGCGTTTTTAGACC
Found at i:43157523 original size:43 final size:43
Alignment explanation
Indices: 43157444--43157525 Score: 101
Period size: 43 Copynumber: 1.9 Consensus size: 43
43157434 TTTTTAGTCC
* * * *
43157444 AAACGCCGCTAAAAACTGAGCAATAATGACGTTTTTGGACCAA
1 AAACCCCGCTAAAAACTGAACAATAACGACGCTTTTGGACCAA
* **
43157487 AAACCCCGCTAAAAACTGAACAATAGCGGTGCTTTTGGA
1 AAACCCCGCTAAAAACTGAACAATAACGACGCTTTTGGA
43157526 AAAACGCCGC
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
43 32 1.00
ACGTcount: A:0.38, C:0.22, G:0.20, T:0.21
Consensus pattern (43 bp):
AAACCCCGCTAAAAACTGAACAATAACGACGCTTTTGGACCAA
Found at i:43157624 original size:41 final size:41
Alignment explanation
Indices: 43157567--43157695 Score: 231
Period size: 41 Copynumber: 3.1 Consensus size: 41
43157557 CGCTTCTGGA
**
43157567 GCTTTTGGAGAAACGCCGCTATAGATCGAGGTTTTAGCAAC
1 GCTTTTGGAGAAACGCCGCTATAGATCGAGGTTTTAGCGGC
*
43157608 GCTTTTGGAGAAACGCCGCTATAGATTGAGGTTTTAGCGGC
1 GCTTTTGGAGAAACGCCGCTATAGATCGAGGTTTTAGCGGC
43157649 GCTTTTGGAGAAACGCCGCTATAGATCGAGGTTTTAGCGGC
1 GCTTTTGGAGAAACGCCGCTATAGATCGAGGTTTTAGCGGC
43157690 GCTTTT
1 GCTTTT
43157696 TGAAAAATGC
Statistics
Matches: 84, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 84 1.00
ACGTcount: A:0.22, C:0.19, G:0.29, T:0.29
Consensus pattern (41 bp):
GCTTTTGGAGAAACGCCGCTATAGATCGAGGTTTTAGCGGC
Found at i:43158424 original size:43 final size:43
Alignment explanation
Indices: 43158305--43158426 Score: 104
Period size: 43 Copynumber: 2.9 Consensus size: 43
43158295 GTTTAGGGGA
* * *
43158305 TAGGG-TTATGATATAATGTTTATTATTTTGGGGTTT-ATGATT
1 TAGGGTTTATGATATAATGTTTATTGTTTT-TGGTTTAAGGATT
* * * * * * *** *
43158347 TATGATTTAAGATTTAAGGTTTAATGTCCATGGTTTAAGGGTT
1 TAGGGTTTATGATATAATGTTTATTGTTTTTGGTTTAAGGATT
43158390 TAGGGTTTATGATATAATGTTTATTGTTTTTGGTTTA
1 TAGGGTTTATGATATAATGTTTATTGTTTTTGGTTTA
43158427 GAGTTTTTGA
Statistics
Matches: 56, Mismatches: 22, Indels: 3
0.69 0.27 0.04
Matches are distributed among these distances:
42 8 0.14
43 48 0.86
ACGTcount: A:0.25, C:0.02, G:0.23, T:0.51
Consensus pattern (43 bp):
TAGGGTTTATGATATAATGTTTATTGTTTTTGGTTTAAGGATT
Found at i:43158425 original size:14 final size:14
Alignment explanation
Indices: 43158415--43158467 Score: 79
Period size: 14 Copynumber: 3.8 Consensus size: 14
43158405 AATGTTTATT
43158415 GTTTTTGGTTTAGA
1 GTTTTTGGTTTAGA
* *
43158429 GTTTTTGATTTAGG
1 GTTTTTGGTTTAGA
*
43158443 GTTTATGGTTTAGA
1 GTTTTTGGTTTAGA
43158457 GTTTTTGGTTT
1 GTTTTTGGTTT
43158468 TTTGTTTTAC
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 33 1.00
ACGTcount: A:0.13, C:0.00, G:0.28, T:0.58
Consensus pattern (14 bp):
GTTTTTGGTTTAGA
Found at i:43158440 original size:28 final size:28
Alignment explanation
Indices: 43158409--43158475 Score: 89
Period size: 28 Copynumber: 2.4 Consensus size: 28
43158399 TGATATAATG
43158409 TTTATTGTTTTTGGTTTAGAGTTTTTGA
1 TTTATTGTTTTTGGTTTAGAGTTTTTGA
** * *
43158437 TTTAGGGTTTATGGTTTAGAGTTTTTGG
1 TTTATTGTTTTTGGTTTAGAGTTTTTGA
*
43158465 TTTTTTGTTTT
1 TTTATTGTTTT
43158476 ACAGTTAGGA
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.12, C:0.00, G:0.24, T:0.64
Consensus pattern (28 bp):
TTTATTGTTTTTGGTTTAGAGTTTTTGA
Found at i:43158649 original size:20 final size:20
Alignment explanation
Indices: 43158626--43158665 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
43158616 ATCCCTTGTA
*
43158626 ATATATATTTAGGGTTTAGG
1 ATATAGATTTAGGGTTTAGG
* *
43158646 ATATAGGTTTATGGTTTAGG
1 ATATAGATTTAGGGTTTAGG
43158666 GTTTACTGTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.28, C:0.00, G:0.28, T:0.45
Consensus pattern (20 bp):
ATATAGATTTAGGGTTTAGG
Found at i:43158891 original size:19 final size:20
Alignment explanation
Indices: 43158869--43158911 Score: 56
Period size: 18 Copynumber: 2.3 Consensus size: 20
43158859 AATATAATAT
43158869 TTATTTTAATAT-ATTAAAA
1 TTATTTTAATATAATTAAAA
*
43158888 TTA--TTAATATAATTTAAA
1 TTATTTTAATATAATTAAAA
43158906 TTATTT
1 TTATTT
43158912 AAGAGATAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 5
0.77 0.04 0.19
Matches are distributed among these distances:
17 7 0.35
18 9 0.45
19 3 0.15
20 1 0.05
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (20 bp):
TTATTTTAATATAATTAAAA
Found at i:43163723 original size:40 final size:40
Alignment explanation
Indices: 43163668--43163845 Score: 234
Period size: 40 Copynumber: 4.5 Consensus size: 40
43163658 CGGATGATAA
43163668 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTACTATAT
* * *
43163708 CCGGGCTAAGACCCGAAGGTATTTGTGCTAGTTGCTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTACTATAT
* * * *
43163748 TCGGGCTAAGTCCCGAAGGCATTTGGGCTAGTTACTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTACTATAT
* * * *
43163788 CCGGGCTAAGACCTGAAGGCATTTATGCGAGTTGCTTTAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTACTATAT
43163828 CC-GGCTAA-ATCCCGAAGG
1 CCGGGCTAAGA-CCCGAAGG
43163846 TACTTGAGTT
Statistics
Matches: 120, Mismatches: 17, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
38 1 0.01
39 13 0.11
40 106 0.88
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.27
Consensus pattern (40 bp):
CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:43167031 original size:31 final size:33
Alignment explanation
Indices: 43166993--43167065 Score: 93
Period size: 31 Copynumber: 2.3 Consensus size: 33
43166983 TTGTTGTATT
43166993 TTATTTATTTTTA-TATTT-AATCTA-ATTTTTA
1 TTATTTATTTTTAGT-TTTGAATCTATATTTTTA
*
43167024 TTATTTA-TTTTAGTTTTGATTCTATATTTTTA
1 TTATTTATTTTTAGTTTTGAATCTATATTTTTA
43167056 TT-TTTATTTT
1 TTATTTATTTT
43167066 AATTTGATAA
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
30 8 0.22
31 17 0.46
32 12 0.32
ACGTcount: A:0.23, C:0.03, G:0.03, T:0.71
Consensus pattern (33 bp):
TTATTTATTTTTAGTTTTGAATCTATATTTTTA
Found at i:43167040 original size:19 final size:18
Alignment explanation
Indices: 43166992--43167063 Score: 58
Period size: 19 Copynumber: 3.9 Consensus size: 18
43166982 CTTGTTGTAT
43166992 TTTA-TTTATTTTTA-TA
1 TTTATTTTATTTTTATTA
* *
43167008 TTTAATCTAATTTTTATTA
1 TTT-ATTTTATTTTTATTA
* *
43167027 TTTATTTTAGTTTTGATTC
1 TTTATTTTA-TTTTTATTA
*
43167046 TATATTTTTATTTTTATT
1 TTTA-TTTTATTTTTATT
43167064 TTAATTTGAT
Statistics
Matches: 43, Mismatches: 8, Indels: 7
0.74 0.14 0.12
Matches are distributed among these distances:
16 3 0.07
17 1 0.02
18 12 0.28
19 22 0.51
20 5 0.12
ACGTcount: A:0.24, C:0.03, G:0.03, T:0.71
Consensus pattern (18 bp):
TTTATTTTATTTTTATTA
Found at i:43167057 original size:6 final size:6
Alignment explanation
Indices: 43166996--43167070 Score: 53
Period size: 6 Copynumber: 12.2 Consensus size: 6
43166986 TTGTATTTTA
* * * * *
43166996 TTTATT TTTATA TTTAAT CTAATT TTTATT ATTTA-T TTTAGTT TTGATT
1 TTTATT TTTATT TTTATT TTTATT TTTATT -TTTATT TTTA-TT TTTATT
* *
43167045 CTATATT TTTATT TTTATT TTAATT T
1 -TTTATT TTTATT TTTATT TTTATT T
43167071 GATAATGAAT
Statistics
Matches: 52, Mismatches: 13, Indels: 8
0.71 0.18 0.11
Matches are distributed among these distances:
5 4 0.08
6 36 0.69
7 12 0.23
ACGTcount: A:0.24, C:0.03, G:0.03, T:0.71
Consensus pattern (6 bp):
TTTATT
Found at i:43167106 original size:12 final size:11
Alignment explanation
Indices: 43167073--43167106 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
43167063 TTTAATTTGA
43167073 TAAT-GAATTT
1 TAATAGAATTT
43167083 TAATAGAATTT
1 TAATAGAATTT
43167094 TAATAGAAATTT
1 TAATAG-AATTT
43167106 T
1 T
43167107 TTATATTTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 4 0.18
11 12 0.55
12 6 0.27
ACGTcount: A:0.44, C:0.00, G:0.09, T:0.47
Consensus pattern (11 bp):
TAATAGAATTT
Found at i:43168788 original size:12 final size:12
Alignment explanation
Indices: 43168771--43168795 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
43168761 CTTGTAAGAA
43168771 TAATCATATTAT
1 TAATCATATTAT
43168783 TAATCATATTAT
1 TAATCATATTAT
43168795 T
1 T
43168796 TTTAGGACAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.08, G:0.00, T:0.52
Consensus pattern (12 bp):
TAATCATATTAT
Found at i:43175075 original size:214 final size:219
Alignment explanation
Indices: 43174724--43175134 Score: 602
Period size: 214 Copynumber: 1.9 Consensus size: 219
43174714 GTCGAAGTAA
43174724 ACAACAACATTATAATAATAAAAAACATAAGAAAATGTCCAAAATACAATAGAAACCTACACCAC
1 ACAACAACATTATAATAATAAAAAACATAAGAAAATGTCCAAAATACAATAGAAACCTACACCAC
* * *
43174789 TCCAAACAAACAAACAAAAAAAAAAAGAACACAACAAAAGTTCAATTAACCAATAACAATAACAA
66 TCC--AC--AC--ACAAAAAAAAAAAGAACACAACAAAAGCTCAATTAACCAACAACAAAAACAA
* * * *
43174854 ACCAAACCAAACTAACAACAATAACACATCAGTTTAAAAACCATTATAGAATAGTTTAAA-TTTC
125 ACCAAACCAAACTAACAACAATAACACATCAATTCAAAAACCATTAAAGAATA-ATTAAACTTTC
43174918 TTCATGAGTCCAAATAAATAACAAAAACAAT
189 TTCATGAGTCCAAATAAATAACAAAAACAAT
*
43174949 ACAACAACATTGTAATAA-AAAAAACATAAGCAAAA-GTCCAAAATACAATAGAAACCTACACCA
1 ACAACAACATTATAATAATAAAAAACATAAG-AAAATGTCCAAAATACAATAGAAACCTACACCA
* *
43175012 GTCC-C-C-C-AAAAAAAAAAGAACACAACAAAAGCTCAATTATCCAACAACAAAAACAAACCAA
65 CTCCACACACAAAAAAAAAAAGAACACAACAAAAGCTCAATTAACCAACAACAAAAACAAACCAA
*
43175073 ACCAAACTAATAACAATAACACATCAATTCAAAAACCATTAAAGAATAATTAAACTTTCTTC
130 ACCAAACTAACAACAATAACACATCAATTCAAAAACCATTAAAGAATAATTAAACTTTCTTC
43175135 TTGTGCTTCA
Statistics
Matches: 173, Mismatches: 11, Indels: 15
0.87 0.06 0.08
Matches are distributed among these distances:
213 5 0.03
214 101 0.58
215 1 0.01
218 1 0.01
221 1 0.01
224 43 0.25
225 21 0.12
ACGTcount: A:0.57, C:0.21, G:0.04, T:0.17
Consensus pattern (219 bp):
ACAACAACATTATAATAATAAAAAACATAAGAAAATGTCCAAAATACAATAGAAACCTACACCAC
TCCACACACAAAAAAAAAAAGAACACAACAAAAGCTCAATTAACCAACAACAAAAACAAACCAAA
CCAAACTAACAACAATAACACATCAATTCAAAAACCATTAAAGAATAATTAAACTTTCTTCATGA
GTCCAAATAAATAACAAAAACAAT
Found at i:43179728 original size:28 final size:26
Alignment explanation
Indices: 43179688--43179739 Score: 77
Period size: 28 Copynumber: 1.9 Consensus size: 26
43179678 ATTCGCTAGA
*
43179688 TAAGTTGCGAACTGAAGGGTTTGCCAGT
1 TAAGTTGCAAACTG--GGGTTTGCCAGT
43179716 TAAGTTGCAAACTGGGGTTTGCCA
1 TAAGTTGCAAACTGGGGTTTGCCA
43179740 ATCACAGTCA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 10 0.43
28 13 0.57
ACGTcount: A:0.25, C:0.15, G:0.31, T:0.29
Consensus pattern (26 bp):
TAAGTTGCAAACTGGGGTTTGCCAGT
Found at i:43180358 original size:14 final size:14
Alignment explanation
Indices: 43180339--43180384 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
43180329 TGAACCTATG
43180339 TTTTAAGATATGTT
1 TTTTAAGATATGTT
*
43180353 TTTTAAGATACGATT
1 TTTTAAGATATG-TT
*
43180368 TTATAA-AT-TGTT
1 TTTTAAGATATGTT
43180380 TTTTA
1 TTTTA
43180385 CAAACTTATA
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
12 6 0.22
13 1 0.04
14 13 0.48
15 7 0.26
ACGTcount: A:0.30, C:0.02, G:0.11, T:0.57
Consensus pattern (14 bp):
TTTTAAGATATGTT
Found at i:43182831 original size:39 final size:39
Alignment explanation
Indices: 43182778--43182918 Score: 212
Period size: 39 Copynumber: 3.6 Consensus size: 39
43182768 CATATTCACT
* *
43182778 TTTAAGCA-AGTATCACATTACACATATAATCACATAACA
1 TTTAAGCATA-TATCACAATACTCATATAATCACATAACA
43182817 TTTAAGCATATATCACAATACTCATATAATCACATAACA
1 TTTAAGCATATATCACAATACTCATATAATCACATAACA
* * *
43182856 TTTAAGCATATATCACAATGCTCATATAATAACATAACG
1 TTTAAGCATATATCACAATACTCATATAATCACATAACA
*
43182895 TTCAAGCATATATCACAATACTCA
1 TTTAAGCATATATCACAATACTCA
43182919 AAAACATGTT
Statistics
Matches: 94, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
39 93 0.99
40 1 0.01
ACGTcount: A:0.45, C:0.21, G:0.05, T:0.30
Consensus pattern (39 bp):
TTTAAGCATATATCACAATACTCATATAATCACATAACA
Found at i:43184147 original size:24 final size:24
Alignment explanation
Indices: 43184115--43184161 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
43184105 CTGTCAGGAG
**
43184115 AGGATTTAGGAGTTGATAAGGGAT
1 AGGATTTAGGAGCAGATAAGGGAT
43184139 AGGATTTAGGAGCAGATAAGGGA
1 AGGATTTAGGAGCAGATAAGGGA
43184162 GGAAATCTAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.36, C:0.02, G:0.38, T:0.23
Consensus pattern (24 bp):
AGGATTTAGGAGCAGATAAGGGAT
Found at i:43185593 original size:27 final size:26
Alignment explanation
Indices: 43185553--43185664 Score: 134
Period size: 27 Copynumber: 4.2 Consensus size: 26
43185543 AGGAAGCGTC
*
43185553 CTGGTGGCTATGCCACAATTATCTGAT
1 CTGGTGGCTCTGCCAC-ATTATCTGAT
*
43185580 CTGGTGGCTCTGCCACATATATCTGTT
1 CTGGTGGCTCTGCCACAT-TATCTGAT
*
43185607 CTGGTGGTTCTGCCACGATTATCTGTAT
1 CTGGTGGCTCTGCCAC-ATTATCTG-AT
* * *
43185635 CTGGTGACTCTGTCACATTATCTGTT
1 CTGGTGGCTCTGCCACATTATCTGAT
43185661 CTGG
1 CTGG
43185665 CAGCCATGCT
Statistics
Matches: 74, Mismatches: 8, Indels: 7
0.83 0.09 0.08
Matches are distributed among these distances:
26 7 0.09
27 51 0.69
28 16 0.22
ACGTcount: A:0.16, C:0.23, G:0.23, T:0.38
Consensus pattern (26 bp):
CTGGTGGCTCTGCCACATTATCTGAT
Found at i:43185657 original size:54 final size:54
Alignment explanation
Indices: 43185553--43185664 Score: 163
Period size: 54 Copynumber: 2.1 Consensus size: 54
43185543 AGGAAGCGTC
*
43185553 CTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATATCTGTT
1 CTGGTGGCTATGCCACAATTATCTGATCTGGTGACTCTGCCACATATATCTGTT
* * * *
43185607 CTGGTGGTTCTGCCACGATTATCTGTATCTGGTGACTCTGTCACAT-TATCTGTT
1 CTGGTGGCTATGCCACAATTATCTG-ATCTGGTGACTCTGCCACATATATCTGTT
43185661 CTGG
1 CTGG
43185665 CAGCCATGCT
Statistics
Matches: 52, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
54 34 0.65
55 18 0.35
ACGTcount: A:0.16, C:0.23, G:0.23, T:0.38
Consensus pattern (54 bp):
CTGGTGGCTATGCCACAATTATCTGATCTGGTGACTCTGCCACATATATCTGTT
Found at i:43189731 original size:51 final size:51
Alignment explanation
Indices: 43189668--43189767 Score: 137
Period size: 51 Copynumber: 2.0 Consensus size: 51
43189658 CTACCTTATA
* ** *
43189668 ACATGTAACACATCCATAATGAACTCGGACCTTTCAATGAGCTCAGATGTT
1 ACATGTAACACATCCATAATGAACTCAGACCACTCAACGAGCTCAGATGTT
* * *
43189719 ACATGTATCACATCCATTATGAACTCAGACCACTCAACGAGCTCGGATG
1 ACATGTAACACATCCATAATGAACTCAGACCACTCAACGAGCTCAGATG
43189768 CCACATATAT
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
51 42 1.00
ACGTcount: A:0.33, C:0.26, G:0.16, T:0.25
Consensus pattern (51 bp):
ACATGTAACACATCCATAATGAACTCAGACCACTCAACGAGCTCAGATGTT
Found at i:43189779 original size:51 final size:51
Alignment explanation
Indices: 43189676--43189779 Score: 127
Period size: 51 Copynumber: 2.0 Consensus size: 51
43189666 TAACATGTAA
* ** * ** *
43189676 CACATCCATAATGAACTCGGACCTTTCAATGAGCTCAGATGTTACATGTAT
1 CACATCCATAATGAACTCAGACCACTCAACGAGCTCAGATGCCACATATAT
* *
43189727 CACATCCATTATGAACTCAGACCACTCAACGAGCTCGGATGCCACATATAT
1 CACATCCATAATGAACTCAGACCACTCAACGAGCTCAGATGCCACATATAT
43189778 CA
1 CA
43189780 TGAACTTGGA
Statistics
Matches: 44, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
51 44 1.00
ACGTcount: A:0.33, C:0.28, G:0.14, T:0.25
Consensus pattern (51 bp):
CACATCCATAATGAACTCAGACCACTCAACGAGCTCAGATGCCACATATAT
Found at i:43196385 original size:15 final size:16
Alignment explanation
Indices: 43196365--43196398 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
43196355 AATATTTATT
*
43196365 TATTTATTTTTA-TAA
1 TATTTATATTTAGTAA
43196380 TATTTATATTTAGTAA
1 TATTTATATTTAGTAA
43196396 TAT
1 TAT
43196399 AATTTATTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 11 0.65
16 6 0.35
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (16 bp):
TATTTATATTTAGTAA
Found at i:43198300 original size:12 final size:12
Alignment explanation
Indices: 43198283--43198307 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
43198273 TTTGGACAGC
43198283 AGCAGTAGTCTA
1 AGCAGTAGTCTA
43198295 AGCAGTAGTCTA
1 AGCAGTAGTCTA
43198307 A
1 A
43198308 CTTTGAAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.16, G:0.24, T:0.24
Consensus pattern (12 bp):
AGCAGTAGTCTA
Found at i:43203092 original size:23 final size:23
Alignment explanation
Indices: 43203066--43203110 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
43203056 TTAAAATGTA
*
43203066 TGTTCTTAATTGT-AATATAATTG
1 TGTTATTAATTGTGAA-ATAATTG
*
43203089 TGTTATTCATTGTGAAATAATT
1 TGTTATTAATTGTGAAATAATT
43203111 TATGAAAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 17 0.89
24 2 0.11
ACGTcount: A:0.31, C:0.04, G:0.13, T:0.51
Consensus pattern (23 bp):
TGTTATTAATTGTGAAATAATTG
Found at i:43205151 original size:46 final size:46
Alignment explanation
Indices: 43204985--43205160 Score: 169
Period size: 46 Copynumber: 3.8 Consensus size: 46
43204975 TGTAACCCGC
* * *
43204985 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGACATTTGCAT
* * * * * *
43205031 CCATGAGTGAACTCGGACTCAACTCAATGAGTTCGGATGCCTAGTTACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGA---C-ATTTGCAT
* *
43205081 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGACATTTGCAT
* **
43205124 CCATAAGTGAACTCAAACTCAACTCAACGAGCTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGA
43205161 TGCTCAACCA
Statistics
Matches: 104, Mismatches: 19, Indels: 14
0.76 0.14 0.10
Matches are distributed among these distances:
43 6 0.06
44 2 0.02
45 2 0.02
46 58 0.56
47 28 0.27
48 2 0.02
49 2 0.02
50 4 0.04
ACGTcount: A:0.30, C:0.29, G:0.20, T:0.21
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGACATTTGCAT
Found at i:43205160 original size:93 final size:93
Alignment explanation
Indices: 43204992--43205163 Score: 263
Period size: 93 Copynumber: 1.8 Consensus size: 93
43204982 CGCCCATAAG
* * * **
43204992 CGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATGAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCAAACTCAACTCA
* *
43205057 ATGAGTTCGGATGCCTAGTTACATCTCA
66 ACGAGCTCGGATGCCTAGTTACATCTCA
* *
43205085 CGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCATAAGTGAACTCAAACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCAAACTCAACTCA
43205150 ACGAGCTCGGATGC
66 ACGAGCTCGGATGC
43205164 TCAACCATCC
Statistics
Matches: 70, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
93 70 1.00
ACGTcount: A:0.28, C:0.29, G:0.21, T:0.22
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCAAACTCAACTCA
ACGAGCTCGGATGCCTAGTTACATCTCA
Found at i:43207567 original size:15 final size:15
Alignment explanation
Indices: 43207535--43207598 Score: 89
Period size: 15 Copynumber: 4.4 Consensus size: 15
43207525 CAAAGATAAC
43207535 AAGAAA-CC-GAATA
1 AAGAAATCCAGAATA
43207548 AAGAAATCCA-AGATA
1 AAGAAATCCAGA-ATA
*
43207563 GAGAAATCCAGAATA
1 AAGAAATCCAGAATA
43207578 AAGAAATCCAGAATA
1 AAGAAATCCAGAATA
43207593 AAGAAA
1 AAGAAA
43207599 CCCAAGATAC
Statistics
Matches: 45, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
13 6 0.13
14 3 0.07
15 35 0.78
16 1 0.02
ACGTcount: A:0.61, C:0.12, G:0.16, T:0.11
Consensus pattern (15 bp):
AAGAAATCCAGAATA
Found at i:43212192 original size:40 final size:40
Alignment explanation
Indices: 43212137--43212353 Score: 298
Period size: 40 Copynumber: 5.5 Consensus size: 40
43212127 TGGATGATAA
* * *
43212137 CCGGGCTAAGTCCCGAAGGCATTTGCGCTAGTGACTAGT-T
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-TAT
*
43212177 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGCTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
43212217 CCGGGCTAAGTTCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
43212257 CCGGGCTAAGTCCCGAAGGCATTGGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* *
43212297 CCGGGCTATGTCCCGAAGGCA-TTGAGCGAG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAT
* *
43212336 CC-GGTTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
43212354 TACTTGGCTT
Statistics
Matches: 161, Mismatches: 14, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
38 15 0.09
39 16 0.10
40 130 0.81
ACGTcount: A:0.23, C:0.24, G:0.29, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:43213966 original size:46 final size:45
Alignment explanation
Indices: 43213891--43214065 Score: 158
Period size: 46 Copynumber: 3.8 Consensus size: 45
43213881 TGTAACCCGC
*
43213891 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTT-GCAT
* * * *
43213937 CCATGAGTGAACTCGGACTCAACTCAACGAGTTTGGATGCCTAGTTACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG--G-C--GTTGCAT
* * * *** *
43213987 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCATACATTTGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGC-GTTGCAT
43214030 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG
43214066 ATGCTCAACC
Statistics
Matches: 103, Mismatches: 18, Indels: 16
0.75 0.13 0.12
Matches are distributed among these distances:
43 6 0.06
44 2 0.02
45 2 0.02
46 57 0.55
47 25 0.24
48 3 0.03
49 2 0.02
50 3 0.03
51 3 0.03
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.22
Consensus pattern (45 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTGCAT
Found at i:43214057 original size:93 final size:93
Alignment explanation
Indices: 43213898--43214069 Score: 263
Period size: 93 Copynumber: 1.8 Consensus size: 93
43213888 CGCCCATAAG
* * * *
43213898 CGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATGAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCAGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
* *
43213963 ACGAGTTTGGATGCCTAGTTACATCTCA
66 ACGAGCTCGGATGCCTAGTTACATCTCA
* * *
43213991 CGAACTCGGACTCAACTCAACGAGTTCATACATTTGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCAGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
43214056 ACGAGCTCGGATGC
66 ACGAGCTCGGATGC
43214070 TCAACCATCC
Statistics
Matches: 70, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
93 70 1.00
ACGTcount: A:0.28, C:0.29, G:0.21, T:0.22
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCAGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGCTCGGATGCCTAGTTACATCTCA
Found at i:43225310 original size:23 final size:23
Alignment explanation
Indices: 43225284--43225328 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
43225274 TTAAAATGTA
*
43225284 TGTTCTTAATTGT-AATATAATTG
1 TGTTATTAATTGTGAA-ATAATTG
*
43225307 TGTTATTCATTGTGAAATAATT
1 TGTTATTAATTGTGAAATAATT
43225329 TATGAAAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 17 0.89
24 2 0.11
ACGTcount: A:0.31, C:0.04, G:0.13, T:0.51
Consensus pattern (23 bp):
TGTTATTAATTGTGAAATAATTG
Found at i:43237712 original size:68 final size:68
Alignment explanation
Indices: 43237633--43237808 Score: 175
Period size: 68 Copynumber: 2.6 Consensus size: 68
43237623 CATCATGTGT
** * * *
43237633 ACAAGAGAGCTACGAGATACTATGTAGTAGCTAGGTCACATGTGTGA-T-ACGGGATGTATC-CC
1 ACAAGAGAGCTACGAGATA-TAAAT-GTAGCTAGGTCACATGTGTGATTCAAGGGAAGGA-CACC
43237695 ATGTAG
63 ATGTAG
* * *
43237701 ACAAGAGAGCTACGGGAGAGATAAATGTAGCTAGGTCGCATGTGTGATTCCAAGTGAAGGACACC
1 ACAAGAGAGCTAC--GAGATATAAATGTAGCTAGGTCACATGTGTGATT-CAAGGGAAGGACACC
43237766 ATGTAG
63 ATGTAG
*
43237772 ACAAGAGAGCTACGAG--ATAAAT-TGGCTAGGTCACATG
1 ACAAGAGAGCTACGAGATATAAATGTAGCTAGGTCACATG
43237809 GGTGGTACTA
Statistics
Matches: 92, Mismatches: 10, Indels: 14
0.79 0.09 0.12
Matches are distributed among these distances:
66 13 0.14
67 6 0.07
68 33 0.36
69 7 0.08
70 6 0.07
71 27 0.29
ACGTcount: A:0.34, C:0.16, G:0.29, T:0.22
Consensus pattern (68 bp):
ACAAGAGAGCTACGAGATATAAATGTAGCTAGGTCACATGTGTGATTCAAGGGAAGGACACCATG
TAG
Found at i:43245122 original size:27 final size:26
Alignment explanation
Indices: 43245081--43245193 Score: 127
Period size: 27 Copynumber: 4.2 Consensus size: 26
43245071 CAACATAGCT
* * *
43245081 ACCAGAACAGGTAATGTGACAGAGTC
1 ACCAGAACAGATAATGTGGCAGAGCC
*
43245107 ACCAGATACAGATAATCGTGGTAGAGCC
1 ACCAGA-ACAGATAAT-GTGGCAGAGCC
*
43245135 ACCAGAACAGATATATGTGGCAGAACC
1 ACCAGAACAGATA-ATGTGGCAGAGCC
* *
43245162 ACCAGATCAGATAATTGTGGCATAGCC
1 ACCAGAACAGATAA-TGTGGCAGAGCC
43245189 ACCAG
1 ACCAG
43245194 GACGCTTCCT
Statistics
Matches: 74, Mismatches: 9, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
26 7 0.09
27 51 0.69
28 16 0.22
ACGTcount: A:0.37, C:0.22, G:0.24, T:0.17
Consensus pattern (26 bp):
ACCAGAACAGATAATGTGGCAGAGCC
Found at i:43245173 original size:54 final size:54
Alignment explanation
Indices: 43245081--43245193 Score: 147
Period size: 54 Copynumber: 2.1 Consensus size: 54
43245071 CAACATAGCT
* ** *
43245081 ACCAGAACAGGTAATGTGACAGAGTCACCAGATACAGATAATCGTGGTAGAGCC
1 ACCAGAACAGATAATGTGACAGAACCACCAGATACAGATAATCGTGGCAGAGCC
* * *
43245135 ACCAGAACAGATATATGTGGCAGAACCACCAGAT-CAGATAATTGTGGCATAGCC
1 ACCAGAACAGATA-ATGTGACAGAACCACCAGATACAGATAATCGTGGCAGAGCC
43245189 ACCAG
1 ACCAG
43245194 GACGCTTCCT
Statistics
Matches: 51, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
54 34 0.67
55 17 0.33
ACGTcount: A:0.37, C:0.22, G:0.24, T:0.17
Consensus pattern (54 bp):
ACCAGAACAGATAATGTGACAGAACCACCAGATACAGATAATCGTGGCAGAGCC
Found at i:43256001 original size:133 final size:133
Alignment explanation
Indices: 43255801--43256070 Score: 423
Period size: 133 Copynumber: 2.0 Consensus size: 133
43255791 ATTTAATTAT
* * * ** *
43255801 ATGAAGTGTTATGAGATCATGATAGATGAAATGGAAAATGTTGGCATAATTTTTTTGGTTGGAAT
1 ATGAAATGTTATGAGATCATGATAGATGAAAAGGAAAATGTTGGCATAAATGATTTGATTGGAAT
* *
43255866 GAGTAATGCAAATTGGAATTGGATGAATGAAATGTATATTGAGATGTTACTAGTACATGTTTTAT
66 GAGTAATGCAAATTGGAATTGGATGAATAAAATGTATATTGAGATATTACTAGTACATGTTTTAT
43255931 ATA
131 ATA
43255934 ATGAAATGTTATGAGATCATGATAGATGAAAAGGAAAATGTTGGCATAAATGATTTGATTGGAAT
1 ATGAAATGTTATGAGATCATGATAGATGAAAAGGAAAATGTTGGCATAAATGATTTGATTGGAAT
** * *
43255999 GAGTAATGCAAATTGGAATTTTATTAATAAAATGTATATTGAGATATTATTAGTACATGTTTTAT
66 GAGTAATGCAAATTGGAATTGGATGAATAAAATGTATATTGAGATATTACTAGTACATGTTTTAT
*
43256064 TTA
131 ATA
43256067 ATGA
1 ATGA
43256071 TAAGATTATA
Statistics
Matches: 124, Mismatches: 13, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
133 124 1.00
ACGTcount: A:0.38, C:0.03, G:0.22, T:0.37
Consensus pattern (133 bp):
ATGAAATGTTATGAGATCATGATAGATGAAAAGGAAAATGTTGGCATAAATGATTTGATTGGAAT
GAGTAATGCAAATTGGAATTGGATGAATAAAATGTATATTGAGATATTACTAGTACATGTTTTAT
ATA
Found at i:43264156 original size:37 final size:37
Alignment explanation
Indices: 43264106--43264180 Score: 123
Period size: 37 Copynumber: 2.0 Consensus size: 37
43264096 TAAATATTCT
** *
43264106 TTTGATAAGTACATTCGTTGTTCTAAGAGAAAAAAAA
1 TTTGATAAGTACATTCACTATTCTAAGAGAAAAAAAA
43264143 TTTGATAAGTACATTCACTATTCTAAGAGAAAAAAAA
1 TTTGATAAGTACATTCACTATTCTAAGAGAAAAAAAA
43264180 T
1 T
43264181 ATGGATATCG
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.45, C:0.09, G:0.13, T:0.32
Consensus pattern (37 bp):
TTTGATAAGTACATTCACTATTCTAAGAGAAAAAAAA
Found at i:43265886 original size:23 final size:23
Alignment explanation
Indices: 43265860--43265905 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
43265850 GTATGTGGTT
43265860 AGAGTACAC-AGTTGTATGGTTCA
1 AGAGTACACGA-TTGTATGGTTCA
43265883 AGAGTACACGATTGTATGGTTCA
1 AGAGTACACGATTGTATGGTTCA
43265906 GCACCACACG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
23 21 0.95
24 1 0.05
ACGTcount: A:0.30, C:0.13, G:0.26, T:0.30
Consensus pattern (23 bp):
AGAGTACACGATTGTATGGTTCA
Found at i:43265914 original size:23 final size:23
Alignment explanation
Indices: 43265871--43265915 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
43265861 GAGTACACAG
**
43265871 TTGTATGGTTCAAGAGTACACGA
1 TTGTATGGTTCAAGACCACACGA
43265894 TTGTATGGTTC-AGCACCACACG
1 TTGTATGGTTCAAG-ACCACACG
43265916 GCATCAGCCT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 2 0.11
23 17 0.89
ACGTcount: A:0.27, C:0.20, G:0.24, T:0.29
Consensus pattern (23 bp):
TTGTATGGTTCAAGACCACACGA
Found at i:43275826 original size:26 final size:25
Alignment explanation
Indices: 43275777--43275829 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 25
43275767 AATGGTAGTT
43275777 AAATGTTAAATTTATATGCTGTTATG
1 AAATGTTAAATTTATATGC-GTTATG
43275803 AAATGTTAGAATTTATATTG-GTTATG
1 AAATGTTA-AATTTATA-TGCGTTATG
43275829 A
1 A
43275830 CTAAATATGA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
26 15 0.60
27 8 0.32
28 2 0.08
ACGTcount: A:0.36, C:0.02, G:0.17, T:0.45
Consensus pattern (25 bp):
AAATGTTAAATTTATATGCGTTATG
Found at i:43280862 original size:20 final size:20
Alignment explanation
Indices: 43280839--43280877 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
43280829 TATTCATTTA
43280839 TTTATATAAATTTTATAAAT
1 TTTATATAAATTTTATAAAT
* **
43280859 TTTATGTATTTTTTATAAA
1 TTTATATAAATTTTATAAA
43280878 ATCTTATGTA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (20 bp):
TTTATATAAATTTTATAAAT
Found at i:43280874 original size:31 final size:32
Alignment explanation
Indices: 43280834--43280894 Score: 81
Period size: 31 Copynumber: 1.9 Consensus size: 32
43280824 ATATATATTC
*
43280834 ATTTATTTATATAAATTTTAT-AAATTTTATGT
1 ATTTATTTATA-AAATCTTATGAAATTTTATGT
*
43280866 ATTT-TTTATAAAATCTTATGTAATTTTAT
1 ATTTATTTATAAAATCTTATGAAATTTTAT
43280895 TGAAAAATGA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 8 0.31
31 14 0.54
32 4 0.15
ACGTcount: A:0.36, C:0.02, G:0.03, T:0.59
Consensus pattern (32 bp):
ATTTATTTATAAAATCTTATGAAATTTTATGT
Found at i:43280884 original size:21 final size:20
Alignment explanation
Indices: 43280849--43280892 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
43280839 TTTATATAAA
* *
43280849 TTTTATAAATTTTATGTATT
1 TTTTATAAATCTTATGTAAT
43280869 TTTTATAAAATCTTATGTAAT
1 TTTTAT-AAATCTTATGTAAT
43280890 TTT
1 TTT
43280893 ATTGAAAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 6 0.29
21 15 0.71
ACGTcount: A:0.32, C:0.02, G:0.05, T:0.61
Consensus pattern (20 bp):
TTTTATAAATCTTATGTAAT
Found at i:43280892 original size:20 final size:19
Alignment explanation
Indices: 43280847--43280894 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 19
43280837 TATTTATATA
*
43280847 AATTTTATAAATTTTATGT
1 AATTTTATAAATCTTATGT
*
43280866 ATTTTTTATAAAATCTTATGT
1 A-ATTTTAT-AAATCTTATGT
43280887 AATTTTAT
1 AATTTTAT
43280895 TGAAAAATGA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
19 1 0.04
20 12 0.50
21 11 0.46
ACGTcount: A:0.35, C:0.02, G:0.04, T:0.58
Consensus pattern (19 bp):
AATTTTATAAATCTTATGT
Found at i:43280997 original size:60 final size:62
Alignment explanation
Indices: 43280933--43281051 Score: 152
Period size: 60 Copynumber: 2.0 Consensus size: 62
43280923 CAATTTTTAA
* * * *
43280933 TTTTTAAGGATCAAGACTAAATTGATAGAATGTGTAAA-GTTG-AGGGCTAAATTTATTGAT
1 TTTTTAAGAATCAAGACTAAATTGATAAAATCTGTAAATATTGAAGGGCTAAATTTATTGAT
* * * *
43280993 TTTTTTAGAATTAGGACTAAATTGATAAAATCTGTAAATATTGAAGGGTTAAATTTATT
1 TTTTTAAGAATCAAGACTAAATTGATAAAATCTGTAAATATTGAAGGGCTAAATTTATT
43281052 ATTATACTAA
Statistics
Matches: 49, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
60 32 0.65
61 3 0.06
62 14 0.29
ACGTcount: A:0.38, C:0.04, G:0.18, T:0.39
Consensus pattern (62 bp):
TTTTTAAGAATCAAGACTAAATTGATAAAATCTGTAAATATTGAAGGGCTAAATTTATTGAT
Found at i:43286071 original size:28 final size:28
Alignment explanation
Indices: 43286037--43286092 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
43286027 GTACGAGTAA
43286037 GACCATGGCATCGATATGTGATTCCAAT
1 GACCATGGCATCGATATGTGATTCCAAT
43286065 GACCATGGCATCGATATGTGATTCCAAT
1 GACCATGGCATCGATATGTGATTCCAAT
43286093 ATGTGATTAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.29, C:0.21, G:0.21, T:0.29
Consensus pattern (28 bp):
GACCATGGCATCGATATGTGATTCCAAT
Found at i:43294839 original size:74 final size:74
Alignment explanation
Indices: 43294703--43294854 Score: 234
Period size: 74 Copynumber: 2.1 Consensus size: 74
43294693 TTACATAAAT
* * * * *
43294703 AATACAAAGTTTATTATTTAAATTGAAAAAATCACTAAAATTAATAATTGAAATGGTGAAAAAGT
1 AATACAAAGTTGACTATTTAAATTGAAAAAAACACTAAAATTAATAATTAAAATGGTAAAAAAGT
43294768 CATTACATA
66 CATTACATA
*
43294777 AATACAAAGTTGACTATTTAAATTGAAAAAAAACCCTAAAATTAATAATTAAAATGG-AAAAAAG
1 AATACAAAGTTGACTATTTAAATTG-AAAAAAACACTAAAATTAATAATTAAAATGGTAAAAAAG
43294841 TCATTACATA
65 TCATTACATA
43294851 AATA
1 AATA
43294855 TAAAATTATT
Statistics
Matches: 71, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
74 43 0.61
75 28 0.39
ACGTcount: A:0.54, C:0.08, G:0.09, T:0.30
Consensus pattern (74 bp):
AATACAAAGTTGACTATTTAAATTGAAAAAAACACTAAAATTAATAATTAAAATGGTAAAAAAGT
CATTACATA
Found at i:43295097 original size:33 final size:33
Alignment explanation
Indices: 43295055--43295130 Score: 98
Period size: 33 Copynumber: 2.3 Consensus size: 33
43295045 AGTCAGAAGT
* * *
43295055 AGTGGAGTACAGCGGTGGATACATGCCGGGAGG
1 AGTGGAGTACAGCGGAGGATACAGGCCGAGAGG
* * *
43295088 AGTGGAGTACGGCGGAGGATACGGGCTGAGAGG
1 AGTGGAGTACAGCGGAGGATACAGGCCGAGAGG
43295121 AGTGGAGTAC
1 AGTGGAGTAC
43295131 TAAGGTGGAG
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
33 37 1.00
ACGTcount: A:0.25, C:0.13, G:0.47, T:0.14
Consensus pattern (33 bp):
AGTGGAGTACAGCGGAGGATACAGGCCGAGAGG
Found at i:43297140 original size:14 final size:16
Alignment explanation
Indices: 43297108--43297142 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
43297098 AAAATCAAAT
43297108 AAAATTACATTATAAA
1 AAAATTACATTATAAA
*
43297124 AAAATTACATTAGAAA
1 AAAATTACATTATAAA
43297140 AAA
1 AAA
43297143 GCACAAAACA
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:0.66, C:0.06, G:0.03, T:0.26
Consensus pattern (16 bp):
AAAATTACATTATAAA
Found at i:43297247 original size:99 final size:97
Alignment explanation
Indices: 43297122--43297497 Score: 387
Period size: 99 Copynumber: 3.9 Consensus size: 97
43297112 TTACATTATA
* * *
43297122 AAAAAATTACATTA-GAAAAAAGCACAAAACACTAAACTAAACACTAACAATTTATATAATCTAA
1 AAAAATTTACATTACTAAAAAATCACAAAACACT-AACTAAACACTAACAATTTATA-AA-CTAA
* * *
43297186 TCCTAAATTACTAACAAAATTATTATAATTTTTTT
63 TCATAAATTACTAACAAAATAACTATAATTTTTTT
*
43297221 AAAAA-TTAAATTACTAAAAAATCACAAAAC-CTTAAACTAAACACTAACAATTTATAAACTAAT
1 AAAAATTTACATTACTAAAAAATCACAAAACAC-T-AACTAAACACTAACAATTTATAAACTAAT
* * ***
43297284 CATAAATTACTAACAAAGTAACTATAACATTTAAA
64 CATAAATTACTAACAAAATAACTATAA-TTTTTTT
* * * *
43297319 AAAAATTTACATTACTAATAAATTACAACACAC-AA--AAA-ACTAGCAATTTATAAACTAATCA
1 AAAAATTTACATTACTAAAAAATCACAAAACACTAACTAAACACTAACAATTTATAAACTAATCA
43297380 TAAATTACTAACAAAATAACTATAAATATATATATTT
66 TAAATTACTAACAAAATAACTAT-AAT-T-T-T-TTT
* *
43297417 AAAAAATTTACATTACTAAAAAATCAC-AAA-A-T-ACAAAACACTAACAATTTATAACCTAATC
1 -AAAAATTTACATTACTAAAAAATCACAAAACACTAACTAAACACTAACAATTTATAAACTAATC
* *
43297478 ATAAATTGCTAACCAAATAA
65 ATAAATTACTAACAAAATAA
43297498 TTTTACATTA
Statistics
Matches: 234, Mismatches: 28, Indels: 30
0.80 0.10 0.10
Matches are distributed among these distances:
94 44 0.19
95 6 0.03
96 2 0.01
97 32 0.14
98 23 0.10
99 126 0.54
100 1 0.00
ACGTcount: A:0.55, C:0.15, G:0.01, T:0.28
Consensus pattern (97 bp):
AAAAATTTACATTACTAAAAAATCACAAAACACTAACTAAACACTAACAATTTATAAACTAATCA
TAAATTACTAACAAAATAACTATAATTTTTTT
Found at i:43297507 original size:76 final size:76
Alignment explanation
Indices: 43297423--43297656 Score: 276
Period size: 75 Copynumber: 3.1 Consensus size: 76
43297413 ATTTAAAAAA
* *
43297423 TTTACATTACTAAAAAATCACAAAATACAAAACACTAACAATTTATAACCTAATCATAAATTGCT
1 TTTACATTAATAAAAAATCACAAAATACAAAACACTAACAATTTATAACCTAATCATAAATTACT
*
43297488 AACCAAATAAT
66 AACAAAATAAT
* **** *
43297499 TTTACATTAATAAAAAATCACAAAACACAAAGTTTTAACAATTTATAA-CTTATCATAAATTACT
1 TTTACATTAATAAAAAATCACAAAATACAAAACACTAACAATTTATAACCTAATCATAAATTACT
43297563 AACAAAATAAT
66 AACAAAATAAT
* * * * *
43297574 TTTACATTAATAAAATATCAAAAAATACTAAACTAAACAC-AACAAATTATAACATAATCCTAAA
1 TTTACATTAATAAAAAATCACAAAATAC---A--AAACACTAACAATTTATAACCTAATCATAAA
43297638 TTACTAACAAAAT-AT
61 TTACTAACAAAATAAT
43297653 TTTA
1 TTTA
43297657 AAACAATTAT
Statistics
Matches: 132, Mismatches: 20, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
75 49 0.37
76 42 0.32
78 1 0.01
79 17 0.13
80 23 0.17
ACGTcount: A:0.54, C:0.15, G:0.01, T:0.30
Consensus pattern (76 bp):
TTTACATTAATAAAAAATCACAAAATACAAAACACTAACAATTTATAACCTAATCATAAATTACT
AACAAAATAAT
Found at i:43297571 original size:75 final size:76
Alignment explanation
Indices: 43297423--43297656 Score: 267
Period size: 76 Copynumber: 3.1 Consensus size: 76
43297413 ATTTAAAAAA
* * *
43297423 TTTACATTACTAAAAAATCACAAAATACAAAACACTAACAATTTATAACCTAATCATAAATTGCT
1 TTTACATTAATAAAAAATCACAAAACACAAAACACTAACAATTTATAACCTAATCATAAATTACT
*
43297488 AACCAAATAAT
66 AACAAAATAAT
**** *
43297499 TTTACATTAATAAAAAATCACAAAACACAAAGTTTTAACAATTTATAA-CTTATCATAAATTACT
1 TTTACATTAATAAAAAATCACAAAACACAAAACACTAACAATTTATAACCTAATCATAAATTACT
43297563 AACAAAATAAT
66 AACAAAATAAT
* * * * * *
43297574 TTTACATTAATAAAATATCAAAAAATACTAAACTAAACAC-AACAAATTATAACATAATCCTAAA
1 TTTACATTAATAAAAAATC-ACAAA-AC---ACAAAACACTAACAATTTATAACCTAATCATAAA
43297638 TTACTAACAAAAT-AT
61 TTACTAACAAAATAAT
43297653 TTTA
1 TTTA
43297657 AAACAATTAT
Statistics
Matches: 132, Mismatches: 20, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
75 42 0.32
76 46 0.35
77 2 0.02
79 17 0.13
80 25 0.19
ACGTcount: A:0.54, C:0.15, G:0.01, T:0.30
Consensus pattern (76 bp):
TTTACATTAATAAAAAATCACAAAACACAAAACACTAACAATTTATAACCTAATCATAAATTACT
AACAAAATAAT
Found at i:43297996 original size:18 final size:19
Alignment explanation
Indices: 43297969--43298016 Score: 66
Period size: 18 Copynumber: 2.7 Consensus size: 19
43297959 GTTTATATAA
43297969 ATTT-TAAAAAAATAT-TT
1 ATTTATAAAAAAATATATT
*
43297986 ATTTATAAAAAAATGTATT
1 ATTTATAAAAAAATATATT
43298005 A-TTATAAAAAAA
1 ATTTATAAAAAAA
43298017 AAGGTGATGG
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
17 4 0.14
18 21 0.75
19 3 0.11
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (19 bp):
ATTTATAAAAAAATATATT
Found at i:43299414 original size:27 final size:27
Alignment explanation
Indices: 43299384--43299443 Score: 77
Period size: 27 Copynumber: 2.2 Consensus size: 27
43299374 AACAAAATTG
*
43299384 CCAGTATCAGTATATATGGCAAAG-CT
1 CCAGTAACAGTATATATGGCAAAGCCT
* *
43299410 ACCAGTAACAGTATATGTGGCGAAGCCT
1 -CCAGTAACAGTATATATGGCAAAGCCT
43299438 CCAGTA
1 CCAGTA
43299444 CAATACACTT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
27 27 0.93
28 2 0.07
ACGTcount: A:0.33, C:0.22, G:0.22, T:0.23
Consensus pattern (27 bp):
CCAGTAACAGTATATATGGCAAAGCCT
Found at i:43299789 original size:20 final size:18
Alignment explanation
Indices: 43299742--43299789 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 18
43299732 GTGTGGAGCC
*
43299742 CATGAGCCCATTGGGCCCA
1 CATG-GCCCATTCGGCCCA
*
43299761 CACGGCCCATTTCGGCCCAA
1 CATGGCCCA-TTCGGCCC-A
43299781 CATGGCCCA
1 CATGGCCCA
43299790 AAATAACCTA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
18 5 0.21
19 10 0.42
20 9 0.38
ACGTcount: A:0.21, C:0.42, G:0.23, T:0.15
Consensus pattern (18 bp):
CATGGCCCATTCGGCCCA
Found at i:43306305 original size:47 final size:44
Alignment explanation
Indices: 43306192--43306403 Score: 135
Period size: 47 Copynumber: 4.6 Consensus size: 44
43306182 TATGCGTGCT
43306192 GATGCATGTCCCAGACATGTCTTACACTAGCACAACTCTTGGCC
1 GATGCATGTCCCAGACATGTCTTACACTAGCACAACTCTTGGCC
* * * * *
43306236 GATGCGTGTCCCAGACACGTCTTACACTGGC-TATCTCTGTCAAGGCC
1 GATGCATGTCCCAGACATGTCTTACACTAGCACAACTCT-T---GGCC
* * * * * * *
43306283 GATGCATGTCCCAAACATGTCTT-CTCTGGCACTCATAAT-ATGACT
1 GATGCATGTCCCAGACATGTCTTACACTAGCA--CA-ACTCTTGGCC
* * ** *
43306328 AAAGCATGTCCCAGACATGTCTTACACTAGC-CCTCGTCTGGATGCC
1 GATGCATGTCCCAGACATGTCTTACACTAGCACAAC-TCTTG--GCC
43306374 GATGCCATGTCCCAGACATGGTCTTACACT
1 GATG-CATGTCCCAGACAT-GTCTTACACT
43306404 GATACACAAA
Statistics
Matches: 124, Mismatches: 29, Indels: 26
0.69 0.16 0.15
Matches are distributed among these distances:
43 7 0.06
44 30 0.24
45 22 0.18
46 14 0.11
47 38 0.31
48 11 0.09
49 1 0.01
50 1 0.01
ACGTcount: A:0.24, C:0.31, G:0.19, T:0.26
Consensus pattern (44 bp):
GATGCATGTCCCAGACATGTCTTACACTAGCACAACTCTTGGCC
Found at i:43307128 original size:12 final size:12
Alignment explanation
Indices: 43307111--43307135 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
43307101 TAAAAATGTA
43307111 AAAATCATCAAG
1 AAAATCATCAAG
43307123 AAAATCATCAAG
1 AAAATCATCAAG
43307135 A
1 A
43307136 TCACTTACAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.60, C:0.16, G:0.08, T:0.16
Consensus pattern (12 bp):
AAAATCATCAAG
Found at i:43311687 original size:30 final size:30
Alignment explanation
Indices: 43311653--43311713 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
43311643 TCCTTAACTC
*
43311653 AAACTTTGGCAAAATTACAATTTTGCCCCT
1 AAACTTTGGCAAAATTACAATTTTCCCCCT
* * * *
43311683 AAACTTTTGCATATTTACACTTTTCCCCCT
1 AAACTTTGGCAAAATTACAATTTTCCCCCT
43311713 A
1 A
43311714 GGCTCGGGAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.30, C:0.26, G:0.07, T:0.38
Consensus pattern (30 bp):
AAACTTTGGCAAAATTACAATTTTCCCCCT
Found at i:43324697 original size:80 final size:76
Alignment explanation
Indices: 43324604--43324855 Score: 245
Period size: 88 Copynumber: 3.1 Consensus size: 76
43324594 ATAACTGTTT
* * *
43324604 TAAAATTATTTTGTTAGTAATTTAGGATTATGTTATAAATT-TTTGTGTTTAGTTTAGTATTTTG
1 TAAAATTAGTTTGTTAGTAATTTAGGATTAGGTTATAAATTGTTAGTG--T--TTT-GTATTTTG
43324668 TGATTTTTTATTAATG
61 TGATTTTTTATTAATG
* *
43324684 TAAAATTAGTTTGTTAGTAATTTATGATTAGGTTATAAATTGTTAGTGTTTTGTGTTTTGTGATT
1 TAAAATTAGTTTGTTAGTAATTTAGGATTAGGTTATAAATTGTTAGTGTTTTGTATTTTGTGATT
43324749 TTTTATTAATG
66 TTTTATTAATG
* *
43324760 TAAAATTGTTTTGTTAATTATTTTGTTAGTAATTTATGATTAGGTTATAAATTGTTAGTGTTTTG
1 T-AAA----------A-TTAGTTTGTTAGTAATTTAGGATTAGGTTATAAATTGTTAGTGTTTTG
* *
43324825 TGTTTTGTGATTTTTTTTAGTAATG
54 TATTTTGTGA--TTTTTTATTAATG
43324850 TAAAAT
1 TAAAAT
43324856 ATTTAAAAAA
Statistics
Matches: 150, Mismatches: 7, Indels: 32
0.79 0.04 0.17
Matches are distributed among these distances:
76 24 0.16
77 6 0.04
78 1 0.01
79 2 0.01
80 38 0.25
81 5 0.03
87 1 0.01
88 57 0.38
89 3 0.02
90 13 0.09
ACGTcount: A:0.27, C:0.00, G:0.17, T:0.56
Consensus pattern (76 bp):
TAAAATTAGTTTGTTAGTAATTTAGGATTAGGTTATAAATTGTTAGTGTTTTGTATTTTGTGATT
TTTTATTAATG
Found at i:43324773 original size:76 final size:78
Alignment explanation
Indices: 43324604--43324775 Score: 235
Period size: 76 Copynumber: 2.2 Consensus size: 78
43324594 ATAACTGTTT
* * *
43324604 TAAAATTATTTTGTTAGTAATTTAGGATTATGTTATAAATTTTTGTGTTTAGTTTAGTATTTTGT
1 TAAAATTGTTTTGTTAGTAATTTAGGATTAGGTTATAAATTTTAGTG-TTA-TTTAGTATTTTGT
43324669 GATTTTTTATTAATG
64 GATTTTTTATTAATG
* *
43324684 TAAAATTAG-TTTGTTAGTAATTTATGATTAGGTTATAAATTGTTAGTG-T-TTT-GTGTTTTGT
1 TAAAATT-GTTTTGTTAGTAATTTAGGATTAGGTTATAAATT-TTAGTGTTATTTAGTATTTTGT
43324745 GATTTTTTATTAATG
64 GATTTTTTATTAATG
43324760 TAAAATTGTTTTGTTA
1 TAAAATTGTTTTGTTA
43324776 ATTATTTTGT
Statistics
Matches: 84, Mismatches: 5, Indels: 10
0.85 0.05 0.10
Matches are distributed among these distances:
75 1 0.01
76 37 0.44
77 3 0.04
79 1 0.01
80 37 0.44
81 5 0.06
ACGTcount: A:0.27, C:0.00, G:0.16, T:0.56
Consensus pattern (78 bp):
TAAAATTGTTTTGTTAGTAATTTAGGATTAGGTTATAAATTTTAGTGTTATTTAGTATTTTGTGA
TTTTTTATTAATG
Found at i:43324793 original size:88 final size:89
Alignment explanation
Indices: 43324687--43324855 Score: 304
Period size: 88 Copynumber: 1.9 Consensus size: 89
43324677 ATTAATGTAA
43324687 AATTAGTTTGTTAGTAATTTATGATTAGGTTATAAATTGTTAGTGTTTTGTGTTTTGTGA-TTTT
1 AATTAGTTTGTTAGTAATTTATGATTAGGTTATAAATTGTTAGTGTTTTGTGTTTTGTGATTTTT
*
43324751 TTATTAATGTAAAATTGTTTTGTT
66 TTAGTAATGTAAAATTGTTTTGTT
*
43324775 AATTATTTTGTTAGTAATTTATGATTAGGTTATAAATTGTTAGTGTTTTGTGTTTTGTGATTTTT
1 AATTAGTTTGTTAGTAATTTATGATTAGGTTATAAATTGTTAGTGTTTTGTGTTTTGTGA-TTTT
43324840 TTTAGTAATGTAAAAT
65 TTTAGTAATGTAAAAT
43324856 ATTTAAAAAA
Statistics
Matches: 77, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
88 59 0.77
90 18 0.23
ACGTcount: A:0.26, C:0.00, G:0.18, T:0.56
Consensus pattern (89 bp):
AATTAGTTTGTTAGTAATTTATGATTAGGTTATAAATTGTTAGTGTTTTGTGTTTTGTGATTTTT
TTAGTAATGTAAAATTGTTTTGTT
Found at i:43325049 original size:104 final size:104
Alignment explanation
Indices: 43324777--43325067 Score: 429
Period size: 102 Copynumber: 2.8 Consensus size: 104
43324767 GTTTTGTTAA
43324777 TTATTTTGTTAGTAATTTATGATTAGG-TTATAAATTGTTAGTG--T--TTT-GTGTTTTGTGAT
1 TTATTTTGTTAGTAATTTATGATTAGGTTTATAAATTGTTAGTGTTTAGTTTAGTGTTTTGTGA-
*
43324836 TTTTTTTAGTAATGTAAAATATTTAAAAAAAATATTTTTATAG
65 -TTTTTTAGTAATGT-AAAT-TTTTAAAAAAATATTTTTATAG
*
43324879 TTATTTTGTTAGTAATTTATGATTA-GTTTATAAATTGTTTGTGTTTAGTTTAG-GATTTTGTGA
1 TTATTTTGTTAGTAATTTATGATTAGGTTTATAAATTGTTAGTGTTTAGTTTAGTG-TTTTGTGA
*
43324942 TTTTTTAGTAATGT-AATTTTTAAAAATATATTTTTATAG
65 TTTTTTAGTAATGTAAATTTTTAAAAAAATATTTTTATAG
43324981 TTATTTTGTTAGTAATTTATGATTAGGTTATATAAATTGTTAGTGTTTAGTTTAGTGTTTTGTGA
1 TTATTTTGTTAGTAATTTATGATTAGGTT-TATAAATTGTTAGTGTTTAGTTTAGTGTTTTGTGA
*
43325046 TTTTTTATTAATGTAAATTTTT
65 TTTTTTAGTAATGTAAATTTTT
43325068 TATAATGTAA
Statistics
Matches: 173, Mismatches: 5, Indels: 19
0.88 0.03 0.10
Matches are distributed among these distances:
101 1 0.01
102 85 0.49
103 6 0.03
104 46 0.27
105 22 0.13
106 4 0.02
107 9 0.05
ACGTcount: A:0.29, C:0.00, G:0.15, T:0.56
Consensus pattern (104 bp):
TTATTTTGTTAGTAATTTATGATTAGGTTTATAAATTGTTAGTGTTTAGTTTAGTGTTTTGTGAT
TTTTTAGTAATGTAAATTTTTAAAAAAATATTTTTATAG
Found at i:43325073 original size:16 final size:16
Alignment explanation
Indices: 43325045--43325081 Score: 58
Period size: 17 Copynumber: 2.3 Consensus size: 16
43325035 GTGTTTTGTG
43325045 ATTTTTTATTAATGTAA
1 ATTTTTTATTAATGT-A
43325062 ATTTTTTA-TAATGTA
1 ATTTTTTATTAATGTA
43325077 ATTTT
1 ATTTT
43325082 ATTTGATTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 6 0.30
16 6 0.30
17 8 0.40
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.62
Consensus pattern (16 bp):
ATTTTTTATTAATGTA
Found at i:43333735 original size:5 final size:5
Alignment explanation
Indices: 43333727--43333751 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
43333717 ATGCAATCAT
43333727 AAACA AAACA AAACA AAACA AAACA
1 AAACA AAACA AAACA AAACA AAACA
43333752 CGTCAGTACA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.20, G:0.00, T:0.00
Consensus pattern (5 bp):
AAACA
Found at i:43333809 original size:12 final size:12
Alignment explanation
Indices: 43333788--43333821 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
43333778 AATAGAGCAC
*
43333788 CTACTCGGGTGA
1 CTACTAGGGTGA
43333800 CTACTAGGGTGA
1 CTACTAGGGTGA
43333812 CTACTAGGGT
1 CTACTAGGGT
43333822 TTGGTGTGGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.21, C:0.21, G:0.32, T:0.26
Consensus pattern (12 bp):
CTACTAGGGTGA
Found at i:43334871 original size:132 final size:129
Alignment explanation
Indices: 43334727--43334974 Score: 318
Period size: 132 Copynumber: 1.9 Consensus size: 129
43334717 GAAAATAAGC
* *
43334727 TTACCTTTATTTTTTATTTGAAATCTTATGCATTTT-AATTTAAAAGGATATTCGATTATTTAGA
1 TTACCTTTATTTTTTATTT-AAAACTTAAGCATTTTAAATTTAAAAGGATATTCGATTATTTAGA
* *
43334791 TCCAACGGGAAAAAATTGAAACCCCGTAAGTTAGGGCACGACTTTCTCGAGTTTCTAAACATAGA
65 TCCAAC--GAAAAAATCGAAACCCCGTAAGTTAGGGCACGAC-TTCTCGAATTTCTAAACATAGA
43334856 ATA
127 ATA
* * * * *
43334859 TTACCTTTATTTTTTATTTAAAACTTAAGTATTTTAAATTTAGAAGGATGTTCGGTTGTTTAGAT
1 TTACCTTTATTTTTTATTTAAAACTTAAGCATTTTAAATTTAAAAGGATATTCGATTATTTAGAT
** * * * *
43334924 TTAACGAGAAAATCGAAACCTCGTAAGTTAGGGTATGACTTCTCGAATTTC
66 CCAACGAAAAAATCGAAACCCCGTAAGTTAGGGCACGACTTCTCGAATTTC
43334975 CAAAAACGAA
Statistics
Matches: 100, Mismatches: 15, Indels: 5
0.83 0.12 0.04
Matches are distributed among these distances:
129 11 0.11
130 29 0.29
131 13 0.13
132 47 0.47
ACGTcount: A:0.33, C:0.13, G:0.15, T:0.39
Consensus pattern (129 bp):
TTACCTTTATTTTTTATTTAAAACTTAAGCATTTTAAATTTAAAAGGATATTCGATTATTTAGAT
CCAACGAAAAAATCGAAACCCCGTAAGTTAGGGCACGACTTCTCGAATTTCTAAACATAGAATA
Found at i:43335329 original size:26 final size:26
Alignment explanation
Indices: 43335300--43335499 Score: 121
Period size: 26 Copynumber: 7.9 Consensus size: 26
43335290 AAGCGAAACA
*
43335300 AAATAATATATAAAAAAATTTGAAG-T
1 AAATAATATATAAAACAATTT-AAGAT
*
43335326 AAAT-A-GTATAAAACAATTTAAGAT
1 AAATAATATATAAAACAATTTAAGAT
* *
43335350 AAATAATATGTAAAACAA-TTAA-AA
1 AAATAATATATAAAACAATTTAAGAT
* * * * * *
43335374 AAACAATAAACAAAGCAATTTAAAAC
1 AAATAATATATAAAACAATTTAAGAT
* * * *
43335400 AAATAATACATAAGACAACTTAAAAT
1 AAATAATATATAAAACAATTTAAGAT
* *
43335426 -AAT-ATATGA-AAAAC-GTTTAAAAT
1 AAATAATAT-ATAAAACAATTTAAGAT
* * *
43335449 AAATAATATGTAAAAAGAAATTTAAAAT
1 AAATAATATAT-AAAA-CAATTTAAGAT
*
43335477 AAATAATATACAAAACAATTTAA
1 AAATAATATATAAAACAATTTAA
43335500 AAAAGAATAA
Statistics
Matches: 134, Mismatches: 28, Indels: 24
0.72 0.15 0.13
Matches are distributed among these distances:
23 10 0.07
24 41 0.31
25 18 0.13
26 44 0.33
27 4 0.03
28 17 0.13
ACGTcount: A:0.62, C:0.06, G:0.06, T:0.26
Consensus pattern (26 bp):
AAATAATATATAAAACAATTTAAGAT
Found at i:43335343 original size:24 final size:23
Alignment explanation
Indices: 43335304--43335369 Score: 71
Period size: 24 Copynumber: 2.7 Consensus size: 23
43335294 GAAACAAAAT
*
43335304 AATATATAAAAAAATTTGAAG-TA
1 AATATATAAAACAATTT-AAGATA
43335327 AATAGTATAAAACAATTTAAGATA
1 AATA-TATAAAACAATTTAAGATA
43335351 AATAATATGTAAAACAATT
1 AAT-ATA--TAAAACAATT
43335370 AAAAAAACAA
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
23 7 0.19
24 19 0.51
25 1 0.03
26 10 0.27
ACGTcount: A:0.59, C:0.03, G:0.08, T:0.30
Consensus pattern (23 bp):
AATATATAAAACAATTTAAGATA
Found at i:43335393 original size:50 final size:50
Alignment explanation
Indices: 43335336--43335501 Score: 149
Period size: 50 Copynumber: 3.3 Consensus size: 50
43335326 AAATAGTATA
* *
43335336 AAACAATTTAAGATAAATAATATGTAAAACAA-TTAAAAAAACAATAAAC
1 AAACAATTTAAAATAAATAATATGTAAAACAACTTAAAAAAATAATAAAC
* ** * * *
43335385 AAAGCAATTTAAAACAAATAATACATAAGACAACTTAAAATAATATATGAA-
1 AAA-CAATTTAAAATAAATAATATGTAAAACAACTTAAAAAAATA-ATAAAC
* * * *
43335436 AAAC-GTTTAAAATAAATAATATGTAAAAAGAAATTTAAAATAAATAATATAC
1 AAACAATTTAAAATAAATAATATGT-AAAA-CAACTTAAAA-AAATAATAAAC
43335488 AAAACAATTTAAAA
1 -AAACAATTTAAAA
43335502 AAGAATAAAT
Statistics
Matches: 89, Mismatches: 19, Indels: 13
0.74 0.16 0.11
Matches are distributed among these distances:
49 19 0.21
50 28 0.31
51 23 0.26
52 8 0.09
53 4 0.04
54 7 0.08
ACGTcount: A:0.63, C:0.07, G:0.05, T:0.25
Consensus pattern (50 bp):
AAACAATTTAAAATAAATAATATGTAAAACAACTTAAAAAAATAATAAAC
Found at i:43335452 original size:27 final size:28
Alignment explanation
Indices: 43335422--43335491 Score: 88
Period size: 28 Copynumber: 2.5 Consensus size: 28
43335412 AGACAACTTA
* **
43335422 AAATAATATATGAAAA-ACGTTTAAAAT
1 AAATAATATATAAAAAGAAATTTAAAAT
*
43335449 AAATAATATGTAAAAAGAAATTTAAAAT
1 AAATAATATATAAAAAGAAATTTAAAAT
*
43335477 AAATAATATACAAAA
1 AAATAATATATAAAA
43335492 CAATTTAAAA
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
27 14 0.39
28 22 0.61
ACGTcount: A:0.64, C:0.03, G:0.06, T:0.27
Consensus pattern (28 bp):
AAATAATATATAAAAAGAAATTTAAAAT
Found at i:43335553 original size:36 final size:36
Alignment explanation
Indices: 43335473--43335555 Score: 93
Period size: 36 Copynumber: 2.4 Consensus size: 36
43335463 AAGAAATTTA
* *
43335473 AAATAAATA-ATATACAAAACAATTTAAAAAAGAAT
1 AAATATATATATATACAAAACAATTCAAAAAAGAAT
*
43335508 AAATGATATATATATA-AAAACAATTCAAAATA-AAT
1 AAAT-ATATATATATACAAAACAATTCAAAAAAGAAT
43335543 AACA-ATATATATA
1 AA-ATATATATATA
43335556 ACAGTTTTAA
Statistics
Matches: 42, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
34 9 0.21
35 9 0.21
36 19 0.45
37 5 0.12
ACGTcount: A:0.65, C:0.06, G:0.02, T:0.27
Consensus pattern (36 bp):
AAATATATATATATACAAAACAATTCAAAAAAGAAT
Found at i:43335652 original size:25 final size:26
Alignment explanation
Indices: 43335612--43335688 Score: 88
Period size: 25 Copynumber: 3.0 Consensus size: 26
43335602 TTTAAATTAG
* *
43335612 TTTAAAATACATAATATGTGAAAAAA
1 TTTAAAATAAATAATATATGAAAAAA
*
43335638 -TTAAAATAAACAATA-AT-AAAACAA
1 TTTAAAATAAATAATATATGAAAA-AA
43335662 TTTAAAATAAATAATATATGAGAAAAA
1 TTTAAAATAAATAATATATGA-AAAAA
43335689 AAGGTTGAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 9
0.76 0.07 0.16
Matches are distributed among these distances:
23 4 0.10
24 3 0.07
25 27 0.64
26 2 0.05
27 3 0.07
28 3 0.07
ACGTcount: A:0.64, C:0.04, G:0.05, T:0.27
Consensus pattern (26 bp):
TTTAAAATAAATAATATATGAAAAAA
Found at i:43336538 original size:40 final size:40
Alignment explanation
Indices: 43336480--43336559 Score: 142
Period size: 40 Copynumber: 2.0 Consensus size: 40
43336470 CGACGGAGAG
*
43336480 GAAGGTCAATCAATAGGTAAGATTTCTAATATTTATTCAT
1 GAAGGTCAATCAACAGGTAAGATTTCTAATATTTATTCAT
*
43336520 GAAGGTCAATCGACAGGTAAGATTTCTAATATTTATTCAT
1 GAAGGTCAATCAACAGGTAAGATTTCTAATATTTATTCAT
43336560 TTATTTCGAA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.36, C:0.11, G:0.16, T:0.36
Consensus pattern (40 bp):
GAAGGTCAATCAACAGGTAAGATTTCTAATATTTATTCAT
Found at i:43337502 original size:76 final size:77
Alignment explanation
Indices: 43337368--43337752 Score: 456
Period size: 76 Copynumber: 5.0 Consensus size: 77
43337358 TTTTTTAAAT
* * * * ** * * *
43337368 AACTTTATATTTGTATAATGACTTTTTTGCCATTTTAGTTATTAA-TTTAATGTGTTTTTTTGCT
1 AACTTTGTATTTATGTAATGACTTTTTTGCCATTTCAGTTATTAATTTTAGGGTTTTTTTTTACA
43337432 ATTTAAATAGTC
66 ATTTAAATAGTC
* ** * * *
43337444 AACTTTGTATTTATGTAATTACTTTTTCACCATTTCAGTTATTAA-TTTATGGTTTTTTTATGCA
1 AACTTTGTATTTATGTAATGACTTTTTTGCCATTTCAGTTATTAATTTTAGGGTTTTTTTTTACA
43337508 ATTTAAATAGTC
66 ATTTAAATAGTC
*
43337520 AACTTTGTATTTATGTAATGACTTTTTTGCCATTTCATTTATTAATTTTAGGGTTTTTTTTGTTT
1 AACTTTGTATTTATGTAATGACTTTTTTGCCATTTCAGTTATTAATTTTAGGG-------T-TTT
*
43337585 TTTTTACAATTTACATAGTC
58 TTTTTACAATTTAAATAGTC
* *
43337605 AACTTTGTATTTATGTAATGACTTTTTCGCTATTTCAGTTATTAATTTTAGGGTTTTTTTTTACA
1 AACTTTGTATTTATGTAATGACTTTTTTGCCATTTCAGTTATTAATTTTAGGGTTTTTTTTTACA
43337670 ATTTAAATAGTC
66 ATTTAAATAGTC
* ** *
43337682 AACTTTGTATTTATGTAATGACTTTTTTGCTATTTCAACTATTAATTTTAAGG--TTTTTTT-CA
1 AACTTTGTATTTATGTAATGACTTTTTTGCCATTTCAGTTATTAATTTTAGGGTTTTTTTTTACA
43337744 ATTTAAATA
66 ATTTAAATA
43337753 ATAAAATTTG
Statistics
Matches: 272, Mismatches: 28, Indels: 20
0.85 0.09 0.06
Matches are distributed among these distances:
74 11 0.04
75 7 0.03
76 105 0.39
77 77 0.28
78 1 0.00
84 1 0.00
85 70 0.26
ACGTcount: A:0.26, C:0.09, G:0.10, T:0.55
Consensus pattern (77 bp):
AACTTTGTATTTATGTAATGACTTTTTTGCCATTTCAGTTATTAATTTTAGGGTTTTTTTTTACA
ATTTAAATAGTC
Found at i:43337610 original size:85 final size:85
Alignment explanation
Indices: 43337495--43337741 Score: 357
Period size: 77 Copynumber: 3.0 Consensus size: 85
43337485 TTAATTTATG
* * *
43337495 GTTTTTTTATGCAATTTAAATAGTCAACTTTGTATTTATGTAATGACTTTTTTGCCATTTCATTT
1 GTTTTTTT-TACAATTTAAATAGTCAACTTTGTATTTATGTAATGACTTTTTTGCTATTTCAATT
43337560 ATTAATTTTAGGGTTTTTTTT
65 ATTAATTTTAGGGTTTTTTTT
* * *
43337581 GTTTTTTTTACAATTTACATAGTCAACTTTGTATTTATGTAATGACTTTTTCGCTATTTCAGTTA
1 GTTTTTTTTACAATTTAAATAGTCAACTTTGTATTTATGTAATGACTTTTTTGCTATTTCAATTA
43337646 TTAATTTTAGGG-------T
66 TTAATTTTAGGGTTTTTTTT
*
43337659 -TTTTTTTTACAATTTAAATAGTCAACTTTGTATTTATGTAATGACTTTTTTGCTATTTCAACTA
1 GTTTTTTTTACAATTTAAATAGTCAACTTTGTATTTATGTAATGACTTTTTTGCTATTTCAATTA
*
43337723 TTAATTTTAAGGTTTTTTT
66 TTAATTTTAGGGTTTTTTT
43337742 CAATTTAAAT
Statistics
Matches: 144, Mismatches: 10, Indels: 16
0.85 0.06 0.09
Matches are distributed among these distances:
77 71 0.49
78 1 0.01
85 64 0.44
86 8 0.06
ACGTcount: A:0.25, C:0.09, G:0.11, T:0.55
Consensus pattern (85 bp):
GTTTTTTTTACAATTTAAATAGTCAACTTTGTATTTATGTAATGACTTTTTTGCTATTTCAATTA
TTAATTTTAGGGTTTTTTTT
Found at i:43337631 original size:43 final size:43
Alignment explanation
Indices: 43337497--43337631 Score: 98
Period size: 42 Copynumber: 3.1 Consensus size: 43
43337487 AATTTATGGT
*
43337497 TTTTTTATGCAATTTAAATAGTCAACTTTGTATTTATGTAATGAC
1 TTTTTTA--CAATTTACATAGTCAACTTTGTATTTATGTAATGAC
* * * * ** ** **
43337542 TTTTTTGCCATTT-CATTTA-TTAATTTTAGGGTTT-T-TTTTGTT
1 TTTTTTACAATTTACA--TAGTCAACTTT-GTATTTATGTAATGAC
43337584 TTTTTTACAATTTACATAGTCAACTTTGTATTTATGTAATGAC
1 TTTTTTACAATTTACATAGTCAACTTTGTATTTATGTAATGAC
43337627 TTTTT
1 TTTTT
43337632 CGCTATTTCA
Statistics
Matches: 62, Mismatches: 21, Indels: 16
0.63 0.21 0.16
Matches are distributed among these distances:
41 6 0.10
42 22 0.35
43 22 0.35
44 6 0.10
45 6 0.10
ACGTcount: A:0.24, C:0.09, G:0.10, T:0.56
Consensus pattern (43 bp):
TTTTTTACAATTTACATAGTCAACTTTGTATTTATGTAATGAC
Found at i:43337727 original size:162 final size:161
Alignment explanation
Indices: 43337422--43337741 Score: 514
Period size: 162 Copynumber: 2.0 Consensus size: 161
43337412 ATTTAATGTG
* * *
43337422 TTTTTTTGCTATTTAAATAGTCAACTTTGTATTTATGTAATTACTTTTTCACCATTTCAGTTATT
1 TTTTTTTACAATTTAAATAGTCAACTTTGTATTTATGTAATGACTTTTTCACCATTTCAGTTATT
* *
43337487 AATTTATGGTTTTTTTATGCAATTTAAATAGTCAACTTTGTATTTATGTAATGACTTTTTTGCCA
66 AATTTAGGGTTTTTTTATACAATTTAAATAGTCAACTTTGTATTTATGTAATGACTTTTTTGCCA
** *
43337552 TTTCATTTATTAATTTTAGGGTTTTTTTTGT
131 TTTCAACTATTAATTTTAAGGTTTTTTTTGT
* * *
43337583 TTTTTTTACAATTTACATAGTCAACTTTGTATTTATGTAATGACTTTTTCGCTATTTCAGTTATT
1 TTTTTTTACAATTTAAATAGTCAACTTTGTATTTATGTAATGACTTTTTCACCATTTCAGTTATT
* *
43337648 AATTTTAGGGTTTTTTTTTACAATTTAAATAGTCAACTTTGTATTTATGTAATGACTTTTTTGCT
66 AA-TTTAGGGTTTTTTTATACAATTTAAATAGTCAACTTTGTATTTATGTAATGACTTTTTTGCC
43337713 ATTTCAACTATTAATTTTAAGGTTTTTTT
130 ATTTCAACTATTAATTTTAAGGTTTTTTT
43337742 CAATTTAAAT
Statistics
Matches: 145, Mismatches: 13, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
161 61 0.42
162 84 0.58
ACGTcount: A:0.25, C:0.09, G:0.10, T:0.55
Consensus pattern (161 bp):
TTTTTTTACAATTTAAATAGTCAACTTTGTATTTATGTAATGACTTTTTCACCATTTCAGTTATT
AATTTAGGGTTTTTTTATACAATTTAAATAGTCAACTTTGTATTTATGTAATGACTTTTTTGCCA
TTTCAACTATTAATTTTAAGGTTTTTTTTGT
Found at i:43337771 original size:77 final size:76
Alignment explanation
Indices: 43337581--43337768 Score: 247
Period size: 77 Copynumber: 2.5 Consensus size: 76
43337571 GGTTTTTTTT
* * * * **
43337581 GTTTTTTTTACAATTTACATAGTCAACTTTGTATTTATGTAATGACTTTTTCGCTATTTCAGTTA
1 GTTTTTTTTACAATTTAAATAATAAAATTTGTATTTATGTAATGACTTTTTCGCTATTTCAACTA
*
43337646 TTAATTTTAGG
66 TTAATTTTAAG
* * * *
43337657 GTTTTTTTTTACAATTTAAATAGTCAACTTTGTATTTATGTAATGACTTTTTTGCTATTTCAACT
1 G-TTTTTTTTACAATTTAAATAATAAAATTTGTATTTATGTAATGACTTTTTCGCTATTTCAACT
43337722 ATTAATTTTAAG
65 ATTAATTTTAAG
43337734 G-TTTTTTT-CAATTTAAATAATAAAATTTGT-TTTAT
1 GTTTTTTTTACAATTTAAATAATAAAATTTGTATTTAT
43337769 TTACATAAAA
Statistics
Matches: 103, Mismatches: 8, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
73 5 0.05
74 19 0.18
75 7 0.07
76 1 0.01
77 71 0.69
ACGTcount: A:0.28, C:0.09, G:0.10, T:0.54
Consensus pattern (76 bp):
GTTTTTTTTACAATTTAAATAATAAAATTTGTATTTATGTAATGACTTTTTCGCTATTTCAACTA
TTAATTTTAAG
Found at i:43341009 original size:3 final size:3
Alignment explanation
Indices: 43341001--43341041 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
43340991 CTTTAGCAAA
43341001 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
43341042 ACATTAAATG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:43341931 original size:17 final size:17
Alignment explanation
Indices: 43341909--43341945 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
43341899 TAGGTGAAGA
43341909 TAAGGATTTGAATTTAC
1 TAAGGATTTGAATTTAC
43341926 TAAGGATTTGAATTTAC
1 TAAGGATTTGAATTTAC
43341943 TAA
1 TAA
43341946 AAATAGGTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.38, C:0.05, G:0.16, T:0.41
Consensus pattern (17 bp):
TAAGGATTTGAATTTAC
Found at i:43343652 original size:3 final size:3
Alignment explanation
Indices: 43343644--43343696 Score: 106
Period size: 3 Copynumber: 17.7 Consensus size: 3
43343634 ACTAACATAG
43343644 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
43343692 AAT AA
1 AAT AA
43343697 AATCTAAACT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:43343737 original size:16 final size:17
Alignment explanation
Indices: 43343716--43343748 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
43343706 TTTGTAATAC
43343716 ATTAAAAT-AATAAACA
1 ATTAAAATAAATAAACA
43343732 ATTAAAATAAATAAACA
1 ATTAAAATAAATAAACA
43343749 CAAAGGTGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.70, C:0.06, G:0.00, T:0.24
Consensus pattern (17 bp):
ATTAAAATAAATAAACA
Found at i:43343998 original size:15 final size:15
Alignment explanation
Indices: 43343980--43344018 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
43343970 ATGTGTAAGT
43343980 AAATAATAATGGATA-
1 AAATAATAAT-GATAG
43343995 AAATAATAATGATAG
1 AAATAATAATGATAG
*
43344010 TAATAATAA
1 AAATAATAA
43344019 ATAATATATA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 4 0.18
15 18 0.82
ACGTcount: A:0.62, C:0.00, G:0.10, T:0.28
Consensus pattern (15 bp):
AAATAATAATGATAG
Found at i:43344104 original size:12 final size:12
Alignment explanation
Indices: 43344089--43344113 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
43344079 AATAAATAAA
43344089 TAAATTAAATAT
1 TAAATTAAATAT
43344101 TAAATTAAATAT
1 TAAATTAAATAT
43344113 T
1 T
43344114 TAATAAAACA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (12 bp):
TAAATTAAATAT
Found at i:43350564 original size:21 final size:21
Alignment explanation
Indices: 43350540--43350584 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
43350530 TTCTGTTCTG
*
43350540 CTCTGCCTCCCTCGCTGCTGC
1 CTCTGCCTCCCGCGCTGCTGC
43350561 CTCTGCCTCCCGCGCTGCTGC
1 CTCTGCCTCCCGCGCTGCTGC
43350582 CTC
1 CTC
43350585 CGCCCTAAGT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.00, C:0.53, G:0.20, T:0.27
Consensus pattern (21 bp):
CTCTGCCTCCCGCGCTGCTGC
Found at i:43354038 original size:9 final size:9
Alignment explanation
Indices: 43354024--43354073 Score: 50
Period size: 9 Copynumber: 5.6 Consensus size: 9
43354014 TATTTATGTT
43354024 TTATGTAAG
1 TTATGTAAG
43354033 TTATGT-AG
1 TTATGTAAG
43354041 ATTATGTAAG
1 -TTATGTAAG
*
43354051 GTATGT-AG
1 TTATGTAAG
*
43354059 ATTATGTAAA
1 -TTATGTAAG
43354069 TTATG
1 TTATG
43354074 AAATTTGAAC
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
8 4 0.12
9 27 0.79
10 3 0.09
ACGTcount: A:0.34, C:0.00, G:0.22, T:0.44
Consensus pattern (9 bp):
TTATGTAAG
Found at i:43354047 original size:18 final size:18
Alignment explanation
Indices: 43354024--43354073 Score: 82
Period size: 18 Copynumber: 2.8 Consensus size: 18
43354014 TATTTATGTT
43354024 TTATGTAAGTTATGTAGA
1 TTATGTAAGTTATGTAGA
*
43354042 TTATGTAAGGTATGTAGA
1 TTATGTAAGTTATGTAGA
*
43354060 TTATGTAAATTATG
1 TTATGTAAGTTATG
43354074 AAATTTGAAC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.34, C:0.00, G:0.22, T:0.44
Consensus pattern (18 bp):
TTATGTAAGTTATGTAGA
Found at i:43354150 original size:9 final size:9
Alignment explanation
Indices: 43354136--43354252 Score: 99
Period size: 9 Copynumber: 12.3 Consensus size: 9
43354126 ATGTATTAGT
43354136 TAAGTTATG
1 TAAGTTATG
43354145 TAAGTTGTTATG
1 TAA---GTTATG
*
43354157 TACGTTATG
1 TAAGTTATG
* *
43354166 TGAGTAATG
1 TAAGTTATG
*
43354175 TAAATTATG
1 TAAGTTATG
43354184 TAAGTTATG
1 TAAGTTATG
*
43354193 TGAGTTATG
1 TAAGTTATG
*
43354202 TAAGTTGTTACG
1 TAA---GTTATG
*
43354214 TAAATTATG
1 TAAGTTATG
*
43354223 TAAGTTATA
1 TAAGTTATG
*
43354232 TGAGTTATG
1 TAAGTTATG
43354241 TAAGTTATG
1 TAAGTTATG
43354250 TAA
1 TAA
43354253 TTTTTTTAAG
Statistics
Matches: 84, Mismatches: 18, Indels: 12
0.74 0.16 0.11
Matches are distributed among these distances:
9 68 0.81
12 16 0.19
ACGTcount: A:0.32, C:0.02, G:0.22, T:0.44
Consensus pattern (9 bp):
TAAGTTATG
Found at i:43354222 original size:57 final size:57
Alignment explanation
Indices: 43354138--43354250 Score: 154
Period size: 57 Copynumber: 2.0 Consensus size: 57
43354128 GTATTAGTTA
* ** * *
43354138 AGTTATGTAAGTTGTTATGTACGTTATGTGAGTAATGTAAATTATGTAAGTTATGTG
1 AGTTATGTAAGTTGTTACGTAAATTATGTAAGTAATATAAATTATGTAAGTTATGTG
* * *
43354195 AGTTATGTAAGTTGTTACGTAAATTATGTAAGTTATATGAGTTATGTAAGTTATGT
1 AGTTATGTAAGTTGTTACGTAAATTATGTAAGTAATATAAATTATGTAAGTTATGT
43354251 AATTTTTTTA
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
57 48 1.00
ACGTcount: A:0.31, C:0.02, G:0.23, T:0.44
Consensus pattern (57 bp):
AGTTATGTAAGTTGTTACGTAAATTATGTAAGTAATATAAATTATGTAAGTTATGTG
Found at i:43355245 original size:10 final size:10
Alignment explanation
Indices: 43355230--43355258 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
43355220 AATAAAATTA
43355230 ATTCATACTT
1 ATTCATACTT
43355240 ATTCATACTT
1 ATTCATACTT
43355250 ATTCATACT
1 ATTCATACT
43355259 CCACTCTCAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.31, C:0.21, G:0.00, T:0.48
Consensus pattern (10 bp):
ATTCATACTT
Found at i:43355754 original size:183 final size:183
Alignment explanation
Indices: 43355446--43355814 Score: 729
Period size: 183 Copynumber: 2.0 Consensus size: 183
43355436 CCTAGAACAG
43355446 ATGTAAGATTATAAGAGTAGCACCAAATATATTTCAGTTTAAGCAAATATAAAAACTTTATCTAT
1 ATGTAAGATTATAAGAGTAGCACCAAATATATTTCAGTTTAAGCAAATATAAAAACTTTATCTAT
43355511 ATCAGTACCAAATATTAATTCGAAGATTAAATGGCAGCTTCAGTTGAACCAATAGTTGCAGGAGG
66 ATCAGTACCAAATATTAATTCGAAGATTAAATGGCAGCTTCAGTTGAACCAATAGTTGCAGGAGG
*
43355576 AGCAGGAAGCAGTAACTGAAATATATACAACATTAATTCACTAATACAGACAC
131 AGCAGGAAGCAGTAACTGAAATACATACAACATTAATTCACTAATACAGACAC
43355629 ATGTAAGATTATAAGAGTAGCACCAAATATATTTCAGTTTAAGCAAATATAAAAACTTTATCTAT
1 ATGTAAGATTATAAGAGTAGCACCAAATATATTTCAGTTTAAGCAAATATAAAAACTTTATCTAT
43355694 ATCAGTACCAAATATTAATTCGAAGATTAAATGGCAGCTTCAGTTGAACCAATAGTTGCAGGAGG
66 ATCAGTACCAAATATTAATTCGAAGATTAAATGGCAGCTTCAGTTGAACCAATAGTTGCAGGAGG
43355759 AGCAGGAAGCAGTAACTGAAATACATACAACATTAATTCACTAATACAGACAC
131 AGCAGGAAGCAGTAACTGAAATACATACAACATTAATTCACTAATACAGACAC
43355812 ATG
1 ATG
43355815 GAACTATATC
Statistics
Matches: 185, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
183 185 1.00
ACGTcount: A:0.43, C:0.15, G:0.15, T:0.27
Consensus pattern (183 bp):
ATGTAAGATTATAAGAGTAGCACCAAATATATTTCAGTTTAAGCAAATATAAAAACTTTATCTAT
ATCAGTACCAAATATTAATTCGAAGATTAAATGGCAGCTTCAGTTGAACCAATAGTTGCAGGAGG
AGCAGGAAGCAGTAACTGAAATACATACAACATTAATTCACTAATACAGACAC
Found at i:43355904 original size:14 final size:13
Alignment explanation
Indices: 43355885--43355914 Score: 51
Period size: 14 Copynumber: 2.2 Consensus size: 13
43355875 CAATATAATT
43355885 TTACTTCATATATA
1 TTACTTCATATA-A
43355899 TTACTTCATATAA
1 TTACTTCATATAA
43355912 TTA
1 TTA
43355915 TTATAGTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.25
14 12 0.75
ACGTcount: A:0.37, C:0.13, G:0.00, T:0.50
Consensus pattern (13 bp):
TTACTTCATATAA
Found at i:43357203 original size:37 final size:37
Alignment explanation
Indices: 43357125--43357245 Score: 152
Period size: 37 Copynumber: 3.2 Consensus size: 37
43357115 CTATGAAGTA
*
43357125 GATGCACGGGGCGAAGGAGATGGAGGCCGAGATGGGTTGC
1 GATGCACGGGGCGAAGGCGATGGA-G--GAGATGGGTTGC
* * *
43357165 GATGAACGGTGCGAAGGCGATGGAGGAGATGGTTTGC
1 GATGCACGGGGCGAAGGCGATGGAGGAGATGGGTTGC
* *
43357202 GATGCACGGGGAGAAGGCGATGGAGGAGATGTGTTGC
1 GATGCACGGGGCGAAGGCGATGGAGGAGATGGGTTGC
*
43357239 AATGCAC
1 GATGCAC
43357246 AGGGAGATTT
Statistics
Matches: 71, Mismatches: 10, Indels: 3
0.85 0.12 0.04
Matches are distributed among these distances:
37 49 0.69
39 1 0.01
40 21 0.30
ACGTcount: A:0.25, C:0.13, G:0.46, T:0.16
Consensus pattern (37 bp):
GATGCACGGGGCGAAGGCGATGGAGGAGATGGGTTGC
Found at i:43357322 original size:24 final size:25
Alignment explanation
Indices: 43357272--43357322 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 25
43357262 AAACTTACCG
* * *
43357272 ATTTGGGGAATTTGGGGATTTCTGA
1 ATTTAGGGAAATTGGGGATTTCAGA
43357297 ATTTAGGGAAATT-GGGATTTCAGA
1 ATTTAGGGAAATTGGGGATTTCAGA
43357321 AT
1 AT
43357323 CAGGGCAAAC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
24 12 0.52
25 11 0.48
ACGTcount: A:0.27, C:0.04, G:0.31, T:0.37
Consensus pattern (25 bp):
ATTTAGGGAAATTGGGGATTTCAGA
Found at i:43362250 original size:47 final size:47
Alignment explanation
Indices: 43362184--43362616 Score: 652
Period size: 47 Copynumber: 9.1 Consensus size: 47
43362174 GAAATGATAG
*
43362184 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATACGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
*
43362231 TAGGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
*
43362278 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGAGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
43362325 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTGA
*
43362374 TAGGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTGA
* * *
43362423 TAGGGCCTAATGGCCGACGTGATGAATGTGAAAGTGTATATACGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
43362470 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
* *
43362517 TAAGGCCTAATGGTCGATGTGATGAATGTGGAAGTGTATATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTGA
* * * * * * *
43362566 -CAGGGCTGAGTGGCCAACGTGATGGATGTGAAAGTGTATAAATGTGA
1 TAAGGCCT-AATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
43362613 TAAG
1 TAAG
43362617 TCCCGAAGGG
Statistics
Matches: 357, Mismatches: 23, Indels: 11
0.91 0.06 0.03
Matches are distributed among these distances:
47 224 0.63
48 7 0.02
49 126 0.35
ACGTcount: A:0.31, C:0.09, G:0.31, T:0.29
Consensus pattern (47 bp):
TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
Found at i:43362512 original size:192 final size:192
Alignment explanation
Indices: 43362187--43362614 Score: 713
Period size: 192 Copynumber: 2.2 Consensus size: 192
43362177 ATGATAGTAA
* *
43362187 GGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATACGTGATAGGGCCTAATGGCCGATG
1 GGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAGGGCCTAATGGCCGACG
*
43362250 TGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGT
66 TGATGAATGTGAAAGTGTATATACGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGT
*
43362315 ATATATGAGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAG
131 ATATATGAGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGACAG
43362377 GGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAGGGCCTAATGGCCGACG
1 GGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAGGGCCTAATGGCCGACG
43362442 TGATGAATGTGAAAGTGTATATACGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGT
66 TGATGAATGTGAAAGTGTATATACGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGT
* * *
43362507 ATATATGTGATAAGGCCTAATGGTCGATGTGATGAATGTGGAAGTGTATATATATGTGACAG
131 ATATATGAGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGACAG
* * * *
43362569 GG-CTGAGTGGCCAACGTGATGGATGTGAAAGTGTATA-A-ATGTGATA
1 GGCCT-AATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATA
43362615 AGTCCCGAAG
Statistics
Matches: 224, Mismatches: 11, Indels: 6
0.93 0.05 0.02
Matches are distributed among these distances:
190 41 0.18
191 3 0.01
192 180 0.80
ACGTcount: A:0.31, C:0.09, G:0.31, T:0.29
Consensus pattern (192 bp):
GGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAGGGCCTAATGGCCGACG
TGATGAATGTGAAAGTGTATATACGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGT
ATATATGAGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGACAG
Found at i:43362613 original size:143 final size:142
Alignment explanation
Indices: 43362184--43362616 Score: 681
Period size: 143 Copynumber: 3.0 Consensus size: 142
43362174 GAAATGATAG
*
43362184 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATACGTGATAGGGCCTAATGGCCGAT
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAGGGCCTAATGGCCGAT
* *
43362249 GTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAG
66 GTGATGAATGTGAAAGTGTATATATATGTGA-AAGGGCTAATGGCCGACGTGATGAATGTGAAAG
*
43362312 TGTATATATGAGA
130 TGTATATATGTGA
43362325 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAGGGCCTAATGGCCG
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTGATAGGGCCTAATGGCCG
*
43362390 ATGTGATGAATGTGAAAGTGTATATATATGTGATAGGGCCTAATGGCCGACGTGATGAATGTGAA
64 ATGTGATGAATGTGAAAGTGTATATATATGTGAAAGGG-CTAATGGCCGACGTGATGAATGTGAA
*
43362455 AGTGTATATACGTGA
128 AGTGTATATATGTGA
* *
43362470 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGTCGAT
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAGGGCCTAATGGCCGAT
* * * * *
43362535 GTGATGAATGTGGAAGTGTATATATATGTGACAGGGCTGAGTGGCCAACGTGATGGATGTGAAAG
66 GTGATGAATGTGAAAGTGTATATATATGTGAAAGGGCT-AATGGCCGACGTGATGAATGTGAAAG
*
43362600 TGTATAAATGTGA
130 TGTATATATGTGA
43362613 TAAG
1 TAAG
43362617 TCCCGAAGGG
Statistics
Matches: 271, Mismatches: 15, Indels: 10
0.92 0.05 0.03
Matches are distributed among these distances:
141 36 0.13
142 2 0.01
143 145 0.54
144 3 0.01
145 85 0.31
ACGTcount: A:0.31, C:0.09, G:0.31, T:0.29
Consensus pattern (142 bp):
TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAGGGCCTAATGGCCGAT
GTGATGAATGTGAAAGTGTATATATATGTGAAAGGGCTAATGGCCGACGTGATGAATGTGAAAGT
GTATATATGTGA
Found at i:43362791 original size:37 final size:37
Alignment explanation
Indices: 43362735--43362813 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
43362725 CCGAGCTCTA
* * *
43362735 AAGACCCGATGACTACGTGTGGGGATTTTGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
*
43362772 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
43362809 AAGAC
1 AAGAC
43362814 TTCGTAATAA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.24, C:0.19, G:0.32, T:0.25
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
Found at i:43365656 original size:15 final size:14
Alignment explanation
Indices: 43365638--43365676 Score: 53
Period size: 13 Copynumber: 2.8 Consensus size: 14
43365628 CATTTAATTA
43365638 TATTAGTATTTTTT
1 TATTAGTATTTTTT
*
43365652 CTATTAGGA-TTTTT
1 -TATTAGTATTTTTT
43365666 TATTAGTATTT
1 TATTAGTATTT
43365677 ATTAGTATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
13 7 0.33
14 7 0.33
15 7 0.33
ACGTcount: A:0.23, C:0.03, G:0.10, T:0.64
Consensus pattern (14 bp):
TATTAGTATTTTTT
Found at i:43372297 original size:16 final size:18
Alignment explanation
Indices: 43372276--43372309 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
43372266 TGTGGATTTA
43372276 GGTTTTTA-AAAA-AATT
1 GGTTTTTATAAAATAATT
43372292 GGTTTTTATAAAATAATT
1 GGTTTTTATAAAATAATT
43372310 TGTAAAATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.50
17 4 0.25
18 4 0.25
ACGTcount: A:0.41, C:0.00, G:0.12, T:0.47
Consensus pattern (18 bp):
GGTTTTTATAAAATAATT
Found at i:43372317 original size:12 final size:12
Alignment explanation
Indices: 43372300--43372333 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
43372290 TTGGTTTTTA
43372300 TAAAATAATTTG
1 TAAAATAATTTG
43372312 TAAAATAATTTG
1 TAAAATAATTTG
43372324 --AAATAATTTG
1 TAAAATAATTTG
43372334 GATAACAAGT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 10 0.45
12 12 0.55
ACGTcount: A:0.50, C:0.00, G:0.09, T:0.41
Consensus pattern (12 bp):
TAAAATAATTTG
Found at i:43378454 original size:20 final size:20
Alignment explanation
Indices: 43378429--43378467 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
43378419 GGCCGTGTGA
*
43378429 GTCACATGGGCGTGTGGGCG
1 GTCACACGGGCGTGTGGGCG
43378449 GTCACACGGGCGTGTGGGC
1 GTCACACGGGCGTGTGGGC
43378468 TCGATTTGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.10, C:0.23, G:0.49, T:0.18
Consensus pattern (20 bp):
GTCACACGGGCGTGTGGGCG
Found at i:43378858 original size:40 final size:40
Alignment explanation
Indices: 43378794--43378872 Score: 113
Period size: 40 Copynumber: 2.0 Consensus size: 40
43378784 GTACGGTACC
* *
43378794 ACTTGGTGTGTAGGGTTGAATGGGTTGATTCTATCCCCAT
1 ACTTGGTGTGCAGGGCTGAATGGGTTGATTCTATCCCCAT
** *
43378834 ACTTGGTGTGCAGGGCTGGGTGGGTTGATTTTATCCCCA
1 ACTTGGTGTGCAGGGCTGAATGGGTTGATTCTATCCCCA
43378873 CATGGTGTGT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.15, C:0.16, G:0.33, T:0.35
Consensus pattern (40 bp):
ACTTGGTGTGCAGGGCTGAATGGGTTGATTCTATCCCCAT
Found at i:43379804 original size:22 final size:22
Alignment explanation
Indices: 43379774--43379847 Score: 55
Period size: 22 Copynumber: 3.3 Consensus size: 22
43379764 ACACCAATCA
43379774 TCACATACTTGAATTTATCAGAT
1 TCAC-TACTTGAATTTATCAGAT
***
43379797 TCACTACTTAGACACCAATC--A-
1 TCACTACTT-GA-ATTTATCAGAT
*
43379818 TCATATACTTGAATTTATCAGAT
1 TCA-CTACTTGAATTTATCAGAT
43379841 TCACTAC
1 TCACTAC
43379848 CAATATACAT
Statistics
Matches: 37, Mismatches: 8, Indels: 13
0.64 0.14 0.22
Matches are distributed among these distances:
20 4 0.11
21 5 0.14
22 15 0.41
23 9 0.24
24 4 0.11
ACGTcount: A:0.35, C:0.23, G:0.07, T:0.35
Consensus pattern (22 bp):
TCACTACTTGAATTTATCAGAT
Done.