Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr12 103066607
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: 103066607
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Warning! 238 characters in sequence are not A, C, G, or T
File 79 of 345
Found at i:21781432 original size:27 final size:27
Alignment explanation
Indices: 21781395--21781661 Score: 252
Period size: 27 Copynumber: 10.0 Consensus size: 27
21781385 ATATATACAT
*
21781395 CACAT-AGGGCAAAACAGTCATCTTAC
1 CACATAAGGGCAAAACAGTCATTTTAC
* * * *
21781421 CACATAAGGGCAGAACAATTATTTTAT
1 CACATAAGGGCAAAACAGTCATTTTAC
* * *
21781448 TACATAAGGGCTAAACAATCATTTTAC
1 CACATAAGGGCAAAACAGTCATTTTAC
* * * *
21781475 CACTTAAGGGAAAAATAGTTATTTTAC
1 CACATAAGGGCAAAACAGTCATTTTAC
*
21781502 CACATAAGGG-AAGAACAGTCATTTTAT
1 CACATAAGGGCAA-AACAGTCATTTTAC
* * *
21781529 CACATAAAGGCGAAACAATCA-TTTAC
1 CACATAAGGGCAAAACAGTCATTTTAC
* * * *
21781555 CACTTAAGGGCAAAATAGTTATTCTAC
1 CACATAAGGGCAAAACAGTCATTTTAC
* *
21781582 CACATAAGGGCAAAATAGTCATTTTAT
1 CACATAAGGGCAAAACAGTCATTTTAC
* *
21781609 CACATAAGGGTAAAATAGTCATTTTAC
1 CACATAAGGGCAAAACAGTCATTTTAC
* * **
21781636 CACTTAAGGGTAAAACAACCATTTTA
1 CACATAAGGGCAAAACAGTCATTTTA
21781662 TCAATTAGGG
Statistics
Matches: 195, Mismatches: 42, Indels: 7
0.80 0.17 0.03
Matches are distributed among these distances:
26 26 0.13
27 168 0.86
28 1 0.01
ACGTcount: A:0.41, C:0.18, G:0.14, T:0.27
Consensus pattern (27 bp):
CACATAAGGGCAAAACAGTCATTTTAC
Found at i:21781633 original size:134 final size:134
Alignment explanation
Indices: 21781393--21781664 Score: 332
Period size: 134 Copynumber: 2.0 Consensus size: 134
21781383 ATATATATAC
* * * * **
21781393 ATCACATAGGGCAAAACAGTCATCTTACCACATAAGGGCAGAACAATTATTTTATTACATAAGGG
1 ATCACATAAGGCAAAACAATCATCTTACCACATAAGGGCAAAACAATTATTCTACCACATAAGGG
* * * **
21781458 CTAAACAATCATTTTACCACTTAAGGGAAAAATAGTTATTTTACCACATAAGGG-AAGAACAGTC
66 CAAAACAATCATTTTACCACATAAGGGAAAAATAGTCATTTTACCACATAAGGGTAA-AACAACC
21781522 ATTTT
130 ATTTT
* * * *
21781527 ATCACATAAAGGCGAAACAATCAT-TTACCACTTAAGGGCAAAATAGTTATTCTACCACATAAGG
1 ATCACAT-AAGGCAAAACAATCATCTTACCACATAAGGGCAAAACAATTATTCTACCACATAAGG
* * * * *
21781591 GCAAAATAGTCATTTTATCACATAAGGGTAAAATAGTCATTTTACCACTTAAGGGTAAAACAACC
65 GCAAAACAATCATTTTACCACATAAGGGAAAAATAGTCATTTTACCACATAAGGGTAAAACAACC
21781656 ATTTT
130 ATTTT
21781661 ATCA
1 ATCA
21781665 ATTAGGGGTT
Statistics
Matches: 116, Mismatches: 20, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
134 101 0.87
135 15 0.13
ACGTcount: A:0.41, C:0.18, G:0.14, T:0.28
Consensus pattern (134 bp):
ATCACATAAGGCAAAACAATCATCTTACCACATAAGGGCAAAACAATTATTCTACCACATAAGGG
CAAAACAATCATTTTACCACATAAGGGAAAAATAGTCATTTTACCACATAAGGGTAAAACAACCA
TTTT
Found at i:21781673 original size:27 final size:27
Alignment explanation
Indices: 21781601--21781673 Score: 76
Period size: 27 Copynumber: 2.7 Consensus size: 27
21781591 GCAAAATAGT
* **
21781601 CATTTTATCACA-TAAGGGTAAAATAGT
1 CATTTTATCA-ATTAAGGGTAAAACAAC
* *
21781628 CATTTTACCACTTAAGGGTAAAACAAC
1 CATTTTATCAATTAAGGGTAAAACAAC
*
21781655 CATTTTATCAATTAGGGGT
1 CATTTTATCAATTAAGGGT
21781674 TGAGGCACAC
Statistics
Matches: 37, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.33
Consensus pattern (27 bp):
CATTTTATCAATTAAGGGTAAAACAAC
Found at i:21786936 original size:24 final size:24
Alignment explanation
Indices: 21786891--21786974 Score: 91
Period size: 24 Copynumber: 3.5 Consensus size: 24
21786881 CAGATCGTTT
21786891 GAGCTTACTGATATTTCAGCTCATAA
1 GAGCTTACTG-T-TTTCAGCTCATAA
* *
21786917 GAGCTTACTGTTTTCAGCTCGTCA
1 GAGCTTACTGTTTTCAGCTCATAA
*
21786941 GAGCTTACCG-TTTCAGCTCA-ATA
1 GAGCTTACTGTTTTCAGCTCATA-A
*
21786964 GATCTTACTGT
1 GAGCTTACTGT
21786975 CCATCAGCTC
Statistics
Matches: 49, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
23 18 0.37
24 20 0.41
25 1 0.02
26 10 0.20
ACGTcount: A:0.24, C:0.23, G:0.18, T:0.36
Consensus pattern (24 bp):
GAGCTTACTGTTTTCAGCTCATAA
Found at i:21787194 original size:35 final size:35
Alignment explanation
Indices: 21787155--21787225 Score: 124
Period size: 35 Copynumber: 2.0 Consensus size: 35
21787145 CGTCGTGCCC
*
21787155 AGCGTCGTGCCCACGACTCTAGCCGCGACAGAATA
1 AGCGTCGTGCCCACGACTCCAGCCGCGACAGAATA
*
21787190 AGCGTCGTGCCCACGACTCCAGCCGTGACAGAATA
1 AGCGTCGTGCCCACGACTCCAGCCGCGACAGAATA
21787225 A
1 A
21787226 AAAAACTGCA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.27, C:0.34, G:0.25, T:0.14
Consensus pattern (35 bp):
AGCGTCGTGCCCACGACTCCAGCCGCGACAGAATA
Found at i:21787968 original size:24 final size:25
Alignment explanation
Indices: 21787941--21787989 Score: 73
Period size: 24 Copynumber: 2.0 Consensus size: 25
21787931 CAAATCATCA
21787941 AACTTTTTTTAT-TTTTTTATTTTT
1 AACTTTTTTTATCTTTTTTATTTTT
* *
21787965 AACTTTTTTTCTCTTTTTTCTTTTT
1 AACTTTTTTTATCTTTTTTATTTTT
21787990 TTTCTTTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 11 0.50
25 11 0.50
ACGTcount: A:0.12, C:0.10, G:0.00, T:0.78
Consensus pattern (25 bp):
AACTTTTTTTATCTTTTTTATTTTT
Found at i:21787980 original size:10 final size:10
Alignment explanation
Indices: 21787967--21788003 Score: 51
Period size: 9 Copynumber: 3.9 Consensus size: 10
21787957 TTATTTTTAA
21787967 CTTTTTTTCT
1 CTTTTTTTCT
21787977 C-TTTTTTCT
1 CTTTTTTTCT
21787986 -TTTTTTTCT
1 CTTTTTTTCT
*
21787995 TTTTTTTTC
1 CTTTTTTTC
21788004 GAATTATTTC
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
9 16 0.64
10 9 0.36
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (10 bp):
CTTTTTTTCT
Found at i:21787981 original size:18 final size:16
Alignment explanation
Indices: 21787952--21787998 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 16
21787942 ACTTTTTTTA
*
21787952 TTTTTTTATTTTTAACT
1 TTTTTTTCTTTTT-ACT
*
21787969 TTTTTTCTCTTTTTTCT
1 TTTTTT-TCTTTTTACT
21787986 TTTTTTTCTTTTT
1 TTTTTTTCTTTTT
21787999 TTTTCGAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
16 7 0.26
17 14 0.52
18 6 0.22
ACGTcount: A:0.06, C:0.11, G:0.00, T:0.83
Consensus pattern (16 bp):
TTTTTTTCTTTTTACT
Found at i:21787997 original size:8 final size:8
Alignment explanation
Indices: 21787943--21788000 Score: 62
Period size: 8 Copynumber: 7.0 Consensus size: 8
21787933 AATCATCAAA
21787943 CTTTTTTT
1 CTTTTTTT
*
21787951 ATTTTTTT
1 CTTTTTTT
* **
21787959 ATTTTTAA
1 CTTTTTTT
21787967 CTTTTTTT
1 CTTTTTTT
21787975 CTCTTTTTT
1 CT-TTTTTT
21787984 CTTTTTTTT
1 C-TTTTTTT
21787993 CTTTTTTT
1 CTTTTTTT
21788001 TTCGAATTAT
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
8 27 0.64
9 14 0.33
10 1 0.02
ACGTcount: A:0.07, C:0.10, G:0.00, T:0.83
Consensus pattern (8 bp):
CTTTTTTT
Found at i:21788035 original size:10 final size:10
Alignment explanation
Indices: 21788020--21788055 Score: 63
Period size: 10 Copynumber: 3.6 Consensus size: 10
21788010 TTTCTTCTTC
21788020 TTTTTTTGTT
1 TTTTTTTGTT
*
21788030 TTTTTTTGCT
1 TTTTTTTGTT
21788040 TTTTTTTGTT
1 TTTTTTTGTT
21788050 TTTTTT
1 TTTTTT
21788056 GTGGAACATG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 24 1.00
ACGTcount: A:0.00, C:0.03, G:0.08, T:0.89
Consensus pattern (10 bp):
TTTTTTTGTT
Found at i:21789411 original size:27 final size:28
Alignment explanation
Indices: 21789381--21789499 Score: 113
Period size: 27 Copynumber: 4.4 Consensus size: 28
21789371 TTTAGTTTAC
21789381 TAAAATTACCGAAATACCCTTAG-TTTG
1 TAAAATTACCGAAATACCCTTAGATTTG
* * *
21789408 TAAAAATACTGAAATACCC-TCGATTTG
1 TAAAATTACCGAAATACCCTTAGATTTG
* * *
21789435 TAAATTTACCGAAATA-CCTTCGACTTG
1 TAAAATTACCGAAATACCCTTAGATTTG
* *
21789462 TAAAATTACC-AAAGTACCC-TCGATTTA
1 TAAAATTACCGAAA-TACCCTTAGATTTG
*
21789489 CAAAATTACCG
1 TAAAATTACCG
21789500 TTTTACCCCT
Statistics
Matches: 76, Mismatches: 11, Indels: 9
0.79 0.11 0.09
Matches are distributed among these distances:
26 7 0.09
27 67 0.88
28 2 0.03
ACGTcount: A:0.39, C:0.21, G:0.10, T:0.30
Consensus pattern (28 bp):
TAAAATTACCGAAATACCCTTAGATTTG
Found at i:21789448 original size:54 final size:54
Alignment explanation
Indices: 21789381--21789499 Score: 143
Period size: 54 Copynumber: 2.2 Consensus size: 54
21789371 TTTAGTTTAC
* *
21789381 TAAAATTACCGAAATACCCTTAG-TTTGTAAAAATACTGAAA-TACCCTCGATTTG
1 TAAAATTACCGAAATA-CCTTAGACTTGTAAAAATAC-CAAAGTACCCTCGATTTG
* * * *
21789435 TAAATTTACCGAAATACCTTCGACTTGTAAAATTACCAAAGTACCCTCGATTTA
1 TAAAATTACCGAAATACCTTAGACTTGTAAAAATACCAAAGTACCCTCGATTTG
*
21789489 CAAAATTACCG
1 TAAAATTACCG
21789500 TTTTACCCCT
Statistics
Matches: 55, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
53 8 0.15
54 47 0.85
ACGTcount: A:0.39, C:0.21, G:0.10, T:0.30
Consensus pattern (54 bp):
TAAAATTACCGAAATACCTTAGACTTGTAAAAATACCAAAGTACCCTCGATTTG
Found at i:21789714 original size:27 final size:27
Alignment explanation
Indices: 21789476--21789714 Score: 252
Period size: 27 Copynumber: 8.9 Consensus size: 27
21789466 ATTACCAAAG
* *
21789476 TACCCTCGATTTACAAAATTACCGTTT
1 TACCCTCGATTTACAGAATTACTGTTT
* *
21789503 TACCC-CTAATTTACATAATTA-TCGTTT
1 TACCCTC-GATTTACAGAATTACT-GTTT
*
21789530 TACCC-CTGATTTACATAATTA-TCGTTT
1 TACCCTC-GATTTACAGAATTACT-GTTT
* * *
21789557 TATCCTCGACTTACAGAATTACCGTTT
1 TACCCTCGATTTACAGAATTACTGTTT
*
21789584 TACCCTCGATTTACTGAATTACTGTTT
1 TACCCTCGATTTACAGAATTACTGTTT
* * *
21789611 TACCCTTGATTTATAGAATTACTATTT
1 TACCCTCGATTTACAGAATTACTGTTT
* * *
21789638 TACCCTTGATTTATAGAATTATTGTTT
1 TACCCTCGATTTACAGAATTACTGTTT
* *
21789665 TACCCTTGATTTATAGAATTACTGTTT
1 TACCCTCGATTTACAGAATTACTGTTT
*
21789692 TACCCTCGATTTACAAAATTACT
1 TACCCTCGATTTACAGAATTACT
21789715 AAAATACCCT
Statistics
Matches: 186, Mismatches: 22, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
26 1 0.01
27 184 0.99
28 1 0.01
ACGTcount: A:0.28, C:0.21, G:0.08, T:0.44
Consensus pattern (27 bp):
TACCCTCGATTTACAGAATTACTGTTT
Found at i:21789722 original size:27 final size:27
Alignment explanation
Indices: 21789692--21789859 Score: 76
Period size: 27 Copynumber: 6.1 Consensus size: 27
21789682 ATTACTGTTT
21789692 TACCCTCGATTTACAAAATTACTAAAA
1 TACCCTCGATTTACAAAATTACTAAAA
* * *** *
21789719 TACCCTTGGTTTGTGAAATTACCGAAAA
1 TACCCTCGATTTACAAAATTA-CTAAAA
* ** *
21789747 -ACCCTCAATTTGTAAAATTACCAAAA
1 TACCCTCGATTTACAAAATTACTAAAA
* *
21789773 TACCC-CTAATTTACAAAGTTAC-AGAAA
1 TACCCTC-GATTTACAAAATTACTA-AAA
* *
21789800 TACCCTTGACTTT-CTAAAAATTA-TAGGAA
1 TACCCTCGA-TTTAC--AAAATTACTA-AAA
* * * *
21789829 TACCATTGGTTTACAAAATTACTGAAA
1 TACCCTCGATTTACAAAATTACTAAAA
21789856 TACC
1 TACC
21789860 TTTGGTTTGT
Statistics
Matches: 108, Mismatches: 22, Indels: 22
0.71 0.14 0.14
Matches are distributed among these distances:
26 7 0.06
27 71 0.66
28 12 0.11
29 18 0.17
ACGTcount: A:0.40, C:0.20, G:0.09, T:0.30
Consensus pattern (27 bp):
TACCCTCGATTTACAAAATTACTAAAA
Found at i:21789985 original size:27 final size:27
Alignment explanation
Indices: 21789921--21789985 Score: 78
Period size: 27 Copynumber: 2.4 Consensus size: 27
21789911 ACCCCTAAAA
* *
21789921 GGTAAAAAGATCGTAAAGCCCCTGTAG
1 GGTAAAATGACCGTAAAGCCCCTGTAG
* *
21789948 GGTAAAGTGACCGTAATA-CCCCTGTAT
1 GGTAAAATGACCGTAA-AGCCCCTGTAG
21789975 GGTAAAATGAC
1 GGTAAAATGAC
21789986 GAATATGCCC
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
27 31 0.97
28 1 0.03
ACGTcount: A:0.35, C:0.18, G:0.25, T:0.22
Consensus pattern (27 bp):
GGTAAAATGACCGTAAAGCCCCTGTAG
Found at i:21791172 original size:25 final size:25
Alignment explanation
Indices: 21791143--21791190 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
21791133 TTATAATATG
* * *
21791143 AAAATGACCGTTTTGCCCCTAGGTA
1 AAAATGACCATTATACCCCTAGGTA
21791168 AAAATGACCATTATACCCCTAGG
1 AAAATGACCATTATACCCCTAGG
21791191 GTTTATGTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (25 bp):
AAAATGACCATTATACCCCTAGGTA
Found at i:21791278 original size:20 final size:20
Alignment explanation
Indices: 21791233--21791291 Score: 102
Period size: 19 Copynumber: 3.0 Consensus size: 20
21791223 ATAAATATGG
21791233 TATGTATGATATGCACATGA
1 TATGTATGATATGCACATGA
*
21791253 -ATGTATGCTATGCACATGA
1 TATGTATGATATGCACATGA
21791272 TATGTATGATATGCACATGA
1 TATGTATGATATGCACATGA
21791292 GGTAATCATA
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
19 18 0.50
20 18 0.50
ACGTcount: A:0.34, C:0.12, G:0.20, T:0.34
Consensus pattern (20 bp):
TATGTATGATATGCACATGA
Found at i:21791369 original size:24 final size:24
Alignment explanation
Indices: 21791342--21791484 Score: 209
Period size: 24 Copynumber: 6.0 Consensus size: 24
21791332 GAGGAAGTGA
21791342 AAAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATC
21791366 AAAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATC
21791390 AAAAGGGCTTATGCCCCAGTTAT-
1 AAAAGGGCTTATGCCCCAGTTATC
*
21791413 AAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATC
* * *
21791437 GAAAGGGCTTTTGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATC
*
21791461 AAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAG-GGCTTATGCC-CCAGTTAT
21791485 ATGATAAAGC
Statistics
Matches: 111, Mismatches: 5, Indels: 5
0.92 0.04 0.04
Matches are distributed among these distances:
23 23 0.21
24 77 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:21791435 original size:47 final size:47
Alignment explanation
Indices: 21791342--21791484 Score: 207
Period size: 47 Copynumber: 3.0 Consensus size: 47
21791332 GAGGAAGTGA
21791342 AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTAT-AAAAGGGCTTATGCCCCAGTTATC
*
21791390 AAAAGGGCTTATGCCCCAGTTATAAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATAAAAGGGCTTATGCCCCAGTTATC
* * *
21791437 GAAAGGGCTTTTGCCCCAGTTATTAAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAGGGCTTATGCCCCAGTTA-TAAAAG-GGCTTATGCC-CCAGTTAT
21791485 ATGATAAAGC
Statistics
Matches: 88, Mismatches: 4, Indels: 5
0.91 0.04 0.05
Matches are distributed among these distances:
47 43 0.49
48 34 0.39
49 11 0.12
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.27
Consensus pattern (47 bp):
AAAAGGGCTTATGCCCCAGTTATAAAAGGGCTTATGCCCCAGTTATC
Found at i:21791458 original size:71 final size:72
Alignment explanation
Indices: 21791342--21791485 Score: 220
Period size: 71 Copynumber: 2.0 Consensus size: 72
21791332 GAGGAAGTGA
*
21791342 AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATCAAAAG-GGCTTATGCC-
1 AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATCAAAAGAGGC-TAGGCCT
21791405 CCAGTTAT
65 CCAGTTAT
** * *
21791413 AAAAGGGCTTATGCCCCAGTTATTGAAAGGGCTTTTGCCCCAGTTATTAAAAGAGGCTAGGCCTC
1 AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATCAAAAGAGGCTAGGCCTC
21791478 CAGTTAT
66 CAGTTAT
21791485 A
1 A
21791486 TGATAAAGCA
Statistics
Matches: 66, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
71 54 0.82
72 12 0.18
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.26
Consensus pattern (72 bp):
AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATCAAAAGAGGCTAGGCCTC
CAGTTAT
Found at i:21791710 original size:31 final size:31
Alignment explanation
Indices: 21791672--21791753 Score: 155
Period size: 31 Copynumber: 2.6 Consensus size: 31
21791662 ATACCGTTTA
21791672 CAGTAATATGAAATATGAAAAGGCTTCGGCC
1 CAGTAATATGAAATATGAAAAGGCTTCGGCC
21791703 CAGTAATATGAAATATGAAAAGGCTTCGGCC
1 CAGTAATATGAAATATGAAAAGGCTTCGGCC
*
21791734 CAGTATTATGAAATATGAAA
1 CAGTAATATGAAATATGAAA
21791754 TATGAAAAGG
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 50 1.00
ACGTcount: A:0.41, C:0.13, G:0.21, T:0.24
Consensus pattern (31 bp):
CAGTAATATGAAATATGAAAAGGCTTCGGCC
Found at i:21794538 original size:53 final size:53
Alignment explanation
Indices: 21794474--21794588 Score: 144
Period size: 53 Copynumber: 2.2 Consensus size: 53
21794464 TAGTTTACTA
* * **
21794474 AAATTACCGAAATACCCTTAG-TTTGTAAAAATACTGAAA-TACCCTCGATTTGT
1 AAATTACCGAAATA-CCTTAGACTTGTAAAAATAC-CAAAGTACCCTCGATTTAC
* *
21794527 AAATTACCGAAATACCTTCGACTTGTAAAATTACCAAAGTACCCTCGATTTAC
1 AAATTACCGAAATACCTTAGACTTGTAAAAATACCAAAGTACCCTCGATTTAC
21794580 AAATTACCG
1 AAATTACCG
21794589 TTTTACCCCT
Statistics
Matches: 54, Mismatches: 6, Indels: 4
0.84 0.09 0.06
Matches are distributed among these distances:
52 8 0.15
53 46 0.85
ACGTcount: A:0.38, C:0.22, G:0.10, T:0.30
Consensus pattern (53 bp):
AAATTACCGAAATACCTTAGACTTGTAAAAATACCAAAGTACCCTCGATTTAC
Found at i:21794547 original size:26 final size:27
Alignment explanation
Indices: 21794472--21794577 Score: 128
Period size: 27 Copynumber: 4.0 Consensus size: 27
21794462 TTTAGTTTAC
*
21794472 TAAAATTACCGAAATACCCT-TAGTTTG
1 TAAAATTACCGAAATACCCTCGA-TTTG
* *
21794499 TAAAAATACTGAAATACCCTCGATTTG
1 TAAAATTACCGAAATACCCTCGATTTG
* *
21794526 T-AAATTACCGAAATACCTTCGACTTG
1 TAAAATTACCGAAATACCCTCGATTTG
21794552 TAAAATTACC-AAAGTACCCTCGATTT
1 TAAAATTACCGAAA-TACCCTCGATTT
21794578 ACAAATTACC
Statistics
Matches: 67, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
26 25 0.37
27 41 0.61
28 1 0.01
ACGTcount: A:0.38, C:0.21, G:0.10, T:0.31
Consensus pattern (27 bp):
TAAAATTACCGAAATACCCTCGATTTG
Found at i:21794574 original size:27 final size:25
Alignment explanation
Indices: 21794472--21794587 Score: 101
Period size: 26 Copynumber: 4.4 Consensus size: 25
21794462 TTTAGTTTAC
* *
21794472 TAAAATTACCGAAATACCCTTAGTTTG
1 TAAAATTACC-AAATACCC-TCGATTG
* *
21794499 TAAAAATACTGAAATACCCTCGATTTG
1 TAAAATTAC-CAAATACCCTCGA-TTG
*
21794526 T-AAATTACCGAAATACCTTCGACTTG
1 TAAAATTACC-AAATACCCTCGA-TTG
21794552 TAAAATTACCAAAGTACCCTCGATT-
1 TAAAATTACCAAA-TACCCTCGATTG
21794577 TACAAATTACC
1 TA-AAATTACC
21794588 GTTTTACCCC
Statistics
Matches: 74, Mismatches: 9, Indels: 13
0.77 0.09 0.14
Matches are distributed among these distances:
25 2 0.03
26 36 0.49
27 36 0.49
ACGTcount: A:0.39, C:0.22, G:0.09, T:0.30
Consensus pattern (25 bp):
TAAAATTACCAAATACCCTCGATTG
Found at i:21794803 original size:27 final size:27
Alignment explanation
Indices: 21794566--21794803 Score: 261
Period size: 27 Copynumber: 8.9 Consensus size: 27
21794556 ATTACCAAAG
*
21794566 TACCCTCGATTTACA-AATTACCGTTT
1 TACCCTCGATTTACAGAATTACTGTTT
* *
21794592 TACCC-CTAATTTACATAATTA-TCGTTT
1 TACCCTC-GATTTACAGAATTACT-GTTT
*
21794619 TACCC-CTGATTTACATAATTA-TCGTTT
1 TACCCTC-GATTTACAGAATTACT-GTTT
* *
21794646 TACCCTCGACTTACAGAATTACCGTTT
1 TACCCTCGATTTACAGAATTACTGTTT
*
21794673 TACCCTCGATTTACTGAATTACTGTTT
1 TACCCTCGATTTACAGAATTACTGTTT
* * *
21794700 TACCCTTGATTTATAGAATTACTATTT
1 TACCCTCGATTTACAGAATTACTGTTT
* * *
21794727 TACCCTTGATTTATAGAATTATTGTTT
1 TACCCTCGATTTACAGAATTACTGTTT
* *
21794754 TACCCTTGATTTATAGAATTACTGTTT
1 TACCCTCGATTTACAGAATTACTGTTT
*
21794781 TACCCTCGATTTACAAAATTACT
1 TACCCTCGATTTACAGAATTACT
21794804 AAAATACCCT
Statistics
Matches: 188, Mismatches: 19, Indels: 9
0.87 0.09 0.04
Matches are distributed among these distances:
25 1 0.01
26 12 0.06
27 174 0.93
28 1 0.01
ACGTcount: A:0.27, C:0.21, G:0.08, T:0.43
Consensus pattern (27 bp):
TACCCTCGATTTACAGAATTACTGTTT
Found at i:21794811 original size:27 final size:27
Alignment explanation
Indices: 21794781--21794945 Score: 97
Period size: 26 Copynumber: 6.1 Consensus size: 27
21794771 ATTACTGTTT
21794781 TACCCTCGATTTACAAAATTACTAAAA
1 TACCCTCGATTTACAAAATTACTAAAA
* * *** **
21794808 TACCCTTGGTTTGTGAAATTACCGAAA
1 TACCCTCGATTTACAAAATTACTAAAA
* ** *
21794835 -ACCCTCAATTTGTAAAATTACCAAAA
1 TACCCTCGATTTACAAAATTACTAAAA
* *
21794861 TACCC-CTATTTACAAAGTTAC-AGAAA
1 TACCCTCGATTTACAAAATTACTA-AAA
*
21794887 TACCCTTGACTTTTA-AAAATTA-TAGAAA
1 TACCCTCGA--TTTACAAAATTACTA-AAA
* * * *
21794915 TACCATTGGTTTACAAAATTACTGAAA
1 TACCCTCGATTTACAAAATTACTAAAA
21794942 TACC
1 TACC
21794946 TTTGGTTTGT
Statistics
Matches: 108, Mismatches: 22, Indels: 16
0.74 0.15 0.11
Matches are distributed among these distances:
25 1 0.01
26 45 0.42
27 39 0.36
28 19 0.18
29 4 0.04
ACGTcount: A:0.41, C:0.20, G:0.08, T:0.31
Consensus pattern (27 bp):
TACCCTCGATTTACAAAATTACTAAAA
Found at i:21794950 original size:27 final size:27
Alignment explanation
Indices: 21794869--21794953 Score: 84
Period size: 27 Copynumber: 3.1 Consensus size: 27
21794859 AATACCCCTA
* * * *
21794869 TTTACAAAGTTACAGAAATACCCTTGACT
1 TTTACAAAATTACTGAAATACCATTG--G
21794898 TTTA-AAAATTA-TAGAAATACCATTGG
1 TTTACAAAATTACT-GAAATACCATTGG
*
21794924 TTTACAAAATTACTGAAATACCTTTGG
1 TTTACAAAATTACTGAAATACCATTGG
21794951 TTT
1 TTT
21794954 GTTGATTTAC
Statistics
Matches: 48, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
26 4 0.08
27 22 0.46
28 18 0.38
29 4 0.08
ACGTcount: A:0.39, C:0.14, G:0.11, T:0.36
Consensus pattern (27 bp):
TTTACAAAATTACTGAAATACCATTGG
Found at i:21795070 original size:27 final size:27
Alignment explanation
Indices: 21795006--21795070 Score: 87
Period size: 27 Copynumber: 2.4 Consensus size: 27
21794996 TACCCCTAAA
*
21795006 GGTAAAAAGACCGTAAAGCCCCTGTAG
1 GGTAAAATGACCGTAAAGCCCCTGTAG
* *
21795033 GGTAAAGTGACCGTAATA-CCCCTGTAT
1 GGTAAAATGACCGTAA-AGCCCCTGTAG
21795060 GGTAAAATGAC
1 GGTAAAATGAC
21795071 GAATATGCCC
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
27 32 0.97
28 1 0.03
ACGTcount: A:0.35, C:0.20, G:0.25, T:0.20
Consensus pattern (27 bp):
GGTAAAATGACCGTAAAGCCCCTGTAG
Found at i:21796248 original size:25 final size:25
Alignment explanation
Indices: 21796219--21796266 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
21796209 TTATAATATG
* * *
21796219 AAAATGACCGTTTTGCCCCTAGGTA
1 AAAATGACCATTATACCCCTAGGTA
21796244 AAAATGACCATTATACCCCTAGG
1 AAAATGACCATTATACCCCTAGG
21796267 GTTTATGTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (25 bp):
AAAATGACCATTATACCCCTAGGTA
Found at i:21796347 original size:11 final size:11
Alignment explanation
Indices: 21796314--21796367 Score: 55
Period size: 11 Copynumber: 5.4 Consensus size: 11
21796304 TATGGTATGT
21796314 ATGATATGCAC
1 ATGATATGCAC
*
21796325 ATGA-ATG--T
1 ATGATATGCAC
21796333 ATGATATGCAC
1 ATGATATGCAC
*
21796344 ATGATATG--T
1 ATGATATGCAC
21796353 ATGATATGCAC
1 ATGATATGCAC
21796364 ATGA
1 ATGA
21796368 GGTAATCATA
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
8 4 0.12
9 11 0.32
10 3 0.09
11 16 0.47
ACGTcount: A:0.37, C:0.11, G:0.20, T:0.31
Consensus pattern (11 bp):
ATGATATGCAC
Found at i:21796354 original size:20 final size:20
Alignment explanation
Indices: 21796309--21796367 Score: 111
Period size: 19 Copynumber: 3.0 Consensus size: 20
21796299 ATAAATATGG
21796309 TATGTATGATATGCACATGA
1 TATGTATGATATGCACATGA
21796329 -ATGTATGATATGCACATGA
1 TATGTATGATATGCACATGA
21796348 TATGTATGATATGCACATGA
1 TATGTATGATATGCACATGA
21796368 GGTAATCATA
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
19 19 0.50
20 19 0.50
ACGTcount: A:0.36, C:0.10, G:0.20, T:0.34
Consensus pattern (20 bp):
TATGTATGATATGCACATGA
Found at i:21796445 original size:24 final size:24
Alignment explanation
Indices: 21796418--21796560 Score: 209
Period size: 24 Copynumber: 6.0 Consensus size: 24
21796408 GAGGAAGTGA
21796418 AAAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATC
21796442 AAAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATC
21796466 AAAAGGGCTTATGCCCCAGTTAT-
1 AAAAGGGCTTATGCCCCAGTTATC
*
21796489 AAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATC
* * *
21796513 GAAAGGGCTTTTGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATC
*
21796537 AAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAG-GGCTTATGCC-CCAGTTAT
21796561 ATGATAAAGC
Statistics
Matches: 111, Mismatches: 5, Indels: 5
0.92 0.04 0.04
Matches are distributed among these distances:
23 23 0.21
24 77 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:21796511 original size:47 final size:47
Alignment explanation
Indices: 21796418--21796560 Score: 207
Period size: 47 Copynumber: 3.0 Consensus size: 47
21796408 GAGGAAGTGA
21796418 AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTAT-AAAAGGGCTTATGCCCCAGTTATC
*
21796466 AAAAGGGCTTATGCCCCAGTTATAAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATAAAAGGGCTTATGCCCCAGTTATC
* * *
21796513 GAAAGGGCTTTTGCCCCAGTTATTAAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAGGGCTTATGCCCCAGTTA-TAAAAG-GGCTTATGCC-CCAGTTAT
21796561 ATGATAAAGC
Statistics
Matches: 88, Mismatches: 4, Indels: 5
0.91 0.04 0.05
Matches are distributed among these distances:
47 43 0.49
48 34 0.39
49 11 0.12
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.27
Consensus pattern (47 bp):
AAAAGGGCTTATGCCCCAGTTATAAAAGGGCTTATGCCCCAGTTATC
Found at i:21796534 original size:71 final size:72
Alignment explanation
Indices: 21796418--21796561 Score: 220
Period size: 71 Copynumber: 2.0 Consensus size: 72
21796408 GAGGAAGTGA
*
21796418 AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATCAAAAG-GGCTTATGCC-
1 AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATCAAAAGAGGC-TAGGCCT
21796481 CCAGTTAT
65 CCAGTTAT
** * *
21796489 AAAAGGGCTTATGCCCCAGTTATTGAAAGGGCTTTTGCCCCAGTTATTAAAAGAGGCTAGGCCTC
1 AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATCAAAAGAGGCTAGGCCTC
21796554 CAGTTAT
66 CAGTTAT
21796561 A
1 A
21796562 TGATAAAGCA
Statistics
Matches: 66, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
71 54 0.82
72 12 0.18
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.26
Consensus pattern (72 bp):
AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATCAAAAGAGGCTAGGCCTC
CAGTTAT
Found at i:21796786 original size:31 final size:31
Alignment explanation
Indices: 21796748--21796829 Score: 155
Period size: 31 Copynumber: 2.6 Consensus size: 31
21796738 ATACCGTTTA
21796748 CAGTAATATGAAATATGAAAAGGCTTCGGCC
1 CAGTAATATGAAATATGAAAAGGCTTCGGCC
21796779 CAGTAATATGAAATATGAAAAGGCTTCGGCC
1 CAGTAATATGAAATATGAAAAGGCTTCGGCC
*
21796810 CAGTATTATGAAATATGAAA
1 CAGTAATATGAAATATGAAA
21796830 TATGAAAAGG
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 50 1.00
ACGTcount: A:0.41, C:0.13, G:0.21, T:0.24
Consensus pattern (31 bp):
CAGTAATATGAAATATGAAAAGGCTTCGGCC
Found at i:21797994 original size:17 final size:17
Alignment explanation
Indices: 21797964--21798001 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 17
21797954 AACAAATGAC
21797964 AAATAGAAATAAAAATA
1 AAATAGAAATAAAAATA
21797981 AAATA-AAATAAAAATTA
1 AAATAGAAATAAAAA-TA
21797998 AAAT
1 AAAT
21798002 TGATGAAAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 9 0.45
17 11 0.55
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (17 bp):
AAATAGAAATAAAAATA
Found at i:21804647 original size:35 final size:35
Alignment explanation
Indices: 21804608--21804678 Score: 124
Period size: 35 Copynumber: 2.0 Consensus size: 35
21804598 CGTCGTGCCC
21804608 AGCGTCGTGCCCACGACTCCAGCCACGACAGAATA
1 AGCGTCGTGCCCACGACTCCAGCCACGACAGAATA
**
21804643 AGCGTCGTGCCCACGACTCCAGCCGTGACAGAATA
1 AGCGTCGTGCCCACGACTCCAGCCACGACAGAATA
21804678 A
1 A
21804679 AAAAAAACTG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.28, C:0.35, G:0.24, T:0.13
Consensus pattern (35 bp):
AGCGTCGTGCCCACGACTCCAGCCACGACAGAATA
Found at i:21806176 original size:17 final size:19
Alignment explanation
Indices: 21806134--21806177 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
21806124 ATGAAATTTT
*
21806134 AATTAGTATTATGAGATAA
1 AATTATTATTATGAGATAA
*
21806153 AATTATTATTATTAGA-AA
1 AATTATTATTATGAGATAA
21806171 AA-TATTA
1 AATTATTA
21806178 CTGTATGTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 5 0.22
18 4 0.17
19 14 0.61
ACGTcount: A:0.50, C:0.00, G:0.09, T:0.41
Consensus pattern (19 bp):
AATTATTATTATGAGATAA
Found at i:21808003 original size:28 final size:28
Alignment explanation
Indices: 21807971--21808039 Score: 113
Period size: 28 Copynumber: 2.5 Consensus size: 28
21807961 GCGTAGATCA
*
21807971 CGAAATTACCCCTAAAGAGCAAAATTAT
1 CGAAATTACCCCTAAAGAGCAAAATTAC
21807999 CGAAATTACCCCTAAAGAGCAAAATTAC
1 CGAAATTACCCCTAAAGAGCAAAATTAC
*
21808027 CGATA-TACCCCTA
1 CGAAATTACCCCTA
21808040 GGGTTTTAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
27 8 0.21
28 31 0.79
ACGTcount: A:0.43, C:0.26, G:0.10, T:0.20
Consensus pattern (28 bp):
CGAAATTACCCCTAAAGAGCAAAATTAC
Found at i:21815082 original size:27 final size:27
Alignment explanation
Indices: 21814527--21815081 Score: 683
Period size: 27 Copynumber: 20.6 Consensus size: 27
21814517 AAAGTACTCC
21814527 CGATTTACAGAATTACCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
21814554 C-AGTTTACAGAATTACCGTTTTACCCT
1 CGA-TTTACAGAATTACCGTTTTACCCT
* *
21814581 C-AGTTTATAGAATTACTGTTTTACCCT
1 CGA-TTTACAGAATTACCGTTTTACCCT
** *
21814608 CGATTTGTAAAATTACCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
* *
21814635 CGATTTACAGAATTATCATTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
**
21814662 C-ATTTACAGAATTACTATTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
21814688 CGATTTACAGAATTACCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
***
21814715 C-AGTTTACAGAATTATTATTTTACCCT
1 CGA-TTTACAGAATTACCGTTTTACCCT
* *
21814742 TGATTTACAGAATTACTGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
*
21814769 CGATTTATAGAATTACCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
** *
21814796 CGATTTGTAAAATTACCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
* *
21814823 CGATTTATAGAATTACCATTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
**
21814850 C-AGTTTACAGAATTACTATTTTACCCT
1 CGA-TTTACAGAATTACCGTTTTACCCT
*
21814877 CGATTTATAGAATTACCGTTTTACCC-
1 CGATTTACAGAATTACCGTTTTACCCT
* * *
21814903 CTAATTTACATAATTACCATTTTAACCC-
1 C-GATTTACAGAATTACCGTTTT-ACCCT
* *
21814931 CGATTTACATAATTATCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
21814958 CGATTTACAGAATTACCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
* * *
21814985 CGATTTACAGTATTTCCATTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
* *
21815012 CGATTTATAGAATTACTGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
* *
21815039 TGATTTACAGAATTACTGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
*
21815066 CGATTTACAAAATTAC
1 CGATTTACAGAATTAC
21815082 TAAAATACCC
Statistics
Matches: 464, Mismatches: 54, Indels: 20
0.86 0.10 0.04
Matches are distributed among these distances:
26 32 0.07
27 424 0.91
28 8 0.02
ACGTcount: A:0.28, C:0.22, G:0.09, T:0.41
Consensus pattern (27 bp):
CGATTTACAGAATTACCGTTTTACCCT
Found at i:21816350 original size:25 final size:25
Alignment explanation
Indices: 21816322--21816369 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
21816312 TTATACCATG
* * *
21816322 AAAATGACCGTTTTGCCCCTAGGTA
1 AAAATGACCATTATACCCCTAGGTA
21816347 AAAATGACCATTATACCCCTAGG
1 AAAATGACCATTATACCCCTAGG
21816370 GTTTATGTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (25 bp):
AAAATGACCATTATACCCCTAGGTA
Found at i:21816472 original size:20 final size:20
Alignment explanation
Indices: 21816412--21816472 Score: 104
Period size: 20 Copynumber: 3.0 Consensus size: 20
21816402 ATAAATATGG
*
21816412 TATGTATGAGATGCACATGA
1 TATGTATGATATGCACATGA
*
21816432 CATGTATGATATGCACATGA
1 TATGTATGATATGCACATGA
21816452 TATGTATGATATGCACATGA
1 TATGTATGATATGCACATGA
21816472 T
1 T
21816473 GTAATCATAA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.34, C:0.11, G:0.21, T:0.33
Consensus pattern (20 bp):
TATGTATGATATGCACATGA
Found at i:21816549 original size:24 final size:24
Alignment explanation
Indices: 21816522--21816664 Score: 209
Period size: 24 Copynumber: 6.0 Consensus size: 24
21816512 GAGGAAGTGA
21816522 AAAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATC
21816546 AAAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATC
21816570 AAAAGGGCTTATGCCCCAGTTAT-
1 AAAAGGGCTTATGCCCCAGTTATC
*
21816593 AAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATC
* * *
21816617 GAAAGGGCTTTTGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATC
*
21816641 AAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAG-GGCTTATGCC-CCAGTTAT
21816665 ATGATAAAGC
Statistics
Matches: 111, Mismatches: 5, Indels: 5
0.92 0.04 0.04
Matches are distributed among these distances:
23 23 0.21
24 77 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:21816615 original size:47 final size:47
Alignment explanation
Indices: 21816522--21816664 Score: 207
Period size: 47 Copynumber: 3.0 Consensus size: 47
21816512 GAGGAAGTGA
21816522 AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTAT-AAAAGGGCTTATGCCCCAGTTATC
*
21816570 AAAAGGGCTTATGCCCCAGTTATAAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATAAAAGGGCTTATGCCCCAGTTATC
* * *
21816617 GAAAGGGCTTTTGCCCCAGTTATTAAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAGGGCTTATGCCCCAGTTA-TAAAAG-GGCTTATGCC-CCAGTTAT
21816665 ATGATAAAGC
Statistics
Matches: 88, Mismatches: 4, Indels: 5
0.91 0.04 0.05
Matches are distributed among these distances:
47 43 0.49
48 34 0.39
49 11 0.12
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.27
Consensus pattern (47 bp):
AAAAGGGCTTATGCCCCAGTTATAAAAGGGCTTATGCCCCAGTTATC
Found at i:21816638 original size:71 final size:72
Alignment explanation
Indices: 21816522--21816665 Score: 220
Period size: 71 Copynumber: 2.0 Consensus size: 72
21816512 GAGGAAGTGA
*
21816522 AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATCAAAAG-GGCTTATGCC-
1 AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATCAAAAGAGGC-TAGGCCT
21816585 CCAGTTAT
65 CCAGTTAT
** * *
21816593 AAAAGGGCTTATGCCCCAGTTATTGAAAGGGCTTTTGCCCCAGTTATTAAAAGAGGCTAGGCCTC
1 AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATCAAAAGAGGCTAGGCCTC
21816658 CAGTTAT
66 CAGTTAT
21816665 A
1 A
21816666 TGATAAAGCA
Statistics
Matches: 66, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
71 54 0.82
72 12 0.18
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.26
Consensus pattern (72 bp):
AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATCAAAAGAGGCTAGGCCTC
CAGTTAT
Found at i:21816891 original size:31 final size:31
Alignment explanation
Indices: 21816856--21816919 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
21816846 CGTTTACAGT
*
21816856 AAAGGCTTCGGCCCAGTAATATGAAATTTGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
**
21816887 AAAGGCTTCGGCCCAGTGTTATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
21816918 AA
1 AA
21816920 TATGAAAAGG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.36, C:0.16, G:0.23, T:0.25
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTAATATGAAATATGA
Found at i:21818560 original size:26 final size:24
Alignment explanation
Indices: 21818528--21818585 Score: 71
Period size: 24 Copynumber: 2.3 Consensus size: 24
21818518 CAGACCGTAT
21818528 GAGCTTACTAATATTTCAGCTCATAA
1 GAGCTTACT-AT-TTTCAGCTCATAA
* * *
21818554 GATCTTACTGTTTTCAGCTCATCA
1 GAGCTTACTATTTTCAGCTCATAA
21818578 GAGCTTAC
1 GAGCTTAC
21818586 CGTTTCAGCT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
24 19 0.68
25 1 0.04
26 8 0.29
ACGTcount: A:0.28, C:0.22, G:0.14, T:0.36
Consensus pattern (24 bp):
GAGCTTACTATTTTCAGCTCATAA
Found at i:21818595 original size:23 final size:24
Alignment explanation
Indices: 21818541--21818597 Score: 80
Period size: 24 Copynumber: 2.4 Consensus size: 24
21818531 CTTACTAATA
* *
21818541 TTTCAGCTCATAAGATCTTACTGT
1 TTTCAGCTCATAAGAGCTTACCGT
*
21818565 TTTCAGCTCATCAGAGCTTACCG-
1 TTTCAGCTCATAAGAGCTTACCGT
21818588 TTTCAGCTCA
1 TTTCAGCTCA
21818598 ATACAGCTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
23 10 0.33
24 20 0.67
ACGTcount: A:0.23, C:0.26, G:0.14, T:0.37
Consensus pattern (24 bp):
TTTCAGCTCATAAGAGCTTACCGT
Found at i:21819724 original size:338 final size:338
Alignment explanation
Indices: 21819108--21819783 Score: 1316
Period size: 338 Copynumber: 2.0 Consensus size: 338
21819098 CAATAGCTCA
21819108 CTCGATTCGGATAAAGTCAGAGATACGCATCACATTATCTAGTTATGCTTACTTGAGCTAGTGAT
1 CTCGATTCGGATAAAGTCAGAGATACGCATCACATTATCTAGTTATGCTTACTTGAGCTAGTGAT
* *
21819173 TTTGGTACATGTTGTGGTATAAGATAAAGCCATGTGATTTGGCTTAACTTGGTATACTATGTGTA
66 TTTGGTACATGTTGTGGTATAAGATAAAGACATGTGATTTGGCTTAACTTGGTATAATATGTGTA
21819238 TGAAATGTTATGGATTAGCTGCCTATTAAGTTATAAAATGTTGCAAATTATGCTTGTGTAGGTAT
131 TGAAATGTTATGGATTAGCTGCCTATTAAGTTATAAAATGTTGCAAATTATGCTTGTGTAGGTAT
21819303 TTAAAAATAGGGTGGCAAATTGGCTTAGTAAATAGCCTATTTTTGTCCACACGGGCAAAGACACG
196 TTAAAAATAGGGTGGCAAATTGGCTTAGTAAATAGCCTATTTTTGTCCACACGGGCAAAGACACG
21819368 GGCGTGTGTCTCAGTCGTGTGTGACACACGGTTATGTTACACGGTCGTGTGTCCCTTGGTGTTGA
261 GGCGTGTGTCTCAGTCGTGTGTGACACACGGTTATGTTACACGGTCGTGTGTCCCTTGGTGTTGA
21819433 AATTAAAATCAAT
326 AATTAAAATCAAT
21819446 CTCGATTCGGATAAAGTCAGAGATACGCATCACATTATCTAGTTATGCTTACTTGAGCTAGTGAT
1 CTCGATTCGGATAAAGTCAGAGATACGCATCACATTATCTAGTTATGCTTACTTGAGCTAGTGAT
21819511 TTTGGTACATGTTGTGGTATAAGATAAAGACATGTGATTTGGCTTAACTTGGTATAATATGTGTA
66 TTTGGTACATGTTGTGGTATAAGATAAAGACATGTGATTTGGCTTAACTTGGTATAATATGTGTA
*
21819576 TGAAATGTTATGGATTAGCTGCCTATTGAGTTATAAAATGTTGCAAATTATGCTTGTGTAGGTAT
131 TGAAATGTTATGGATTAGCTGCCTATTAAGTTATAAAATGTTGCAAATTATGCTTGTGTAGGTAT
*
21819641 TTAAAAATAGGGTGGCAAATTGGCTTAGTAAATAGCCTATTTTTGTCCACACGGGCAGAGACACG
196 TTAAAAATAGGGTGGCAAATTGGCTTAGTAAATAGCCTATTTTTGTCCACACGGGCAAAGACACG
21819706 GGCGTGTGTCTCAGTCGTGTGTGACACACGGTTATGTTACACGGTCGTGTGTCCCTTGGTGTTGA
261 GGCGTGTGTCTCAGTCGTGTGTGACACACGGTTATGTTACACGGTCGTGTGTCCCTTGGTGTTGA
21819771 AATTAAAATCAAT
326 AATTAAAATCAAT
21819784 TCAGTATGTT
Statistics
Matches: 334, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
338 334 1.00
ACGTcount: A:0.28, C:0.14, G:0.24, T:0.34
Consensus pattern (338 bp):
CTCGATTCGGATAAAGTCAGAGATACGCATCACATTATCTAGTTATGCTTACTTGAGCTAGTGAT
TTTGGTACATGTTGTGGTATAAGATAAAGACATGTGATTTGGCTTAACTTGGTATAATATGTGTA
TGAAATGTTATGGATTAGCTGCCTATTAAGTTATAAAATGTTGCAAATTATGCTTGTGTAGGTAT
TTAAAAATAGGGTGGCAAATTGGCTTAGTAAATAGCCTATTTTTGTCCACACGGGCAAAGACACG
GGCGTGTGTCTCAGTCGTGTGTGACACACGGTTATGTTACACGGTCGTGTGTCCCTTGGTGTTGA
AATTAAAATCAAT
Found at i:21823533 original size:29 final size:29
Alignment explanation
Indices: 21823500--21823573 Score: 139
Period size: 29 Copynumber: 2.6 Consensus size: 29
21823490 CCTTCGAGCT
21823500 CGCACACTTAGTGCCATATATTTCCAGCA
1 CGCACACTTAGTGCCATATATTTCCAGCA
*
21823529 TGCACACTTAGTGCCATATATTTCCAGCA
1 CGCACACTTAGTGCCATATATTTCCAGCA
21823558 CGCACACTTAGTGCCA
1 CGCACACTTAGTGCCA
21823574 ATCTCGTCAC
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 43 1.00
ACGTcount: A:0.27, C:0.31, G:0.15, T:0.27
Consensus pattern (29 bp):
CGCACACTTAGTGCCATATATTTCCAGCA
Found at i:21823534 original size:58 final size:58
Alignment explanation
Indices: 21823441--21823573 Score: 133
Period size: 58 Copynumber: 2.3 Consensus size: 58
21823431 ATACTCGATT
* * * * *
21823441 TCGCACACTTAGTGCCATGCGATTTAAGCCCGCACACACAGTGCCATGCCCTTCGAGC
1 TCGCACACTTAGTGCCATGAGATTTAAGCACGCACACACAGTGCCATACACTTCCAGC
* * * ** * *
21823499 TCGCACACTTAGTGCCAT-ATATTTCCAGCATGCACACTTAGTGCCATATATTTCCAGC
1 TCGCACACTTAGTGCCATGAGATTT-AAGCACGCACACACAGTGCCATACACTTCCAGC
*
21823557 ACGCACACTTAGTGCCA
1 TCGCACACTTAGTGCCA
21823574 ATCTCGTCAC
Statistics
Matches: 61, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
57 4 0.07
58 57 0.93
ACGTcount: A:0.25, C:0.33, G:0.17, T:0.25
Consensus pattern (58 bp):
TCGCACACTTAGTGCCATGAGATTTAAGCACGCACACACAGTGCCATACACTTCCAGC
Found at i:21826321 original size:26 final size:25
Alignment explanation
Indices: 21826291--21826453 Score: 109
Period size: 23 Copynumber: 6.8 Consensus size: 25
21826281 AGACTCACCA
21826291 CAGCTCGTATGAGCTTACTGATATAT
1 CAGCTCGTATGAGCTTACTGATAT-T
* *
21826317 CAGCTCGTAAGAGCTTACTG-TTTT
1 CAGCTCGTATGAGCTTACTGATATT
* *
21826341 CAGCTCAT-TGGAGCTTAC-CA-ATT
1 CAGCTCGTAT-GAGCTTACTGATATT
*
21826364 CAGCTCGTATGAGCTTACTG-TTTT
1 CAGCTCGTATGAGCTTACTGATATT
*
21826388 CAGCTCAT-TGGAGCTTATCT-AT-TT
1 CAGCTCGTAT-GAGCTTA-CTGATATT
*
21826412 -AGCTCG-ATAGAGCTTACCG-T-TT
1 CAGCTCGTAT-GAGCTTACTGATATT
*
21826434 CAGCTC-AATAGAGCTTACTG
1 CAGCTCGTAT-GAGCTTACTG
21826454 TTTATCATCT
Statistics
Matches: 111, Mismatches: 14, Indels: 27
0.73 0.09 0.18
Matches are distributed among these distances:
22 4 0.04
23 48 0.43
24 35 0.32
25 5 0.05
26 19 0.17
ACGTcount: A:0.23, C:0.22, G:0.20, T:0.35
Consensus pattern (25 bp):
CAGCTCGTATGAGCTTACTGATATT
Found at i:21826378 original size:47 final size:47
Alignment explanation
Indices: 21826316--21826451 Score: 186
Period size: 47 Copynumber: 2.9 Consensus size: 47
21826306 TACTGATATA
*
21826316 TCAGCTCGTAAGAGCTTACTGTTTTCAGCTCATTGGAGCTTACCAAT
1 TCAGCTCGTATGAGCTTACTGTTTTCAGCTCATTGGAGCTTACCAAT
* *
21826363 TCAGCTCGTATGAGCTTACTGTTTTCAGCTCATTGGAGCTTATCTAT
1 TCAGCTCGTATGAGCTTACTGTTTTCAGCTCATTGGAGCTTACCAAT
* * * *
21826410 TTAGCTCG-ATAGAGCTTACCG-TTTCAGCTCAATAGAGCTTAC
1 TCAGCTCGTAT-GAGCTTACTGTTTTCAGCTCATTGGAGCTTAC
21826452 TGTTTATCAT
Statistics
Matches: 80, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
46 20 0.25
47 60 0.75
ACGTcount: A:0.23, C:0.23, G:0.19, T:0.35
Consensus pattern (47 bp):
TCAGCTCGTATGAGCTTACTGTTTTCAGCTCATTGGAGCTTACCAAT
Found at i:21826437 original size:70 final size:71
Alignment explanation
Indices: 21826291--21826465 Score: 178
Period size: 70 Copynumber: 2.4 Consensus size: 71
21826281 AGACTCACCA
* * * *
21826291 CAGCTCGTATGAGCTTACTGATATATCAGCTCGTAAGAGCTTACTGTTTTCAGCTCATTGGAGCT
1 CAGCTCGTATGAGCTTACTG-T-TTTCAGCTCATAAGAGCTTACTGATTTCAGCTCATTAGAGCT
21826356 TACCAATT
64 TACCAATT
**
21826364 CAGCTCGTATGAGCTTACTGTTTTCAGCTCATTGGAGCTTATCT-ATTT-AGCTCGA-TAGAGCT
1 CAGCTCGTATGAGCTTACTGTTTTCAGCTCATAAGAGCTTA-CTGATTTCAGCTC-ATTAGAGCT
**
21826426 TACCGTTT
64 TACCAATT
* *
21826434 CAGCTC-AATAGAGCTTACTGTTTATCATCTCA
1 CAGCTCGTAT-GAGCTTACTGTTT-TCAGCTCA
21826466 GGAGGAGTTT
Statistics
Matches: 88, Mismatches: 10, Indels: 10
0.81 0.09 0.09
Matches are distributed among these distances:
69 2 0.02
70 36 0.41
71 27 0.31
72 3 0.03
73 20 0.23
ACGTcount: A:0.23, C:0.22, G:0.18, T:0.36
Consensus pattern (71 bp):
CAGCTCGTATGAGCTTACTGTTTTCAGCTCATAAGAGCTTACTGATTTCAGCTCATTAGAGCTTA
CCAATT
Found at i:21826456 original size:23 final size:23
Alignment explanation
Indices: 21826326--21826456 Score: 113
Period size: 23 Copynumber: 5.6 Consensus size: 23
21826316 TCAGCTCGTA
*
21826326 AGAGCTTACTGTTTTCAGCTCATT
1 AGAGCTTACTG-TTTCAGCTCAAT
* *** *
21826350 GGAGCTTACCAATTCAGCTC-GT
1 AGAGCTTACTGTTTCAGCTCAAT
*
21826372 ATGAGCTTACTGTTTTCAGCTCATT
1 A-GAGCTTACTG-TTTCAGCTCAAT
* * *
21826397 GGAGCTTATCTATTT-AGCTCGAT
1 AGAGCTTA-CTGTTTCAGCTCAAT
*
21826420 AGAGCTTACCGTTTCAGCTCAAT
1 AGAGCTTACTGTTTCAGCTCAAT
21826443 AGAGCTTACTGTTT
1 AGAGCTTACTGTTT
21826457 ATCATCTCAG
Statistics
Matches: 83, Mismatches: 19, Indels: 11
0.73 0.17 0.10
Matches are distributed among these distances:
22 5 0.06
23 49 0.59
24 26 0.31
25 3 0.04
ACGTcount: A:0.22, C:0.21, G:0.19, T:0.37
Consensus pattern (23 bp):
AGAGCTTACTGTTTCAGCTCAAT
Found at i:21826655 original size:20 final size:20
Alignment explanation
Indices: 21826612--21826659 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
21826602 CGATTATATG
*
21826612 AATTACTGTTGAAATGAATG
1 AATTACTGTTGAAATGAATA
* **
21826632 AATTACTGTTGATATGGTTA
1 AATTACTGTTGAAATGAATA
21826652 AATTACTG
1 AATTACTG
21826660 ATATACTGAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.35, C:0.06, G:0.19, T:0.40
Consensus pattern (20 bp):
AATTACTGTTGAAATGAATA
Found at i:21826690 original size:20 final size:20
Alignment explanation
Indices: 21826629--21826726 Score: 76
Period size: 20 Copynumber: 5.0 Consensus size: 20
21826619 GTTGAAATGA
*
21826629 ATGAATTACT-GTTGATATGG
1 ATGAATTACTAGTT-ATACGG
* * * *
21826649 TTAAATTACT-GATATACTG
1 ATGAATTACTAGTTATACGG
*
21826668 ATGAATTGCTAGTTATACGG
1 ATGAATTACTAGTTATACGG
* * *
21826688 ATGATTTACTAGTTATATGA
1 ATGAATTACTAGTTATACGG
21826708 ATGAATTAC-AGTTTATACG
1 ATGAATTACTAG-TTATACG
21826727 AATAAAAATG
Statistics
Matches: 60, Mismatches: 16, Indels: 4
0.75 0.20 0.05
Matches are distributed among these distances:
19 13 0.22
20 47 0.78
ACGTcount: A:0.34, C:0.08, G:0.18, T:0.40
Consensus pattern (20 bp):
ATGAATTACTAGTTATACGG
Found at i:21831532 original size:28 final size:28
Alignment explanation
Indices: 21831500--21831589 Score: 99
Period size: 28 Copynumber: 3.2 Consensus size: 28
21831490 ATGTACCATC
21831500 ATTTTATAGATTTTATAGTTCTGCCACA
1 ATTTTATAGATTTTATAGTTCTGCCACA
* * * * *
21831528 ATTTTTTAGATTTTACAATTTTTCCACA
1 ATTTTATAGATTTTATAGTTCTGCCACA
* * *
21831556 GGTTTTACAGATTTTATAGTTCTGCCACT
1 -ATTTTATAGATTTTATAGTTCTGCCACA
21831585 ATTTT
1 ATTTT
21831590 TCCATATTTT
Statistics
Matches: 47, Mismatches: 14, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
28 27 0.57
29 20 0.43
ACGTcount: A:0.26, C:0.14, G:0.10, T:0.50
Consensus pattern (28 bp):
ATTTTATAGATTTTATAGTTCTGCCACA
Found at i:21831533 original size:29 final size:29
Alignment explanation
Indices: 21831501--21831590 Score: 101
Period size: 29 Copynumber: 3.1 Consensus size: 29
21831491 TGTACCATCA
21831501 TTTTATAGATTTTATAGTTCTGCCACAAT
1 TTTTATAGATTTTATAGTTCTGCCACAAT
* * * * **
21831530 TTTT-TAGATTTTACAATTTTTCCACAGG
1 TTTTATAGATTTTATAGTTCTGCCACAAT
* *
21831558 TTTTACAGATTTTATAGTTCTGCCACTAT
1 TTTTATAGATTTTATAGTTCTGCCACAAT
21831587 TTTT
1 TTTT
21831591 CCATATTTTA
Statistics
Matches: 46, Mismatches: 14, Indels: 2
0.74 0.23 0.03
Matches are distributed among these distances:
28 22 0.48
29 24 0.52
ACGTcount: A:0.24, C:0.14, G:0.10, T:0.51
Consensus pattern (29 bp):
TTTTATAGATTTTATAGTTCTGCCACAAT
Found at i:21831598 original size:29 final size:27
Alignment explanation
Indices: 21831499--21831600 Score: 80
Period size: 29 Copynumber: 3.6 Consensus size: 27
21831489 AATGTACCAT
21831499 CATTTTAT-AGATTTTATAGTTCTGCCA
1 CATTTT-TCAGATTTTATAGTTCTGCCA
* * * * *
21831526 CAATTTTTTAGATTTTACAATTTTTCCA
1 C-ATTTTTCAGATTTTATAGTTCTGCCA
*
21831554 CAGGTTTTACAGATTTTATAGTTCTGCCA
1 CA--TTTTTCAGATTTTATAGTTCTGCCA
*
21831583 CTATTTTTCCATATTTTA
1 C-ATTTTT-CAGATTTTA
21831601 CAATTCTACT
Statistics
Matches: 57, Mismatches: 12, Indels: 10
0.72 0.15 0.13
Matches are distributed among these distances:
27 3 0.05
28 25 0.44
29 28 0.49
30 1 0.02
ACGTcount: A:0.25, C:0.16, G:0.09, T:0.50
Consensus pattern (27 bp):
CATTTTTCAGATTTTATAGTTCTGCCA
Found at i:21842496 original size:29 final size:29
Alignment explanation
Indices: 21842441--21842620 Score: 170
Period size: 29 Copynumber: 6.3 Consensus size: 29
21842431 GTGTTACATC
* * *
21842441 TGCCACAAG-TTTCTAGATTTTATAGTTT
1 TGCCACTAGTTTTCCAGATTTTACAGTTT
* *
21842469 TGCCACTAGTTTTCCAGAATTTACAGTTC
1 TGCCACTAGTTTTCCAGATTTTACAGTTT
* ** *
21842498 TGCCAC-AATTTTTGAAATTTTACAGTTT
1 TGCCACTAGTTTTCCAGATTTTACAGTTT
* *
21842526 TGCCACTAGTTTTCCAGATTTTTACAATTC
1 TGCCACTAGTTTTCCAGA-TTTTACAGTTT
* * *
21842556 TACCA-TTGTTTTCCAGATTTTATAGTTT
1 TGCCACTAGTTTTCCAGATTTTACAGTTT
**
21842584 TGCCACT-GTTTTTTTAGATTTTACAGTTT
1 TGCCACTAG-TTTTCCAGATTTTACAGTTT
21842613 TGCCACTA
1 TGCCACTA
21842621 TTCTTCAAAA
Statistics
Matches: 120, Mismatches: 26, Indels: 10
0.77 0.17 0.06
Matches are distributed among these distances:
28 43 0.36
29 64 0.53
30 13 0.11
ACGTcount: A:0.23, C:0.18, G:0.12, T:0.46
Consensus pattern (29 bp):
TGCCACTAGTTTTCCAGATTTTACAGTTT
Found at i:21842595 original size:57 final size:57
Alignment explanation
Indices: 21842443--21842595 Score: 182
Period size: 57 Copynumber: 2.7 Consensus size: 57
21842433 GTTACATCTG
* * * *
21842443 CCACAAGTTTCTAGATTTTATAGTTTTGCCACTAGTTTTCCAGAATTTACAGTTCTG
1 CCACAATTTTCCAGATTTTATAGTTTTGCCACTAGTTTTCCAGAATTTACAATTCTA
** * * *
21842500 CCACAATTTTTGAAATTTTACAGTTTTGCCACTAGTTTTCCAGATTTTTACAATTCTA
1 CCACAATTTTCCAGATTTTATAGTTTTGCCACTAGTTTTCCAGA-ATTTACAATTCTA
***
21842558 CCATTGTTTTCCAGATTTTATAGTTTTGCCACT-GTTTT
1 CCACAATTTTCCAGATTTTATAGTTTTGCCACTAGTTTT
21842596 TTTAGATTTT
Statistics
Matches: 80, Mismatches: 15, Indels: 2
0.82 0.15 0.02
Matches are distributed among these distances:
57 44 0.55
58 36 0.45
ACGTcount: A:0.24, C:0.19, G:0.12, T:0.46
Consensus pattern (57 bp):
CCACAATTTTCCAGATTTTATAGTTTTGCCACTAGTTTTCCAGAATTTACAATTCTA
Found at i:21842969 original size:11 final size:11
Alignment explanation
Indices: 21842953--21842978 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
21842943 CTTGCAATGA
21842953 GATAGAATGTT
1 GATAGAATGTT
21842964 GATAGAATGTT
1 GATAGAATGTT
21842975 GATA
1 GATA
21842979 ATGATATTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.38, C:0.00, G:0.27, T:0.35
Consensus pattern (11 bp):
GATAGAATGTT
Found at i:21852203 original size:43 final size:43
Alignment explanation
Indices: 21852147--21852271 Score: 135
Period size: 43 Copynumber: 2.9 Consensus size: 43
21852137 TTTACATGTT
* * * *
21852147 ATCACATATCGATGCTACTGTCCTAAACAGGGTCTTACACGAA
1 ATCACATAGCGATGCCAATGTCCCAAACAGGGTCTTACACGAA
* * * *
21852190 ATCATATAGCGATGCCAATGTCCCAGACATGGTCTTACACGTA
1 ATCACATAGCGATGCCAATGTCCCAAACAGGGTCTTACACGAA
* * *
21852233 ATCACAATA-CAATGCCAATGTCCCATACATGGTCTTACA
1 ATCAC-ATAGCGATGCCAATGTCCCAAACAGGGTCTTACA
21852272 TGTAACCACA
Statistics
Matches: 70, Mismatches: 11, Indels: 2
0.84 0.13 0.02
Matches are distributed among these distances:
43 67 0.96
44 3 0.04
ACGTcount: A:0.33, C:0.26, G:0.15, T:0.26
Consensus pattern (43 bp):
ATCACATAGCGATGCCAATGTCCCAAACAGGGTCTTACACGAA
Found at i:21853232 original size:22 final size:22
Alignment explanation
Indices: 21853181--21853232 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 22
21853171 ACTTAATTTA
21853181 TTTCA-TAATTACCATTATAAC
1 TTTCATTAATTACCATTATAAC
* *
21853202 TTT-ATTAATTAACC-TTGTAAT
1 TTTCATTAATT-ACCATTATAAC
21853223 TTTCATTAAT
1 TTTCATTAAT
21853233 AAAGCACATA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
20 1 0.04
21 16 0.62
22 9 0.35
ACGTcount: A:0.35, C:0.13, G:0.02, T:0.50
Consensus pattern (22 bp):
TTTCATTAATTACCATTATAAC
Found at i:21874404 original size:25 final size:25
Alignment explanation
Indices: 21874375--21874422 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
21874365 CCTTATAATG
* * *
21874375 AAAATGACCGTTTTGCCCCTAGGTA
1 AAAATGACCATTATACCCCTAGGTA
21874400 AAAATGACCATTATACCCCTAGG
1 AAAATGACCATTATACCCCTAGG
21874423 GTTTATGTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (25 bp):
AAAATGACCATTATACCCCTAGGTA
Found at i:21874491 original size:20 final size:20
Alignment explanation
Indices: 21874466--21874504 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
21874456 TAAATATGGT
21874466 ATGTATGATATGCACATGAA
1 ATGTATGATATGCACATGAA
21874486 ATGTATGATATGCACATGA
1 ATGTATGATATGCACATGA
21874505 GGTACTCATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.38, C:0.10, G:0.21, T:0.31
Consensus pattern (20 bp):
ATGTATGATATGCACATGAA
Found at i:21874585 original size:23 final size:24
Alignment explanation
Indices: 21874555--21874649 Score: 124
Period size: 24 Copynumber: 4.0 Consensus size: 24
21874545 GAGGAAGTGA
21874555 AAAAGGGCTTATGCCCCAGTTA-T
1 AAAAGGGCTTATGCCCCAGTTATT
21874578 AAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
*
21874602 GAAAGGGCTT-TGGCCCCAGTTATT
1 AAAAGGGCTTAT-GCCCCAGTTATT
*
21874626 AAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAG-GGCTTATGCC-CCAGTTAT
21874650 ATGATAAAGC
Statistics
Matches: 64, Mismatches: 3, Indels: 8
0.85 0.04 0.11
Matches are distributed among these distances:
23 23 0.36
24 30 0.47
25 11 0.17
ACGTcount: A:0.28, C:0.21, G:0.24, T:0.26
Consensus pattern (24 bp):
AAAAGGGCTTATGCCCCAGTTATT
Found at i:21874623 original size:47 final size:49
Alignment explanation
Indices: 21874556--21874649 Score: 133
Period size: 47 Copynumber: 2.0 Consensus size: 49
21874546 AGGAAGTGAA
*
21874556 AAAGGGCTTATGCCCCAGTTA-TAAAAG-GGCTTATGCC-CCAGTTATTG
1 AAAGGGCTTATGCCCCAGTTATTAAAAGAGGC-TAGGCCTCCAGTTATTG
21874603 AAAGGGCTT-TGGCCCCAGTTATTAAAAGAGGCTAGGCCTCCAGTTAT
1 AAAGGGCTTAT-GCCCCAGTTATTAAAAGAGGCTAGGCCTCCAGTTAT
21874650 ATGATAAAGC
Statistics
Matches: 42, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
46 1 0.02
47 19 0.45
48 11 0.26
49 11 0.26
ACGTcount: A:0.28, C:0.21, G:0.24, T:0.27
Consensus pattern (49 bp):
AAAGGGCTTATGCCCCAGTTATTAAAAGAGGCTAGGCCTCCAGTTATTG
Found at i:21874892 original size:38 final size:38
Alignment explanation
Indices: 21874841--21875002 Score: 232
Period size: 38 Copynumber: 4.4 Consensus size: 38
21874831 CGTTTACAGT
21874841 AAAGGCTTCGGCCCAGTATTATGAAATATGAAACATGA
1 AAAGGCTTCGGCCCAGTATTATGAAATATGAAACATGA
*
21874879 AAAGGCTTCGGCCCAG-----T--AATATGAAATATG-
1 AAAGGCTTCGGCCCAGTATTATGAAATATGAAACATGA
21874909 AAAGGCTTCGGCCCAGTATTATGAAATATGAAACATGA
1 AAAGGCTTCGGCCCAGTATTATGAAATATGAAACATGA
*
21874947 AAAGGCTTCGGCCCAGTATTATGAAATATGAAATATGA
1 AAAGGCTTCGGCCCAGTATTATGAAATATGAAACATGA
*
21874985 AAAGGGCTACGGCCCAGT
1 AAA-GGCTTCGGCCCAGT
21875003 GCATGATTGA
Statistics
Matches: 111, Mismatches: 4, Indels: 17
0.84 0.03 0.13
Matches are distributed among these distances:
30 16 0.14
31 12 0.11
33 1 0.01
35 1 0.01
37 12 0.11
38 56 0.50
39 13 0.12
ACGTcount: A:0.38, C:0.17, G:0.23, T:0.23
Consensus pattern (38 bp):
AAAGGCTTCGGCCCAGTATTATGAAATATGAAACATGA
Found at i:21874915 original size:30 final size:30
Alignment explanation
Indices: 21874865--21874941 Score: 127
Period size: 30 Copynumber: 2.5 Consensus size: 30
21874855 AGTATTATGA
*
21874865 AATATGAAACATGAAAAGGCTTCGGCCCAGT
1 AATATGAAATATG-AAAGGCTTCGGCCCAGT
21874896 AATATGAAATATGAAAGGCTTCGGCCCAGT
1 AATATGAAATATGAAAGGCTTCGGCCCAGT
*
21874926 ATTATGAAATATGAAA
1 AATATGAAATATGAAA
21874942 CATGAAAAGG
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
30 32 0.73
31 12 0.27
ACGTcount: A:0.42, C:0.14, G:0.21, T:0.23
Consensus pattern (30 bp):
AATATGAAATATGAAAGGCTTCGGCCCAGT
Found at i:21874915 original size:68 final size:68
Alignment explanation
Indices: 21874841--21874979 Score: 269
Period size: 68 Copynumber: 2.0 Consensus size: 68
21874831 CGTTTACAGT
21874841 AAAGGCTTCGGCCCAGTATTATGAAATATGAAACATGAAAAGGCTTCGGCCCAGTAATATGAAAT
1 AAAGGCTTCGGCCCAGTATTATGAAATATGAAACATGAAAAGGCTTCGGCCCAGTAATATGAAAT
21874906 ATG
66 ATG
*
21874909 AAAGGCTTCGGCCCAGTATTATGAAATATGAAACATGAAAAGGCTTCGGCCCAGTATTATGAAAT
1 AAAGGCTTCGGCCCAGTATTATGAAATATGAAACATGAAAAGGCTTCGGCCCAGTAATATGAAAT
21874974 ATG
66 ATG
21874977 AAA
1 AAA
21874980 TATGAAAAGG
Statistics
Matches: 70, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
68 70 1.00
ACGTcount: A:0.39, C:0.16, G:0.22, T:0.24
Consensus pattern (68 bp):
AAAGGCTTCGGCCCAGTATTATGAAATATGAAACATGAAAAGGCTTCGGCCCAGTAATATGAAAT
ATG
Found at i:21882453 original size:25 final size:25
Alignment explanation
Indices: 21882424--21882471 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
21882414 CCTTATAATG
* * *
21882424 AAAATGACCGTTTTGCCCCTAGGTA
1 AAAATGACCATTATACCCCTAGGTA
21882449 AAAATGACCATTATACCCCTAGG
1 AAAATGACCATTATACCCCTAGG
21882472 GTTTATGTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (25 bp):
AAAATGACCATTATACCCCTAGGTA
Found at i:21882540 original size:20 final size:20
Alignment explanation
Indices: 21882515--21882573 Score: 100
Period size: 20 Copynumber: 3.0 Consensus size: 20
21882505 TAAATATGGT
21882515 ATGTATGATATGCACATGAA
1 ATGTATGATATGCACATGAA
* *
21882535 ATGTATGATACGCACATGAT
1 ATGTATGATATGCACATGAA
21882555 ATGTATGATATGCACATGA
1 ATGTATGATATGCACATGA
21882574 GGTAATCATA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.37, C:0.12, G:0.20, T:0.31
Consensus pattern (20 bp):
ATGTATGATATGCACATGAA
Found at i:21882654 original size:23 final size:24
Alignment explanation
Indices: 21882624--21882718 Score: 124
Period size: 24 Copynumber: 4.0 Consensus size: 24
21882614 GAGGAAGTGA
21882624 AAAAGGGCTTATGCCCCAGTTA-T
1 AAAAGGGCTTATGCCCCAGTTATT
21882647 AAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
*
21882671 GAAAGGGCTT-TGGCCCCAGTTATT
1 AAAAGGGCTTAT-GCCCCAGTTATT
*
21882695 AAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAG-GGCTTATGCC-CCAGTTAT
21882719 ATGATAAAGC
Statistics
Matches: 64, Mismatches: 3, Indels: 8
0.85 0.04 0.11
Matches are distributed among these distances:
23 23 0.36
24 30 0.47
25 11 0.17
ACGTcount: A:0.28, C:0.21, G:0.24, T:0.26
Consensus pattern (24 bp):
AAAAGGGCTTATGCCCCAGTTATT
Found at i:21882692 original size:47 final size:49
Alignment explanation
Indices: 21882625--21882718 Score: 133
Period size: 47 Copynumber: 2.0 Consensus size: 49
21882615 AGGAAGTGAA
*
21882625 AAAGGGCTTATGCCCCAGTTA-TAAAAG-GGCTTATGCC-CCAGTTATTG
1 AAAGGGCTTATGCCCCAGTTATTAAAAGAGGC-TAGGCCTCCAGTTATTG
21882672 AAAGGGCTT-TGGCCCCAGTTATTAAAAGAGGCTAGGCCTCCAGTTAT
1 AAAGGGCTTAT-GCCCCAGTTATTAAAAGAGGCTAGGCCTCCAGTTAT
21882719 ATGATAAAGC
Statistics
Matches: 42, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
46 1 0.02
47 19 0.45
48 11 0.26
49 11 0.26
ACGTcount: A:0.28, C:0.21, G:0.24, T:0.27
Consensus pattern (49 bp):
AAAGGGCTTATGCCCCAGTTATTAAAAGAGGCTAGGCCTCCAGTTATTG
Found at i:21896527 original size:37 final size:37
Alignment explanation
Indices: 21896486--21896560 Score: 123
Period size: 37 Copynumber: 2.0 Consensus size: 37
21896476 TGTTTCTAAC
* * *
21896486 TACAACCTTAAAGAAATTCTGTACGGTTTCATTTTGG
1 TACAACCTCAAAGAAATTCTCTACAGTTTCATTTTGG
21896523 TACAACCTCAAAGAAATTCTCTACAGTTTCATTTTGG
1 TACAACCTCAAAGAAATTCTCTACAGTTTCATTTTGG
21896560 T
1 T
21896561 GTTCCTACTA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.31, C:0.19, G:0.13, T:0.37
Consensus pattern (37 bp):
TACAACCTCAAAGAAATTCTCTACAGTTTCATTTTGG
Found at i:21897864 original size:5 final size:5
Alignment explanation
Indices: 21897848--21897877 Score: 51
Period size: 5 Copynumber: 5.8 Consensus size: 5
21897838 AGTTTCGAGT
21897848 TTGAG TTTGAG TTGAG TTGAG TTGAG TTGA
1 TTGAG -TTGAG TTGAG TTGAG TTGAG TTGA
21897878 ATTTCACAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 19 0.79
6 5 0.21
ACGTcount: A:0.20, C:0.00, G:0.37, T:0.43
Consensus pattern (5 bp):
TTGAG
Found at i:21898027 original size:19 final size:21
Alignment explanation
Indices: 21897999--21898101 Score: 63
Period size: 20 Copynumber: 5.0 Consensus size: 21
21897989 TACAAAAAAA
*
21897999 AAAATAATTT-TCAAAAATTC
1 AAAATAATTTATAAAAAATTC
21898019 AAAAT-ATTTATAAAAAATTC
1 AAAATAATTTATAAAAAATTC
* * * *
21898039 AAATTTCATTTTTTAAAAAATTAT
1 AAA-AT-AATTTATAAAAAATT-C
*
21898063 AAAAAAATTTA-AAAAAA-TC
1 AAAATAATTTATAAAAAATTC
* *
21898082 TAAA-AATATATAAAGAAATT
1 AAAATAATTTATAAA-AAATT
21898102 TAATTTTTTT
Statistics
Matches: 63, Mismatches: 12, Indels: 15
0.70 0.13 0.17
Matches are distributed among these distances:
18 5 0.08
19 10 0.16
20 21 0.33
21 8 0.13
22 4 0.06
23 12 0.19
24 3 0.05
ACGTcount: A:0.59, C:0.05, G:0.01, T:0.35
Consensus pattern (21 bp):
AAAATAATTTATAAAAAATTC
Found at i:21915732 original size:40 final size:40
Alignment explanation
Indices: 21915684--21915765 Score: 155
Period size: 40 Copynumber: 2.0 Consensus size: 40
21915674 TGATTACTCG
*
21915684 TCTGAGCTAAATTCCATCTGCAACAAATGCAAGACCTTAT
1 TCTGAGCTAAATTCCATCTGAAACAAATGCAAGACCTTAT
21915724 TCTGAGCTAAATTCCATCTGAAACAAATGCAAGACCTTAT
1 TCTGAGCTAAATTCCATCTGAAACAAATGCAAGACCTTAT
21915764 TC
1 TC
21915766 ATTTCGGGAA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.35, C:0.24, G:0.12, T:0.28
Consensus pattern (40 bp):
TCTGAGCTAAATTCCATCTGAAACAAATGCAAGACCTTAT
Found at i:21928176 original size:8 final size:8
Alignment explanation
Indices: 21928163--21928190 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
21928153 AGGGTTCTTT
21928163 GTTTTCGG
1 GTTTTCGG
21928171 GTTTTCGG
1 GTTTTCGG
21928179 GTTTTCGG
1 GTTTTCGG
21928187 GTTT
1 GTTT
21928191 AATTTTTATC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.00, C:0.11, G:0.36, T:0.54
Consensus pattern (8 bp):
GTTTTCGG
Found at i:21928706 original size:19 final size:19
Alignment explanation
Indices: 21928678--21928756 Score: 117
Period size: 19 Copynumber: 4.2 Consensus size: 19
21928668 AATCTTTAAG
*
21928678 GATATACAATCTTAGATAT
1 GATATGCAATCTTAGATAT
21928697 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
21928716 GATA--CAATCTTAGATAT
1 GATATGCAATCTTAGATAT
21928733 GATATGCAATCTTGAAGATAT
1 GATATGCAATCTT--AGATAT
21928754 GAT
1 GAT
21928757 CTTGTAATCT
Statistics
Matches: 55, Mismatches: 1, Indels: 6
0.89 0.02 0.10
Matches are distributed among these distances:
17 17 0.31
19 29 0.53
21 9 0.16
ACGTcount: A:0.39, C:0.10, G:0.15, T:0.35
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:21928708 original size:36 final size:36
Alignment explanation
Indices: 21928668--21928753 Score: 115
Period size: 36 Copynumber: 2.4 Consensus size: 36
21928658 ATGGAAATAT
21928668 AATCTTTAAGGATATACAATCTTAGATATGATATGC
1 AATCTTTAAGGATATACAATCTTAGATATGATATGC
*
21928704 AATC-TT-AGATATGATACAATCTTAGATATGATATGC
1 AATCTTTAAG-GAT-ATACAATCTTAGATATGATATGC
*
21928740 AATCTTGAA-GATAT
1 AATCTTTAAGGATAT
21928754 GATCTTGTAA
Statistics
Matches: 43, Mismatches: 3, Indels: 9
0.78 0.05 0.16
Matches are distributed among these distances:
34 2 0.05
35 6 0.14
36 33 0.77
37 1 0.02
38 1 0.02
ACGTcount: A:0.40, C:0.10, G:0.14, T:0.36
Consensus pattern (36 bp):
AATCTTTAAGGATATACAATCTTAGATATGATATGC
Found at i:21929286 original size:25 final size:25
Alignment explanation
Indices: 21929258--21929306 Score: 73
Period size: 26 Copynumber: 2.0 Consensus size: 25
21929248 GTGCATAGTT
21929258 TTATTT-TTTTATATGCTATGTTTAA
1 TTATTTCTTTTATATGCTAT-TTTAA
*
21929283 TTATTTCTTTTATGTGCTATTTTA
1 TTATTTCTTTTATATGCTATTTTA
21929307 TGATATATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 10 0.45
26 12 0.55
ACGTcount: A:0.20, C:0.06, G:0.08, T:0.65
Consensus pattern (25 bp):
TTATTTCTTTTATATGCTATTTTAA
Found at i:21931558 original size:20 final size:19
Alignment explanation
Indices: 21931535--21931728 Score: 88
Period size: 19 Copynumber: 10.2 Consensus size: 19
21931525 TAAAAATAAG
21931535 AAAAATTATAAATATA-TA
1 AAAAATTATAAATATATTA
*
21931553 TAAAAATTATTAAGTAT-TTA
1 -AAAAATTA-TAAATATATTA
*
21931573 AAATATATTA-AAAT-TGTTA
1 AAA-A-ATTATAAATATATTA
* *
21931592 TAAACTTATAAATAT-TTA
1 AAAAATTATAAATATATTA
* *
21931610 AAAAATAATAAAT-TAATA
1 AAAAATTATAAATATATTA
*
21931628 AAATATATT-TAAA-ATTTTA
1 AAA-A-ATTATAAATATATTA
*
21931647 TAAAAACATATAAA-A-ATTCA
1 -AAAAA-TTATAAATATATT-A
*
21931667 TAAAAACTTATAAAAATATTA
1 -AAAAA-TTATAAATATATTA
*
21931688 AAAAATTCT-AATATATTA
1 AAAAATTATAAATATATTA
*
21931706 TAAAAATTATTAAAAAT-TTA
1 -AAAAATTA-TAAATATATTA
21931726 AAA
1 AAA
21931729 CTATAAAAAA
Statistics
Matches: 137, Mismatches: 18, Indels: 40
0.70 0.09 0.21
Matches are distributed among these distances:
17 4 0.03
18 33 0.24
19 45 0.33
20 42 0.31
21 10 0.07
22 3 0.02
ACGTcount: A:0.59, C:0.03, G:0.01, T:0.37
Consensus pattern (19 bp):
AAAAATTATAAATATATTA
Found at i:21931603 original size:29 final size:28
Alignment explanation
Indices: 21931571--21931650 Score: 85
Period size: 29 Copynumber: 2.9 Consensus size: 28
21931561 ATTAAGTATT
21931571 TAAAATATATTAAAATTGTTATAAACTT-A
1 TAAAATATATTAAAATT-TTATAAA-TTAA
** *
21931600 T-AAATAT-TTAAAAAATAATAAATTAA
1 TAAAATATATTAAAATTTTATAAATTAA
21931626 TAAAATATATTTAAAATTTTATAAA
1 TAAAATATA-TTAAAATTTTATAAA
21931651 AACATATAAA
Statistics
Matches: 41, Mismatches: 6, Indels: 8
0.75 0.11 0.15
Matches are distributed among these distances:
25 2 0.05
26 8 0.20
27 12 0.29
28 6 0.15
29 13 0.32
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.40
Consensus pattern (28 bp):
TAAAATATATTAAAATTTTATAAATTAA
Found at i:21931612 original size:55 final size:56
Alignment explanation
Indices: 21931540--21931650 Score: 140
Period size: 55 Copynumber: 2.0 Consensus size: 56
21931530 ATAAGAAAAA
* *
21931540 TTATAAATATATATAAAAATTATTAAGTATT-TAAAATATA-TTAAAATTGTTATAAAC
1 TTATAAATATATATAAAAAATAATAA--ATTATAAAATATATTTAAAATT-TTATAAAC
21931597 TTATAAATAT-T-TAAAAAATAATAAATTAATAAAATATATTTAAAATTTTATAAA
1 TTATAAATATATATAAAAAATAATAAATT-ATAAAATATATTTAAAATTTTATAAA
21931651 AACATATAAA
Statistics
Matches: 49, Mismatches: 2, Indels: 8
0.83 0.03 0.14
Matches are distributed among these distances:
53 3 0.06
55 27 0.55
56 9 0.18
57 10 0.20
ACGTcount: A:0.56, C:0.01, G:0.02, T:0.41
Consensus pattern (56 bp):
TTATAAATATATATAAAAAATAATAAATTATAAAATATATTTAAAATTTTATAAAC
Found at i:21931691 original size:29 final size:28
Alignment explanation
Indices: 21931644--21931737 Score: 97
Period size: 30 Copynumber: 3.3 Consensus size: 28
21931634 ATTTAAAATT
*
21931644 TTATAAAAACATATAAAAATTCATAAAAAC
1 TTATAAAAATAT-TAAAAATTC-TAAAAAC
*
21931674 TTATAAAAATATTAAAAAATTCTAATATA-
1 TTATAAAAATATT-AAAAATTCTAA-AAAC
21931703 TTATAAAAATTATTAAAAATT-T-AAAAC
1 TTATAAAAA-TATTAAAAATTCTAAAAAC
21931730 -TATAAAAA
1 TTATAAAAA
21931738 AGTCATTTAA
Statistics
Matches: 57, Mismatches: 3, Indels: 12
0.79 0.04 0.17
Matches are distributed among these distances:
26 10 0.18
27 1 0.02
28 1 0.02
29 20 0.35
30 25 0.44
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (28 bp):
TTATAAAAATATTAAAAATTCTAAAAAC
Found at i:21933919 original size:29 final size:29
Alignment explanation
Indices: 21933886--21933982 Score: 106
Period size: 29 Copynumber: 3.3 Consensus size: 29
21933876 AGTAGTGATC
* *
21933886 AAATCAAAAACTCTAAACTAATATCTCAA
1 AAATAAAAAACTCTAAACTAAAATCTCAA
* *
21933915 AAATCAAAAACTCTAAA-TAAAAATATCAA
1 AAATAAAAAACTCTAAACT-AAAATCTCAA
* * * *
21933944 AAATAAAAAACCCTAATCCAAAATCCCAA
1 AAATAAAAAACTCTAAACTAAAATCTCAA
21933973 AAATAAAAAA
1 AAATAAAAAA
21933983 TCCTAAAGCA
Statistics
Matches: 58, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
28 1 0.02
29 57 0.98
ACGTcount: A:0.63, C:0.19, G:0.00, T:0.19
Consensus pattern (29 bp):
AAATAAAAAACTCTAAACTAAAATCTCAA
Found at i:21933994 original size:29 final size:29
Alignment explanation
Indices: 21933886--21933996 Score: 96
Period size: 29 Copynumber: 3.8 Consensus size: 29
21933876 AGTAGTGATC
* * * * *
21933886 AAATCAAAAACTCTAAACTAATATCTCAA
1 AAATAAAAAACCCTAAACCAAAATCCCAA
* * ** **
21933915 AAATCAAAAACTCTAAATAAAAATATCAA
1 AAATAAAAAACCCTAAACCAAAATCCCAA
*
21933944 AAATAAAAAACCCTAATCCAAAATCCCAA
1 AAATAAAAAACCCTAAACCAAAATCCCAA
* *
21933973 AAATAAAAAATCCTAAAGCAAAAT
1 AAATAAAAAACCCTAAACCAAAAT
21933997 TTCCAAGCTT
Statistics
Matches: 68, Mismatches: 14, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 68 1.00
ACGTcount: A:0.61, C:0.19, G:0.01, T:0.19
Consensus pattern (29 bp):
AAATAAAAAACCCTAAACCAAAATCCCAA
Found at i:21951275 original size:16 final size:16
Alignment explanation
Indices: 21951254--21951284 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
21951244 TGAGGTAATC
21951254 TCAATTTCTATTTTTT
1 TCAATTTCTATTTTTT
*
21951270 TCAATTTCTGTTTTT
1 TCAATTTCTATTTTT
21951285 CAAATTTCTG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.16, C:0.13, G:0.03, T:0.68
Consensus pattern (16 bp):
TCAATTTCTATTTTTT
Found at i:21951300 original size:14 final size:15
Alignment explanation
Indices: 21951266--21951298 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
21951256 AATTTCTATT
21951266 TTTTTC-AATTTCTG
1 TTTTTCAAATTTCTG
21951280 TTTTTCAAATTTCTG
1 TTTTTCAAATTTCTG
21951295 TTTT
1 TTTT
21951299 CAGAAATCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 6 0.33
15 12 0.67
ACGTcount: A:0.15, C:0.12, G:0.06, T:0.67
Consensus pattern (15 bp):
TTTTTCAAATTTCTG
Found at i:21951631 original size:92 final size:92
Alignment explanation
Indices: 21951369--21951680 Score: 472
Period size: 92 Copynumber: 3.4 Consensus size: 92
21951359 TTTATGTTTC
* * *
21951369 AAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCGGCTCATATGCTGAGGTATTTTCAATT
1 AAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTTGGCTCACATGCTGAGGTATTTTCAATT
* *
21951434 TCTGTTTTTTTAATTTATATTTTTC--
66 TCTGTTCTTTCAATTTATATTTTTCAA
* * * *
21951459 AAAAAGCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAGG---ACACGCTGATGTATTTTCAAT
1 AAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCT-TGGCTCACATGCTGAGGTATTTTCAAT
21951521 TTCTGTTCTTTCAATTTATATTTTTCAA
65 TTCTGTTCTTTCAATTTATATTTTTCAA
*
21951549 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGCTCACATGCTGAGGTATTTTCAATT
1 AAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTTGGCTCACATGCTGAGGTATTTTCAATT
21951614 TCTGTTCTTTCAATTTATATTTTTCAA
66 TCTGTTCTTTCAATTTATATTTTTCAA
* *
21951641 AAAAATCAACTCATGTTGCGAGAGGTGAGTTGAGCCTTGG
1 AAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTTGG
21951681 GGCACGCTGA
Statistics
Matches: 202, Mismatches: 14, Indels: 10
0.89 0.06 0.04
Matches are distributed among these distances:
88 42 0.21
89 2 0.01
90 70 0.35
91 2 0.01
92 86 0.43
ACGTcount: A:0.29, C:0.16, G:0.18, T:0.38
Consensus pattern (92 bp):
AAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTTGGCTCACATGCTGAGGTATTTTCAATT
TCTGTTCTTTCAATTTATATTTTTCAA
Found at i:21951776 original size:73 final size:73
Alignment explanation
Indices: 21951641--21951776 Score: 200
Period size: 73 Copynumber: 1.9 Consensus size: 73
21951631 TATTTTTCAA
* * ** * *
21951641 AAAAATCAACTCATGTTGCGAGAGGTGAGTTGAGCCTTGGGGCACGCTGAGTTAATTGCAATTCC
1 AAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTGCAATTCC
21951706 TGTTTGTC
66 TGTTTGTC
* *
21951714 AAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATT
1 AAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTGCAATT
21951777 TCCGTTTTTC
Statistics
Matches: 55, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
73 55 1.00
ACGTcount: A:0.29, C:0.18, G:0.25, T:0.29
Consensus pattern (73 bp):
AAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTGCAATTCC
TGTTTGTC
Found at i:21951837 original size:160 final size:162
Alignment explanation
Indices: 21951549--21951870 Score: 452
Period size: 160 Copynumber: 2.0 Consensus size: 162
21951539 TATTTTTCAA
* * *
21951549 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGCTCACATGCTGAGGTATTTTCAATT
1 AAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTAGG--CACACGCTGAGGTATTTTCAATT
* * * * *
21951614 TCTGTTCTTTCAATTTATATTTTTCAAAAAAATCAACTCATGTTGCGAGAGGTGAGTTGAGCCTT
64 TCCGTTCTTTCAAGTTATACTCTTC-AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTT
* *
21951679 GGGGCACGCTGAGTTAATTGCAATTCCTGTTTGTC
128 AGGGCACGCTGAGGTAATTGCAATTCCTGTTTGTC
21951714 AAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCAGG-ACACGCTGAGGTATTTTCAATTT
1 AAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCT-AGGCACACGCTGAGGTATTTTCAATTT
*
21951778 CCGTT-TTTCAAGTTATGCTCTTC-AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTAG
65 CCGTTCTTTCAAGTTATACTCTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTAG
* * * *
21951841 GGCATGCTGAGGTATTTTCAATTTCTGTTT
130 GGCACGCTGAGGTAATTGCAATTCCTGTTT
21951871 TTTCAAGTTA
Statistics
Matches: 141, Mismatches: 15, Indels: 7
0.87 0.09 0.04
Matches are distributed among these distances:
160 63 0.45
162 14 0.10
163 26 0.18
165 36 0.26
166 2 0.01
ACGTcount: A:0.27, C:0.17, G:0.22, T:0.34
Consensus pattern (162 bp):
AAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTAGGCACACGCTGAGGTATTTTCAATTTC
CGTTCTTTCAAGTTATACTCTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTAGG
GCACGCTGAGGTAATTGCAATTCCTGTTTGTC
Found at i:21951918 original size:88 final size:86
Alignment explanation
Indices: 21951712--21952049 Score: 369
Period size: 87 Copynumber: 3.9 Consensus size: 86
21951702 TTCCTGTTTG
* * * *
21951712 TCAAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATT
1 TCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTAGGGCATGCTGAGGTATTTTCAATT
* * *
21951777 TCCGTTTTTCAAGTTATGCTCT
66 TCTGTTTTTCAAGTTAT-ATTT
21951799 TCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTAGGGCATGCTGAGGTATTTTCAATT
1 TCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTAGGGCATGCTGAGGTATTTTCAATT
21951864 TCTGTTTTTTCAAGTTATATTTT
66 TCTG-TTTTTCAAGTTATA-TTT
* *
21951887 TCAAAAATCAACTCATATTGTGAGAGGTGAGTTGAGCC-TCGGGTCACATG-TCGAGGTATTTTC
1 TCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTAGGG---CATGCT-GAGGTATTTTC
** * * *
21951950 AAAATCTGCTTTTCAAATTA-AGTT
62 AATTTCTGTTTTTCAAGTTATATTT
* ** * * * *
21951974 TCAAAAACCAACTCATATTGCGAGAAATGAGTTGAGCCTT-GGCTCACGTGCTAAGCTATATTCA
1 TCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTAGG-GCA--TGCTGAGGTATTTTCA
21952038 ATTTCTGTTTTT
63 ATTTCTGTTTTT
21952050 AATGTCTGTT
Statistics
Matches: 215, Mismatches: 25, Indels: 22
0.82 0.10 0.08
Matches are distributed among these distances:
85 2 0.01
87 126 0.59
88 55 0.26
89 11 0.05
90 21 0.10
ACGTcount: A:0.28, C:0.17, G:0.20, T:0.35
Consensus pattern (86 bp):
TCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTAGGGCATGCTGAGGTATTTTCAATT
TCTGTTTTTCAAGTTATATTT
Found at i:21952007 original size:175 final size:176
Alignment explanation
Indices: 21951712--21952049 Score: 443
Period size: 175 Copynumber: 1.9 Consensus size: 176
21951702 TTCCTGTTTG
**
21951712 TCAAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATT
1 TCAAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAAAA
* * * * **
21951777 TCCGTTTTTCAAGTTATGCTCTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTAGG
66 TCCGCTTTTCAAATTAAGCTCTTCAAAAACCAACTCATATTGCGAGAAATGAGTTGAGCCTT-GG
* * *
21951842 -GCA-TGCTGAGGTATTTTCAATTTCTGTTTTTTCAAGTTATATTTT
130 CGCACTGCTAAGCTATATTCAATTTCTGTTTTTTCAAGTTATATTTT
** * *
21951887 TCAAAAATCAACTCATATTGTGAGAGGTGAGTTGAGCCTCGGGTCACATG-TCGAGGTATTTTCA
1 TCAAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCAGG--ACACGCT-GAGGTATTTTCA
*
21951951 AAATCTGCTTTTCAAATTAAG-T-TTCAAAAACCAACTCATATTGCGAGAAATGAGTTGAGCCTT
63 AAATCCGCTTTTCAAATTAAGCTCTTCAAAAACCAACTCATATTGCGAGAAATGAGTTGAGCCTT
*
21952014 GGCTCACGTGCTAAGCTATATTCAATTTCTGTTTTT
128 GGCGCAC-TGCTAAGCTATATTCAATTTCTGTTTTT
21952050 AATGTCTGTT
Statistics
Matches: 140, Mismatches: 17, Indels: 10
0.84 0.10 0.06
Matches are distributed among these distances:
174 2 0.01
175 80 0.57
176 2 0.01
177 56 0.40
ACGTcount: A:0.28, C:0.17, G:0.20, T:0.35
Consensus pattern (176 bp):
TCAAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAAAA
TCCGCTTTTCAAATTAAGCTCTTCAAAAACCAACTCATATTGCGAGAAATGAGTTGAGCCTTGGC
GCACTGCTAAGCTATATTCAATTTCTGTTTTTTCAAGTTATATTTT
Found at i:21952248 original size:21 final size:21
Alignment explanation
Indices: 21952206--21952249 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
21952196 GCAGAGCCTT
* *
21952206 GAAGTTACAGTGGAGCTAATC
1 GAAGTTACAGTGAAACTAATC
* *
21952227 GAAGTTGCAGTGAAACTGATC
1 GAAGTTACAGTGAAACTAATC
21952248 GA
1 GA
21952250 GGATATTAGA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.34, C:0.14, G:0.30, T:0.23
Consensus pattern (21 bp):
GAAGTTACAGTGAAACTAATC
Found at i:21952605 original size:25 final size:25
Alignment explanation
Indices: 21952568--21952615 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
21952558 AAAAGTCTTT
*
21952568 ACTCTATTCTCGTCACACGACAACA
1 ACTCTATTATCGTCACACGACAACA
* * *
21952593 ACTCTGTTATCGTTATACGACAA
1 ACTCTATTATCGTCACACGACAA
21952616 TGAGTAAAGA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.31, C:0.29, G:0.10, T:0.29
Consensus pattern (25 bp):
ACTCTATTATCGTCACACGACAACA
Found at i:21953994 original size:17 final size:17
Alignment explanation
Indices: 21953974--21954012 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
21953964 CTTCGTTATT
*
21953974 TTATTTCATTTTAATTA
1 TTATTTCATTATAATTA
* *
21953991 TTATTTGATTATCATTA
1 TTATTTCATTATAATTA
21954008 TTATT
1 TTATT
21954013 ATATTAGTGT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.28, C:0.05, G:0.03, T:0.64
Consensus pattern (17 bp):
TTATTTCATTATAATTA
Found at i:21954084 original size:15 final size:16
Alignment explanation
Indices: 21954064--21954098 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
21954054 ATCTACATAG
21954064 TATTTT-TTTTAAAAT
1 TATTTTATTTTAAAAT
*
21954079 TATTTTATTTTAATAT
1 TATTTTATTTTAAAAT
21954095 TATT
1 TATT
21954099 AAATTATGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 6 0.33
16 12 0.67
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (16 bp):
TATTTTATTTTAAAAT
Found at i:21954135 original size:3 final size:3
Alignment explanation
Indices: 21954127--21954226 Score: 62
Period size: 3 Copynumber: 32.3 Consensus size: 3
21954117 TGAATTTCTA
* * * *
21954127 TAT TAT TAT TAT TAT TAT TGT TACT TAT TAT TAC TGT TAT GTACA TAT
1 TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT -TA-T TAT
* * *
21954175 TAT T-T ATAC TA- TACT TAA TAT TAT TAT TAT TAT TA- TATT TAC TAT
1 TAT TAT -TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT
21954220 TAT TAT T
1 TAT TAT T
21954227 TATAAATATT
Statistics
Matches: 75, Mismatches: 13, Indels: 18
0.71 0.12 0.17
Matches are distributed among these distances:
2 5 0.07
3 59 0.79
4 11 0.15
ACGTcount: A:0.32, C:0.06, G:0.03, T:0.59
Consensus pattern (3 bp):
TAT
Found at i:21954199 original size:24 final size:24
Alignment explanation
Indices: 21954172--21954230 Score: 75
Period size: 24 Copynumber: 2.5 Consensus size: 24
21954162 GTTATGTACA
21954172 TATTATTTATACTATACTTAATAT
1 TATTATTTATACTATACTTAATAT
* * *
21954196 TATTA-TTATTATTATATTTACTAT
1 TATTATTTA-TACTATACTTAATAT
21954220 TATTATTTATA
1 TATTATTTATA
21954231 AATATTAGTG
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
23 3 0.10
24 24 0.80
25 3 0.10
ACGTcount: A:0.36, C:0.05, G:0.00, T:0.59
Consensus pattern (24 bp):
TATTATTTATACTATACTTAATAT
Found at i:21954908 original size:11 final size:11
Alignment explanation
Indices: 21954886--21954916 Score: 53
Period size: 11 Copynumber: 2.7 Consensus size: 11
21954876 ATATTTATTT
21954886 TATATATATATG
1 TATATAT-TATG
21954898 TATATATTATG
1 TATATATTATG
21954909 TATATATT
1 TATATATT
21954917 TTAACATTAC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 12 0.63
12 7 0.37
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.55
Consensus pattern (11 bp):
TATATATTATG
Found at i:21955298 original size:11 final size:11
Alignment explanation
Indices: 21955282--21955306 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
21955272 TAATATCCCG
21955282 AATTAGGGCCT
1 AATTAGGGCCT
21955293 AATTAGGGCCT
1 AATTAGGGCCT
21955304 AAT
1 AAT
21955307 CGGAGTAGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.32, C:0.16, G:0.24, T:0.28
Consensus pattern (11 bp):
AATTAGGGCCT
Found at i:21956878 original size:49 final size:49
Alignment explanation
Indices: 21956801--21957145 Score: 411
Period size: 49 Copynumber: 6.9 Consensus size: 49
21956791 ACTATTGTGA
*
21956801 GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATT
1 GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT
* * ** * *
21956850 GGTCGCATGTGTAGTACTAAGTGCAGGCTACTATGCATACCCGAAAACTGT
1 GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAA-T-T
* * * **
21956901 GATCACTTGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATTGTT
1 GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT
* * * *
21956950 GGTCGCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCTGATAACTT
1 GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAA-TT
* * * **
21957000 CGATCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGATGGTT
1 -GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT
* *
21957050 AGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCTGATAATT
1 -GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT
* * *
21957100 GGTCGCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGATA
1 GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATA
21957146 GCTTCGGCTA
Statistics
Matches: 250, Mismatches: 42, Indels: 8
0.83 0.14 0.03
Matches are distributed among these distances:
49 123 0.49
50 50 0.20
51 77 0.31
ACGTcount: A:0.26, C:0.19, G:0.26, T:0.29
Consensus pattern (49 bp):
GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT
Found at i:21956981 original size:100 final size:99
Alignment explanation
Indices: 21956803--21957146 Score: 483
Period size: 100 Copynumber: 3.5 Consensus size: 99
21956793 TATTGTGAGG
* *
21956803 TCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTGGTCGCATGTGTAGTACT
1 TCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAGTTGGTCGCATGTGTAGTACT
* * *
21956868 AAGTGCAGGCTACTATGCATACCCGAAAACTGTGA
66 AAGTGCAGGCTACTATGCGTACCTGATAACT-TGA
* * *
21956903 TCACTTGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATTGTTGGTCGCATGTGTAGTACT
1 TCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAGTTGGTCGCATGTGTAGTACT
21956968 AAGTGCAGGCTACTATGCGTACCTGATAACTTCGA
66 AAGTGCAGGCTACTATGCGTACCTGATAACTT-GA
* * * * *
21957003 TCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGATGGTTAGGTCACGTGTGTAGTAC
1 TCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAGTT-GGTCGCATGTGTAGTAC
* * *
21957068 TAAGTGCAGGCTACTACGTGTACCTGATAA-TTGG
65 TAAGTGCAGGCTACTATGCGTACCTGATAACTTGA
* * *
21957102 TCGCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGATAG
1 TCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAG
21957147 CTTCGGCTAC
Statistics
Matches: 219, Mismatches: 23, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
99 41 0.19
100 135 0.62
101 43 0.20
ACGTcount: A:0.26, C:0.19, G:0.26, T:0.29
Consensus pattern (99 bp):
TCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAGTTGGTCGCATGTGTAGTACT
AAGTGCAGGCTACTATGCGTACCTGATAACTTGA
Found at i:21957037 original size:28 final size:28
Alignment explanation
Indices: 21957005--21957088 Score: 83
Period size: 28 Copynumber: 3.2 Consensus size: 28
21956995 AACTTCGATC
21957005 ACGTGTGTAGTACTAAGTGCAGGCTACT
1 ACGTGTGTAGTACTAAGTGCAGGCTACT
* * *
21957033 ACGTGTATCAG-A-T-GGT-TAGG-T-C-
1 ACGTGTGT-AGTACTAAGTGCAGGCTACT
21957055 ACGTGTGTAGTACTAAGTGCAGGCTACT
1 ACGTGTGTAGTACTAAGTGCAGGCTACT
21957083 ACGTGT
1 ACGTGT
21957089 ACCTGATAAT
Statistics
Matches: 42, Mismatches: 6, Indels: 16
0.66 0.09 0.25
Matches are distributed among these distances:
21 2 0.05
22 8 0.19
23 2 0.05
24 3 0.07
25 6 0.14
26 3 0.07
27 2 0.05
28 14 0.33
29 2 0.05
ACGTcount: A:0.24, C:0.17, G:0.30, T:0.30
Consensus pattern (28 bp):
ACGTGTGTAGTACTAAGTGCAGGCTACT
Found at i:21960384 original size:45 final size:45
Alignment explanation
Indices: 21960334--21960480 Score: 267
Period size: 45 Copynumber: 3.3 Consensus size: 45
21960324 GCAAAAATAA
* *
21960334 AAACTTTGTAATTTTGAATGACATGTGTTGAAAGAAACTTGGAAC
1 AAACTTTGTAATTTTAAATGACATGTGTTGAAACAAACTTGGAAC
*
21960379 AAACTTTATAATTTTAAATGACATGTGTTGAAACAAACTTGGAAC
1 AAACTTTGTAATTTTAAATGACATGTGTTGAAACAAACTTGGAAC
21960424 AAACTTTGTAATTTTAAATGACATGTGTTGAAACAAACTTGGAAC
1 AAACTTTGTAATTTTAAATGACATGTGTTGAAACAAACTTGGAAC
21960469 AAACTTTGTAAT
1 AAACTTTGTAAT
21960481 ATAAATTAGA
Statistics
Matches: 98, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 98 1.00
ACGTcount: A:0.40, C:0.10, G:0.16, T:0.34
Consensus pattern (45 bp):
AAACTTTGTAATTTTAAATGACATGTGTTGAAACAAACTTGGAAC
Found at i:21963146 original size:20 final size:19
Alignment explanation
Indices: 21963110--21963160 Score: 54
Period size: 20 Copynumber: 2.7 Consensus size: 19
21963100 AATGACTATT
*
21963110 TTGTAAA-GTTGTAAAATAA
1 TTGTAAATG-TGTGAAATAA
21963129 GTTGTAAATGTGTGAAATAA
1 -TTGTAAATGTGTGAAATAA
21963149 TTG-AAAT-TGTGA
1 TTGTAAATGTGTGA
21963161 GTTGCTATAG
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
17 5 0.17
18 4 0.14
19 3 0.10
20 16 0.55
21 1 0.03
ACGTcount: A:0.41, C:0.00, G:0.22, T:0.37
Consensus pattern (19 bp):
TTGTAAATGTGTGAAATAA
Found at i:21963948 original size:44 final size:44
Alignment explanation
Indices: 21963875--21963961 Score: 120
Period size: 44 Copynumber: 2.0 Consensus size: 44
21963865 TATATATGAG
* * * *
21963875 GCATCTGAGCTCGTTGAGTTAGTCTGAGTTCACTATGGATGCGA
1 GCATCCGAACTCGTTGAATTAGTCCGAGTTCACTATGGATGCGA
* *
21963919 GCATCCGAACTCGTTGAATTGGTCCGAGTTCATTATGGATGCG
1 GCATCCGAACTCGTTGAATTAGTCCGAGTTCACTATGGATGCG
21963962 GTACATGTAA
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
44 37 1.00
ACGTcount: A:0.21, C:0.20, G:0.29, T:0.31
Consensus pattern (44 bp):
GCATCCGAACTCGTTGAATTAGTCCGAGTTCACTATGGATGCGA
Found at i:21967911 original size:24 final size:24
Alignment explanation
Indices: 21967883--21967973 Score: 76
Period size: 24 Copynumber: 3.8 Consensus size: 24
21967873 AAATTACCCG
* *
21967883 TTAAGCTCGCATGAGCTTTCTGAT
1 TTAAGCTCGCATAAGCTTCCTGAT
** * *
21967907 TTAAGCTCTTATGAGCTTCCTGTT
1 TTAAGCTCGCATAAGCTTCCTGAT
* *
21967931 ATTAAACTCGAATAAGCTTCCT-AT
1 -TTAAGCTCGCATAAGCTTCCTGAT
*
21967955 TATAAGCTCACATAAGCTT
1 T-TAAGCTCGCATAAGCTT
21967974 TCTATTATTT
Statistics
Matches: 53, Mismatches: 12, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
23 1 0.02
24 35 0.66
25 17 0.32
ACGTcount: A:0.27, C:0.21, G:0.14, T:0.37
Consensus pattern (24 bp):
TTAAGCTCGCATAAGCTTCCTGAT
Found at i:21967948 original size:25 final size:25
Alignment explanation
Indices: 21967920--21967982 Score: 76
Period size: 24 Copynumber: 2.6 Consensus size: 25
21967910 AGCTCTTATG
*
21967920 AGCTTCCTGTTATTAAACTCGA-ATA
1 AGCTTCCTATTATTAAACTC-ACATA
*
21967945 AGCTTCCTATTA-TAAGCTCACATA
1 AGCTTCCTATTATTAAACTCACATA
*
21967969 AGCTTTCTATTATT
1 AGCTTCCTATTATT
21967983 TGGCTTGGAA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
23 1 0.03
24 20 0.61
25 12 0.36
ACGTcount: A:0.30, C:0.21, G:0.10, T:0.40
Consensus pattern (25 bp):
AGCTTCCTATTATTAAACTCACATA
Found at i:21968645 original size:2 final size:2
Alignment explanation
Indices: 21968638--21968681 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
21968628 GATATAGTTT
21968638 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
21968680 TA
1 TA
21968682 AGGTCTTAAT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:21973345 original size:84 final size:84
Alignment explanation
Indices: 21973246--21973412 Score: 307
Period size: 84 Copynumber: 2.0 Consensus size: 84
21973236 CTTATATTCA
* * *
21973246 ACTACTCATTCTCTCTTTCTCTCTCTCTCAAATTCTTAGTTTTGGTTAAATATGTTCAAGAAAAG
1 ACTACTCATTCTCTCTCTCTCTCTCTCTCAAATTCTTAGTTTTGGTGAAATATGTTCAAAAAAAG
21973311 CTTGGGCTGCATTTTTTTT
66 CTTGGGCTGCATTTTTTTT
21973330 ACTACTCATTCTCTCTCTCTCTCTCTCTCAAATTCTTAGTTTTGGTGAAATATGTTCAAAAAAAG
1 ACTACTCATTCTCTCTCTCTCTCTCTCTCAAATTCTTAGTTTTGGTGAAATATGTTCAAAAAAAG
21973395 CTTGGGCTGCATTTTTTT
66 CTTGGGCTGCATTTTTTT
21973413 GTAGTGGCAG
Statistics
Matches: 80, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
84 80 1.00
ACGTcount: A:0.22, C:0.21, G:0.12, T:0.45
Consensus pattern (84 bp):
ACTACTCATTCTCTCTCTCTCTCTCTCTCAAATTCTTAGTTTTGGTGAAATATGTTCAAAAAAAG
CTTGGGCTGCATTTTTTTT
Found at i:21983953 original size:22 final size:22
Alignment explanation
Indices: 21983927--21983981 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
21983917 ACATAAAGAC
21983927 AATTTATAAAATTATAAATGTA
1 AATTTATAAAATTATAAATGTA
*
21983949 AATTTATAAAATTATAAATGTT
1 AATTTATAAAATTATAAATGTA
*
21983971 AATTAATAAAA
1 AATTTATAAAA
21983982 AAGTAAATAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (22 bp):
AATTTATAAAATTATAAATGTA
Found at i:21983988 original size:22 final size:22
Alignment explanation
Indices: 21983927--21983989 Score: 65
Period size: 22 Copynumber: 2.9 Consensus size: 22
21983917 ACATAAAGAC
* *
21983927 AATTTATAAAATTATAAATGTA
1 AATTAATAAAATAATAAATGTA
* * *
21983949 AATTTATAAAATTATAAATGTT
1 AATTAATAAAATAATAAATGTA
21983971 AATTAATAAAA-AAGTAAAT
1 AATTAATAAAATAA-TAAAT
21983990 ATTTTTATAA
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
21 1 0.03
22 36 0.97
ACGTcount: A:0.57, C:0.00, G:0.05, T:0.38
Consensus pattern (22 bp):
AATTAATAAAATAATAAATGTA
Found at i:21984607 original size:47 final size:47
Alignment explanation
Indices: 21984538--21984630 Score: 177
Period size: 47 Copynumber: 2.0 Consensus size: 47
21984528 AACCAATTCA
*
21984538 TCTCTAACTCATTGTACAGTATCATGATCCATATGCATTCTCAGCTT
1 TCTCTAACTCATCGTACAGTATCATGATCCATATGCATTCTCAGCTT
21984585 TCTCTAACTCATCGTACAGTATCATGATCCATATGCATTCTCAGCT
1 TCTCTAACTCATCGTACAGTATCATGATCCATATGCATTCTCAGCT
21984631 AAAGATGCAA
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 45 1.00
ACGTcount: A:0.26, C:0.27, G:0.11, T:0.37
Consensus pattern (47 bp):
TCTCTAACTCATCGTACAGTATCATGATCCATATGCATTCTCAGCTT
Found at i:21993535 original size:16 final size:16
Alignment explanation
Indices: 21993513--21993565 Score: 65
Period size: 15 Copynumber: 3.4 Consensus size: 16
21993503 TTTGACATAA
21993513 TATTTTTTGAATATAT
1 TATTTTTTGAATATAT
* * *
21993529 CA-TTTTTCACT-TAT
1 TATTTTTTGAATATAT
21993543 TATTTTTTGAATATAT
1 TATTTTTTGAATATAT
21993559 TATTTTT
1 TATTTTT
21993566 AAATTTCTTT
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
14 4 0.14
15 14 0.48
16 11 0.38
ACGTcount: A:0.26, C:0.06, G:0.04, T:0.64
Consensus pattern (16 bp):
TATTTTTTGAATATAT
Found at i:21993581 original size:30 final size:30
Alignment explanation
Indices: 21993513--21993570 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
21993503 TTTGACATAA
* *
21993513 TATTTTTTGAATATATCATTTTTCACTTAT
1 TATTTTTTGAATATATCATTTTTAAATTAT
*
21993543 TATTTTTTGAATATATTATTTTTAAATT
1 TATTTTTTGAATATATCATTTTTAAATT
21993571 TCTTTATTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.29, C:0.05, G:0.03, T:0.62
Consensus pattern (30 bp):
TATTTTTTGAATATATCATTTTTAAATTAT
Done.