Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr2
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: 41236440
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 2030548 characters in sequence are not A, C, G, or T
File 43 of 106
Found at i:16275460 original size:37 final size:37
Alignment explanation
Indices: 16275418--16275534 Score: 150
Period size: 37 Copynumber: 3.2 Consensus size: 37
16275408 TAATGTTGTG
*
16275418 TGATGATGTTGAAGTGTGCGAGCAGGAAGTGCACACA
1 TGATGATGTTGAAGTGTGCGAGCAGGGAGTGCACACA
* * *
16275455 TGATGATGAT--AGTGTGAGAGTAGGGAGTGCACACA
1 TGATGATGTTGAAGTGTGCGAGCAGGGAGTGCACACA
* *
16275490 TGATGATGTTGAAGTGTGCGAGTC-GGGAGTGAACAAA
1 TGATGATGTTGAAGTGTGCGAG-CAGGGAGTGCACACA
16275527 TGATGATG
1 TGATGATG
16275535 ATATTGTGTT
Statistics
Matches: 68, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
35 31 0.46
37 37 0.54
ACGTcount: A:0.30, C:0.09, G:0.37, T:0.24
Consensus pattern (37 bp):
TGATGATGTTGAAGTGTGCGAGCAGGGAGTGCACACA
Found at i:16275484 original size:35 final size:35
Alignment explanation
Indices: 16275420--16275542 Score: 140
Period size: 35 Copynumber: 3.5 Consensus size: 35
16275410 ATGTTGTGTG
* * *
16275420 ATGATGTTGA-AGTGTGCGAGCAGGAAGTGCACAC
1 ATGATGATGATAGTGTGCGAGTAGGGAGTGCACAC
*
16275454 ATGATGATGATAGTGTGAGAGTAGGGAGTGCACAC
1 ATGATGATGATAGTGTGCGAGTAGGGAGTGCACAC
* * * *
16275489 ATGATGATGTTGAAGTGTGCGAGTCGGGAGTGAACAA
1 ATGATGATGAT--AGTGTGCGAGTAGGGAGTGCACAC
*
16275526 ATGATGATGATATTGTG
1 ATGATGATGATAGTGTG
16275543 TTGAAATGAG
Statistics
Matches: 75, Mismatches: 11, Indels: 5
0.82 0.12 0.05
Matches are distributed among these distances:
34 9 0.12
35 36 0.48
37 30 0.40
ACGTcount: A:0.30, C:0.09, G:0.36, T:0.25
Consensus pattern (35 bp):
ATGATGATGATAGTGTGCGAGTAGGGAGTGCACAC
Found at i:16280215 original size:16 final size:16
Alignment explanation
Indices: 16280196--16280226 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
16280186 ATAAAAATAT
16280196 AAAAAAATCAAAATCG
1 AAAAAAATCAAAATCG
*
16280212 AAAAGAATCAAAATC
1 AAAAAAATCAAAATC
16280227 TAAATTTTGG
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:0.68, C:0.13, G:0.06, T:0.13
Consensus pattern (16 bp):
AAAAAAATCAAAATCG
Found at i:16284544 original size:43 final size:43
Alignment explanation
Indices: 16284470--16284588 Score: 141
Period size: 43 Copynumber: 2.8 Consensus size: 43
16284460 TCACCAGCTC
* * **** *
16284470 ATGCGCACTCCTTACTCACACATGGTTGGGTCATCAC-CGGGTT
1 ATGCGCACTCCCTACTCGCACATAACCGGGTCATC-CTCGGCTT
16284513 ATGCGCACTCCCTACTCGCACATAACCGGGTCATCCTCGGCTT
1 ATGCGCACTCCCTACTCGCACATAACCGGGTCATCCTCGGCTT
* *
16284556 ATGCGCACTCCCTACTAGCACATAACCGAGTCA
1 ATGCGCACTCCCTACTCGCACATAACCGGGTCA
16284589 ATATAATTAC
Statistics
Matches: 66, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
42 1 0.02
43 65 0.98
ACGTcount: A:0.22, C:0.35, G:0.19, T:0.24
Consensus pattern (43 bp):
ATGCGCACTCCCTACTCGCACATAACCGGGTCATCCTCGGCTT
Found at i:16294431 original size:5 final size:5
Alignment explanation
Indices: 16294421--16294458 Score: 69
Period size: 5 Copynumber: 7.8 Consensus size: 5
16294411 ACCTAATCTG
16294421 ACTTA ACTTA AC-TA ACTTA ACTTA ACTTA ACTTA ACTT
1 ACTTA ACTTA ACTTA ACTTA ACTTA ACTTA ACTTA ACTT
16294459 GGGCCACGCA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
4 4 0.12
5 28 0.88
ACGTcount: A:0.39, C:0.21, G:0.00, T:0.39
Consensus pattern (5 bp):
ACTTA
Found at i:16294513 original size:15 final size:15
Alignment explanation
Indices: 16294493--16294538 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
16294483 TTCTTAAAAT
16294493 AACTTTAAAACCAAA
1 AACTTTAAAACCAAA
16294508 AACTTTAAAATCC-AA
1 AACTTTAAAA-CCAAA
* *
16294523 AGCTTTAAAATCAAA
1 AACTTTAAAACCAAA
16294538 A
1 A
16294539 TCTCTTATCT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
14 1 0.04
15 24 0.89
16 2 0.07
ACGTcount: A:0.57, C:0.17, G:0.02, T:0.24
Consensus pattern (15 bp):
AACTTTAAAACCAAA
Found at i:16301013 original size:40 final size:40
Alignment explanation
Indices: 16300920--16301054 Score: 202
Period size: 40 Copynumber: 3.4 Consensus size: 40
16300910 ATAGTGCCTG
* * * * * *
16300920 TGTGCACGATGTGGGGGGATGTACACGACGGC-ACTGAT-
1 TGTGCACGATGTGGGGGGATGCACATGATGGCGCCGGCTA
16300958 TGTGCACGATGTGGGGGGATGCACATGATGGCGCCGGCTA
1 TGTGCACGATGTGGGGGGATGCACATGATGGCGCCGGCTA
16300998 TGTGCACGATGTGGGGGGATGCACATGATGGCGCCGGCTA
1 TGTGCACGATGTGGGGGGATGCACATGATGGCGCCGGCTA
16301038 TGTGCACGATGTGGGGG
1 TGTGCACGATGTGGGGG
16301055 AATGTATATG
Statistics
Matches: 89, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
38 29 0.33
39 3 0.03
40 57 0.64
ACGTcount: A:0.18, C:0.19, G:0.43, T:0.21
Consensus pattern (40 bp):
TGTGCACGATGTGGGGGGATGCACATGATGGCGCCGGCTA
Found at i:16302707 original size:73 final size:73
Alignment explanation
Indices: 16302608--16302789 Score: 194
Period size: 73 Copynumber: 2.5 Consensus size: 73
16302598 AACAGAATGA
16302608 TCTTAGTCGACTAA-TTGCGC-TCTTAGTCGACTAAGTTGTCTTTGTCTTCTGAA-CCCAG-TTT
1 TCTTAGTCGACTAACTT-C-CTTCTTAGTCGACTAAGTTGTCTTTGTC-T-TGAAGCCCAGATTT
* *
16302669 TTGGCAGT-GAGC
62 CTGGCAATAG-GC
* * * *
16302681 TCTTAGTCGACTAACTTCCTTTTTAGTCGATTAAGTTGTTTTTGTCTTGAAGTCCAGATTTCTGG
1 TCTTAGTCGACTAACTTCCTTCTTAGTCGACTAAGTTGTCTTTGTCTTGAAGCCCAGATTTCTGG
*
16302746 TAATAGGC
66 CAATAGGC
* * *
16302754 TCTTAGTCGACTAACTTACTTCTTGGTCAACTAAGT
1 TCTTAGTCGACTAACTTCCTTCTTAGTCGACTAAGT
16302790 CTTCTCTGTC
Statistics
Matches: 92, Mismatches: 12, Indels: 10
0.81 0.11 0.09
Matches are distributed among these distances:
71 4 0.04
72 6 0.07
73 79 0.86
74 3 0.03
ACGTcount: A:0.20, C:0.20, G:0.19, T:0.41
Consensus pattern (73 bp):
TCTTAGTCGACTAACTTCCTTCTTAGTCGACTAAGTTGTCTTTGTCTTGAAGCCCAGATTTCTGG
CAATAGGC
Found at i:16309603 original size:35 final size:34
Alignment explanation
Indices: 16309564--16309740 Score: 145
Period size: 35 Copynumber: 5.2 Consensus size: 34
16309554 TCAAGCTTAG
* *
16309564 CCAAAACCTTTCACAATGGTTTTT-ACCAGGATCAA
1 CCAAAACC-TTCACAATGGTTTTTCA-AAGGCTCAA
* *
16309599 CCAAAA--TCCA-AAGTGGTTTTTCAAAGGCTTAA
1 CCAAAACCTTCACAA-TGGTTTTTCAAAGGCTCAA
* **
16309631 CCACAACCTTTCACAATGGTTTTTCACGGGCTCAA
1 CCAAAACC-TTCACAATGGTTTTTCAAAGGCTCAA
16309666 CCAAAACC--CA-AAGTGGTTTTTCAAAGGCTCAA
1 CCAAAACCTTCACAA-TGGTTTTTCAAAGGCTCAA
* * *
16309698 CCACAACCTACAACAATGGTTTTTC-AAGAGATCAA
1 CCAAAACCTTC-ACAATGGTTTTTCAAAG-GCTCAA
16309733 CCAAAACC
1 CCAAAACC
16309741 GAACAACTAA
Statistics
Matches: 115, Mismatches: 15, Indels: 24
0.75 0.10 0.16
Matches are distributed among these distances:
31 4 0.03
32 48 0.42
33 1 0.01
34 4 0.03
35 54 0.47
36 4 0.03
ACGTcount: A:0.36, C:0.27, G:0.13, T:0.25
Consensus pattern (34 bp):
CCAAAACCTTCACAATGGTTTTTCAAAGGCTCAA
Found at i:16309633 original size:32 final size:32
Alignment explanation
Indices: 16309595--16309700 Score: 115
Period size: 32 Copynumber: 3.2 Consensus size: 32
16309585 TTTACCAGGA
16309595 TCAACCAAAATCCAAAGTGGTTTTTCAAAGGC
1 TCAACCAAAATCCAAAGTGGTTTTTCAAAGGC
* * * **
16309627 TTAACCACAACCTTTCACAA-TGGTTTTTCACGGGC
1 TCAACCA-AA--ATCCA-AAGTGGTTTTTCAAAGGC
*
16309662 TCAACCAAAACCCAAAGTGGTTTTTCAAAGGC
1 TCAACCAAAATCCAAAGTGGTTTTTCAAAGGC
16309694 TCAACCA
1 TCAACCA
16309701 CAACCTACAA
Statistics
Matches: 58, Mismatches: 11, Indels: 10
0.73 0.14 0.13
Matches are distributed among these distances:
31 2 0.03
32 28 0.48
33 2 0.03
34 2 0.03
35 22 0.38
36 2 0.03
ACGTcount: A:0.34, C:0.26, G:0.14, T:0.25
Consensus pattern (32 bp):
TCAACCAAAATCCAAAGTGGTTTTTCAAAGGC
Found at i:16309647 original size:67 final size:66
Alignment explanation
Indices: 16309558--16309740 Score: 251
Period size: 67 Copynumber: 2.7 Consensus size: 66
16309548 CTTTTATCAA
* * *
16309558 GCTTAGCCAAAACCTTTCACAATGGTTTTTACCAGGATCAACCAAAATCCAAAGTGGTTTTTCAA
1 GCTTAACCACAACCTTTCACAATGGTTTTT-CCAGGATCAACCAAAACCCAAAGTGGTTTTTCAA
16309623 AG
65 AG
* *
16309625 GCTTAACCACAACCTTTCACAATGGTTTTTCACGGGCTCAACCAAAACCCAAAGTGGTTTTTCAA
1 GCTTAACCACAACCTTTCACAATGGTTTTTC-CAGGATCAACCAAAACCCAAAGTGGTTTTTCAA
16309690 AG
65 AG
* * *
16309692 GCTCAACCACAACC-TACAACAATGGTTTTTCAAGAGATCAACCAAAACC
1 GCTTAACCACAACCTTTC-ACAATGGTTTTTCCAG-GATCAACCAAAACC
16309741 GAACAACTAA
Statistics
Matches: 103, Mismatches: 10, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
66 4 0.04
67 99 0.96
ACGTcount: A:0.35, C:0.26, G:0.14, T:0.25
Consensus pattern (66 bp):
GCTTAACCACAACCTTTCACAATGGTTTTTCCAGGATCAACCAAAACCCAAAGTGGTTTTTCAAA
G
Found at i:16313670 original size:31 final size:31
Alignment explanation
Indices: 16313618--16313710 Score: 90
Period size: 25 Copynumber: 3.1 Consensus size: 31
16313608 CTTCTCCATT
* *
16313618 TTTCCTATTTGGGCTAAGCCCATTTATTTTTA
1 TTTCCTA-TTGGGCCATGCCCATTTATTTTTA
*
16313650 TTTCCTATTGGGCCATGCCCACTTA---TT-
1 TTTCCTATTGGGCCATGCCCATTTATTTTTA
*
16313677 TTT--TATTGGGTCATGCCCATTTATTTTCTA
1 TTTCCTATTGGGCCATGCCCATTTATTTT-TA
16313707 TTTC
1 TTTC
16313711 TTTTTCTTTC
Statistics
Matches: 50, Mismatches: 5, Indels: 13
0.74 0.07 0.19
Matches are distributed among these distances:
25 18 0.36
27 3 0.06
28 3 0.06
29 1 0.02
30 3 0.06
31 15 0.30
32 7 0.14
ACGTcount: A:0.16, C:0.22, G:0.13, T:0.49
Consensus pattern (31 bp):
TTTCCTATTGGGCCATGCCCATTTATTTTTA
Found at i:16313683 original size:32 final size:32
Alignment explanation
Indices: 16313618--16313679 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 32
16313608 CTTCTCCATT
* *
16313618 TTTCCTATTTGGGCTAAGCCCATTTATTTTTA
1 TTTCCTATTTGGGCCAAGCCCACTTATTTTTA
*
16313650 TTTCCTA-TTGGGCCATGCCCACTTATTTTT
1 TTTCCTATTTGGGCCAAGCCCACTTATTTTT
16313680 TATTGGGTCA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
31 20 0.74
32 7 0.26
ACGTcount: A:0.16, C:0.23, G:0.13, T:0.48
Consensus pattern (32 bp):
TTTCCTATTTGGGCCAAGCCCACTTATTTTTA
Found at i:16313959 original size:24 final size:25
Alignment explanation
Indices: 16313927--16313973 Score: 62
Period size: 24 Copynumber: 1.9 Consensus size: 25
16313917 CTCAAATTTC
16313927 CAGCAACAAAACT-TCTCAATTTTGG
1 CAGCAACAAAACTGTC-CAATTTTGG
*
16313952 CAGC-ACAAAGCTGTCCAATTTT
1 CAGCAACAAAACTGTCCAATTTT
16313974 CCTGCACAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.34, C:0.26, G:0.13, T:0.28
Consensus pattern (25 bp):
CAGCAACAAAACTGTCCAATTTTGG
Found at i:16314104 original size:22 final size:22
Alignment explanation
Indices: 16314079--16314122 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
16314069 AGCAAAAACC
*
16314079 TTCA-AAAATTTCTAGCAGCAAA
1 TTCACAAAATTTC-AGCAACAAA
*
16314101 TTCACACAATTTCAGCAACAAA
1 TTCACAAAATTTCAGCAACAAA
16314123 AACCTTGAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.45, C:0.23, G:0.07, T:0.25
Consensus pattern (22 bp):
TTCACAAAATTTCAGCAACAAA
Found at i:16333235 original size:22 final size:23
Alignment explanation
Indices: 16333209--16333258 Score: 59
Period size: 21 Copynumber: 2.3 Consensus size: 23
16333199 CTAATCTTAT
* *
16333209 TTAAACAACCAAATTTAAAT-TA
1 TTAAACAAACAAAATTAAATCTA
16333231 TTAAA-AAACAAAATTAAATCTA
1 TTAAACAAACAAAATTAAATCTA
*
16333253 ATAAAC
1 TTAAAC
16333259 TAAAACTAGA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
21 12 0.52
22 11 0.48
ACGTcount: A:0.60, C:0.12, G:0.00, T:0.28
Consensus pattern (23 bp):
TTAAACAAACAAAATTAAATCTA
Found at i:16336359 original size:5 final size:5
Alignment explanation
Indices: 16336349--16336396 Score: 62
Period size: 5 Copynumber: 9.4 Consensus size: 5
16336339 ATATATATAT
*
16336349 TTTTC TTTTC TTTTC TCTTT- TTTTC TTTTC TTTTA TTTTC TTTCTC TT
1 TTTTC TTTTC TTTTC T-TTTC TTTTC TTTTC TTTTC TTTTC TTT-TC TT
16336397 CCTCTTCTCT
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
4 3 0.08
5 28 0.74
6 7 0.18
ACGTcount: A:0.02, C:0.19, G:0.00, T:0.79
Consensus pattern (5 bp):
TTTTC
Found at i:16336644 original size:35 final size:33
Alignment explanation
Indices: 16336567--16336644 Score: 95
Period size: 33 Copynumber: 2.3 Consensus size: 33
16336557 TATCCACACC
* * *
16336567 AAAATCAGCAGTTAAGTTGCTCTATTTCTTCGC
1 AAAATCAGCAGCTAAGCTGCTCTATTTCTTCGA
16336600 AAAATCAGCAGCTAAGCTGCTCTATTTTCCCTTC-A
1 AAAATCAGCAGCTAAGCTGCTCTA-TTT--CTTCGA
16336635 AAAATCAGCA
1 AAAATCAGCA
16336645 CCCAAAGCTA
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
33 22 0.56
34 3 0.08
35 10 0.26
36 4 0.10
ACGTcount: A:0.32, C:0.24, G:0.13, T:0.31
Consensus pattern (33 bp):
AAAATCAGCAGCTAAGCTGCTCTATTTCTTCGA
Found at i:16336701 original size:34 final size:34
Alignment explanation
Indices: 16336663--16336737 Score: 82
Period size: 35 Copynumber: 2.2 Consensus size: 34
16336653 TACAAAGATT
16336663 AGCAACAAAA-TCGCACCTTT-CAGCCTTCAAAATC
1 AGCAACAAAACT-GCA-CTTTCCAGCCTTCAAAATC
** *
16336697 AGCAACCAAAACTTTATTTTCCAGCCTTCAAAATC
1 AGCAA-CAAAACTGCACTTTCCAGCCTTCAAAATC
16336732 AGCAAC
1 AGCAAC
16336738 TAAAGCTACT
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
34 9 0.26
35 25 0.71
36 1 0.03
ACGTcount: A:0.39, C:0.31, G:0.08, T:0.23
Consensus pattern (34 bp):
AGCAACAAAACTGCACTTTCCAGCCTTCAAAATC
Found at i:16340606 original size:2 final size:2
Alignment explanation
Indices: 16340601--16340638 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
16340591 ACTATATACG
* *
16340601 AT AT AT GT AT AT AT GT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
16340639 CAATCATCAT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (2 bp):
AT
Found at i:16340733 original size:42 final size:42
Alignment explanation
Indices: 16340686--16340805 Score: 168
Period size: 42 Copynumber: 2.9 Consensus size: 42
16340676 TATTCAACAA
* * *
16340686 CTTATGTGCACTCCCACTCACACATAGTCGGGTCAGCAACGG
1 CTTATGTGCACTCCCACTCACACATAGCCAGGTCAACAACGG
*
16340728 CTTATGTGCACTCCCACTCGCACATAGCCAGGTCAACAACGG
1 CTTATGTGCACTCCCACTCACACATAGCCAGGTCAACAACGG
* ** *
16340770 CTTATGTGCACTCCTACTCGTATATAGCCAGGTCAA
1 CTTATGTGCACTCCCACTCACACATAGCCAGGTCAA
16340806 TATCTTTACA
Statistics
Matches: 71, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 71 1.00
ACGTcount: A:0.25, C:0.33, G:0.19, T:0.23
Consensus pattern (42 bp):
CTTATGTGCACTCCCACTCACACATAGCCAGGTCAACAACGG
Found at i:16350488 original size:62 final size:62
Alignment explanation
Indices: 16350418--16350541 Score: 212
Period size: 62 Copynumber: 2.0 Consensus size: 62
16350408 GCTGGTGCAG
*
16350418 AAACTGAGAAACAACAGGCCTCTTCTCCGAACTCAAAGGAAGTTTCCATTATGGACATTTTT
1 AAACTGAGAAACAACAAGCCTCTTCTCCGAACTCAAAGGAAGTTTCCATTATGGACATTTTT
* * *
16350480 AAACTGAGAAACAGCAAGCCTCTTCTCCGAACTCAGAGGAAGTTTCCATTATGGATATTTTT
1 AAACTGAGAAACAACAAGCCTCTTCTCCGAACTCAAAGGAAGTTTCCATTATGGACATTTTT
16350542 TATCAAATGG
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
62 58 1.00
ACGTcount: A:0.33, C:0.22, G:0.17, T:0.28
Consensus pattern (62 bp):
AAACTGAGAAACAACAAGCCTCTTCTCCGAACTCAAAGGAAGTTTCCATTATGGACATTTTT
Found at i:16352854 original size:38 final size:39
Alignment explanation
Indices: 16352768--16352872 Score: 131
Period size: 38 Copynumber: 2.7 Consensus size: 39
16352758 ACCCGGCTCA
*
16352768 TGTACATCCCCCCACATCGTGCACATAGCCGGCGCCATCG
1 TGTACATCCCCCCACATCGTGCACA-AGCCAGCGCCATCG
** * * *
16352808 TGCGCATCCCCCCACATCATGCACAA-TCAGTGCCATCG
1 TGTACATCCCCCCACATCGTGCACAAGCCAGCGCCATCG
*
16352846 TGTACATCCCTCCACATCGTGCACAAG
1 TGTACATCCCCCCACATCGTGCACAAG
16352873 GGCACTATCA
Statistics
Matches: 54, Mismatches: 10, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
38 31 0.57
39 1 0.02
40 22 0.41
ACGTcount: A:0.23, C:0.41, G:0.17, T:0.19
Consensus pattern (39 bp):
TGTACATCCCCCCACATCGTGCACAAGCCAGCGCCATCG
Found at i:16366588 original size:20 final size:21
Alignment explanation
Indices: 16366553--16366591 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
16366543 AGAGCTAATC
16366553 AATAATAAACAAATTAAAAGA
1 AATAATAAACAAATTAAAAGA
*
16366574 AATAATATA-AAATTAAAA
1 AATAATAAACAAATTAAAA
16366592 TAACTAACTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.72, C:0.03, G:0.03, T:0.23
Consensus pattern (21 bp):
AATAATAAACAAATTAAAAGA
Found at i:16369283 original size:43 final size:43
Alignment explanation
Indices: 16369112--16369286 Score: 219
Period size: 43 Copynumber: 4.1 Consensus size: 43
16369102 GTAATTATGT
* *
16369112 TGACTCGGCTATGTGCGAGTAGGGAGTGCGCATAAGCCGAG-GA
1 TGACCCGGTTATGTGCGAGTAGGGAGTGCGCATAAGCCG-GTGA
* *
16369155 TGACCTGGTTATGTGCGAGTAGGGAGTGCGCATAACCCGGTGA
1 TGACCCGGTTATGTGCGAGTAGGGAGTGCGCATAAGCCGGTGA
*
16369198 TGACCCGGTTATGTGCGAGTAGGGAGTGTGCATAA-CTCGGTGA
1 TGACCCGGTTATGTGCGAGTAGGGAGTGCGCATAAGC-CGGTGA
* ** * * *
16369241 TGACCCAGCCATGTGCGAGTAGGGAGTGTGCATGAGCTGGTGA
1 TGACCCGGTTATGTGCGAGTAGGGAGTGCGCATAAGCCGGTGA
16369284 TGA
1 TGA
16369287 TGATGATGAG
Statistics
Matches: 118, Mismatches: 11, Indels: 6
0.87 0.08 0.04
Matches are distributed among these distances:
42 2 0.02
43 115 0.97
44 1 0.01
ACGTcount: A:0.22, C:0.18, G:0.38, T:0.22
Consensus pattern (43 bp):
TGACCCGGTTATGTGCGAGTAGGGAGTGCGCATAAGCCGGTGA
Found at i:16369303 original size:20 final size:20
Alignment explanation
Indices: 16369272--16369334 Score: 67
Period size: 20 Copynumber: 3.2 Consensus size: 20
16369262 GGGAGTGTGC
*
16369272 ATGAGCTGGTGATGATGATG
1 ATGAGTTGGTGATGATGATG
* *
16369292 ATGAGTCT-GTGATGATGGTA
1 ATGAGT-TGGTGATGATGATG
*
16369312 ATGGGTTGGTGA-GATGATG
1 ATGAGTTGGTGATGATGATG
16369331 ATGA
1 ATGA
16369335 TGTATATATA
Statistics
Matches: 34, Mismatches: 7, Indels: 5
0.74 0.15 0.11
Matches are distributed among these distances:
19 9 0.26
20 24 0.71
21 1 0.03
ACGTcount: A:0.25, C:0.03, G:0.40, T:0.32
Consensus pattern (20 bp):
ATGAGTTGGTGATGATGATG
Found at i:16379352 original size:2 final size:2
Alignment explanation
Indices: 16379345--16379369 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
16379335 TAGCATGAGA
16379345 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
16379370 ATCATCCAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:16383412 original size:21 final size:20
Alignment explanation
Indices: 16383382--16383421 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
16383372 GCGCATGAGC
16383382 TGGTGATGATGATGATGGGA
1 TGGTGATGATGATGATGGGA
*
16383402 TGGTGCATGATGGTGATGGG
1 TGGTG-ATGATGATGATGGG
16383422 TATATGTATA
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:0.20, C:0.03, G:0.47, T:0.30
Consensus pattern (20 bp):
TGGTGATGATGATGATGGGA
Found at i:16386969 original size:21 final size:21
Alignment explanation
Indices: 16386945--16386993 Score: 98
Period size: 21 Copynumber: 2.3 Consensus size: 21
16386935 TGAGAGTTTC
16386945 TCACTGCAGCGAGAATGAAGT
1 TCACTGCAGCGAGAATGAAGT
16386966 TCACTGCAGCGAGAATGAAGT
1 TCACTGCAGCGAGAATGAAGT
16386987 TCACTGC
1 TCACTGC
16386994 GAAAAGTTTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.31, C:0.22, G:0.27, T:0.20
Consensus pattern (21 bp):
TCACTGCAGCGAGAATGAAGT
Found at i:16387247 original size:40 final size:38
Alignment explanation
Indices: 16387199--16387301 Score: 127
Period size: 38 Copynumber: 2.7 Consensus size: 38
16387189 ACCCGACTCA
*
16387199 TGTACATCCCCCCACATCGTGCACATAGCCG-GCACCATCG
1 TGTACATCCCCCCACATCGTGCACA-AGCAGTG--CCATCG
* * *
16387239 TGTGCATCCCCCCCCATCGTGCACAATCAGTGCCATCG
1 TGTACATCCCCCCACATCGTGCACAAGCAGTGCCATCG
*
16387277 TGTACATACCCCCACATCGTGCACA
1 TGTACATCCCCCCACATCGTGCACA
16387302 CGGGCACTAT
Statistics
Matches: 55, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
38 28 0.51
39 3 0.05
40 24 0.44
ACGTcount: A:0.22, C:0.42, G:0.17, T:0.19
Consensus pattern (38 bp):
TGTACATCCCCCCACATCGTGCACAAGCAGTGCCATCG
Found at i:16388671 original size:21 final size:21
Alignment explanation
Indices: 16388631--16388679 Score: 50
Period size: 21 Copynumber: 2.3 Consensus size: 21
16388621 AGTCATGTGC
16388631 TGCTCAAACTAGTGTCCAA-GT
1 TGCTC-AACTAGTGTCCAAGGT
16388652 TGCTCAACTAG-GTGCTCAAGGT
1 TGCTCAACTAGTGT-C-CAAGGT
16388674 T-CTCAA
1 TGCTCAA
16388680 TTCTCTAAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
19 2 0.08
20 7 0.28
21 13 0.52
22 3 0.12
ACGTcount: A:0.27, C:0.24, G:0.20, T:0.29
Consensus pattern (21 bp):
TGCTCAACTAGTGTCCAAGGT
Found at i:16392499 original size:42 final size:42
Alignment explanation
Indices: 16392440--16392564 Score: 196
Period size: 42 Copynumber: 3.0 Consensus size: 42
16392430 TGTTGATATG
* *
16392440 GACCCGGCTATGTGCGAGTAGGAGTGCACATAAGCCGTTGCT
1 GACCCGACTATGTGCGAGTGGGAGTGCACATAAGCCGTTGCT
*
16392482 GACCCGACTATGTGCGAGTGGGAGTGCACATAAGCCATTGCT
1 GACCCGACTATGTGCGAGTGGGAGTGCACATAAGCCGTTGCT
* * *
16392524 GACCCGACTATGTGCAAGTGGGAGTGCGCATAAGTCGTTGC
1 GACCCGACTATGTGCGAGTGGGAGTGCACATAAGCCGTTGC
16392565 ATATGAGATG
Statistics
Matches: 76, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 76 1.00
ACGTcount: A:0.22, C:0.23, G:0.33, T:0.22
Consensus pattern (42 bp):
GACCCGACTATGTGCGAGTGGGAGTGCACATAAGCCGTTGCT
Found at i:16392618 original size:2 final size:2
Alignment explanation
Indices: 16392605--16392638 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
16392595 ATGATGATTG
* *
16392605 AT AT AT AC AT AT AT AT AT AT AT AT AT AC AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
16392639 CGTATATGGT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:16392620 original size:10 final size:10
Alignment explanation
Indices: 16392605--16392638 Score: 59
Period size: 10 Copynumber: 3.4 Consensus size: 10
16392595 ATGATGATTG
16392605 ATATATACAT
1 ATATATACAT
*
16392615 ATATATATAT
1 ATATATACAT
16392625 ATATATACAT
1 ATATATACAT
16392635 ATAT
1 ATAT
16392639 CGTATATGGT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (10 bp):
ATATATACAT
Found at i:16401865 original size:22 final size:22
Alignment explanation
Indices: 16401839--16401882 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
16401829 CTTAGTGGTA
16401839 ACATGTAAA-TGAGAATAGTGTT
1 ACATGTAAACTGAGAA-AGTGTT
*
16401861 ACATGTAAACTTAGAAAGTGTT
1 ACATGTAAACTGAGAAAGTGTT
16401883 TGATGGAAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.41, C:0.07, G:0.20, T:0.32
Consensus pattern (22 bp):
ACATGTAAACTGAGAAAGTGTT
Found at i:16405598 original size:21 final size:22
Alignment explanation
Indices: 16405574--16405620 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 22
16405564 TTGAATGGAG
16405574 GCATCAATCTTTGTCAT-AAAT
1 GCATCAATCTTTGTCATGAAAT
* *
16405595 GCATCAGTCTTTGTCATGAATT
1 GCATCAATCTTTGTCATGAAAT
16405617 GCAT
1 GCAT
16405621 GAACATATCC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 16 0.70
22 7 0.30
ACGTcount: A:0.28, C:0.19, G:0.15, T:0.38
Consensus pattern (22 bp):
GCATCAATCTTTGTCATGAAAT
Found at i:16406859 original size:30 final size:30
Alignment explanation
Indices: 16406825--16406885 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
16406815 TTTCTTAACT
*
16406825 TAGTTTAATAGATAAGTTGCTACCCTAGAG
1 TAGTTTAATAGATAAGTTGCTAACCTAGAG
*
16406855 TAGTTTAATGGATAAGTTGCTAACCTAGAG
1 TAGTTTAATAGATAAGTTGCTAACCTAGAG
16406885 T
1 T
16406886 CTTAAATTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.33, C:0.11, G:0.21, T:0.34
Consensus pattern (30 bp):
TAGTTTAATAGATAAGTTGCTAACCTAGAG
Found at i:16408512 original size:21 final size:19
Alignment explanation
Indices: 16408481--16408521 Score: 55
Period size: 21 Copynumber: 2.1 Consensus size: 19
16408471 ACATATTGAG
16408481 TAGTTAATTTAAGTTATTT
1 TAGTTAATTTAAGTTATTT
*
16408500 TAGTTAGATTTTATGTTATTT
1 TAGTTA-A-TTTAAGTTATTT
16408521 T
1 T
16408522 GTTTTAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 6 0.32
20 1 0.05
21 12 0.63
ACGTcount: A:0.27, C:0.00, G:0.12, T:0.61
Consensus pattern (19 bp):
TAGTTAATTTAAGTTATTT
Found at i:16409503 original size:465 final size:466
Alignment explanation
Indices: 16408631--16409563 Score: 1719
Period size: 465 Copynumber: 2.0 Consensus size: 466
16408621 TATATGTTTT
16408631 GGCATTTTGACTATATCTCTCTCTAAAATACTCCAAATGAGGTGATTCTTAATCACTAGAATTCA
1 GGCATTTTGACTATATCTCTCTCTAAAATACTCCAAATGAGGTGATTCTTAATCACTAGAATTCA
* * *
16408696 AAGAGATAGGGCTACAACTTTTATTTTTACCACTTTTCCCAATTCTTGATCAGATCATGATCAAA
66 AAGAGATAGCGCTACAACTTTTATGTTTACCACTTTGCCCAATTCTTGATCAGATCATGATCAAA
16408761 ATATTTGTCTAAGTCGGAGCACTACAGCAATATGCATGGACTGGACATGATGCAGTATTTGGAGC
131 ATATTTGTCTAAGTCGGAGCACTACAGCAATATGCATGGACTGGACATGATGCAGTATTTGGAGC
16408826 ATATCTTTCAATCCAGAAGTCCAATTGACGTGATTCTTAAGCCACTAGAAAGCTAAGAGATAGAG
196 ATATCTTTCAATCCAGAAGTCCAATTGACGTGATTCTTAAGCCACTAGAAAGCTAAGAGATAGAG
16408891 ATAAAACTTTCATGTTTTGCCACTTTACCAGTTCAGGACAAGTCAGGGTGAAAATCATGTTTGAA
261 ATAAAACTTTCATGTTTTGCCACTTTACCAGTTCAGGACAAGTCAGGGTGAAAATCATGTTTGAA
*
16408956 TTTGATTAACTGTCACAGCACTAAGAGAACAAGGCTACAAGCTAGTGAAAGGAAGCACACAACAC
326 TTTGATTAACTGTCACAGCACTAAGAGAACAAGGCTACAAGCTAGTGAAACGAAGCACACAACAC
*
16409021 ATTTTCCCGAGACCTAAGTGCTGCAGTGCTAGAAGAAAAGCACCGTATCACTACTGTAGCAAGAA
391 ATTTTCCCGAGACCTAAGTGCTGCAGTGCTAGAAGAAAAGCACCGTAACACTACTGTAGCAAGAA
16409086 TCCAGCATCGC
456 TCCAGCATCGC
16409097 GGCATTTTGACTATATCTCTCTCTAAAATACTCCAAATGAGGTGATTCTTAATCACTAGAATTCA
1 GGCATTTTGACTATATCTCTCTCTAAAATACTCCAAATGAGGTGATTCTTAATCACTAGAATTCA
* * * *
16409162 AAGAGGA-AGCGCTCCAACTTTTATGTTTACCACTTTGCCCATTTC-TGA-CTGAATCGTGATCA
66 AAGA-GATAGCGCTACAACTTTTATGTTTACCACTTTGCCCAATTCTTGATCAG-ATCATGATCA
16409224 AAATATTTGTCTAAGTCGGAGCACTACAGCAATATGCATGGACTGGACATGATGCAGTATTTGGA
129 AAATATTTGTCTAAGTCGGAGCACTACAGCAATATGCATGGACTGGACATGATGCAGTATTTGGA
*
16409289 GCATATCTTTCAATCCAGAAGTCCAATTGACGTGATTCTTAAGCCACTGGAAAGCTAAGAGATAG
194 GCATATCTTTCAATCCAGAAGTCCAATTGACGTGATTCTTAAGCCACTAGAAAGCTAAGAGATAG
*
16409354 AGATAAAACTTTCATGTTTTGCCACTTTACCAGTTCAGGCCAAGTCAGGGTGAAAATCATGTTTG
259 AGATAAAACTTTCATGTTTTGCCACTTTACCAGTTCAGGACAAGTCAGGGTGAAAATCATGTTTG
*
16409419 AATTTGATTAACTGTCGCAGCACTAAGAGAACAAGGCTACAAGCTAGTGAAACGAAGCACACAAC
324 AATTTGATTAACTGTCACAGCACTAAGAGAACAAGGCTACAAGCTAGTGAAACGAAGCACACAAC
16409484 ACATTTTCCCGAGACCTAAGTGCTGCAGTGCTAGAAGAAAAGCACCGTAACACTACTGTAGCAAG
389 ACATTTTCCCGAGACCTAAGTGCTGCAGTGCTAGAAGAAAAGCACCGTAACACTACTGTAGCAAG
16409549 AATCCAGCATCGC
454 AATCCAGCATCGC
16409562 GG
1 GG
16409564 GGCCAAGATA
Statistics
Matches: 453, Mismatches: 12, Indels: 5
0.96 0.03 0.01
Matches are distributed among these distances:
464 2 0.00
465 347 0.77
466 102 0.23
467 2 0.00
ACGTcount: A:0.33, C:0.21, G:0.19, T:0.27
Consensus pattern (466 bp):
GGCATTTTGACTATATCTCTCTCTAAAATACTCCAAATGAGGTGATTCTTAATCACTAGAATTCA
AAGAGATAGCGCTACAACTTTTATGTTTACCACTTTGCCCAATTCTTGATCAGATCATGATCAAA
ATATTTGTCTAAGTCGGAGCACTACAGCAATATGCATGGACTGGACATGATGCAGTATTTGGAGC
ATATCTTTCAATCCAGAAGTCCAATTGACGTGATTCTTAAGCCACTAGAAAGCTAAGAGATAGAG
ATAAAACTTTCATGTTTTGCCACTTTACCAGTTCAGGACAAGTCAGGGTGAAAATCATGTTTGAA
TTTGATTAACTGTCACAGCACTAAGAGAACAAGGCTACAAGCTAGTGAAACGAAGCACACAACAC
ATTTTCCCGAGACCTAAGTGCTGCAGTGCTAGAAGAAAAGCACCGTAACACTACTGTAGCAAGAA
TCCAGCATCGC
Found at i:16416201 original size:20 final size:20
Alignment explanation
Indices: 16416164--16416202 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
16416154 CGGGGGTGTT
***
16416164 TTTGTTTGTTTTTGCTTATC
1 TTTGTTTGTTTACCCTTATC
16416184 TTTGTTTGTTTACCCTTAT
1 TTTGTTTGTTTACCCTTAT
16416203 TATTTTACAT
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:0.08, C:0.13, G:0.13, T:0.67
Consensus pattern (20 bp):
TTTGTTTGTTTACCCTTATC
Found at i:16420091 original size:15 final size:15
Alignment explanation
Indices: 16420071--16420109 Score: 78
Period size: 15 Copynumber: 2.6 Consensus size: 15
16420061 TCCAAATCTG
16420071 AAAACATGAATTTTA
1 AAAACATGAATTTTA
16420086 AAAACATGAATTTTA
1 AAAACATGAATTTTA
16420101 AAAACATGA
1 AAAACATGA
16420110 GTACGAAACT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.56, C:0.08, G:0.08, T:0.28
Consensus pattern (15 bp):
AAAACATGAATTTTA
Found at i:16420857 original size:2 final size:2
Alignment explanation
Indices: 16420845--16420889 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
16420835 ACCATACACC
*
16420845 AT AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
16420887 AT A
1 AT A
16420890 CTACTACTAC
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:16424463 original size:8 final size:8
Alignment explanation
Indices: 16424450--16424487 Score: 58
Period size: 8 Copynumber: 4.6 Consensus size: 8
16424440 AAATAGGAGA
16424450 AATAAAAT
1 AATAAAAT
*
16424458 AATAAAAC
1 AATAAAAT
16424466 AATAAAAT
1 AATAAAAT
16424474 AATAATAAT
1 AATAA-AAT
16424483 AATAA
1 AATAA
16424488 GAAAAAAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
8 19 0.70
9 8 0.30
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.24
Consensus pattern (8 bp):
AATAAAAT
Found at i:16424894 original size:34 final size:35
Alignment explanation
Indices: 16424845--16424931 Score: 104
Period size: 34 Copynumber: 2.5 Consensus size: 35
16424835 AGAGGCATTG
*
16424845 TGCTGCAAATTTTGAGAGGGAAGAAGCAAAAG-TT
1 TGCTACAAATTTTGAGAGGGAAGAAGCAAAAGTTT
* * * * *
16424879 TGCTACAAAATTTGAGAAGGAAGGAGGAAGAGTTT
1 TGCTACAAATTTTGAGAGGGAAGAAGCAAAAGTTT
*
16424914 TGCTACAAATTTTAAGAG
1 TGCTACAAATTTTGAGAG
16424932 AGAAAACAAG
Statistics
Matches: 43, Mismatches: 9, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
34 26 0.60
35 17 0.40
ACGTcount: A:0.39, C:0.08, G:0.28, T:0.25
Consensus pattern (35 bp):
TGCTACAAATTTTGAGAGGGAAGAAGCAAAAGTTT
Found at i:16426128 original size:2 final size:2
Alignment explanation
Indices: 16426123--16426165 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
16426113 TATACTTATG
16426123 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
16426164 TA
1 TA
16426166 NNNNNNNNNN
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:16426197 original size:2 final size:2
Alignment explanation
Indices: 16426190--16426238 Score: 80
Period size: 2 Copynumber: 24.0 Consensus size: 2
16426180 NNNNNNNNNN
*
16426190 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TT TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
16426232 CTA TA TA
1 -TA TA TA
16426239 GAGAGGTTTG
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
2 42 0.95
3 2 0.05
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:16429592 original size:27 final size:27
Alignment explanation
Indices: 16429561--16429614 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
16429551 CATAGTTTTG
* *
16429561 CTGTAAATTTTTAGAAGGAAATAGAAA
1 CTGTAAATTTCTAAAAGGAAATAGAAA
*
16429588 CTGTAAATTTCTAAAATGAAATAGAAA
1 CTGTAAATTTCTAAAAGGAAATAGAAA
16429615 GAGTTTTGTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.50, C:0.06, G:0.15, T:0.30
Consensus pattern (27 bp):
CTGTAAATTTCTAAAAGGAAATAGAAA
Found at i:16429649 original size:35 final size:35
Alignment explanation
Indices: 16429605--16429714 Score: 177
Period size: 35 Copynumber: 3.2 Consensus size: 35
16429595 TTTCTAAAAT
* * *
16429605 GAAATAGAAAGAGTTTTGTTGCAGATTTTGAGAGG
1 GAAAAAGAAAGAGTTTTGCTGCAAATTTTGAGAGG
16429640 GAAAAAGAAAGAGTTTTGCTGCAAATTTTGAGA-G
1 GAAAAAGAAAGAGTTTTGCTGCAAATTTTGAGAGG
*
16429674 GAAAAAGAAAGAGTTTTGCTGCAAATTTTGAGAGA
1 GAAAAAGAAAGAGTTTTGCTGCAAATTTTGAGAGG
16429709 GAAAAA
1 GAAAAA
16429715 ATAAGAGCTG
Statistics
Matches: 70, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
34 34 0.49
35 36 0.51
ACGTcount: A:0.42, C:0.05, G:0.27, T:0.26
Consensus pattern (35 bp):
GAAAAAGAAAGAGTTTTGCTGCAAATTTTGAGAGG
Found at i:16429816 original size:14 final size:14
Alignment explanation
Indices: 16429789--16429826 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
16429779 TGAAAAGAGG
*
16429789 GAGAAGGAAGAAAAA
1 GAGAA-GAAAAAAAA
16429804 G-GAAGAAAAAAAA
1 GAGAAGAAAAAAAA
16429817 GAGAAGAAAA
1 GAGAAGAAAA
16429827 TTGCTGCCGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
13 9 0.43
14 11 0.52
15 1 0.05
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (14 bp):
GAGAAGAAAAAAAA
Found at i:16431202 original size:13 final size:13
Alignment explanation
Indices: 16431184--16431210 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
16431174 CTAATCAAAC
16431184 TAAATAAAATAAT
1 TAAATAAAATAAT
16431197 TAAATAAAATAAT
1 TAAATAAAATAAT
16431210 T
1 T
16431211 CTATTTTCNT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (13 bp):
TAAATAAAATAAT
Found at i:16431249 original size:99 final size:96
Alignment explanation
Indices: 16431123--16431321 Score: 330
Period size: 99 Copynumber: 2.0 Consensus size: 96
16431113 TATACATTTA
16431123 TTATCTAAAATAATTTAGTAATCTAAATCATCCATTTAAACTAAAA-TTTGGCTAATCAAACTAA
1 TTATCTAAAATAATTTAGTAATCTAAATCATCCATTTAAACTAAAATTTTGGCTAATCAAACTAA
16431187 ATA-AAATAATTAAATAAAATAATTCTATTTTC
66 ATAGAAAT-ATTAAATAAAAT-ATTCTATTTTC
16431219 NTTATCTAAAAATAATTTTAGTAATCTAAATCATCCATTTAAACTAAAATTTTGGCTAATCAAAC
1 -TTATCT-AAAATAA-TTTAGTAATCTAAATCATCCATTTAAACTAAAATTTTGGCTAATCAAAC
*
16431284 TAAATAGAAATATTAAGTAAAATATTCTATTTTC
63 TAAATAGAAATATTAAATAAAATATTCTATTTTC
16431318 TTAT
1 TTAT
16431322 AAAACAATAT
Statistics
Matches: 97, Mismatches: 1, Indels: 7
0.92 0.01 0.07
Matches are distributed among these distances:
97 6 0.06
98 11 0.11
99 44 0.45
100 32 0.33
101 4 0.04
ACGTcount: A:0.46, C:0.11, G:0.04, T:0.39
Consensus pattern (96 bp):
TTATCTAAAATAATTTAGTAATCTAAATCATCCATTTAAACTAAAATTTTGGCTAATCAAACTAA
ATAGAAATATTAAATAAAATATTCTATTTTC
Found at i:16433526 original size:42 final size:42
Alignment explanation
Indices: 16433460--16433575 Score: 160
Period size: 42 Copynumber: 2.8 Consensus size: 42
16433450 GATGTGGACT
* * *
16433460 CAGCTATGTGCAAGTAGGAATGCACATAAGCCGTAGCTGACC
1 CAGCTATGTGCGAGTGGGAGTGCACATAAGCCGTAGCTGACC
* * *
16433502 TAGCTATGTGCGAGTGGGAGTGCACATAAGCCTTTGCTGACC
1 CAGCTATGTGCGAGTGGGAGTGCACATAAGCCGTAGCTGACC
* *
16433544 CGGCTATGTGCGAGTGGGAGTGCGCATAAGCC
1 CAGCTATGTGCGAGTGGGAGTGCACATAAGCC
16433576 ATTGCATATG
Statistics
Matches: 65, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 65 1.00
ACGTcount: A:0.24, C:0.22, G:0.32, T:0.22
Consensus pattern (42 bp):
CAGCTATGTGCGAGTGGGAGTGCACATAAGCCGTAGCTGACC
Found at i:16433633 original size:2 final size:2
Alignment explanation
Indices: 16433621--16433659 Score: 51
Period size: 2 Copynumber: 19.0 Consensus size: 2
16433611 ATGATGATTG
* *
16433621 AT AT CT AT AT AT AT AT AT AT AT AT AC AT AT AT GAT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT
16433660 GGCTGTAAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
2 30 0.94
3 2 0.06
ACGTcount: A:0.46, C:0.05, G:0.03, T:0.46
Consensus pattern (2 bp):
AT
Found at i:16440858 original size:43 final size:43
Alignment explanation
Indices: 16440810--16440936 Score: 209
Period size: 43 Copynumber: 3.0 Consensus size: 43
16440800 TGTGATAATT
*
16440810 ATGACCTAGCTATGTGCAGTGTAGGAGTGCACATGAGCTGATC
1 ATGACCTAGCTATGTGCGGTGTAGGAGTGCACATGAGCTGATC
* * *
16440853 ATGACCCAGCTATGTGTGGTGTAGGAGTGCACATGAGCTGATG
1 ATGACCTAGCTATGTGCGGTGTAGGAGTGCACATGAGCTGATC
*
16440896 ATGACCTAGCTATGTGCGGTGTAGGAGTGCACATAAGCTGA
1 ATGACCTAGCTATGTGCGGTGTAGGAGTGCACATGAGCTGA
16440937 GAGAGAGTTG
Statistics
Matches: 77, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
43 77 1.00
ACGTcount: A:0.25, C:0.17, G:0.32, T:0.25
Consensus pattern (43 bp):
ATGACCTAGCTATGTGCGGTGTAGGAGTGCACATGAGCTGATC
Found at i:16442426 original size:45 final size:45
Alignment explanation
Indices: 16442377--16442465 Score: 178
Period size: 45 Copynumber: 2.0 Consensus size: 45
16442367 TATGGTTCAG
16442377 TATGCAACCTATGATGTAAATGATTAGTTTTGAATATGTTTTCTT
1 TATGCAACCTATGATGTAAATGATTAGTTTTGAATATGTTTTCTT
16442422 TATGCAACCTATGATGTAAATGATTAGTTTTGAATATGTTTTCT
1 TATGCAACCTATGATGTAAATGATTAGTTTTGAATATGTTTTCT
16442466 CTAAAGGTAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.29, C:0.09, G:0.16, T:0.46
Consensus pattern (45 bp):
TATGCAACCTATGATGTAAATGATTAGTTTTGAATATGTTTTCTT
Found at i:16448218 original size:40 final size:40
Alignment explanation
Indices: 16448161--16448279 Score: 154
Period size: 40 Copynumber: 3.0 Consensus size: 40
16448151 CAGCCCTGGT
16448161 TTTCA-CTGCAGCGAGAATGCAATCTCGCTGTAGTGAGAAA
1 TTTCACCT-CAGCGAGAATGCAATCTCGCTGTAGTGAGAAA
* * *
16448201 TTTCACCTCAGCAAGAATGCAATCTCACTGCAGTGAGAAA
1 TTTCACCTCAGCGAGAATGCAATCTCGCTGTAGTGAGAAA
* *
16448241 -TTCTACCTTAGCGAGAATG-AATCTCGCTGTAGAGAGAAA
1 TTTC-ACCTCAGCGAGAATGCAATCTCGCTGTAGTGAGAAA
16448280 CTCTCGAGTT
Statistics
Matches: 69, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
39 20 0.29
40 47 0.68
41 2 0.03
ACGTcount: A:0.33, C:0.21, G:0.22, T:0.24
Consensus pattern (40 bp):
TTTCACCTCAGCGAGAATGCAATCTCGCTGTAGTGAGAAA
Found at i:16448239 original size:22 final size:22
Alignment explanation
Indices: 16448163--16448239 Score: 56
Period size: 22 Copynumber: 3.7 Consensus size: 22
16448153 GCCCTGGTTT
16448163 TCACTGCAGCGAGAATGCAATC
1 TCACTGCAGCGAGAATGCAATC
* * * *
16448185 TCGCTGTAGTGAG-A---AATT
1 TCACTGCAGCGAGAATGCAATC
*
16448203 TCACCT-CAGCAAGAATGCAATC
1 TCA-CTGCAGCGAGAATGCAATC
*
16448225 TCACTGCAGTGAGAA
1 TCACTGCAGCGAGAA
16448240 ATTCTACCTT
Statistics
Matches: 38, Mismatches: 11, Indels: 12
0.62 0.18 0.20
Matches are distributed among these distances:
18 9 0.24
19 3 0.08
21 3 0.08
22 23 0.61
ACGTcount: A:0.32, C:0.23, G:0.22, T:0.22
Consensus pattern (22 bp):
TCACTGCAGCGAGAATGCAATC
Found at i:16449973 original size:43 final size:43
Alignment explanation
Indices: 16449890--16450136 Score: 372
Period size: 43 Copynumber: 5.8 Consensus size: 43
16449880 TGTGATAATT
* * * *
16449890 ATGACCTAGCTATATGCGGTGT-AGAGTGCACATGAGCTGATC
1 ATGACCCAGCCATGTGCGGTGTAAGAGTGCACATGAGCTGATG
*
16449932 ATGACCCAGCTATGTGCGGTGTAAGAGTGCACATGAGCTGATG
1 ATGACCCAGCCATGTGCGGTGTAAGAGTGCACATGAGCTGATG
*
16449975 ATGACCCAGCCATGTGCGGTGTAGGAGTGCACATGAGCTGATG
1 ATGACCCAGCCATGTGCGGTGTAAGAGTGCACATGAGCTGATG
*
16450018 ATGACCCAGCCATGTGCGGTGTAAGAGTGCACATGAGC-AATG
1 ATGACCCAGCCATGTGCGGTGTAAGAGTGCACATGAGCTGATG
*
16450060 ATGACCCAGCCATGTGTGGTGTAAGAGTGCACATGAGCTGATG
1 ATGACCCAGCCATGTGCGGTGTAAGAGTGCACATGAGCTGATG
* * **
16450103 ATGACCCAACTATGTGCGGTGTGGGAGTGCACAT
1 ATGACCCAGCCATGTGCGGTGTAAGAGTGCACAT
16450137 AAGTTGAGAG
Statistics
Matches: 189, Mismatches: 14, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
42 60 0.32
43 129 0.68
ACGTcount: A:0.26, C:0.20, G:0.32, T:0.23
Consensus pattern (43 bp):
ATGACCCAGCCATGTGCGGTGTAAGAGTGCACATGAGCTGATG
Found at i:16450075 original size:128 final size:128
Alignment explanation
Indices: 16449890--16450136 Score: 388
Period size: 128 Copynumber: 1.9 Consensus size: 128
16449880 TGTGATAATT
* * * *
16449890 ATGACCTAGCTATATGCGGTGTAGAGTGCACATGAGCTGATCATGACCCAGCTATGTGCGGTGTA
1 ATGACCCAGCCATATGCGGTGTAGAGTGCACATGAGCTAATCATGACCCAGCCATGTGCGGTGTA
*
16449955 AGAGTGCACATGAGCTGATGATGACCCAGCCATGTGCGGTGTAGGAGTGCACATGAGCTGATG
66 AGAGTGCACATGAGCTGATGATGACCCAACCATGTGCGGTGTAGGAGTGCACATGAGCTGATG
* * *
16450018 ATGACCCAGCCATGTGCGGTGTAAGAGTGCACATGAGC-AATGATGACCCAGCCATGTGTGGTGT
1 ATGACCCAGCCATATGCGGTGT-AGAGTGCACATGAGCTAATCATGACCCAGCCATGTGCGGTGT
* *
16450082 AAGAGTGCACATGAGCTGATGATGACCCAACTATGTGCGGTGTGGGAGTGCACAT
65 AAGAGTGCACATGAGCTGATGATGACCCAACCATGTGCGGTGTAGGAGTGCACAT
16450137 AAGTTGAGAG
Statistics
Matches: 108, Mismatches: 10, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
128 93 0.86
129 15 0.14
ACGTcount: A:0.26, C:0.20, G:0.32, T:0.23
Consensus pattern (128 bp):
ATGACCCAGCCATATGCGGTGTAGAGTGCACATGAGCTAATCATGACCCAGCCATGTGCGGTGTA
AGAGTGCACATGAGCTGATGATGACCCAACCATGTGCGGTGTAGGAGTGCACATGAGCTGATG
Found at i:16450081 original size:85 final size:85
Alignment explanation
Indices: 16449885--16450136 Score: 380
Period size: 85 Copynumber: 3.0 Consensus size: 85
16449875 TATTGTGTGA
* * * * *
16449885 TAATTATGACCTAGCTATATGCGGTGTAGAGTGCACATGAGCTGATCATGACCCAGCTATGTGCG
1 TAATGATGACCCAGCCATGTGCGGTGTAGAGTGCACATGAGCTGATGATGACCCAGCTATGTGCG
16449950 GTGTAAGAGTGCACATGAGC
66 GTGTAAGAGTGCACATGAGC
* *
16449970 TGATGATGACCCAGCCATGTGCGGTGTAGGAGTGCACATGAGCTGATGATGACCCAGCCATGTGC
1 TAATGATGACCCAGCCATGTGCGGTGTA-GAGTGCACATGAGCTGATGATGACCCAGCTATGTGC
16450035 GGTGTAAGAGTGCACATGAGC
65 GGTGTAAGAGTGCACATGAGC
* *
16450056 -AATGATGACCCAGCCATGTGTGGTGTAAGAGTGCACATGAGCTGATGATGACCCAACTATGTGC
1 TAATGATGACCCAGCCATGTGCGGTGT-AGAGTGCACATGAGCTGATGATGACCCAGCTATGTGC
**
16450120 GGTGTGGGAGTGCACAT
65 GGTGTAAGAGTGCACAT
16450137 AAGTTGAGAG
Statistics
Matches: 152, Mismatches: 13, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
85 96 0.63
86 56 0.37
ACGTcount: A:0.26, C:0.19, G:0.31, T:0.23
Consensus pattern (85 bp):
TAATGATGACCCAGCCATGTGCGGTGTAGAGTGCACATGAGCTGATGATGACCCAGCTATGTGCG
GTGTAAGAGTGCACATGAGC
Found at i:16451002 original size:13 final size:13
Alignment explanation
Indices: 16450984--16451011 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
16450974 ACCTAATAAC
16450984 TTAATTAAACAAT
1 TTAATTAAACAAT
16450997 TTAATTAAACAAT
1 TTAATTAAACAAT
16451010 TT
1 TT
16451012 TAATCAAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (13 bp):
TTAATTAAACAAT
Found at i:16451164 original size:35 final size:35
Alignment explanation
Indices: 16450997--16451165 Score: 169
Period size: 35 Copynumber: 4.8 Consensus size: 35
16450987 ATTAAACAAT
* * *
16450997 TTAATTAAACAATTTTAATCAAATAGGCCCAATGAC
1 TTAATTAAACAA-TTTAATTAATTAGGCCTAATGAC
* * *
16451033 TTAATTAAACAAATTTAATCAATTAGGTCC-GATAAC
1 TTAATTAAAC-AATTTAATTAATTAGG-CCTAATGAC
**** * *
16451069 TTAATTGTTTAATTTAATTAATTAGCCCTTATGAC
1 TTAATTAAACAATTTAATTAATTAGGCCTAATGAC
* * *
16451104 TTAATTAAATAATTGAATTAATTAGGCCTAATGAT
1 TTAATTAAACAATTTAATTAATTAGGCCTAATGAC
16451139 TTAATTAAACAATTTAATTAATTAGGC
1 TTAATTAAACAATTTAATTAATTAGGC
16451166 ACAACTTAAT
Statistics
Matches: 110, Mismatches: 20, Indels: 7
0.80 0.15 0.05
Matches are distributed among these distances:
34 2 0.02
35 71 0.65
36 33 0.30
37 4 0.04
ACGTcount: A:0.41, C:0.11, G:0.09, T:0.38
Consensus pattern (35 bp):
TTAATTAAACAATTTAATTAATTAGGCCTAATGAC
Found at i:16455930 original size:15 final size:16
Alignment explanation
Indices: 16455911--16455946 Score: 65
Period size: 15 Copynumber: 2.3 Consensus size: 16
16455901 CTCCATCCTT
16455911 TCTTTCTTCCTTTCTC
1 TCTTTCTTCCTTTCTC
16455927 -CTTTCTTCCTTTCTC
1 TCTTTCTTCCTTTCTC
16455942 TCTTT
1 TCTTT
16455947 GCTTTTAAGC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 15 0.79
16 4 0.21
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (16 bp):
TCTTTCTTCCTTTCTC
Found at i:16459577 original size:45 final size:47
Alignment explanation
Indices: 16459527--16459615 Score: 121
Period size: 47 Copynumber: 1.9 Consensus size: 47
16459517 TGCACGACGT
* *
16459527 GGGGGGATGTACATGAT-G-GCACTGAT-TGTGCACGATGTGGGGGGG
1 GGGGGGATGCACACGATGGTGC-CTGATATGTGCACGATGTGGGGGGG
*
16459572 GGGGGGATGCACACGATGGTGCCTGCTATGTGCACGATGTGGGG
1 GGGGGGATGCACACGATGGTGCCTGATATGTGCACGATGTGGGG
16459616 AGATGTACAT
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
45 15 0.39
46 5 0.13
47 18 0.47
ACGTcount: A:0.17, C:0.15, G:0.47, T:0.21
Consensus pattern (47 bp):
GGGGGGATGCACACGATGGTGCCTGATATGTGCACGATGTGGGGGGG
Found at i:16464246 original size:37 final size:38
Alignment explanation
Indices: 16464194--16464303 Score: 170
Period size: 37 Copynumber: 2.9 Consensus size: 38
16464184 TGAGGATGTT
**
16464194 GAAGTGTGTGAGTAGGGAGTGCACACATGATGATGATA
1 GAAGTGTGCAAGTAGGGAGTGCACACATGATGATGATA
*
16464232 G-AGTGTGCAAGTAGGGAGTGCACACATGATGATG-TT
1 GAAGTGTGCAAGTAGGGAGTGCACACATGATGATGATA
*
16464268 GAAGTGTGCGAGTAGGGAGTGCACACATGATGATGA
1 GAAGTGTGCAAGTAGGGAGTGCACACATGATGATGA
16464304 ATGCATATGT
Statistics
Matches: 66, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
36 2 0.03
37 63 0.95
38 1 0.02
ACGTcount: A:0.30, C:0.10, G:0.37, T:0.23
Consensus pattern (38 bp):
GAAGTGTGCAAGTAGGGAGTGCACACATGATGATGATA
Found at i:16467671 original size:2 final size:2
Alignment explanation
Indices: 16467666--16467695 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
16467656 CACATGAGTA
16467666 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
16467696 GTTGCAAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:16471276 original size:37 final size:37
Alignment explanation
Indices: 16471235--16471357 Score: 138
Period size: 37 Copynumber: 3.1 Consensus size: 37
16471225 GTTGTGTGAG
*
16471235 GATGTTAAAGTGTGCGAGTAGGGAGTGCACACATGGT
1 GATGTTAAAGTGTGCGAGTAGGGAGTGCACACATGAT
*
16471272 GATGTTAGAGTGTGCGAGTAGGGAGTGTCGCAGTGCACATATGAT
1 GATGTTAAAGTGTGCGAGTAGGGA--GT-GCA---CAC--ATGAT
* *
16471317 GATGTTGAAGTGTGCAAGTAGGGAGTGCACACATGAT
1 GATGTTAAAGTGTGCGAGTAGGGAGTGCACACATGAT
16471354 GATG
1 GATG
16471358 AATGAATATG
Statistics
Matches: 73, Mismatches: 5, Indels: 16
0.78 0.05 0.17
Matches are distributed among these distances:
37 32 0.44
39 5 0.07
40 3 0.04
42 3 0.04
43 5 0.07
45 25 0.34
ACGTcount: A:0.27, C:0.11, G:0.37, T:0.25
Consensus pattern (37 bp):
GATGTTAAAGTGTGCGAGTAGGGAGTGCACACATGAT
Found at i:16471322 original size:45 final size:45
Alignment explanation
Indices: 16471258--16471343 Score: 129
Period size: 45 Copynumber: 1.9 Consensus size: 45
16471248 GCGAGTAGGG
* *
16471258 AGTGCACACATGGTGATGTT-AGAGTGTGCGAGTAGGGAGTGTCGC
1 AGTGCACACATGATGATGTTGA-AGTGTGCAAGTAGGGAGTGTCGC
*
16471303 AGTGCACATATGATGATGTTGAAGTGTGCAAGTAGGGAGTG
1 AGTGCACACATGATGATGTTGAAGTGTGCAAGTAGGGAGTG
16471344 CACACATGAT
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
45 36 0.97
46 1 0.03
ACGTcount: A:0.26, C:0.10, G:0.38, T:0.26
Consensus pattern (45 bp):
AGTGCACACATGATGATGTTGAAGTGTGCAAGTAGGGAGTGTCGC
Found at i:16476172 original size:23 final size:23
Alignment explanation
Indices: 16476142--16476201 Score: 84
Period size: 23 Copynumber: 2.6 Consensus size: 23
16476132 TGAGCTGGTG
* * *
16476142 ATGATGATGATGTGATGGTGTGT
1 ATGATGATGATGGGATGATGTGC
16476165 ATGATGATGATGGGATGATGTGC
1 ATGATGATGATGGGATGATGTGC
*
16476188 ATGATAATGATGGG
1 ATGATGATGATGGG
16476202 TATACGTATA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.27, C:0.02, G:0.38, T:0.33
Consensus pattern (23 bp):
ATGATGATGATGGGATGATGTGC
Found at i:16476558 original size:21 final size:21
Alignment explanation
Indices: 16476534--16476576 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
16476524 TTTCATCAGC
16476534 AGAAT-TTCGCTACAGCGAGAA
1 AGAATCTT-GCTACAGCGAGAA
**
16476555 AGAATCTTGCTGTAGCGAGAA
1 AGAATCTTGCTACAGCGAGAA
16476576 A
1 A
16476577 CCTTATGTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 17 0.89
22 2 0.11
ACGTcount: A:0.37, C:0.16, G:0.26, T:0.21
Consensus pattern (21 bp):
AGAATCTTGCTACAGCGAGAA
Found at i:16476600 original size:60 final size:61
Alignment explanation
Indices: 16476480--16476613 Score: 141
Period size: 60 Copynumber: 2.2 Consensus size: 61
16476470 CTGTAGCTTC
* *
16476480 TCGCTACAGC-AAAAAGGAATCTCACTATAGCGAGAAACTCTTTGTTTCATCAGCAGAATT
1 TCGCTACAGCGAGAAAGGAATCTCACTATAGCGAGAAACTCTTTGTTTCATCAGCACAATT
** * **
16476540 TCGCTACAGCGAGAAA-GAATCTTGCTGTAGCGAGAAAC-CTTATGTTTC-TGGGTCACAATT
1 TCGCTACAGCGAGAAAGGAATCTCACTATAGCGAGAAACTCTT-TGTTTCATCAG-CACAATT
* *
16476600 TCGCTGCATCGAGA
1 TCGCTACAGCGAGA
16476614 TTCAATCTCG
Statistics
Matches: 62, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
59 5 0.08
60 53 0.85
61 4 0.06
ACGTcount: A:0.31, C:0.22, G:0.21, T:0.27
Consensus pattern (61 bp):
TCGCTACAGCGAGAAAGGAATCTCACTATAGCGAGAAACTCTTTGTTTCATCAGCACAATT
Found at i:16480314 original size:128 final size:126
Alignment explanation
Indices: 16480157--16480410 Score: 490
Period size: 128 Copynumber: 2.0 Consensus size: 126
16480147 TTTCTTACTT
16480157 CTTTCTTCTCCAAACTTCTTGGGCACTAAACCTGTAGCTTCTAACCCTAATTTTCAGCACATCTA
1 CTTTCTTCTCCAAACTTCTTGGGCACTAAACCTGTAGCTTCTAACCCTAATTTTCAGCACATCTA
16480222 AACCCTAAGAGAAGAAGAAAGAAAAAGAAAGAAAGGAAGAAAAGCTTGGTTTTGTAATTCAA
66 AACCCTAAGAGAAGAAGAAAG-AAAAGAAAGAAAGGAAGAAAAGCTTGGTTTTGTAATTCAA
16480284 NCTTTCTTCTCCAAACTTCTTGGGCACTAAACCTGTAGCTTCTAACCCTAATTTTCAGCACATCT
1 -CTTTCTTCTCCAAACTTCTTGGGCACTAAACCTGTAGCTTCTAACCCTAATTTTCAGCACATCT
16480349 AAACCCTAAGAGAAGAAGAAAGAAAAGAAAGAAAGGAAGAAAAGCTTGGTTTTGTAATTCAA
65 AAACCCTAAGAGAAGAAGAAAGAAAAGAAAGAAAGGAAGAAAAGCTTGGTTTTGTAATTCAA
16480411 GGAAGCTAAG
Statistics
Matches: 126, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
127 40 0.32
128 86 0.68
ACGTcount: A:0.38, C:0.20, G:0.16, T:0.26
Consensus pattern (126 bp):
CTTTCTTCTCCAAACTTCTTGGGCACTAAACCTGTAGCTTCTAACCCTAATTTTCAGCACATCTA
AACCCTAAGAGAAGAAGAAAGAAAAGAAAGAAAGGAAGAAAAGCTTGGTTTTGTAATTCAA
Found at i:16481404 original size:43 final size:42
Alignment explanation
Indices: 16481234--16481405 Score: 193
Period size: 43 Copynumber: 4.0 Consensus size: 42
16481224 TTGTGTGATA
** * *
16481234 ATGATGACCCAGCTATGTGCGTGT-GGGAGTGCACATGAGCTT
1 ATGATGACCTGGCCATGTGCG-GTAGGGAGTGCACATGAGCTG
** * * *
16481276 ATGATGACCCAGCTATGTGCGGTGTGGGAGTGCACATGAGTTG
1 ATGATGACCTGGCCATGTGCGGT-AGGGAGTGCACATGAGCTG
* *
16481319 ATGATGACCTGGCCATGTGCGGCATGGGAGTGCACACGAGCTG
1 ATGATGACCTGGCCATGTGCGGTA-GGGAGTGCACATGAGCTG
*
16481362 ATGATGACTTGGCCATGTGCGAGTAGGGAGTGCACATGAGCTG
1 ATGATGACCTGGCCATGTGCG-GTAGGGAGTGCACATGAGCTG
16481405 A
1 A
16481406 GTGTGGGGGG
Statistics
Matches: 114, Mismatches: 12, Indels: 7
0.86 0.09 0.05
Matches are distributed among these distances:
41 2 0.02
42 21 0.18
43 89 0.78
44 2 0.02
ACGTcount: A:0.22, C:0.19, G:0.36, T:0.23
Consensus pattern (42 bp):
ATGATGACCTGGCCATGTGCGGTAGGGAGTGCACATGAGCTG
Found at i:16486920 original size:2 final size:2
Alignment explanation
Indices: 16486913--16486942 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
16486903 GCCTAGCCAC
16486913 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
16486943 CACAGGTCGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:16488213 original size:19 final size:19
Alignment explanation
Indices: 16488173--16488215 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
16488163 TTGTCTTTTT
*
16488173 TTTCTTTCTCCATCCTTTC
1 TTTCTTTCTCCATCCTTCC
* *
16488192 TTTCTTTCTCCTTTCTTCC
1 TTTCTTTCTCCATCCTTCC
16488211 TTTCT
1 TTTCT
16488216 CTCTTTGCTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.02, C:0.35, G:0.00, T:0.63
Consensus pattern (19 bp):
TTTCTTTCTCCATCCTTCC
Found at i:16488226 original size:17 final size:15
Alignment explanation
Indices: 16488185--16488226 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
16488175 TCTTTCTCCA
*
16488185 TCCTTTCTTTCTTTC
1 TCCTTTCTTCCTTTC
16488200 TCCTTTCTTCCTTTC
1 TCCTTTCTTCCTTTC
16488215 TCTCTTTGCTTC
1 TC-CTTT-CTTC
16488227 AAAGTCGATT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
15 16 0.67
16 4 0.17
17 4 0.17
ACGTcount: A:0.00, C:0.36, G:0.02, T:0.62
Consensus pattern (15 bp):
TCCTTTCTTCCTTTC
Found at i:16499925 original size:180 final size:180
Alignment explanation
Indices: 16499701--16500051 Score: 494
Period size: 180 Copynumber: 1.9 Consensus size: 180
16499691 GGCCAGGAAA
*
16499701 ATTTTCAGAAATAATCCTCATTGAACATTTTAATAAAGATAATTTTTCTAGAACTTTTT-AGGAT
1 ATTTTCAGAAATAATCCTCATTGAACATTTTAATAAAGATAATTTTTCTAGAA-TTTTTCAGAAT
* * *
16499765 TAATTTTCAAGAGTTTCTTGTCAATTAAAATTGAAATTCATGCCAAAACAGTGAACTGGA-TAGA
65 TAATTTCCAAGACTTTCTTGTCAATTAAAACTGAAATTCATGCCAAAACAGTGAACTGGACT-GA
*
16499829 TTT-A-TATTTGCACCAATTTTCTTGCTTGAAATCAGCATATTTGACCATGAT
129 TTTCACTATTTGCACCAA-TTTCTTGCTTAAAATCAGCATATTTGACCATGAT
* * *
16499880 ATTTTCCAGAAGTAATCCTTATTGAACATTTTAATAAAGATAATTTTTCTGGAATTTTTCAGAAT
1 ATTTT-CAGAAATAATCCTCATTGAACATTTTAATAAAGATAATTTTTCTAGAATTTTTCAGAAT
* * * * *
16499945 TAATTTCCAAGACTTTCTTGTCAATTAATACTGAAATTCATGTCATAACAGTGAGCTGGACTGCT
65 TAATTTCCAAGACTTTCTTGTCAATTAAAACTGAAATTCATGCCAAAACAGTGAACTGGACTGAT
* * *
16500010 TTCACTTTTTGCTCCAATTTCTTGCTTAAAATCAGCCTATTT
130 TTCACTATTTGCACCAATTTCTTGCTTAAAATCAGCATATTT
16500052 AATCATGAAC
Statistics
Matches: 151, Mismatches: 16, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
179 10 0.07
180 106 0.70
181 25 0.17
182 10 0.07
ACGTcount: A:0.33, C:0.15, G:0.12, T:0.40
Consensus pattern (180 bp):
ATTTTCAGAAATAATCCTCATTGAACATTTTAATAAAGATAATTTTTCTAGAATTTTTCAGAATT
AATTTCCAAGACTTTCTTGTCAATTAAAACTGAAATTCATGCCAAAACAGTGAACTGGACTGATT
TCACTATTTGCACCAATTTCTTGCTTAAAATCAGCATATTTGACCATGAT
Found at i:16501238 original size:3 final size:3
Alignment explanation
Indices: 16501230--16501254 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
16501220 TTTCTAGCAG
16501230 CTT CTT CTT CTT CTT CTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT C
16501255 CCATCTCTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (3 bp):
CTT
Found at i:16502025 original size:2 final size:2
Alignment explanation
Indices: 16502018--16502067 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
16502008 TATTATGTGG
16502018 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
16502060 AT AT AT AT
1 AT AT AT AT
16502068 GTTGTGTATG
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:16503804 original size:32 final size:32
Alignment explanation
Indices: 16503768--16503887 Score: 116
Period size: 36 Copynumber: 3.5 Consensus size: 32
16503758 TTTAATTGTT
16503768 TAATTTAATCAATTAGACCCAATTTAATTAAA
1 TAATTTAATCAATTAGACCCAATTTAATTAAA
* *
16503800 TAATTTAATTAATTA-AGCCAAATAATTTAATTAAA
1 TAATTTAATCAATTAGA-CC---CAATTTAATTAAA
*
16503835 TAATTTTAATCAATTAGGCCCAATGACTTAATTAAA
1 TAA-TTTAATCAATTAGACCCAAT---TTAATTAAA
*
16503871 CAAATTTAATCAATTAG
1 -TAATTTAATCAATTAG
16503888 GCTCAGTAAC
Statistics
Matches: 72, Mismatches: 6, Indels: 16
0.77 0.06 0.17
Matches are distributed among these distances:
31 1 0.01
32 16 0.22
33 3 0.04
35 15 0.21
36 35 0.49
37 2 0.03
ACGTcount: A:0.47, C:0.11, G:0.05, T:0.38
Consensus pattern (32 bp):
TAATTTAATCAATTAGACCCAATTTAATTAAA
Found at i:16503834 original size:35 final size:35
Alignment explanation
Indices: 16503768--16503989 Score: 191
Period size: 35 Copynumber: 6.4 Consensus size: 35
16503758 TTTAATTGTT
* *
16503768 TAATTTAATCAATTAGACCCAAT---TTAATTAAA
1 TAATTTAATTAATTAGGCCCAATAACTTAATTAAA
* * *
16503800 TAATTTAATTAATTAAGCCAAATAATTTAATTAAA
1 TAATTTAATTAATTAGGCCCAATAACTTAATTAAA
* *
16503835 TAATTTTAATCAATTAGGCCCAATGACTTAATTAAA
1 TAA-TTTAATTAATTAGGCCCAATAACTTAATTAAA
* * * * ***
16503871 CAAATTTAATCAATTAGGCTCAGTAACTTAATTGTT
1 -TAATTTAATTAATTAGGCCCAATAACTTAATTAAA
* **
16503907 TAATGTAATTAATT-GGCCCAACGACTTAATTAAA
1 TAATTTAATTAATTAGGCCCAATAACTTAATTAAA
* * * * *
16503941 CAATTTAATTAATTAAGCCCGATGATTTAATTAAA
1 TAATTTAATTAATTAGGCCCAATAACTTAATTAAA
*
16503976 CAATTTAATTAATT
1 TAATTTAATTAATT
16503990 TGGCACAACT
Statistics
Matches: 152, Mismatches: 32, Indels: 9
0.79 0.17 0.05
Matches are distributed among these distances:
32 19 0.12
34 25 0.16
35 53 0.35
36 53 0.35
37 2 0.01
ACGTcount: A:0.43, C:0.12, G:0.07, T:0.38
Consensus pattern (35 bp):
TAATTTAATTAATTAGGCCCAATAACTTAATTAAA
Found at i:16530043 original size:13 final size:14
Alignment explanation
Indices: 16530020--16530080 Score: 52
Period size: 13 Copynumber: 4.1 Consensus size: 14
16530010 ACATTTATTA
16530020 TATTCAAATAATAT
1 TATTCAAATAATAT
16530034 TATT-AAATAATAT
1 TATTCAAATAATAT
* *
16530047 TCTTCATAATATTTAT
1 TATTCA-AATA-ATAT
*
16530063 TATAATTAAATAATAT
1 TAT--TCAAATAATAT
16530079 TA
1 TA
16530081 ATATATTTTC
Statistics
Matches: 37, Mismatches: 5, Indels: 8
0.74 0.10 0.16
Matches are distributed among these distances:
13 12 0.32
14 5 0.14
15 4 0.11
16 10 0.27
17 4 0.11
18 2 0.05
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.48
Consensus pattern (14 bp):
TATTCAAATAATAT
Found at i:16530047 original size:45 final size:45
Alignment explanation
Indices: 16529992--16530080 Score: 117
Period size: 45 Copynumber: 2.0 Consensus size: 45
16529982 TAAATAATAC
* * * *
16529992 TAAATGATATTTTTTATTACATTTATTAT-ATTCAAATAATATTAT
1 TAAATAATATTCTTCATAACATTTATTATAATT-AAATAATATTAT
*
16530037 TAAATAATATTCTTCATAATATTTATTATAATTAAATAATATTA
1 TAAATAATATTCTTCATAACATTTATTATAATTAAATAATATTA
16530081 ATATATTTTC
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
45 35 0.92
46 3 0.08
ACGTcount: A:0.44, C:0.04, G:0.01, T:0.51
Consensus pattern (45 bp):
TAAATAATATTCTTCATAACATTTATTATAATTAAATAATATTAT
Found at i:16531617 original size:16 final size:16
Alignment explanation
Indices: 16531596--16531626 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
16531586 TCGCAATAAA
*
16531596 GGGAGAGAGGGAGAGG
1 GGGAGAGAGAGAGAGG
16531612 GGGAGAGAGAGAGAG
1 GGGAGAGAGAGAGAG
16531627 CGAATAGGCC
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:0.35, C:0.00, G:0.65, T:0.00
Consensus pattern (16 bp):
GGGAGAGAGAGAGAGG
Found at i:16538894 original size:16 final size:16
Alignment explanation
Indices: 16538875--16538908 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
16538865 TTTAATTACT
16538875 ATTAAATTAAATTTTA
1 ATTAAATTAAATTTTA
* *
16538891 ATTAAGTTAGATTTTA
1 ATTAAATTAAATTTTA
16538907 AT
1 AT
16538909 CGGATTACAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (16 bp):
ATTAAATTAAATTTTA
Found at i:16539521 original size:30 final size:30
Alignment explanation
Indices: 16539481--16539541 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
16539471 TTATTTAAAA
*
16539481 TTAACTTGGTAATTAGCATCATTACATCTT
1 TTAACGTGGTAATTAGCATCATTACATCTT
* *
16539511 TTAACGTGGTAATTAGCGTCATTCCATCTT
1 TTAACGTGGTAATTAGCATCATTACATCTT
16539541 T
1 T
16539542 GGTGCATTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.26, C:0.18, G:0.13, T:0.43
Consensus pattern (30 bp):
TTAACGTGGTAATTAGCATCATTACATCTT
Found at i:16540419 original size:2 final size:2
Alignment explanation
Indices: 16540412--16540437 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
16540402 AAATTAAAGA
16540412 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
16540438 CTATTTAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:16549393 original size:22 final size:22
Alignment explanation
Indices: 16549363--16549407 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
16549353 GTTTAATTAA
* *
16549363 GTTGTGCCTAATTAATTAAATT
1 GTTGGGCCTAATAAATTAAATT
16549385 GTTGGGCCTAATAAATTAAATT
1 GTTGGGCCTAATAAATTAAATT
16549407 G
1 G
16549408 ATTAATTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.33, C:0.09, G:0.18, T:0.40
Consensus pattern (22 bp):
GTTGGGCCTAATAAATTAAATT
Found at i:16549415 original size:35 final size:35
Alignment explanation
Indices: 16549373--16549476 Score: 163
Period size: 35 Copynumber: 3.0 Consensus size: 35
16549363 GTTGTGCCTA
16549373 ATTAATTAAATTGTTGGGCCTAATAAATTAAATTG
1 ATTAATTAAATTGTTGGGCCTAATAAATTAAATTG
16549408 ATTAATTAAATTGTTGGGCCTAATAAATTAAATTG
1 ATTAATTAAATTGTTGGGCCTAATAAATTAAATTG
* * * **
16549443 TTTAATTAAGTTATTGGGCCTAATTGATTAAATT
1 ATTAATTAAATTGTTGGGCCTAATAAATTAAATT
16549477 AAACAATTAA
Statistics
Matches: 64, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
35 64 1.00
ACGTcount: A:0.38, C:0.06, G:0.14, T:0.42
Consensus pattern (35 bp):
ATTAATTAAATTGTTGGGCCTAATAAATTAAATTG
Found at i:16552481 original size:184 final size:183
Alignment explanation
Indices: 16552143--16552511 Score: 562
Period size: 184 Copynumber: 2.0 Consensus size: 183
16552133 TATGTAATAA
* * ** *
16552143 TTTTCAACAAGAGGGATAAGTACCTTTATGTTTGAAGTCCACTTGATTACTCTAACCTTCAAGCT
1 TTTTCAACAAGAGGGACAAGCACCTTTATGTTTGAAGTCCACTCAATTACTCCAACCTTCAAGCT
*
16552208 AGTGTGTGTACAAGATATCATTTATGTTAATGTATGAATGCTATAATGAACATGCTTGATATGTT
66 AGTGTGGGTACAAGATATCATTTATGTTAATGTATGAATGCTATAATGAACATGCTTGATATGTT
16552273 GATACATGTGATGTATGATGGATCATATAATGTTTTCCATCTAAGATACTATG
131 GATACATGTGATGTATGATGGATCATATAATGTTTTCCATCTAAGATACTATG
* * ** *
16552326 TTTTCAACAATAGGGGACAAGCACCTTTATGTTTGAAGTCCACTCAATTTCTCCAGTCTTCGAGC
1 TTTTCAACAAGA-GGGACAAGCACCTTTATGTTTGAAGTCCACTCAATTACTCCAACCTTCAAGC
* *
16552391 TAGTGTGGGTACGAGATATTATTTATGTTAATGTATGAATGCTA-AGATGAACATGCTTGATATG
65 TAGTGTGGGTACAAGATATCATTTATGTTAATGTATGAATGCTATA-ATGAACATGCTTGATATG
* *
16552455 TTGATACATGTGATGT-TTACTGGATCATATGATGTTTTCCATCTAAGATACTATG
129 TTGATACATGTGATGTATGA-TGGATCATATAATGTTTTCCATCTAAGATACTATG
16552510 TT
1 TT
16552512 ATGTATATGA
Statistics
Matches: 168, Mismatches: 15, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
183 14 0.08
184 154 0.92
ACGTcount: A:0.30, C:0.14, G:0.19, T:0.38
Consensus pattern (183 bp):
TTTTCAACAAGAGGGACAAGCACCTTTATGTTTGAAGTCCACTCAATTACTCCAACCTTCAAGCT
AGTGTGGGTACAAGATATCATTTATGTTAATGTATGAATGCTATAATGAACATGCTTGATATGTT
GATACATGTGATGTATGATGGATCATATAATGTTTTCCATCTAAGATACTATG
Found at i:16558061 original size:2 final size:2
Alignment explanation
Indices: 16558042--16558096 Score: 74
Period size: 2 Copynumber: 27.0 Consensus size: 2
16558032 TATGACGCTG
* * *
16558042 AT AT GT AT AT AA AG AT AT AT GAT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT AT AT AT AT AT AT
16558085 AT AT AT AT AT AT
1 AT AT AT AT AT AT
16558097 TATTAAGTAG
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
2 45 0.96
3 2 0.04
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.45
Consensus pattern (2 bp):
AT
Found at i:16558181 original size:2 final size:2
Alignment explanation
Indices: 16558174--16558208 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
16558164 AGTGACAATN
16558174 AT AT AT AT AT AT AT -T AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
16558209 TGTTAAGTAG
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:16558215 original size:112 final size:110
Alignment explanation
Indices: 16558063--16558280 Score: 366
Period size: 112 Copynumber: 2.0 Consensus size: 110
16558053 AAGATATATG
*
16558063 ATATATATATATATATATATATATATATATATATTATTAAGTAGTTTTGTATAATTGATGTAACC
1 ATATATATATATATATATATATATATATATATATTATTAAGTAGTTTTGTATAATTGATATAACC
16558128 GTGCATGTGCAG-AGTGGGCAGTGCACATGCCAGTTGAGTGACAAT
66 GTGCATGTGC-GTAGTGGGCAGTGCACATGCCAGTTGAGTGACAAT
* *
16558173 NATATATATATATATTATATATATATATATATATATTGTTAAGTAGTTTTGTATAATTGATATTA
1 -ATATATATATATA-TATATATATATATATATATATTATTAAGTAGTTTTGTATAATTGATATAA
*
16558238 CCGTGCATGTGCGTAGTGGGCAGTGCACATGCCGGTTGAGTGA
64 CCGTGCATGTGCGTAGTGGGCAGTGCACATGCCAGTTGAGTGA
16558281 TAATGTAGCT
Statistics
Matches: 101, Mismatches: 4, Indels: 3
0.94 0.04 0.03
Matches are distributed among these distances:
111 14 0.14
112 87 0.86
ACGTcount: A:0.33, C:0.09, G:0.20, T:0.39
Consensus pattern (110 bp):
ATATATATATATATATATATATATATATATATATTATTAAGTAGTTTTGTATAATTGATATAACC
GTGCATGTGCGTAGTGGGCAGTGCACATGCCAGTTGAGTGACAAT
Found at i:16559118 original size:21 final size:21
Alignment explanation
Indices: 16559094--16559152 Score: 55
Period size: 21 Copynumber: 2.8 Consensus size: 21
16559084 AGACTTTCTA
*
16559094 GCTGTAGCGAGATCCATTTTG
1 GCTGCAGCGAGATCCATTTTG
* **
16559115 GCTGCAGTGAGATTTATTTTG
1 GCTGCAGCGAGATCCATTTTG
* *
16559136 GCTACAGTGAGAATCCA
1 GCTGCAGCGAG-ATCCA
16559153 ATTTAGCTAC
Statistics
Matches: 30, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
21 27 0.90
22 3 0.10
ACGTcount: A:0.24, C:0.17, G:0.27, T:0.32
Consensus pattern (21 bp):
GCTGCAGCGAGATCCATTTTG
Found at i:16569161 original size:2 final size:2
Alignment explanation
Indices: 16569154--16569180 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
16569144 AGATTCGTAT
16569154 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
16569181 GATTTGAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:16570961 original size:17 final size:17
Alignment explanation
Indices: 16570931--16570963 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
16570921 TTTAATTAGG
16570931 AATTAGTTATATATTAT
1 AATTAGTTATATATTAT
16570948 AATT-GTTATAATATTA
1 AATTAGTTAT-ATATTA
16570964 AGGACTTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (17 bp):
AATTAGTTATATATTAT
Found at i:16580964 original size:2 final size:2
Alignment explanation
Indices: 16580957--16580981 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
16580947 TTATCTGTAG
16580957 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
16580982 TTATGCAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:16587893 original size:15 final size:15
Alignment explanation
Indices: 16587873--16587902 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
16587863 AATAATATCC
16587873 AATATTAATTAATTA
1 AATATTAATTAATTA
*
16587888 AATATTTATTAATTA
1 AATATTAATTAATTA
16587903 TTTATAAATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
AATATTAATTAATTA
Found at i:16592352 original size:3 final size:3
Alignment explanation
Indices: 16592344--16592373 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
16592334 TTTAAGGACT
16592344 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
16592374 TATTTACCAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:16593443 original size:16 final size:16
Alignment explanation
Indices: 16593422--16593454 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
16593412 ATTGGCTCAA
16593422 CACTAGACCAATGCGC
1 CACTAGACCAATGCGC
16593438 CACTAGACCAATGCGC
1 CACTAGACCAATGCGC
16593454 C
1 C
16593455 CGTCGTGGTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.30, C:0.39, G:0.18, T:0.12
Consensus pattern (16 bp):
CACTAGACCAATGCGC
Found at i:16594431 original size:29 final size:29
Alignment explanation
Indices: 16594394--16594451 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
16594384 AATAATTAAT
* *
16594394 TATAAAA-TTTATTTAATTTAAAATAAAAA
1 TATAAAATTTTAATTAATAT-AAATAAAAA
*
16594423 TATATAATTTTAATTAATATAAATAAAAA
1 TATAAAATTTTAATTAATATAAATAAAAA
16594452 ATTAAGATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 15 0.60
30 10 0.40
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (29 bp):
TATAAAATTTTAATTAATATAAATAAAAA
Found at i:16595341 original size:4 final size:4
Alignment explanation
Indices: 16595334--16595360 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
16595324 AAAAAAATGC
16595334 TTAT TTAT TTAT TTAT TTAT TTAT TTA
1 TTAT TTAT TTAT TTAT TTAT TTAT TTA
16595361 GGTAGCTTGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (4 bp):
TTAT
Found at i:16606549 original size:20 final size:19
Alignment explanation
Indices: 16606521--16606570 Score: 73
Period size: 19 Copynumber: 2.6 Consensus size: 19
16606511 TTGTGAGAAA
* **
16606521 TTTTTAAAAGAAATAACTT
1 TTTTTAAAAAAAATAAAAT
16606540 TTTTTAAAAAAAATAAAAT
1 TTTTTAAAAAAAATAAAAT
16606559 TTTTTAAAAAAA
1 TTTTTAAAAAAA
16606571 GAGTTTAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (19 bp):
TTTTTAAAAAAAATAAAAT
Found at i:16612394 original size:39 final size:39
Alignment explanation
Indices: 16612304--16612480 Score: 243
Period size: 39 Copynumber: 4.6 Consensus size: 39
16612294 TCAACTCAGC
* * * *
16612304 TCATGTGCACTCCCACACCGCATATAGCA-A-AT-ATCC
1 TCATGTGCTCTCCCACACCGCACATGGCATATATCATCA
*
16612340 TCATGTGCACTCCCACACCGCACATGGCATATATCATCA
1 TCATGTGCTCTCCCACACCGCACATGGCATATATCATCA
16612379 TCATGTGCTCTCCCACACCGCACATGGCATATATCATCA
1 TCATGTGCTCTCCCACACCGCACATGGCATATATCATCA
* * *
16612418 TCATGTGCTCTCTCACACCGTACATGGCATATATCATCG
1 TCATGTGCTCTCCCACACCGCACATGGCATATATCATCA
* *
16612457 GCGTGTGCTCTCCCACACCGCACA
1 TCATGTGCTCTCCCACACCGCACA
16612481 CTACCGGCAC
Statistics
Matches: 127, Mismatches: 11, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
36 27 0.21
37 1 0.01
38 2 0.02
39 97 0.76
ACGTcount: A:0.25, C:0.36, G:0.14, T:0.24
Consensus pattern (39 bp):
TCATGTGCTCTCCCACACCGCACATGGCATATATCATCA
Found at i:16612449 original size:78 final size:75
Alignment explanation
Indices: 16612304--16612516 Score: 239
Period size: 78 Copynumber: 2.8 Consensus size: 75
16612294 TCAACTCAGC
* * *
16612304 TCATGTGCACTCCCACACCGCATATAGCAAATATCCTCATGTGCACTCCCACACCGCACATGGCA
1 TCATGTGCTCTCCCACACCGCACATAGCAAATATCATCATGTGCACTCCCACACCGCACATGGCA
16612369 TATATCATCA
66 TATATCATCA
* * * *
16612379 TCATGTGCTCTCCCACACCGCACATGGCATATATCATCATCATGTGCTCTCTCACACCGTACATG
1 TCATGTGCTCTCCCACACCGCACATAGCA-A-AT-ATCATCATGTGCACTCCCACACCGCACATG
*
16612444 GCATATATCATCG
63 GCATATATCATCA
* * **** * *
16612457 GCGTGTGCTCTCCCACACCGCACACTA-CCGGCACCGTCATGTGCACTCCCACACCGCACA
1 TCATGTGCTCTCCCACACCGCACA-TAGCAAATATCATCATGTGCACTCCCACACCGCACA
16612517 CGCATGGTTA
Statistics
Matches: 114, Mismatches: 20, Indels: 8
0.80 0.14 0.06
Matches are distributed among these distances:
75 49 0.43
76 1 0.01
77 2 0.02
78 61 0.54
79 1 0.01
ACGTcount: A:0.25, C:0.38, G:0.15, T:0.23
Consensus pattern (75 bp):
TCATGTGCTCTCCCACACCGCACATAGCAAATATCATCATGTGCACTCCCACACCGCACATGGCA
TATATCATCA
Found at i:16616694 original size:43 final size:43
Alignment explanation
Indices: 16616568--16616697 Score: 163
Period size: 43 Copynumber: 3.0 Consensus size: 43
16616558 CCCACCATAC
* * * * *
16616568 TCAGCTCATGTGCATTCCCTAC-TTGAACATAGCAGGGTTATCA
1 TCAGCTCATGTGCACTCCC-ACATCGCACATAGCTGGGTCATCA
* * *
16616611 TCAGCTCATGTGCACTCCCACACCGCCCATAGCTGAGTCATCA
1 TCAGCTCATGTGCACTCCCACATCGCACATAGCTGGGTCATCA
*
16616654 TCAGCTCATGTGCACTCCCACATCGCACATAGTTGGGTCATCA
1 TCAGCTCATGTGCACTCCCACATCGCACATAGCTGGGTCATCA
16616697 T
1 T
16616698 TATCACACAA
Statistics
Matches: 74, Mismatches: 12, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
42 2 0.03
43 72 0.97
ACGTcount: A:0.24, C:0.32, G:0.18, T:0.26
Consensus pattern (43 bp):
TCAGCTCATGTGCACTCCCACATCGCACATAGCTGGGTCATCA
Found at i:16617530 original size:21 final size:21
Alignment explanation
Indices: 16617505--16617545 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
16617495 GAAGAAGAAA
16617505 AAGAAGCT-ACTGGAAAATGAG
1 AAGAAGCTGA-TGGAAAATGAG
*
16617526 AAGAAGTTGATGGAAAATGA
1 AAGAAGCTGATGGAAAATGA
16617546 TATTCAAACT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 17 0.94
22 1 0.06
ACGTcount: A:0.49, C:0.05, G:0.29, T:0.17
Consensus pattern (21 bp):
AAGAAGCTGATGGAAAATGAG
Found at i:16624504 original size:39 final size:39
Alignment explanation
Indices: 16624442--16624582 Score: 196
Period size: 39 Copynumber: 3.6 Consensus size: 39
16624432 GCTAATATCC
*
16624442 TCATGTGCAT-TCCCACATTGCACATGGCATATATCATCA
1 TCATGTGC-TCTCCCACATCGCACATGGCATATATCATCA
*
16624481 TCATGTGCTCTCCTACATCGCACATGGCATATATCATCA
1 TCATGTGCTCTCCCACATCGCACATGGCATATATCATCA
* * *
16624520 TCATGTGCTCTTCCACACCGCACATGGCATATATCATTGA
1 TCATGTGCTCTCCCACATCGCACATGGCATATATCA-TCA
*
16624560 -CGTGTGCTCTCCCACATCGCACA
1 TCATGTGCTCTCCCACATCGCACA
16624583 CTACCAGCAC
Statistics
Matches: 91, Mismatches: 9, Indels: 4
0.88 0.09 0.04
Matches are distributed among these distances:
38 1 0.01
39 88 0.97
40 2 0.02
ACGTcount: A:0.25, C:0.32, G:0.14, T:0.29
Consensus pattern (39 bp):
TCATGTGCTCTCCCACATCGCACATGGCATATATCATCA
Found at i:16625485 original size:20 final size:20
Alignment explanation
Indices: 16625460--16625501 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
16625450 AAGGGAGGAG
*
16625460 AAGGAAGGAGTAAGAAAA-GA
1 AAGGAAGGA-AAAGAAAATGA
16625480 AAGGAAGGAAAAGAAAATGA
1 AAGGAAGGAAAAGAAAATGA
16625500 AA
1 AA
16625502 AATTTGATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.64, C:0.00, G:0.31, T:0.05
Consensus pattern (20 bp):
AAGGAAGGAAAAGAAAATGA
Found at i:16632759 original size:5 final size:5
Alignment explanation
Indices: 16632749--16632773 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
16632739 AGTGTGGCCC
16632749 AAGTT AAGTT AAGTT AAGTT AAGTT
1 AAGTT AAGTT AAGTT AAGTT AAGTT
16632774 TGATAGAATA
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:0.40, C:0.00, G:0.20, T:0.40
Consensus pattern (5 bp):
AAGTT
Found at i:16639139 original size:101 final size:99
Alignment explanation
Indices: 16638963--16639164 Score: 386
Period size: 101 Copynumber: 2.0 Consensus size: 99
16638953 TCTCACCACC
16638963 CTCATTTTCACCCATTTCAGGCTCAAGATAGTCTATAGATAGCTGATTTCATCGAGGACTACCAT
1 CTCATTTTCACCCATTTCAGGCTCAAGATAGTCTATAGATAGCTGATTTCATCGAGGACTACCAT
16639028 TGGATTTGCATCCGTCAAACTGTAGGTTCACTAAT
66 TGGATTTGCATCCGTCAAACTGTAGGTTCAC-AAT
16639063 CNTCATTTTCACCCATTTCAGGCTCAAGATAGTCTATAGATAGCTGATTTCATCGAGGACTACCA
1 C-TCATTTTCACCCATTTCAGGCTCAAGATAGTCTATAGATAGCTGATTTCATCGAGGACTACCA
16639128 TTGGATTTGCATCCGTCAAACTGTAGGTTCACAAT
65 TTGGATTTGCATCCGTCAAACTGTAGGTTCACAAT
16639163 CT
1 CT
16639165 TTCTTACTTT
Statistics
Matches: 101, Mismatches: 0, Indels: 3
0.97 0.00 0.03
Matches are distributed among these distances:
99 1 0.01
100 5 0.05
101 95 0.94
ACGTcount: A:0.27, C:0.23, G:0.17, T:0.33
Consensus pattern (99 bp):
CTCATTTTCACCCATTTCAGGCTCAAGATAGTCTATAGATAGCTGATTTCATCGAGGACTACCAT
TGGATTTGCATCCGTCAAACTGTAGGTTCACAAT
Found at i:16647612 original size:73 final size:73
Alignment explanation
Indices: 16647514--16647673 Score: 223
Period size: 73 Copynumber: 2.2 Consensus size: 73
16647504 CAAGTAATGG
* * * *
16647514 GTTAGTCAACTAAGAATCTACTGCCAGAAATTTGGACTTCAAGACAGAACCAACTTAATCGACCA
1 GTTAGTCGACTAAGAATCTACTGCCAGAAATTTGGACTTCAAAACAAAAACAACTTAATCGACCA
*
16647579 AGAAGTAA
66 AGAAGGAA
* * *
16647587 GTTAGTCGACTAAGAA-CATATTGCCAGAAATTTGGACTTCAAAACAAAAACAACTTATTCGACT
1 GTTAGTCGACTAAGAATC-TACTGCCAGAAATTTGGACTTCAAAACAAAAACAACTTAATCGACC
16647651 AAGAAGGAA
65 AAGAAGGAA
*
16647660 GTTAGTAGACTAAG
1 GTTAGTCGACTAAG
16647674 TGCTCACTGC
Statistics
Matches: 77, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
72 1 0.01
73 76 0.99
ACGTcount: A:0.42, C:0.17, G:0.17, T:0.23
Consensus pattern (73 bp):
GTTAGTCGACTAAGAATCTACTGCCAGAAATTTGGACTTCAAAACAAAAACAACTTAATCGACCA
AGAAGGAA
Found at i:16648156 original size:67 final size:68
Alignment explanation
Indices: 16648055--16648202 Score: 219
Period size: 67 Copynumber: 2.2 Consensus size: 68
16648045 AAAGTGTGCT
* * *
16648055 AGCCTTAGAAAAGTTAGTTTTGGGTTTTGATTGATCCC-GTGAAAAACCATTGTTAAAGGTTGTG
1 AGCCTTTGAAAAGTCAGCTTTGGGTTTTGATTGATCCCGGT-AAAAACCATTGTTAAAGGTTGTG
16648119 CTTG
65 CTTG
* *
16648123 AGCCTTTGAAAAGTCA-CTTTGGGTTTTGGTTGATCCCGGTAAAAACCATTGTTAAAGGTTGTGG
1 AGCCTTTGAAAAGTCAGCTTTGGGTTTTGATTGATCCCGGTAAAAACCATTGTTAAAGGTTGTGC
16648187 TTG
66 TTG
*
16648190 AGCCTGTGAAAAG
1 AGCCTTTGAAAAG
16648203 CCATTGTAAA
Statistics
Matches: 73, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
67 57 0.78
68 16 0.22
ACGTcount: A:0.26, C:0.13, G:0.26, T:0.34
Consensus pattern (68 bp):
AGCCTTTGAAAAGTCAGCTTTGGGTTTTGATTGATCCCGGTAAAAACCATTGTTAAAGGTTGTGC
TTG
Found at i:16648207 original size:35 final size:35
Alignment explanation
Indices: 16648093--16648214 Score: 108
Period size: 35 Copynumber: 3.6 Consensus size: 35
16648083 GATTGATCCC
*
16648093 GTGAAAAACCATTGTTAAAGGTTGTGCTTGAGCCT
1 GTGAAAAACCATTGTTAAAGGTTGTGGTTGAGCCT
* ** * * * * *
16648128 TTGAAAAGTCACT-TT--GGGTTTTGGTTGATCCC
1 GTGAAAAACCATTGTTAAAGGTTGTGGTTGAGCCT
16648160 G-GTAAAAACCATTGTTAAAGGTTGTGGTTGAGCCT
1 GTG-AAAAACCATTGTTAAAGGTTGTGGTTGAGCCT
* *
16648195 GTGAAAAGCCATTGTAAAAG
1 GTGAAAAACCATTGTTAAAG
16648215 CTTGGTGGGA
Statistics
Matches: 63, Mismatches: 19, Indels: 10
0.68 0.21 0.11
Matches are distributed among these distances:
31 1 0.02
32 19 0.30
33 2 0.03
34 2 0.03
35 38 0.60
36 1 0.02
ACGTcount: A:0.29, C:0.13, G:0.26, T:0.32
Consensus pattern (35 bp):
GTGAAAAACCATTGTTAAAGGTTGTGGTTGAGCCT
Found at i:16657787 original size:43 final size:43
Alignment explanation
Indices: 16657723--16657947 Score: 281
Period size: 43 Copynumber: 5.2 Consensus size: 43
16657713 TTGTGTGATA
** * * * *
16657723 ATGATGACCTAGCTATATGCGATGT-GGGAGTGCACATGAGCTG
1 ATGATGACCCGGCTATGTGCGA-GTAGGGAGTGCGCATAAGCCG
*
16657766 ATGATGACCCGGCTATGTGCGAGTAGGGAGTACGCATAAGCCG
1 ATGATGACCCGGCTATGTGCGAGTAGGGAGTGCGCATAAGCCG
* *
16657809 ATGATGACCTGGCTATGTGCGAGTAGGGAGTGGGCATAAGCCG
1 ATGATGACCCGGCTATGTGCGAGTAGGGAGTGCGCATAAGCCG
** *
16657852 ATCATGATGACCCTACTATGTGCGAGTAGGGAGTGCGTATAAGCCG
1 ---ATGATGACCCGGCTATGTGCGAGTAGGGAGTGCGCATAAGCCG
* *
16657898 ATGATGACCCGACTATGTGCGAGTAGGGAGTGTGCATAAGCCG
1 ATGATGACCCGGCTATGTGCGAGTAGGGAGTGCGCATAAGCCG
16657941 ATGATGA
1 ATGATGA
16657948 TGACCCGACT
Statistics
Matches: 160, Mismatches: 18, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
42 2 0.01
43 120 0.75
46 38 0.24
ACGTcount: A:0.26, C:0.18, G:0.34, T:0.22
Consensus pattern (43 bp):
ATGATGACCCGGCTATGTGCGAGTAGGGAGTGCGCATAAGCCG
Found at i:16657883 original size:89 final size:89
Alignment explanation
Indices: 16657766--16657957 Score: 312
Period size: 89 Copynumber: 2.2 Consensus size: 89
16657756 ACATGAGCTG
* * *
16657766 ATGATGACCCGGCTATGTGCGAGTAGGGAGTACGCATAAGCCGATGATGACCTGGCTATGTGCGA
1 ATGATGACCCGACTATGTGCGAGTAGGGAGTACGCATAAGCCGATGATGACCCGACTATGTGCGA
16657831 GTAGGGAGTGGGCATAAGCCGATC
66 GTAGGGAGTGGGCATAAGCCGATC
* * *
16657855 ATGATGACCCTACTATGTGCGAGTAGGGAGTGCGTATAAGCCGATGATGACCCGACTATGTGCGA
1 ATGATGACCCGACTATGTGCGAGTAGGGAGTACGCATAAGCCGATGATGACCCGACTATGTGCGA
* *
16657920 GTAGGGAGTGTGCATAAGCCGATG
66 GTAGGGAGTGGGCATAAGCCGATC
16657944 ATGATGACCCGACT
1 ATGATGACCCGACT
16657958 GTGACGATGA
Statistics
Matches: 94, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
89 94 1.00
ACGTcount: A:0.26, C:0.19, G:0.34, T:0.21
Consensus pattern (89 bp):
ATGATGACCCGACTATGTGCGAGTAGGGAGTACGCATAAGCCGATGATGACCCGACTATGTGCGA
GTAGGGAGTGGGCATAAGCCGATC
Found at i:16661618 original size:21 final size:20
Alignment explanation
Indices: 16661593--16661636 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 20
16661583 TTAATTTCAG
16661593 TTATTTTAG-TTCAATTTTACT
1 TTATTTT-GTTTCAA-TTTACT
*
16661614 TTATTTTGTTTTAATTTACT
1 TTATTTTGTTTCAATTTACT
16661634 TTA
1 TTA
16661637 AGAAGAGTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 10 0.48
21 11 0.52
ACGTcount: A:0.23, C:0.07, G:0.05, T:0.66
Consensus pattern (20 bp):
TTATTTTGTTTCAATTTACT
Found at i:16662626 original size:11 final size:11
Alignment explanation
Indices: 16662606--16662635 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
16662596 AATAACTTTT
16662606 TATTAATAAAA
1 TATTAATAAAA
*
16662617 TATTATTAAAA
1 TATTAATAAAA
16662628 TATTAATA
1 TATTAATA
16662636 TTTAATTCAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (11 bp):
TATTAATAAAA
Found at i:16663176 original size:13 final size:13
Alignment explanation
Indices: 16663159--16663199 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
16663149 GAAGGAAGGA
16663159 GAAAGGAAAGAAA-
1 GAAA-GAAAGAAAG
*
16663172 GAAAG-GAGAAAG
1 GAAAGAAAGAAAG
16663184 GAAAGAAAGAAAG
1 GAAAGAAAGAAAG
16663197 GAA
1 GAA
16663200 GATAAAGCTT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
11 5 0.21
12 6 0.25
13 13 0.54
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (13 bp):
GAAAGAAAGAAAG
Found at i:16663179 original size:20 final size:20
Alignment explanation
Indices: 16663154--16663198 Score: 90
Period size: 20 Copynumber: 2.2 Consensus size: 20
16663144 AGTTGGAAGG
16663154 AAGGAGAAAGGAAAGAAAGA
1 AAGGAGAAAGGAAAGAAAGA
16663174 AAGGAGAAAGGAAAGAAAGA
1 AAGGAGAAAGGAAAGAAAGA
16663194 AAGGA
1 AAGGA
16663199 AGATAAAGCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (20 bp):
AAGGAGAAAGGAAAGAAAGA
Done.