Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013022.1 Kokia drynarioides strain JFW-HI SEQ_128040, whole genome shotgun sequence
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: 273959
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 12 characters in sequence are not A, C, G, or T
Found at i:3426 original size:96 final size:96
Alignment explanation
Indices: 3262--3453 Score: 384
Period size: 96 Copynumber: 2.0 Consensus size: 96
3252 TTTAGATGGT
3262 ATTGAAGTTGTAGAACACATTAATATTGTATATCACATCTGCTGGGTAAGTTAGCAATGCACTAT
1 ATTGAAGTTGTAGAACACATTAATATTGTATATCACATCTGCTGGGTAAGTTAGCAATGCACTAT
3327 GGAATACTGGGTGGCCATTTCATTTTATGTA
66 GGAATACTGGGTGGCCATTTCATTTTATGTA
3358 ATTGAAGTTGTAGAACACATTAATATTGTATATCACATCTGCTGGGTAAGTTAGCAATGCACTAT
1 ATTGAAGTTGTAGAACACATTAATATTGTATATCACATCTGCTGGGTAAGTTAGCAATGCACTAT
3423 GGAATACTGGGTGGCCATTTCATTTTATGTA
66 GGAATACTGGGTGGCCATTTCATTTTATGTA
3454 CTTTATGTTG
Statistics
Matches: 96, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
96 96 1.00
ACGTcount: A:0.30, C:0.14, G:0.21, T:0.35
Consensus pattern (96 bp):
ATTGAAGTTGTAGAACACATTAATATTGTATATCACATCTGCTGGGTAAGTTAGCAATGCACTAT
GGAATACTGGGTGGCCATTTCATTTTATGTA
Found at i:4985 original size:18 final size:18
Alignment explanation
Indices: 4962--4999 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 18
4952 TAAAAAAAAA
4962 GATGAAT-TTTATATATTT
1 GATGAATATTT-TATATTT
4980 GATGAATATTTTATATTT
1 GATGAATATTTTATATTT
4998 GA
1 GA
5000 AATTTATTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 16 0.84
19 3 0.16
ACGTcount: A:0.34, C:0.00, G:0.13, T:0.53
Consensus pattern (18 bp):
GATGAATATTTTATATTT
Found at i:5450 original size:16 final size:16
Alignment explanation
Indices: 5431--5465 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
5421 GAAAATGTGG
5431 AAAGAAAAAAAAAATT
1 AAAGAAAAAAAAAATT
5447 AAAGAAAAAAAAAATT
1 AAAGAAAAAAAAAATT
5463 AAA
1 AAA
5466 TGTGCTTCGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.83, C:0.00, G:0.06, T:0.11
Consensus pattern (16 bp):
AAAGAAAAAAAAAATT
Found at i:6356 original size:25 final size:25
Alignment explanation
Indices: 6327--6382 Score: 94
Period size: 25 Copynumber: 2.2 Consensus size: 25
6317 ATCCTCAATC
6327 TTTTTTAATTTTATTAGGGTTAGGG
1 TTTTTTAATTTTATTAGGGTTAGGG
* *
6352 TTTTTTAATTTTGTTAGGGTTATGG
1 TTTTTTAATTTTATTAGGGTTAGGG
6377 TTTTTT
1 TTTTTT
6383 TAGGATTTAG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.16, C:0.00, G:0.21, T:0.62
Consensus pattern (25 bp):
TTTTTTAATTTTATTAGGGTTAGGG
Found at i:7883 original size:108 final size:108
Alignment explanation
Indices: 7756--7966 Score: 336
Period size: 108 Copynumber: 2.0 Consensus size: 108
7746 AATAAAGAAA
* * *
7756 ATTTATGTATTTAAAATAGGATACTCGATTATTTATGTTTAAAG-AAAAATCATACATAGTACGT
1 ATTTATGTATTTAAAATAGGATACTCGATTATTTAGGTTCAAAGAAAAAATCATAC-CAGTACGT
*
7820 TTGAGCATAATTTCTCGAATTCCCTAAATAAAAGAACATCAAAC
65 TTGAGCACAATTTCTCGAATTCCCTAAATAAAAGAACATCAAAC
*
7864 ATTTAT-TGATTTTAAATAGGATACTCGATTATTTAGGTTCAAAGAAAAAATCATACCAGTACGT
1 ATTTATGT-ATTTAAAATAGGATACTCGATTATTTAGGTTCAAAGAAAAAATCATACCAGTACGT
*
7928 TTGAGCACAATTTCTTGAATTCCCTAAATAAAAGAACAT
65 TTGAGCACAATTTCTCGAATTCCCTAAATAAAAGAACAT
7967 TACATTTTTT
Statistics
Matches: 95, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
107 1 0.01
108 83 0.87
109 11 0.12
ACGTcount: A:0.41, C:0.13, G:0.12, T:0.34
Consensus pattern (108 bp):
ATTTATGTATTTAAAATAGGATACTCGATTATTTAGGTTCAAAGAAAAAATCATACCAGTACGTT
TGAGCACAATTTCTCGAATTCCCTAAATAAAAGAACATCAAAC
Found at i:8420 original size:31 final size:29
Alignment explanation
Indices: 8296--8423 Score: 89
Period size: 31 Copynumber: 4.3 Consensus size: 29
8286 ATAGAAGAGC
* * * *
8296 AAATTTAAAAGGAATAAAAACAAAAGGGTT
1 AAATTTAAAA-AAAAAAAAATAAAAGGATT
* *
8326 AAATTTTAACAAAAATAAAAATAACAGGATT
1 AAA-TTTAA-AAAAAAAAAAATAAAAGGATT
* * * * * *
8357 TAATTT-AAAATAATAGAAT-AAATGAGT
1 AAATTTAAAAAAAAAAAAATAAAAGGATT
8384 AAATTTAAAAGAGAAAAAAAATAAAAGGATT
1 AAATTTAAAA-A-AAAAAAAATAAAAGGATT
8415 AAATTTAAA
1 AAATTTAAA
8424 TTAAAAATAA
Statistics
Matches: 74, Mismatches: 18, Indels: 11
0.72 0.17 0.11
Matches are distributed among these distances:
27 10 0.14
28 11 0.15
29 2 0.03
30 12 0.16
31 37 0.50
32 2 0.03
ACGTcount: A:0.62, C:0.02, G:0.11, T:0.25
Consensus pattern (29 bp):
AAATTTAAAAAAAAAAAAATAAAAGGATT
Found at i:8436 original size:17 final size:17
Alignment explanation
Indices: 8414--8447 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
8404 ATAAAAGGAT
*
8414 TAAATTTAAATTAAAAA
1 TAAATTTAAAGTAAAAA
8431 TAAATTTAAAGTAAAAA
1 TAAATTTAAAGTAAAAA
8448 GGACAAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (17 bp):
TAAATTTAAAGTAAAAA
Found at i:13694 original size:25 final size:25
Alignment explanation
Indices: 13593--13686 Score: 143
Period size: 25 Copynumber: 3.8 Consensus size: 25
13583 ATACTGGTTA
*
13593 AACTCTATCTGGGCTCGTAAAAGCT
1 AACTTTATCTGGGCTCGTAAAAGCT
*
13618 AACTTTATCTGGGGTCGTAAAAGCT
1 AACTTTATCTGGGCTCGTAAAAGCT
*
13643 AACTTTATCTGGGCTCGTAAGAGCT
1 AACTTTATCTGGGCTCGTAAAAGCT
* *
13668 AACCTTATCTAGGCTCGTA
1 AACTTTATCTGGGCTCGTA
13687 TGAGCTAAAT
Statistics
Matches: 63, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 63 1.00
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.31
Consensus pattern (25 bp):
AACTTTATCTGGGCTCGTAAAAGCT
Found at i:16631 original size:24 final size:24
Alignment explanation
Indices: 16604--16661 Score: 80
Period size: 24 Copynumber: 2.4 Consensus size: 24
16594 TGTTGTCTCT
* *
16604 ATCTTCATCTCCACTCTTAACTTC
1 ATCTTCATCTCCACCCTCAACTTC
* *
16628 ATCTTCATCCCCACCCTCGACTTC
1 ATCTTCATCTCCACCCTCAACTTC
16652 ATCTTCATCT
1 ATCTTCATCT
16662 TCATCGCCTT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.19, C:0.41, G:0.02, T:0.38
Consensus pattern (24 bp):
ATCTTCATCTCCACCCTCAACTTC
Found at i:19111 original size:19 final size:20
Alignment explanation
Indices: 19069--19105 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 20
19059 GCTAAAATGA
19069 TTTTAACCAAGTAAAACTTC
1 TTTTAACCAAGTAAAACTTC
*
19089 TTTTAA-CAAGTCAAACT
1 TTTTAACCAAGTAAAACT
19106 ATTTTTCAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 10 0.62
20 6 0.38
ACGTcount: A:0.41, C:0.19, G:0.05, T:0.35
Consensus pattern (20 bp):
TTTTAACCAAGTAAAACTTC
Found at i:31002 original size:38 final size:38
Alignment explanation
Indices: 30951--31029 Score: 149
Period size: 38 Copynumber: 2.1 Consensus size: 38
30941 AAGCTGCACC
30951 TTTATCTTTTGTGACTCATCAAGCTCTTTAAACAAGGA
1 TTTATCTTTTGTGACTCATCAAGCTCTTTAAACAAGGA
*
30989 TTTATCTTTTGTGACTCATCAAGCTCTTTGAACAAGGA
1 TTTATCTTTTGTGACTCATCAAGCTCTTTAAACAAGGA
31027 TTT
1 TTT
31030 GGTACCTGTC
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.27, C:0.18, G:0.14, T:0.42
Consensus pattern (38 bp):
TTTATCTTTTGTGACTCATCAAGCTCTTTAAACAAGGA
Found at i:41635 original size:21 final size:22
Alignment explanation
Indices: 41594--41644 Score: 70
Period size: 21 Copynumber: 2.4 Consensus size: 22
41584 GAATATTATG
41594 TAATTTAAATAAAATTAGTAAA
1 TAATTTAAATAAAATTAGTAAA
*
41616 TAATTTATAAT-AAA-TAGTAAT
1 TAATTTA-AATAAAATTAGTAAA
41637 TAATTTAA
1 TAATTTAA
41645 TCAAATATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
20 1 0.04
21 13 0.48
22 10 0.37
23 3 0.11
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.41
Consensus pattern (22 bp):
TAATTTAAATAAAATTAGTAAA
Found at i:44496 original size:43 final size:43
Alignment explanation
Indices: 44275--44503 Score: 202
Period size: 43 Copynumber: 5.3 Consensus size: 43
44265 AAACCGTTAT
* * *
44275 AGAACATGGTATTTAGCGGC-ACTTTCC-AACAAACGCCGTTAA
1 AGAACATGGTCTTTAGCGGCGA-TTTCCTCACAAACGCCGCTAA
** * * * * *
44317 AGAACATAAAT-TTTAGCGGCGCTTTTCC-CAAAAACTCTGTTAA
1 AGAACAT-GGTCTTTAGCGGCG-ATTTCCTCACAAACGCCGCTAA
* *
44360 ATAACATGATCTTTAGCGGCG-TTTCAAC-CACAAACGCCGCTAA
1 AGAACATGGTCTTTAGCGGCGATTTC--CTCACAAACGCCGCTAA
* *
44403 AAAACATGGTCTTTAGCGGCGATTTCCTCACAAACACCGCTAA
1 AGAACATGGTCTTTAGCGGCGATTTCCTCACAAACGCCGCTAA
* * *
44446 AGAACATGGTCTTTAGCTGCGCA-TTCCTCACAAACGCCGTTAC
1 AGAACATGGTCTTTAGCGGCG-ATTTCCTCACAAACGCCGCTAA
44489 AGAACATGGTCTTTA
1 AGAACATGGTCTTTA
44504 CCGATGCTTT
Statistics
Matches: 157, Mismatches: 21, Indels: 17
0.81 0.11 0.09
Matches are distributed among these distances:
41 4 0.03
42 19 0.12
43 129 0.82
44 5 0.03
ACGTcount: A:0.32, C:0.25, G:0.17, T:0.26
Consensus pattern (43 bp):
AGAACATGGTCTTTAGCGGCGATTTCCTCACAAACGCCGCTAA
Found at i:44519 original size:43 final size:42
Alignment explanation
Indices: 44388--44532 Score: 155
Period size: 43 Copynumber: 3.4 Consensus size: 42
44378 GCGTTTCAAC
* * *
44388 CACAAACGCCGCTAAAAAACATGGTCTTTAGCGGCGATTTCCT
1 CACAAACGCCGCTAAAGAACATGGTCTTTA-CCGCGCTTTCCT
* * *
44431 CACAAACACCGCTAAAGAACATGGTCTTTAGCTGCGCATTCCT
1 CACAAACGCCGCTAAAGAACATGGTCTTTA-CCGCGCTTTCCT
* * * *
44474 CACAAACGCCGTTACAGAACATGGTCTTTACCGATGCTTTTCT
1 CACAAACGCCGCTAAAGAACATGGTCTTTACCG-CGCTTTCCT
* *
44517 CACAAAAGCTGCTAAA
1 CACAAACGCCGCTAAA
44533 ATTAACATAT
Statistics
Matches: 85, Mismatches: 16, Indels: 2
0.83 0.16 0.02
Matches are distributed among these distances:
42 2 0.02
43 83 0.98
ACGTcount: A:0.31, C:0.28, G:0.17, T:0.24
Consensus pattern (42 bp):
CACAAACGCCGCTAAAGAACATGGTCTTTACCGCGCTTTCCT
Found at i:50736 original size:14 final size:14
Alignment explanation
Indices: 50717--50743 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
50707 TATAATTAAA
50717 TAATTAAATATTTT
1 TAATTAAATATTTT
50731 TAATTAAATATTT
1 TAATTAAATATTT
50744 GGGTTTAGGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (14 bp):
TAATTAAATATTTT
Found at i:50779 original size:58 final size:58
Alignment explanation
Indices: 50708--50913 Score: 175
Period size: 58 Copynumber: 3.5 Consensus size: 58
50698 TTATTTAAAT
*
50708 ATAATTAAATAATTAAATATTTTTAATTAAATATTTGGGTTTAGGGTTTAATAAATAA
1 ATAATTAAATAATTAAATATTTTTAATTAAATATTTGAGTTTAGGGTTTAATAAATAA
* * * * ** *** *
50766 CTAATTAAATAATTAATTATTTTT-ATTGAGT-TTTGTTTTTAATAATTTAATATTTATTTAAA
1 ATAATTAAATAATTAAATATTTTTAATTAAATATTTGAGTTT-AGGGTTTAATA---A-AT-AA
* * * *
50828 TATAATTTAATATTTTAATATTTTAAATTAAATATTTGAGTTTAGGGTTTAATAAATAA
1 -ATAATTAAATAATTAAATATTTTTAATTAAATATTTGAGTTTAGGGTTTAATAAATAA
* *
50887 GTAATTAAATAATTAATTA-TTTTAATT
1 ATAATTAAATAATTAAATATTTTTAATT
50914 GAGTTTTGTT
Statistics
Matches: 109, Mismatches: 30, Indels: 19
0.69 0.19 0.12
Matches are distributed among these distances:
56 7 0.06
57 20 0.18
58 36 0.33
59 2 0.02
60 2 0.02
61 2 0.02
62 2 0.02
63 18 0.17
64 13 0.12
65 7 0.06
ACGTcount: A:0.42, C:0.00, G:0.07, T:0.50
Consensus pattern (58 bp):
ATAATTAAATAATTAAATATTTTTAATTAAATATTTGAGTTTAGGGTTTAATAAATAA
Found at i:50858 original size:121 final size:121
Alignment explanation
Indices: 50610--50990 Score: 615
Period size: 121 Copynumber: 3.1 Consensus size: 121
50600 TCTTTTTAAT
* *
50610 AATTAAATAGTTGGATTTAGGGTTTAATAAATAACTAATTAAATAATTAATTATTTAAATAATTC
1 AATTAAATATTTGGGTTTAGGGTTTAATAAATAACTAATTAAATAATTAATTATTT---TAATT-
* *
50675 GA---TTGTTTTTAATAATTTAATATTTATTTAAATATAATTAAATAATTAAATATTTTT
62 GAGTTTTGTTTTTAATAATTTAATATTTATTTAAATATAATTAAATAATTTAATATTTTA
*
50732 AATTAAATATTTGGGTTTAGGGTTTAATAAATAACTAATTAAATAATTAATTATTTTTATTGAGT
1 AATTAAATATTTGGGTTTAGGGTTTAATAAATAACTAATTAAATAATTAATTATTTTAATTGAGT
* *
50797 TTTGTTTTTAATAATTTAATATTTATTTAAATATAATTTAATATTTTAATATTTTA
66 TTTGTTTTTAATAATTTAATATTTATTTAAATATAATTAAATAATTTAATATTTTA
* *
50853 AATTAAATATTTGAGTTTAGGGTTTAATAAATAAGTAATTAAATAATTAATTATTTTAATTGAGT
1 AATTAAATATTTGGGTTTAGGGTTTAATAAATAACTAATTAAATAATTAATTATTTTAATTGAGT
*
50918 TTTGTTTTTAATAATTTAATATTTATTTAAATATAATTAAATAATTTAATATTTTG
66 TTTGTTTTTAATAATTTAATATTTATTTAAATATAATTAAATAATTTAATATTTTA
50974 AATTAAATATTTGGGTT
1 AATTAAATATTTGGGTT
50991 GTTTTTTAAC
Statistics
Matches: 242, Mismatches: 14, Indels: 7
0.92 0.05 0.03
Matches are distributed among these distances:
118 2 0.01
119 4 0.02
121 182 0.75
122 54 0.22
ACGTcount: A:0.41, C:0.01, G:0.08, T:0.50
Consensus pattern (121 bp):
AATTAAATATTTGGGTTTAGGGTTTAATAAATAACTAATTAAATAATTAATTATTTTAATTGAGT
TTTGTTTTTAATAATTTAATATTTATTTAAATATAATTAAATAATTTAATATTTTA
Found at i:52916 original size:21 final size:21
Alignment explanation
Indices: 52887--52929 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
52877 ATTATATCAG
52887 ACATATCAGACA-ATAAAACCA
1 ACATATCAG-CAGATAAAACCA
* *
52908 ACATTTCAGCAGTTAAAACCA
1 ACATATCAGCAGATAAAACCA
52929 A
1 A
52930 TACCCTAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 2 0.11
21 17 0.89
ACGTcount: A:0.51, C:0.23, G:0.07, T:0.19
Consensus pattern (21 bp):
ACATATCAGCAGATAAAACCA
Found at i:54982 original size:80 final size:79
Alignment explanation
Indices: 54853--55016 Score: 283
Period size: 80 Copynumber: 2.1 Consensus size: 79
54843 TTAATATCCT
*
54853 TAAAATTTTTATAAATTTTGGTTTAAATTATGATAAAATGATTTAAAATTAAATTATTAGTTTTT
1 TAAAACTTTTATAAATTTTGGTTTAAATTATGATAAAATGATTTAAAATTAAATTATTAG-TTTT
**
54918 TTTTTCGATTGAAAA
65 TTTGACGATTGAAAA
54933 TAAAACTTTTATAAATTTTGGTTTAAATTATGATAAAATGATTTAAAATTAAATTATTAGTTTTT
1 TAAAACTTTTATAAATTTTGGTTTAAATTATGATAAAATGATTTAAAATTAAATTATTAGTTTTT
*
54998 TTGACGGTTGAAAA
66 TTGACGATTGAAAA
55012 TAAAA
1 TAAAA
55017 TTTGTTTATC
Statistics
Matches: 80, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
79 21 0.26
80 59 0.74
ACGTcount: A:0.41, C:0.02, G:0.10, T:0.47
Consensus pattern (79 bp):
TAAAACTTTTATAAATTTTGGTTTAAATTATGATAAAATGATTTAAAATTAAATTATTAGTTTTT
TTGACGATTGAAAA
Found at i:70605 original size:28 final size:28
Alignment explanation
Indices: 70541--70703 Score: 209
Period size: 28 Copynumber: 5.8 Consensus size: 28
70531 CATTCTCCAT
* * *
70541 AAAGGCTTCCCTTTTCAAAGGTTCACCAA
1 AAAGGCTTTCC-TTTCAAAGGTTCGCCAC
* *
70570 AAAGGCTTTCCTTTAAAAGGTTCGCCAT
1 AAAGGCTTTCCTTTCAAAGGTTCGCCAC
* * *
70598 AAATGCTTTCCTTTCAAAGATTTGCCAC
1 AAAGGCTTTCCTTTCAAAGGTTCGCCAC
*
70626 AAAGGCTTTCCTTTCAAAGGTTCTCCAC
1 AAAGGCTTTCCTTTCAAAGGTTCGCCAC
* *
70654 AAAGGCTTTCCTTTCAGAGATTCGCCAC
1 AAAGGCTTTCCTTTCAAAGGTTCGCCAC
*
70682 AAAGGCTTTCCTTTTAAAGGTT
1 AAAGGCTTTCCTTTCAAAGGTT
70704 ACCATGAAGG
Statistics
Matches: 115, Mismatches: 19, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
28 105 0.91
29 10 0.09
ACGTcount: A:0.28, C:0.25, G:0.15, T:0.33
Consensus pattern (28 bp):
AAAGGCTTTCCTTTCAAAGGTTCGCCAC
Found at i:70645 original size:15 final size:15
Alignment explanation
Indices: 70625--70669 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
70615 AGATTTGCCA
70625 CAAAGGCTTTCCTTT
1 CAAAGGCTTTCCTTT
*
70640 CAAAGG-TTCTCC--A
1 CAAAGGCTT-TCCTTT
70653 CAAAGGCTTTCCTTT
1 CAAAGGCTTTCCTTT
70668 CA
1 CA
70670 GAGATTCGCC
Statistics
Matches: 24, Mismatches: 2, Indels: 8
0.71 0.06 0.24
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.24, C:0.29, G:0.13, T:0.33
Consensus pattern (15 bp):
CAAAGGCTTTCCTTT
Found at i:70659 original size:84 final size:85
Alignment explanation
Indices: 70541--70700 Score: 232
Period size: 84 Copynumber: 1.9 Consensus size: 85
70531 CATTCTCCAT
* * *
70541 AAAGGCTTCCCTTTTCAAAGGTTCACCAAAAAGGCTTTCCTTTAAAAGGTTCGCCATAAATGCTT
1 AAAGGCTTCCCTTTTCAAAGGTTCACCAAAAAGGCTTTCCTTTAAAAGATTCGCCACAAAGGCTT
70606 TCCTTTCAAAGATTTGCCAC
66 TCCTTTCAAAGATTTGCCAC
* * * * *
70626 AAAGGCTTTCC-TTTCAAAGGTTCTCCACAAAGGCTTTCCTTTCAGAGATTCGCCACAAAGGCTT
1 AAAGGCTTCCCTTTTCAAAGGTTCACCAAAAAGGCTTTCCTTTAAAAGATTCGCCACAAAGGCTT
*
70690 TCCTTTTAAAG
66 TCCTTTCAAAG
70701 GTTACCATGA
Statistics
Matches: 66, Mismatches: 9, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
84 56 0.85
85 10 0.15
ACGTcount: A:0.28, C:0.25, G:0.15, T:0.32
Consensus pattern (85 bp):
AAAGGCTTCCCTTTTCAAAGGTTCACCAAAAAGGCTTTCCTTTAAAAGATTCGCCACAAAGGCTT
TCCTTTCAAAGATTTGCCAC
Found at i:72659 original size:14 final size:14
Alignment explanation
Indices: 72635--72673 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
72625 AAAATTTGAA
*
72635 AATAGTTTTATTTT
1 AATATTTTTATTTT
*
72649 TATATTTTTATTTT
1 AATATTTTTATTTT
72663 AATATTATTTA
1 AATATT-TTTA
72674 GTAATTAATA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
14 17 0.81
15 4 0.19
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.67
Consensus pattern (14 bp):
AATATTTTTATTTT
Found at i:74305 original size:30 final size:30
Alignment explanation
Indices: 74248--74306 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
74238 TAAAAAAGTT
**
74248 AAATAAAAAAACTAAAATAATTTTTATATA
1 AAATAAAAAAACTAAAATAATCATTATATA
*
74278 AAATTAAAAAACT-AAATAAATCATTATAT
1 AAATAAAAAAACTAAAAT-AATCATTATAT
74307 TTTGGGTAAG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 4 0.16
30 21 0.84
ACGTcount: A:0.63, C:0.05, G:0.00, T:0.32
Consensus pattern (30 bp):
AAATAAAAAAACTAAAATAATCATTATATA
Found at i:83325 original size:26 final size:27
Alignment explanation
Indices: 83275--83338 Score: 80
Period size: 26 Copynumber: 2.4 Consensus size: 27
83265 AAATTTTTTT
*
83275 GAATCGAGTCGAGTAATATGAAA-TTC
1 GAATCGAATCGAGTAATATGAAATTTC
*
83301 GAATCGAATCGAGTGAA-ATGGAATTTC
1 GAATCGAATCGAGT-AATATGAAATTTC
83328 G-ATCGAATCGA
1 GAATCGAATCGA
83339 ACTGAATATA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
26 28 0.82
27 6 0.18
ACGTcount: A:0.38, C:0.12, G:0.25, T:0.25
Consensus pattern (27 bp):
GAATCGAATCGAGTAATATGAAATTTC
Found at i:84451 original size:24 final size:24
Alignment explanation
Indices: 84407--84452 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
84397 ATATTAAGAT
* *
84407 AATTATATATTATTATTATTATTA
1 AATTATATATTATAATAATTATTA
84431 AATTATAT-TTAATAATAATTAT
1 AATTATATATT-ATAATAATTAT
84453 ATTAAATTGT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 2 0.11
24 17 0.89
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (24 bp):
AATTATATATTATAATAATTATTA
Found at i:84915 original size:28 final size:28
Alignment explanation
Indices: 84883--84942 Score: 111
Period size: 28 Copynumber: 2.1 Consensus size: 28
84873 GTTTAAAATC
84883 ATTTGAATCCTATGGGAGAATACATTTT
1 ATTTGAATCCTATGGGAGAATACATTTT
*
84911 ATTTGAATCCTATGGGGGAATACATTTT
1 ATTTGAATCCTATGGGAGAATACATTTT
84939 ATTT
1 ATTT
84943 TAACCAAAGT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.30, C:0.10, G:0.18, T:0.42
Consensus pattern (28 bp):
ATTTGAATCCTATGGGAGAATACATTTT
Found at i:86792 original size:88 final size:88
Alignment explanation
Indices: 86643--86819 Score: 336
Period size: 88 Copynumber: 2.0 Consensus size: 88
86633 AATTACCACC
86643 ACATCGCAATGAGAATCAACCTGACGTCGCGATGATGTGACAACACGACGTGACTCTTTCTCCAT
1 ACATCGCAATGAGAATCAACCTGACGTCGCGATGATGTGACAACACGACGTGACTCTTTCTCCAT
*
86708 CAATTTTGATTCAACCAAACTGT
66 CAATTTCGATTCAACCAAACTGT
*
86731 ACATCGCGATGAGAATCAACCTGACGTCGCGATGATGTGACAACACGACGTGACTCTTTCTCCAT
1 ACATCGCAATGAGAATCAACCTGACGTCGCGATGATGTGACAACACGACGTGACTCTTTCTCCAT
86796 CAATTTCGATTCAACCAAACTGT
66 CAATTTCGATTCAACCAAACTGT
86819 A
1 A
86820 GCACATGCGA
Statistics
Matches: 87, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
88 87 1.00
ACGTcount: A:0.31, C:0.27, G:0.18, T:0.25
Consensus pattern (88 bp):
ACATCGCAATGAGAATCAACCTGACGTCGCGATGATGTGACAACACGACGTGACTCTTTCTCCAT
CAATTTCGATTCAACCAAACTGT
Found at i:89377 original size:25 final size:25
Alignment explanation
Indices: 89346--89394 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
89336 TCTCTCGATC
*
89346 TCTTTTCT-CTTTTGTTTTCCTTTCT
1 TCTTTTCTCCTTTT-TTCTCCTTTCT
89371 TCTTTTCTCCTTTTTTCTCCTTTC
1 TCTTTTCTCCTTTTTTCTCCTTTC
89395 ATAACACTCT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 17 0.77
26 5 0.23
ACGTcount: A:0.00, C:0.29, G:0.02, T:0.69
Consensus pattern (25 bp):
TCTTTTCTCCTTTTTTCTCCTTTCT
Found at i:89915 original size:45 final size:45
Alignment explanation
Indices: 89821--89941 Score: 129
Period size: 45 Copynumber: 2.7 Consensus size: 45
89811 TCAATTTCTC
* * *
89821 TTATACCTATCCCTTTTATTA-CCATTTATCCCTCTGTCTTCAAT
1 TTATACCTACCCCATTTATTAGCCGTTTATCCCTCTGTCTTCAAT
* * *
89865 CTATACCTACACCATTTATTAGCCGTTTATCACCT-TGTCTTCCAT
1 TTATACCTACCCCATTTATTAGCCGTTTATC-CCTCTGTCTTCAAT
* *
89910 TTATACATACCCCCCATTTATTAGTCGTTTAT
1 TTATACCTA--CCCCATTTATTAGCCGTTTAT
89942 ATCTCTCTCG
Statistics
Matches: 63, Mismatches: 10, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
44 17 0.27
45 24 0.38
46 3 0.05
47 19 0.30
ACGTcount: A:0.22, C:0.29, G:0.05, T:0.44
Consensus pattern (45 bp):
TTATACCTACCCCATTTATTAGCCGTTTATCCCTCTGTCTTCAAT
Found at i:90740 original size:26 final size:26
Alignment explanation
Indices: 90690--90740 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 26
90680 TTGAGATTCG
*
90690 AGGTTTGGTGTTTGAGATTTGGGTTT
1 AGGTTTGGTGTTTGAGATTTAGGTTT
90716 AGGTTTAGG-GTTTGAG-TTTAAGGTT
1 AGGTTT-GGTGTTTGAGATTT-AGGTT
90741 CAGTGCTTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
25 3 0.14
26 17 0.77
27 2 0.09
ACGTcount: A:0.16, C:0.00, G:0.37, T:0.47
Consensus pattern (26 bp):
AGGTTTGGTGTTTGAGATTTAGGTTT
Found at i:90786 original size:22 final size:22
Alignment explanation
Indices: 90761--90819 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
90751 TATTTATGAG
*
90761 TTAGGTGTTAAGGTTTTAGTGT
1 TTAGGTGTTAAGGTTTTAATGT
* **
90783 TTAGGGGTTATTGTTTTAATGT
1 TTAGGTGTTAAGGTTTTAATGT
*
90805 TTAGAGTTTTAAGGT
1 TTAG-GTGTTAAGGT
90820 GTTGATCATT
Statistics
Matches: 28, Mismatches: 8, Indels: 1
0.76 0.22 0.03
Matches are distributed among these distances:
22 22 0.79
23 6 0.21
ACGTcount: A:0.20, C:0.00, G:0.29, T:0.51
Consensus pattern (22 bp):
TTAGGTGTTAAGGTTTTAATGT
Found at i:94086 original size:24 final size:24
Alignment explanation
Indices: 94051--94105 Score: 83
Period size: 24 Copynumber: 2.3 Consensus size: 24
94041 AATCTTTTAG
*
94051 TTAAACTCTGTTTATTTGTTTCAA
1 TTAAACTATGTTTATTTGTTTCAA
* *
94075 TTAAACTATGTTTATTTGTTTGAG
1 TTAAACTATGTTTATTTGTTTCAA
94099 TTAAACT
1 TTAAACT
94106 CTTATTAGTG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.27, C:0.09, G:0.11, T:0.53
Consensus pattern (24 bp):
TTAAACTATGTTTATTTGTTTCAA
Found at i:94529 original size:18 final size:18
Alignment explanation
Indices: 94506--94542 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
94496 ATGGGAAGCT
94506 TATATAAAT-TATAATTAA
1 TATATAAATAT-TAATTAA
94524 TATATAAATATTAATTAA
1 TATATAAATATTAATTAA
94542 T
1 T
94543 GGAATTAACC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 17 0.94
19 1 0.06
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
TATATAAATATTAATTAA
Found at i:94742 original size:38 final size:39
Alignment explanation
Indices: 94700--94773 Score: 114
Period size: 38 Copynumber: 1.9 Consensus size: 39
94690 CCATTAAAGA
* *
94700 CCAACACTCAAATAATAATAACTTTTTA-TTTAAAATGG
1 CCAACACCCAAAAAATAATAACTTTTTATTTTAAAATGG
*
94738 CCAACACCCAAAAAATAATAATTTTTTATTTTAAAA
1 CCAACACCCAAAAAATAATAACTTTTTATTTTAAAA
94774 AATTGGTGTC
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
38 25 0.78
39 7 0.22
ACGTcount: A:0.47, C:0.16, G:0.03, T:0.34
Consensus pattern (39 bp):
CCAACACCCAAAAAATAATAACTTTTTATTTTAAAATGG
Found at i:96200 original size:202 final size:200
Alignment explanation
Indices: 95931--96328 Score: 724
Period size: 202 Copynumber: 2.0 Consensus size: 200
95921 TAAAAACTAA
95931 ACCCCAAAACCTAATAATAAGAACCTCAAAACTTAAACACAAAATTCCCTAAAAGCTTGTAAAAG
1 ACCCCAAAACCTAATAATAAGAACCTCAAAACTTAAACACAAAATTCCCTAAAAGCTTGTAAAAG
*
95996 CTAATACTAAATTATTATGGGTTAAAATCTTTATAGGGTAGAAAAATGCCTATGTATAGACTAAA
66 CTAATACTAAATTATTATGGGTTAAAATCTTTATAGGGTAGAAAAATGCCTATGTATAGAATAAA
*
96061 TTTTGTGTACAAATTTAACTAAAACATTCCTAAAGTAACAAGAGTTTAACTAGGAGAAAAAAATC
131 TTTTGTGTACAAATTTAACTAAAACATTCCTAAAATAACAAGAGTTTAACTAGG-GAAAAAAATC
96126 AAGAAG
195 AAGAAG
* *
96132 ACCCCAAAACCTAATAATAAGAATCCTCAAAATTTAAACACAAAATTCTCTAAAAGCTTGTAAAA
1 ACCCCAAAACCTAATAATAAGAA-CCTCAAAACTTAAACACAAAATTCCCTAAAAGCTTGTAAAA
96197 GCTAATACTAAATTATTATGGGTTAAAATCTTTATAGGGTAGAAAAATGCCTATGTATAGAATAA
65 GCTAATACTAAATTATTATGGGTTAAAATCTTTATAGGGTAGAAAAATGCCTATGTATAGAATAA
* *
96262 ATTTTGTGTACAAATTTAACTAAAACATTTCTAAAATAACAAGAGTTTAAGTAGGGAAAAAAATC
130 ATTTTGTGTACAAATTTAACTAAAACATTCCTAAAATAACAAGAGTTTAACTAGGGAAAAAAATC
96327 AA
195 AA
96329 AATTTAACTA
Statistics
Matches: 190, Mismatches: 6, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
201 35 0.18
202 155 0.82
ACGTcount: A:0.47, C:0.14, G:0.12, T:0.28
Consensus pattern (200 bp):
ACCCCAAAACCTAATAATAAGAACCTCAAAACTTAAACACAAAATTCCCTAAAAGCTTGTAAAAG
CTAATACTAAATTATTATGGGTTAAAATCTTTATAGGGTAGAAAAATGCCTATGTATAGAATAAA
TTTTGTGTACAAATTTAACTAAAACATTCCTAAAATAACAAGAGTTTAACTAGGGAAAAAAATCA
AGAAG
Found at i:97370 original size:19 final size:20
Alignment explanation
Indices: 97321--97371 Score: 61
Period size: 19 Copynumber: 2.6 Consensus size: 20
97311 AATTTAAAAA
97321 AATTATAATTTTTAATATTT
1 AATTATAATTTTTAATATTT
* *
97341 -ATAATATTTTTTAAT-TTT
1 AATTATAATTTTTAATATTT
*
97359 AATTTTAATTTTT
1 AATTATAATTTTT
97372 TTAAAAAATA
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
18 3 0.12
19 22 0.88
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (20 bp):
AATTATAATTTTTAATATTT
Found at i:97521 original size:13 final size:13
Alignment explanation
Indices: 97488--97521 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
97478 ATAAAAAGAA
*
97488 TAAATTTAAAAAT
1 TAAATTAAAAAAT
97501 TAAA-TAAAAAAT
1 TAAATTAAAAAAT
97513 TAAATTAAA
1 TAAATTAAA
97522 TTTTTATAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (13 bp):
TAAATTAAAAAAT
Found at i:101745 original size:2 final size:2
Alignment explanation
Indices: 101738--101771 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
101728 ATTATCATTA
101738 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
101772 TAAATTAAAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:102608 original size:41 final size:41
Alignment explanation
Indices: 102515--102957 Score: 384
Period size: 41 Copynumber: 10.5 Consensus size: 41
102505 TCTTGATGTA
* *
102515 TAAATGGAAGACTCATGTCTCGGGATGAGCATGAGGGGATAT
1 TAAA-GGAAGACTCATGTCTCGGGATGAGCATGAGAGAATAT
* * * *
102557 TAAAGGAAAGGAAGACTGATGTCTCGGGATGAGCATAAGGGGATAT
1 T-----AAAGGAAGACTCATGTCTCGGGATGAGCATGAGAGAATAT
* * ** *
102603 TAAAGGAAGACTCGTGTCTTGGGATGAGCATGATCGGATAT
1 TAAAGGAAGACTCATGTCTCGGGATGAGCATGAGAGAATAT
* * * *
102644 TAAAGGAAGATTTATGTCTCTGGATGAGCATGAGGGAATAT
1 TAAAGGAAGACTCATGTCTCGGGATGAGCATGAGAGAATAT
* * * * * *
102685 TGAAGGAAGACTCATGTCTTGGGTTGAGCATGAGATTATGTGT
1 TAAAGGAAGACTCATGTCTCGGGATGAGCATGAGA-GA-ATAT
**
102728 TAAAGGAAGACTCATGTCTCAAGATGAGCATGAGAGAATAT
1 TAAAGGAAGACTCATGTCTCGGGATGAGCATGAGAGAATAT
**
102769 TAAAGGAAGACTCATGTCTCAAGATGAGCATGAGAGAATAT
1 TAAAGGAAGACTCATGTCTCGGGATGAGCATGAGAGAATAT
* * * *
102810 TAAAGGAAGACTCATGTCTCGGGTTGAGCATGAGATTATGTGT
1 TAAAGGAAGACTCATGTCTCGGGATGAGCATGAGA-GA-ATAT
* * * * * *
102853 TAAAGGAAGACTCATGTCTTGGGTTGATCATGA-ATTTATGTGT
1 TAAAGGAAGACTCATGTCTCGGGATGAGCATGAGA--GA-ATAT
* * * * *
102896 TAAAGGAAGACTCATGTCTCAGGTTGAGCATGAGATTATGTGT
1 TAAAGGAAGACTCATGTCTCGGGATGAGCATGAGA-GA-ATAT
102939 TAAAGGAAGACTCATGTCT
1 TAAAGGAAGACTCATGTCT
102958 TGAAAAGAGC
Statistics
Matches: 345, Mismatches: 45, Indels: 21
0.84 0.11 0.05
Matches are distributed among these distances:
41 170 0.49
42 5 0.01
43 130 0.38
44 1 0.00
46 36 0.10
47 3 0.01
ACGTcount: A:0.33, C:0.11, G:0.29, T:0.27
Consensus pattern (41 bp):
TAAAGGAAGACTCATGTCTCGGGATGAGCATGAGAGAATAT
Found at i:102696 original size:82 final size:82
Alignment explanation
Indices: 102515--102957 Score: 384
Period size: 84 Copynumber: 5.2 Consensus size: 82
102505 TCTTGATGTA
* *
102515 TAAATGGAAGACTCATGTCTCGGGATGAGCATGAGGGGATATTAAAGGAAAGGAAGACTGATGTC
1 TAAA-GGAAGACTCATGTCTCGGGATGAGCATGAGAGGATATT-----AAAGGAAGACTCATGTC
* *
102580 TCGGGATGAGCATAAGGGGATAT
60 TCGGGATGAGCATGAGGGAATAT
* * ** * * *
102603 TAAAGGAAGACTCGTGTCTTGGGATGAGCATGATCGGATATTAAAGGAAGATTTATGTCTCTGGA
1 TAAAGGAAGACTCATGTCTCGGGATGAGCATGAGAGGATATTAAAGGAAGACTCATGTCTCGGGA
102668 TGAGCATGAGGGAATAT
66 TGAGCATGAGGGAATAT
* * * ** * **
102685 TGAAGGAAGACTCATGTCTTGGGTTGAGCATGAGATTATGTGTTAAAGGAAGACTCATGTCTCAA
1 TAAAGGAAGACTCATGTCTCGGGATGAGCATGAGAGGA--TATTAAAGGAAGACTCATGTCTCGG
*
102750 GATGAGCATGAGAGAATAT
64 GATGAGCATGAGGGAATAT
** * *
102769 TAAAGGAAGACTCATGTCTCAAGATGAGCATGAGAGAATATTAAAGGAAGACTCATGTCTCGGGT
1 TAAAGGAAGACTCATGTCTCGGGATGAGCATGAGAGGATATTAAAGGAAGACTCATGTCTCGGGA
** * *
102834 TGAGCATGAGATTATGTGT
66 TGAGCATGAG-GGA-ATAT
* * * ** * *
102853 TAAAGGAAGACTCATGTCTTGGGTTGATCATGA-ATTTATGTGTTAAAGGAAGACTCATGTCTCA
1 TAAAGGAAGACTCATGTCTCGGGATGAGCATGAGA-GGA--TATTAAAGGAAGACTCATGTCTCG
* ** * *
102917 GGTTGAGCATGAGATTATGTGT
63 GGATGAGCATGAG-GGA-ATAT
102939 TAAAGGAAGACTCATGTCT
1 TAAAGGAAGACTCATGTCT
102958 TGAAAAGAGC
Statistics
Matches: 302, Mismatches: 46, Indels: 16
0.83 0.13 0.04
Matches are distributed among these distances:
82 99 0.33
83 2 0.01
84 100 0.33
86 63 0.21
87 34 0.11
88 4 0.01
ACGTcount: A:0.33, C:0.11, G:0.29, T:0.27
Consensus pattern (82 bp):
TAAAGGAAGACTCATGTCTCGGGATGAGCATGAGAGGATATTAAAGGAAGACTCATGTCTCGGGA
TGAGCATGAGGGAATAT
Found at i:102744 original size:43 final size:43
Alignment explanation
Indices: 102687--103042 Score: 361
Period size: 43 Copynumber: 8.5 Consensus size: 43
102677 GGGAATATTG
*
102687 AAGGAAGACTCATGTCTTGGGTTGAGCATGAGATTATGTGTTA
1 AAGGAAGACTCATGTCTCGGGTTGAGCATGAGATTATGTGTTA
** * * * *
102730 AAGGAAGACTCATGTCTCAAGATGAGCATGAGA-GA-ATATTA
1 AAGGAAGACTCATGTCTCGGGTTGAGCATGAGATTATGTGTTA
** * * * *
102771 AAGGAAGACTCATGTCTCAAGATGAGCATGAGA-GA-ATATTA
1 AAGGAAGACTCATGTCTCGGGTTGAGCATGAGATTATGTGTTA
102812 AAGGAAGACTCATGTCTCGGGTTGAGCATGAGATTATGTGTTA
1 AAGGAAGACTCATGTCTCGGGTTGAGCATGAGATTATGTGTTA
* *
102855 AAGGAAGACTCATGTCTTGGGTTGATCATGA-ATTTATGTGTTA
1 AAGGAAGACTCATGTCTCGGGTTGAGCATGAGA-TTATGTGTTA
*
102898 AAGGAAGACTCATGTCTCAGGTTGAGCATGAGATTATGTGTTA
1 AAGGAAGACTCATGTCTCGGGTTGAGCATGAGATTATGTGTTA
* **** *
102941 AAGGAAGACTCATGTCTTGAAAAGAGCATGAGACTATGT-TTA
1 AAGGAAGACTCATGTCTCGGGTTGAGCATGAGATTATGTGTTA
* * * * * * *
102983 ATGGAAGACTTATGACT-TGGTAGAGCATAAGATTAT-T-TGA
1 AAGGAAGACTCATGTCTCGGGTTGAGCATGAGATTATGTGTTA
* *
103023 AAGGAAGACTTATGACTCGG
1 AAGGAAGACTCATGTCTCGG
103043 AGTAACATAA
Statistics
Matches: 271, Mismatches: 37, Indels: 12
0.85 0.12 0.04
Matches are distributed among these distances:
40 19 0.07
41 89 0.33
42 20 0.07
43 142 0.52
44 1 0.00
ACGTcount: A:0.34, C:0.11, G:0.27, T:0.29
Consensus pattern (43 bp):
AAGGAAGACTCATGTCTCGGGTTGAGCATGAGATTATGTGTTA
Found at i:102773 original size:125 final size:125
Alignment explanation
Indices: 102515--102992 Score: 424
Period size: 125 Copynumber: 3.8 Consensus size: 125
102505 TCTTGATGTA
** * * *
102515 TAAATGGAAGACTCATGTCTCGGGATGAGCATGAGGGGATATTAAAGGAAAGGAAGACTGATGTC
1 TAAA-GGAAGACTCATGTCTCAAGATGAGCATGAGAGAATATT-----AAAGGAAGACTCATGTC
* * *** * * *** ** *
102580 TCGGGATGAGCATAAGGGGA--TATTAAAGGAAGACTCGTGTCTTGGGATGAGCATGATCGGATA
60 TCGGGTTGAGCATGAGATTATGTGTTAAAGGAAGACTCATGTCTCAAGATGAGCATGAGAGAATA
102643 T
125 T
* * ** * * *
102644 TAAAGGAAGATTTATGTCTCTGGATGAGCATGAGGGAATATTGAAGGAAGACTCATGTCTTGGGT
1 TAAAGGAAGACTCATGTCTCAAGATGAGCATGAGAGAATATTAAAGGAAGACTCATGTCTCGGGT
102709 TGAGCATGAGATTATGTGTTAAAGGAAGACTCATGTCTCAAGATGAGCATGAGAGAATAT
66 TGAGCATGAGATTATGTGTTAAAGGAAGACTCATGTCTCAAGATGAGCATGAGAGAATAT
102769 TAAAGGAAGACTCATGTCTCAAGATGAGCATGAGAGAATATTAAAGGAAGACTCATGTCTCGGGT
1 TAAAGGAAGACTCATGTCTCAAGATGAGCATGAGAGAATATTAAAGGAAGACTCATGTCTCGGGT
*** * * * * *
102834 TGAGCATGAGATTATGTGTTAAAGGAAGACTCATGTCTTGGGTTGATCATGA-ATTTATGTGT
66 TGAGCATGAGATTATGTGTTAAAGGAAGACTCATGTCTCAAGATGAGCATGAGA--GA-ATAT
* * * * * * *
102896 TAAAGGAAGACTCATGTCTCAGGTTGAGCATGAGATTATGTGTTAAAGGAAGACTCATGTCTTGA
1 TAAAGGAAGACTCATGTCTCAAGATGAGCATGAGA-GA-ATATTAAAGGAAGACTCATGTCTCGG
*** * *
102961 AAAGAGCATGAGACTATGT-TTAATGGAAGACT
64 GTTGAGCATGAGATTATGTGTTAAAGGAAGACT
102993 TATGACTTGG
Statistics
Matches: 295, Mismatches: 47, Indels: 15
0.83 0.13 0.04
Matches are distributed among these distances:
123 29 0.10
124 1 0.00
125 141 0.48
126 1 0.00
127 35 0.12
128 47 0.16
129 41 0.14
ACGTcount: A:0.33, C:0.11, G:0.29, T:0.27
Consensus pattern (125 bp):
TAAAGGAAGACTCATGTCTCAAGATGAGCATGAGAGAATATTAAAGGAAGACTCATGTCTCGGGT
TGAGCATGAGATTATGTGTTAAAGGAAGACTCATGTCTCAAGATGAGCATGAGAGAATAT
Found at i:103028 original size:168 final size:168
Alignment explanation
Indices: 102563--103032 Score: 454
Period size: 166 Copynumber: 2.8 Consensus size: 168
102553 ATATTAAAGG
* ** * * * * *** *
102563 AAAGGAAGACTGATGTCTCGGGATGAGCATAAGGGGATATTAAAGGAAGACTCGTGTCTTGGGAT
1 AAAGGAAGACTCATGTCTCAAGATGAGCATGAGAGAATATTAAAGGAAGACTCATGTCTCAAGAA
* * * * * * * *** *
102628 GAGCATGA-TCGGATATTAAAGGAAGATTTATGTCTCTGG-ATGAGCATGAGGGAATAT-TG-AA
66 GAGCATGAGAC-AATATTAAAGGAAGACTCATGACTCGGGTA-GAGCATAAGATTATGTGTGAAA
102689 GGAAGACTCATGTCTTGGGTTGAGCATGAGATTATGTGTT
129 GGAAGACTCATGTCTTGGGTTGAGCATGAGATTATGTGTT
*
102729 AAAGGAAGACTCATGTCTCAAGATGAGCATGAGAGAATATTAAAGGAAGACTCATGTCTCAAGAT
1 AAAGGAAGACTCATGTCTCAAGATGAGCATGAGAGAATATTAAAGGAAGACTCATGTCTCAAGAA
* * * * *
102794 GAGCATGAGAGAATATTAAAGGAAGACTCATGTCTCGGGTTGAGCATGAGATTATGTGTTAAAGG
66 GAGCATGAGACAATATTAAAGGAAGACTCATGACTCGGGTAGAGCATAAGATTATGTGTGAAAGG
*
102859 AAGACTCATGTCTTGGGTTGATCATGA-ATTTATGTGTT
131 AAGACTCATGTCTTGGGTTGAGCATGAGA-TTATGTGTT
* * * * * *
102897 AAAGGAAGACTCATGTCTCAGGTTGAGCATGAGATTATGTGTTAAAGGAAGACTCATGTCTTGAA
1 AAAGGAAGACTCATGTCTCAAGATGAGCATGAGA-GA-ATATTAAAGGAAGACTCATGTC-TCAA
* * * * *
102962 -AAGAGCATGAGACTATGTTTAATGGAAGACTTATGACT-TGGTAGAGCATAAGATTAT-T-TGA
63 GAAGAGCATGAGACAAT-ATTAAAGGAAGACTCATGACTCGGGTAGAGCATAAGATTATGTGTGA
103023 AAGGAAGACT
127 AAGGAAGACT
103033 TATGACTCGG
Statistics
Matches: 255, Mismatches: 40, Indels: 16
0.82 0.13 0.05
Matches are distributed among these distances:
166 99 0.39
167 2 0.01
168 83 0.33
169 2 0.01
170 49 0.19
171 20 0.08
ACGTcount: A:0.34, C:0.10, G:0.28, T:0.28
Consensus pattern (168 bp):
AAAGGAAGACTCATGTCTCAAGATGAGCATGAGAGAATATTAAAGGAAGACTCATGTCTCAAGAA
GAGCATGAGACAATATTAAAGGAAGACTCATGACTCGGGTAGAGCATAAGATTATGTGTGAAAGG
AAGACTCATGTCTTGGGTTGAGCATGAGATTATGTGTT
Found at i:103707 original size:21 final size:21
Alignment explanation
Indices: 103679--103731 Score: 83
Period size: 21 Copynumber: 2.6 Consensus size: 21
103669 AGAGTTTTTA
103679 GTAT-GGTAGAAG-CATGACTT
1 GTATCGGTAGAAGTCAT-ACTT
103699 GTATCGGTAGAAGTCATACTT
1 GTATCGGTAGAAGTCATACTT
103720 GTATCGGTAGAA
1 GTATCGGTAGAA
103732 CTAGCACAGG
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
20 4 0.13
21 24 0.77
22 3 0.10
ACGTcount: A:0.30, C:0.11, G:0.28, T:0.30
Consensus pattern (21 bp):
GTATCGGTAGAAGTCATACTT
Found at i:104190 original size:32 final size:32
Alignment explanation
Indices: 104034--104296 Score: 217
Period size: 32 Copynumber: 8.2 Consensus size: 32
104024 AATTTCATAA
* * *
104034 TATGCTTATAAGAGCTAATCAATTAGT-ATCTAG
1 TATGCTCATAAGAGCT-ATCAATCAGTAAAC-AG
* * * * * *
104067 TAAGCTCGTATGAGTTAATCAATCATTATACAG
1 TATGCTCATAAGAGCT-ATCAATCAGTAAACAG
* * * * *
104100 TATGCTCATGAGAGTTATTAATTAGT-AATAG
1 TATGCTCATAAGAGCTATCAATCAGTAAACAG
* * * *
104131 TAAGCTCATATGAACTGATCAATCAGTATACAG
1 TATGCTCATAAGAGCT-ATCAATCAGTAAACAG
* *
104164 TATGCTCATGAGAGCTATCATTCAGTAAACAG
1 TATGCTCATAAGAGCTATCAATCAGTAAACAG
* *
104196 TATGC-CGTAAGAGCTATCAATCAGTAAACAA
1 TATGCTCATAAGAGCTATCAATCAGTAAACAG
* * *
104227 TATGCTCGTAAGAGCTATCAATCAGTAAATAA
1 TATGCTCATAAGAGCTATCAATCAGTAAACAG
* *
104259 TATGCTCGTAAGAGCTATCAATCAGTAAATAG
1 TATGCTCATAAGAGCTATCAATCAGTAAACAG
*
104291 TTTGCT
1 TATGCT
104297 TGTAAGAGTT
Statistics
Matches: 186, Mismatches: 40, Indels: 9
0.79 0.17 0.04
Matches are distributed among these distances:
31 41 0.22
32 95 0.51
33 49 0.26
34 1 0.01
ACGTcount: A:0.37, C:0.15, G:0.17, T:0.31
Consensus pattern (32 bp):
TATGCTCATAAGAGCTATCAATCAGTAAACAG
Found at i:104191 original size:64 final size:64
Alignment explanation
Indices: 104064--104285 Score: 243
Period size: 64 Copynumber: 3.5 Consensus size: 64
104054 AATTAGTATC
* * * * *
104064 TAGTAAGCTCGTATGAGTTAATCAATCATTATACAGTATGCTCATGAGAGTTATTAATT-AGT-A
1 TAGTAAGCTCGTAAGAGCT-ATCAATCAGTATACAGTATGCTCATGAGAGCTA-TCATTCAGTAA
104127 A
64 A
* * *
104128 TAGTAAGCTCATATGAACTGATCAATCAGTATACAGTATGCTCATGAGAGCTATCATTCAGTAAA
1 TAGTAAGCTCGTAAGAGCT-ATCAATCAGTATACAGTATGCTCATGAGAGCTATCATTCAGTAAA
* * * * * * *
104193 CAGTATGC-CGTAAGAGCTATCAATCAGTAAACAATATGCTCGTAAGAGCTATCAATCAGTAAA
1 TAGTAAGCTCGTAAGAGCTATCAATCAGTATACAGTATGCTCATGAGAGCTATCATTCAGTAAA
* *
104256 TAATATGCTCGTAAGAGCTATCAATCAGTA
1 TAGTAAGCTCGTAAGAGCTATCAATCAGTA
104286 AATAGTTTGC
Statistics
Matches: 136, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
63 50 0.37
64 78 0.57
65 8 0.06
ACGTcount: A:0.37, C:0.16, G:0.17, T:0.30
Consensus pattern (64 bp):
TAGTAAGCTCGTAAGAGCTATCAATCAGTATACAGTATGCTCATGAGAGCTATCATTCAGTAAA
Found at i:104304 original size:64 final size:63
Alignment explanation
Indices: 104148--104287 Score: 208
Period size: 63 Copynumber: 2.2 Consensus size: 63
104138 ATATGAACTG
* * * * * *
104148 ATCAATCAGTATACAGTATGCTCATGAGAGCTATCATTCAGTAAACAGTATGCCGTAAGAGCT
1 ATCAATCAGTAAACAATATGCTCGTAAGAGCTATCAATCAGTAAACAATATGCCGTAAGAGCT
*
104211 ATCAATCAGTAAACAATATGCTCGTAAGAGCTATCAATCAGTAAATAATATGCTCGTAAGAGCT
1 ATCAATCAGTAAACAATATGCTCGTAAGAGCTATCAATCAGTAAACAATATGC-CGTAAGAGCT
104275 ATCAATCAGTAAA
1 ATCAATCAGTAAA
104288 TAGTTTGCTT
Statistics
Matches: 69, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
63 46 0.67
64 23 0.33
ACGTcount: A:0.39, C:0.18, G:0.16, T:0.26
Consensus pattern (63 bp):
ATCAATCAGTAAACAATATGCTCGTAAGAGCTATCAATCAGTAAACAATATGCCGTAAGAGCT
Found at i:110196 original size:79 final size:78
Alignment explanation
Indices: 110105--110252 Score: 217
Period size: 79 Copynumber: 1.9 Consensus size: 78
110095 TACTGTTAAC
* * *
110105 AACAGAAATTGAATAAATTATGTTGAAC-GACGGGAATAAAATCCTGAAACAAAATTGTTCAATT
1 AACAGAAATTGAATAAATTATATTGAACGGA-AGGAATAAAATCCTAAAACAAAATTGTTCAATT
110169 GATTTTTGTTTAGA
65 GATTTTTGTTTAGA
* * *
110183 AACAGAAAATTGAATAAATTCTATTGAACGGAAGGAATAAAATCCTAAAATAGAATTGTTCAATT
1 AACAG-AAATTGAATAAATTATATTGAACGGAAGGAATAAAATCCTAAAACAAAATTGTTCAATT
110248 GATTT
65 GATTT
110253 CTATTTACAA
Statistics
Matches: 62, Mismatches: 6, Indels: 3
0.87 0.08 0.04
Matches are distributed among these distances:
78 5 0.08
79 55 0.89
80 2 0.03
ACGTcount: A:0.45, C:0.09, G:0.16, T:0.31
Consensus pattern (78 bp):
AACAGAAATTGAATAAATTATATTGAACGGAAGGAATAAAATCCTAAAACAAAATTGTTCAATTG
ATTTTTGTTTAGA
Found at i:113460 original size:24 final size:23
Alignment explanation
Indices: 113421--113466 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 23
113411 ACAAAAACTA
113421 AACCCCAAAACCTAAAAACAAAG
1 AACCCCAAAACCTAAAAACAAAG
* *
113444 AACCCTCAAAACGTAAACACAAA
1 AACCC-CAAAACCTAAAAACAAA
113467 ATTCTCTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 5 0.25
24 15 0.75
ACGTcount: A:0.59, C:0.30, G:0.04, T:0.07
Consensus pattern (23 bp):
AACCCCAAAACCTAAAAACAAAG
Found at i:114387 original size:8 final size:7
Alignment explanation
Indices: 114370--114403 Score: 50
Period size: 8 Copynumber: 4.6 Consensus size: 7
114360 TTTATTTTAT
114370 TTTAATA
1 TTTAATA
114377 TTTAATAA
1 TTTAAT-A
114385 TTTAATAA
1 TTTAAT-A
114393 TTTAATA
1 TTTAATA
114400 TTTA
1 TTTA
114404 TTAAAAATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
7 11 0.42
8 15 0.58
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (7 bp):
TTTAATA
Found at i:114388 original size:15 final size:15
Alignment explanation
Indices: 114370--114403 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
114360 TTTATTTTAT
114370 TTTAATATTTAATAA
1 TTTAATATTTAATAA
114385 TTTAATAATTTAAT-A
1 TTTAAT-ATTTAATAA
114400 TTTA
1 TTTA
114404 TTAAAAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 11 0.61
16 7 0.39
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
TTTAATATTTAATAA
Found at i:116179 original size:9 final size:9
Alignment explanation
Indices: 116165--116224 Score: 61
Period size: 9 Copynumber: 6.6 Consensus size: 9
116155 TCGAATACAT
116165 TTTTTTTTC
1 TTTTTTTTC
116174 TTTTTTTTC
1 TTTTTTTTC
116183 TTTTTTTT-
1 TTTTTTTTC
116191 TTTCAATTTTTC
1 TTT---TTTTTC
**
116203 -TTTTTGAC
1 TTTTTTTTC
116211 TTTTTTTTC
1 TTTTTTTTC
116220 TTTTT
1 TTTTT
116225 CTAAACAATA
Statistics
Matches: 42, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
8 7 0.17
9 28 0.67
11 7 0.17
ACGTcount: A:0.05, C:0.10, G:0.02, T:0.83
Consensus pattern (9 bp):
TTTTTTTTC
Found at i:117151 original size:6 final size:6
Alignment explanation
Indices: 117130--117266 Score: 88
Period size: 6 Copynumber: 23.3 Consensus size: 6
117120 AGTGCATAAT
* * *
117130 AAAAT- AAAAT- AAAATA AAAAT- AAAATA AAACTA AAACTA AAACTA
1 AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA
* * * * * * *
117175 AAAATA AGAATGA AAAAGA AAAA-G AAAATG GAAATG AAAATG AAAATAA
1 AAAATA AAAAT-A AAAATA AAAATA AAAATA AAAATA AAAATA AAAAT-A
* * *
117224 AAAATGA AAAAGA AAAAGA AAAA-G AAAATA AAAAT- AAAATA AA
1 AAAAT-A AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AA
117267 TGTACTAACT
Statistics
Matches: 112, Mismatches: 13, Indels: 13
0.81 0.09 0.09
Matches are distributed among these distances:
5 28 0.25
6 70 0.62
7 14 0.12
ACGTcount: A:0.76, C:0.02, G:0.09, T:0.13
Consensus pattern (6 bp):
AAAATA
Found at i:117238 original size:37 final size:36
Alignment explanation
Indices: 117175--117262 Score: 113
Period size: 37 Copynumber: 2.4 Consensus size: 36
117165 ACTAAAACTA
* * * * *
117175 AAAATAAGAATGAAAAAGAAAAAGAAAATGGAAATG
1 AAAATAAAAATAAAAAAGAAAAAGAAAAAGAAAAAG
*
117211 AAAATGAAAATAAAAAATGAAAAAGAAAAAGAAAAAG
1 AAAATAAAAATAAAAAA-GAAAAAGAAAAAGAAAAAG
117248 AAAATAAAAATAAAA
1 AAAATAAAAATAAAA
117263 TAAATGTACT
Statistics
Matches: 44, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
36 14 0.32
37 30 0.68
ACGTcount: A:0.76, C:0.00, G:0.14, T:0.10
Consensus pattern (36 bp):
AAAATAAAAATAAAAAAGAAAAAGAAAAAGAAAAAG
Found at i:119444 original size:12 final size:13
Alignment explanation
Indices: 119417--119446 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
119407 TATAAAATAA
119417 AAAAATTAAATGT
1 AAAAATTAAATGT
119430 AAAAATTAAAT-T
1 AAAAATTAAATGT
119442 AAAAA
1 AAAAA
119447 CAAAAAATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 6 0.35
13 11 0.65
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (13 bp):
AAAAATTAAATGT
Found at i:131889 original size:290 final size:290
Alignment explanation
Indices: 131362--131911 Score: 1001
Period size: 290 Copynumber: 1.9 Consensus size: 290
131352 AGCTAACTAA
* *
131362 CAACACTCCCCTTCAAGTTGGTGGATGGAAAGTGTTTTTAACCTCCAACTTGGACAACATATAAC
1 CAACACTCCCCTTCAAGTTGGTGGATGGAAAATGTTTTTAACCTCCAACTTGGACAACAAATAAC
* *
131427 TATGCTGTTAAACTCCCAATGCCTTATTCAAGATGTTTACAACCTGATCTGCAGTAGACACATAT
66 TATGCTGTTAAACTCCCAATGCCTTATTCAAGATGTCTACAACCTGATCTACAGTAGACACATAT
* * *
131492 TCTGTTTGTATTAATCTCGCTTGTATCTTTTCTCGAACAAAATGATAGTCTATCTCAATATGCTT
131 TCTATTTGTATTAATCTCGCTTGTATCTTCTCTAGAACAAAATGATAGTCTATCTCAATATGCTT
131557 AGTCCTTTCATGAAACATAGGATTAGAAGCTATTTGAATGGCTGACTTGCTATCACTGAACAATT
196 AGTCCTTTCATGAAACATAGGATTAGAAGCTATTTGAATGGCTGACTTGCTATCACTGAACAATT
131622 AACAGCTAATTAATCTGCAGTTGCTTCCTT
261 AACAGCTAATTAATCTGCAGTTGCTTCCTT
* *
131652 CAACACTCCTCTTCAAGTTGGTGGATGGAAAATGTTTTTAACCTCCAACTTGGACAATAAATAAC
1 CAACACTCCCCTTCAAGTTGGTGGATGGAAAATGTTTTTAACCTCCAACTTGGACAACAAATAAC
*
131717 TATGCTGTTGAACTCCCAATGCCTTATTCAAGATGTCTACAACCTGATCTACAGTAGACACATAT
66 TATGCTGTTAAACTCCCAATGCCTTATTCAAGATGTCTACAACCTGATCTACAGTAGACACATAT
131782 TCTATTTGTATTAATCTCGCTTGTATCTTCTCTAGAACAAAATGATAGTCTATCTCAATATGCTT
131 TCTATTTGTATTAATCTCGCTTGTATCTTCTCTAGAACAAAATGATAGTCTATCTCAATATGCTT
*
131847 AGTCCTTTCATGAAACATAGGATTAGAAGCTATTTTAATGGCTGACTTGCTATCACTGAACAATT
196 AGTCCTTTCATGAAACATAGGATTAGAAGCTATTTGAATGGCTGACTTGCTATCACTGAACAATT
131912 TAACTTGTGT
Statistics
Matches: 249, Mismatches: 11, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
290 249 1.00
ACGTcount: A:0.30, C:0.21, G:0.15, T:0.34
Consensus pattern (290 bp):
CAACACTCCCCTTCAAGTTGGTGGATGGAAAATGTTTTTAACCTCCAACTTGGACAACAAATAAC
TATGCTGTTAAACTCCCAATGCCTTATTCAAGATGTCTACAACCTGATCTACAGTAGACACATAT
TCTATTTGTATTAATCTCGCTTGTATCTTCTCTAGAACAAAATGATAGTCTATCTCAATATGCTT
AGTCCTTTCATGAAACATAGGATTAGAAGCTATTTGAATGGCTGACTTGCTATCACTGAACAATT
AACAGCTAATTAATCTGCAGTTGCTTCCTT
Found at i:136369 original size:2 final size:2
Alignment explanation
Indices: 136362--136387 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
136352 CCAATTGTAG
136362 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
136388 TTAAATGGTT
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:136448 original size:2 final size:2
Alignment explanation
Indices: 136405--136430 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
136395 GTTGGTTGTG
136405 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
136431 AATGATTAAG
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):
TA
Found at i:137242 original size:80 final size:80
Alignment explanation
Indices: 137109--137263 Score: 238
Period size: 80 Copynumber: 1.9 Consensus size: 80
137099 GCGCAAACCA
* * * * *
137109 TTGGTTAATCCAACTAGAGTTGGGCTCACTTATCACGGTTTATCCGCTAGGCACTAGGTGCCATG
1 TTGGTTAATCCAACTAGAGCTGGACTCACTTATCACGGTTTAACCACTAGGCACCAGGTGCCATG
137174 AATTGACGGATTTTG
66 AATTGACGGATTTTG
* **
137189 TTGGTTAATCCAACTAGAGCTGGATTCACTTATCGTGGTTTAACCACTAGGCACCAGGTGCCATG
1 TTGGTTAATCCAACTAGAGCTGGACTCACTTATCACGGTTTAACCACTAGGCACCAGGTGCCATG
137254 AATTGACGGA
66 AATTGACGGA
137264 AATTATGAAC
Statistics
Matches: 67, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
80 67 1.00
ACGTcount: A:0.25, C:0.21, G:0.25, T:0.30
Consensus pattern (80 bp):
TTGGTTAATCCAACTAGAGCTGGACTCACTTATCACGGTTTAACCACTAGGCACCAGGTGCCATG
AATTGACGGATTTTG
Found at i:139460 original size:16 final size:16
Alignment explanation
Indices: 139439--139471 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
139429 TACGACAATC
139439 ACCATCAAGGAAGCCT
1 ACCATCAAGGAAGCCT
139455 ACCATCAAGGAAGCCT
1 ACCATCAAGGAAGCCT
139471 A
1 A
139472 ACTCATTCTT
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:0.39, C:0.30, G:0.18, T:0.12
Consensus pattern (16 bp):
ACCATCAAGGAAGCCT
Found at i:139885 original size:18 final size:18
Alignment explanation
Indices: 139834--139887 Score: 90
Period size: 18 Copynumber: 3.0 Consensus size: 18
139824 ACTACATTTG
*
139834 CAACTAACAGCTAACCAA
1 CAACTAACAGCTAACTAA
*
139852 CAACTAACAGTTAACTAA
1 CAACTAACAGCTAACTAA
139870 CAACTAACAGCTAACTAA
1 CAACTAACAGCTAACTAA
139888 TCTGCAGTTG
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 33 1.00
ACGTcount: A:0.50, C:0.28, G:0.06, T:0.17
Consensus pattern (18 bp):
CAACTAACAGCTAACTAA
Found at i:141024 original size:23 final size:22
Alignment explanation
Indices: 140974--141024 Score: 57
Period size: 23 Copynumber: 2.3 Consensus size: 22
140964 AGGGATCAAA
* **
140974 ATTAAAGAGTAATTTTTACGAT
1 ATTAAAAAGTAATTTTTAAAAT
*
140996 AATAAAAATGTAATTTTTAAAAT
1 ATTAAAAA-GTAATTTTTAAAAT
141019 ATTAAA
1 ATTAAA
141025 TTAAATTTTT
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
22 6 0.26
23 17 0.74
ACGTcount: A:0.51, C:0.02, G:0.08, T:0.39
Consensus pattern (22 bp):
ATTAAAAAGTAATTTTTAAAAT
Found at i:143865 original size:6 final size:7
Alignment explanation
Indices: 143850--143875 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
143840 CCAAATTGTA
143850 TTTTATT
1 TTTTATT
143857 TTTTATT
1 TTTTATT
143864 TTTTATT
1 TTTTATT
143871 TTTTA
1 TTTTA
143876 CTAATAAATG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (7 bp):
TTTTATT
Found at i:144379 original size:22 final size:21
Alignment explanation
Indices: 144343--144394 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 21
144333 CGCTCATATT
144343 AATT-TTTAATTTTTT-TTTA
1 AATTATTTAATTTTTTATTTA
*
144362 AATTATTTATATTGTTTTATTTT
1 AATTATTTA-ATT-TTTTATTTA
144385 AA-TATTTAAT
1 AATTATTTAAT
144395 AATTTTATAA
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
19 4 0.14
20 4 0.14
21 5 0.18
22 10 0.36
23 5 0.18
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (21 bp):
AATTATTTAATTTTTTATTTA
Found at i:144402 original size:21 final size:24
Alignment explanation
Indices: 144349--144402 Score: 60
Period size: 24 Copynumber: 2.4 Consensus size: 24
144339 TATTAATTTT
*
144349 TAATTTTTTTTTAAATTATTTATA
1 TAATTTTATTTTAAATTATTTATA
**
144373 TTGTTTTATTTT-AA-TATTTA-A
1 TAATTTTATTTTAAATTATTTATA
144394 TAATTTTAT
1 TAATTTTAT
144403 AAATTTTTTA
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
21 8 0.32
22 6 0.24
23 2 0.08
24 9 0.36
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (24 bp):
TAATTTTATTTTAAATTATTTATA
Found at i:145401 original size:2 final size:2
Alignment explanation
Indices: 145394--145422 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
145384 ATTAAAATGT
145394 TA 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 TA T
145423 TAAAATATCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:147401 original size:20 final size:20
Alignment explanation
Indices: 147373--147410 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
147363 TTATTGTTTA
147373 AATTGTAAAAAATAAATAAT
1 AATTGTAAAAAATAAATAAT
* *
147393 AATTTTAAATAATAAATA
1 AATTGTAAAAAATAAATA
147411 TTAACTTTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (20 bp):
AATTGTAAAAAATAAATAAT
Found at i:147419 original size:20 final size:20
Alignment explanation
Indices: 147378--147419 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
147368 GTTTAAATTG
*
147378 TAAAAAATAAATAATAATTT
1 TAAAAAATAAATAATAACTT
* *
147398 TAAATAATAAATATTAACTT
1 TAAAAAATAAATAATAACTT
147418 TA
1 TA
147420 TTAAAAATAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (20 bp):
TAAAAAATAAATAATAACTT
Found at i:153017 original size:37 final size:35
Alignment explanation
Indices: 152976--153113 Score: 114
Period size: 37 Copynumber: 3.7 Consensus size: 35
152966 AGTCCACTAA
*
152976 ACTTGTCTTCATGATTCAAGTTATGACAGTCAGTTGG
1 ACTTGTCCTCATG-TTCAAGTTATGACAGTCAGTT-G
* * * *
153013 ACTTGTCCTCCTGTTCCAAGTTATAACGGTCCGCTTG
1 ACTTGTCCTCATGTT-CAAGTTATGACAGTCAG-TTG
* * * **
153050 AATTTTCCTCATGTTCTAAGTTATGACTGTTTGTTAG
1 ACTTGTCCTCATGTTC-AAGTTATGACAGTCAGTT-G
*
153087 ATTTGTCCTCATGTTTCAAGTTATGAC
1 ACTTGTCCTCATG-TTCAAGTTATGAC
153114 GGTTCATTGA
Statistics
Matches: 82, Mismatches: 14, Indels: 10
0.77 0.13 0.09
Matches are distributed among these distances:
36 5 0.06
37 72 0.88
38 5 0.06
ACGTcount: A:0.21, C:0.20, G:0.18, T:0.41
Consensus pattern (35 bp):
ACTTGTCCTCATGTTCAAGTTATGACAGTCAGTTG
Found at i:153133 original size:74 final size:74
Alignment explanation
Indices: 152979--153134 Score: 163
Period size: 74 Copynumber: 2.1 Consensus size: 74
152969 CCACTAAACT
* * *
152979 TGTCTTCATGATTCAAGTTATGACAGTCAGTTGGACTTGTCCTCCTGTTCCAAGTTATAACGGTC
1 TGTCCTCATGATTCAAGTTATGACAGTCAGTTAGACTTGTCCTCATGTTCCAAGTTATAACGGTC
* *
153044 CGCTTGAAT
66 CGATTGAAG
* * ** * * *
153053 TTTCCTCATG-TTCTAAGTTATGACTGTTTGTTAGATTTGTCCTCATGTTTCAAGTTATGACGGT
1 TGTCCTCATGATTC-AAGTTATGACAGTCAGTTAGACTTGTCCTCATGTTCCAAGTTATAACGGT
*
153117 TC-ATTGAAGG
65 CCGATTGAA-G
153127 TGTCCTCA
1 TGTCCTCA
153135 AGTTTCCATG
Statistics
Matches: 66, Mismatches: 14, Indels: 4
0.79 0.17 0.05
Matches are distributed among these distances:
73 8 0.12
74 58 0.88
ACGTcount: A:0.21, C:0.19, G:0.20, T:0.40
Consensus pattern (74 bp):
TGTCCTCATGATTCAAGTTATGACAGTCAGTTAGACTTGTCCTCATGTTCCAAGTTATAACGGTC
CGATTGAAG
Found at i:153667 original size:28 final size:28
Alignment explanation
Indices: 153275--153660 Score: 381
Period size: 28 Copynumber: 13.8 Consensus size: 28
153265 TTATCCATGA
*
153275 ATCTTTCAAGCAAGAGTCTTCATGGACT
1 ATCTTTCAAGCAAGAGTCTGCATGGACT
* *
153303 ATCTTTCAACCAAGAGT-TCGCATAGACT
1 ATCTTTCAAGCAAGAGTCT-GCATGGACT
* *
153331 AT-TCTTCAAGCAAGTGTCCGCATGGACT
1 ATCT-TTCAAGCAAGAGTCTGCATGGACT
*
153359 ATCTTTCAAGCAAGAGTCTGAATGGACT
1 ATCTTTCAAGCAAGAGTCTGCATGGACT
* * *
153387 AT-TCTTCAAGCAAGAATCAGCACGGACT
1 ATCT-TTCAAGCAAGAGTCTGCATGGACT
* * *
153415 ATCTTACAAGAAAGAGTCTGCATGGATT
1 ATCTTTCAAGCAAGAGTCTGCATGGACT
* * **
153443 ATCATTCAAGTAAGAGTCCACATGGACT
1 ATCTTTCAAGCAAGAGTCTGCATGGACT
* *
153471 ATCTTTCAAGCAAGTGTCTACA-GAGACT
1 ATCTTTCAAGCAAGAGTCTGCATG-GACT
* *
153499 ATTCTTT-GAGCAAGAGTCAGCATGGACT
1 A-TCTTTCAAGCAAGAGTCTGCATGGACT
* **
153527 ATCTTACAAGCAAGAGTCTATATGGACT
1 ATCTTTCAAGCAAGAGTCTGCATGGACT
*
153555 ATCGTTCAAGCAAGAGTCTGCATGGACT
1 ATCTTTCAAGCAAGAGTCTGCATGGACT
* **
153583 AT-TCTTCAAGCAAGAATCCACATGGACT
1 ATCT-TTCAAGCAAGAGTCTGCATGGACT
* * **
153611 ATCGTTT-AAGTAAGAATCCACATGGACT
1 ATC-TTTCAAGCAAGAGTCTGCATGGACT
153639 ATCTTTCAAGCAAGAGTCTGCA
1 ATCTTTCAAGCAAGAGTCTGCA
153661 AGAACTAACT
Statistics
Matches: 292, Mismatches: 52, Indels: 28
0.78 0.14 0.08
Matches are distributed among these distances:
27 11 0.04
28 270 0.92
29 10 0.03
30 1 0.00
ACGTcount: A:0.32, C:0.21, G:0.19, T:0.27
Consensus pattern (28 bp):
ATCTTTCAAGCAAGAGTCTGCATGGACT
Found at i:156601 original size:29 final size:28
Alignment explanation
Indices: 156554--156611 Score: 66
Period size: 30 Copynumber: 2.0 Consensus size: 28
156544 TAAATTATTG
156554 AAAATTTTTATTTATA-TTTAATATTTT
1 AAAATTTTTATTTATATTTTAATATTTT
*
156581 AAAATTTTT-TTATAATCATTTTAATTTTTT
1 AAAATTTTTATT-T-AT-ATTTTAATATTTT
156611 A
1 A
156612 CTCGATATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
26 2 0.08
27 10 0.38
28 2 0.08
29 1 0.04
30 11 0.42
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (28 bp):
AAAATTTTTATTTATATTTTAATATTTT
Found at i:163168 original size:31 final size:32
Alignment explanation
Indices: 163103--163174 Score: 92
Period size: 32 Copynumber: 2.3 Consensus size: 32
163093 TTAATATAAT
* * * *
163103 ATTTGGTACTTGAACTTGATATTTTTTTCTTA
1 ATTTGGTACTTAAACTTGACATCTTTTTCCTA
*
163135 ATTTGGTACTTAAATTTGACA-CTTTTTCCTA
1 ATTTGGTACTTAAACTTGACATCTTTTTCCTA
163166 ATTTGGTAC
1 ATTTGGTAC
163175 CTAATTTTTT
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
31 17 0.49
32 18 0.51
ACGTcount: A:0.24, C:0.12, G:0.12, T:0.51
Consensus pattern (32 bp):
ATTTGGTACTTAAACTTGACATCTTTTTCCTA
Found at i:163393 original size:31 final size:29
Alignment explanation
Indices: 163357--163463 Score: 112
Period size: 31 Copynumber: 3.6 Consensus size: 29
163347 AAAAAAAAGC
163357 TTAGGTACCAAATTAGGAAAAAATGCCAAGT
1 TTAGGTACCAAATTAGGAAAAAAT--CAAGT
**
163388 TTAGGTACCAAATT-GGTTCCAAAA--AAGT
1 TTAGGTACCAAATTAGG--AAAAAATCAAGT
*
163416 TTAGGTACCAAATTAGAAAAAAATATCAAGT
1 TTAGGTACCAAATTAG-GAAAAA-ATCAAGT
163447 TTAGGTACCAAATTAGG
1 TTAGGTACCAAATTAGG
163464 TCAAAAAAAA
Statistics
Matches: 63, Mismatches: 6, Indels: 15
0.75 0.07 0.18
Matches are distributed among these distances:
28 21 0.33
29 2 0.03
30 2 0.03
31 34 0.54
32 4 0.06
ACGTcount: A:0.44, C:0.12, G:0.18, T:0.26
Consensus pattern (29 bp):
TTAGGTACCAAATTAGGAAAAAATCAAGT
Found at i:163430 original size:59 final size:59
Alignment explanation
Indices: 163348--163518 Score: 227
Period size: 59 Copynumber: 2.9 Consensus size: 59
163338 ATTGAATCTA
* * *
163348 AAAAAAAGCTTAGGTACCAAATTAGGAAAAAATGCCAAGTTTAGGTACCAAATT-GGTTC
1 AAAAAAAGATTAGGTACCAAATTAGAAAAAAATGTCAAGTTTAGGTACCAAATTAGG-TC
* * *
163407 CAAAAAAGTTTAGGTACCAAATTAGAAAAAAATATCAAGTTTAGGTACCAAATTAGGTC
1 AAAAAAAGATTAGGTACCAAATTAGAAAAAAATGTCAAGTTTAGGTACCAAATTAGGTC
* * * **
163466 AAAAAAAAATTAAGTACCAAATTAAAAAAAAATGTCAAGTTTAAATACCAAAT
1 AAAAAAAGATTAGGTACCAAATTAGAAAAAAATGTCAAGTTTAGGTACCAAAT
163519 GTTATATTAA
Statistics
Matches: 98, Mismatches: 13, Indels: 2
0.87 0.12 0.02
Matches are distributed among these distances:
59 96 0.98
60 2 0.02
ACGTcount: A:0.51, C:0.12, G:0.13, T:0.24
Consensus pattern (59 bp):
AAAAAAAGATTAGGTACCAAATTAGAAAAAAATGTCAAGTTTAGGTACCAAATTAGGTC
Found at i:178150 original size:12 final size:12
Alignment explanation
Indices: 178109--178141 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
178099 CATTCACAAC
178109 AATTCTTATGGT
1 AATTCTTATGGT
178121 AATTCTTATGGT
1 AATTCTTATGGT
178133 AATTCTTAT
1 AATTCTTAT
178142 AATAATTCTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.27, C:0.09, G:0.12, T:0.52
Consensus pattern (12 bp):
AATTCTTATGGT
Found at i:183492 original size:36 final size:36
Alignment explanation
Indices: 183445--183544 Score: 155
Period size: 36 Copynumber: 2.8 Consensus size: 36
183435 TGGTAACAGA
*
183445 CATGACCTTTGGATCAACAGGGAGTAAAACAACCAT
1 CATGACCTTTGGGTCAACAGGGAGTAAAACAACCAT
* * *
183481 CATGACCTTTGGGTCAATAGGGAGTAAAACGAGCAT
1 CATGACCTTTGGGTCAACAGGGAGTAAAACAACCAT
*
183517 CATGACCTTTGGGTCAACAAGGAGTAAA
1 CATGACCTTTGGGTCAACAGGGAGTAAA
183545 TCAAATATCG
Statistics
Matches: 58, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 58 1.00
ACGTcount: A:0.36, C:0.19, G:0.24, T:0.21
Consensus pattern (36 bp):
CATGACCTTTGGGTCAACAGGGAGTAAAACAACCAT
Found at i:187005 original size:70 final size:70
Alignment explanation
Indices: 186922--187061 Score: 210
Period size: 70 Copynumber: 2.0 Consensus size: 70
186912 CAAAAAGAAA
*
186922 TTATAAGAATCTAA-TCAAATTCACTCGACTAAACCAACAAACCTCAATTCTTCTAACCCCAAAT
1 TTATAAGAATCTAACT-AAATCCACTCGACTAAACCAACAAACCTCAATTCTTCTAACCCCAAAT
186986 TTTAGG
65 TTTAGG
* * * * *
186992 TTATAAGAATCTAACTGAATCCACTTGACTCAACCAATAGACCTCAATTCTTCTAACCCCAAATT
1 TTATAAGAATCTAACTAAATCCACTCGACTAAACCAACAAACCTCAATTCTTCTAACCCCAAATT
187057 TTAGG
66 TTAGG
187062 GTGTTACATT
Statistics
Matches: 63, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
70 62 0.98
71 1 0.02
ACGTcount: A:0.38, C:0.26, G:0.07, T:0.29
Consensus pattern (70 bp):
TTATAAGAATCTAACTAAATCCACTCGACTAAACCAACAAACCTCAATTCTTCTAACCCCAAATT
TTAGG
Found at i:190530 original size:25 final size:25
Alignment explanation
Indices: 190479--190537 Score: 75
Period size: 25 Copynumber: 2.4 Consensus size: 25
190469 TTAAACATAA
* * *
190479 TTAAATTTATTATTAATAATTATAT
1 TTAATTTTATTATTAATAATAACAT
190504 TTAATTTTATTATTAATTAA-AACAT
1 TTAATTTTATTATTAA-TAATAACAT
190529 TTAATTTTA
1 TTAATTTTA
190538 GAAAATATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
25 27 0.90
26 3 0.10
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (25 bp):
TTAATTTTATTATTAATAATAACAT
Found at i:191044 original size:18 final size:18
Alignment explanation
Indices: 191017--191058 Score: 75
Period size: 18 Copynumber: 2.3 Consensus size: 18
191007 AAGCAATAAA
*
191017 CATCATTAACTATCGGAC
1 CATCACTAACTATCGGAC
191035 CATCACTAACTATCGGAC
1 CATCACTAACTATCGGAC
191053 CATCAC
1 CATCAC
191059 ATGGGGTGGT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.33, C:0.33, G:0.10, T:0.24
Consensus pattern (18 bp):
CATCACTAACTATCGGAC
Found at i:191305 original size:24 final size:24
Alignment explanation
Indices: 191278--191346 Score: 111
Period size: 24 Copynumber: 2.9 Consensus size: 24
191268 AATCTTTTAG
*
191278 TTAAACTCTGTTTAATTGTTTCAA
1 TTAAACTCTGTTTATTTGTTTCAA
*
191302 TTAAACTCTATTTATTTGTTTCAA
1 TTAAACTCTGTTTATTTGTTTCAA
*
191326 TTAAATTCTGTTTATTTGTTT
1 TTAAACTCTGTTTATTTGTTT
191347 GAGTCAAACT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 41 1.00
ACGTcount: A:0.26, C:0.10, G:0.07, T:0.57
Consensus pattern (24 bp):
TTAAACTCTGTTTATTTGTTTCAA
Found at i:193344 original size:24 final size:24
Alignment explanation
Indices: 193293--193347 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 24
193283 TCTTTAAGTT
*
193293 AAACTCTATTTATCTGTTTCAATT
1 AAACTCTATTTATCTGTTTCAATC
* * * *
193317 AAACTCTGTTTATTTGTTTGAGTC
1 AAACTCTATTTATCTGTTTCAATC
193341 AAACTCT
1 AAACTCT
193348 TATTAGTCTA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.27, C:0.16, G:0.09, T:0.47
Consensus pattern (24 bp):
AAACTCTATTTATCTGTTTCAATC
Found at i:194670 original size:3 final size:3
Alignment explanation
Indices: 194662--194687 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
194652 ATATTTTTTA
194662 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
194688 ATTTTTATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:203023 original size:28 final size:28
Alignment explanation
Indices: 202952--203023 Score: 74
Period size: 28 Copynumber: 2.5 Consensus size: 28
202942 CACAGTCAAA
* **
202952 ATTCTGATTCTGGCTCGAAAAAAGTGAT
1 ATTCTGACTCTGGCTCGAAAAAAGCAAT
* *
202980 ATTCTAACTCTGGGCTCG-AAAGAGCAAT
1 ATTCTGACTCT-GGCTCGAAAAAAGCAAT
203008 ATTCTGGACTCTGGCT
1 ATTCT-GACTCTGGCT
203024 TTAAAGAAGT
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
28 25 0.69
29 11 0.31
ACGTcount: A:0.28, C:0.19, G:0.22, T:0.31
Consensus pattern (28 bp):
ATTCTGACTCTGGCTCGAAAAAAGCAAT
Found at i:211400 original size:22 final size:22
Alignment explanation
Indices: 211375--211439 Score: 69
Period size: 22 Copynumber: 3.0 Consensus size: 22
211365 AGCACCGTAA
211375 TGTTAAACAAAGAGCATAGAAG
1 TGTTAAACAAAGAGCATAGAAG
* * *
211397 TGTTAAGCAAAGAGAACCA-AAG
1 TGTTAAACAAAGAGCA-TAGAAG
* *
211419 TGTTGAACAGAGAGCATAGAA
1 TGTTAAACAAAGAGCATAGAA
211440 TTGCTGAATG
Statistics
Matches: 33, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
21 1 0.03
22 31 0.94
23 1 0.03
ACGTcount: A:0.48, C:0.11, G:0.25, T:0.17
Consensus pattern (22 bp):
TGTTAAACAAAGAGCATAGAAG
Found at i:215471 original size:23 final size:23
Alignment explanation
Indices: 215429--215475 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
215419 ATCTTTAATG
*
215429 TTTATTTGTTTCAATTAAACTCT
1 TTTATTTGTTTCAATCAAACTCT
* *
215452 TTTATTTGTTTGAGTCAAACTCT
1 TTTATTTGTTTCAATCAAACTCT
215475 T
1 T
215476 ATTAGTCTAG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.23, C:0.13, G:0.09, T:0.55
Consensus pattern (23 bp):
TTTATTTGTTTCAATCAAACTCT
Found at i:217718 original size:2 final size:2
Alignment explanation
Indices: 217713--217738 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
217703 TCACTTGGAC
217713 CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA
217739 TATATACTAA
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:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:222448 original size:20 final size:20
Alignment explanation
Indices: 222423--222464 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
222413 TTTTGCACTA
222423 ACTTATTGTTCACATAAAGT
1 ACTTATTGTTCACATAAAGT
222443 ACTTATTGTTCACATAAAGT
1 ACTTATTGTTCACATAAAGT
222463 AC
1 AC
222465 CTTTAATTGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.36, C:0.17, G:0.10, T:0.38
Consensus pattern (20 bp):
ACTTATTGTTCACATAAAGT
Found at i:222817 original size:17 final size:17
Alignment explanation
Indices: 222795--222828 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
222785 AACAACATGC
222795 ATATATAATATATAAGT
1 ATATATAATATATAAGT
222812 ATATATAATATATAAGT
1 ATATATAATATATAAGT
222829 GTAGTCTTAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.41
Consensus pattern (17 bp):
ATATATAATATATAAGT
Found at i:224817 original size:58 final size:58
Alignment explanation
Indices: 224694--225120 Score: 291
Period size: 59 Copynumber: 7.3 Consensus size: 58
224684 TAAGCATTGG
* * * ***
224694 GGGT-AAAATGGTAATTTT-TATAAAATCGAGGT-AAAAATAGAGTTTTTGG-AGATCCCA
1 GGGTAAAAAT-GTAATTTTGGA-AAAATCGAGGTCAAAAATGGAATTTTTGGAAG-TTTGA
* * *
224751 GGGT-AAAATGATAATTTTGGAGAAATCGAGGTCAAGAATGGAATTTTTGGAAGTTTGG
1 GGGTAAAAATG-TAATTTTGGAAAAATCGAGGTCAAAAATGGAATTTTTGGAAGTTTGA
* *** * *
224809 GGGTAAAATTGT-ATGTTTGGAAGTTTCGAGGTCAAAAATGGAATTTTTGAAAGTTCG-
1 GGGTAAAAATGTAAT-TTTGGAAAAATCGAGGTCAAAAATGGAATTTTTGGAAGTTTGA
* * *
224866 GGGTAAAAATGTAATTTTTGGAAAAATTTGA-GTCAAAAATGGAATTTTGGGGAAGTTAGA
1 GGGTAAAAATGTAA-TTTTGGAAAAA-TCGAGGTCAAAAATGGAATTTT-TGGAAGTTTGA
** ** *
224926 GGGTCGAAATGTAATTTTTGGAAAAATCGATATCAAAAATGGAA-TTTTGGAAAGTTTAA
1 GGGTAAAAATGTAA-TTTTGGAAAAATCGAGGTCAAAAATGGAATTTTTGG-AAGTTTGA
* ** ** * * *
224985 GGGTAAAAATGTAATTTTTGGGAAGTTTAAGGTTAAAAATGGAA-TTTTGGAAATTTTA
1 GGGTAAAAATGTAA-TTTTGGAAAAATCGAGGTCAAAAATGGAATTTTTGGAAGTTTGA
* * ** * * **
225043 GGGGTAAAAATGTAATTTTTTGCAAGTTTG-GAGTCAAAAATGGAAATTTTAAAAGTTTGA
1 -GGGTAAAAATGTAA-TTTTGGAAAAATCGAG-GTCAAAAATGGAATTTTTGGAAGTTTGA
*
225103 GGGTAAAAATGTTATTTT
1 GGGTAAAAATGTAATTTT
225121 CAAAAATTTT
Statistics
Matches: 301, Mismatches: 53, Indels: 31
0.78 0.14 0.08
Matches are distributed among these distances:
56 1 0.00
57 39 0.13
58 94 0.31
59 121 0.40
60 46 0.15
ACGTcount: A:0.37, C:0.04, G:0.25, T:0.34
Consensus pattern (58 bp):
GGGTAAAAATGTAATTTTGGAAAAATCGAGGTCAAAAATGGAATTTTTGGAAGTTTGA
Found at i:224863 original size:30 final size:29
Alignment explanation
Indices: 224778--225113 Score: 186
Period size: 30 Copynumber: 11.4 Consensus size: 29
224768 TGGAGAAATC
* *
224778 GAGGTCAAGAATGGAATTTTTGGAAGTTT
1 GAGGTCAAAAATGGAATTTTTGAAAGTTT
* * * * *
224807 GGGGGT--AAAATTGTATGTTTGGAAGTTT
1 -GAGGTCAAAAATGGAATTTTTGAAAGTTT
*
224835 CGAGGTCAAAAATGGAATTTTTGAAAGTTC
1 -GAGGTCAAAAATGGAATTTTTGAAAGTTT
* * *
224865 GGGGT-AAAAATGTAATTTTTGGAAAAATTT
1 GAGGTCAAAAATGGAATTTTT-G-AAAGTTT
* * *
224895 GA-GTCAAAAATGGAATTTTGGGGAAGTTA
1 GAGGTCAAAAATGGAATTTT-TGAAAGTTT
* * ** *
224924 GAGGGTC-GAAATGTAATTTTTGGAAAAATC
1 GA-GGTCAAAAATGGAATTTTT-GAAAGTTT
** *
224954 GATATCAAAAATGGAATTTTGGAAAGTTT
1 GAGGTCAAAAATGGAATTTTTGAAAGTTT
* * *
224983 AAGGGT-AAAAATGTAATTTTTGGGAAGTTT
1 GA-GGTCAAAAATGGAATTTTT-GAAAGTTT
* * * *
225013 AAGGTTAAAAATGGAATTTTGGAAATTTT
1 GAGGTCAAAAATGGAATTTTTGAAAGTTT
* * *
225042 AGGGGT-AAAAATGTAATTTTTTGCAAGTTT
1 -GAGGTCAAAAATGGAA-TTTTTGAAAGTTT
* *
225072 G-GAGTCAAAAATGGAAATTTTAAAAGTTT
1 GAG-GTCAAAAATGGAATTTTTGAAAGTTT
225101 GAGGGT-AAAAATG
1 GA-GGTCAAAAATG
225114 TTATTTTCAA
Statistics
Matches: 230, Mismatches: 57, Indels: 39
0.71 0.17 0.12
Matches are distributed among these distances:
28 37 0.16
29 73 0.32
30 116 0.50
31 4 0.02
ACGTcount: A:0.37, C:0.03, G:0.26, T:0.34
Consensus pattern (29 bp):
GAGGTCAAAAATGGAATTTTTGAAAGTTT
Found at i:225023 original size:59 final size:59
Alignment explanation
Indices: 224779--225194 Score: 328
Period size: 59 Copynumber: 7.1 Consensus size: 59
224769 GGAGAAATCG
* * * * *
224779 AGGTCAAGAATGGAATTTTTGG-AAGTTTGGGGGTAAAATTGT-ATGTTTGG-AAGTTTCG
1 AGGTCAAAAATGGAA-TTTTGGAAAGTTTAGGGGTAAAAATGTAATTTTTGGAAAGTTT-A
* * * *
224837 AGGTCAAAAATGGAATTTTTGAAAG-TTCGGGGTAAAAATGTAATTTTTGGAAAAATTTG
1 AGGTCAAAAATGGAATTTTGGAAAGTTTAGGGGTAAAAATGTAATTTTTGG-AAAGTTTA
* ** ** **
224896 A-GTCAAAAATGGAATTTTGGGGAAG-TTAGAGGGTCGAAATGTAATTTTTGGAAAAATCG
1 AGGTCAAAAATGGAATTTT-GGAAAGTTTAG-GGGTAAAAATGTAATTTTTGGAAAGTTTA
** * *
224955 ATATCAAAAATGGAATTTTGGAAAGTTTAAGGGTAAAAATGTAATTTTTGGGAAGTTTA
1 AGGTCAAAAATGGAATTTTGGAAAGTTTAGGGGTAAAAATGTAATTTTTGGAAAGTTTA
* * * *
225014 AGGTTAAAAATGGAATTTTGGAAATTTTAGGGGTAAAAATGTAATTTTTTGCAAGTTT-
1 AGGTCAAAAATGGAATTTTGGAAAGTTTAGGGGTAAAAATGTAATTTTTGGAAAGTTTA
* * * *** *
225072 GGAGTCAAAAATGGAAATTTT-AAAAGTTT-GAGGGTAAAAATGTTATTTTCAAAAATTTTA
1 AG-GTCAAAAATGG-AATTTTGGAAAGTTTAG-GGGTAAAAATGTAATTTTTGGAAAGTTTA
* ** * * ** * *
225132 AGGTTAAAAATATAATTTTAGGGAAGTTTGGGGGTCGAAATATAATTTTTGGACAGTTTA
1 AGGTCAAAAATGGAATTTT-GGAAAGTTTAGGGGTAAAAATGTAATTTTTGGAAAGTTTA
225192 AGG
1 AGG
225195 ACCTCCAGGG
Statistics
Matches: 288, Mismatches: 55, Indels: 28
0.78 0.15 0.08
Matches are distributed among these distances:
57 19 0.07
58 49 0.17
59 140 0.49
60 79 0.27
61 1 0.00
ACGTcount: A:0.37, C:0.03, G:0.25, T:0.35
Consensus pattern (59 bp):
AGGTCAAAAATGGAATTTTGGAAAGTTTAGGGGTAAAAATGTAATTTTTGGAAAGTTTA
Found at i:229140 original size:22 final size:22
Alignment explanation
Indices: 229115--229200 Score: 68
Period size: 22 Copynumber: 3.9 Consensus size: 22
229105 CAATAGTAGA
229115 CACACAAAATGCT-AATCAGAAG
1 CACACAAAATGCTGAA-CAGAAG
* *
229137 CACACATAGTGCTGAACAGAAG
1 CACACAAAATGCTGAACAGAAG
* * *
229159 CACACATAGTGCTGAA-AGAGGG
1 CACACAAAATGCTGAACAGA-AG
* * *
229181 CGCACATAGTGCTGAACAGA
1 CACACAAAATGCTGAACAGA
229201 GGGCACGAAA
Statistics
Matches: 57, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
21 3 0.05
22 49 0.86
23 5 0.09
ACGTcount: A:0.41, C:0.22, G:0.23, T:0.14
Consensus pattern (22 bp):
CACACAAAATGCTGAACAGAAG
Found at i:229215 original size:23 final size:23
Alignment explanation
Indices: 229136--229227 Score: 118
Period size: 22 Copynumber: 4.1 Consensus size: 23
229126 CTAATCAGAA
*
229136 GCACACATAGTGCTGAACAGA-A
1 GCACACATAGTGCTGAACAGAGG
229158 GCACACATAGTGCTGAA-AGAGG
1 GCACACATAGTGCTGAACAGAGG
*
229180 GCGCACATAGTGCTGAACAGAGG
1 GCACACATAGTGCTGAACAGAGG
* *
229203 GCACGAAAT-GTGCTAAACAGAGG
1 GCAC-ACATAGTGCTGAACAGAGG
229226 GC
1 GC
229228 GCTAGTGTTC
Statistics
Matches: 62, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
21 3 0.05
22 33 0.53
23 23 0.37
24 3 0.05
ACGTcount: A:0.36, C:0.21, G:0.30, T:0.13
Consensus pattern (23 bp):
GCACACATAGTGCTGAACAGAGG
Found at i:235444 original size:22 final size:22
Alignment explanation
Indices: 235419--235465 Score: 78
Period size: 22 Copynumber: 2.1 Consensus size: 22
235409 AGCACTAATC
235419 AGAAGCACACACAGTGCTA-AAT
1 AGAAGCACACACAGTGC-AGAAT
235441 AGAAGCACACACAGTGCAGAAT
1 AGAAGCACACACAGTGCAGAAT
235463 AGA
1 AGA
235466 GGGCACGAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 1 0.04
22 23 0.96
ACGTcount: A:0.47, C:0.21, G:0.21, T:0.11
Consensus pattern (22 bp):
AGAAGCACACACAGTGCAGAAT
Found at i:240741 original size:87 final size:87
Alignment explanation
Indices: 240645--240812 Score: 264
Period size: 87 Copynumber: 1.9 Consensus size: 87
240635 ACTTTCGACA
* * *
240645 TCGGACCTTTCATCTCGACCATCATAGGCCCAATTTAATAACTCACGATGCCATAGAAAATCCGC
1 TCGGACCTTTAATCTCAACCATCATAGGCCCAATTTAATAACTCACGATGCCATAAAAAATCCGC
240710 AACAAATGCAGGATTTCCATCT
66 AACAAATGCAGGATTTCCATCT
* * * *
240732 TCGGACCTTTAATCTCAACCGTCATAGGCCCATTTTGATAACTCACGATGTCATAAAAAATCCGC
1 TCGGACCTTTAATCTCAACCATCATAGGCCCAATTTAATAACTCACGATGCCATAAAAAATCCGC
*
240797 AACAAATGTAGGATTT
66 AACAAATGCAGGATTT
240813 TTGTCATGGG
Statistics
Matches: 73, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
87 73 1.00
ACGTcount: A:0.33, C:0.26, G:0.14, T:0.27
Consensus pattern (87 bp):
TCGGACCTTTAATCTCAACCATCATAGGCCCAATTTAATAACTCACGATGCCATAAAAAATCCGC
AACAAATGCAGGATTTCCATCT
Found at i:241731 original size:2 final size:2
Alignment explanation
Indices: 241724--241754 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
241714 ATTCTATTTC
241724 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
241755 CTTAATGGCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:247168 original size:22 final size:22
Alignment explanation
Indices: 247140--247184 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
247130 ATTTAAGAAC
247140 TTAGAATCAAACTCTTGCATAT
1 TTAGAATCAAACTCTTGCATAT
247162 TTAGAATCAAACTCTTGCATAT
1 TTAGAATCAAACTCTTGCATAT
247184 T
1 T
247185 CTTCACCTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.36, C:0.18, G:0.09, T:0.38
Consensus pattern (22 bp):
TTAGAATCAAACTCTTGCATAT
Found at i:254352 original size:43 final size:43
Alignment explanation
Indices: 254291--254374 Score: 168
Period size: 43 Copynumber: 2.0 Consensus size: 43
254281 CAACAAACGA
254291 GATTCATTTATATTTTGTTTTGCTCAGCCAAAACATTTTACGG
1 GATTCATTTATATTTTGTTTTGCTCAGCCAAAACATTTTACGG
254334 GATTCATTTATATTTTGTTTTGCTCAGCCAAAACATTTTAC
1 GATTCATTTATATTTTGTTTTGCTCAGCCAAAACATTTTAC
254375 TATGAGATAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 41 1.00
ACGTcount: A:0.26, C:0.17, G:0.12, T:0.45
Consensus pattern (43 bp):
GATTCATTTATATTTTGTTTTGCTCAGCCAAAACATTTTACGG
Found at i:259527 original size:23 final size:22
Alignment explanation
Indices: 259436--259516 Score: 103
Period size: 22 Copynumber: 3.7 Consensus size: 22
259426 TATATTGTTG
* *
259436 TTTTGG-TGCTGTTTTTTATTA
1 TTTTGGTTGTTGTTTTTTACTA
* *
259457 TTTTGGTTGCTGTTTTTTGCTA
1 TTTTGGTTGTTGTTTTTTACTA
259479 TTTTGG-TGTTGTTTTTTTACTA
1 TTTTGGTTGTTG-TTTTTTACTA
259501 TTTTGGTTGTTGTTTT
1 TTTTGGTTGTTGTTTT
259517 GGTACTTTTT
Statistics
Matches: 53, Mismatches: 4, Indels: 5
0.85 0.06 0.08
Matches are distributed among these distances:
21 10 0.19
22 38 0.72
23 5 0.09
ACGTcount: A:0.06, C:0.05, G:0.21, T:0.68
Consensus pattern (22 bp):
TTTTGGTTGTTGTTTTTTACTA
Found at i:259535 original size:44 final size:44
Alignment explanation
Indices: 259447--259537 Score: 103
Period size: 44 Copynumber: 2.1 Consensus size: 44
259437 TTTGGTGCTG
* * * *
259447 TTTTTTATTATTTTGGTTGCTGTTTTTTGCTATTTTGGTGTTGT
1 TTTTTTACTATTTTGGTTGCTGTTTTGTACTATTTTGGTATTGT
* **
259491 TTTTTTACTATTTTGGTTGTTGTTTTGGTACT-TTTTTTTATTGT
1 TTTTTTACTATTTTGGTTGCTGTTTT-GTACTATTTTGGTATTGT
259535 TTT
1 TTT
259538 GATGCTGTTA
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
44 36 0.92
45 3 0.08
ACGTcount: A:0.08, C:0.04, G:0.18, T:0.70
Consensus pattern (44 bp):
TTTTTTACTATTTTGGTTGCTGTTTTGTACTATTTTGGTATTGT
Found at i:259582 original size:47 final size:46
Alignment explanation
Indices: 259499--259632 Score: 139
Period size: 44 Copynumber: 2.9 Consensus size: 46
259489 GTTTTTTTAC
* * * * *
259499 TATTTTGGTTGTTGTTTTGGTACTTTTTTTTATTGTTTTGATGCTGT
1 TATTTTTGTTGCTGTTTTGTTA-TTATTTTTGTTGTTTTGATGCTGT
259546 TATTTTTGTTGCTGCTTTTGTTATTATTTTTGTTG-TTT--TGCTGT
1 TATTTTTGTTGCTG-TTTTGTTATTATTTTTGTTGTTTTGATGCTGT
** * *
259590 TATTTTTGTTGCTGTTTTGATTGCTATTTTGGTTGTTTGGATG
1 TATTTTTGTTGCTGTTTTG-TTATTATTTTTGTTGTTTTGATG
259633 TTATTTTTAT
Statistics
Matches: 73, Mismatches: 9, Indels: 10
0.79 0.10 0.11
Matches are distributed among these distances:
43 5 0.07
44 32 0.44
45 2 0.03
46 3 0.04
47 24 0.33
48 7 0.10
ACGTcount: A:0.08, C:0.05, G:0.22, T:0.65
Consensus pattern (46 bp):
TATTTTTGTTGCTGTTTTGTTATTATTTTTGTTGTTTTGATGCTGT
Found at i:259590 original size:23 final size:22
Alignment explanation
Indices: 259507--259608 Score: 68
Period size: 23 Copynumber: 4.5 Consensus size: 22
259497 ACTATTTTGG
*
259507 TTGTTGTTTTG-G-TACTTTTTT
1 TTGTTGTTTTGTGTTA-TTATTT
* * *
259528 TTATTGTTTTGATGCTGTTATTT
1 TTGTTGTTTTG-TGTTATTATTT
259551 TTGTTGCTGCTTT-TGTTATTATTT
1 TTGTTG-T--TTTGTGTTATTATTT
259575 TTGTTGTTTTGCTGTTATT-TTT
1 TTGTTGTTTTG-TGTTATTATTT
*
259597 GTTGCTGTTTTG
1 -TTGTTGTTTTG
259609 ATTGCTATTT
Statistics
Matches: 65, Mismatches: 7, Indels: 16
0.74 0.08 0.18
Matches are distributed among these distances:
21 13 0.20
22 3 0.05
23 29 0.45
24 17 0.26
26 3 0.05
ACGTcount: A:0.07, C:0.06, G:0.20, T:0.68
Consensus pattern (22 bp):
TTGTTGTTTTGTGTTATTATTT
Found at i:259618 original size:44 final size:44
Alignment explanation
Indices: 259540--259640 Score: 141
Period size: 44 Copynumber: 2.3 Consensus size: 44
259530 ATTGTTTTGA
* *
259540 TGCTGTTATTTTTGTTGCTGCTTTTGTTATTATTTTTGTTGTTT
1 TGCTGTTATTTTTGTTGCTGCTTTTGTTACTATTTTGGTTGTTT
*
259584 TGCTGTTATTTTTGTTGCTG-TTTTGATTGCTATTTTGGTTGTTT
1 TGCTGTTATTTTTGTTGCTGCTTTTG-TTACTATTTTGGTTGTTT
* *
259628 GGATGTTATTTTT
1 TGCTGTTATTTTT
259641 ATGCGTTTTA
Statistics
Matches: 51, Mismatches: 5, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
43 5 0.10
44 46 0.90
ACGTcount: A:0.08, C:0.06, G:0.21, T:0.65
Consensus pattern (44 bp):
TGCTGTTATTTTTGTTGCTGCTTTTGTTACTATTTTGGTTGTTT
Found at i:261657 original size:30 final size:28
Alignment explanation
Indices: 261588--261657 Score: 77
Period size: 31 Copynumber: 2.4 Consensus size: 28
261578 AAGTTGTAGG
* *
261588 TTTAGTCTTTGTATTTTTATTTGATCAAT
1 TTTAGTC-TTGTATTTTTAGTTGATAAAT
*
261617 TTTAGTTCTTGTAATTTTTTAGTTGGTAAAT
1 TTTAG-TCTTGT-A-TTTTTAGTTGATAAAT
261648 TTTAGTCTTG
1 TTTAGTCTTG
261658 GCCCAACCAG
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
29 9 0.26
30 8 0.23
31 18 0.51
ACGTcount: A:0.20, C:0.06, G:0.14, T:0.60
Consensus pattern (28 bp):
TTTAGTCTTGTATTTTTAGTTGATAAAT
Found at i:262636 original size:14 final size:16
Alignment explanation
Indices: 262606--262642 Score: 51
Period size: 14 Copynumber: 2.4 Consensus size: 16
262596 AATAGAATGA
262606 AAATAAATCTATAATT
1 AAATAAATCTATAATT
262622 AAATAAAT-T-TAATT
1 AAATAAATCTATAATT
*
262636 AATTAAA
1 AAATAAA
262643 AATTTTAAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 11 0.55
15 1 0.05
16 8 0.40
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (16 bp):
AAATAAATCTATAATT
Found at i:266952 original size:23 final size:23
Alignment explanation
Indices: 266899--266968 Score: 104
Period size: 23 Copynumber: 3.0 Consensus size: 23
266889 TCATTAACAT
* *
266899 TGTTCGTGAACGTGTTCAATTATA
1 TGTTCGTGAACATGTTCGATTA-A
*
266923 TGTTCGTGAACATGTTTGATTAA
1 TGTTCGTGAACATGTTCGATTAA
266946 TGTTCGTGAACATGTTCGATTAA
1 TGTTCGTGAACATGTTCGATTAA
266969 GTTAAATGAA
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
23 23 0.55
24 19 0.45
ACGTcount: A:0.26, C:0.11, G:0.21, T:0.41
Consensus pattern (23 bp):
TGTTCGTGAACATGTTCGATTAA
Found at i:266978 original size:23 final size:23
Alignment explanation
Indices: 266905--266986 Score: 67
Period size: 23 Copynumber: 3.5 Consensus size: 23
266895 ACATTGTTCG
* * **
266905 TGAACGTGTTCAATTATATGTTCG
1 TGAACATGTTCGATTA-ATGTTAA
* **
266929 TGAACATGTTTGATTAATGTTCG
1 TGAACATGTTCGATTAATGTTAA
266952 TGAACATGTTCGATTAA-GTTAAA
1 TGAACATGTTCGATTAATGTT-AA
*
266975 TGAATATGTTCG
1 TGAACATGTTCG
266987 TGAACATTAA
Statistics
Matches: 50, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
22 3 0.06
23 34 0.68
24 13 0.26
ACGTcount: A:0.29, C:0.10, G:0.21, T:0.40
Consensus pattern (23 bp):
TGAACATGTTCGATTAATGTTAA
Found at i:267432 original size:3 final size:3
Alignment explanation
Indices: 267424--267468 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
267414 TTTAAAATTA
267424 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
267469 GCTCAATCAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:270595 original size:23 final size:23
Alignment explanation
Indices: 270536--270711 Score: 127
Period size: 23 Copynumber: 7.8 Consensus size: 23
270526 AAGAGTACCG
* *
270536 AAGTACTAAACAGAGAGCACA-T
1 AAGTGCTAAACAGAGAGCACACA
*
270558 AAGTGCTGGGTAACAGAGAGCACACA
1 AAGTGCT---AAACAGAGAGCACACA
*
270584 AAGTGCTAAACAGAGAGTACACA
1 AAGTGCTAAACAGAGAGCACACA
*
270607 AA--G-T--AC--TGAGCACACA
1 AAGTGCTAAACAGAGAGCACACA
* * *
270623 AAGTGTTAATCAGAGAGCACACG
1 AAGTGCTAAACAGAGAGCACACA
270646 AAGTGCTAATAACAGAGAGCACA-A
1 AAGTGCT-A-AACAGAGAGCACACA
* *
270670 GACGTGCTAAACAGAGAGCACATA
1 -AAGTGCTAAACAGAGAGCACACA
* *
270694 CAGTGCTAATCAGAGAGC
1 AAGTGCTAAACAGAGAGC
270712 GCGCTAGTGT
Statistics
Matches: 122, Mismatches: 17, Indels: 29
0.73 0.10 0.17
Matches are distributed among these distances:
16 10 0.08
18 3 0.02
19 1 0.01
20 1 0.01
21 2 0.02
22 6 0.05
23 58 0.48
24 3 0.02
25 31 0.25
26 7 0.06
ACGTcount: A:0.43, C:0.19, G:0.24, T:0.14
Consensus pattern (23 bp):
AAGTGCTAAACAGAGAGCACACA
Found at i:270637 original size:39 final size:39
Alignment explanation
Indices: 270575--270649 Score: 114
Period size: 39 Copynumber: 1.9 Consensus size: 39
270565 GGGTAACAGA
*
270575 GAGCACACAAAGTGCTAAACAGAGAGTACACAAAGTACT
1 GAGCACACAAAGTGCTAAACAGAGAGCACACAAAGTACT
* * *
270614 GAGCACACAAAGTGTTAATCAGAGAGCACACGAAGT
1 GAGCACACAAAGTGCTAAACAGAGAGCACACAAAGT
270650 GCTAATAACA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 32 1.00
ACGTcount: A:0.44, C:0.20, G:0.23, T:0.13
Consensus pattern (39 bp):
GAGCACACAAAGTGCTAAACAGAGAGCACACAAAGTACT
Done.