Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014379.1 Kokia drynarioides strain JFW-HI SEQ_129417, 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: 260798
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.34
Warning! 106 characters in sequence are not A, C, G, or T
Found at i:12341 original size:20 final size:21
Alignment explanation
Indices: 12316--12355 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
12306 TTTTTCATAT
*
12316 ATTTTTATTGAAAAT-TTTAA
1 ATTTTTATTAAAAATGTTTAA
*
12336 ATTTTTTTTAAAAATGTTTA
1 ATTTTTATTAAAAATGTTTA
12356 TATATATATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (21 bp):
ATTTTTATTAAAAATGTTTAA
Found at i:14330 original size:20 final size:20
Alignment explanation
Indices: 14305--14360 Score: 69
Period size: 20 Copynumber: 2.8 Consensus size: 20
14295 TCAAATATTC
14305 TACAATCGATTTAAATCTA-T
1 TACAATCGATTTAAATC-AGT
* * *
14325 TTCAATCGACTTCAATCAGT
1 TACAATCGATTTAAATCAGT
14345 TACAATCGATTTAAAT
1 TACAATCGATTTAAAT
14361 TTGCTACAAC
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
19 1 0.03
20 28 0.97
ACGTcount: A:0.38, C:0.18, G:0.07, T:0.38
Consensus pattern (20 bp):
TACAATCGATTTAAATCAGT
Found at i:14368 original size:20 final size:20
Alignment explanation
Indices: 14290--14379 Score: 65
Period size: 20 Copynumber: 4.5 Consensus size: 20
14280 ACTGTTTCAC
* * *
14290 TCGATTCAAATATTCTACAA
1 TCGATTTAAATCTGCTACAA
** *
14310 TCGATTTAAATCTATTTCAA
1 TCGATTTAAATCTGCTACAA
* * * *
14330 TCGACTTCAATCAGTTACAA
1 TCGATTTAAATCTGCTACAA
*
14350 TCGATTTAAATTTGCTACAA
1 TCGATTTAAATCTGCTACAA
14370 -CAGATTTAAA
1 TC-GATTTAAA
14380 CATGTTTTAT
Statistics
Matches: 54, Mismatches: 15, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
19 1 0.02
20 53 0.98
ACGTcount: A:0.38, C:0.18, G:0.08, T:0.37
Consensus pattern (20 bp):
TCGATTTAAATCTGCTACAA
Found at i:16498 original size:42 final size:42
Alignment explanation
Indices: 16439--16537 Score: 135
Period size: 42 Copynumber: 2.4 Consensus size: 42
16429 GAGGGTTGTT
*
16439 ACTTTTTGTATGTGTAATTGAGTGCGGTGATGAACTAATATC
1 ACTTTTTGTATGTGTAATTGAGTGCGGTGATGAACTAATATA
* * * * * *
16481 ACTTTTTGTACGTGTAATTGGGTGTGGTGGTGGAGTAATATA
1 ACTTTTTGTATGTGTAATTGAGTGCGGTGATGAACTAATATA
16523 ACTTTTTGTATGTGT
1 ACTTTTTGTATGTGT
16538 GTAATCGAGT
Statistics
Matches: 49, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 49 1.00
ACGTcount: A:0.22, C:0.07, G:0.27, T:0.43
Consensus pattern (42 bp):
ACTTTTTGTATGTGTAATTGAGTGCGGTGATGAACTAATATA
Found at i:22686 original size:33 final size:33
Alignment explanation
Indices: 22635--22698 Score: 101
Period size: 33 Copynumber: 1.9 Consensus size: 33
22625 AACATTTTGT
* *
22635 TCAGTTCTTGTTCGTTTATCAAATTAAATAAGA
1 TCAGTTCTTATTCATTTATCAAATTAAATAAGA
*
22668 TCAGTTTTTATTCATTTATCAAATTAAATAA
1 TCAGTTCTTATTCATTTATCAAATTAAATAA
22699 ATGAATATTA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.36, C:0.11, G:0.08, T:0.45
Consensus pattern (33 bp):
TCAGTTCTTATTCATTTATCAAATTAAATAAGA
Found at i:22815 original size:14 final size:14
Alignment explanation
Indices: 22798--22829 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
22788 CTATTGCTCA
22798 ATTACTATAATATT
1 ATTACTATAATATT
22812 ATTACTATAATATT
1 ATTACTATAATATT
22826 ATTA
1 ATTA
22830 TTGTTGGTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (14 bp):
ATTACTATAATATT
Found at i:33742 original size:39 final size:40
Alignment explanation
Indices: 33689--33784 Score: 131
Period size: 39 Copynumber: 2.4 Consensus size: 40
33679 TTTAAAAAAA
* *
33689 AAAAGGAAAACTTATGATTCAATAAAGCATAAAAGTGATT
1 AAAAGGAAGACTTATGACTCAATAAAGCATAAAAGTGATT
* * * *
33729 TAAAGG-AGACTTATGACTCAGTAGAGCATAAGAGTGATT
1 AAAAGGAAGACTTATGACTCAATAAAGCATAAAAGTGATT
33768 AAAAGGAAGACTTATGA
1 AAAAGGAAGACTTATGA
33785 ACCTATGAAG
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
39 33 0.69
40 15 0.31
ACGTcount: A:0.47, C:0.08, G:0.21, T:0.24
Consensus pattern (40 bp):
AAAAGGAAGACTTATGACTCAATAAAGCATAAAAGTGATT
Found at i:48985 original size:41 final size:41
Alignment explanation
Indices: 48887--48987 Score: 157
Period size: 41 Copynumber: 2.5 Consensus size: 41
48877 TCGATATTTA
*
48887 AAAGGAAGACTCATGTATCGAGATGAGAATGAGATCATATT
1 AAAGGAAGACTCATGTCTCGAGATGAGAATGAGATCATATT
* * *
48928 AAAGGAAGACCCATGTCTCGGGATGAGAATGAGATTATATT
1 AAAGGAAGACTCATGTCTCGAGATGAGAATGAGATCATATT
*
48969 AAAGAAAGACTCATGTCTC
1 AAAGGAAGACTCATGTCTC
48988 AAAATTTGCA
Statistics
Matches: 54, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 54 1.00
ACGTcount: A:0.40, C:0.13, G:0.24, T:0.24
Consensus pattern (41 bp):
AAAGGAAGACTCATGTCTCGAGATGAGAATGAGATCATATT
Found at i:50644 original size:29 final size:29
Alignment explanation
Indices: 50602--50660 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
50592 TCCTTTTTAC
*
50602 ATAGTCTTAAACAATGAAGAAGAAAGAAA
1 ATAGTATTAAACAATGAAGAAGAAAGAAA
50631 ATAGTATTAAACAATGAAGAAGAAAGAAA
1 ATAGTATTAAACAATGAAGAAGAAAGAAA
50660 A
1 A
50661 CAACAAAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.61, C:0.05, G:0.17, T:0.17
Consensus pattern (29 bp):
ATAGTATTAAACAATGAAGAAGAAAGAAA
Found at i:50698 original size:24 final size:27
Alignment explanation
Indices: 50671--50729 Score: 88
Period size: 24 Copynumber: 2.3 Consensus size: 27
50661 CAACAAAAAT
50671 AAAATCTAATCT-AAAA-GAAAAG-AG
1 AAAATCTAATCTAAAAATGAAAAGAAG
*
50695 AAAATATAATCTAAAAATGAAAAGAAG
1 AAAATCTAATCTAAAAATGAAAAGAAG
50722 AAAATCTA
1 AAAATCTA
50730 GCCCTAAAAC
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
24 11 0.37
25 4 0.13
26 6 0.20
27 9 0.30
ACGTcount: A:0.64, C:0.07, G:0.10, T:0.19
Consensus pattern (27 bp):
AAAATCTAATCTAAAAATGAAAAGAAG
Found at i:51354 original size:24 final size:24
Alignment explanation
Indices: 51326--51400 Score: 105
Period size: 24 Copynumber: 3.1 Consensus size: 24
51316 AGAAATAATC
*
51326 TTTCAGTTAAACTCTGTTTATTTG
1 TTTCAATTAAACTCTGTTTATTTG
* *
51350 TTTCAATTAAATTATGTTTATTTG
1 TTTCAATTAAACTCTGTTTATTTG
* *
51374 TTTCAATTAAACTTTGTATATTTG
1 TTTCAATTAAACTCTGTTTATTTG
51398 TTT
1 TTT
51401 GAGTCAAACT
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 45 1.00
ACGTcount: A:0.25, C:0.08, G:0.09, T:0.57
Consensus pattern (24 bp):
TTTCAATTAAACTCTGTTTATTTG
Found at i:54317 original size:20 final size:20
Alignment explanation
Indices: 54281--54318 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
54271 TTTTTAAGTT
*
54281 TTATATTTTATATATTTTTA
1 TTATATTTTATAAATTTTTA
54301 TTATATTTT-TAAAATTTT
1 TTATATTTTAT-AAATTTT
54319 CAAATGATGA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 1 0.06
20 15 0.94
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (20 bp):
TTATATTTTATAAATTTTTA
Found at i:55254 original size:22 final size:22
Alignment explanation
Indices: 55227--55280 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
55217 TAAATTAAAT
55227 TTTTATAATAGTAAAAG-TATAA
1 TTTTATAAT-GTAAAAGTTATAA
* * *
55249 TTTTATCATTTAAAAGTTTATAT
1 TTTTATAATGTAAAAG-TTATAA
55272 TTTTATAAT
1 TTTTATAAT
55281 TTTTAAAGAA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
21 6 0.23
22 8 0.31
23 12 0.46
ACGTcount: A:0.41, C:0.02, G:0.06, T:0.52
Consensus pattern (22 bp):
TTTTATAATGTAAAAGTTATAA
Found at i:58927 original size:10 final size:11
Alignment explanation
Indices: 58896--58927 Score: 50
Period size: 10 Copynumber: 3.1 Consensus size: 11
58886 CCTTAAAAAT
58896 AGAGAGAGAG-
1 AGAGAGAGAGA
58906 AGAGAGAGAGA
1 AGAGAGAGAGA
58917 AG-GAGAGAGA
1 AGAGAGAGAGA
58927 A
1 A
58928 TATCAGAAGG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 19 0.90
11 2 0.10
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (11 bp):
AGAGAGAGAGA
Found at i:62608 original size:92 final size:92
Alignment explanation
Indices: 62443--62619 Score: 300
Period size: 92 Copynumber: 1.9 Consensus size: 92
62433 TTAAGTGTTC
* * *
62443 TTTGTTTTTGAGTTTTTCGAGGTTTAGTTTTTATCTCCATCTTTTGTACTCTTTGTTGTTTTTCC
1 TTTGGTTTTGAGTTTTTCGAGATTTAGTTTTTATCTCCATCTTTTGTACTCTTTGTTGTTTTGCC
62508 ATTATAGTAAAATTATCTTTTGTACTA
66 ATTATAGTAAAATTATCTTTTGTACTA
* *
62535 TTTGGTTTTGAGTTTTTCGAGATTTAGTTTTTATTTCCGTCTTTTGTACTCTTTGTTGTTTTGCC
1 TTTGGTTTTGAGTTTTTCGAGATTTAGTTTTTATCTCCATCTTTTGTACTCTTTGTTGTTTTGCC
*
62600 ATTGTAGTAAAATTATCTTT
66 ATTATAGTAAAATTATCTTT
62620 GCCTGTAATT
Statistics
Matches: 79, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
92 79 1.00
ACGTcount: A:0.16, C:0.11, G:0.15, T:0.58
Consensus pattern (92 bp):
TTTGGTTTTGAGTTTTTCGAGATTTAGTTTTTATCTCCATCTTTTGTACTCTTTGTTGTTTTGCC
ATTATAGTAAAATTATCTTTTGTACTA
Found at i:64825 original size:6 final size:6
Alignment explanation
Indices: 64814--64845 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
64804 TTTAAGTTTT
64814 TTCCCC TTCCCC TTCCCC TTCCCC TTCCCC TT
1 TTCCCC TTCCCC TTCCCC TTCCCC TTCCCC TT
64846 GAATGAAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.00, C:0.62, G:0.00, T:0.38
Consensus pattern (6 bp):
TTCCCC
Found at i:65875 original size:28 final size:29
Alignment explanation
Indices: 65799--65874 Score: 109
Period size: 29 Copynumber: 2.6 Consensus size: 29
65789 ATTGGAAAAT
*
65799 AAAATTATTTAATAATTTTATTATTTCAA
1 AAAATAATTTAATAATTTTATTATTTCAA
* *
65828 AAAATAATTTAAAAATTTTA-TATTTTAA
1 AAAATAATTTAATAATTTTATTATTTCAA
65856 AAAATAATTTTAATAATTT
1 AAAATAA-TTTAATAATTT
65875 AAAATAATTT
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
28 14 0.33
29 28 0.67
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (29 bp):
AAAATAATTTAATAATTTTATTATTTCAA
Found at i:65880 original size:19 final size:19
Alignment explanation
Indices: 65830--65884 Score: 62
Period size: 19 Copynumber: 2.9 Consensus size: 19
65820 TATTTCAAAA
65830 AATAATTT-AAA-AATTTT
1 AATAATTTAAAATAATTTT
*
65847 -ATATTTTAAAAAATAATTTT
1 AATAATTT--AAAATAATTTT
65867 AATAATTTAAAATAATTT
1 AATAATTTAAAATAATTT
65885 ACTGACATGA
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
16 6 0.19
19 13 0.42
20 6 0.19
21 6 0.19
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
AATAATTTAAAATAATTTT
Found at i:68648 original size:15 final size:14
Alignment explanation
Indices: 68624--68653 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
68614 TAACAGTATG
68624 TGGAGAACCATTTC
1 TGGAGAACCATTTC
68638 TGGATGAACCATTTC
1 TGGA-GAACCATTTC
68653 T
1 T
68654 CATGCGCACA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.27
15 11 0.73
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.33
Consensus pattern (14 bp):
TGGAGAACCATTTC
Found at i:69945 original size:25 final size:25
Alignment explanation
Indices: 69917--69966 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
69907 CTACACTTAT
* *
69917 CAGAGTTTAAGTGTAAAACTAAAAA
1 CAGAGTTTAAATGGAAAACTAAAAA
69942 CAGAGTTTAAATGGAAAACTAAAAA
1 CAGAGTTTAAATGGAAAACTAAAAA
69967 AAATGTAAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.54, C:0.08, G:0.16, T:0.22
Consensus pattern (25 bp):
CAGAGTTTAAATGGAAAACTAAAAA
Found at i:71310 original size:17 final size:16
Alignment explanation
Indices: 71271--71312 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 16
71261 GAAAATTTTA
*
71271 ACTTTTGCTCAAAAGT
1 ACTTTTGATCAAAAGT
71287 ACTTTTTGATCCAAAAGT
1 AC-TTTTGAT-CAAAAGT
71305 ACTTTTGA
1 ACTTTTGA
71313 GAAACAATGC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
16 2 0.09
17 12 0.52
18 9 0.39
ACGTcount: A:0.31, C:0.17, G:0.12, T:0.40
Consensus pattern (16 bp):
ACTTTTGATCAAAAGT
Found at i:74766 original size:6 final size:6
Alignment explanation
Indices: 74755--74779 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
74745 TTAAAATATG
74755 GGTCGA GGTCGA GGTCGA GGTCGA G
1 GGTCGA GGTCGA GGTCGA GGTCGA G
74780 CTTGAATATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.16, G:0.52, T:0.16
Consensus pattern (6 bp):
GGTCGA
Found at i:76627 original size:2 final size:2
Alignment explanation
Indices: 76622--76654 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
76612 ATTTTTTTTG
76622 TA TA 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 TA TA T
76655 TATTAATTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:77602 original size:24 final size:24
Alignment explanation
Indices: 77557--77602 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
77547 GTTTTTTAAA
*
77557 TTAATATTGTTAATAGTAGTTAGT
1 TTAATATTGTTAATAATAGTTAGT
77581 TTAATATTGTTAA-AATATGTTA
1 TTAATATTGTTAATAATA-GTTA
77603 TATTTTTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 3 0.15
24 17 0.85
ACGTcount: A:0.37, C:0.00, G:0.13, T:0.50
Consensus pattern (24 bp):
TTAATATTGTTAATAATAGTTAGT
Found at i:78877 original size:2 final size:2
Alignment explanation
Indices: 78870--78894 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
78860 CTATTTTGAG
78870 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
78895 TTGCATATTC
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:89883 original size:30 final size:30
Alignment explanation
Indices: 89826--89883 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
89816 TTTCACTTCT
* * *
89826 TTTGGAATTTTTCTCATTGTTAACCCTTTC
1 TTTGGAATTTTTCCCAGTCTTAACCCTTTC
*
89856 TTTGGAATTTTTCCCAGTCTTAGCCCTT
1 TTTGGAATTTTTCCCAGTCTTAACCCTT
89884 AGTGTTATAG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.16, C:0.22, G:0.12, T:0.50
Consensus pattern (30 bp):
TTTGGAATTTTTCCCAGTCTTAACCCTTTC
Found at i:97643 original size:33 final size:33
Alignment explanation
Indices: 97603--97666 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 33
97593 AAAATAAAAG
* *
97603 AAAACCACTTACCCTATTTTATATGAAATTCTA
1 AAAACCACCTACACTATTTTATATGAAATTCTA
* *
97636 AAAACCACCTATACTATTTTATATGGAATTC
1 AAAACCACCTACACTATTTTATATGAAATTC
97667 ATGCAAATAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.39, C:0.20, G:0.05, T:0.36
Consensus pattern (33 bp):
AAAACCACCTACACTATTTTATATGAAATTCTA
Found at i:101523 original size:3 final size:3
Alignment explanation
Indices: 101515--101580 Score: 51
Period size: 3 Copynumber: 21.0 Consensus size: 3
101505 TAAAAACAAT
* * * *
101515 TAA TAA TAA TAA CAA TAA TAA TAAA TAA TAG TAA TAAA TAA CAT TAA
1 TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA T-AA TAA TAA TAA
* *
101562 TAAA TAT TAA TAA AAA TAA
1 T-AA TAA TAA TAA TAA TAA
101581 AAAGGGAAAA
Statistics
Matches: 48, Mismatches: 12, Indels: 6
0.73 0.18 0.09
Matches are distributed among these distances:
3 39 0.81
4 9 0.19
ACGTcount: A:0.65, C:0.03, G:0.02, T:0.30
Consensus pattern (3 bp):
TAA
Found at i:101541 original size:16 final size:16
Alignment explanation
Indices: 101505--101564 Score: 58
Period size: 16 Copynumber: 4.0 Consensus size: 16
101495 TTGTTTATTT
101505 TAAA-AACAATTAATAA
1 TAAATAACAA-TAATAA
101521 T-AATAACAATAATAA
1 TAAATAACAATAATAA
*
101536 TAAAT---AATAGTAA
1 TAAATAACAATAATAA
*
101549 TAAATAACATTAATAA
1 TAAATAACAATAATAA
101565 ATATTAATAA
Statistics
Matches: 36, Mismatches: 3, Indels: 10
0.73 0.06 0.20
Matches are distributed among these distances:
13 12 0.33
15 9 0.25
16 15 0.42
ACGTcount: A:0.65, C:0.05, G:0.02, T:0.28
Consensus pattern (16 bp):
TAAATAACAATAATAA
Found at i:101549 original size:13 final size:13
Alignment explanation
Indices: 101515--101580 Score: 73
Period size: 13 Copynumber: 5.2 Consensus size: 13
101505 TAAAAACAAT
101515 TAATAATAAT-AA
1 TAATAATAATAAA
*
101527 CAATAATAATAAA
1 TAATAATAATAAA
*
101540 TAATAGTAATAAA
1 TAATAATAATAAA
* *
101553 TAACATTAATAAA
1 TAATAATAATAAA
*
101566 TATTAATAA-AAA
1 TAATAATAATAAA
101578 TAA
1 TAA
101581 AAAGGGAAAA
Statistics
Matches: 44, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
12 14 0.32
13 30 0.68
ACGTcount: A:0.65, C:0.03, G:0.02, T:0.30
Consensus pattern (13 bp):
TAATAATAATAAA
Found at i:102639 original size:30 final size:29
Alignment explanation
Indices: 102603--102910 Score: 291
Period size: 30 Copynumber: 10.3 Consensus size: 29
102593 CCCTGAATTA
*
102603 TCCAAAAATCATATTTTAACCACCAAACTT
1 TCCAAAAATTATATTTTAACC-CCAAACTT
102633 TCCAAAAATTATATTTTAACCCCTAAACTT
1 TCCAAAAATTATATTTTAACCCC-AAACTT
* *
102663 TCTAAAAATTATAATTTT-GCCTCCAAACTT
1 TCCAAAAATTAT-ATTTTAACC-CCAAACTT
* *
102693 TCCAAAAATTATATTTTGACCCCTAAATTT
1 TCCAAAAATTATATTTTAACCCC-AAACTT
* * * *
102723 TCTAAAAAATACATTTTAACCCTTAAACTT
1 TCCAAAAATTATATTTTAACCC-CAAACTT
* *
102753 TCTAAAAAATATATTTTAACCCCTAAACTT
1 TCCAAAAATTATATTTTAACCCC-AAACTT
* * *
102783 TCCAAAAATTACATTTT-ACCCCTATATTT
1 TCCAAAAATTATATTTTAACCCC-AAACTT
*
102812 TCCAAAAATTATATTTTTACCTCTCAAAC-T
1 TCCAAAAATTATATTTTAACC-C-CAAACTT
* * *
102842 TCACAAAAATTACATTTT-ACCTCGAACTT
1 TC-CAAAAATTATATTTTAACCCCAAACTT
* * *
102871 TCCAAAAATTATATTTTGACCCTTAAAATT
1 TCCAAAAATTATATTTTAACCC-CAAACTT
102901 TCCAAAAATT
1 TCCAAAAATT
102911 CCATTTTGAC
Statistics
Matches: 234, Mismatches: 30, Indels: 28
0.80 0.10 0.10
Matches are distributed among these distances:
28 18 0.08
29 41 0.18
30 150 0.64
31 24 0.10
32 1 0.00
ACGTcount: A:0.40, C:0.22, G:0.01, T:0.37
Consensus pattern (29 bp):
TCCAAAAATTATATTTTAACCCCAAACTT
Found at i:102699 original size:60 final size:58
Alignment explanation
Indices: 102603--102975 Score: 358
Period size: 60 Copynumber: 6.3 Consensus size: 58
102593 CCCTGAATTA
* *
102603 TCCAAAAATCATATTTTAACCACCAAACTTTCCAAAAATTATATTTTAACCCCTAAACTT
1 TCCAAAAATTACATTTT-ACC-CCAAACTTTCCAAAAATTATATTTTAACCCCTAAACTT
* * * * *
102663 TCTAAAAATTATAATTTTGCCTCCAAACTTTCCAAAAATTATATTTTGACCCCTAAATTT
1 TCCAAAAATTA-CATTTTACC-CCAAACTTTCCAAAAATTATATTTTAACCCCTAAACTT
* * * * *
102723 TCTAAAAAATACATTTTAACCCTTAAACTTTCTAAAAAATATATTTTAACCCCTAAACTT
1 TCCAAAAATTACATTTT-ACCC-CAAACTTTCCAAAAATTATATTTTAACCCCTAAACTT
* * * *
102783 TCCAAAAATTACATTTTACCCCTATATTTTCCAAAAATTATATTTTTACCTCTCAAAC-T
1 TCCAAAAATTACATTTTACCCC-AAACTTTCCAAAAATTATATTTTAACCCCT-AAACTT
* * * * *
102842 TCACAAAAATTACATTTTACCTCGAACTTTCCAAAAATTATATTTTGACCCTTAAAATT
1 TC-CAAAAATTACATTTTACCCCAAACTTTCCAAAAATTATATTTTAACCCCTAAACTT
* * * * *
102901 TCCAAAAATTCCATTTTGACCACGAAC-TTCTCAAAAATTACCATTTT-ACCCTTAAA-TT
1 TCCAAAAATTACATTTT-ACCCCAAACTTTC-CAAAAATTA-TATTTTAACCCCTAAACTT
* *
102959 TCTAAAAATTCCATTTT
1 TCCAAAAATTACATTTT
102976 TCCTCTGAGT
Statistics
Matches: 267, Mismatches: 36, Indels: 22
0.82 0.11 0.07
Matches are distributed among these distances:
58 38 0.14
59 90 0.34
60 134 0.50
61 5 0.02
ACGTcount: A:0.39, C:0.22, G:0.02, T:0.38
Consensus pattern (58 bp):
TCCAAAAATTACATTTTACCCCAAACTTTCCAAAAATTATATTTTAACCCCTAAACTT
Found at i:102756 original size:90 final size:89
Alignment explanation
Indices: 102603--102917 Score: 361
Period size: 90 Copynumber: 3.5 Consensus size: 89
102593 CCCTGAATTA
* * * * *
102603 TCCAAAAATCATATTTTAACCACC-AAACTTTCCAAAAATTATATTTTAACCCCTAAACTTTCTA
1 TCCAAAAATTATATTTTGACC-CCTAAATTTTCCAAAAATTACATTTTAACCCTTAAACTTTCTA
*
102667 AAAATTATAATTTTGCCTCCAAACTT
65 AAAATTAT-ATTTTACCTCCAAACTT
* *
102693 TCCAAAAATTATATTTTGACCCCTAAATTTTCTAAAAAATACATTTTAACCCTTAAACTTTCTAA
1 TCCAAAAATTATATTTTGACCCCTAAATTTTCCAAAAATTACATTTTAACCCTTAAACTTTCTAA
*
102758 AAAATATATTTTAACC-CCTAAACTT
66 AAATTATATTTT-ACCTCC-AAACTT
* * * * * *
102783 TCCAAAAATTACATTTT-ACCCCTATATTTTCCAAAAATTATATTTTTACCTCTCAAAC-TTCAC
1 TCCAAAAATTATATTTTGACCCCTAAATTTTCCAAAAATTACATTTTAACC-CTTAAACTTTC-T
* *
102846 AAAAATTACATTTTACCT-CGAACTT
64 AAAAATTATATTTTACCTCCAAACTT
* * *
102871 TCCAAAAATTATATTTTGACCCTTAAAATTTCCAAAAATTCCATTTT
1 TCCAAAAATTATATTTTGACCCCTAAATTTTCCAAAAATTACATTTT
102918 GACCACGAAC
Statistics
Matches: 192, Mismatches: 26, Indels: 15
0.82 0.11 0.06
Matches are distributed among these distances:
88 21 0.11
89 68 0.35
90 103 0.54
ACGTcount: A:0.39, C:0.22, G:0.01, T:0.38
Consensus pattern (89 bp):
TCCAAAAATTATATTTTGACCCCTAAATTTTCCAAAAATTACATTTTAACCCTTAAACTTTCTAA
AAATTATATTTTACCTCCAAACTT
Found at i:102917 original size:30 final size:29
Alignment explanation
Indices: 102631--102975 Score: 209
Period size: 30 Copynumber: 11.7 Consensus size: 29
102621 ACCACCAAAC
* * *
102631 TTTCCAAAAATTATATTTTAACCCCTAAAC
1 TTTCCAAAAATTACATTTT-ACCCTTAAAA
* * * * *
102661 TTTCTAAAAATTATAATTTT-GCCTCCAAAC
1 TTTCCAAAAATTA-CATTTTACCCT-TAAAA
* * *
102691 TTTCCAAAAATTATATTTTGACCCCTAAAT
1 TTTCCAAAAATTACATTTT-ACCCTTAAAA
* * *
102721 TTTCTAAAAAATACATTTTAACCCTTAAAC
1 TTTCCAAAAATTACATTTT-ACCCTTAAAA
* * * * *
102751 TTTCTAAAAAATATATTTTAACCCCTAAAC
1 TTTCCAAAAATTACATTTT-ACCCTTAAAA
* * *
102781 TTTCCAAAAATTACATTTTACCCCTATAT
1 TTTCCAAAAATTACATTTTACCCTTAAAA
* *
102810 TTTCCAAAAATTATATTTTTA-CCTCTCAAA
1 TTTCCAAAAATTACA-TTTTACCCT-TAAAA
* ** *
102840 CTTCACAAAAATTACATTTTA-CCTCGAAC
1 TTTC-CAAAAATTACATTTTACCCTTAAAA
*
102869 TTTCCAAAAATTATATTTTGACCCTTAAAA
1 TTTCCAAAAATTACATTTT-ACCCTTAAAA
* *
102899 TTTCCAAAAATTCCATTTTGA-CC--ACGAA
1 TTTCCAAAAATTACATTTT-ACCCTTA-AAA
*
102927 CTTCTCAAAAATTACCATTTTACCCTT-AAA
1 TTTC-CAAAAATTA-CATTTTACCCTTAAAA
* *
102957 TTTCTAAAAATTCCATTTT
1 TTTCCAAAAATTACATTTT
102976 TCCTCTGAGT
Statistics
Matches: 252, Mismatches: 48, Indels: 32
0.76 0.14 0.10
Matches are distributed among these distances:
27 1 0.00
28 25 0.10
29 55 0.22
30 154 0.61
31 17 0.07
ACGTcount: A:0.38, C:0.22, G:0.02, T:0.39
Consensus pattern (29 bp):
TTTCCAAAAATTACATTTTACCCTTAAAA
Found at i:108632 original size:12 final size:11
Alignment explanation
Indices: 108585--108632 Score: 55
Period size: 12 Copynumber: 4.3 Consensus size: 11
108575 TAAAATTATC
108585 ATTTTTTTAAA
1 ATTTTTTTAAA
108596 TATTTTTTTAAA
1 -ATTTTTTTAAA
108608 ATTATTTTT--A
1 ATT-TTTTTAAA
108618 ATTTTTTTATAA
1 ATTTTTTTA-AA
108630 ATT
1 ATT
108633 ACCAAATAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
9 5 0.16
10 4 0.12
11 3 0.09
12 20 0.62
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (11 bp):
ATTTTTTTAAA
Found at i:110581 original size:34 final size:34
Alignment explanation
Indices: 110537--110602 Score: 114
Period size: 34 Copynumber: 1.9 Consensus size: 34
110527 TTTGTACTAT
*
110537 AATACACAAAGCTGAATTTTAGTATTTGAACTGC
1 AATACACAAAGCTAAATTTTAGTATTTGAACTGC
*
110571 AATACCCAAAGCTAAATTTTAGTATTTGAACT
1 AATACACAAAGCTAAATTTTAGTATTTGAACT
110603 AGCAGCTAGG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.39, C:0.15, G:0.12, T:0.33
Consensus pattern (34 bp):
AATACACAAAGCTAAATTTTAGTATTTGAACTGC
Found at i:111692 original size:25 final size:25
Alignment explanation
Indices: 111664--111751 Score: 70
Period size: 29 Copynumber: 3.2 Consensus size: 25
111654 AAATATAAAC
111664 TATTAAAAAAATAAAATTACATTTT
1 TATTAAAAAAATAAAATTACATTTT
111689 TATTACCGTAAAAAATATACAATTTA-ATTTT
1 TATTA----AAAAAATA-A-AA-TTACATTTT
* *
111720 GACCTTAAAATAATAAAATTACATTTT
1 TA--TTAAAAAAATAAAATTACATTTT
111747 TATTA
1 TATTA
111752 CCGTAAAAAT
Statistics
Matches: 50, Mismatches: 3, Indels: 20
0.68 0.04 0.27
Matches are distributed among these distances:
25 8 0.16
26 3 0.06
27 8 0.16
28 1 0.02
29 15 0.30
30 1 0.02
31 8 0.16
32 3 0.06
33 3 0.06
ACGTcount: A:0.49, C:0.08, G:0.02, T:0.41
Consensus pattern (25 bp):
TATTAAAAAAATAAAATTACATTTT
Found at i:111703 original size:30 final size:30
Alignment explanation
Indices: 111667--111769 Score: 106
Period size: 30 Copynumber: 3.5 Consensus size: 30
111657 TATAAACTAT
111667 TAAAAAAATAAAATTACATTTTTATTACCG
1 TAAAAAAATAAAATTACATTTTTATTACCG
* * *
111697 TAAAAAATATACAATTTA-A--TTT-TGACCT
1 TAAAAAA-ATA-AAATTACATTTTTATTACCG
*
111725 TAAAATAATAAAATTACATTTTTATTACCG
1 TAAAAAAATAAAATTACATTTTTATTACCG
* *
111755 TAAAAATATATAATT
1 TAAAAAAATAAAATT
111770 TAATTTCGAC
Statistics
Matches: 57, Mismatches: 10, Indels: 12
0.72 0.13 0.15
Matches are distributed among these distances:
26 5 0.09
27 4 0.07
28 10 0.18
29 6 0.11
30 23 0.40
31 4 0.07
32 5 0.09
ACGTcount: A:0.50, C:0.09, G:0.03, T:0.39
Consensus pattern (30 bp):
TAAAAAAATAAAATTACATTTTTATTACCG
Found at i:111729 original size:26 final size:25
Alignment explanation
Indices: 111700--111787 Score: 68
Period size: 26 Copynumber: 3.2 Consensus size: 25
111690 ATTACCGTAA
111700 AAAATATACAATTTAATTTTGACCTT
1 AAAATATA-AATTTAATTTTGACCTT
* * *
111726 AAAATAATAAAATTACATTTTTATTACCGTA
1 AAAAT-ATAAATTTA-A--TTT-TGACC-TT
*
111757 AAAATATATAATTTAATTTCGACCTT
1 AAAATATA-AATTTAATTTTGACCTT
111783 AAAAT
1 AAAAT
111788 TTTTTTAATT
Statistics
Matches: 48, Mismatches: 7, Indels: 14
0.70 0.10 0.20
Matches are distributed among these distances:
26 16 0.33
27 7 0.15
28 3 0.06
29 3 0.06
30 8 0.17
31 11 0.23
ACGTcount: A:0.47, C:0.10, G:0.03, T:0.40
Consensus pattern (25 bp):
AAAATATAAATTTAATTTTGACCTT
Found at i:111787 original size:57 final size:58
Alignment explanation
Indices: 111666--111787 Score: 210
Period size: 58 Copynumber: 2.1 Consensus size: 58
111656 ATATAAACTA
* *
111666 TTAAAAAAATAAAATTACATTTTTATTACCGTAAAAAATATACAATTTAATTTTGACC
1 TTAAAATAATAAAATTACATTTTTATTACCGTAAAAAATATACAATTTAATTTCGACC
*
111724 TTAAAATAATAAAATTACATTTTTATTACCGT-AAAAATATATAATTTAATTTCGACC
1 TTAAAATAATAAAATTACATTTTTATTACCGTAAAAAATATACAATTTAATTTCGACC
111781 TTAAAAT
1 TTAAAAT
111788 TTTTTTAATT
Statistics
Matches: 61, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
57 30 0.49
58 31 0.51
ACGTcount: A:0.48, C:0.10, G:0.03, T:0.39
Consensus pattern (58 bp):
TTAAAATAATAAAATTACATTTTTATTACCGTAAAAAATATACAATTTAATTTCGACC
Found at i:114268 original size:20 final size:20
Alignment explanation
Indices: 114243--114283 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
114233 AATCTATGGG
114243 AGTAAAAGAAAAAGGTTTTA
1 AGTAAAAGAAAAAGGTTTTA
114263 AGTAAAAGAAAAAGGTTTTA
1 AGTAAAAGAAAAAGGTTTTA
114283 A
1 A
114284 CTTCATTATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.56, C:0.00, G:0.20, T:0.24
Consensus pattern (20 bp):
AGTAAAAGAAAAAGGTTTTA
Found at i:114835 original size:25 final size:26
Alignment explanation
Indices: 114791--114844 Score: 83
Period size: 26 Copynumber: 2.1 Consensus size: 26
114781 TAAAATATTA
* *
114791 TTTTTTAATTTTTAAGAGGTTAATTT
1 TTTTTTAATTTTTAAGAGGTCAAATT
114817 TTTTTTAATTTTTAA-AGGTCAAATT
1 TTTTTTAATTTTTAAGAGGTCAAATT
114842 TTT
1 TTT
114845 CATCAACTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
25 11 0.42
26 15 0.58
ACGTcount: A:0.28, C:0.02, G:0.09, T:0.61
Consensus pattern (26 bp):
TTTTTTAATTTTTAAGAGGTCAAATT
Found at i:114872 original size:30 final size:29
Alignment explanation
Indices: 114837--114899 Score: 92
Period size: 30 Copynumber: 2.1 Consensus size: 29
114827 TTTAAAGGTC
114837 AAATTTTTCATC-AACTTTTAAAAAATTTCA
1 AAATTTTTC-TCTAACTTTTAAAAAATTT-A
*
114867 AAATTTTTCTCTAATTTTTAAAAAATTTA
1 AAATTTTTCTCTAACTTTTAAAAAATTTA
114896 AAAT
1 AAAT
114900 CTTATTTTAT
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
29 7 0.23
30 24 0.77
ACGTcount: A:0.44, C:0.10, G:0.00, T:0.46
Consensus pattern (29 bp):
AAATTTTTCTCTAACTTTTAAAAAATTTA
Found at i:129141 original size:52 final size:52
Alignment explanation
Indices: 129068--129409 Score: 434
Period size: 52 Copynumber: 6.6 Consensus size: 52
129058 ATTTCATTTA
* * * * * *
129068 ATACTCATGATAACACATAGTCATCAGACCTCTTAATCCGTAAAGCATTCAT
1 ATACTCACGATGACACTTAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
* * * * * *
129120 GTACTCACAATGACGCGTAGTCATCGAAACTCATAATCCG-AAAGGATTCAT
1 ATACTCACGATGACACTTAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
*
129171 ATACTCACGATGACACTTAGTCATCGGACCTCATAATCCGTAAAGAATTCAT
1 ATACTCACGATGACACTTAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
* *
129223 ATACTCACGGTGACACTTAGTCATCGGACCTCATATTCCGTAAAGGATTCAT
1 ATACTCACGATGACACTTAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
* * * * * **
129275 AAACTCACAATGACACTTAGTCATTGGACTTCATATTCTATAAAGGATTCAT
1 ATACTCACGATGACACTTAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
* *
129327 ATACTCACGATGACACATAGTCATCGGACCTCATATTCCGTAAAGGATTCAT
1 ATACTCACGATGACACTTAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
* * *
129379 ATACTCACGATGACACATAGTTATCGAACCT
1 ATACTCACGATGACACTTAGTCATCGGACCT
129410 TTTTGCATTT
Statistics
Matches: 252, Mismatches: 37, Indels: 2
0.87 0.13 0.01
Matches are distributed among these distances:
51 44 0.17
52 208 0.83
ACGTcount: A:0.34, C:0.24, G:0.14, T:0.28
Consensus pattern (52 bp):
ATACTCACGATGACACTTAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
Found at i:132323 original size:109 final size:109
Alignment explanation
Indices: 132054--132324 Score: 364
Period size: 109 Copynumber: 2.5 Consensus size: 109
132044 GCTTAGGATA
* * * * * *
132054 CTGCTCACACAAGCTATTGAGAATCTGTAACATATGCAGGATCTTAGCCATAGCGACGGTTTGTA
1 CTGCTCACACAAGCTGTAGAGAATCTGCAACATATGCAGGATCTTAGCCATCGCAACAGTTTGTA
**
132119 TCATCATATGATAGTATCCATTCAATAGTCACCAGCTCACGACG
66 TCATCATAACATAGTATCCATTCAATAGTCACCAGCTCACGACG
* * *
132163 CTGCTCACACAAGCTGTCGAGAATCTGCAACATATGTAGGATCTTAACCATCGCAACAGTTTGTA
1 CTGCTCACACAAGCTGTAGAGAATCTGCAACATATGCAGGATCTTAGCCATCGCAACAGTTTGTA
* *
132228 TCATCATAACATAGTATCCATTCAATAGTCACTAGCTCACGATG
66 TCATCATAACATAGTATCCATTCAATAGTCACCAGCTCACGACG
* * * * *
132272 CTGTTCATACAAGCTGTAGAGAATCCGCAACAAATGCAAGAT-TTCAGCCATCG
1 CTGCTCACACAAGCTGTAGAGAATCTGCAACATATGCAGGATCTT-AGCCATCG
132325 TGATAGTTTA
Statistics
Matches: 141, Mismatches: 20, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
108 2 0.01
109 139 0.99
ACGTcount: A:0.32, C:0.24, G:0.17, T:0.27
Consensus pattern (109 bp):
CTGCTCACACAAGCTGTAGAGAATCTGCAACATATGCAGGATCTTAGCCATCGCAACAGTTTGTA
TCATCATAACATAGTATCCATTCAATAGTCACCAGCTCACGACG
Found at i:134146 original size:40 final size:40
Alignment explanation
Indices: 134089--134188 Score: 175
Period size: 40 Copynumber: 2.5 Consensus size: 40
134079 CTACACAAGT
*
134089 TCATATGTCTTCC-TTTTAACAATCTTATGCTCTACCGAG
1 TCATAAGTCTTCCTTTTTAACAATCTTATGCTCTACCGAG
*
134128 TCATAAGTCTTCCTTTTTAATAATCTTATGCTCTACCGAG
1 TCATAAGTCTTCCTTTTTAACAATCTTATGCTCTACCGAG
134168 TCATAAGTCTTCCTTTTTAAC
1 TCATAAGTCTTCCTTTTTAAC
134189 GATATTCTCA
Statistics
Matches: 57, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
39 12 0.21
40 45 0.79
ACGTcount: A:0.24, C:0.24, G:0.09, T:0.43
Consensus pattern (40 bp):
TCATAAGTCTTCCTTTTTAACAATCTTATGCTCTACCGAG
Found at i:139197 original size:10 final size:10
Alignment explanation
Indices: 139174--139207 Score: 59
Period size: 10 Copynumber: 3.3 Consensus size: 10
139164 AATAGACGTG
139174 AAAATAAATA
1 AAAATAAATA
139184 AAAATGAAATA
1 AAAAT-AAATA
139195 AAAATAAATA
1 AAAATAAATA
139205 AAA
1 AAA
139208 TTATACAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 13 0.57
11 10 0.43
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.18
Consensus pattern (10 bp):
AAAATAAATA
Found at i:139937 original size:152 final size:149
Alignment explanation
Indices: 139764--140085 Score: 398
Period size: 152 Copynumber: 2.1 Consensus size: 149
139754 ATTTTTTTTT
* * *
139764 AAATCACTAATTTTCTTAAAGATAAAAGTTTTTATTTCGAAATAATTAAAAAAAATTAAAA-TTT
1 AAATCACTAATTTTCTTAAAGATAAAAGCTTTTATTTCAAAATAATT-AAAAAAATCAAAACTTT
*
139828 ATTT-AAAAATTTAAAATTTTTCTTTTAAAACTACTAAAAAACAAATTTTTATTTTTAAAAAAAA
65 ATTTAAAAAATTT-AAATTTTTCCTTTAAAACTACTAAAAAACAAATTTTTA-TTTT--AAAAAA
139892 TCTAAACCTTCA-TTTTTTAAAAGA
126 TCTAAACCTTCATTTTTTTAAAA-A
* * * * *
139916 AAATCACTACTTTTCTTAAAGATCAAAGCTTTTATTTTAAAATAGTTAAAAAAATCAAAACTTTG
1 AAATCACTAATTTTCTTAAAGATAAAAGCTTTTATTTCAAAATAATTAAAAAAATCAAAACTTTA
* ** * * *
139981 TTTAAAAAATTTAACTTTTTCCTTTAAATTTACTAAAAAATAATTTTTTATTTTGAAAAATCTAA
66 TTTAAAAAATTTAAATTTTTCCTTTAAAACTACTAAAAAACAAATTTTTATTTTAAAAAATCTAA
* *
140046 ACTTTCATTTTTTTTTAAAA
131 ACCTTCA-TTTTTTTAAAAA
*
140066 AAATCACTATTTTTCTTAAA
1 AAATCACTAATTTTCTTAAA
140086 TATCAAAATA
Statistics
Matches: 148, Mismatches: 18, Indels: 10
0.84 0.10 0.06
Matches are distributed among these distances:
149 16 0.11
150 20 0.14
151 25 0.17
152 79 0.53
153 8 0.05
ACGTcount: A:0.45, C:0.09, G:0.03, T:0.43
Consensus pattern (149 bp):
AAATCACTAATTTTCTTAAAGATAAAAGCTTTTATTTCAAAATAATTAAAAAAATCAAAACTTTA
TTTAAAAAATTTAAATTTTTCCTTTAAAACTACTAAAAAACAAATTTTTATTTTAAAAAATCTAA
ACCTTCATTTTTTTAAAAA
Found at i:142219 original size:170 final size:172
Alignment explanation
Indices: 141933--142251 Score: 389
Period size: 170 Copynumber: 1.9 Consensus size: 172
141923 TAATTAAGGT
* * * *
141933 AGTAAAATTTTAAAAGAAAAAATTAAAAAAAATTGAAGGGGGTGAATGGGTTTGGGGTAGATAGG
1 AGTAAAATTTTAAAAGAAAAAATTAAAAAAAATT-AAGGAGGTAAATGAGTTTGGGATAGATAGG
* * *
141998 GGTTGGGATGGGAGGGGAGTAAAACTTTTAGGGGGAAAGTGAGATGGAGTAAAAGTTTTAGAGGA
65 GGTTGGGATGGGAGGGGAGTAAAACTTTGAGGAGGAAAGTGAGAAGGAGTAAAAGTTTTAGAGGA
*
142063 AAA-TAAAAAGTTTTGAGGGTTTTTTTTGGAAAGTAAATGTAGG
130 AAAGTAAAAAGGTTT-AGGGTTTTTTTTGGAAAGTAAATGTAGG
** * *
142106 AGTAAAATTTTGAAGGGAAAATATTAAAAAAAATT-ATGAGG-AAATGAGTTTGGGATAGAT-GA
1 AGTAAAATTTT-AAAAGAAAAAATTAAAAAAAATTAAGGAGGTAAATGAGTTTGGGATAGATAG-
* * * * * *
142168 GGG-TGGGATGTGAGGTGAGTAAAAGGTTTGA-GAGGAAAGTGGGAAGGAGTAAATGTTTTAGGG
64 GGGTTGGGATGGGAGGGGAGTAAAA-CTTTGAGGAGGAAAGTGAGAAGGAGTAAAAGTTTTAGAG
142231 GAAAAGTAAAAAGGTTTAGGG
128 GAAAAGTAAAAAGGTTTAGGG
142252 GTTTAGGGGT
Statistics
Matches: 124, Mismatches: 18, Indels: 11
0.81 0.12 0.07
Matches are distributed among these distances:
170 56 0.45
171 33 0.27
172 4 0.03
173 11 0.09
174 20 0.16
ACGTcount: A:0.39, C:0.00, G:0.34, T:0.26
Consensus pattern (172 bp):
AGTAAAATTTTAAAAGAAAAAATTAAAAAAAATTAAGGAGGTAAATGAGTTTGGGATAGATAGGG
GTTGGGATGGGAGGGGAGTAAAACTTTGAGGAGGAAAGTGAGAAGGAGTAAAAGTTTTAGAGGAA
AAGTAAAAAGGTTTAGGGTTTTTTTTGGAAAGTAAATGTAGG
Found at i:142256 original size:8 final size:8
Alignment explanation
Indices: 142243--142267 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
142233 AAAGTAAAAA
142243 GGTTTAGG
1 GGTTTAGG
142251 GGTTTAGG
1 GGTTTAGG
142259 GGTTTAGG
1 GGTTTAGG
142267 G
1 G
142268 CAAAAGTGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.12, C:0.00, G:0.52, T:0.36
Consensus pattern (8 bp):
GGTTTAGG
Found at i:144611 original size:132 final size:132
Alignment explanation
Indices: 144369--144648 Score: 344
Period size: 132 Copynumber: 2.1 Consensus size: 132
144359 GAAATGGGTC
* * * *
144369 TGCTCACACGAGCTGTGGATCGAGATGTGCGGCTACACGATACTGCTCACACGAGTTGTGGAGAA
1 TGCTCACACGAGCTGTGGATCGAGATATGAGGCTACACGATACTACTCACACGAGCTGTGGAGAA
* * * * * * * *
144434 TCCTCAATAAATTTCGAACCTCAAACATTGATAGGACATCTAAGACCAGTACCCATATAACTTGT
66 TCCGCAACAAATGTAGAACCTCAAACATCGATAGGACATCCAAGACCAGCACCCATATAACCTGT
144499 AA
131 AA
* * * ** *
144501 TGCTCACACGAGCTGTGGGTCGAGATATTAGGCTACGCGATGTTACTTACACGAGCTGTGGAGAA
1 TGCTCACACGAGCTGTGGATCGAGATATGAGGCTACACGATACTACTCACACGAGCTGTGGAGAA
* * ** *
144566 TCCGCAACCAATGTAGGACCTCAGCCATCGGTAGGACATCCAAGACCAGCACCCATATAACCTGT
66 TCCGCAACAAATGTAGAACCTCAAACATCGATAGGACATCCAAGACCAGCACCCATATAACCTGT
144631 AA
131 AA
*
144633 TACTCACACGAGCTGT
1 TGCTCACACGAGCTGT
144649 AACTGTAACA
Statistics
Matches: 124, Mismatches: 24, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
132 124 1.00
ACGTcount: A:0.30, C:0.25, G:0.22, T:0.23
Consensus pattern (132 bp):
TGCTCACACGAGCTGTGGATCGAGATATGAGGCTACACGATACTACTCACACGAGCTGTGGAGAA
TCCGCAACAAATGTAGAACCTCAAACATCGATAGGACATCCAAGACCAGCACCCATATAACCTGT
AA
Found at i:144754 original size:69 final size:69
Alignment explanation
Indices: 144671--144822 Score: 259
Period size: 69 Copynumber: 2.2 Consensus size: 69
144661 TAATCATATA
* * *
144671 TGCTCACATGAGCTGTGAAATGGGCCTGCTCACACGAGCTGTGGGTCGGGATGTTAGGTTACACG
1 TGCTCACACGAGCTGTGAAATGGGCCTGCTCACACAAGCTGTGGGTCGGGATGTTAGGCTACACG
144736 ATGC
66 ATGC
*
144740 TGCTCACACGAGCTGTGAAATGGGTCTGCTCACACAAGCTGTGGGTCGGGATGTTAGGCTACACG
1 TGCTCACACGAGCTGTGAAATGGGCCTGCTCACACAAGCTGTGGGTCGGGATGTTAGGCTACACG
*
144805 ATGT
66 ATGC
144809 TGCTCACACGAGCT
1 TGCTCACACGAGCT
144823 TTGGACAATC
Statistics
Matches: 78, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
69 78 1.00
ACGTcount: A:0.21, C:0.23, G:0.32, T:0.24
Consensus pattern (69 bp):
TGCTCACACGAGCTGTGAAATGGGCCTGCTCACACAAGCTGTGGGTCGGGATGTTAGGCTACACG
ATGC
Found at i:144974 original size:265 final size:265
Alignment explanation
Indices: 144501--144979 Score: 778
Period size: 265 Copynumber: 1.8 Consensus size: 265
144491 TAACTTGTAA
* * * *
144501 TGCTCACACGAGCTGTGGGTCGAGATATTAGGCTACGCGATGTTACTTACACGAGCTGTGGAGAA
1 TGCTCACACAAGCTGTGGGTCGAGATATTAGGCTACACGATGTTACTCACACGAGCTGTGGACAA
* * * * *
144566 TCCGCAACCAATGTAGGACCTCAGCCATCGGTAGGACATCCAAGACCAGCACCCATATAACCTGT
66 TCCGCAACAAATGGAAGACCTCAACCATCGGTAGGACATCCAAGACCAACACCCATATAACCTGT
*
144631 AATACTCACACGAGCTGTAACTGTAACATGTAATCATATATGCTCACATGAGCTGTGAAATGGGC
131 AATACTCACACGAGCTGTAACTGTAACATGTAATCATATATGCTCACACGAGCTGTGAAATGGGC
144696 CTGCTCACACGAGCTGTGGGTCGGGATGTTAGGTTACACGATGCTGCTCACACGAGCTGTGAAAT
196 CTGCTCACACGAGCTGTGGGTCGGGATGTTAGGTTACACGATGCTGCTCACACGAGCTGTGAAAT
144761 GGGTC
261 GGGTC
* * * *
144766 TGCTCACACAAGCTGTGGGTCGGGATGTTAGGCTACACGATGTTGCTCACACGAGCTTTGGACAA
1 TGCTCACACAAGCTGTGGGTCGAGATATTAGGCTACACGATGTTACTCACACGAGCTGTGGACAA
* *
144831 TCCGCAACAAATGGAAGTCCTCAACCATCGGTAGGACATCCAAGACCAACGCCCATATAACCTGT
66 TCCGCAACAAATGGAAGACCTCAACCATCGGTAGGACATCCAAGACCAACACCCATATAACCTGT
* * * *
144896 AATGCTTACATGAGCTGTAACTGTAACATGTAATCATATATGCTCACACGAGCTGTGAAATGGGT
131 AATACTCACACGAGCTGTAACTGTAACATGTAATCATATATGCTCACACGAGCTGTGAAATGGGC
144961 CTGCTCACACGAGCTGTGG
196 CTGCTCACACGAGCTGTGG
144980 AGAATCCGCA
Statistics
Matches: 194, Mismatches: 20, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
265 194 1.00
ACGTcount: A:0.28, C:0.24, G:0.25, T:0.23
Consensus pattern (265 bp):
TGCTCACACAAGCTGTGGGTCGAGATATTAGGCTACACGATGTTACTCACACGAGCTGTGGACAA
TCCGCAACAAATGGAAGACCTCAACCATCGGTAGGACATCCAAGACCAACACCCATATAACCTGT
AATACTCACACGAGCTGTAACTGTAACATGTAATCATATATGCTCACACGAGCTGTGAAATGGGC
CTGCTCACACGAGCTGTGGGTCGGGATGTTAGGTTACACGATGCTGCTCACACGAGCTGTGAAAT
GGGTC
Found at i:145682 original size:15 final size:16
Alignment explanation
Indices: 145652--145685 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
145642 TGATTTAGAT
*
145652 AATCATTTATTCATTC
1 AATCATTCATTCATTC
145668 AATCATTCA-TCATTC
1 AATCATTCATTCATTC
145683 AAT
1 AAT
145686 TTAATGACTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.35, C:0.21, G:0.00, T:0.44
Consensus pattern (16 bp):
AATCATTCATTCATTC
Found at i:150383 original size:22 final size:22
Alignment explanation
Indices: 150352--150406 Score: 85
Period size: 22 Copynumber: 2.5 Consensus size: 22
150342 CTTACTATTT
150352 AGCACTGTGTGTG-TTTCTGTTC
1 AGCACTGTGTGTGCTTT-TGTTC
*
150374 AGGACTGTGTGTGCTTTTGTTC
1 AGCACTGTGTGTGCTTTTGTTC
150396 AGCACTGTGTG
1 AGCACTGTGTG
150407 AGCCTATTGT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
22 27 0.90
23 3 0.10
ACGTcount: A:0.11, C:0.16, G:0.31, T:0.42
Consensus pattern (22 bp):
AGCACTGTGTGTGCTTTTGTTC
Found at i:159828 original size:31 final size:30
Alignment explanation
Indices: 159790--159878 Score: 96
Period size: 31 Copynumber: 3.0 Consensus size: 30
159780 TCAAATATTT
159790 GATATTTGAGTTTGGTTTTAATATTTAATTA
1 GATATTTGAGTTT-GTTTTAATATTTAATTA
159821 GATATTTGAGTTT-TTTT--TATCTTAATTTA
1 GATATTTGAGTTTGTTTTAATAT-TTAA-TTA
* *
159850 -ATACTTGAGTTTGATTTTAATGTTTAATT
1 GATATTTGAGTTTG-TTTTAATATTTAATT
159879 TTAGTATCTA
Statistics
Matches: 50, Mismatches: 2, Indels: 13
0.77 0.03 0.20
Matches are distributed among these distances:
27 3 0.06
28 15 0.30
29 7 0.14
30 6 0.12
31 17 0.34
32 2 0.04
ACGTcount: A:0.27, C:0.02, G:0.13, T:0.57
Consensus pattern (30 bp):
GATATTTGAGTTTGTTTTAATATTTAATTA
Found at i:160744 original size:22 final size:22
Alignment explanation
Indices: 160719--160760 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
160709 TCAATAACAC
*
160719 AATTAAGAGAGAATTTTGTAGG
1 AATTAAGAGAGAACTTTGTAGG
* *
160741 AATTTAGGGAGAACTTTGTA
1 AATTAAGAGAGAACTTTGTA
160761 TCTTGGGTTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.38, C:0.02, G:0.26, T:0.33
Consensus pattern (22 bp):
AATTAAGAGAGAACTTTGTAGG
Found at i:164762 original size:52 final size:52
Alignment explanation
Indices: 164689--164983 Score: 339
Period size: 52 Copynumber: 5.7 Consensus size: 52
164679 TAAACGAAGA
*
164689 GGTCCAATGACTAAGTGTCATCGTGAGTATATGAATCTTTTACGGATTAAAC
1 GGTCCGATGACTAAGTGTCATCGTGAGTATATGAATCTTTTACGGATTAAAC
*
164741 GGTCCGATGACTAAGTGTCATCATGAGTATATGAATCTTTT-CAGGATTAAAC
1 GGTCCGATGACTAAGTGTCATCGTGAGTATATGAATCTTTTAC-GGATTAAAC
* * * *
164793 GGTTCGATGACTAAGTATCATCATGAGTATATGAATCCTTTA-GGATTAAAC
1 GGTCCGATGACTAAGTGTCATCGTGAGTATATGAATCTTTTACGGATTAAAC
* * *
164844 AGTCCGATGACTAAGTGTTATCGTGAGTATATGGATCTTTTACGGATTAAGA-
1 GGTCCGATGACTAAGTGTCATCGTGAGTATATGAATCTTTTACGGATTAA-AC
* ** ** * *
164896 GGTCCGATGACTTTA-TGTCATCGTGAGTATACAAATCCCTTGCGGA-TAATAA
1 GGTCCGATGAC-TAAGTGTCATCGTGAGTATATGAATCTTTTACGGATTAA-AC
* * * *
164948 GCTCCGGTGGCTATGTGTCATCGTGAGTATATGAAT
1 GGTCCGATGACTAAGTGTCATCGTGAGTATATGAAT
164984 GAAGTGAAAT
Statistics
Matches: 207, Mismatches: 29, Indels: 14
0.83 0.12 0.06
Matches are distributed among these distances:
51 50 0.24
52 154 0.74
53 3 0.01
ACGTcount: A:0.29, C:0.15, G:0.23, T:0.33
Consensus pattern (52 bp):
GGTCCGATGACTAAGTGTCATCGTGAGTATATGAATCTTTTACGGATTAAAC
Found at i:164875 original size:103 final size:104
Alignment explanation
Indices: 164685--164983 Score: 331
Period size: 103 Copynumber: 2.9 Consensus size: 104
164675 GCCATAAACG
* * * * *
164685 AAGAGGTCCAATGACTAAGTGTCATCGTGAGTATATGAATCTTTTACGGATTAAACGGTCCGATG
1 AAGAGGTCCGATGACTAAGTATCATCATGAGTATATGAATCCTTTACGGATTAAACAGTCCGATG
164750 ACTAAGTGTCATCATGAGTATATGAATCTTTT-CAGGATT
66 ACTAAGTGTCATCATGAGTATATGAATCTTTTAC-GGATT
*
164789 AA-ACGGTTCGATGACTAAGTATCATCATGAGTATATGAATCCTTTA-GGATTAAACAGTCCGAT
1 AAGA-GGTCCGATGACTAAGTATCATCATGAGTATATGAATCCTTTACGGATTAAACAGTCCGAT
* * *
164852 GACTAAGTGTTATCGTGAGTATATGGATCTTTTACGGATT
65 GACTAAGTGTCATCATGAGTATATGAATCTTTTACGGATT
* * * ** * *
164892 AAGAGGTCCGATGACTTTA-TGTCATCGTGAGTATACAAATCCCTTGCGGA-TAATA-AGCTCCG
1 AAGAGGTCCGATGAC-TAAGTATCATCATGAGTATATGAATCCTTTACGGATTAA-ACAG-TCCG
* * * *
164954 GTGGCTATGTGTCATCGTGAGTATATGAAT
63 ATGACTAAGTGTCATCATGAGTATATGAAT
164984 GAAGTGAAAT
Statistics
Matches: 166, Mismatches: 22, Indels: 14
0.82 0.11 0.07
Matches are distributed among these distances:
103 90 0.54
104 76 0.46
ACGTcount: A:0.30, C:0.15, G:0.23, T:0.32
Consensus pattern (104 bp):
AAGAGGTCCGATGACTAAGTATCATCATGAGTATATGAATCCTTTACGGATTAAACAGTCCGATG
ACTAAGTGTCATCATGAGTATATGAATCTTTTACGGATT
Found at i:164977 original size:155 final size:155
Alignment explanation
Indices: 164690--164983 Score: 371
Period size: 155 Copynumber: 1.9 Consensus size: 155
164680 AAACGAAGAG
164690 GTCCAATGACTAAGTGTCATCGTGAGTATATGAATCTTTTACGGATTAAACGGTCCGATGACTAA
1 GTCCAATGACTAAGTGTCATCGTGAGTATATGAATCTTTTACGGATTAAACGGTCCGATGACTAA
** * * * * *
164755 GTGTCATCATGAGTATATGAATCTTTTCAGGATTAAACGGTTCGATGACTAAGTATCATCATGAG
66 GTGTCATCATGAGTATACAAATCCTTGCAGGATTAAAAGCTCCGATGACTAAGTATCATCATGAG
164820 TATATGAATCCTTTAGGATTAAACA
131 TATATGAATCCTTTAGGATTAAACA
* * *
164845 GTCCGATGACTAAGTGTTATCGTGAGTATATGGATCTTTTACGGATTAAGA-GGTCCGATGACTT
1 GTCCAATGACTAAGTGTCATCGTGAGTATATGAATCTTTTACGGATTAA-ACGGTCCGATGAC-T
* * * * * * *
164909 TA-TGTCATCGTGAGTATACAAATCCCTTGC-GGA-TAATAAGCTCCGGTGGCTATGTGTCATCG
64 AAGTGTCATCATGAGTATACAAAT-CCTTGCAGGATTAA-AAGCTCCGATGACTAAGTATCATCA
164971 TGAGTATATGAAT
127 TGAGTATATGAAT
164984 GAAGTGAAAT
Statistics
Matches: 118, Mismatches: 17, Indels: 8
0.83 0.12 0.06
Matches are distributed among these distances:
154 3 0.03
155 108 0.92
156 7 0.06
ACGTcount: A:0.29, C:0.15, G:0.22, T:0.33
Consensus pattern (155 bp):
GTCCAATGACTAAGTGTCATCGTGAGTATATGAATCTTTTACGGATTAAACGGTCCGATGACTAA
GTGTCATCATGAGTATACAAATCCTTGCAGGATTAAAAGCTCCGATGACTAAGTATCATCATGAG
TATATGAATCCTTTAGGATTAAACA
Found at i:171791 original size:52 final size:52
Alignment explanation
Indices: 171716--172007 Score: 338
Period size: 52 Copynumber: 5.6 Consensus size: 52
171706 CGACGAGGTT
* *
171716 CGATGACTAAGTGTCATCGTGAGTATATGAATCCTTTACGGCTTAAACGGTC
1 CGATGACTAAGTGTCATCGTGAGTATATGAATCCTTTACGGATTAAATGGTC
* * * * * *
171768 CGATGTCTAGGTGCCATCATGAGTATATGGATCCTTTACGGATTAAATGGTT
1 CGATGACTAAGTGTCATCGTGAGTATATGAATCCTTTACGGATTAAATGGTC
* *
171820 CGATGACTAAGTGTCATCGTGAGTATATGAATCCTTTATGAATTAAATGGTC
1 CGATGACTAAGTGTCATCGTGAGTATATGAATCCTTTACGGATTAAATGGTC
*
171872 CGATGACTAAGTGTCATCGTGAGTATAT-AGATCTTTTACGGATTAAGA-GGTC
1 CGATGACTAAGTGTCATCGTGAGTATATGA-ATCCTTTACGGATTAA-ATGGTC
* ** * * *
171924 TGATGACTTTGTGTCATCGTGAGTATACGAATCCCTTACGGATTATAA-GCTC
1 CGATGACTAAGTGTCATCGTGAGTATATGAATCCTTTACGGATTA-AATGGTC
* * * * *
171976 CGGTGGCTATGTGTGATTGTGAGTATATGAAT
1 CGATGACTAAGTGTCATCGTGAGTATATGAAT
172008 GAAGTGAAAT
Statistics
Matches: 203, Mismatches: 33, Indels: 8
0.83 0.14 0.03
Matches are distributed among these distances:
51 1 0.00
52 199 0.98
53 3 0.01
ACGTcount: A:0.27, C:0.15, G:0.24, T:0.34
Consensus pattern (52 bp):
CGATGACTAAGTGTCATCGTGAGTATATGAATCCTTTACGGATTAAATGGTC
Found at i:172007 original size:156 final size:156
Alignment explanation
Indices: 171716--172007 Score: 374
Period size: 156 Copynumber: 1.9 Consensus size: 156
171706 CGACGAGGTT
* *
171716 CGATGACTAAGTGTCATCGTGAGTATATGAATCCTTTACGGCTTAAACGGTCCGATGTCTAGGTG
1 CGATGACTAAGTGTCATCGTGAGTATATGAATCCTTTACGGATTAAACGGTCCGATGACTAGGTG
* * * * *
171781 CCATCATGAGTATATGGATCCTTTACGGATTAAATGGTTCGATGACTAAGTGTCATCGTGAGTAT
66 CCATCATGAGTATACGAATCCCTTACGGATTAAATGCTCCGATGACTAAGTGTCATCGTGAGTAT
171846 ATGAATCCTTTATGAATTAAATGGTC
131 ATGAATCCTTTATGAATTAAATGGTC
* * **
171872 CGATGACTAAGTGTCATCGTGAGTATAT-AGATCTTTTACGGATTAAGA-GGTCTGATGACTTTG
1 CGATGACTAAGTGTCATCGTGAGTATATGA-ATCCTTTACGGATTAA-ACGGTCCGATGACTAGG
* * * * * * *
171935 TGTCATCGTGAGTATACGAATCCCTTACGGATTATAA-GCTCCGGTGGCTATGTGTGATTGTGAG
64 TGCCATCATGAGTATACGAATCCCTTACGGATTA-AATGCTCCGATGACTAAGTGTCATCGTGAG
171999 TATATGAAT
128 TATATGAAT
172008 GAAGTGAAAT
Statistics
Matches: 115, Mismatches: 18, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
155 1 0.01
156 111 0.97
157 3 0.03
ACGTcount: A:0.27, C:0.15, G:0.24, T:0.34
Consensus pattern (156 bp):
CGATGACTAAGTGTCATCGTGAGTATATGAATCCTTTACGGATTAAACGGTCCGATGACTAGGTG
CCATCATGAGTATACGAATCCCTTACGGATTAAATGCTCCGATGACTAAGTGTCATCGTGAGTAT
ATGAATCCTTTATGAATTAAATGGTC
Found at i:175643 original size:15 final size:15
Alignment explanation
Indices: 175623--175652 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
175613 TTATTTGAAC
*
175623 TTTGGTATTGATATT
1 TTTGGTATTAATATT
175638 TTTGGTATTAATATT
1 TTTGGTATTAATATT
175653 GATACATGTT
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:0.23, C:0.00, G:0.17, T:0.60
Consensus pattern (15 bp):
TTTGGTATTAATATT
Found at i:176488 original size:83 final size:83
Alignment explanation
Indices: 176395--176563 Score: 284
Period size: 83 Copynumber: 2.0 Consensus size: 83
176385 TAATTGGCCG
* *
176395 ATTTTCAACCGAATTAACTGTTAATCGAACTTTCAAAAAATCATTAACCAACCCCCGATCGAATT
1 ATTTTCAACCGAATTAACTGTTAATCAAACTTTCAAAAAATCATTAACCAACCCCCAATCGAATT
* *
176460 AATTCGGTTAACTGGTCA
66 AATTCGGTTAACCGATCA
* *
176478 ATTTTCAACCGAATTAACTGTTAATCAAACTTTCAAAAAATTATTAACCAACCTCCAATCGAATT
1 ATTTTCAACCGAATTAACTGTTAATCAAACTTTCAAAAAATCATTAACCAACCCCCAATCGAATT
176543 AATTCGGTTAACCGATCA
66 AATTCGGTTAACCGATCA
176561 ATT
1 ATT
176564 AACCGAATTT
Statistics
Matches: 80, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
83 80 1.00
ACGTcount: A:0.38, C:0.22, G:0.09, T:0.31
Consensus pattern (83 bp):
ATTTTCAACCGAATTAACTGTTAATCAAACTTTCAAAAAATCATTAACCAACCCCCAATCGAATT
AATTCGGTTAACCGATCA
Found at i:181615 original size:25 final size:25
Alignment explanation
Indices: 181587--181646 Score: 84
Period size: 25 Copynumber: 2.4 Consensus size: 25
181577 AACGAACATG
*
181587 GATTTCTCTAGAAAGCTTTTGTGGT
1 GATTTCTCTAGAAAGCCTTTGTGGT
* *
181612 GATTTCTTTGGAAAGCCTTTGTGGT
1 GATTTCTCTAGAAAGCCTTTGTGGT
*
181637 AATTTCTCTA
1 GATTTCTCTA
181647 AAAAACTTAT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.20, C:0.13, G:0.22, T:0.45
Consensus pattern (25 bp):
GATTTCTCTAGAAAGCCTTTGTGGT
Found at i:188085 original size:29 final size:28
Alignment explanation
Indices: 188030--188099 Score: 97
Period size: 29 Copynumber: 2.5 Consensus size: 28
188020 GTTGAACTGT
*
188030 ATTA-TTATTTTTACTATGTAATTAATA
1 ATTAGTTATATTTACTATGTAATTAATA
*
188057 ATTAGTTATATTTACATATTTAATTAATA
1 ATTAGTTATATTTAC-TATGTAATTAATA
*
188086 ATTAGTTAGATTTA
1 ATTAGTTATATTTA
188100 TATTGAATTT
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
27 4 0.11
28 9 0.24
29 25 0.66
ACGTcount: A:0.39, C:0.03, G:0.06, T:0.53
Consensus pattern (28 bp):
ATTAGTTATATTTACTATGTAATTAATA
Found at i:188201 original size:40 final size:38
Alignment explanation
Indices: 188116--188202 Score: 102
Period size: 40 Copynumber: 2.2 Consensus size: 38
188106 ATTTTATCTG
*
188116 ATTTTTTTAAATATTTTGTAGTGTTAATTATAAGTTTTA
1 ATTTTTTTAAATATTTTGTAGTATTAATTATAAG-TTTA
* * * *
188155 TATTTTTGTGAATCTTTTGTATTATTAATTATAAGTCTTA
1 -ATTTTTTTAAATATTTTGTAGTATTAATTATAAGT-TTA
188195 ATTTTTTT
1 ATTTTTTT
188203 TTTTCATTTT
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
39 8 0.20
40 32 0.80
ACGTcount: A:0.28, C:0.02, G:0.09, T:0.61
Consensus pattern (38 bp):
ATTTTTTTAAATATTTTGTAGTATTAATTATAAGTTTA
Found at i:188293 original size:34 final size:34
Alignment explanation
Indices: 188250--188344 Score: 145
Period size: 34 Copynumber: 2.8 Consensus size: 34
188240 TCTGCTATTA
*
188250 AAGTTTTATTATTTTTGTTTCATTTTGTAGTTTT
1 AAGTCTTATTATTTTTGTTTCATTTTGTAGTTTT
* * *
188284 AAGTCTTATTATTCTTGTTACATTTTTTAGTTTT
1 AAGTCTTATTATTTTTGTTTCATTTTGTAGTTTT
*
188318 AAGCCTTATTATTTTTGTTTCATTTTG
1 AAGTCTTATTATTTTTGTTTCATTTTG
188345 GTGAATATTT
Statistics
Matches: 53, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
34 53 1.00
ACGTcount: A:0.19, C:0.07, G:0.11, T:0.63
Consensus pattern (34 bp):
AAGTCTTATTATTTTTGTTTCATTTTGTAGTTTT
Found at i:196857 original size:34 final size:34
Alignment explanation
Indices: 196814--196969 Score: 144
Period size: 34 Copynumber: 4.7 Consensus size: 34
196804 AATATTCACC
* *
196814 AAAATGAAACAAAAATGATAAGGCTTAAAACTAA
1 AAAATGAAACAAAAATAATAAGACTTAAAACTAA
*
196848 AAAATGAAACAAAAATAATAAGACTTAAAACTAC
1 AAAATGAAACAAAAATAATAAGACTTAAAACTAA
* *
196882 CAAATGAAACAAAAATAATAAAAC-T----CT-A
1 AAAATGAAACAAAAATAATAAGACTTAAAACTAA
* ****
196910 ACAATGGAAACACTGCTAATAAGACTTAAAACTAA
1 AAAAT-GAAACAAAAATAATAAGACTTAAAACTAA
* *
196945 AAAATGGAAAAAAAAATTATAAGAC
1 AAAAT-GAAACAAAAATAATAAGAC
196970 CTATAATTAA
Statistics
Matches: 95, Mismatches: 20, Indels: 13
0.74 0.16 0.10
Matches are distributed among these distances:
28 3 0.03
29 16 0.17
30 1 0.01
33 1 0.01
34 55 0.58
35 19 0.20
ACGTcount: A:0.62, C:0.12, G:0.09, T:0.18
Consensus pattern (34 bp):
AAAATGAAACAAAAATAATAAGACTTAAAACTAA
Found at i:200954 original size:5 final size:5
Alignment explanation
Indices: 200944--200985 Score: 57
Period size: 5 Copynumber: 8.0 Consensus size: 5
200934 AAAAATCATT
*
200944 TGAAA TGAAA TGTAA TGAAA TGAAAA TGAAAA TGAAA TGAAA
1 TGAAA TGAAA TGAAA TGAAA TG-AAA TG-AAA TGAAA TGAAA
200986 AAAGAATTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
5 23 0.68
6 11 0.32
ACGTcount: A:0.60, C:0.00, G:0.19, T:0.21
Consensus pattern (5 bp):
TGAAA
Found at i:201056 original size:20 final size:20
Alignment explanation
Indices: 201018--201057 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
201008 AATAAAAGTT
*
201018 AAAATTATTAAATTTAAAAA
1 AAAATTATTAAATTGAAAAA
201038 AAAATTTATTAAA-TGAAAAA
1 AAAA-TTATTAAATTGAAAAA
201058 TAATTAGTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.33
Consensus pattern (20 bp):
AAAATTATTAAATTGAAAAA
Found at i:201057 original size:21 final size:20
Alignment explanation
Indices: 201018--201057 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
201008 AATAAAAGTT
*
201018 AAAATTATTAAATTTAAAAAA
1 AAAATTATTAAA-TGAAAAAA
*
201039 AAATTTATTAAATGAAAAA
1 AAAATTATTAAATGAAAAA
201058 TAATTAGTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.33
Consensus pattern (20 bp):
AAAATTATTAAATGAAAAAA
Found at i:201153 original size:12 final size:12
Alignment explanation
Indices: 201118--201186 Score: 57
Period size: 12 Copynumber: 5.3 Consensus size: 12
201108 ATTGAAGAAG
201118 TTAAAATAAAAT
1 TTAAAATAAAAT
** *
201130 TTAAGTTGAAAT
1 TTAAAATAAAAT
201142 TTAAAATAAAATT
1 TTAAAATAAAA-T
*
201155 TTAGTTAAGTTAAAAT
1 TTA---AA-ATAAAAT
201171 TTAAAATAAAAT
1 TTAAAATAAAAT
201183 TTAA
1 TTAA
201187 GTTAAAATAA
Statistics
Matches: 44, Mismatches: 8, Indels: 10
0.71 0.13 0.16
Matches are distributed among these distances:
12 27 0.61
13 6 0.14
16 6 0.14
17 5 0.11
ACGTcount: A:0.55, C:0.00, G:0.06, T:0.39
Consensus pattern (12 bp):
TTAAAATAAAAT
Found at i:201162 original size:29 final size:29
Alignment explanation
Indices: 201130--201191 Score: 106
Period size: 29 Copynumber: 2.1 Consensus size: 29
201120 AAAATAAAAT
* *
201130 TTAAGTTGAAATTTAAAATAAAATTTTAG
1 TTAAGTTAAAATTTAAAATAAAATTTAAG
201159 TTAAGTTAAAATTTAAAATAAAATTTAAG
1 TTAAGTTAAAATTTAAAATAAAATTTAAG
201188 TTAA
1 TTAA
201192 AATAAAATCA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.08, T:0.40
Consensus pattern (29 bp):
TTAAGTTAAAATTTAAAATAAAATTTAAG
Found at i:201192 original size:12 final size:12
Alignment explanation
Indices: 201159--201228 Score: 63
Period size: 12 Copynumber: 6.0 Consensus size: 12
201149 AAAATTTTAG
201159 TTAAGTTAAAAT
1 TTAAGTTAAAAT
**
201171 TTAAAATAAAAT
1 TTAAGTTAAAAT
201183 TTAAGTTAAAA-
1 TTAAGTTAAAAT
** * *
201194 -TAAAATCAATT
1 TTAAGTTAAAAT
*
201205 TTAAGTTGAAAT
1 TTAAGTTAAAAT
201217 TTAAGTTAAAAT
1 TTAAGTTAAAAT
201229 AGATTTTTTT
Statistics
Matches: 43, Mismatches: 13, Indels: 4
0.72 0.22 0.07
Matches are distributed among these distances:
10 6 0.14
12 37 0.86
ACGTcount: A:0.53, C:0.01, G:0.07, T:0.39
Consensus pattern (12 bp):
TTAAGTTAAAAT
Found at i:201197 original size:29 final size:29
Alignment explanation
Indices: 201138--201199 Score: 97
Period size: 29 Copynumber: 2.1 Consensus size: 29
201128 ATTTAAGTTG
* **
201138 AAATTTAAAATAAAATTTTAGTTAAGTTA
1 AAATTTAAAATAAAATTTAAGTTAAAATA
201167 AAATTTAAAATAAAATTTAAGTTAAAATA
1 AAATTTAAAATAAAATTTAAGTTAAAATA
201196 AAAT
1 AAAT
201200 CAATTTTAAG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.58, C:0.00, G:0.05, T:0.37
Consensus pattern (29 bp):
AAATTTAAAATAAAATTTAAGTTAAAATA
Found at i:201207 original size:22 final size:22
Alignment explanation
Indices: 201159--201216 Score: 71
Period size: 22 Copynumber: 2.5 Consensus size: 22
201149 AAAATTTTAG
201159 TTAAGTTAAAATTTAAAATAAAAT
1 TTAAGTTAAAA--TAAAATAAAAT
* *
201183 TTAAGTTAAAATAAAATCAATT
1 TTAAGTTAAAATAAAATAAAAT
*
201205 TTAAGTTGAAAT
1 TTAAGTTAAAAT
201217 TTAAGTTAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
22 20 0.65
24 11 0.35
ACGTcount: A:0.53, C:0.02, G:0.07, T:0.38
Consensus pattern (22 bp):
TTAAGTTAAAATAAAATAAAAT
Found at i:201208 original size:17 final size:17
Alignment explanation
Indices: 201168--201205 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
201158 GTTAAGTTAA
*
201168 AATTTAAAATAAAATTT
1 AATTTAAAATAAAATTC
*
201185 AAGTTAAAATAAAA-TC
1 AATTTAAAATAAAATTC
201201 AATTT
1 AATTT
201206 TAAGTTGAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
16 5 0.28
17 13 0.72
ACGTcount: A:0.58, C:0.03, G:0.03, T:0.37
Consensus pattern (17 bp):
AATTTAAAATAAAATTC
Found at i:201473 original size:30 final size:29
Alignment explanation
Indices: 201437--201543 Score: 70
Period size: 30 Copynumber: 3.3 Consensus size: 29
201427 AAACTTTTAA
*
201437 AAAATAATAATAATTTTTAATATATAATTT
1 AAAA-AATAATAATTTTTAATATATATTTT
* *
201467 AAAATAAAAATTTATTTTTATTTTTAATATATATTTTT
1 AAAA-AATAA--TA---AT-TTTT-AATATATA-TTTT
* *
201505 AAAAAATATATAAATTTGAATATATATTTT
1 AAAAAATA-ATAATTTTTAATATATATTTT
201535 AAAAAATAA
1 AAAAAATAA
201544 AACTTATAAA
Statistics
Matches: 61, Mismatches: 7, Indels: 19
0.70 0.08 0.22
Matches are distributed among these distances:
29 1 0.02
30 21 0.34
31 8 0.13
32 5 0.08
35 1 0.02
36 6 0.10
37 11 0.18
38 8 0.13
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.47
Consensus pattern (29 bp):
AAAAAATAATAATTTTTAATATATATTTT
Found at i:201591 original size:10 final size:9
Alignment explanation
Indices: 201559--201590 Score: 55
Period size: 9 Copynumber: 3.4 Consensus size: 9
201549 ATAAAAGGGG
201559 AAAATTATT
1 AAAATTATT
201568 AAAATATATT
1 AAAAT-TATT
201578 AAAATTATT
1 AAAATTATT
201587 AAAA
1 AAAA
201591 AATAAAACTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 13 0.59
10 9 0.41
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (9 bp):
AAAATTATT
Found at i:201696 original size:14 final size:16
Alignment explanation
Indices: 201660--201696 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
201650 AAAAATAACA
201660 ATAAA-TTTTAATTAT
1 ATAAATTTTTAATTAT
201675 ATAAATTTTTAATT-T
1 ATAAATTTTTAATTAT
201690 A-AAATTT
1 ATAAATTT
201697 ATATTTTAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 6 0.29
15 7 0.33
16 8 0.38
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (16 bp):
ATAAATTTTTAATTAT
Found at i:204795 original size:29 final size:31
Alignment explanation
Indices: 204736--204795 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
204726 TTCTCGCTTC
*
204736 ACATTACAGTATATAATTCAAATCCGAGAAT
1 ACATTACAGTATATAATTCAAATCCAAGAAT
204767 ACATTACAGTATATAATT-AAA-CCAAGAAT
1 ACATTACAGTATATAATTCAAATCCAAGAAT
204796 TCGGTTGCAC
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 7 0.25
30 3 0.11
31 18 0.64
ACGTcount: A:0.48, C:0.15, G:0.08, T:0.28
Consensus pattern (31 bp):
ACATTACAGTATATAATTCAAATCCAAGAAT
Found at i:213079 original size:27 final size:27
Alignment explanation
Indices: 213041--213093 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
213031 GAACAACGTT
213041 GGAATCTAACGGGGAGTGGCGATGGTC
1 GGAATCTAACGGGGAGTGGCGATGGTC
*
213068 GGAATCTAACGGGGAGTGGCGGTGGT
1 GGAATCTAACGGGGAGTGGCGATGGT
213094 GGCGTCAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.21, C:0.13, G:0.47, T:0.19
Consensus pattern (27 bp):
GGAATCTAACGGGGAGTGGCGATGGTC
Found at i:223958 original size:43 final size:45
Alignment explanation
Indices: 223910--224023 Score: 126
Period size: 43 Copynumber: 2.6 Consensus size: 45
223900 AATAACATCC
** *
223910 AAACAACA-AAAATAACAACCAAAATAGCAGTAAAAACAATAG-A
1 AAACAACATAAAATAACAACCAAAATAGCAACAAAAACAACAGAA
* * * *
223953 AAACAACATTAAA-AAGAACAAAAATAGCAACAAAAATAACAGCAA
1 AAACAACATAAAATAACAACCAAAATAGCAACAAAAACAACAG-AA
223998 AAACAACATGAAAATAACAACCAAAA
1 AAACAACAT-AAAATAACAACCAAAA
224024 CAGTAAAAAA
Statistics
Matches: 56, Mismatches: 10, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
43 31 0.55
44 3 0.05
45 10 0.18
46 3 0.05
47 9 0.16
ACGTcount: A:0.68, C:0.17, G:0.06, T:0.09
Consensus pattern (45 bp):
AAACAACATAAAATAACAACCAAAATAGCAACAAAAACAACAGAA
Found at i:224055 original size:31 final size:31
Alignment explanation
Indices: 224028--224089 Score: 92
Period size: 30 Copynumber: 2.1 Consensus size: 31
224018 CCAAAACAGT
*
224028 AAAAAAAAAGC-ATCAAAACAATAAAAACAC
1 AAAAAAAAAGCAACCAAAACAATAAAAACAC
*
224058 AAAAAAAAAGCAACCAAAACAGTAAAAA-AC
1 AAAAAAAAAGCAACCAAAACAATAAAAACAC
224088 AA
1 AA
224090 CACCAAAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 15 0.52
31 14 0.48
ACGTcount: A:0.74, C:0.16, G:0.05, T:0.05
Consensus pattern (31 bp):
AAAAAAAAAGCAACCAAAACAATAAAAACAC
Found at i:229765 original size:11 final size:12
Alignment explanation
Indices: 229751--229793 Score: 58
Period size: 11 Copynumber: 3.9 Consensus size: 12
229741 AGAATAACCC
229751 ATAAA-TAAATA
1 ATAAATTAAATA
229762 ATAAA-T-AATA
1 ATAAATTAAATA
229772 ATAAATTAAATA
1 ATAAATTAAATA
229784 A-AAATTAAAT
1 ATAAATTAAAT
229794 GTCAGTAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
10 9 0.30
11 16 0.53
12 5 0.17
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (12 bp):
ATAAATTAAATA
Found at i:231634 original size:45 final size:44
Alignment explanation
Indices: 231565--231921 Score: 296
Period size: 45 Copynumber: 8.0 Consensus size: 44
231555 TAATCTATCT
* * * *
231565 CTCT-GATTAAGGGTAGAAGATTGGATGGTGACTTCAACTTGTCC
1 CTCTGGATT-AGGGTAAAAGGTTGGATGATGACTTCAACTTGCCC
* *
231609 CTCTGGATTAGGTGTAAAATGTTGGATTG-TGACTTCAACCTGCCC
1 CTCTGGATTAGG-GTAAAAGGTTGGA-TGATGACTTCAACTTGCCC
* * **
231654 CTTTGGATTAATGGT-AAAGGTTGGATGATGGTTTCAA-TCTGCCC
1 CTCTGGATT-AGGGTAAAAGGTTGGATGATGACTTCAACT-TGCCC
* * * *
231698 CTCTGGATTAAAGGTAAAAGGTTGGCTGAT-AGCTT-AAATCTACCC
1 CTCTGGATT-AGGGTAAAAGGTTGGATGATGA-CTTCAACT-TGCCC
* * *
231743 CTCTAGG-TTAGGGGTAAAAGATTGGATGATGGCTTCAATTTGCCC
1 CTCT-GGATTA-GGGTAAAAGGTTGGATGATGACTTCAACTTGCCC
* *
231788 CTCTGGATTAGAGGTAAAAGATTGGATGATGACTTCAACTTGTCC
1 CTCTGGATTAG-GGTAAAAGGTTGGATGATGACTTCAACTTGCCC
* * * * *
231833 CTCTAGATTAGGGGTAAAAGGTTGGATGGTAACTTCAACCTGCCT
1 CTCTGGATTA-GGGTAAAAGGTTGGATGATGACTTCAACTTGCCC
* * * *
231878 CTTTGGATTATGGGTAAAAGGTCGGATGATGGCTTCAACCTGCC
1 CTCTGGATTA-GGGTAAAAGGTTGGATGATGACTTCAACTTGCC
231922 GCTTGGTAAC
Statistics
Matches: 257, Mismatches: 40, Indels: 31
0.78 0.12 0.09
Matches are distributed among these distances:
43 2 0.01
44 47 0.18
45 198 0.77
46 10 0.04
ACGTcount: A:0.25, C:0.17, G:0.26, T:0.31
Consensus pattern (44 bp):
CTCTGGATTAGGGTAAAAGGTTGGATGATGACTTCAACTTGCCC
Found at i:231914 original size:90 final size:90
Alignment explanation
Indices: 231514--231916 Score: 336
Period size: 90 Copynumber: 4.5 Consensus size: 90
231504 TAACTTCATT
* * * * *
231514 CTGCCCCTCTAGATTAGGGGTAAAA-GTCTGGATAATGGCTTTAA-TCTATCTCTCT-GATTAAG
1 CTGCCCCTCTGGATTA-GGGTAAAAGGT-TGGATGATGGCTTCAACTCTACCCCTCTAGATTAAG
* *
231576 GGTAGAAGATTGGATGGTGACTTCAAC
64 GGTAAAAGATTGGATGATGACTTCAAC
* * * * * * * *
231603 TTGTCCCTCTGGATTAGGTGTAAAATGTTGGATTG-TGACTTCAAC-CTGCCCCTTTGGATTAAT
1 CTGCCCCTCTGGATTAGG-GTAAAAGGTTGGA-TGATGGCTTCAACTCTACCCCTCTAGATTAAG
* ** *
231666 GGT-AAAGGTTGGATGATGGTTTCAAT
64 GGTAAAAGATTGGATGATGACTTCAAC
* * * * * *
231692 CTGCCCCTCTGGATTAAAGGTAAAAGGTTGGCTGATAGCTT-AAATCTACCCCTCTAGGTTAGGG
1 CTGCCCCTCTGGATT-AGGGTAAAAGGTTGGATGATGGCTTCAACTCTACCCCTCTAGATTAAGG
* *
231756 GTAAAAGATTGGATGATGGCTTCAAT
65 GTAAAAGATTGGATGATGACTTCAAC
* * * ** *
231782 TTGCCCCTCTGGATTAGAGGTAAAAGATTGGATGATGACTTCAACT-TGTCCCTCTAGATTAGGG
1 CTGCCCCTCTGGATTAG-GGTAAAAGGTTGGATGATGGCTTCAACTCTACCCCTCTAGATTAAGG
* * *
231846 GTAAAAGGTTGGATGGTAACTTCAAC
65 GTAAAAGATTGGATGATGACTTCAAC
* * *
231872 CTGCCTCTTTGGATTATGGGTAAAAGGTCGGATGATGGCTTCAAC
1 CTGCCCCTCTGGATTA-GGGTAAAAGGTTGGATGATGGCTTCAAC
231917 CTGCCGCTTG
Statistics
Matches: 248, Mismatches: 54, Indels: 23
0.76 0.17 0.07
Matches are distributed among these distances:
88 6 0.02
89 97 0.39
90 141 0.57
91 4 0.02
ACGTcount: A:0.26, C:0.17, G:0.26, T:0.32
Consensus pattern (90 bp):
CTGCCCCTCTGGATTAGGGTAAAAGGTTGGATGATGGCTTCAACTCTACCCCTCTAGATTAAGGG
TAAAAGATTGGATGATGACTTCAAC
Found at i:231986 original size:26 final size:26
Alignment explanation
Indices: 231947--231997 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
231937 CCTGCCTCTT
* *
231947 TGGATTATGGGTAAAAGGTTGGATGA
1 TGGATTAAGGGTAAAAGGCTGGATGA
*
231973 TGGATTAAGTGTAAAAGGCTGGATG
1 TGGATTAAGGGTAAAAGGCTGGATG
231998 GCTTCAACCT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.31, C:0.02, G:0.37, T:0.29
Consensus pattern (26 bp):
TGGATTAAGGGTAAAAGGCTGGATGA
Found at i:232040 original size:42 final size:44
Alignment explanation
Indices: 231973--232082 Score: 125
Period size: 45 Copynumber: 2.5 Consensus size: 44
231963 GGTTGGATGA
* * *
231973 TGGATTAAGTGTAAAAGGCTGGAT-G-GCTTCAACCTGCCCTTT
1 TGGATTAAGGGTAAAAGGCTAGATGGTGCTTCAACCTGCCCTTC
* * *
232015 TGGATTAAGGGTAAAAGGTTAGATGGTTGTTTCAATCTGCCCTTC
1 TGGATTAAGGGTAAAAGGCTAGATGG-TGCTTCAACCTGCCCTTC
* *
232060 TGGATTAGGGGTAAAAGACTAGA
1 TGGATTAAGGGTAAAAGGCTAGA
232083 AGGCTACTTC
Statistics
Matches: 56, Mismatches: 9, Indels: 3
0.82 0.13 0.04
Matches are distributed among these distances:
42 21 0.38
43 1 0.02
45 34 0.61
ACGTcount: A:0.27, C:0.14, G:0.28, T:0.31
Consensus pattern (44 bp):
TGGATTAAGGGTAAAAGGCTAGATGGTGCTTCAACCTGCCCTTC
Found at i:232167 original size:45 final size:45
Alignment explanation
Indices: 231994--232167 Score: 118
Period size: 45 Copynumber: 3.9 Consensus size: 45
231984 TAAAAGGCTG
* * * * **
231994 GATGGCTTCAACCTGCCCTTTTGGATTAA-GGGTAAAAGGTTAGAT
1 GATGGCTTCAATCTGCCCCTCTAGA-TAAGGGGTAAAAGACTAGAT
* * * * * * *
232039 GGTTGTTTCAATCTGCCCTTCTGGATTAGGGGTAAAAGACTAGAAG
1 GATGGCTTCAATCTGCCCCTCTAGATAAGGGGTAAAAGACTAG-AT
* * * * * * * * *
232085 GCT-ACTTCATTCTACCCCTTTATATTAGAGGTGAAAGACTAGAT
1 GATGGCTTCAATCTGCCCCTCTAGATAAGGGGTAAAAGACTAGAT
232129 GATGGCTTCAATCTGCCCCTCTAGATAAGGGGTAAAAGA
1 GATGGCTTCAATCTGCCCCTCTAGATAAGGGGTAAAAGA
232168 TTGAATGGCG
Statistics
Matches: 96, Mismatches: 30, Indels: 6
0.73 0.23 0.05
Matches are distributed among these distances:
44 5 0.05
45 88 0.92
46 3 0.03
ACGTcount: A:0.28, C:0.18, G:0.24, T:0.30
Consensus pattern (45 bp):
GATGGCTTCAATCTGCCCCTCTAGATAAGGGGTAAAAGACTAGAT
Found at i:239361 original size:29 final size:31
Alignment explanation
Indices: 239310--239368 Score: 95
Period size: 29 Copynumber: 2.0 Consensus size: 31
239300 TTAACACTAC
*
239310 AAATTAAATGCAACATATATAAAA-AAAATA
1 AAATGAAATGCAACATATATAAAATAAAATA
239340 AAATGAAA-GCAACATATATAAAATAAAAT
1 AAATGAAATGCAACATATATAAAATAAAAT
239369 GCAAAAGATC
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 15 0.56
30 12 0.44
ACGTcount: A:0.66, C:0.07, G:0.05, T:0.22
Consensus pattern (31 bp):
AAATGAAATGCAACATATATAAAATAAAATA
Found at i:241718 original size:21 final size:20
Alignment explanation
Indices: 241689--241750 Score: 65
Period size: 21 Copynumber: 3.0 Consensus size: 20
241679 AAATCAATAT
*
241689 AAATTAAAAATTAAT-TAAA
1 AAATGAAAAATTAATATAAA
241708 AATCATGAAAAA-TAATATAACA
1 AA--ATGAAAAATTAATATAA-A
*
241730 AAATGAAAAATAAATATAAA
1 AAATGAAAAATTAATATAAA
241750 A
1 A
241751 TAATAATTAT
Statistics
Matches: 36, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
19 2 0.06
20 14 0.39
21 17 0.47
22 3 0.08
ACGTcount: A:0.69, C:0.03, G:0.03, T:0.24
Consensus pattern (20 bp):
AAATGAAAAATTAATATAAA
Found at i:241851 original size:19 final size:19
Alignment explanation
Indices: 241806--241852 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 19
241796 TAACAAAATT
241806 ATCTATTT-AAATTTATAA
1 ATCTATTTAAAATTTATAA
241824 AT-TATTTTAAAATTT-TAA
1 ATCTA-TTTAAAATTTATAA
241842 ATACTATTTAA
1 AT-CTATTTAA
241853 TTTCTAAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
17 2 0.08
18 10 0.40
19 11 0.44
20 2 0.08
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (19 bp):
ATCTATTTAAAATTTATAA
Found at i:242117 original size:26 final size:26
Alignment explanation
Indices: 242044--242117 Score: 73
Period size: 26 Copynumber: 2.8 Consensus size: 26
242034 TTAAAATAAG
*
242044 ATTATAAATATGATCTTGTTATGAAT
1 ATTATAAATATGATCTTGTTATCAAT
* *
242070 ATTTTATTAAGTA-GAT-GT-TTATCAAT
1 A--TTA-TAAATATGATCTTGTTATCAAT
242096 ATTATAAATATGATCTTGTTAT
1 ATTATAAATATGATCTTGTTAT
242118 ATGATCTTGT
Statistics
Matches: 37, Mismatches: 5, Indels: 12
0.69 0.09 0.22
Matches are distributed among these distances:
23 5 0.14
24 6 0.16
25 1 0.03
26 13 0.35
27 1 0.03
28 6 0.16
29 5 0.14
ACGTcount: A:0.36, C:0.04, G:0.11, T:0.49
Consensus pattern (26 bp):
ATTATAAATATGATCTTGTTATCAAT
Found at i:242121 original size:13 final size:13
Alignment explanation
Indices: 242103--242130 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
242093 AATATTATAA
242103 ATATGATCTTGTT
1 ATATGATCTTGTT
242116 ATATGATCTTGTT
1 ATATGATCTTGTT
242129 AT
1 AT
242131 GAATATTTTA
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:0.25, C:0.07, G:0.14, T:0.54
Consensus pattern (13 bp):
ATATGATCTTGTT
Found at i:245659 original size:57 final size:59
Alignment explanation
Indices: 245542--245687 Score: 172
Period size: 58 Copynumber: 2.5 Consensus size: 59
245532 ATATGTTATG
* * * *
245542 ATTTTTA-TCAATTCATAATTTAATAATAGTTATATTAAAAATGTTATTAAATTATATATT
1 ATTTTTATTAAATT-AT-ATTTAATAATAATTATATTAAAAATATAATTAAATTATATATT
* * * * *
245602 A-TTTTATTTAATTTTATTTAATAATAATTTTGTT-AAAATATAATTAAATTATTTATT
1 ATTTTTATTAAATTATATTTAATAATAATTATATTAAAAATATAATTAAATTATATATT
245659 ATTTTTATTAAATTATATTTAATAATAAT
1 ATTTTTATTAAATTATATTTAATAATAAT
245688 AATAATAATA
Statistics
Matches: 74, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
57 21 0.28
58 41 0.55
59 6 0.08
60 6 0.08
ACGTcount: A:0.42, C:0.01, G:0.02, T:0.54
Consensus pattern (59 bp):
ATTTTTATTAAATTATATTTAATAATAATTATATTAAAAATATAATTAAATTATATATT
Found at i:245879 original size:16 final size:16
Alignment explanation
Indices: 245860--245906 Score: 67
Period size: 16 Copynumber: 2.9 Consensus size: 16
245850 AGTCTTATCC
245860 CATTACAACTCTATTA
1 CATTACAACTCTATTA
* *
245876 CATTACAAATCTATTC
1 CATTACAACTCTATTA
*
245892 CATTACATCTCTATT
1 CATTACAACTCTATT
245907 TCACTACAGC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.34, C:0.26, G:0.00, T:0.40
Consensus pattern (16 bp):
CATTACAACTCTATTA
Found at i:245882 original size:32 final size:31
Alignment explanation
Indices: 245845--245915 Score: 79
Period size: 32 Copynumber: 2.2 Consensus size: 31
245835 TGAAATATTG
245845 ATTACAGTCTTATCCCATTACAACTCTATTAC
1 ATTACAGTC-TATCCCATTACAACTCTATTAC
* * * *
245877 ATTACAAATCTATTCCATTACATCTCTATTTC
1 ATTAC-AGTCTATCCCATTACAACTCTATTAC
*
245909 ACTACAG
1 ATTACAG
245916 CAAACCAAAC
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
31 1 0.03
32 28 0.88
33 3 0.09
ACGTcount: A:0.32, C:0.27, G:0.03, T:0.38
Consensus pattern (31 bp):
ATTACAGTCTATCCCATTACAACTCTATTAC
Found at i:258318 original size:18 final size:18
Alignment explanation
Indices: 258291--258327 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
258281 CATAATTCTA
258291 GAGGCAGAGGTGGACGTG
1 GAGGCAGAGGTGGACGTG
* *
258309 GAGGCGGAGGTGGAGGTG
1 GAGGCAGAGGTGGACGTG
258327 G
1 G
258328 TCGGGGACGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.19, C:0.08, G:0.62, T:0.11
Consensus pattern (18 bp):
GAGGCAGAGGTGGACGTG
Done.