Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014906.1 Kokia drynarioides strain JFW-HI SEQ_129949, 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: 242657
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Warning! 399 characters in sequence are not A, C, G, or T
Found at i:6548 original size:15 final size:16
Alignment explanation
Indices: 6530--6562 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
6520 TAAAATAATT
*
6530 AAAAATA-AAATTTTA
1 AAAAATAGAAAATTTA
6545 AAAAATAGAAAATTTA
1 AAAAATAGAAAATTTA
6561 AA
1 AA
6563 TATTAAGGTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (16 bp):
AAAAATAGAAAATTTA
Found at i:6597 original size:22 final size:22
Alignment explanation
Indices: 6556--6617 Score: 70
Period size: 22 Copynumber: 2.8 Consensus size: 22
6546 AAAATAGAAA
* *
6556 ATTTAAATATTAAGGTAAATAAT
1 ATTTATAT-TTAAGATAAATAAT
* * *
6579 TTTTATCTTTATGATAAATAAT
1 ATTTATATTTAAGATAAATAAT
6601 ATTTATATTTAAGATAA
1 ATTTATATTTAAGATAA
6618 TATTACGATA
Statistics
Matches: 31, Mismatches: 8, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
22 26 0.84
23 5 0.16
ACGTcount: A:0.45, C:0.02, G:0.06, T:0.47
Consensus pattern (22 bp):
ATTTATATTTAAGATAAATAAT
Found at i:6909 original size:26 final size:27
Alignment explanation
Indices: 6865--6916 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
6855 TTTCATATAC
6865 ATTTTTAGATTATACATTTTAAAATTT
1 ATTTTTAGATTATACATTTTAAAATTT
** *
6892 ATTTTTATTTTATA-ATTTTTAAATT
1 ATTTTTAGATTATACATTTTAAAATT
6917 ATATATGTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 10 0.45
27 12 0.55
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.62
Consensus pattern (27 bp):
ATTTTTAGATTATACATTTTAAAATTT
Found at i:32538 original size:23 final size:25
Alignment explanation
Indices: 32491--32543 Score: 83
Period size: 23 Copynumber: 2.2 Consensus size: 25
32481 AAATTAATCC
*
32491 AAATATAAATAGGAGTGTTGAATTT
1 AAATAGAAATAGGAGTGTTGAATTT
32516 AAATAGAAATAGGA-T-TTGAATTT
1 AAATAGAAATAGGAGTGTTGAATTT
32539 AAATA
1 AAATA
32544 CAAAATAGCA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 13 0.48
24 1 0.04
25 13 0.48
ACGTcount: A:0.49, C:0.00, G:0.17, T:0.34
Consensus pattern (25 bp):
AAATAGAAATAGGAGTGTTGAATTT
Found at i:32556 original size:24 final size:23
Alignment explanation
Indices: 32508--32556 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
32498 AATAGGAGTG
* *
32508 TTGAATTTAAATAGAAATAGGAT
1 TTGAATTTAAATAAAAATAGCAT
32531 TTGAATTTAAATACAAAATAGCAT
1 TTGAATTTAAATA-AAAATAGCAT
32555 TT
1 TT
32557 ATTGGGTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 13 0.57
24 10 0.43
ACGTcount: A:0.47, C:0.04, G:0.12, T:0.37
Consensus pattern (23 bp):
TTGAATTTAAATAAAAATAGCAT
Found at i:40255 original size:21 final size:21
Alignment explanation
Indices: 40231--40271 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
40221 TATATTGTAA
*
40231 TTTT-AATTTTAGTCTTTTTTT
1 TTTTAAATTATAGT-TTTTTTT
40252 TTTTAAATTATAGTTTTTTT
1 TTTTAAATTATAGTTTTTTT
40272 AATATAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.20, C:0.02, G:0.05, T:0.73
Consensus pattern (21 bp):
TTTTAAATTATAGTTTTTTTT
Found at i:50999 original size:2 final size:2
Alignment explanation
Indices: 50992--51028 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
50982 CACCAATCAT
50992 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
51029 TGCCCAATTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:52585 original size:43 final size:43
Alignment explanation
Indices: 52536--52622 Score: 174
Period size: 43 Copynumber: 2.0 Consensus size: 43
52526 ATTCAATCCA
52536 AGTTTATGTGCACAAATTGAAATGTGTTTATAAATTCTACACT
1 AGTTTATGTGCACAAATTGAAATGTGTTTATAAATTCTACACT
52579 AGTTTATGTGCACAAATTGAAATGTGTTTATAAATTCTACACT
1 AGTTTATGTGCACAAATTGAAATGTGTTTATAAATTCTACACT
52622 A
1 A
52623 ACCTATAAGA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.36, C:0.11, G:0.14, T:0.39
Consensus pattern (43 bp):
AGTTTATGTGCACAAATTGAAATGTGTTTATAAATTCTACACT
Found at i:69546 original size:30 final size:33
Alignment explanation
Indices: 69466--69549 Score: 86
Period size: 30 Copynumber: 2.6 Consensus size: 33
69456 GTTATATTTG
69466 AATATTTAAAATATAAT-TTATATAATCTAATTA
1 AATATTTAAAAT-TAATATTATATAATCTAATTA
* * *
69499 AATTTTTAAATAATTAATATTA-ATTA-CTTA-TA
1 AATATTT-AA-AATTAATATTATATAATCTAATTA
69531 AATATTTAAAATTAATATT
1 AATATTTAAAATTAATATT
69550 TCATATATTA
Statistics
Matches: 44, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
30 10 0.23
31 2 0.05
32 8 0.18
33 9 0.20
34 9 0.20
35 6 0.14
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (33 bp):
AATATTTAAAATTAATATTATATAATCTAATTA
Found at i:77779 original size:11 final size:12
Alignment explanation
Indices: 77758--77783 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
77748 ACATATTATT
77758 AAAAAGAAAAAA
1 AAAAAGAAAAAA
77770 AAAAAGAAAAAA
1 AAAAAGAAAAAA
77782 AA
1 AA
77784 TAGAGTATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (12 bp):
AAAAAGAAAAAA
Found at i:80182 original size:25 final size:25
Alignment explanation
Indices: 80154--80203 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
80144 TCTTTTTTTA
80154 AAAAAAATACTTCCTTTTGTTCTTC
1 AAAAAAATACTTCCTTTTGTTCTTC
*
80179 AAAAAATTACTTCCTTTTGTTCTTC
1 AAAAAAATACTTCCTTTTGTTCTTC
80204 TTATTACAGC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.30, C:0.20, G:0.04, T:0.46
Consensus pattern (25 bp):
AAAAAAATACTTCCTTTTGTTCTTC
Found at i:85671 original size:47 final size:46
Alignment explanation
Indices: 85604--85694 Score: 121
Period size: 45 Copynumber: 2.0 Consensus size: 46
85594 TAATAAAAAC
* **
85604 GATTGAAATTAAAATATAATCAATTTTTTTTATAATATATAAAAAAGG
1 GATTAAAATTAAAATATAATC-A-TTTTTCCATAATATATAAAAAAGG
*
85652 GATTAAAATTAAAAT-TAATCATTTTTCCATAATGTATAAAAAA
1 GATTAAAATTAAAATATAATCATTTTTCCATAATATATAAAAAA
85695 AGCGCACCAA
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
45 19 0.49
46 1 0.03
47 5 0.13
48 14 0.36
ACGTcount: A:0.51, C:0.04, G:0.07, T:0.38
Consensus pattern (46 bp):
GATTAAAATTAAAATATAATCATTTTTCCATAATATATAAAAAAGG
Found at i:85695 original size:47 final size:48
Alignment explanation
Indices: 85604--85696 Score: 111
Period size: 48 Copynumber: 2.0 Consensus size: 48
85594 TAATAAAAAC
* ** *
85604 GATTGAAATTAAAATATAATCAATTTTTTTTATAATATATAAAAAAGG
1 GATTAAAATTAAAATATAATCAATTTTTTCCATAATATAAAAAAAAGG
*
85652 GATTAAAATTAAAAT-TAATC-A-TTTTTCCATAATGTATAAAAAAAG
1 GATTAAAATTAAAATATAATCAATTTTTTCCATAATATA-AAAAAAAG
85697 CGCACCAATG
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
45 12 0.31
46 8 0.21
47 5 0.13
48 14 0.36
ACGTcount: A:0.51, C:0.04, G:0.08, T:0.38
Consensus pattern (48 bp):
GATTAAAATTAAAATATAATCAATTTTTTCCATAATATAAAAAAAAGG
Found at i:98208 original size:16 final size:16
Alignment explanation
Indices: 98189--98228 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
98179 AAAATAATAT
98189 ATTATTAAT-TAATAAA
1 ATTATTAATCT-ATAAA
*
98205 ATTATAAATCTATAAA
1 ATTATTAATCTATAAA
98221 ATTATTAA
1 ATTATTAA
98229 ATACAGTTGT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
16 20 0.95
17 1 0.05
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (16 bp):
ATTATTAATCTATAAA
Found at i:98267 original size:22 final size:23
Alignment explanation
Indices: 98242--98291 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
98232 CAGTTGTATA
*
98242 AATT-AAAGATAAATAAAAACCC
1 AATTCAAACATAAATAAAAACCC
**
98264 AATTCTTACATAAATAAAAACCC
1 AATTCAAACATAAATAAAAACCC
98287 AATTC
1 AATTC
98292 TTACATATAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
22 4 0.17
23 20 0.83
ACGTcount: A:0.56, C:0.18, G:0.02, T:0.24
Consensus pattern (23 bp):
AATTCAAACATAAATAAAAACCC
Found at i:98278 original size:23 final size:23
Alignment explanation
Indices: 98250--98298 Score: 98
Period size: 23 Copynumber: 2.1 Consensus size: 23
98240 TAAATTAAAG
98250 ATAAATAAAAACCCAATTCTTAC
1 ATAAATAAAAACCCAATTCTTAC
98273 ATAAATAAAAACCCAATTCTTAC
1 ATAAATAAAAACCCAATTCTTAC
98296 ATA
1 ATA
98299 TAAATATGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.53, C:0.20, G:0.00, T:0.27
Consensus pattern (23 bp):
ATAAATAAAAACCCAATTCTTAC
Found at i:101516 original size:3 final size:3
Alignment explanation
Indices: 101508--101540 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
101498 TTGACATATC
*
101508 CTT CTT CTT CTT CTT CTT CTT CTG CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
101541 TTTTTTTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.00, C:0.33, G:0.03, T:0.64
Consensus pattern (3 bp):
CTT
Found at i:102176 original size:134 final size:134
Alignment explanation
Indices: 101936--102205 Score: 522
Period size: 134 Copynumber: 2.0 Consensus size: 134
101926 AGCCAGATTC
101936 ATAGCCCAAAATTCACTTAGAAATTTTCCACACCGTGCAGGTAACGCTTGCTGAAAACGCCTATT
1 ATAGCCCAAAATTCACTTAGAAATTTTCCACACCGTGCAGGTAACGCTTGCTGAAAACGCCTATT
102001 AACCCAATAGAAGTATTTTCCAAATTGTCAAAAAGTCCTCATAATTGATGATGATTATTACTTGA
66 AACCCAATAGAAGTATTTTCCAAATTGTCAAAAAGTCCTCATAATTGATGATGATTATTACTTGA
102066 TTTG
131 TTTG
* *
102070 ATAGCCCAAAATTCACTTAGAAATTTTCCACACCGTTCAGGTAACGCTTGCTGAAAATGCCTATT
1 ATAGCCCAAAATTCACTTAGAAATTTTCCACACCGTGCAGGTAACGCTTGCTGAAAACGCCTATT
102135 AACCCAATAGAAGTATTTTCCAAATTGTCAAAAAGTCCTCATAATTGATGATGATTATTACTTGA
66 AACCCAATAGAAGTATTTTCCAAATTGTCAAAAAGTCCTCATAATTGATGATGATTATTACTTGA
102200 TTTG
131 TTTG
102204 AT
1 AT
102206 GTACCATTTG
Statistics
Matches: 134, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
134 134 1.00
ACGTcount: A:0.34, C:0.20, G:0.14, T:0.32
Consensus pattern (134 bp):
ATAGCCCAAAATTCACTTAGAAATTTTCCACACCGTGCAGGTAACGCTTGCTGAAAACGCCTATT
AACCCAATAGAAGTATTTTCCAAATTGTCAAAAAGTCCTCATAATTGATGATGATTATTACTTGA
TTTG
Found at i:113196 original size:2 final size:2
Alignment explanation
Indices: 113189--113217 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
113179 GGAAGAAAAT
113189 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
113218 ATAGGAAAGG
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:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:114261 original size:18 final size:18
Alignment explanation
Indices: 114212--114261 Score: 50
Period size: 18 Copynumber: 2.8 Consensus size: 18
114202 ACATACGTAC
114212 ATTTAAAAATAATATACA
1 ATTTAAAAATAATATACA
* *
114230 A-TTATAATTAAATATA-A
1 ATTTAAAAAT-AATATACA
114247 GATTTAAAAATAATA
1 -ATTTAAAAATAATA
114262 ATAACAATAC
Statistics
Matches: 25, Mismatches: 4, Indels: 6
0.71 0.11 0.17
Matches are distributed among these distances:
17 7 0.28
18 12 0.48
19 6 0.24
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (18 bp):
ATTTAAAAATAATATACA
Found at i:122529 original size:12 final size:13
Alignment explanation
Indices: 122510--122539 Score: 51
Period size: 14 Copynumber: 2.2 Consensus size: 13
122500 CGTGTGTGTA
122510 TATATATATATATT
1 TATATATATA-ATT
122524 TATATATATAATT
1 TATATATATAATT
122537 TAT
1 TAT
122540 TAAGAAACTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.38
14 10 0.62
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (13 bp):
TATATATATAATT
Found at i:127568 original size:22 final size:19
Alignment explanation
Indices: 127543--127586 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 19
127533 TTTAATAATG
127543 AATTTTAACAGTAATGATTTTA
1 AATTTTAA-A-TAAT-ATTTTA
127565 AATTTTAAATAATATTTTA
1 AATTTTAAATAATATTTTA
127584 AAT
1 AAT
127587 ATATTATCGA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 9 0.41
20 4 0.18
21 1 0.05
22 8 0.36
ACGTcount: A:0.45, C:0.02, G:0.05, T:0.48
Consensus pattern (19 bp):
AATTTTAAATAATATTTTA
Found at i:127690 original size:24 final size:24
Alignment explanation
Indices: 127663--127712 Score: 59
Period size: 23 Copynumber: 2.1 Consensus size: 24
127653 AATAATAAAT
127663 TTTTTACAGTATA-AAATATGAATA
1 TTTTTA-AGTATATAAATATGAATA
* *
127687 -TTTTAATTATATAAATATGAGTA
1 TTTTTAAGTATATAAATATGAATA
127710 TTT
1 TTT
127713 GTTTAGATCA
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
22 5 0.23
23 15 0.68
24 2 0.09
ACGTcount: A:0.42, C:0.02, G:0.08, T:0.48
Consensus pattern (24 bp):
TTTTTAAGTATATAAATATGAATA
Found at i:130882 original size:18 final size:18
Alignment explanation
Indices: 130859--130899 Score: 82
Period size: 18 Copynumber: 2.3 Consensus size: 18
130849 TTCCTTTTAT
130859 ACAATTCTTAAATTGTCC
1 ACAATTCTTAAATTGTCC
130877 ACAATTCTTAAATTGTCC
1 ACAATTCTTAAATTGTCC
130895 ACAAT
1 ACAAT
130900 CCTTCAATCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.37, C:0.22, G:0.05, T:0.37
Consensus pattern (18 bp):
ACAATTCTTAAATTGTCC
Found at i:141353 original size:20 final size:20
Alignment explanation
Indices: 141328--141368 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
141318 TAATCCACAT
**
141328 TGCAAATATAATTTCTAGGA
1 TGCAAATATAAAGTCTAGGA
*
141348 TGCAAATTTAAAGTCTAGGA
1 TGCAAATATAAAGTCTAGGA
141368 T
1 T
141369 ACTTCACATG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.39, C:0.10, G:0.17, T:0.34
Consensus pattern (20 bp):
TGCAAATATAAAGTCTAGGA
Found at i:143532 original size:19 final size:19
Alignment explanation
Indices: 143504--143568 Score: 57
Period size: 17 Copynumber: 3.6 Consensus size: 19
143494 ATTTTTGAAT
*
143504 TAATAATTAATATAAATAA
1 TAATATTTAATATAAATAA
*
143523 TAATATTTAAAAT-AA-AA
1 TAATATTTAATATAAATAA
* *
143540 TAAAATTT-A-ATAAATTA
1 TAATATTTAATATAAATAA
143557 TAATTATTTAAT
1 TAA-TATTTAAT
143569 TTATCAAAAT
Statistics
Matches: 36, Mismatches: 5, Indels: 9
0.72 0.10 0.18
Matches are distributed among these distances:
15 2 0.06
16 3 0.08
17 13 0.36
18 6 0.17
19 12 0.33
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (19 bp):
TAATATTTAATATAAATAA
Found at i:144383 original size:14 final size:15
Alignment explanation
Indices: 144353--144406 Score: 53
Period size: 15 Copynumber: 3.8 Consensus size: 15
144343 TGATTTCGGC
144353 TTAAATATAATATAT
1 TTAAATATAATATAT
*
144368 TTAAGTATAA-ATATT
1 TTAAATATAATATA-T
144383 TTAAA-AT-ATA-AT
1 TTAAATATAATATAT
*
144395 TTTAATATAATA
1 TTAAATATAATA
144407 ATATGTTTTA
Statistics
Matches: 32, Mismatches: 3, Indels: 9
0.73 0.07 0.20
Matches are distributed among these distances:
12 5 0.16
13 4 0.12
14 9 0.28
15 14 0.44
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (15 bp):
TTAAATATAATATAT
Found at i:144392 original size:16 final size:16
Alignment explanation
Indices: 144353--144393 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
144343 TGATTTCGGC
144353 TTAAATAT-AATATAT
1 TTAAATATAAATATAT
*
144368 TTAAGTATAAATAT-T
1 TTAAATATAAATATAT
144383 TTAAAATATAA
1 TT-AAATATAA
144394 TTTTAATATA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
15 10 0.45
16 12 0.55
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (16 bp):
TTAAATATAAATATAT
Found at i:144406 original size:16 final size:15
Alignment explanation
Indices: 144356--144406 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 15
144346 TTTCGGCTTA
144356 AATATAATATA-TTT
1 AATATAATATATTTT
144370 AAGTATAA-ATATTTT
1 AA-TATAATATATTTT
*
144385 AAAAT-ATA-ATTTT
1 AATATAATATATTTT
144398 AATATAATA
1 AATATAATA
144407 ATATGTTTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
13 10 0.32
14 11 0.35
15 10 0.32
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (15 bp):
AATATAATATATTTT
Found at i:150158 original size:20 final size:22
Alignment explanation
Indices: 150119--150159 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 22
150109 GTGAAAGATG
*
150119 GACGGTAGAGATTCAAACCGTT
1 GACGGTAGAGATTAAAACCGTT
150141 GACGG-AGAG-TTAAAACCGT
1 GACGGTAGAGATTAAAACCGT
150160 GAGTGTTGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 9 0.50
21 4 0.22
22 5 0.28
ACGTcount: A:0.34, C:0.17, G:0.29, T:0.20
Consensus pattern (22 bp):
GACGGTAGAGATTAAAACCGTT
Found at i:151269 original size:14 final size:15
Alignment explanation
Indices: 151241--151273 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
151231 AAATATATTG
151241 ATAAATATAAATTTA
1 ATAAATATAAATTTA
*
151256 ATAAA-ATAATTTTA
1 ATAAATATAAATTTA
151270 ATAA
1 ATAA
151274 TATTAACAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 12 0.71
15 5 0.29
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (15 bp):
ATAAATATAAATTTA
Found at i:151927 original size:11 final size:11
Alignment explanation
Indices: 151862--151931 Score: 50
Period size: 11 Copynumber: 6.0 Consensus size: 11
151852 GCCAATGTTT
*
151862 TAAAATAGTAA
1 TAAAATAATAA
*
151873 CAAAATTAATAA
1 TAAAA-TAATAA
*
151885 TAAAATAAAAA
1 TAAAATAATAA
* * *
151896 TTATATAATATC
1 TAAAATAATA-A
151908 TAAATAATAATAA
1 T-AA-AATAATAA
151921 TAAAATAATAA
1 TAAAATAATAA
151932 CAGTATAATG
Statistics
Matches: 44, Mismatches: 11, Indels: 8
0.70 0.17 0.13
Matches are distributed among these distances:
11 24 0.55
12 12 0.27
13 2 0.05
14 6 0.14
ACGTcount: A:0.66, C:0.03, G:0.01, T:0.30
Consensus pattern (11 bp):
TAAAATAATAA
Found at i:153324 original size:34 final size:34
Alignment explanation
Indices: 153281--153350 Score: 140
Period size: 34 Copynumber: 2.1 Consensus size: 34
153271 TAAAAATAAA
153281 TTAAATTAAATAGTGTCCCTCTTATTATTATTAG
1 TTAAATTAAATAGTGTCCCTCTTATTATTATTAG
153315 TTAAATTAAATAGTGTCCCTCTTATTATTATTAG
1 TTAAATTAAATAGTGTCCCTCTTATTATTATTAG
153349 TT
1 TT
153351 GTGGACTGCA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.31, C:0.11, G:0.09, T:0.49
Consensus pattern (34 bp):
TTAAATTAAATAGTGTCCCTCTTATTATTATTAG
Found at i:170310 original size:23 final size:23
Alignment explanation
Indices: 170237--170385 Score: 115
Period size: 23 Copynumber: 6.4 Consensus size: 23
170227 TATACGAAAC
* *
170237 AAACAGAGAGTAC-CAAAGTAC-
1 AAACAGAGAGCACACAAAGTGCT
* *
170258 CAACAGAGAGCACA-TAAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
* *
170280 GGGCAACAGAGAGCACACACAGTGCT
1 ---AAACAGAGAGCACACAAAGTGCT
* * *
170306 AAACAGGGAGTACACAAAGTACT
1 AAACAGAGAGCACACAAAGTGCT
*
170329 AATCAGAGAGCACACAAAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
* * *
170352 AATCAGAGAGAACACACAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
170375 AATAACAGAGA
1 -A-AACAGAGA
170386 ACACGAGACA
Statistics
Matches: 102, Mismatches: 18, Indels: 12
0.77 0.14 0.09
Matches are distributed among these distances:
21 16 0.16
23 58 0.57
24 1 0.01
25 21 0.21
26 6 0.06
ACGTcount: A:0.45, C:0.21, G:0.23, T:0.11
Consensus pattern (23 bp):
AAACAGAGAGCACACAAAGTGCT
Found at i:170336 original size:46 final size:46
Alignment explanation
Indices: 170286--170377 Score: 130
Period size: 46 Copynumber: 2.0 Consensus size: 46
170276 TGCTGGGCAA
* * *
170286 CAGAGAGCACACACAGTGCTAAACAGGGAGTACACAAAGTACTAAT
1 CAGAGAGCACACAAAGTGCTAAACAGAGAGAACACAAAGTACTAAT
* * *
170332 CAGAGAGCACACAAAGTGCTAATCAGAGAGAACACACAGTGCTAAT
1 CAGAGAGCACACAAAGTGCTAAACAGAGAGAACACAAAGTACTAAT
170378 AACAGAGAAC
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
46 40 1.00
ACGTcount: A:0.43, C:0.22, G:0.22, T:0.13
Consensus pattern (46 bp):
CAGAGAGCACACAAAGTGCTAAACAGAGAGAACACAAAGTACTAAT
Found at i:170359 original size:69 final size:66
Alignment explanation
Indices: 170237--170385 Score: 174
Period size: 69 Copynumber: 2.1 Consensus size: 66
170227 TATACGAAAC
* *
170237 AAACAGAGAGTACCAAAGTACCAACAGAGAGCACATAAGTGCTGGGCAACAGAGAGCACACACAG
1 AAACAGAGAGTACCAAAGTACCAACAGAGAGCACAAAAGTGCT--G-AACAGAGAGAACACACAG
170302 TGCT
63 TGCT
* *
170306 AAACAGGGAGTACACAAAGTACTAATCAGAGAGCACACAAAGTGCT-AATCAGAGAGAACACACA
1 AAACAGAGAGTAC-CAAAGTACCAA-CAGAGAGCACA-AAAGTGCTGAA-CAGAGAGAACACACA
170370 GTGCT
62 GTGCT
170375 AATAACAGAGA
1 -A-AACAGAGA
170386 ACACGAGACA
Statistics
Matches: 69, Mismatches: 5, Indels: 10
0.82 0.06 0.12
Matches are distributed among these distances:
68 2 0.03
69 31 0.45
70 11 0.16
71 18 0.26
72 7 0.10
ACGTcount: A:0.45, C:0.21, G:0.23, T:0.11
Consensus pattern (66 bp):
AAACAGAGAGTACCAAAGTACCAACAGAGAGCACAAAAGTGCTGAACAGAGAGAACACACAGTGC
T
Found at i:174933 original size:23 final size:23
Alignment explanation
Indices: 174843--174944 Score: 98
Period size: 23 Copynumber: 4.3 Consensus size: 23
174833 GCTGGGCAAC
* *
174843 AGAGAGCACACACAGTGCTAAACT
1 AGAGAGCACACAAAGTGCT-AATT
* * *
174867 -GAGAGTACACAAAGTACTAATC
1 AGAGAGCACACAAAGTGCTAATT
* *
174889 AGAGAGCACGCAAAATGCTAATT
1 AGAGAGCACACAAAGTGCTAATT
*
174912 AGAGAGCACACACAGTGCTAATAAT
1 AGAGAGCACACAAAGTGCTAAT--T
174937 AGAGAGCA
1 AGAGAGCA
174945 TGAGACGTGC
Statistics
Matches: 62, Mismatches: 13, Indels: 5
0.77 0.16 0.06
Matches are distributed among these distances:
22 2 0.03
23 51 0.82
25 9 0.15
ACGTcount: A:0.44, C:0.20, G:0.22, T:0.15
Consensus pattern (23 bp):
AGAGAGCACACAAAGTGCTAATT
Found at i:179641 original size:23 final size:24
Alignment explanation
Indices: 179596--179640 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 24
179586 TCCAAATGTA
179596 ATTTTTATTAATTACTTTTAAAAT
1 ATTTTTATTAATTACTTTTAAAAT
*
179620 ATTTTTA-TAATT-GTTTTAAAA
1 ATTTTTATTAATTACTTTTAAAA
179641 AATTACTGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 8 0.40
23 5 0.25
24 7 0.35
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (24 bp):
ATTTTTATTAATTACTTTTAAAAT
Found at i:188357 original size:32 final size:32
Alignment explanation
Indices: 188320--188391 Score: 81
Period size: 32 Copynumber: 2.2 Consensus size: 32
188310 ACGAACTGAT
** *
188320 TGAATCGGTTAAAAATAGATTCAACCAACAAC
1 TGAATCGACTAAAAATAGATTAAACCAACAAC
* * * *
188352 TGAATCGACTAAAATTTGATTAAACTAACAAT
1 TGAATCGACTAAAAATAGATTAAACCAACAAC
188384 TGAATCGA
1 TGAATCGA
188392 ATTTTTTAAA
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.46, C:0.15, G:0.12, T:0.26
Consensus pattern (32 bp):
TGAATCGACTAAAAATAGATTAAACCAACAAC
Found at i:189645 original size:15 final size:15
Alignment explanation
Indices: 189602--189647 Score: 51
Period size: 15 Copynumber: 3.2 Consensus size: 15
189592 GGGTATGATG
* *
189602 ATTTCTAATATTATA
1 ATTTCAAATATTATT
*
189617 AATTCAAATA--ATT
1 ATTTCAAATATTATT
189630 ATTTCAAATATTATT
1 ATTTCAAATATTATT
189645 ATT
1 ATT
189648 ATTTTTATAG
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
13 11 0.44
15 14 0.56
ACGTcount: A:0.43, C:0.07, G:0.00, T:0.50
Consensus pattern (15 bp):
ATTTCAAATATTATT
Found at i:190437 original size:44 final size:45
Alignment explanation
Indices: 190347--190446 Score: 141
Period size: 45 Copynumber: 2.2 Consensus size: 45
190337 GTAATTATAG
* *
190347 AAAAATTAAATGGTTTAATATTAAAAAAAGTTAAAATATAAGTTT
1 AAAAATTAAACGGTTTAAAATTAAAAAAAGTTAAAATATAAGTTT
*
190392 AAAAATTAAACGGTTTAAAATTAAAAAAA-TTAAAATGT-AGATTT
1 AAAAATTAAACGGTTTAAAATTAAAAAAAGTTAAAATATAAG-TTT
190436 AAAATATTAAA
1 AAAA-ATTAAA
190447 ATTTTATACC
Statistics
Matches: 50, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
43 2 0.04
44 15 0.30
45 33 0.66
ACGTcount: A:0.58, C:0.01, G:0.08, T:0.33
Consensus pattern (45 bp):
AAAAATTAAACGGTTTAAAATTAAAAAAAGTTAAAATATAAGTTT
Found at i:190817 original size:17 final size:17
Alignment explanation
Indices: 190797--190832 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
190787 ATATTTAATA
190797 ATTT-TTTACAATTTTTT
1 ATTTATTTA-AATTTTTT
190814 ATTTATTTAAATTTTTT
1 ATTTATTTAAATTTTTT
190831 AT
1 AT
190833 ATAAATATCT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 14 0.78
18 4 0.22
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (17 bp):
ATTTATTTAAATTTTTT
Found at i:193365 original size:26 final size:26
Alignment explanation
Indices: 193328--193380 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
193318 TAATAATAGG
*
193328 AACAATAGGGTATGGGACTGATCTGC
1 AACAATACGGTATGGGACTGATCTGC
193354 AACAATACGGTATGGGACTGATCTGC
1 AACAATACGGTATGGGACTGATCTGC
193380 A
1 A
193381 TTACATAAAG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.32, C:0.17, G:0.28, T:0.23
Consensus pattern (26 bp):
AACAATACGGTATGGGACTGATCTGC
Found at i:193462 original size:16 final size:16
Alignment explanation
Indices: 193441--193474 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
193431 AAAATTCTCC
193441 TCAATGTTGCATGTAA
1 TCAATGTTGCATGTAA
*
193457 TCAATGTTGCCTGTAA
1 TCAATGTTGCATGTAA
193473 TC
1 TC
193475 CAACTTCAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.26, C:0.18, G:0.18, T:0.38
Consensus pattern (16 bp):
TCAATGTTGCATGTAA
Found at i:209726 original size:30 final size:30
Alignment explanation
Indices: 209690--209749 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
209680 CCAAATCCCT
209690 TAGTACCATATCTCATAGAATAAAGAATTA
1 TAGTACCATATCTCATAGAATAAAGAATTA
209720 TAGTACCATATCTCATAGAATAAAGAATTA
1 TAGTACCATATCTCATAGAATAAAGAATTA
209750 ACTAGGATCT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.47, C:0.13, G:0.10, T:0.30
Consensus pattern (30 bp):
TAGTACCATATCTCATAGAATAAAGAATTA
Found at i:210126 original size:16 final size:16
Alignment explanation
Indices: 210105--210137 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
210095 TAAAATTTCT
*
210105 CAGAGATCAACTAATA
1 CAGAGATAAACTAATA
210121 CAGAGATAAACTAATA
1 CAGAGATAAACTAATA
210137 C
1 C
210138 GTTGCTCCCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.52, C:0.18, G:0.12, T:0.18
Consensus pattern (16 bp):
CAGAGATAAACTAATA
Found at i:217022 original size:6 final size:6
Alignment explanation
Indices: 217011--217039 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
217001 TATTTTTCAC
217011 ATTTTT ATTTTT ATTTTT ATTTTT ATTTT
1 ATTTTT ATTTTT ATTTTT ATTTTT ATTTT
217040 CATAATAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (6 bp):
ATTTTT
Found at i:220402 original size:33 final size:31
Alignment explanation
Indices: 220352--220423 Score: 74
Period size: 32 Copynumber: 2.3 Consensus size: 31
220342 TAGAAAAATT
* *
220352 AATATTTTTGATGTTTAA-ATAAATTTGTGTAA
1 AATATTTTTGATATTTAACA-AATTTTGTG-AA
* *
220384 AATATTTTTTATTATTTAACAAATTTTTTGAA
1 AATATTTTTGA-TATTTAACAAATTTTGTGAA
220416 AATATTTT
1 AATATTTT
220424 ATAAAAGCCT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
32 20 0.59
33 13 0.38
34 1 0.03
ACGTcount: A:0.38, C:0.01, G:0.07, T:0.54
Consensus pattern (31 bp):
AATATTTTTGATATTTAACAAATTTTGTGAA
Found at i:221779 original size:204 final size:204
Alignment explanation
Indices: 221429--221905 Score: 724
Period size: 204 Copynumber: 2.3 Consensus size: 204
221419 AATGGGTCAA
* * *
221429 GAAAATGGGGATATCGGAAGCAATCTCAACACTGAGGAGGCTCAAACACAGGGAATAATATGAAT
1 GAAAATGGGGATATTGGAAGCAATCTCAACACTGAGGAGGCTCAAACACAAGGAATGATATGAAT
* *
221494 GACAGCCATTCAGGTGTGGTTGTGAAACCAGCTGATAGATTATTGATGATTCTTCTTACTATTAT
66 GACAGCCATTCAGGTGTGGTGGTGAAACCAACTGATAGATTATTGATGATTCTTCTTACTATTAT
* * * * * * *
221559 TCACTCCTTCCGCTTTGTTCTAAGTTGAGAAGACTGTCGAGTTTATCCCTGCTGAGGTCCATGGT
131 TCACTCCTTCCGCTTTGTTCCAAGTTAACAAGACTCTCGAGTTGATCCCTACTGAGGTCCATAGT
221624 GATGAAGAG
196 GATGAAGAG
*
221633 GAAAATGGGGATATTGGAAGCAATCTCAACGCTGAGGAGGCTCAAACACAAGGAATGATATGAAT
1 GAAAATGGGGATATTGGAAGCAATCTCAACACTGAGGAGGCTCAAACACAAGGAATGATATGAAT
*
221698 GACAGCCATTCATGTGTGGTGGTGAAACCAACTGATAGATTATTGATGATTCTTCTTACTATTAT
66 GACAGCCATTCAGGTGTGGTGGTGAAACCAACTGATAGATTATTGATGATTCTTCTTACTATTAT
* * *
221763 TCATTCCTTCCGCTTTGTTCCAAGTTAACAAGACTCTCGAGTTGATTCCTATTGAGGTCCATAGT
131 TCACTCCTTCCGCTTTGTTCCAAGTTAACAAGACTCTCGAGTTGATCCCTACTGAGGTCCATAGT
221828 GATGAAGAG
196 GATGAAGAG
* *
221837 GAAAATGGGGATA-TCGAGAGCAATCTCAACACTAGAAGGGAGGCTCGAACA-AAGGGAATGATA
1 GAAAATGGGGATATTGGA-AGCAATCTCAACACT-G-A-GGAGGCTCAAACACAA-GGAATGATA
221900 TGAATG
61 TGAATG
221906 GAAAAACCAT
Statistics
Matches: 248, Mismatches: 20, Indels: 7
0.90 0.07 0.03
Matches are distributed among these distances:
203 3 0.01
204 214 0.86
205 1 0.00
206 3 0.01
207 27 0.11
ACGTcount: A:0.31, C:0.17, G:0.25, T:0.27
Consensus pattern (204 bp):
GAAAATGGGGATATTGGAAGCAATCTCAACACTGAGGAGGCTCAAACACAAGGAATGATATGAAT
GACAGCCATTCAGGTGTGGTGGTGAAACCAACTGATAGATTATTGATGATTCTTCTTACTATTAT
TCACTCCTTCCGCTTTGTTCCAAGTTAACAAGACTCTCGAGTTGATCCCTACTGAGGTCCATAGT
GATGAAGAG
Found at i:223866 original size:14 final size:15
Alignment explanation
Indices: 223828--223860 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
223818 TGTTTGATTG
223828 AAAAT-AATTTTTGA
1 AAAATAAATTTTTGA
223842 AAAATAAATTTTT-A
1 AAAATAAATTTTTGA
223856 AAAAT
1 AAAAT
223861 TGATTTATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 11 0.61
15 7 0.39
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (15 bp):
AAAATAAATTTTTGA
Found at i:223941 original size:32 final size:33
Alignment explanation
Indices: 223883--223955 Score: 96
Period size: 32 Copynumber: 2.2 Consensus size: 33
223873 TAAATAAATT
* *
223883 AATATTTTTTATTGTTTGGATGAATTTGTAT-AA
1 AATATTTTTTATTATTTGGATAAATTT-TATAAA
*
223916 AATATTTTTTATTATTT-GATAAATTTTTTAAA
1 AATATTTTTTATTATTTGGATAAATTTTATAAA
223948 AATATTTT
1 AATATTTT
223956 ATAAAAACTT
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
31 2 0.06
32 18 0.50
33 16 0.44
ACGTcount: A:0.34, C:0.00, G:0.08, T:0.58
Consensus pattern (33 bp):
AATATTTTTTATTATTTGGATAAATTTTATAAA
Found at i:224278 original size:32 final size:32
Alignment explanation
Indices: 224242--224305 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
224232 TAAATTCCAA
224242 TTCAACCATTTCTCGTCTCCTTCTCCATCAAC
1 TTCAACCATTTCTCGTCTCCTTCTCCATCAAC
224274 TTCAACCATTTCTCGTCTCCTTCTCCATCAAC
1 TTCAACCATTTCTCGTCTCCTTCTCCATCAAC
224306 CAGTCCACTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.19, C:0.41, G:0.03, T:0.38
Consensus pattern (32 bp):
TTCAACCATTTCTCGTCTCCTTCTCCATCAAC
Found at i:231540 original size:31 final size:31
Alignment explanation
Indices: 231499--231559 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
231489 GATCAGTGAT
* * *
231499 CTATTTAAAAGTTTTTATTTAAGTTACTGAA
1 CTATTCAAAAGCTTTTATTTAAGTCACTGAA
231530 CTATTCAAAAGCTTTTATTTAAGTCACTGA
1 CTATTCAAAAGCTTTTATTTAAGTCACTGA
231560 GTTGTTAATT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.34, C:0.11, G:0.10, T:0.44
Consensus pattern (31 bp):
CTATTCAAAAGCTTTTATTTAAGTCACTGAA
Found at i:231615 original size:20 final size:20
Alignment explanation
Indices: 231592--231632 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
231582 TTGTTAGCAA
231592 GCTCTAAGCAATGATTCGAT
1 GCTCTAAGCAATGATTCGAT
231612 GCTCTAAGCAATGATTCGAT
1 GCTCTAAGCAATGATTCGAT
231632 G
1 G
231633 ATGTATATGG
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:0.29, C:0.20, G:0.22, T:0.29
Consensus pattern (20 bp):
GCTCTAAGCAATGATTCGAT
Found at i:241395 original size:12 final size:12
Alignment explanation
Indices: 241378--241409 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
241368 GGAGAAGTTT
241378 GAAGATGAGGAC
1 GAAGATGAGGAC
*
241390 GAAGATGAGGAT
1 GAAGATGAGGAC
241402 GAAGATGA
1 GAAGATGA
241410 ATCTGGCTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.44, C:0.03, G:0.41, T:0.12
Consensus pattern (12 bp):
GAAGATGAGGAC
Done.