Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012674.1 Kokia drynarioides strain JFW-HI SEQ_127685, 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: 212605
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.34
Warning! 212 characters in sequence are not A, C, G, or T
Found at i:604 original size:9 final size:9
Alignment explanation
Indices: 592--667 Score: 81
Period size: 9 Copynumber: 8.7 Consensus size: 9
582 AAACACATTA
592 CCTTTCTTT
1 CCTTTCTTT
601 CC-TTC-TT
1 CCTTTCTTT
608 -CTTTCTTT
1 CCTTTCTTT
*
616 CCTCTCCTTCTT
1 CCT-TTC-T-TT
628 CCTTTCTTT
1 CCTTTCTTT
637 -CTTTCTTT
1 CCTTTCTTT
645 CCTTTCTTT
1 CCTTTCTTT
654 CCTTTCTTT
1 CCTTTCTTT
663 -CTTTC
1 CCTTTC
668 CCATTTATTT
Statistics
Matches: 58, Mismatches: 2, Indels: 15
0.77 0.03 0.20
Matches are distributed among these distances:
6 1 0.02
7 5 0.09
8 18 0.31
9 23 0.40
10 3 0.05
11 3 0.05
12 5 0.09
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (9 bp):
CCTTTCTTT
Found at i:613 original size:4 final size:4
Alignment explanation
Indices: 593--667 Score: 80
Period size: 4 Copynumber: 18.2 Consensus size: 4
583 AACACATTAC
* * * *
593 CTTT CTTT CCTT C-TT CTTT CTTT CCTCT CCTT CTTC CTTT CTTT CTTT
1 CTTT CTTT CTTT CTTT CTTT CTTT -CTTT CTTT CTTT CTTT CTTT CTTT
641 CTTT CCTTT CTTT CCTTT CTTT CTTT C
1 CTTT -CTTT CTTT -CTTT CTTT CTTT C
668 CCATTTATTT
Statistics
Matches: 60, Mismatches: 7, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
3 3 0.05
4 46 0.77
5 11 0.18
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (4 bp):
CTTT
Found at i:627 original size:17 final size:17
Alignment explanation
Indices: 593--668 Score: 79
Period size: 17 Copynumber: 4.6 Consensus size: 17
583 AACACATTAC
593 CTTTCTTTCC-TT-CTT
1 CTTTCTTTCCTTTCCTT
*
608 CTTTCTTTCCTCTCCTT
1 CTTTCTTTCCTTTCCTT
* *
625 CTTCCTTT-CTTTCTTT
1 CTTTCTTTCCTTTCCTT
641 CTTTCCTTT-CTTTCCTTT
1 CTTT-CTTTCCTTTCC-TT
659 CTTTCTTTCC
1 CTTTCTTTCC
669 CATTTATTTG
Statistics
Matches: 50, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
15 10 0.20
16 10 0.20
17 23 0.46
18 7 0.14
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (17 bp):
CTTTCTTTCCTTTCCTT
Found at i:5569 original size:16 final size:16
Alignment explanation
Indices: 5548--5581 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
5538 TATAATGCTT
* *
5548 TATAATTTTTATTTTA
1 TATAATTTATATATTA
5564 TATAATTTATATATTA
1 TATAATTTATATATTA
5580 TA
1 TA
5582 AAAAAACTGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (16 bp):
TATAATTTATATATTA
Found at i:8042 original size:163 final size:163
Alignment explanation
Indices: 7730--8382 Score: 1067
Period size: 163 Copynumber: 4.0 Consensus size: 163
7720 CTAAGCAAGT
* *
7730 GGTCTGCACTACATGAACATCCTATTACTACATGGAAAGGGATACACAAAGCAGAGTCCACTGCA
1 GGTCTGCACTACATGAACATCCTATTACTACATGGAAAGGGATACACAAAGCAAAGTCCACTACA
*
7795 TAATGAAATGA-TATACCATTGATATGTGGAAAAGAAGGGAAAAAGCAGGCTGCAGATACATGTT
66 TAATGAAATGATTATACCATTGATATGTGAAAAAGAAGGGAAAAAGCAGGCTGCAGATACATGTT
7859 CATCTGTTTATCGACTACCATAAGTGTTGTGAG
131 CATCTGTTTATCGACTACCATAAGTGTTGTGAG
*
7892 GGTCTGCACTACATGAACATCCTATTACTACATGGAAAGGGATACACAAAGCAAAGTCCACTGCA
1 GGTCTGCACTACATGAACATCCTATTACTACATGGAAAGGGATACACAAAGCAAAGTCCACTACA
* *
7957 TAATGAAATGCTTATACCATTGATATGTGGAAAAGAAGGGAAAAAGCAGGCTGCAGATACATGTT
66 TAATGAAATGATTATACCATTGATATGTGAAAAAGAAGGGAAAAAGCAGGCTGCAGATACATGTT
*
8022 CATCTGTTTATCGACTACCATAAGTGTTGTGGG
131 CATCTGTTTATCGACTACCATAAGTGTTGTGAG
* * **
8055 GGTATGCACTAAATGAACATCCTATTACTACATGGAAAGGGATACGTAAAGCAAAGTCCACTACA
1 GGTCTGCACTACATGAACATCCTATTACTACATGGAAAGGGATACACAAAGCAAAGTCCACTACA
*
8120 TAATGAAATGATTATACCATTTG-TATGTGAAAAAGAAGAGAAAAAGCAGCAGGCTGCAGATACA
66 TAATGAAATGATTATACCA-TTGATATGTGAAAAAGAAG-GGAAAA--AGCAGGCTGCAGATACA
*
8184 TTTTCATCTGTTTATCGACTACCATAAGTGTTGTGAG
127 TGTTCATCTGTTTATCGACTACCATAAGTGTTGTGAG
* * *
8221 GGTGTGCACTACATGAACATCCTATTACAACATGGAAAGGGATACACAAAGTAAAGTCCACTACA
1 GGTCTGCACTACATGAACATCCTATTACTACATGGAAAGGGATACACAAAGCAAAGTCCACTACA
* *
8286 TAATGAAATGATTATGCCATTGATATGTGAAAAAGAAGGGAAAATGCAGGCTGCAGATACATGTT
66 TAATGAAATGATTATACCATTGATATGTGAAAAAGAAGGGAAAAAGCAGGCTGCAGATACATGTT
* **
8351 CATGTGTTTATTTACTACCATAAGTGTTGTGA
131 CATCTGTTTATCGACTACCATAAGTGTTGTGA
8383 AGGCTTTCAT
Statistics
Matches: 459, Mismatches: 26, Indels: 11
0.93 0.05 0.02
Matches are distributed among these distances:
162 74 0.16
163 225 0.49
164 8 0.02
165 8 0.02
166 144 0.31
ACGTcount: A:0.36, C:0.16, G:0.21, T:0.26
Consensus pattern (163 bp):
GGTCTGCACTACATGAACATCCTATTACTACATGGAAAGGGATACACAAAGCAAAGTCCACTACA
TAATGAAATGATTATACCATTGATATGTGAAAAAGAAGGGAAAAAGCAGGCTGCAGATACATGTT
CATCTGTTTATCGACTACCATAAGTGTTGTGAG
Found at i:8328 original size:329 final size:325
Alignment explanation
Indices: 7734--8381 Score: 1073
Period size: 329 Copynumber: 2.0 Consensus size: 325
7724 GCAAGTGGTC
* * *
7734 TGCACTACATGAACATCCTATTACTACATGGAAAGGGATACACAAAGCAGAGTCCACTGCATAAT
1 TGCACTAAATGAACATCCTATTACTACATGGAAAGGGATACACAAAGCAAAGTCCACTACATAAT
* *
7799 GAAATGATATACCATTGATATGTGGAAAAGAAGGGAAAAAGCAGGCTGCAGATACATGTTCATCT
66 GAAATGATATACCATTGATATGTGAAAAAGAAGGAAAAAAGCAGGCTGCAGATACATGTTCATCT
*
7864 GTTTATCGACTACCATAAGTGTTGTGAGGGTCTGCACTACATGAACATCCTATTACTACATGGAA
131 GTTTATCGACTACCATAAGTGTTGTGAGGGTCTGCACTACATGAACATCCTATTACAACATGGAA
* * *
7929 AGGGATACACAAAGCAAAGTCCACTGCATAATGAAATGCTTATACCATTGATATGTGGAAAAGAA
196 AGGGATACACAAAGCAAAGTCCACTACATAATGAAATGATTATACCATTGATATGTGAAAAAGAA
7994 GGGAAAAAGCAGGCTGCAGATACATGTTCATCTGTTTATCGACTACCATAAGTGTTGTGGGGGTA
261 GGGAAAAAGCAGGCTGCAGATACATGTTCATCTGTTTATCGACTACCATAAGTGTTGTGGGGGTA
**
8059 TGCACTAAATGAACATCCTATTACTACATGGAAAGGGATACGTAAAGCAAAGTCCACTACATAAT
1 TGCACTAAATGAACATCCTATTACTACATGGAAAGGGATACACAAAGCAAAGTCCACTACATAAT
*
8124 GAAATGATTATACCATTTG-TATGTGAAAAAGAAGAGAAAAAGCAGCAGGCTGCAGATACATTTT
66 GAAATGA-TATACCA-TTGATATGTGAAAAAGAAG-GAAAAA--AGCAGGCTGCAGATACATGTT
*
8188 CATCTGTTTATCGACTACCATAAGTGTTGTGAGGGTGTGCACTACATGAACATCCTATTACAACA
126 CATCTGTTTATCGACTACCATAAGTGTTGTGAGGGTCTGCACTACATGAACATCCTATTACAACA
* *
8253 TGGAAAGGGATACACAAAGTAAAGTCCACTACATAATGAAATGATTATGCCATTGATATGTGAAA
191 TGGAAAGGGATACACAAAGCAAAGTCCACTACATAATGAAATGATTATACCATTGATATGTGAAA
* * **
8318 AAGAAGGGAAAATGCAGGCTGCAGATACATGTTCATGTGTTTATTTACTACCATAAGTGTTGTG
256 AAGAAGGGAAAAAGCAGGCTGCAGATACATGTTCATCTGTTTATCGACTACCATAAGTGTTGTG
8382 AAGGCTTTCA
Statistics
Matches: 299, Mismatches: 19, Indels: 6
0.92 0.06 0.02
Matches are distributed among these distances:
325 67 0.22
326 21 0.07
327 8 0.03
329 203 0.68
ACGTcount: A:0.37, C:0.16, G:0.21, T:0.26
Consensus pattern (325 bp):
TGCACTAAATGAACATCCTATTACTACATGGAAAGGGATACACAAAGCAAAGTCCACTACATAAT
GAAATGATATACCATTGATATGTGAAAAAGAAGGAAAAAAGCAGGCTGCAGATACATGTTCATCT
GTTTATCGACTACCATAAGTGTTGTGAGGGTCTGCACTACATGAACATCCTATTACAACATGGAA
AGGGATACACAAAGCAAAGTCCACTACATAATGAAATGATTATACCATTGATATGTGAAAAAGAA
GGGAAAAAGCAGGCTGCAGATACATGTTCATCTGTTTATCGACTACCATAAGTGTTGTGGGGGTA
Found at i:15764 original size:29 final size:29
Alignment explanation
Indices: 15704--15765 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 29
15694 CACAATAACG
*** *
15704 TAAATAACTAAAATATAACATTTTAAACA
1 TAAATAACTAAAATATAACATGAGAAAAA
*
15733 TAAATGACTAAAATATAACATGAGAAAAA
1 TAAATAACTAAAATATAACATGAGAAAAA
15762 TAAA
1 TAAA
15766 AGTGACTATC
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.61, C:0.08, G:0.05, T:0.26
Consensus pattern (29 bp):
TAAATAACTAAAATATAACATGAGAAAAA
Found at i:23899 original size:18 final size:18
Alignment explanation
Indices: 23873--23912 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
23863 GCCCAGTCCT
* *
23873 ATTTTTTTTCAAAAAGAA
1 ATTTGTTTTCAAAAAAAA
*
23891 ATTTGTTTTGAAAAAAAA
1 ATTTGTTTTCAAAAAAAA
23909 ATTT
1 ATTT
23913 AAAATTCTGG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.45, C:0.03, G:0.07, T:0.45
Consensus pattern (18 bp):
ATTTGTTTTCAAAAAAAA
Found at i:24044 original size:16 final size:16
Alignment explanation
Indices: 24041--24089 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
24031 GAATTTTTTA
*
24041 TTTTATTTTTTGAATT
1 TTTTATTTTATGAATT
*
24057 TTTTATTTTGA-GAATA
1 TTTTATTTT-ATGAATT
24073 TTTT-TTTTAT-AATT
1 TTTTATTTTATGAATT
24087 TTT
1 TTT
24090 AAATTACTTG
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
14 7 0.25
15 4 0.14
16 17 0.61
ACGTcount: A:0.22, C:0.00, G:0.06, T:0.71
Consensus pattern (16 bp):
TTTTATTTTATGAATT
Found at i:24049 original size:21 final size:21
Alignment explanation
Indices: 24025--24065 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
24015 TCATTTGAAT
24025 TTTTATGAATTTTTTATTTTA
1 TTTTATGAATTTTTTATTTTA
*
24046 TTTTTTGAATTTTTTATTTT
1 TTTTATGAATTTTTTATTTT
24066 GAGAATATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.20, C:0.00, G:0.05, T:0.76
Consensus pattern (21 bp):
TTTTATGAATTTTTTATTTTA
Found at i:30552 original size:70 final size:68
Alignment explanation
Indices: 30466--30598 Score: 248
Period size: 70 Copynumber: 1.9 Consensus size: 68
30456 TCTCATATAA
30466 CATACATAGATTTGTAAGGAAAAGTATAGAGAAAAATGGGTTTTTATTTATTTCTTTTTTAAGAT
1 CATACATAGATTTGTAAGGAAAAGTATAGAGAAAAATGGG-TTTTATTTATTTCTTTTTTAAGAT
30531 GTCT
65 GTCT
30535 CATATCATAGATTTGTAAGGAAAAGTATAGAGAAAAATGGGTTTTATTTATTTCTTTTTTAAGA
1 CATA-CATAGATTTGTAAGGAAAAGTATAGAGAAAAATGGGTTTTATTTATTTCTTTTTTAAGA
30599 GGGAGATATT
Statistics
Matches: 63, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
69 27 0.43
70 36 0.57
ACGTcount: A:0.36, C:0.05, G:0.17, T:0.41
Consensus pattern (68 bp):
CATACATAGATTTGTAAGGAAAAGTATAGAGAAAAATGGGTTTTATTTATTTCTTTTTTAAGATG
TCT
Found at i:36457 original size:1 final size:1
Alignment explanation
Indices: 36453--36478 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
36443 NNNNNNNNNN
36453 AAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAA
36479 CCACAAGAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:39293 original size:33 final size:32
Alignment explanation
Indices: 39248--39321 Score: 96
Period size: 33 Copynumber: 2.3 Consensus size: 32
39238 ATAAAAGTAT
* * *
39248 TCTAAAAAAAAAA-AAAAGAAGAGAAAATCTAA
1 TCTAAAAAAAAAAGAAAAAAAAAG-AAACCTAA
39280 TCTAAAAAGAAAAAGAAAAAAAAAGAAACCTAA
1 TCTAAAAA-AAAAAGAAAAAAAAAGAAACCTAA
39313 TCTAAAAAA
1 TCTAAAAAA
39322 CATGAAAAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
32 9 0.24
33 20 0.54
34 8 0.22
ACGTcount: A:0.72, C:0.08, G:0.08, T:0.12
Consensus pattern (32 bp):
TCTAAAAAAAAAAGAAAAAAAAAGAAACCTAA
Found at i:40267 original size:55 final size:55
Alignment explanation
Indices: 40183--40294 Score: 215
Period size: 55 Copynumber: 2.0 Consensus size: 55
40173 TTGAATAAAA
40183 AAGTAAATCTATGCATATACTAAAACCAGTAAATTATAAAATGGAATCAGGGACT
1 AAGTAAATCTATGCATATACTAAAACCAGTAAATTATAAAATGGAATCAGGGACT
*
40238 AAGTAAATCTATGCATATACTAAAACCAGTAAATTATAGAATGGAATCAGGGACT
1 AAGTAAATCTATGCATATACTAAAACCAGTAAATTATAAAATGGAATCAGGGACT
40293 AA
1 AA
40295 ATTAAAACAA
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
55 56 1.00
ACGTcount: A:0.47, C:0.12, G:0.15, T:0.25
Consensus pattern (55 bp):
AAGTAAATCTATGCATATACTAAAACCAGTAAATTATAAAATGGAATCAGGGACT
Found at i:42405 original size:2 final size:2
Alignment explanation
Indices: 42398--42422 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
42388 ACTCAGTTAA
42398 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
42423 CATACTAAGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:61533 original size:89 final size:89
Alignment explanation
Indices: 61382--61563 Score: 364
Period size: 89 Copynumber: 2.0 Consensus size: 89
61372 ACAATAGAGG
61382 TTAATGAACCCAGAGCTTATCTCTTGACCATGGCTTCCTTTATACCAAACCAAAAATAATAAGGG
1 TTAATGAACCCAGAGCTTATCTCTTGACCATGGCTTCCTTTATACCAAACCAAAAATAATAAGGG
61447 TGTACGCTTGTCTTGTAAGGTCTT
66 TGTACGCTTGTCTTGTAAGGTCTT
61471 TTAATGAACCCAGAGCTTATCTCTTGACCATGGCTTCCTTTATACCAAACCAAAAATAATAAGGG
1 TTAATGAACCCAGAGCTTATCTCTTGACCATGGCTTCCTTTATACCAAACCAAAAATAATAAGGG
61536 TGTACGCTTGTCTTGTAAGGTCTT
66 TGTACGCTTGTCTTGTAAGGTCTT
61560 TTAA
1 TTAA
61564 ATTTTGATTT
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
89 93 1.00
ACGTcount: A:0.30, C:0.21, G:0.16, T:0.33
Consensus pattern (89 bp):
TTAATGAACCCAGAGCTTATCTCTTGACCATGGCTTCCTTTATACCAAACCAAAAATAATAAGGG
TGTACGCTTGTCTTGTAAGGTCTT
Found at i:64774 original size:33 final size:35
Alignment explanation
Indices: 64712--64777 Score: 109
Period size: 33 Copynumber: 1.9 Consensus size: 35
64702 ATAGATGTTT
64712 GTTTAAAATTAATGTAATAAATAATAATATATATA
1 GTTTAAAATTAATGTAATAAATAATAATATATATA
*
64747 GTTTAAAATTAAT-TAAT-TATAATAATATATA
1 GTTTAAAATTAATGTAATAAATAATAATATATA
64778 AAATATGTAT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
33 13 0.43
34 4 0.13
35 13 0.43
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (35 bp):
GTTTAAAATTAATGTAATAAATAATAATATATATA
Found at i:65152 original size:31 final size:31
Alignment explanation
Indices: 65116--65186 Score: 133
Period size: 31 Copynumber: 2.3 Consensus size: 31
65106 AATTTTTAGA
65116 TTTTATAAGTATAATTAGGGTTTGACAATTG
1 TTTTATAAGTATAATTAGGGTTTGACAATTG
*
65147 TTTTATAAATATAATTAGGGTTTGACAATTG
1 TTTTATAAGTATAATTAGGGTTTGACAATTG
65178 TTTTATAAG
1 TTTTATAAG
65187 AGTATAGTAT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.34, C:0.03, G:0.17, T:0.46
Consensus pattern (31 bp):
TTTTATAAGTATAATTAGGGTTTGACAATTG
Found at i:65650 original size:30 final size:30
Alignment explanation
Indices: 65615--65674 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
65605 TTCATAACTT
*
65615 CCTAACTGAATTGATTTCGTAACTTCTTAA
1 CCTAACTGAATTGATTCCGTAACTTCTTAA
* *
65645 CCTAACTGAGTTGATTCCGTAACTTTTTAA
1 CCTAACTGAATTGATTCCGTAACTTCTTAA
65675 TTAAGATGGT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.28, C:0.20, G:0.12, T:0.40
Consensus pattern (30 bp):
CCTAACTGAATTGATTCCGTAACTTCTTAA
Found at i:71491 original size:26 final size:26
Alignment explanation
Indices: 71462--71523 Score: 90
Period size: 26 Copynumber: 2.4 Consensus size: 26
71452 CAATCTTTTA
71462 GAAAAA-TTGAATTGCTTTTTATTAAT
1 GAAAAACTT-AATTGCTTTTTATTAAT
* *
71488 GAAAAACTTACTTTCTTTTTATTAAT
1 GAAAAACTTAATTGCTTTTTATTAAT
71514 GAAAAACTTA
1 GAAAAACTTA
71524 CTAAAACATA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
26 31 0.94
27 2 0.06
ACGTcount: A:0.40, C:0.08, G:0.08, T:0.44
Consensus pattern (26 bp):
GAAAAACTTAATTGCTTTTTATTAAT
Found at i:71524 original size:26 final size:26
Alignment explanation
Indices: 71476--71525 Score: 100
Period size: 26 Copynumber: 1.9 Consensus size: 26
71466 AATTGAATTG
71476 CTTTTTATTAATGAAAAACTTACTTT
1 CTTTTTATTAATGAAAAACTTACTTT
71502 CTTTTTATTAATGAAAAACTTACT
1 CTTTTTATTAATGAAAAACTTACT
71526 AAAACATAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.36, C:0.12, G:0.04, T:0.48
Consensus pattern (26 bp):
CTTTTTATTAATGAAAAACTTACTTT
Found at i:78972 original size:56 final size:56
Alignment explanation
Indices: 78902--79055 Score: 186
Period size: 56 Copynumber: 2.7 Consensus size: 56
78892 TTGTTGTTAA
* *
78902 ATTTTAATAA-GATTATTATTAAATATAATTTAATAAAAAATAAATAATTTAATCAT
1 ATTTTAA-AATGATTATTATTAAATATAATTTAATAAAAAATAAATAATTTAATAAC
* * * *
78958 ATTTTAACATGATTATTATTAAATACAATTTAATAAAATAGTATATAATTTAATAAC
1 ATTTTAAAATGATTATTATTAAATATAATTTAATAAAA-AATAAATAATTTAATAAC
*
79015 ATTCTTAAAATAATTATTATTAAAATATGAA-TTAATAAAAA
1 ATT-TTAAAATGATTATTATT-AAATAT-AATTTAATAAAAA
79056 TCATAATATA
Statistics
Matches: 84, Mismatches: 9, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
55 1 0.01
56 34 0.40
57 17 0.20
58 16 0.19
59 14 0.17
60 2 0.02
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.42
Consensus pattern (56 bp):
ATTTTAAAATGATTATTATTAAATATAATTTAATAAAAAATAAATAATTTAATAAC
Found at i:88312 original size:23 final size:24
Alignment explanation
Indices: 88285--88344 Score: 63
Period size: 23 Copynumber: 2.6 Consensus size: 24
88275 AAGTATATTT
*
88285 ATATTATTGTA-ATTTATTTTTTA
1 ATATTATTATATATTTATTTTTTA
* *
88308 ATATTTTTATATTTTTATTTTTTGA
1 ATATTATTATATATTTATTTTTT-A
88333 A-ATT-TTATATAT
1 ATATTATTATATAT
88345 GATCATACTA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
23 16 0.52
24 13 0.42
25 2 0.06
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (24 bp):
ATATTATTATATATTTATTTTTTA
Found at i:88329 original size:24 final size:25
Alignment explanation
Indices: 88297--88344 Score: 73
Period size: 24 Copynumber: 2.0 Consensus size: 25
88287 ATTATTGTAA
88297 TTTATTTTTT-AATATTTT-TATATT
1 TTTATTTTTTGAA-ATTTTATATATT
88321 TTTATTTTTTGAAATTTTATATAT
1 TTTATTTTTTGAAATTTTATATAT
88345 GATCATACTA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 15 0.68
25 7 0.32
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (25 bp):
TTTATTTTTTGAAATTTTATATATT
Found at i:89212 original size:27 final size:30
Alignment explanation
Indices: 89181--89241 Score: 78
Period size: 25 Copynumber: 2.2 Consensus size: 30
89171 CATAATTTTA
89181 ATTTTTTT-T-CTTTTATA-ATTC-AT-AT
1 ATTTTTTTGTACTTTTATATATTCTATAAT
*
89206 ATTTTTTTGTACTTTTCTATATTCTATAAT
1 ATTTTTTTGTACTTTTATATATTCTATAAT
89236 ATTTTT
1 ATTTTT
89242 AATAATTTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
25 8 0.27
26 1 0.03
27 7 0.23
28 4 0.13
29 2 0.07
30 8 0.27
ACGTcount: A:0.23, C:0.08, G:0.02, T:0.67
Consensus pattern (30 bp):
ATTTTTTTGTACTTTTATATATTCTATAAT
Found at i:89250 original size:29 final size:29
Alignment explanation
Indices: 89218--89279 Score: 74
Period size: 29 Copynumber: 2.1 Consensus size: 29
89208 TTTTTTGTAC
89218 TTTTCTATA-TTCTATAA-TATTTTTAATAA
1 TTTTCTATAGTT-T-TAAGTATTTTTAATAA
* *
89247 TTTTTTATAGTTTTAAGTATTTTTCATAA
1 TTTTCTATAGTTTTAAGTATTTTTAATAA
89276 TTTT
1 TTTT
89280 TTAATTTATA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
28 3 0.10
29 24 0.83
30 2 0.07
ACGTcount: A:0.29, C:0.05, G:0.03, T:0.63
Consensus pattern (29 bp):
TTTTCTATAGTTTTAAGTATTTTTAATAA
Found at i:89425 original size:17 final size:18
Alignment explanation
Indices: 89384--89432 Score: 55
Period size: 17 Copynumber: 2.7 Consensus size: 18
89374 AATTATTTAA
89384 AATTTTAATATAATTATAAT
1 AATTTT-ATAT-ATTATAAT
89404 AATTTTATATATTAT-AT
1 AATTTTATATATTATAAT
* *
89421 GATTTTAAATAT
1 AATTTTATATAT
89433 AAAATACCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 12 0.44
18 5 0.19
19 4 0.15
20 6 0.22
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (18 bp):
AATTTTATATATTATAAT
Found at i:91178 original size:33 final size:34
Alignment explanation
Indices: 91121--91197 Score: 93
Period size: 33 Copynumber: 2.3 Consensus size: 34
91111 TATTTTTTTG
* * * *
91121 TTATATTATGCTTGCAAGTTTTGTTAAGGGATTAC
1 TTATATT-TACTTGAAAGTTTTGTTAAAGGACTAC
*
91156 TTATGTTTACTTGAAAG-TTTGTTAAAGGACTAC
1 TTATATTTACTTGAAAGTTTTGTTAAAGGACTAC
91189 TTATATTTA
1 TTATATTTA
91198 TATTAAATTT
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
33 22 0.61
34 8 0.22
35 6 0.17
ACGTcount: A:0.29, C:0.08, G:0.17, T:0.47
Consensus pattern (34 bp):
TTATATTTACTTGAAAGTTTTGTTAAAGGACTAC
Found at i:91220 original size:11 final size:11
Alignment explanation
Indices: 91189--91222 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
91179 AAAGGACTAC
91189 TTATATTTATA
1 TTATATTTATA
*
91200 TTAAATTTATA
1 TTATATTTATA
*
91211 TTATAGTTATA
1 TTATATTTATA
91222 T
1 T
91223 CATCAATGTC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (11 bp):
TTATATTTATA
Found at i:95451 original size:37 final size:37
Alignment explanation
Indices: 95401--95476 Score: 152
Period size: 37 Copynumber: 2.1 Consensus size: 37
95391 CAGACTGGTT
95401 ATGTTTTCACATATGGTGGTACTATAATTTCTTGGCG
1 ATGTTTTCACATATGGTGGTACTATAATTTCTTGGCG
95438 ATGTTTTCACATATGGTGGTACTATAATTTCTTGGCG
1 ATGTTTTCACATATGGTGGTACTATAATTTCTTGGCG
95475 AT
1 AT
95477 TGTTGTTACT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.22, C:0.13, G:0.21, T:0.43
Consensus pattern (37 bp):
ATGTTTTCACATATGGTGGTACTATAATTTCTTGGCG
Found at i:96115 original size:17 final size:17
Alignment explanation
Indices: 96093--96148 Score: 53
Period size: 17 Copynumber: 3.3 Consensus size: 17
96083 CTCTTAACTT
96093 TTAACCTTCCATCTTCC
1 TTAACCTTCCATCTTCC
* *
96110 TTAACCTCCCTTGACTT--
1 TTAACCTTCCAT--CTTCC
*
96127 TTAACCTTCCATTTTCC
1 TTAACCTTCCATCTTCC
96144 TTAAC
1 TTAAC
96149 TTTTCATATT
Statistics
Matches: 30, Mismatches: 5, Indels: 8
0.70 0.12 0.19
Matches are distributed among these distances:
15 2 0.07
17 25 0.83
19 3 0.10
ACGTcount: A:0.20, C:0.36, G:0.02, T:0.43
Consensus pattern (17 bp):
TTAACCTTCCATCTTCC
Found at i:96934 original size:16 final size:17
Alignment explanation
Indices: 96904--96937 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
96894 CAATACAAAA
96904 TTTATATTTGATCAAATT
1 TTTATATTT-ATCAAATT
96922 TTTATATTT-TCAAATT
1 TTTATATTTATCAAATT
96938 GAGGGATCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
18 9 0.56
ACGTcount: A:0.32, C:0.06, G:0.03, T:0.59
Consensus pattern (17 bp):
TTTATATTTATCAAATT
Found at i:103947 original size:74 final size:74
Alignment explanation
Indices: 103826--103971 Score: 256
Period size: 74 Copynumber: 2.0 Consensus size: 74
103816 GTCTGTTCCA
* *
103826 AAAAATGCATTTCTTTTCTGTTAAGAATCGTCCACACTAAGAAGACAACCTTAAAAGGCATTCTG
1 AAAAATCCATTTCTTCTCTGTTAAGAATCGTCCACACTAAGAAGACAACCTTAAAAGGCATTCTG
103891 ACCAACCAT
66 ACCAACCAT
* *
103900 AAAAATCCATTTCTTCTCTGTTAAGAATCTTCCACACTAAGAAGACAACCTTAAAAGGCATTTTG
1 AAAAATCCATTTCTTCTCTGTTAAGAATCGTCCACACTAAGAAGACAACCTTAAAAGGCATTCTG
103965 ACCAACC
66 ACCAACC
103972 GTAGCATCTT
Statistics
Matches: 68, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
74 68 1.00
ACGTcount: A:0.38, C:0.24, G:0.11, T:0.27
Consensus pattern (74 bp):
AAAAATCCATTTCTTCTCTGTTAAGAATCGTCCACACTAAGAAGACAACCTTAAAAGGCATTCTG
ACCAACCAT
Found at i:107706 original size:14 final size:15
Alignment explanation
Indices: 107677--107709 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
107667 TATTTTTATA
*
107677 ATTTTTTATATTTTT
1 ATTTTTTATATATTT
107692 ATTTTTTATA-ATTT
1 ATTTTTTATATATTT
107706 ATTT
1 ATTT
107710 ATTTTGAACC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 7 0.41
15 10 0.59
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (15 bp):
ATTTTTTATATATTT
Found at i:107712 original size:24 final size:24
Alignment explanation
Indices: 107665--107714 Score: 75
Period size: 25 Copynumber: 2.1 Consensus size: 24
107655 ATAAATAAAA
*
107665 TTTATTTTTATAATTTTTTATATT
1 TTTATTTTTATAATTTATTATATT
107689 TTTATTTTTTATAATTTATT-TATT
1 TTTA-TTTTTATAATTTATTATATT
107713 TT
1 TT
107715 GAACCAATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 10 0.42
25 14 0.58
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (24 bp):
TTTATTTTTATAATTTATTATATT
Found at i:108394 original size:27 final size:27
Alignment explanation
Indices: 108347--108401 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 27
108337 GAACATAGGA
* *
108347 TATTAATAAAAATAAAGTATATTTATT
1 TATTAATAAAAATAAAATATAATTATT
108374 TATTAAT-AAAATAAAAATATAATTATT
1 TATTAATAAAAAT-AAAATATAATTATT
108401 T
1 T
108402 GGAATATGTG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 5 0.20
27 20 0.80
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.44
Consensus pattern (27 bp):
TATTAATAAAAATAAAATATAATTATT
Found at i:114250 original size:13 final size:15
Alignment explanation
Indices: 114217--114254 Score: 62
Period size: 13 Copynumber: 2.7 Consensus size: 15
114207 CTCATACTCG
114217 TATAAATATGAAAAT
1 TATAAATATGAAAAT
114232 TATAAATAT-AAAA-
1 TATAAATATGAAAAT
114245 TATAAATATG
1 TATAAATATG
114255 TATTTAAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 9 0.41
14 4 0.18
15 9 0.41
ACGTcount: A:0.61, C:0.00, G:0.05, T:0.34
Consensus pattern (15 bp):
TATAAATATGAAAAT
Found at i:131200 original size:7 final size:7
Alignment explanation
Indices: 131190--131219 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
131180 GAAAAGTTAA
131190 AAAGGTG
1 AAAGGTG
131197 AAAGGTG
1 AAAGGTG
131204 AAAGGTG
1 AAAGGTG
131211 AAAGGTG
1 AAAGGTG
131218 AA
1 AA
131220 GTAGAGAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.47, C:0.00, G:0.40, T:0.13
Consensus pattern (7 bp):
AAAGGTG
Found at i:142788 original size:3 final size:3
Alignment explanation
Indices: 142780--142814 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
142770 TCATGATCAA
142780 CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT CC
1 CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT CC
142815 ATTGTATAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.00, C:0.69, G:0.00, T:0.31
Consensus pattern (3 bp):
CCT
Found at i:156641 original size:16 final size:16
Alignment explanation
Indices: 156622--156655 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
156612 AAACAATCCT
156622 AAACC-AAAATAATCTA
1 AAACCAAAAAT-ATCTA
156638 AAACCAAAAATATCTA
1 AAACCAAAAATATCTA
156654 AA
1 AA
156656 CATAAAATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.65, C:0.18, G:0.00, T:0.18
Consensus pattern (16 bp):
AAACCAAAAATATCTA
Found at i:158739 original size:15 final size:15
Alignment explanation
Indices: 158719--158751 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
158709 TATTCAAGAT
158719 TTAATAGAAAC-ATTA
1 TTAATA-AAACAATTA
158734 TTAATAAAACAATTA
1 TTAATAAAACAATTA
158749 TTA
1 TTA
158752 TCAAAATAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 4 0.24
15 13 0.76
ACGTcount: A:0.55, C:0.06, G:0.03, T:0.36
Consensus pattern (15 bp):
TTAATAAAACAATTA
Found at i:163312 original size:20 final size:20
Alignment explanation
Indices: 163287--163336 Score: 100
Period size: 20 Copynumber: 2.5 Consensus size: 20
163277 TTTATCTCGA
163287 GTATCGATACTCGTGAAGGG
1 GTATCGATACTCGTGAAGGG
163307 GTATCGATACTCGTGAAGGG
1 GTATCGATACTCGTGAAGGG
163327 GTATCGATAC
1 GTATCGATAC
163337 CAAAATGAGC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.26, C:0.16, G:0.32, T:0.26
Consensus pattern (20 bp):
GTATCGATACTCGTGAAGGG
Found at i:168404 original size:2 final size:2
Alignment explanation
Indices: 168397--168428 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
168387 CTTTAAATCC
168397 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
168429 TACAAATTGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:181015 original size:15 final size:17
Alignment explanation
Indices: 180997--181039 Score: 54
Period size: 15 Copynumber: 2.6 Consensus size: 17
180987 ATTTAATTTT
180997 TAATTATTTATTTAATAA
1 TAATTATTTA-TTAATAA
*
181015 TAATTATTCA-T-ATAA
1 TAATTATTTATTAATAA
181030 TAATTATTTA
1 TAATTATTTA
181040 ATCCACTTAC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
15 13 0.57
16 1 0.04
18 9 0.39
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53
Consensus pattern (17 bp):
TAATTATTTATTAATAA
Found at i:181020 original size:18 final size:18
Alignment explanation
Indices: 180997--181033 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
180987 ATTTAATTTT
* *
180997 TAATTATTTATTTAATAA
1 TAATTATTCATATAATAA
181015 TAATTATTCATATAATAA
1 TAATTATTCATATAATAA
181033 T
1 T
181034 TATTTAATCC
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:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (18 bp):
TAATTATTCATATAATAA
Found at i:181291 original size:29 final size:29
Alignment explanation
Indices: 181221--181291 Score: 72
Period size: 29 Copynumber: 2.4 Consensus size: 29
181211 TATTGTTGAT
* *
181221 AAAATTAAACTTTTATATTTTACTTTTAG
1 AAAATTAAATTTTTATATTTTAATTTTAG
* ** *
181250 AAATTTATTTTTTTATTTTTTAAATTTTA-
1 AAAATTAAATTTTTATATTTT-AATTTTAG
181279 AAAATTAAATTTT
1 AAAATTAAATTTT
181292 GTTGGTCATA
Statistics
Matches: 32, Mismatches: 9, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
29 26 0.81
30 6 0.19
ACGTcount: A:0.38, C:0.03, G:0.01, T:0.58
Consensus pattern (29 bp):
AAAATTAAATTTTTATATTTTAATTTTAG
Found at i:183901 original size:23 final size:23
Alignment explanation
Indices: 183874--183926 Score: 106
Period size: 23 Copynumber: 2.3 Consensus size: 23
183864 TACACAGGAA
183874 AGTGGGAGTGAACGTGCTAAAGT
1 AGTGGGAGTGAACGTGCTAAAGT
183897 AGTGGGAGTGAACGTGCTAAAGT
1 AGTGGGAGTGAACGTGCTAAAGT
183920 AGTGGGA
1 AGTGGGA
183927 TTGAGAGAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.30, C:0.08, G:0.42, T:0.21
Consensus pattern (23 bp):
AGTGGGAGTGAACGTGCTAAAGT
Found at i:189182 original size:28 final size:27
Alignment explanation
Indices: 189142--189204 Score: 76
Period size: 29 Copynumber: 2.3 Consensus size: 27
189132 AAATTATGGA
189142 AAAAAAAATTAAA-ATCATA-AAATTCT
1 AAAAAAAATTAAATAT-ATATAAATTCT
*
189168 AAAAAAAATCCTAAATATATATAATTTCT
1 AAAAAAAAT--TAAATATATATAAATTCT
189197 AAAAAAAA
1 AAAAAAAA
189205 AATCATCATA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
26 9 0.28
28 7 0.22
29 16 0.50
ACGTcount: A:0.65, C:0.08, G:0.00, T:0.27
Consensus pattern (27 bp):
AAAAAAAATTAAATATATATAAATTCT
Found at i:190825 original size:20 final size:21
Alignment explanation
Indices: 190784--190825 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
190774 CAATGAAAAT
*
190784 TTTTGAATATTTTAATGATTA
1 TTTTGAATATTTTAAAGATTA
190805 TTTTGTAAT-TTTTAAAG-TTA
1 TTTTG-AATATTTTAAAGATTA
190825 T
1 T
190826 GTGATCAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 4 0.21
21 12 0.63
22 3 0.16
ACGTcount: A:0.31, C:0.00, G:0.10, T:0.60
Consensus pattern (21 bp):
TTTTGAATATTTTAAAGATTA
Found at i:192490 original size:99 final size:99
Alignment explanation
Indices: 192319--192517 Score: 389
Period size: 99 Copynumber: 2.0 Consensus size: 99
192309 TATGAAGTAG
192319 TTGTGATGGTTGCTTGTTCTACCCCACCCTACTCCACTTTATAAAGCTACTATTTTATCTTTGTA
1 TTGTGATGGTTGCTTGTTCTACCCCACCCTACTCCACTTTATAAAGCTACTATTTTATCTTTGTA
192384 TATATTTAATTATTAAAAGGATAAAATATAATAA
66 TATATTTAATTATTAAAAGGATAAAATATAATAA
192418 TTGTGATGGTTGCTTGTTCTACCCCACCCTACTCCACTTTATAAAGCTACTATTTTATCTTTGTA
1 TTGTGATGGTTGCTTGTTCTACCCCACCCTACTCCACTTTATAAAGCTACTATTTTATCTTTGTA
*
192483 TATATTTAATTATTAAAAGGATAAAATGTAATAA
66 TATATTTAATTATTAAAAGGATAAAATATAATAA
192517 T
1 T
192518 ATATTATACT
Statistics
Matches: 99, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
99 99 1.00
ACGTcount: A:0.32, C:0.16, G:0.11, T:0.42
Consensus pattern (99 bp):
TTGTGATGGTTGCTTGTTCTACCCCACCCTACTCCACTTTATAAAGCTACTATTTTATCTTTGTA
TATATTTAATTATTAAAAGGATAAAATATAATAA
Found at i:193341 original size:20 final size:20
Alignment explanation
Indices: 193316--193353 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
193306 ACATCAACAT
193316 AAAATTTAAAAGAGTAATAA
1 AAAATTTAAAAGAGTAATAA
*
193336 AAAATTTCAAAGAGTAAT
1 AAAATTTAAAAGAGTAAT
193354 TAATTGTGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.61, C:0.03, G:0.11, T:0.26
Consensus pattern (20 bp):
AAAATTTAAAAGAGTAATAA
Found at i:205144 original size:22 final size:22
Alignment explanation
Indices: 205119--205161 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
205109 AAATATTAAA
205119 AATTAATAAAATT-AATTTAATT
1 AATT-ATAAAATTCAATTTAATT
* *
205141 AATTTTTAAATTCAATTTAAT
1 AATTATAAAATTCAATTTAAT
205162 GGATCTAAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (22 bp):
AATTATAAAATTCAATTTAATT
Found at i:205950 original size:18 final size:18
Alignment explanation
Indices: 205924--205958 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
205914 TTATTGTGGA
*
205924 TATTTTATTTGTTTTAAT
1 TATTCTATTTGTTTTAAT
*
205942 TATTCTATTTTTTTTAA
1 TATTCTATTTGTTTTAA
205959 AAATAATGTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.23, C:0.03, G:0.03, T:0.71
Consensus pattern (18 bp):
TATTCTATTTGTTTTAAT
Found at i:206441 original size:22 final size:22
Alignment explanation
Indices: 206385--206441 Score: 62
Period size: 23 Copynumber: 2.5 Consensus size: 22
206375 AGAATAATGT
*
206385 ATCAAATATAATTTCTTTAAAGA
1 ATCAAATATAA-ATCTTTAAAGA
*
206408 ATCAAATATAAATCTTTGAAATA
1 ATCAAATATAAATCTTT-AAAGA
*
206431 ATTAAAT-TAAA
1 ATCAAATATAAA
206442 ATTCAAAGAT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
22 9 0.30
23 21 0.70
ACGTcount: A:0.53, C:0.07, G:0.04, T:0.37
Consensus pattern (22 bp):
ATCAAATATAAATCTTTAAAGA
Found at i:210171 original size:19 final size:20
Alignment explanation
Indices: 210146--210189 Score: 81
Period size: 19 Copynumber: 2.2 Consensus size: 20
210136 AAAAAGTAAT
210146 ATAATGGTAGGGTTATATTG
1 ATAATGGTAGGGTTATATTG
210166 -TAATGGTAGGGTTATATTG
1 ATAATGGTAGGGTTATATTG
210185 ATAAT
1 ATAAT
210190 TTGCTTATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 19 0.83
20 4 0.17
ACGTcount: A:0.32, C:0.00, G:0.27, T:0.41
Consensus pattern (20 bp):
ATAATGGTAGGGTTATATTG
Done.