Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011499.1 Corchorus capsularis cultivar CVL-1 contig11520, 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: 91316
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:82 original size:16 final size:16
Alignment explanation
Indices: 57--87 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
47 TCTACATATT
57 ATAAAGATTTAGTAAA
1 ATAAAGATTTAGTAAA
*
73 ATAAATATTTAGTAA
1 ATAAAGATTTAGTAA
88 TATTTTTCAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.00, G:0.10, T:0.35
Consensus pattern (16 bp):
ATAAAGATTTAGTAAA
Found at i:361 original size:13 final size:13
Alignment explanation
Indices: 343--368 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
333 CTAGTTATAC
343 TTACATTAATCTT
1 TTACATTAATCTT
356 TTACATTAATCTT
1 TTACATTAATCTT
369 AAAAGAATAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.00, T:0.54
Consensus pattern (13 bp):
TTACATTAATCTT
Found at i:527 original size:66 final size:67
Alignment explanation
Indices: 444--569 Score: 209
Period size: 67 Copynumber: 1.9 Consensus size: 67
434 TAGTCTTGAG
* *
444 TTCAAGTCTTGTGAATGGGAAAAAAAA-TCATTGTTGGGAGAGTTTTATCACATAATAGACTTCG
1 TTCAAGTCTTGTGAATGGAAAAAAAAATTCATTGTTAGGAGAGTTTTATCACATAATAGACTTCG
508 AA
66 AA
* *
510 TTCAAGTCTTTTGAATGGAAAAAAAAATTCATTGTTAGGAGAGTTTTTTCACATAATAGA
1 TTCAAGTCTTGTGAATGGAAAAAAAAATTCATTGTTAGGAGAGTTTTATCACATAATAGA
570 TCAACTCATT
Statistics
Matches: 55, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
66 25 0.45
67 30 0.55
ACGTcount: A:0.37, C:0.10, G:0.19, T:0.34
Consensus pattern (67 bp):
TTCAAGTCTTGTGAATGGAAAAAAAAATTCATTGTTAGGAGAGTTTTATCACATAATAGACTTCG
AA
Found at i:588 original size:37 final size:37
Alignment explanation
Indices: 538--614 Score: 154
Period size: 37 Copynumber: 2.1 Consensus size: 37
528 AAAAAAAAAT
538 TCATTGTTAGGAGAGTTTTTTCACATAATAGATCAAC
1 TCATTGTTAGGAGAGTTTTTTCACATAATAGATCAAC
575 TCATTGTTAGGAGAGTTTTTTCACATAATAGATCAAC
1 TCATTGTTAGGAGAGTTTTTTCACATAATAGATCAAC
612 TCA
1 TCA
615 GTTCGAACAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 40 1.00
ACGTcount: A:0.32, C:0.14, G:0.16, T:0.38
Consensus pattern (37 bp):
TCATTGTTAGGAGAGTTTTTTCACATAATAGATCAAC
Found at i:2331 original size:18 final size:18
Alignment explanation
Indices: 2308--2345 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
2298 TTTATCCTTC
2308 TGATGATAGATTTGTTGT
1 TGATGATAGATTTGTTGT
2326 TGATGATAGATTTGTTGT
1 TGATGATAGATTTGTTGT
2344 TG
1 TG
2346 GGAAGACCCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.21, C:0.00, G:0.29, T:0.50
Consensus pattern (18 bp):
TGATGATAGATTTGTTGT
Found at i:16223 original size:31 final size:31
Alignment explanation
Indices: 16186--16294 Score: 137
Period size: 31 Copynumber: 3.5 Consensus size: 31
16176 AAAAAAAGCA
* *
16186 ACACGTGGCATGTCACGTGTCACTTTTTGGT
1 ACACGTGGCATGCCACATGTCACTTTTTGGT
* * *
16217 ACACGTGGCGTGACACATGTCACTTTTTGAT
1 ACACGTGGCATGCCACATGTCACTTTTTGGT
* * *
16248 ACACATGGCATGCCACATGTCACTTTCTAGT
1 ACACGTGGCATGCCACATGTCACTTTTTGGT
*
16279 ACACGTGTCATGCCAC
1 ACACGTGGCATGCCAC
16295 GTCGGACACC
Statistics
Matches: 66, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 66 1.00
ACGTcount: A:0.22, C:0.27, G:0.21, T:0.30
Consensus pattern (31 bp):
ACACGTGGCATGCCACATGTCACTTTTTGGT
Found at i:51133 original size:22 final size:21
Alignment explanation
Indices: 51097--51144 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
51087 TGAAATCTTA
*
51097 ATTTC-AATTTCAATGATGTTG
1 ATTTCAAATTTCAATGAT-TTC
*
51118 ATTTCAAATTTTAATGATTTC
1 ATTTCAAATTTCAATGATTTC
51139 ATTTCA
1 ATTTCA
51145 TGTCCAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 13 0.54
22 11 0.46
ACGTcount: A:0.31, C:0.10, G:0.08, T:0.50
Consensus pattern (21 bp):
ATTTCAAATTTCAATGATTTC
Found at i:58271 original size:36 final size:36
Alignment explanation
Indices: 58231--58301 Score: 142
Period size: 36 Copynumber: 2.0 Consensus size: 36
58221 GATTTATCCG
58231 GAATCAACTTGTATGGAATTCTGGATTGATACGTAT
1 GAATCAACTTGTATGGAATTCTGGATTGATACGTAT
58267 GAATCAACTTGTATGGAATTCTGGATTGATACGTA
1 GAATCAACTTGTATGGAATTCTGGATTGATACGTA
58302 AGTTATAACG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.31, C:0.11, G:0.23, T:0.35
Consensus pattern (36 bp):
GAATCAACTTGTATGGAATTCTGGATTGATACGTAT
Found at i:61576 original size:16 final size:16
Alignment explanation
Indices: 61516--61576 Score: 52
Period size: 16 Copynumber: 3.8 Consensus size: 16
61506 AGAATCCAAT
*
61516 ACAAACTAAGAAATAA
1 ACAAACTAATAAATAA
* *
61532 ACTAA-TTATAAACTAA
1 ACAAACTAATAAA-TAA
* *
61548 ACGAACAAATAAATAA
1 ACAAACTAATAAATAA
*
61564 ACAAACTACTAAA
1 ACAAACTAATAAA
61577 CCCACATTCT
Statistics
Matches: 34, Mismatches: 9, Indels: 4
0.72 0.19 0.09
Matches are distributed among these distances:
15 5 0.15
16 24 0.71
17 5 0.15
ACGTcount: A:0.64, C:0.15, G:0.03, T:0.18
Consensus pattern (16 bp):
ACAAACTAATAAATAA
Found at i:64206 original size:2 final size:2
Alignment explanation
Indices: 64199--64247 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
64189 ACAGGTACCT
64199 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
64241 AG AG AG A
1 AG AG AG A
64248 AGCATATACT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:65484 original size:66 final size:66
Alignment explanation
Indices: 65365--65505 Score: 196
Period size: 66 Copynumber: 2.1 Consensus size: 66
65355 TAAGTAACCA
*
65365 AAAACA-GTCTTTTGACCAATATACACACTTTCCACAAAATAAACGATTAAAGAGCAATATTCCA
1 AAAACATG-CTTTTGACCAATATACACACTTTCCACAAAATAAACAATTAAAGAGCAATATTCCA
65429 AT
65 AT
* * * *
65431 AAAACATGCTTTTGACCAATATACACACTTTCCA-TATATAAACCAATTGAAGAGCAATATTCCT
1 AAAACATGCTTTTGACCAATATACACACTTTCCACAAAATAAA-CAATTAAAGAGCAATATTCCA
65495 AT
65 AT
*
65497 GAAACATGC
1 AAAACATGC
65506 ATAAATTTAT
Statistics
Matches: 67, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
65 6 0.09
66 60 0.90
67 1 0.01
ACGTcount: A:0.43, C:0.21, G:0.09, T:0.27
Consensus pattern (66 bp):
AAAACATGCTTTTGACCAATATACACACTTTCCACAAAATAAACAATTAAAGAGCAATATTCCAA
T
Found at i:72514 original size:12 final size:13
Alignment explanation
Indices: 72490--72521 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
72480 TCGGCAGTTA
72490 TTTATTATTATTT
1 TTTATTATTATTT
72503 TTTATT-TTATTT
1 TTTATTATTATTT
72515 TTT-TTAT
1 TTTATTAT
72522 GATCACTGCC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 2 0.11
12 10 0.56
13 6 0.33
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (13 bp):
TTTATTATTATTT
Found at i:85750 original size:11 final size:11
Alignment explanation
Indices: 85736--85773 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
85726 ATTCATAACA
85736 AATTTATAATT
1 AATTTATAATT
85747 AATTTATAATT
1 AATTTATAATT
85758 -ATTTGATAATT
1 AATTT-ATAATT
*
85769 TATTT
1 AATTT
85774 TATATAGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 4 0.16
11 17 0.68
12 4 0.16
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (11 bp):
AATTTATAATT
Found at i:86026 original size:29 final size:31
Alignment explanation
Indices: 85969--86032 Score: 96
Period size: 29 Copynumber: 2.1 Consensus size: 31
85959 AACTTTATGT
*
85969 TTTCCAGTTGTACCCTTATTTTTAAAACATA
1 TTTCCAATTGTACCCTTATTTTTAAAACATA
*
86000 TTTCCAATTGTA-TCTT-TTTTTAAAACATA
1 TTTCCAATTGTACCCTTATTTTTAAAACATA
86029 TTTC
1 TTTC
86033 TAAATTGCCA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
29 17 0.55
30 3 0.10
31 11 0.35
ACGTcount: A:0.28, C:0.17, G:0.05, T:0.50
Consensus pattern (31 bp):
TTTCCAATTGTACCCTTATTTTTAAAACATA
Found at i:86405 original size:19 final size:20
Alignment explanation
Indices: 86378--86415 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
86368 TACTATTATT
86378 TTTTGAATTT-AATATTTTAC
1 TTTTGAATTTCAAT-TTTTAC
86398 TTTT-AATTTCAATTTTTA
1 TTTTGAATTTCAATTTTTA
86416 AATGTCAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.29, C:0.05, G:0.03, T:0.63
Consensus pattern (20 bp):
TTTTGAATTTCAATTTTTAC
Found at i:86608 original size:22 final size:22
Alignment explanation
Indices: 86580--86709 Score: 122
Period size: 22 Copynumber: 5.9 Consensus size: 22
86570 TGTCTCTATG
*
86580 TGGTTATCAAAATTTCATAAAA
1 TGGTTATCAAAATTTCATAGAA
* * *
86602 TGGTTATTATAATTTCATGAGGA
1 TGGTTATCAAAATTTCAT-AGAA
* **
86625 -GGTTATCAAAGTTTCATAGTG
1 TGGTTATCAAAATTTCATAGAA
*
86646 TGGTTACCAAAATTTCATATGGAA
1 TGGTTATCAAAATTTCATA--GAA
*
86670 --GTTATCAAAATTTCATAGTA
1 TGGTTATCAAAATTTCATAGAA
*
86690 TGGTTACCAAAATTTCATAG
1 TGGTTATCAAAATTTCATAG
86710 GATCATGTTA
Statistics
Matches: 86, Mismatches: 16, Indels: 12
0.75 0.14 0.11
Matches are distributed among these distances:
20 2 0.02
21 2 0.02
22 79 0.92
23 2 0.02
24 1 0.01
ACGTcount: A:0.36, C:0.10, G:0.16, T:0.38
Consensus pattern (22 bp):
TGGTTATCAAAATTTCATAGAA
Found at i:86631 original size:44 final size:44
Alignment explanation
Indices: 86581--86708 Score: 168
Period size: 44 Copynumber: 2.9 Consensus size: 44
86571 GTCTCTATGT
** ** *
86581 GGTTATCAAAATTTCATAAAATGGTTATTATAATTTCATGA-GGA
1 GGTTATCAAAATTTCATAGTATGGTTACCAAAATTTCAT-ATGGA
* *
86625 GGTTATCAAAGTTTCATAGTGTGGTTACCAAAATTTCATATGGA
1 GGTTATCAAAATTTCATAGTATGGTTACCAAAATTTCATATGGA
*
86669 AGTTATCAAAATTTCATAGTATGGTTACCAAAATTTCATA
1 GGTTATCAAAATTTCATAGTATGGTTACCAAAATTTCATA
86709 GGATCATGTT
Statistics
Matches: 73, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
43 1 0.01
44 72 0.99
ACGTcount: A:0.37, C:0.10, G:0.16, T:0.38
Consensus pattern (44 bp):
GGTTATCAAAATTTCATAGTATGGTTACCAAAATTTCATATGGA
Found at i:86684 original size:66 final size:65
Alignment explanation
Indices: 86578--86709 Score: 151
Period size: 66 Copynumber: 2.0 Consensus size: 65
86568 CTTGTCTCTA
* * * * *
86578 TGTGGTTATCAAAATTTCATAAAATGGTTATTATAATTTCATGAGGA-GGTTATCAAAGTTTCAT
1 TGTGGTTACCAAAATTTCATAAAA-GGTTATCAAAATTTCAT-AGGATGGTTACCAAAATTTCAT
86642 AG
64 AG
* *
86644 TGTGGTTACCAAAATTTCATATGGAA-GTTATCAAAATTTCATAGTATGGTTACCAAAATTTCAT
1 TGTGGTTACCAAAATTTCATA--AAAGGTTATCAAAATTTCATAGGATGGTTACCAAAATTTCAT
86708 AG
64 AG
86710 GATCATGTTA
Statistics
Matches: 56, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
65 3 0.05
66 51 0.91
68 2 0.04
ACGTcount: A:0.36, C:0.10, G:0.17, T:0.38
Consensus pattern (65 bp):
TGTGGTTACCAAAATTTCATAAAAGGTTATCAAAATTTCATAGGATGGTTACCAAAATTTCATAG
Found at i:86748 original size:22 final size:22
Alignment explanation
Indices: 86604--86767 Score: 98
Period size: 22 Copynumber: 7.3 Consensus size: 22
86594 TCATAAAATG
*
86604 GTTATTATAATTTCAT-GAGG-A
1 GTTATTAAAATTTCATAG-GGTA
* * * *
86625 GGTTATCAAAGTTTCATAGTGTG
1 -GTTATTAAAATTTCATAGGGTA
** * *
86648 GTTACCAAAATTTCATATGGAA
1 GTTATTAAAATTTCATAGGGTA
* ** *
86670 GTTATCAAAATTTCATAGTATG
1 GTTATTAAAATTTCATAGGGTA
** *
86692 GTTACCAAAATTTCATAGGATCA
1 GTTATTAAAATTTCATAGGGT-A
* *
86715 TGTTATTAAAATTTCTTAGGTTA
1 -GTTATTAAAATTTCATAGGGTA
*
86738 GTTATTGAAATTTCATAGGGTA
1 GTTATTAAAATTTCATAGGGTA
86760 GTTGATTA
1 GTT-ATTA
86768 TGACAATTTT
Statistics
Matches: 109, Mismatches: 28, Indels: 9
0.75 0.19 0.06
Matches are distributed among these distances:
22 87 0.80
23 5 0.05
24 17 0.16
ACGTcount: A:0.34, C:0.09, G:0.18, T:0.40
Consensus pattern (22 bp):
GTTATTAAAATTTCATAGGGTA
Found at i:87025 original size:44 final size:44
Alignment explanation
Indices: 86932--87122 Score: 158
Period size: 44 Copynumber: 4.4 Consensus size: 44
86922 ATAGAGATCA
* * *
86932 GATTATCAAAATTT-ATAGTA-AGATTATCAAAATTTCATAGTGTT
1 GATTATCAAAATTTCAAAG-AGAGGTTATCAAAATTTCATAATG-T
* * *
86976 G-TTATCAAAATTTCAAAGAGAGTTTATCAAAATTACATAATGC
1 GATTATCAAAATTTCAAAGAGAGGTTATCAAAATTTCATAATGT
* * * * * * * *
87019 GATTATCAGAATTTCATAGAGGGGTCAACAAAATTTTATAAAGA
1 GATTATCAAAATTTCAAAGAGAGGTTATCAAAATTTCATAATGT
* * *
87063 GGTTATCAAAATTTCATAA-AGAGGTTATCAAATTTTCAAAATGT
1 GATTATCAAAATTTCA-AAGAGAGGTTATCAAAATTTCATAATGT
87107 GATTA-CAAAAATTTCA
1 GATTATC-AAAATTTCA
87123 TAGTGGTATT
Statistics
Matches: 115, Mismatches: 27, Indels: 10
0.76 0.18 0.07
Matches are distributed among these distances:
43 15 0.13
44 99 0.86
45 1 0.01
ACGTcount: A:0.43, C:0.09, G:0.13, T:0.35
Consensus pattern (44 bp):
GATTATCAAAATTTCAAAGAGAGGTTATCAAAATTTCATAATGT
Found at i:87088 original size:22 final size:22
Alignment explanation
Indices: 86792--87100 Score: 153
Period size: 22 Copynumber: 14.0 Consensus size: 22
86782 AAAAGTTATC
* * *
86792 AAAGAGATTATTAAAATGTCAT
1 AAAGAGGTTATCAAAATTTCAT
**
86814 AGCGAGGTTAT-AAGAATTTCAT
1 AAAGAGGTTATCAA-AATTTCAT
** * *
86836 AGTGTGGTTAACAAAATTTCAT
1 AAAGAGGTTATCAAAATTTCAT
* * *
86858 TAGGAGGTTA-CTAATATTTCAT
1 AAAGAGGTTATC-AAAATTTCAT
** * *
86880 GGAGAGGTTATTAAAATCTCAT
1 AAAGAGGTTATCAAAATTTCAT
** * * *
86902 TGAGTGATTATCGAAATTTCAT
1 AAAGAGGTTATCAAAATTTCAT
* *
86924 AGAGATCAGATTATCAAAATTT-AT
1 A-A-A-GAGGTTATCAAAATTTCAT
86948 AGTAAGA--TTATCAAAATTTCAT
1 A--AAGAGGTTATCAAAATTTCAT
** **
86970 AGTGTTGTTATCAAAATTTCA-
1 AAAGAGGTTATCAAAATTTCAT
* *
86991 AAGAGAGTTTATCAAAATTACAT
1 AA-AGAGGTTATCAAAATTTCAT
* * * *
87014 AATGCGATTATCAGAATTTCAT
1 AAAGAGGTTATCAAAATTTCAT
* * * * *
87036 AGAGGGGTCAACAAAATTTTAT
1 AAAGAGGTTATCAAAATTTCAT
87058 AAAGAGGTTATCAAAATTTCAT
1 AAAGAGGTTATCAAAATTTCAT
*
87080 AAAGAGGTTATCAAATTTTCA
1 AAAGAGGTTATCAAAATTTCA
87101 AAATGTGATT
Statistics
Matches: 215, Mismatches: 59, Indels: 26
0.72 0.20 0.09
Matches are distributed among these distances:
20 1 0.00
21 16 0.07
22 174 0.81
23 5 0.02
24 5 0.02
25 14 0.07
ACGTcount: A:0.40, C:0.09, G:0.16, T:0.35
Consensus pattern (22 bp):
AAAGAGGTTATCAAAATTTCAT
Found at i:87275 original size:22 final size:22
Alignment explanation
Indices: 87248--87650 Score: 176
Period size: 22 Copynumber: 18.5 Consensus size: 22
87238 TAGTATTTAG
*
87248 ATCAAAATTTCATATGGAGATT
1 ATCAAAATTTCATATGGAGGTT
*
87270 AACAAAATTTCATAAT-GAGGTT
1 ATCAAAATTTCAT-ATGGAGGTT
** *
87292 ATCAAAAAATCATAAGGAGGTT
1 ATCAAAATTTCATATGGAGGTT
*
87314 ATCAAAA--T--T-TGTA-GTT
1 ATCAAAATTTCATATGGAGGTT
* * * *
87330 ATCAAGATTTCATAAGAAAGTT
1 ATCAAAATTTCATATGGAGGTT
*
87352 ATCAAAATTTTATA-GAGAGGTTT
1 ATCAAAATTTCATATG-GAGG-TT
* *
87375 ATCAAAATTTTATA-GGAAGATTT
1 ATCAAAATTTCATATGG-AG-GTT
*
87398 ATCAAAATTTCATA-GCCAGGTT
1 ATCAAAATTTCATATG-GAGGTT
* * *
87420 ATCACAATTTCATA-GTATGATT
1 ATCAAAATTTCATATGGA-GGTT
*
87442 ATCAAAATTTCAGAGTGTGA--TT
1 ATCAAAATTTCATA-TG-GAGGTT
*
87464 A-CTAACAA-TTCATATGGTGGTT
1 ATC-AA-AATTTCATATGGAGGTT
* * * *
87486 TTTAAATTTTCATAAT-GTGGTT
1 ATCAAAATTTCAT-ATGGAGGTT
* *
87508 ATCAATATATCATATGGAGGTT
1 ATCAAAATTTCATATGGAGGTT
* * **
87530 ATCAACATCTCATAGTGTTGGTT
1 ATCAAAATTTCATA-TGGAGGTT
* *
87553 ATCAAAATTTTAT-TGGGAAGTT
1 ATCAAAATTTCATAT-GGAGGTT
**
87575 ATCAAAATTTCATATTAAGGTCT
1 ATCAAAATTTCATATGGAGGT-T
* * *
87598 -TCAAAATTCCTTAGGGAGGTT
1 ATCAAAATTTCATATGGAGGTT
* * *
87619 AACAAAATTTCATAAGAAGGTT
1 ATCAAAATTTCATATGGAGGTT
**
87641 AAAAAAATTT
1 ATCAAAATTT
87651 ATAAAAAGGT
Statistics
Matches: 290, Mismatches: 61, Indels: 60
0.71 0.15 0.15
Matches are distributed among these distances:
16 9 0.03
17 2 0.01
18 2 0.01
20 3 0.01
21 13 0.04
22 198 0.68
23 61 0.21
24 1 0.00
25 1 0.00
ACGTcount: A:0.39, C:0.10, G:0.15, T:0.36
Consensus pattern (22 bp):
ATCAAAATTTCATATGGAGGTT
Found at i:87378 original size:23 final size:22
Alignment explanation
Indices: 87225--87453 Score: 124
Period size: 22 Copynumber: 10.6 Consensus size: 22
87215 TCAGGGGGGA
*
87225 TATCAAAATTTCATAGTA--TT
1 TATCAAAATTTCATAGGAGGTT
*
87245 TAGATCAAAATTTCATATGGA-GAT
1 T--ATCAAAATTTCATA-GGAGGTT
* *
87269 TAACAAAATTTCATAATGAGG-T
1 TATCAAAATTTCAT-AGGAGGTT
**
87291 TATCAAAAAATCATAAGGAGG-T
1 TATCAAAATTTCAT-AGGAGGTT
*
87313 TATCAAAA-TT--T-GTA-G-T
1 TATCAAAATTTCATAGGAGGTT
* * *
87329 TATCAAGATTTCATAAGAAAG-T
1 TATCAAAATTTCAT-AGGAGGTT
*
87351 TATCAAAATTTTATAGAGAGGTT
1 TATCAAAATTTCATAG-GAGGTT
* *
87374 TATCAAAATTTTATAGGAAGATT
1 TATCAAAATTTCATAGG-AGGTT
*
87397 TATCAAAATTTCATAGCCAGG-T
1 TATCAAAATTTCATAG-GAGGTT
* * * *
87419 TATCACAATTTCATAGTATGAT
1 TATCAAAATTTCATAGGAGGTT
87441 TATCAAAATTTCA
1 TATCAAAATTTCA
87454 GAGTGTGATT
Statistics
Matches: 168, Mismatches: 24, Indels: 32
0.75 0.11 0.14
Matches are distributed among these distances:
16 9 0.05
17 4 0.02
19 2 0.01
20 1 0.01
21 7 0.04
22 101 0.60
23 42 0.25
24 2 0.01
ACGTcount: A:0.42, C:0.10, G:0.13, T:0.36
Consensus pattern (22 bp):
TATCAAAATTTCATAGGAGGTT
Found at i:87654 original size:21 final size:22
Alignment explanation
Indices: 87614--87661 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
87604 TTCCTTAGGG
* *
87614 AGGTTAACAAAATTTCATAAGA
1 AGGTTAAAAAAATTTCATAAAA
87636 AGGTTAAAAAAATTT-ATAAAA
1 AGGTTAAAAAAATTTCATAAAA
87657 AGGTT
1 AGGTT
87662 CTAGAAATTC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
21 10 0.42
22 14 0.58
ACGTcount: A:0.52, C:0.04, G:0.15, T:0.29
Consensus pattern (22 bp):
AGGTTAAAAAAATTTCATAAAA
Found at i:88552 original size:29 final size:29
Alignment explanation
Indices: 88519--88596 Score: 95
Period size: 29 Copynumber: 2.7 Consensus size: 29
88509 ACTTGTAGCG
*
88519 TTTGGACGTTTTATCCCCC-AAACTTCAAT
1 TTTGGACGTTTT-GCCCCCTAAACTTCAAT
* * *
88548 TTTGGACATTTTGCCCCCTGAATTTCAAT
1 TTTGGACGTTTTGCCCCCTAAACTTCAAT
88577 TTTGGGACGTTTTGCCCCCT
1 TTT-GGACGTTTTGCCCCCT
88597 CAACCTAACA
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
28 5 0.12
29 22 0.52
30 15 0.36
ACGTcount: A:0.18, C:0.27, G:0.15, T:0.40
Consensus pattern (29 bp):
TTTGGACGTTTTGCCCCCTAAACTTCAAT
Done.