Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01004940.1 Corchorus capsularis cultivar CVL-1 contig04958, 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: 7651
ACGTcount: A:0.35, C:0.14, G:0.15, T:0.36
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--36 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
37 GAAAAAAAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4252 original size:103 final size:106
Alignment explanation
Indices: 4125--4336 Score: 274
Period size: 108 Copynumber: 2.0 Consensus size: 106
4115 AGCTGAAAGA
* * *
4125 AAAAGGATTGTTGAGTTAGGAGAGTAAGTGATCCTATG-AT-TT-TGA-TTTTGTAGTCTGTGTG
1 AAAAGGATTGTTGAGCTAGAAGAGTAAGTGATCCTATGCATATTATGATTTTTGT-CTCTGTGTG
*
4186 GTTACCAAAATTTCATAAG-GAGATTATCA-AACTTTCATAAGG
65 GTTACCAAAACTTCAT-AGTGAGATTATCACAA-TTTCATAAGG
4228 AAAAGGATTGTTGAGCTAGAAGAGTAAGTGATCCTATGCATGATTATGATTTTTTGTCTCTGTGT
1 AAAAGGATTGTTGAGCTAGAAGAGTAAGTGATCCTATGCAT-ATTATGA-TTTTTGTCTCTGTGT
* * *
4293 GGTTATCAGAACTTCATAGTGAGGTTATCACAATTTCATAAGG
64 GGTTACCAAAACTTCATAGTGAGATTATCACAATTTCATAAGG
4336 A
1 A
4337 GGTTATCACA
Statistics
Matches: 94, Mismatches: 7, Indels: 11
0.84 0.06 0.10
Matches are distributed among these distances:
103 36 0.38
104 2 0.02
106 2 0.02
107 5 0.05
108 41 0.44
109 8 0.09
ACGTcount: A:0.31, C:0.10, G:0.23, T:0.36
Consensus pattern (106 bp):
AAAAGGATTGTTGAGCTAGAAGAGTAAGTGATCCTATGCATATTATGATTTTTGTCTCTGTGTGG
TTACCAAAACTTCATAGTGAGATTATCACAATTTCATAAGG
Found at i:4371 original size:22 final size:22
Alignment explanation
Indices: 4293--4375 Score: 107
Period size: 22 Copynumber: 3.8 Consensus size: 22
4283 GTCTCTGTGT
* *
4293 GGTTATCAGAACTTCAT-AGTGA
1 GGTTATCACAATTTCATAAG-GA
4315 GGTTATCACAATTTCATAAGGA
1 GGTTATCACAATTTCATAAGGA
*
4337 GGTTATCACAATTTTATAAGGA
1 GGTTATCACAATTTCATAAGGA
4359 GGTTAT-ACAAATTTCAT
1 GGTTATCAC-AATTTCAT
4376 TGTGTGATTA
Statistics
Matches: 55, Mismatches: 4, Indels: 4
0.87 0.06 0.06
Matches are distributed among these distances:
21 2 0.04
22 51 0.93
23 2 0.04
ACGTcount: A:0.35, C:0.12, G:0.18, T:0.35
Consensus pattern (22 bp):
GGTTATCACAATTTCATAAGGA
Found at i:4485 original size:174 final size:174
Alignment explanation
Indices: 4207--4571 Score: 644
Period size: 174 Copynumber: 2.1 Consensus size: 174
4197 TTCATAAGGA
4207 GATTATCAAACTTTCATAAGGAAAAGGATTGTTGAGCTAGAAGAGTAAGTGATCCTATGCATGAT
1 GATTATCAAACTTTCATAAGGAAAAGGATTGTTGAGCTAGAAGAGTAAGTGATCCTATGCATGAT
4272 TATGATTTTTTGTCTCTGTGTGGTTATCAGAACTTCATAGTGAGGTTATC-ACAATTTCATAAGG
66 TATGATTTTTTGTCTCTGTGTGGTTATCAGAACTTCATAGTGAGGTTATCAAC-ATTTCATAAGG
4336 AGGTTATCACAATTTTATAAGGAGGTTATACAAATTTCATTGTGT
130 AGGTTATCACAATTTTATAAGGAGGTTATACAAATTTCATTGTGT
* **
4381 GATTATCAAACTTTCATAAGGAAAAGGATTGTTGAGCTTGAAGAGTGGGTGATCCTATGCATGAT
1 GATTATCAAACTTTCATAAGGAAAAGGATTGTTGAGCTAGAAGAGTAAGTGATCCTATGCATGAT
* * *
4446 TATGATTTTTTGTCTCTGTGTGGTTATCGGAATTTCATAGTGAGTTTATCAACATTTCATAAGGA
66 TATGATTTTTTGTCTCTGTGTGGTTATCAGAACTTCATAGTGAGGTTATCAACATTTCATAAGGA
4511 GGTTATCACAATTTTATAAGGAGGTTATACAAATTTCATTGTGT
131 GGTTATCACAATTTTATAAGGAGGTTATACAAATTTCATTGTGT
*
4555 GATTACCAAA-TTTCATA
1 GATTATCAAACTTTCATA
4572 GGGAGTTTAT
Statistics
Matches: 183, Mismatches: 7, Indels: 3
0.95 0.04 0.02
Matches are distributed among these distances:
173 7 0.04
174 174 0.95
175 2 0.01
ACGTcount: A:0.31, C:0.11, G:0.21, T:0.38
Consensus pattern (174 bp):
GATTATCAAACTTTCATAAGGAAAAGGATTGTTGAGCTAGAAGAGTAAGTGATCCTATGCATGAT
TATGATTTTTTGTCTCTGTGTGGTTATCAGAACTTCATAGTGAGGTTATCAACATTTCATAAGGA
GGTTATCACAATTTTATAAGGAGGTTATACAAATTTCATTGTGT
Found at i:4502 original size:22 final size:22
Alignment explanation
Indices: 4467--4679 Score: 149
Period size: 22 Copynumber: 9.9 Consensus size: 22
4457 GTCTCTGTGT
**
4467 GGTTATCGGAATTTCATAGTGA
1 GGTTATCAAAATTTCATAGTGA
* *
4489 GTTTATCAACATTTCATAAG-GA
1 GGTTATCAAAATTTCAT-AGTGA
* *
4511 GGTTATCACAATTTTATAAG-GA
1 GGTTATCAAAATTTCAT-AGTGA
* *
4533 GGTTAT-ACAAATTTCATTGTGT
1 GGTTATCA-AAATTTCATAGTGA
* * *
4555 GATTA-CCAAATTTCATAGGGA
1 GGTTATCAAAATTTCATAGTGA
*
4576 GTTTATCAAAATTTCATAGTGTA
1 GGTTATCAAAATTTCATAGTG-A
* *
4599 -GTTATCAAAATTATCATATTGT
1 GGTTATCAAAATT-TCATAGTGA
* *
4621 GGTTACCAAAATTTCATAGTGT
1 GGTTATCAAAATTTCATAGTGA
*
4643 GGTTA-CCAAATTGT-ATAG-GA
1 GGTTATCAAAATT-TCATAGTGA
4663 --TTATCAAAATTTCATAG
1 GGTTATCAAAATTTCATAG
4680 AGTAGTTTCA
Statistics
Matches: 152, Mismatches: 28, Indels: 25
0.74 0.14 0.12
Matches are distributed among these distances:
18 4 0.03
19 10 0.07
20 1 0.01
21 27 0.18
22 89 0.59
23 21 0.14
ACGTcount: A:0.34, C:0.11, G:0.17, T:0.38
Consensus pattern (22 bp):
GGTTATCAAAATTTCATAGTGA
Found at i:5276 original size:22 final size:22
Alignment explanation
Indices: 5248--5424 Score: 137
Period size: 22 Copynumber: 7.8 Consensus size: 22
5238 AATTTCATGA
*
5248 GGTTATCAAAATTTCATAAAGT
1 GGTTATCAAAATTTCATATAGT
*
5270 GGTTATCAAAATTT-ATATGGAT
1 GGTTATCAAAATTTCATATAG-T
* * * *
5292 CAGGTCATTAACATTTCATA-AGAA
1 --GGTTATCAAAATTTCATATAG-T
5316 GGTTATCAAAATTTCATATAGT
1 GGTTATCAAAATTTCATATAGT
* *
5338 GGTTATCAAAATTTTATATGGAT
1 GGTTATCAAAATTTCATATAG-T
* **
5361 CGGGTTATGAAAATTTCAT-GGGT
1 --GGTTATCAAAATTTCATATAGT
*
5384 AGATTATCAAAATTTCATAGT-GT
1 -GGTTATCAAAATTTCATA-TAGT
5407 GGTTATCAAAATTTCATA
1 GGTTATCAAAATTTCATA
5425 GGGAGGTTAT
Statistics
Matches: 124, Mismatches: 21, Indels: 20
0.75 0.13 0.12
Matches are distributed among these distances:
21 4 0.03
22 81 0.65
23 6 0.05
24 15 0.12
25 18 0.15
ACGTcount: A:0.37, C:0.09, G:0.16, T:0.38
Consensus pattern (22 bp):
GGTTATCAAAATTTCATATAGT
Found at i:5330 original size:68 final size:64
Alignment explanation
Indices: 5202--5420 Score: 233
Period size: 69 Copynumber: 3.2 Consensus size: 64
5192 TTGTCTCTGT
* **
5202 GTGGTTATCAAAATTTCATAAGGAGGAGGATATT-ACAATTTCATGAGGTTATCAAAATTTCATA
1 GTGGTTATCAAAATTT-ATATGGATCAGG-TATTAAC-ATTTCATGAGGTTATCAAAATTTCATA
5266 AA
63 AA
5268 GTGGTTATCAAAATTTATATGGATCAGGTCATTAACATTTCATAAGAAGGTTATCAAAATTTCAT
1 GTGGTTATCAAAATTTATATGGATCAGGT-ATTAACATTTCAT--G-AGGTTATCAAAATTTCAT
*
5333 ATA
62 AAA
* * * *
5336 GTGGTTATCAAAATTTTATATGGATCGGGTTATGAAAATTTCATGGGTAGATTATCAAAATTTCA
1 GTGGTTATCAAAA-TTTATATGGATCAGG-TATTAACATTTCAT--G-AGGTTATCAAAATTTCA
**
5401 TAGT
61 TAAA
5405 GTGGTTATCAAAATTT
1 GTGGTTATCAAAATTT
5421 CATAGGGAGG
Statistics
Matches: 133, Mismatches: 13, Indels: 12
0.84 0.08 0.08
Matches are distributed among these distances:
64 1 0.01
65 19 0.14
66 18 0.14
67 1 0.01
68 36 0.27
69 57 0.43
70 1 0.01
ACGTcount: A:0.37, C:0.09, G:0.18, T:0.37
Consensus pattern (64 bp):
GTGGTTATCAAAATTTATATGGATCAGGTATTAACATTTCATGAGGTTATCAAAATTTCATAAA
Found at i:5392 original size:69 final size:69
Alignment explanation
Indices: 5250--5420 Score: 238
Period size: 69 Copynumber: 2.5 Consensus size: 69
5240 TTTCATGAGG
* * *
5250 TTATCAAAATTTCATAAAGTGGTTATCAAAA-TTTATATGGATCAGGTCATTAACATTTCATAAG
1 TTATCAAAATTTCATATAGTGGTTATCAAAATTTTATATGGATCAGGTCATGAAAATTTCATAAG
*
5314 AAGG
66 AAGA
* * **
5318 TTATCAAAATTTCATATAGTGGTTATCAAAATTTTATATGGATCGGGTTATGAAAATTTCATGGG
1 TTATCAAAATTTCATATAGTGGTTATCAAAATTTTATATGGATCAGGTCATGAAAATTTCATAAG
*
5383 TAGA
66 AAGA
5387 TTATCAAAATTTCATAGT-GTGGTTATCAAAATTT
1 TTATCAAAATTTCATA-TAGTGGTTATCAAAATTT
5421 CATAGGGAGG
Statistics
Matches: 92, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
68 30 0.33
69 61 0.66
70 1 0.01
ACGTcount: A:0.37, C:0.09, G:0.16, T:0.39
Consensus pattern (69 bp):
TTATCAAAATTTCATATAGTGGTTATCAAAATTTTATATGGATCAGGTCATGAAAATTTCATAAG
AAGA
Found at i:5435 original size:44 final size:44
Alignment explanation
Indices: 5246--5548 Score: 166
Period size: 44 Copynumber: 7.0 Consensus size: 44
5236 ACAATTTCAT
**
5246 GAGGTTATCAAAATTTCATAAAGTGGTTATCAAAATTT-ATATGG
1 GAGGTTATCAAAATTTCATAGTGTGGTTATCAAAATTTCATA-GG
* * * * ** **
5290 ATCAGGTCATTAACATTTCATAAG-AAGGTTATCAAAATTTCATATA
1 --GAGGTTATCAAAATTTCAT-AGTGTGGTTATCAAAATTTCATAGG
* * *
5336 GTGGTTATCAAAATTTTATA-TGGATCGGGTTATGAAAATTTCAT-GG
1 GAGGTTATCAAAATTTCATAGT-G-T--GGTTATCAAAATTTCATAGG
*
5382 GTAGATTATCAAAATTTCATAGTGTGGTTATCAAAATTTCATAGG
1 G-AGGTTATCAAAATTTCATAGTGTGGTTATCAAAATTTCATAGG
* * **
5427 GAGGTTATC------T-A-A--GAGATTATCAAAATTTCATAAC
1 GAGGTTATCAAAATTTCATAGTGTGGTTATCAAAATTTCATAGG
* * * * **
5461 AAGGTTATCAGAATGTCATAGTGTGGTTATCAAAATTTCTTAAA
1 GAGGTTATCAAAATTTCATAGTGTGGTTATCAAAATTTCATAGG
* * * * *
5505 AATGTTATAAAAATCTCATAATGTGGTTATCAAAATTTCATAGG
1 GAGGTTATCAAAATTTCATAGTGTGGTTATCAAAATTTCATAGG
5549 ATGGTTAGAA
Statistics
Matches: 195, Mismatches: 42, Indels: 42
0.70 0.15 0.15
Matches are distributed among these distances:
34 26 0.13
36 1 0.01
37 1 0.01
38 1 0.01
40 1 0.01
41 1 0.01
42 1 0.01
43 1 0.01
44 90 0.46
45 3 0.02
46 31 0.16
47 37 0.19
48 1 0.01
ACGTcount: A:0.38, C:0.09, G:0.17, T:0.36
Consensus pattern (44 bp):
GAGGTTATCAAAATTTCATAGTGTGGTTATCAAAATTTCATAGG
Found at i:5470 original size:56 final size:56
Alignment explanation
Indices: 5384--5491 Score: 144
Period size: 56 Copynumber: 1.9 Consensus size: 56
5374 TTTCATGGGT
**** *
5384 AGATTATCAAAATTTCATAGTGTGGTTATCAAAATTTCATAGGGAGGTTATCTAAG
1 AGATTATCAAAATTTCATAACAAGGTTATCAAAATGTCATAGGGAGGTTATCTAAG
* * *
5440 AGATTATCAAAATTTCATAACAAGGTTATCAGAATGTCATAGTGTGGTTATC
1 AGATTATCAAAATTTCATAACAAGGTTATCAAAATGTCATAGGGAGGTTATC
5492 AAAATTTCTT
Statistics
Matches: 44, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
56 44 1.00
ACGTcount: A:0.36, C:0.10, G:0.19, T:0.35
Consensus pattern (56 bp):
AGATTATCAAAATTTCATAACAAGGTTATCAAAATGTCATAGGGAGGTTATCTAAG
Found at i:5533 original size:22 final size:22
Alignment explanation
Indices: 5508--5564 Score: 62
Period size: 22 Copynumber: 2.6 Consensus size: 22
5498 TCTTAAAAAT
*
5508 GTTATAAAAATCTCATAATG-TG
1 GTTATAAAAATCTCAT-AGGATG
* *
5530 GTTATCAAAATTTCATAGGATG
1 GTTATAAAAATCTCATAGGATG
*
5552 GTTAGAAAAATCT
1 GTTATAAAAATCT
5565 AAACTTCATA
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
21 2 0.07
22 26 0.93
ACGTcount: A:0.40, C:0.09, G:0.16, T:0.35
Consensus pattern (22 bp):
GTTATAAAAATCTCATAGGATG
Found at i:5561 original size:44 final size:44
Alignment explanation
Indices: 5443--5564 Score: 140
Period size: 44 Copynumber: 2.8 Consensus size: 44
5433 ATCTAAGAGA
* * * *
5443 TTATCAAAATTTCATAACAA-GGTTATCAGAATGTCATAGTGTGG
1 TTATCAAAATTTCATAA-AATGGTTATAAAAATCTCATAATGTGG
*
5487 TTATCAAAATTTCTTAAAAAT-GTTATAAAAATCTCATAATGTGG
1 TTATCAAAATTTCAT-AAAATGGTTATAAAAATCTCATAATGTGG
** *
5531 TTATCAAAATTTCATAGGATGGTTAGAAAAATCT
1 TTATCAAAATTTCATAAAATGGTTATAAAAATCT
5565 AAACTTCATA
Statistics
Matches: 66, Mismatches: 9, Indels: 6
0.81 0.11 0.07
Matches are distributed among these distances:
43 3 0.05
44 61 0.92
45 2 0.03
ACGTcount: A:0.40, C:0.10, G:0.14, T:0.36
Consensus pattern (44 bp):
TTATCAAAATTTCATAAAATGGTTATAAAAATCTCATAATGTGG
Found at i:5679 original size:22 final size:22
Alignment explanation
Indices: 5651--5741 Score: 103
Period size: 22 Copynumber: 4.0 Consensus size: 22
5641 TCAGATACCT
5651 AAATTTCATAGGAAGGTTATCA
1 AAATTTCATAGGAAGGTTATCA
* *
5673 AAATTTCATAGTATGGTTATCA
1 AAATTTCATAGGAAGGTTATCA
*
5695 AAATTTCATAATG-AGGTTATCCA
1 AAATTTCAT-AGGAAGGTTAT-CA
**
5718 AAAAATCATAGGGAAGGTTATCA
1 AAATTTCATA-GGAAGGTTATCA
5741 A
1 A
5742 TTTTTTGTTA
Statistics
Matches: 57, Mismatches: 8, Indels: 7
0.79 0.11 0.10
Matches are distributed among these distances:
22 36 0.63
23 14 0.25
24 7 0.12
ACGTcount: A:0.42, C:0.10, G:0.16, T:0.32
Consensus pattern (22 bp):
AAATTTCATAGGAAGGTTATCA
Found at i:5712 original size:44 final size:44
Alignment explanation
Indices: 5651--6034 Score: 152
Period size: 44 Copynumber: 8.7 Consensus size: 44
5641 TCAGATACCT
5651 AAATTTCATAG-GAAGGTTATCAAAATTTCATAGTATGGTTATCA
1 AAATTTCATAGTG-AGGTTATCAAAATTTCATAGTATGGTTATCA
* ** * *
5695 AAATTTCATAATGAGGTTATCCAAAAAATCATAGGGAAGGTTATC-
1 AAATTTCATAGTGAGGTTAT-CAAAATTTCATA-GTATGGTTATCA
* *
5740 -AATTT--T--T--TGTTATCAAAATTTCATA-TATAAGGAGGTTGTCA
1 AAATTTCATAGTGAGGTTATCAAAATTTCATAGTAT-----GGTTATCA
* * * * * * *
5781 AAATTTTATAGGGAAGTTTATTAAAATTTTATAGGATTGTTTATCA
1 AAATTTCATAGTG-AGGTTATCAAAATTTCATAGTA-TGGTTATCA
* * * * * * * *
5827 CAATTTTATAGTGCGATTATCAAAATTTTACAGTGTGATTA-CTA
1 AAATTTCATAGTGAGGTTATCAAAATTTCATAGTATGGTTATC-A
** * * * *
5871 GCATTTCATA-TAGAGGTTATCGAAATTTCATA-AAGTGCTTACCA
1 AAATTTCATAGT-GAGGTTATCAAAATTTCATAGTA-TGGTTATCA
* * * * * *
5915 ACACTTCAGAGGGAGGTTATCAAAACTTCATAGTATGGTTATCG
1 AAATTTCATAGTGAGGTTATCAAAATTTCATAGTATGGTTATCA
* * * *
5959 GAATTTCATTG-GATGGTTATCAAATTTTCATTAG-ATGATTATC-
1 AAATTTCATAGTGA-GGTTATCAAAATTTCA-TAGTATGGTTATCA
* *
6002 AAATTTTATAGTGAGGTTTTCAAAAATTTCATA
1 AAATTTCATAGTGAGGTTATC-AAAATTTCATA
6035 AGGAGGTTAA
Statistics
Matches: 249, Mismatches: 62, Indels: 59
0.67 0.17 0.16
Matches are distributed among these distances:
35 1 0.00
37 10 0.04
38 5 0.02
40 7 0.03
42 6 0.02
43 20 0.08
44 126 0.51
45 32 0.13
46 26 0.10
49 14 0.06
50 1 0.00
51 1 0.00
ACGTcount: A:0.36, C:0.10, G:0.16, T:0.38
Consensus pattern (44 bp):
AAATTTCATAGTGAGGTTATCAAAATTTCATAGTATGGTTATCA
Found at i:5810 original size:23 final size:24
Alignment explanation
Indices: 5778--5837 Score: 79
Period size: 23 Copynumber: 2.6 Consensus size: 24
5768 AAGGAGGTTG
5778 TCAAAATTTTATAGGGA-AGTTTA
1 TCAAAATTTTATAGGGATAGTTTA
* *
5801 TTAAAATTTTATA-GGATTGTTTA
1 TCAAAATTTTATAGGGATAGTTTA
*
5824 TCACAATTTTATAG
1 TCAAAATTTTATAG
5838 TGCGATTATC
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
22 3 0.10
23 28 0.90
ACGTcount: A:0.37, C:0.05, G:0.13, T:0.45
Consensus pattern (24 bp):
TCAAAATTTTATAGGGATAGTTTA
Found at i:5853 original size:22 final size:22
Alignment explanation
Indices: 5821--5867 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
5811 ATAGGATTGT
* *
5821 TTATCACAATTTTATAGTGCGA
1 TTATCAAAATTTTACAGTGCGA
*
5843 TTATCAAAATTTTACAGTGTGA
1 TTATCAAAATTTTACAGTGCGA
5865 TTA
1 TTA
5868 CTAGCATTTC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.34, C:0.11, G:0.13, T:0.43
Consensus pattern (22 bp):
TTATCAAAATTTTACAGTGCGA
Found at i:5901 original size:22 final size:21
Alignment explanation
Indices: 5873--6043 Score: 64
Period size: 22 Copynumber: 7.8 Consensus size: 21
5863 GATTACTAGC
5873 ATTTCATATAGAGGTTATCGAA
1 ATTTCATATAGAGGTTATC-AA
* * * *
5895 ATTTCATAAAGTGCTTACCAA
1 ATTTCATATAGAGGTTATCAA
* * **
5916 CACTTCAGAGGGAGGTTATCAAA
1 -ATTTCATATAGAGGTTATC-AA
* * *
5939 ACTTCATAGTA-TGGTTATCGGA
1 ATTTCATA-TAGAGGTTATC-AA
*
5961 ATTTCAT-TGGATGGTTATCAA
1 ATTTCATATAGA-GGTTATCAA
*
5982 ATTTTCAT-TAGATGATTATCAA
1 A-TTTCATATAGA-GGTTATCAA
* *
6004 ATTTTATAGT-GAGGTTTTCAAAA
1 ATTTCATA-TAGAGGTTATC--AA
6027 ATTTCATA-AGGAGGTTA
1 ATTTCATATA-GAGGTTA
6044 AAAAATTATC
Statistics
Matches: 109, Mismatches: 28, Indels: 23
0.68 0.17 0.14
Matches are distributed among these distances:
20 1 0.01
21 14 0.13
22 76 0.70
23 18 0.17
ACGTcount: A:0.34, C:0.11, G:0.18, T:0.37
Consensus pattern (21 bp):
ATTTCATATAGAGGTTATCAA
Found at i:6049 original size:21 final size:22
Alignment explanation
Indices: 6023--6064 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
6013 TGAGGTTTTC
6023 AAAAATT-TCATAAGG-AGGTTA
1 AAAAATTATCAT-AGGAAGGTTA
6044 AAAAATTATCATAGGAAGGTT
1 AAAAATTATCATAGGAAGGTT
6065 TTTGAAATTC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.48, C:0.05, G:0.19, T:0.29
Consensus pattern (22 bp):
AAAAATTATCATAGGAAGGTTA
Found at i:6547 original size:55 final size:55
Alignment explanation
Indices: 6481--6596 Score: 196
Period size: 55 Copynumber: 2.1 Consensus size: 55
6471 AGGGAGGTAG
6481 CCTTCTACTATCTCTAAACCCACATCGTCCATCCCAGAATTTGAACCCGAGACCT
1 CCTTCTACTATCTCTAAACCCACATCGTCCATCCCAGAATTTGAACCCGAGACCT
* * * *
6536 CCTTCTTCTATCTCTAAATCCACATCGTCCGTCCCAGAATTTGAACCTGAGACCT
1 CCTTCTACTATCTCTAAACCCACATCGTCCATCCCAGAATTTGAACCCGAGACCT
6591 CCTTCT
1 CCTTCT
6597 GGAGGCTCAA
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
55 57 1.00
ACGTcount: A:0.24, C:0.37, G:0.09, T:0.29
Consensus pattern (55 bp):
CCTTCTACTATCTCTAAACCCACATCGTCCATCCCAGAATTTGAACCCGAGACCT
Done.