Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015109.1 Corchorus capsularis cultivar CVL-1 contig15130, 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: 65263
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:20455 original size:156 final size:157
Alignment explanation
Indices: 20070--20455 Score: 394
Period size: 156 Copynumber: 2.5 Consensus size: 157
20060 CATCTAGGTG
* ** * *
20070 AAATTTCATCTCAAACAGACTTAGTATGAAAAACTTATGCTAGTTTTTCAATTGAGGACAGTTTG
1 AAATTTCAGCTCATTCAGACTTAGTATGAAAAACTTATGCTAGTTTTTCATTTAAGGACA-TTTG
** * * * * *
20135 AGGAGTCAAACCAACTTCTCTATGCTAGAGAGTTCGGTTTCACTTAGATTTTTTCCCATATCCTT
65 AGGAGAGAAACCAACTTCACCATGCAAGAGAGCTCGGTTTCACTTAGATTTTTTCACATATCCTT
20200 ATGGTGATAATCTAAGTATACTGGTGAA
130 ATGGTGATAATCTAAGTATACTGGTGAA
* * * **
20228 AAA--TCAGCTTCGTT-GGACTTAGTATGGAAAACTTATGCTAGTTTTTCATTTAAGGACCACCT
1 AAATTTCAGC-TCATTCAGACTTAGTATGAAAAACTTATGCTAGTTTTTCATTTAAGGA-CATTT
* * * * *
20290 GGGGAGAGAAACCTAGTTCACCAT-CAAGGGGAGCTCGGTTTTACTTAGAATTTTTT-ACATAGT
64 GAGGAGAGAAACCAACTTCACCATGCAA-GAGAGCTCGGTTTCACTTAG-ATTTTTTCACATA-T
* * *
20353 -CTTATGCG-GATATTCTAAGT-TTCTTG-GAA
126 CCTTATG-GTGATAATCTAAGTATACTGGTGAA
*
20382 AAATTTCAGCTCATTCAGACTTAGAATGAAAAACTTATGCTAGTTTTTCATTTAAGGACATTTTG
1 AAATTTCAGCTCATTCAGACTTAGTATGAAAAACTTATGCTAGTTTTTCATTTAAGGACA-TTTG
*
20447 AGGTGAGAA
65 AGGAGAGAA
20456 GCTCCGTTTA
Statistics
Matches: 185, Mismatches: 33, Indels: 22
0.77 0.14 0.09
Matches are distributed among these distances:
154 6 0.03
155 12 0.06
156 151 0.82
157 13 0.07
158 3 0.02
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.35
Consensus pattern (157 bp):
AAATTTCAGCTCATTCAGACTTAGTATGAAAAACTTATGCTAGTTTTTCATTTAAGGACATTTGA
GGAGAGAAACCAACTTCACCATGCAAGAGAGCTCGGTTTCACTTAGATTTTTTCACATATCCTTA
TGGTGATAATCTAAGTATACTGGTGAA
Found at i:20987 original size:20 final size:20
Alignment explanation
Indices: 20962--21000 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
20952 AAAAGAGTTC
*
20962 GCCTTCCTCAGCAAGTAAAT
1 GCCTTCCTCAACAAGTAAAT
20982 GCCTTCCTCAACAAGTAAA
1 GCCTTCCTCAACAAGTAAA
21001 GCCCGCCAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.33, C:0.31, G:0.13, T:0.23
Consensus pattern (20 bp):
GCCTTCCTCAACAAGTAAAT
Found at i:24380 original size:51 final size:51
Alignment explanation
Indices: 24294--24551 Score: 381
Period size: 51 Copynumber: 5.1 Consensus size: 51
24284 GGCAGGTTTT
**
24294 GAAGCTAATTACGAGCGCTTAGAAAACAAGGATGATACTGCTGTCAGGACA
1 GAAGCTAATTACGAGCGCTTAGAAAACAAATATGATACTGCTGTCAGGACA
* * * *
24345 AAAACTAATTACGAGCACTTAGAAAACAAATATGATACTGCTGTCTGGACA
1 GAAGCTAATTACGAGCGCTTAGAAAACAAATATGATACTGCTGTCAGGACA
* *
24396 GAAGCTAATTACGAGCGCTTAGAAAACATATATGATACTGCTGGCAGGACA
1 GAAGCTAATTACGAGCGCTTAGAAAACAAATATGATACTGCTGTCAGGACA
* * * * **
24447 GAAGCTAATTACCAGAGTTTAGAAAACAAATATGATACTGTTGTTTGGACA
1 GAAGCTAATTACGAGCGCTTAGAAAACAAATATGATACTGCTGTCAGGACA
*
24498 GAAGCTAATTACGAGCGCTTAGAAAACAAATATGATAGTGCTGTCAGGACA
1 GAAGCTAATTACGAGCGCTTAGAAAACAAATATGATACTGCTGTCAGGACA
24549 GAA
1 GAA
24552 ACGCCAACAT
Statistics
Matches: 180, Mismatches: 27, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
51 180 1.00
ACGTcount: A:0.40, C:0.16, G:0.22, T:0.23
Consensus pattern (51 bp):
GAAGCTAATTACGAGCGCTTAGAAAACAAATATGATACTGCTGTCAGGACA
Found at i:30444 original size:81 final size:81
Alignment explanation
Indices: 30309--30479 Score: 297
Period size: 81 Copynumber: 2.1 Consensus size: 81
30299 GGCAACTCTT
* *
30309 CATTTGGGTTTGCCGAGGTTCCTACAAAGTCAAAATAAGTTTTGTTTTTGTATTCCACTTTCTGC
1 CATTTGTGTTTGCCGAGGTTCCTACAAAGTCAAAATAAGCTTTGTTTTTGTATTCCACTTTCTGC
30374 ACCCAGCCGATTACCC
66 ACCCAGCCGATTACCC
* *
30390 CATTTGTGTTTGCCGAGGTTCCTACAAAGTCAAAATAAGCTTTGTTTTTTTATTCCACTTTTTGC
1 CATTTGTGTTTGCCGAGGTTCCTACAAAGTCAAAATAAGCTTTGTTTTTGTATTCCACTTTCTGC
*
30455 ACCCAGCCGGTTACCC
66 ACCCAGCCGATTACCC
30471 CATTTGTGT
1 CATTTGTGT
30480 GAAGAAACAA
Statistics
Matches: 85, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
81 85 1.00
ACGTcount: A:0.21, C:0.24, G:0.17, T:0.38
Consensus pattern (81 bp):
CATTTGTGTTTGCCGAGGTTCCTACAAAGTCAAAATAAGCTTTGTTTTTGTATTCCACTTTCTGC
ACCCAGCCGATTACCC
Found at i:32050 original size:24 final size:24
Alignment explanation
Indices: 32018--32065 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
32008 ATAGCCACAT
32018 TGGACTTTGACTAATCTAAAGTCG
1 TGGACTTTGACTAATCTAAAGTCG
32042 TGGACTTTGACTAATCTAAAGTCG
1 TGGACTTTGACTAATCTAAAGTCG
32066 AGTCACATCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.29, C:0.17, G:0.21, T:0.33
Consensus pattern (24 bp):
TGGACTTTGACTAATCTAAAGTCG
Found at i:32452 original size:17 final size:17
Alignment explanation
Indices: 32404--32452 Score: 50
Period size: 17 Copynumber: 3.1 Consensus size: 17
32394 ACAGATAATT
32404 ATGATGTGTTCAATCAA
1 ATGATGTGTTCAATCAA
* **
32421 ACG--GT-TTGTATCAA
1 ATGATGTGTTCAATCAA
32435 ATGATGTGTTCAATCAA
1 ATGATGTGTTCAATCAA
32452 A
1 A
32453 GTATGATGTA
Statistics
Matches: 23, Mismatches: 6, Indels: 6
0.66 0.17 0.17
Matches are distributed among these distances:
14 9 0.39
15 2 0.09
16 2 0.09
17 10 0.43
ACGTcount: A:0.35, C:0.12, G:0.18, T:0.35
Consensus pattern (17 bp):
ATGATGTGTTCAATCAA
Found at i:33287 original size:3 final size:3
Alignment explanation
Indices: 33274--33313 Score: 71
Period size: 3 Copynumber: 13.3 Consensus size: 3
33264 TCTCCATGTG
*
33274 GGT GAT GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT G
1 GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT G
33314 ACCCATTCTC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.03, C:0.00, G:0.65, T:0.33
Consensus pattern (3 bp):
GGT
Found at i:39811 original size:2 final size:2
Alignment explanation
Indices: 39804--39837 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
39794 AATTCTATGA
39804 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
39838 TTTCTGTTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:41234 original size:21 final size:21
Alignment explanation
Indices: 41210--41252 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
41200 TAACGGTTTC
*
41210 GTCAAACCCGTGTTAACTGCT
1 GTCAAACACGTGTTAACTGCT
41231 GTCAAACACGTGTTAACTGCT
1 GTCAAACACGTGTTAACTGCT
41252 G
1 G
41253 ACTTGTAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.26, C:0.26, G:0.21, T:0.28
Consensus pattern (21 bp):
GTCAAACACGTGTTAACTGCT
Found at i:41283 original size:18 final size:19
Alignment explanation
Indices: 41248--41286 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
41238 ACGTGTTAAC
*
41248 TGCTGACTTGTAATTTTTT
1 TGCTGACGTGTAATTTTTT
41267 TGCTGACGTGT-ATTTTTT
1 TGCTGACGTGTAATTTTTT
41285 TG
1 TG
41287 TATTTTTTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 9 0.47
19 10 0.53
ACGTcount: A:0.13, C:0.10, G:0.21, T:0.56
Consensus pattern (19 bp):
TGCTGACGTGTAATTTTTT
Found at i:41298 original size:28 final size:28
Alignment explanation
Indices: 41255--41317 Score: 117
Period size: 28 Copynumber: 2.2 Consensus size: 28
41245 AACTGCTGAC
41255 TTGTAATTTTTTTGCTGACGTGTATTTTT
1 TTGT-ATTTTTTTGCTGACGTGTATTTTT
41284 TTGTATTTTTTTGCTGACGTGTATTTTT
1 TTGTATTTTTTTGCTGACGTGTATTTTT
41312 TTGTAT
1 TTGTAT
41318 GGGACAGGTG
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
28 30 0.88
29 4 0.12
ACGTcount: A:0.13, C:0.06, G:0.17, T:0.63
Consensus pattern (28 bp):
TTGTATTTTTTTGCTGACGTGTATTTTT
Found at i:41393 original size:14 final size:14
Alignment explanation
Indices: 41373--41407 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
41363 GAAAAAGAAG
41373 AAGAAAACGGAAAA
1 AAGAAAACGGAAAA
* *
41387 CAGAAAATGGAAAA
1 AAGAAAACGGAAAA
41401 AAGAAAA
1 AAGAAAA
41408 AAACTAAACA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.71, C:0.06, G:0.20, T:0.03
Consensus pattern (14 bp):
AAGAAAACGGAAAA
Found at i:41699 original size:53 final size:53
Alignment explanation
Indices: 41619--41725 Score: 187
Period size: 53 Copynumber: 2.0 Consensus size: 53
41609 ATTCCAACCG
* *
41619 TATTTGCTACAAACAAACTGCTATACATACTAGATCTAAAGAACCAAACACCA
1 TATTTGCTACAAACAAACTGCTATACATACTAAATCCAAAGAACCAAACACCA
*
41672 TATTTGCTACAAACAAACTGCTATACATACTAAATCCAAAGAACCCAACACCA
1 TATTTGCTACAAACAAACTGCTATACATACTAAATCCAAAGAACCAAACACCA
41725 T
1 T
41726 GTATGTCTTT
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
53 51 1.00
ACGTcount: A:0.45, C:0.26, G:0.07, T:0.22
Consensus pattern (53 bp):
TATTTGCTACAAACAAACTGCTATACATACTAAATCCAAAGAACCAAACACCA
Found at i:43232 original size:2 final size:2
Alignment explanation
Indices: 43225--43250 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
43215 CCAGAAAATT
43225 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
43251 GACACACAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:44109 original size:39 final size:39
Alignment explanation
Indices: 44055--44132 Score: 129
Period size: 39 Copynumber: 2.0 Consensus size: 39
44045 GCAAAGTTAG
* *
44055 AATTTCCCATCAATGATTGTTTAGAATAAGATCTGAAGA
1 AATTTCCCATCAATGATTCTTTACAATAAGATCTGAAGA
*
44094 AATTTCCCATCAATGATTCTTTACAATAAGATTTGAAGA
1 AATTTCCCATCAATGATTCTTTACAATAAGATCTGAAGA
44133 GGGATGTAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.38, C:0.14, G:0.13, T:0.35
Consensus pattern (39 bp):
AATTTCCCATCAATGATTCTTTACAATAAGATCTGAAGA
Found at i:44549 original size:19 final size:20
Alignment explanation
Indices: 44511--44550 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
44501 ATTGGCGACG
*
44511 TTGTTGGTTATTCATGCTATT
1 TTGTTGGTCATT-ATGCTATT
44532 TTGTTGGTCATT-TGCTATT
1 TTGTTGGTCATTATGCTATT
44551 AGTATGGGAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 7 0.39
21 11 0.61
ACGTcount: A:0.12, C:0.10, G:0.20, T:0.57
Consensus pattern (20 bp):
TTGTTGGTCATTATGCTATT
Found at i:49825 original size:15 final size:15
Alignment explanation
Indices: 49807--49835 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
49797 TAACTCTCCA
49807 TGGGAGAGTGATTCT
1 TGGGAGAGTGATTCT
49822 TGGGAGAGTGATTC
1 TGGGAGAGTGATTC
49836 CAGGGAAAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.21, C:0.07, G:0.41, T:0.31
Consensus pattern (15 bp):
TGGGAGAGTGATTCT
Found at i:49841 original size:15 final size:15
Alignment explanation
Indices: 49803--49841 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
49793 GGAATAACTC
49803 TCCATGGGAGAGTGAT
1 TCCA-GGGAGAGTGAT
**
49819 TCTTGGGAGAGTGAT
1 TCCAGGGAGAGTGAT
49834 TCCAGGGA
1 TCCAGGGA
49842 AAGTAACGCT
Statistics
Matches: 19, Mismatches: 4, Indels: 1
0.79 0.17 0.04
Matches are distributed among these distances:
15 17 0.89
16 2 0.11
ACGTcount: A:0.23, C:0.13, G:0.38, T:0.26
Consensus pattern (15 bp):
TCCAGGGAGAGTGAT
Found at i:52453 original size:36 final size:34
Alignment explanation
Indices: 52404--52539 Score: 105
Period size: 34 Copynumber: 3.9 Consensus size: 34
52394 TTGCTGATTG
* * *
52404 CCATTACTT-TTTACTGATTAATATTTTACTCTTTA
1 CCATT-CTTCTTTACTGACTAAT-CTTTACTCTTCA
* *
52439 CCATTTTTTCTTTACTGGACTACTCTTTACTCTTCA
1 CCA-TTCTTCTTTACT-GACTAATCTTTACTCTTCA
** * *
52475 CCATTCTTCTTTACTGACTTCTCTTCACTCTTTA
1 CCATTCTTCTTTACTGACTAATCTTTACTCTTCA
* * *
52509 CCATT-TTCCTTTGCTGATTACTCTTTACTCT
1 CCATTCTT-CTTTACTGACTAATCTTTACTCT
52540 ACTCTTTACT
Statistics
Matches: 84, Mismatches: 13, Indels: 9
0.79 0.12 0.08
Matches are distributed among these distances:
33 2 0.02
34 40 0.48
35 16 0.19
36 21 0.25
37 5 0.06
ACGTcount: A:0.18, C:0.26, G:0.04, T:0.51
Consensus pattern (34 bp):
CCATTCTTCTTTACTGACTAATCTTTACTCTTCA
Found at i:52505 original size:34 final size:33
Alignment explanation
Indices: 52428--52798 Score: 133
Period size: 34 Copynumber: 11.2 Consensus size: 33
52418 TGATTAATAT
*
52428 TTTACTCTTTACCATTTTTTCTTTACTGGACTACTC
1 TTTACTCTTTACCA--TTTTCTTTACT-GACTTCTC
*
52464 TTTACTCTTCACCATTCTTCTTTACTGACTTCTC
1 TTTACTCTTTACCATT-TTCTTTACTGACTTCTC
* *
52498 TTCACTCTTTACCATTTTCCTTTGCTGA-TTACTC
1 TTTACTCTTTACCATTTT-CTTTACTGACTT-CTC
* * *
52532 TTTACTC--TACTC-TTTACTCTTTAC-CATTTTTC
1 TTTACTCTTTAC-CATTT--TCTTTACTGACTTCTC
** *
52564 TTTACTGATTACTC-TTCTCTTTACT--CTTTACTC
1 TTTACTCTTTAC-CATTTTCTTTACTGAC-TT-CTC
* *
52597 TTTACTCTTTACCCTTTTGCATTACTGA-TTACTC
1 TTTACTCTTTACCATTTT-CTTTACTGACTT-CTC
*
52631 TTTTACTTTTTACCATTTTACTTTGA-TGA-TTACTC
1 -TTTACTCTTTACCATTTT-CTTT-ACTGACTT-CTC
* * * *
52666 TTTA--CTTTACCCTTTACTCTTTAC-CATTTTTC
1 TTTACTCTTTACCATTT--TCTTTACTGACTTCTC
** *
52698 TTTACTGATTA-C-TCTTC--T-CT---TTACTC
1 TTTACTCTTTACCATTTTCTTTACTGACTT-CTC
*
52724 TTTACTCTTTACCCTTTTTCTTTACTGA-TTACTC
1 TTTACTCTTTA-CCATTTTCTTTACTGACTT-CTC
* *
52758 TTTTACTTTTTACCATTTTACTTTGCTGA-TTACTC
1 -TTTACTCTTTACCATTTT-CTTTACTGACTT-CTC
52793 TTTACT
1 TTTACT
52799 TTGCCCTTTA
Statistics
Matches: 264, Mismatches: 35, Indels: 74
0.71 0.09 0.20
Matches are distributed among these distances:
25 2 0.01
26 11 0.04
27 1 0.00
28 2 0.01
29 4 0.02
30 2 0.01
31 1 0.00
32 46 0.17
33 34 0.13
34 86 0.33
35 61 0.23
36 14 0.05
ACGTcount: A:0.16, C:0.26, G:0.04, T:0.54
Consensus pattern (33 bp):
TTTACTCTTTACCATTTTCTTTACTGACTTCTC
Found at i:52538 original size:7 final size:7
Alignment explanation
Indices: 52526--52770 Score: 121
Period size: 7 Copynumber: 36.6 Consensus size: 7
52516 CCTTTGCTGA
52526 TTACTCT
1 TTACTCT
52533 TTACTC-
1 TTACTCT
52539 -TACTCT
1 TTACTCT
52545 TTACTCT
1 TTACTCT
52552 TTAC-CAT
1 TTACTC-T
*
52559 TT-TTCT
1 TTACTCT
**
52565 TTACTGA
1 TTACTCT
52572 TTACTC-
1 TTACTCT
52578 TT-CTCT
1 TTACTCT
52584 TTACTCT
1 TTACTCT
52591 TTACTCT
1 TTACTCT
52598 TTACTCT
1 TTACTCT
*
52605 TTACCCT
1 TTACTCT
*
52612 TT--TGCA
1 TTACT-CT
**
52618 TTACTGA
1 TTACTCT
52625 TTACTCTT
1 TTACTC-T
*
52633 TTACTTT
1 TTACTCT
52640 TTAC-CATT
1 TTACTC--T
52648 TTACT-T
1 TTACTCT
* **
52654 TGA-TGA
1 TTACTCT
52660 TTACTCT
1 TTACTCT
52667 TTA--CT
1 TTACTCT
*
52672 TTACCCT
1 TTACTCT
52679 TTACTCT
1 TTACTCT
52686 TTAC-CAT
1 TTACTC-T
*
52693 TT-TTCT
1 TTACTCT
**
52699 TTACTGA
1 TTACTCT
52706 TTACTC-
1 TTACTCT
52712 TT-CTCT
1 TTACTCT
52718 TTACTCT
1 TTACTCT
52725 TTACTCT
1 TTACTCT
*
52732 TTACCCT
1 TTACTCT
*
52739 TT-TTCT
1 TTACTCT
**
52745 TTACTGA
1 TTACTCT
52752 TTACTCTT
1 TTACTC-T
*
52760 TTACTTT
1 TTACTCT
52767 TTAC
1 TTAC
52771 CATTTTACTT
Statistics
Matches: 180, Mismatches: 33, Indels: 50
0.68 0.13 0.19
Matches are distributed among these distances:
5 17 0.09
6 28 0.16
7 119 0.66
8 16 0.09
ACGTcount: A:0.16, C:0.25, G:0.03, T:0.56
Consensus pattern (7 bp):
TTACTCT
Found at i:52544 original size:12 final size:12
Alignment explanation
Indices: 52527--52551 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
52517 CTTTGCTGAT
52527 TACTCTTTACTC
1 TACTCTTTACTC
52539 TACTCTTTACTC
1 TACTCTTTACTC
52551 T
1 T
52552 TTACCATTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.32, G:0.00, T:0.52
Consensus pattern (12 bp):
TACTCTTTACTC
Found at i:52551 original size:46 final size:46
Alignment explanation
Indices: 52495--52766 Score: 303
Period size: 46 Copynumber: 6.0 Consensus size: 46
52485 TTACTGACTT
* * * *
52495 CTCTTCACTCTTTACCATTTTCCTTTGCTGATTACTCTTTACTCTA
1 CTCTTTACTCTTTACCATTTTTCTTTACTGATTACTCTTTACTTTA
52541 CTCTTTACTCTTTACCATTTTTCTTTACTGATTACTCTTCT-CTTTA
1 CTCTTTACTCTTTACCATTTTTCTTTACTGATTACTCTT-TACTTTA
** **
52587 CTCTTTACTCTTTACTC-TTTACCCTTT--TGCATTACTGATTAC--T-
1 CTCTTTACTCTTTAC-CATTT-TTCTTTACTG-ATTACTCTTTACTTTA
* *
52630 CT-TTTACTTTTTACCATTTTACTTTGA-TGATTACTCTTTACTTTA
1 CTCTTTACTCTTTACCATTTTTCTTT-ACTGATTACTCTTTACTTTA
*
52675 CCCTTTACTCTTTACCATTTTTCTTTACTGATTACTCTTCT-CTTTA
1 CTCTTTACTCTTTACCATTTTTCTTTACTGATTACTCTT-TACTTTA
*
52721 CTCTTTACTCTTTACCCTTTTTCTTTACTGATTACTCTTTTACTTT
1 CTCTTTACTCTTTACCATTTTTCTTTACTGATTACTC-TTTACTTT
52767 TTACCATTTT
Statistics
Matches: 192, Mismatches: 18, Indels: 31
0.80 0.07 0.13
Matches are distributed among these distances:
41 5 0.03
42 24 0.12
43 4 0.02
44 2 0.01
45 5 0.03
46 139 0.72
47 13 0.07
ACGTcount: A:0.16, C:0.26, G:0.03, T:0.55
Consensus pattern (46 bp):
CTCTTTACTCTTTACCATTTTTCTTTACTGATTACTCTTTACTTTA
Found at i:52600 original size:53 final size:51
Alignment explanation
Indices: 52534--52632 Score: 144
Period size: 53 Copynumber: 1.9 Consensus size: 51
52524 GATTACTCTT
*
52534 TACTCTACTCTTTACTCTTTACCATTTTTCTTTACTGATTACTCTTCTCTT
1 TACTCTACTCTTTACTCTTTACCATTTTCCTTTACTGATTACTCTTCTCTT
* * *
52585 TACTCTTTACTCTTTACTCTTTACCCTTTTGCATTACTGATTACTCTT
1 TACTC--TACTCTTTACTCTTTACCATTTTCCTTTACTGATTACTCTT
52633 TTACTTTTTA
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
51 5 0.12
53 38 0.88
ACGTcount: A:0.16, C:0.27, G:0.03, T:0.54
Consensus pattern (51 bp):
TACTCTACTCTTTACTCTTTACCATTTTCCTTTACTGATTACTCTTCTCTT
Found at i:52720 original size:19 final size:19
Alignment explanation
Indices: 52696--52732 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
52686 TTACCATTTT
*
52696 TCTTTACTGATTACTCTTC
1 TCTTTACTCATTACTCTTC
*
52715 TCTTTACTCTTTACTCTT
1 TCTTTACTCATTACTCTT
52733 TACCCTTTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.14, C:0.27, G:0.03, T:0.57
Consensus pattern (19 bp):
TCTTTACTCATTACTCTTC
Found at i:52736 original size:127 final size:127
Alignment explanation
Indices: 52459--52840 Score: 563
Period size: 127 Copynumber: 3.0 Consensus size: 127
52449 TTTACTGGAC
* * * * *
52459 TACTCTTTACTCTTCACCATTCTTCTTTACTGACTT-CTC-TTCACTCTTTACCATTTTCCTTTG
1 TACTCTTTACTCTTTACCCTT-TTCTTTACTGA-TTACTCTTTTACTTTTTACCATTTTACTTTG
* *
52522 CTGATTACTCTTTACTCTACTCTTTACTCTTTACCATTTTTCTTTACTGATTACTCTTCTCTTTA
64 CTGATTACTCTTTACTTTACCCTTTACTCTTTACCATTTTTCTTTACTGATTA-----CTC-TTA
52587 CTCTT
123 CTCTT
* *
52592 TACTCTTTACTCTTTACCCTTTTGCATTACTGATTACTCTTTTACTTTTTACCATTTTACTTTGA
1 TACTCTTTACTCTTTACCCTTTT-CTTTACTGATTACTCTTTTACTTTTTACCATTTTACTTTGC
52657 TGATTACTCTTTACTTTACCCTTTACTCTTTACCATTTTTCTTTACTGATTACTCTT-CTCTT
65 TGATTACTCTTTACTTTACCCTTTACTCTTTACCATTTTTCTTTACTGATTACTCTTACTCTT
52719 TACTCTTTACTCTTTACCCTTTTTCTTTACTGATTACTCTTTTACTTTTTACCATTTTACTTTGC
1 TACTCTTTACTCTTTACCC-TTTTCTTTACTGATTACTCTTTTACTTTTTACCATTTTACTTTGC
*
52784 TGATTACTCTTTACTTTGCCCTTTACTCTTTACCATTTTTCTTTACTGATTACTCTT
65 TGATTACTCTTTACTTTACCCTTTACTCTTTACCATTTTTCTTTACTGATTACTCTT
52841 GTCTGAATAC
Statistics
Matches: 233, Mismatches: 12, Indels: 14
0.90 0.05 0.05
Matches are distributed among these distances:
127 119 0.51
128 6 0.03
129 3 0.01
132 4 0.02
133 30 0.13
134 71 0.30
ACGTcount: A:0.16, C:0.26, G:0.04, T:0.54
Consensus pattern (127 bp):
TACTCTTTACTCTTTACCCTTTTCTTTACTGATTACTCTTTTACTTTTTACCATTTTACTTTGCT
GATTACTCTTTACTTTACCCTTTACTCTTTACCATTTTTCTTTACTGATTACTCTTACTCTT
Found at i:52755 original size:20 final size:20
Alignment explanation
Indices: 52686--52766 Score: 63
Period size: 20 Copynumber: 3.8 Consensus size: 20
52676 CCTTTACTCT
*
52686 TTACCATTTTTCTTTACTGA
1 TTACCCTTTTTCTTTACTGA
**
52706 TTACTCTTCTCTTTACTCTTTACTCT
1 TTAC-C--CT-TTT--TCTTTACTGA
52732 TTACCCTTTTTCTTTACTGA
1 TTACCCTTTTTCTTTACTGA
* *
52752 TTACTCTTTTACTTT
1 TTACCCTTTTTCTTT
52767 TTACCATTTT
Statistics
Matches: 48, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
20 25 0.52
21 1 0.02
22 3 0.06
23 3 0.06
24 3 0.06
25 1 0.02
26 12 0.25
ACGTcount: A:0.15, C:0.25, G:0.02, T:0.58
Consensus pattern (20 bp):
TTACCCTTTTTCTTTACTGA
Found at i:52763 original size:81 final size:82
Alignment explanation
Indices: 52581--52947 Score: 288
Period size: 81 Copynumber: 4.4 Consensus size: 82
52571 ATTACTCTTC
** * * * *
52581 TCTTTACTCTTTACTC-TTTACTCTTTACCCTTTTGCATTACTGATTACTCTTTTACTTTTTAC-
1 TCTTTACTGATTACTCTTTTACTCTTTACCATTTTTCTTTACTGATTACTCTTCTAC--TTTACT
* ** **
52644 CATTTTACT-TTGATGATTAC
64 C--TTTACTCTTTACCATTTT
*
52664 TCTTTACT--TTAC-CCTTTACTCTTTACCATTTTTCTTTACTGATTACTCTTCT-CTTTACTCT
1 TCTTTACTGATTACTCTTTTACTCTTTACCATTTTTCTTTACTGATTACTCTTCTACTTTACTCT
*
52725 TTACTCTTTACCCTTTT
66 TTACTCTTTACCATTTT
* * * * *
52742 TCTTTACTGATTACTCTTTTACTTTTTACCATTTTACTTTGCTGATTACTCTT-TACTTTGCCCT
1 TCTTTACTGATTACTCTTTTACTCTTTACCATTTTTCTTTACTGATTACTCTTCTACTTTACTCT
52806 TTACTCTTTACCATTTT
66 TTACTCTTTACCATTTT
52823 TCTTTACTGATTACTCTTGTCTGAATACTCTTTTA-C-TTTTTCTTTACTGATTAC-CATTTCCT
1 TCTTTACTGATTACTC-T-T-T---TACTC-TTTACCATTTTTCTTTACTGATTACTC--TT-C-
*
52885 TTGCTGATTACTCTTTACTCTTTACCATTTTTTT
55 -TACT--TTACTCTTTACTCTTTACCA---TTTT
*
52919 TCTTTACTGATTACTCTTTTACTTTTTAC
1 TCTTTACTGATTACTCTTTTACTCTTTAC
52948 TGATTACCAT
Statistics
Matches: 234, Mismatches: 24, Indels: 45
0.77 0.08 0.15
Matches are distributed among these distances:
77 6 0.03
78 18 0.08
79 1 0.00
80 7 0.03
81 111 0.47
82 1 0.00
83 9 0.04
84 1 0.00
85 1 0.00
86 16 0.07
87 7 0.03
88 4 0.02
89 4 0.02
90 4 0.02
91 3 0.01
93 19 0.08
94 1 0.00
95 1 0.00
96 20 0.09
ACGTcount: A:0.16, C:0.24, G:0.04, T:0.56
Consensus pattern (82 bp):
TCTTTACTGATTACTCTTTTACTCTTTACCATTTTTCTTTACTGATTACTCTTCTACTTTACTCT
TTACTCTTTACCATTTT
Found at i:52768 original size:27 final size:26
Alignment explanation
Indices: 52706--52768 Score: 63
Period size: 27 Copynumber: 2.3 Consensus size: 26
52696 TCTTTACTGA
* * *
52706 TTACTCTTCTCTTTACTCTTTACTCT
1 TTACTTTTTTCTTTACTCATTACTCT
* *
52732 TTACCCTTTTTCTTTACTGATTACTCTT
1 TTA-CTTTTTTCTTTACTCATTACTC-T
52760 TTACTTTTT
1 TTACTTTTT
52769 ACCATTTTAC
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
26 3 0.10
27 22 0.76
28 4 0.14
ACGTcount: A:0.13, C:0.25, G:0.02, T:0.60
Consensus pattern (26 bp):
TTACTTTTTTCTTTACTCATTACTCT
Found at i:52798 original size:19 final size:19
Alignment explanation
Indices: 52774--52816 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
52764 TTTTTACCAT
**
52774 TTTACTTTGCTGATTACTC
1 TTTACTTTGCCCATTACTC
*
52793 TTTACTTTGCCCTTTACTC
1 TTTACTTTGCCCATTACTC
52812 TTTAC
1 TTTAC
52817 CATTTTTCTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.14, C:0.26, G:0.07, T:0.53
Consensus pattern (19 bp):
TTTACTTTGCCCATTACTC
Found at i:52854 original size:60 final size:58
Alignment explanation
Indices: 52775--52899 Score: 146
Period size: 59 Copynumber: 2.1 Consensus size: 58
52765 TTTTACCATT
* * *
52775 TTACT-TTGCTGATTACTC-TTTACTTTGCCCTTTACTCTTTACCATTTTTCTTTACTGA
1 TTACTCTTGCTGAATACTCTTTTACTTT-CCCTTTACTCATTACCA-TTTCCTTTACTGA
** * *
52833 TTACTCTTGTCTGAATACTCTTTTACTTTTTCTTTACTGATTACCATTTCCTTTGCTGA
1 TTACTCTTG-CTGAATACTCTTTTACTTTCCCTTTACTCATTACCATTTCCTTTACTGA
52892 TTACTCTT
1 TTACTCTT
52900 TACTCTTTAC
Statistics
Matches: 57, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
58 5 0.09
59 22 0.39
60 22 0.39
61 8 0.14
ACGTcount: A:0.16, C:0.23, G:0.07, T:0.54
Consensus pattern (58 bp):
TTACTCTTGCTGAATACTCTTTTACTTTCCCTTTACTCATTACCATTTCCTTTACTGA
Found at i:52946 original size:22 final size:22
Alignment explanation
Indices: 52892--53139 Score: 147
Period size: 22 Copynumber: 11.4 Consensus size: 22
52882 CCTTTGCTGA
* **
52892 TTACTCTTTACTCTTTACCATT
1 TTACTTTTTACTGATTACCATT
**
52914 TTTTTTCTTTACTGATTACTC-TT
1 TTACTT-TTTACTGATTAC-CATT
52937 TTACTTTTTACTGATTACCATT
1 TTACTTTTTACTGATTACCATT
* *
52959 TTACTCTTTT-CTAATTACTATT
1 TTACT-TTTTACTGATTACCATT
* *
52981 TTACTTTTTACTGATAACCTTT
1 TTACTTTTTACTGATTACCATT
** *
53003 TTACCTTTTTACTG-TTTGC-TA
1 TTA-CTTTTTACTGATTACCATT
* *
53024 TTACTTCTTACTGATT---TTT
1 TTACTTTTTACTGATTACCATT
* * *
53043 ATTACTCTTTACTGATTATCACT
1 -TTACTTTTTACTGATTACCATT
* *
53066 TTACTCTTTACTAATTACCATT
1 TTACTTTTTACTGATTACCATT
** * *
53088 TTACCCTTT-CAGA-TACCTTT
1 TTACTTTTTACTGATTACCATT
*
53108 TTACTTTTTTACTGATTA-CGTT
1 TTAC-TTTTTACTGATTACCATT
53130 TTACTCTTTT
1 TTACT-TTTT
53140 TTAGATTTTT
Statistics
Matches: 176, Mismatches: 34, Indels: 32
0.73 0.14 0.13
Matches are distributed among these distances:
19 1 0.01
20 33 0.19
21 17 0.10
22 91 0.52
23 33 0.19
24 1 0.01
ACGTcount: A:0.20, C:0.20, G:0.04, T:0.56
Consensus pattern (22 bp):
TTACTTTTTACTGATTACCATT
Found at i:53045 original size:20 final size:20
Alignment explanation
Indices: 53022--53059 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
53012 TACTGTTTGC
53022 TATTACT-TCTTACTGATTTT
1 TATTACTCT-TTACTGATTTT
53042 TATTACTCTTTACTGATT
1 TATTACTCTTTACTGATT
53060 ATCACTTTAC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 16 0.94
21 1 0.06
ACGTcount: A:0.21, C:0.16, G:0.05, T:0.58
Consensus pattern (20 bp):
TATTACTCTTTACTGATTTT
Found at i:56431 original size:21 final size:21
Alignment explanation
Indices: 56390--56431 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
56380 GGGTTGCGAG
*
56390 GCAAACCACATGGGGCGCCAA
1 GCAAACCACATGGCGCGCCAA
56411 GCAAACCACATTGGCGC-CCAA
1 GCAAACCACA-TGGCGCGCCAA
56432 CGCTAGTCGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.33, C:0.36, G:0.24, T:0.07
Consensus pattern (21 bp):
GCAAACCACATGGCGCGCCAA
Done.