Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012818.1 Corchorus capsularis cultivar CVL-1 contig12839, 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: 70899
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:2520 original size:25 final size:25
Alignment explanation
Indices: 2472--2521 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
2462 GTATATGAAT
**
2472 CGTGAGGTCTTGAATTTAAATCACA
1 CGTGAGGTCTTGAATACAAATCACA
* *
2497 CGTGAGGTCTTGTATACAAGTCACA
1 CGTGAGGTCTTGAATACAAATCACA
2522 TTACATGTAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.30, C:0.18, G:0.22, T:0.30
Consensus pattern (25 bp):
CGTGAGGTCTTGAATACAAATCACA
Found at i:3683 original size:60 final size:60
Alignment explanation
Indices: 3590--3708 Score: 202
Period size: 60 Copynumber: 2.0 Consensus size: 60
3580 CTAATTGCTC
* *
3590 AAATAAGAGCCTAATGTTTGCCAAAATGCTCAAATAAGGGCCCGATCTTTGAATTTGGCA
1 AAATAAGAGCCTAACGTTTCCCAAAATGCTCAAATAAGGGCCCGATCTTTGAATTTGGCA
* *
3650 AAATAAGGGCCTAACGTTTCCCAAACTGCTCAAATAAGGGCCCGATCTTTGAATTTGGC
1 AAATAAGAGCCTAACGTTTCCCAAAATGCTCAAATAAGGGCCCGATCTTTGAATTTGGC
3709 TCCAAAATGC
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
60 55 1.00
ACGTcount: A:0.33, C:0.21, G:0.20, T:0.26
Consensus pattern (60 bp):
AAATAAGAGCCTAACGTTTCCCAAAATGCTCAAATAAGGGCCCGATCTTTGAATTTGGCA
Found at i:3798 original size:31 final size:31
Alignment explanation
Indices: 3763--3898 Score: 152
Period size: 31 Copynumber: 4.5 Consensus size: 31
3753 TGAAACCAGA
*
3763 CCCTTATTTGAGCATTTTCGATAACGTTAGA
1 CCCTTATTTGAGCATTTTCGATAACGTTAGG
*
3794 CCCTTATTTGAGCATTTTCAATAACGTTAGG
1 CCCTTATTTGAGCATTTTCGATAACGTTAGG
* ** * **
3825 CCCTTATTTGGGCAAATT--A-AAAGATCGGG
1 CCCTTATTTGAGCATTTTCGATAACG-TTAGG
* *
3854 CCCTTATTTGAGCATTTTTGATAACATTAGG
1 CCCTTATTTGAGCATTTTCGATAACGTTAGG
3885 CCCTTATTTGAGCA
1 CCCTTATTTGAGCA
3899 ATTAGCCAAG
Statistics
Matches: 86, Mismatches: 15, Indels: 8
0.79 0.14 0.07
Matches are distributed among these distances:
28 3 0.03
29 19 0.22
31 62 0.72
32 2 0.02
ACGTcount: A:0.26, C:0.19, G:0.18, T:0.37
Consensus pattern (31 bp):
CCCTTATTTGAGCATTTTCGATAACGTTAGG
Found at i:4500 original size:2 final size:2
Alignment explanation
Indices: 4455--4481 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
4445 TCATTTGAAC
4455 AT 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 AT A
4482 ACCTGGATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5965 original size:2 final size:2
Alignment explanation
Indices: 5958--5983 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
5948 AAGTATTAGA
5958 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
5984 GTGGCAATGG
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):
AT
Found at i:7341 original size:1 final size:1
Alignment explanation
Indices: 7335--7359 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
7325 TGTCCCAAGA
7335 TTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTT
7360 ATGTGTTCCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:9870 original size:2 final size:2
Alignment explanation
Indices: 9863--9893 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
9853 CTAATTCACC
9863 AT AT AT 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 AT AT AT A
9894 AGTAAAGTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:15618 original size:398 final size:397
Alignment explanation
Indices: 14855--15652 Score: 1562
Period size: 398 Copynumber: 2.0 Consensus size: 397
14845 GGGACATACC
14855 TTTTTTCATGTATTTATATTTTTGTACGAAAACTACTTTCCATAAATAACTACTATGAATCTTTC
1 TTTTTTCATGTATTTATATTTTTGTACGAAAACTACTTTCCATAAATAACTACTATGAATCTTTC
*
14920 ACCCTATAGCTAGATGATAAGATTTATTAGTCTCTTAAAATAGATTAAATATCCCTAAAAAGAAG
66 ACCCTATAGCTAGATGATAACATTTATTAGTCTCTTAAAATAGATTAAATATCCCTAAAAAGAAG
14985 GAAATATTGAATTTTTTTTTTGGCCAGAAAAAAATATTGAAATTTGAATCTAACTTTTTTGTTTT
131 GAAATATTGAATTTTTTTTTTGGCCAGAAAAAAATATTGAAATTTGAATCTAACTTTTTTGTTTT
15050 TATTTTATTTTTAGAGGAGGATTCTAACCCAAATTGTTAGTGTTGAATGTTTTGGAAATTAATAA
196 TATTTTATTTTTAGAGGAGGATTCTAACCCAAATTGTTAGTGTTGAATGTTTTGGAAATTAATAA
15115 GGTCTGATTTGGCATTGTGTTTGAAGATAAAAAACTGTTTTTGACCCAAAACGCAATACCAAAAA
261 GGTCTGATTTGGCATTGTGTTTGAAGATAAAAAACTGTTTTTGACCCAAAACGCAATACCAAAAA
15180 AATTCTGATTTGTGTCAAAAGTTGATTTTGAACGCAAAACAAACCAACCCGAGAAGCTAATCCTT
326 AATTCTGATTTGTGTCAAAAGTTGATTTTGAACGCAAAACAAACCAACCCGAGAAGCTAATCCTT
15245 AGGTGTT
391 AGGTGTT
15252 TTTTTTCATGTATTTATATTTTTGTACGAAAACTACTTTCCATAAATAACTACTATGAATCTTTC
1 TTTTTTCATGTATTTATATTTTTGTACGAAAACTACTTTCCATAAATAACTACTATGAATCTTTC
15317 ACCCTATAGCTAGATGATAACATTTATTAGTCTCTTAAAATAGATTAAATATCCCTAAAAAGAAG
66 ACCCTATAGCTAGATGATAACATTTATTAGTCTCTTAAAATAGATTAAATATCCCTAAAAAGAAG
15382 GAAATATTGAA-TTTTTTTTTGGCCAGAAAAAAATATTGAAATTTGAATCTAACTTTTTTTGTTT
131 GAAATATTGAATTTTTTTTTTGGCCAGAAAAAAATATTGAAATTTGAATCTAAC-TTTTTTGTTT
15446 TTATTTTATTTTTTAGAGGAGGATTCTAACCCAAATTGTTAGTGTTGAATGTTTTGGAAATTAAT
195 TTATTTTA-TTTTTAGAGGAGGATTCTAACCCAAATTGTTAGTGTTGAATGTTTTGGAAATTAAT
15511 AAGGTCTGATTTGGCATTGTGTTTGAAGATAAAAAACTGTTTTTGACCCAAAACGCAATACCAAA
259 AAGGTCTGATTTGGCATTGTGTTTGAAGATAAAAAACTGTTTTTGACCCAAAACGCAATACCAAA
15576 AAAATTCTGATTTGTGTCAAAAGTTGATTTTGAACGCAAAACAAACCAACCCGAGAAGCTAATCC
324 AAAATTCTGATTTGTGTCAAAAGTTGATTTTGAACGCAAAACAAACCAACCCGAGAAGCTAATCC
15641 TTAGGTGTT
389 TTAGGTGTT
15650 TTT
1 TTT
15653 GTGTTTCAAA
Statistics
Matches: 398, Mismatches: 1, Indels: 3
0.99 0.00 0.01
Matches are distributed among these distances:
396 42 0.11
397 158 0.40
398 198 0.50
ACGTcount: A:0.35, C:0.13, G:0.14, T:0.38
Consensus pattern (397 bp):
TTTTTTCATGTATTTATATTTTTGTACGAAAACTACTTTCCATAAATAACTACTATGAATCTTTC
ACCCTATAGCTAGATGATAACATTTATTAGTCTCTTAAAATAGATTAAATATCCCTAAAAAGAAG
GAAATATTGAATTTTTTTTTTGGCCAGAAAAAAATATTGAAATTTGAATCTAACTTTTTTGTTTT
TATTTTATTTTTAGAGGAGGATTCTAACCCAAATTGTTAGTGTTGAATGTTTTGGAAATTAATAA
GGTCTGATTTGGCATTGTGTTTGAAGATAAAAAACTGTTTTTGACCCAAAACGCAATACCAAAAA
AATTCTGATTTGTGTCAAAAGTTGATTTTGAACGCAAAACAAACCAACCCGAGAAGCTAATCCTT
AGGTGTT
Found at i:16166 original size:42 final size:42
Alignment explanation
Indices: 16099--16183 Score: 134
Period size: 42 Copynumber: 2.0 Consensus size: 42
16089 TACAATTTGT
*
16099 TTTTACATAAGACATCGGATATTAGCTAAGTTTACCAAACAG
1 TTTTACATAAGACATCGAATATTAGCTAAGTTTACCAAACAG
* * *
16141 TTTTACATAAGACGTCGAATGTTAGCTAAGTTTCCCAAACAG
1 TTTTACATAAGACATCGAATATTAGCTAAGTTTACCAAACAG
16183 T
1 T
16184 CACGCCATTA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.35, C:0.18, G:0.15, T:0.32
Consensus pattern (42 bp):
TTTTACATAAGACATCGAATATTAGCTAAGTTTACCAAACAG
Found at i:23381 original size:13 final size:13
Alignment explanation
Indices: 23363--23387 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
23353 TAGCAGGAAA
23363 AAAAAAAGAAAAG
1 AAAAAAAGAAAAG
23376 AAAAAAAGAAAA
1 AAAAAAAGAAAA
23388 CACCCAAGTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (13 bp):
AAAAAAAGAAAAG
Found at i:40347 original size:33 final size:34
Alignment explanation
Indices: 40310--40379 Score: 124
Period size: 34 Copynumber: 2.1 Consensus size: 34
40300 CAAATGGGTA
40310 TTTTTCTGACCC-AAAAACAGATTTTGGTATTGT
1 TTTTTCTGACCCAAAAAACAGATTTTGGTATTGT
*
40343 TTTTTCTTACCCAAAAAACAGATTTTGGTATTGT
1 TTTTTCTGACCCAAAAAACAGATTTTGGTATTGT
40377 TTT
1 TTT
40380 CGACTTGCAA
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
33 11 0.31
34 24 0.69
ACGTcount: A:0.27, C:0.14, G:0.13, T:0.46
Consensus pattern (34 bp):
TTTTTCTGACCCAAAAAACAGATTTTGGTATTGT
Found at i:46709 original size:1 final size:1
Alignment explanation
Indices: 46676--46700 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
46666 TATATATTGC
46676 AAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
46701 TCCAAAAAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:49163 original size:211 final size:211
Alignment explanation
Indices: 48891--49291 Score: 568
Period size: 211 Copynumber: 1.9 Consensus size: 211
48881 TCATTAAGGT
* *
48891 AAATTATACAATACACCGTCAATAGAATTTAGCAGATTACAGAAACGCGTCCTGAAGGGTGAAAT
1 AAATTATACAATACACCGTCAATAGAATTTAGCAGACTACACAAACGCGTCCTGAAGGGTGAAAT
* * *
48956 GTGTCATTTAGGGACTAGATTGAAATATTCAAAACTTAATTAATTAAAAAAATGGACATGTGTCA
66 GTGTCACTTAGGGACTAGAATGAAATATTCAAAACTTAAATAATTAAAAAAATGGACATGTGTCA
* * * *
49021 ACTCCACAACACGTTTGTGGAGTCCAAAATTTACACCGCTAGTGTATCAAATAATTACCCAATCA
131 ACTCCACAACACGCTTGTGGAGTCCAAAATTTACACCGCCAGTATATCAAATAATCACCCAATCA
49086 TTAATTACGAATATGC
196 TTAATTACGAATATGC
** * * * * * * *
49102 AAATTATACAATACACCGTCGGTGGAGTTTAGCATACTACACAAGCGGGTTCTGAAGGGTGACAT
1 AAATTATACAATACACCGTCAATAGAATTTAGCAGACTACACAAACGCGTCCTGAAGGGTGAAAT
* * **
49167 GTGTCCCTTAGGGACTAGAATGAAATATTTAAAACTTAAATAATTTTAAAAATGGACATGTGTCA
66 GTGTCACTTAGGGACTAGAATGAAATATTCAAAACTTAAATAATTAAAAAAATGGACATGTGTCA
* * * *
49232 ACTCCACAACCCGCTTGTGGAGTCCGAAATTTCCACCGCCAGTATATCATATAATCACCC
131 ACTCCACAACACGCTTGTGGAGTCCAAAATTTACACCGCCAGTATATCAAATAATCACCC
49292 TTATAAATAA
Statistics
Matches: 164, Mismatches: 26, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
211 164 1.00
ACGTcount: A:0.37, C:0.19, G:0.17, T:0.27
Consensus pattern (211 bp):
AAATTATACAATACACCGTCAATAGAATTTAGCAGACTACACAAACGCGTCCTGAAGGGTGAAAT
GTGTCACTTAGGGACTAGAATGAAATATTCAAAACTTAAATAATTAAAAAAATGGACATGTGTCA
ACTCCACAACACGCTTGTGGAGTCCAAAATTTACACCGCCAGTATATCAAATAATCACCCAATCA
TTAATTACGAATATGC
Found at i:50727 original size:52 final size:52
Alignment explanation
Indices: 50665--50775 Score: 222
Period size: 52 Copynumber: 2.1 Consensus size: 52
50655 ATAGGAGTAC
50665 AAAATTACAAATTCAATGCATGAAGGGCAAGCAAGAAAGGAGACTTAATATA
1 AAAATTACAAATTCAATGCATGAAGGGCAAGCAAGAAAGGAGACTTAATATA
50717 AAAATTACAAATTCAATGCATGAAGGGCAAGCAAGAAAGGAGACTTAATATA
1 AAAATTACAAATTCAATGCATGAAGGGCAAGCAAGAAAGGAGACTTAATATA
50769 AAAATTA
1 AAAATTA
50776 AACCCATAAG
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 59 1.00
ACGTcount: A:0.51, C:0.11, G:0.18, T:0.20
Consensus pattern (52 bp):
AAAATTACAAATTCAATGCATGAAGGGCAAGCAAGAAAGGAGACTTAATATA
Found at i:56747 original size:91 final size:92
Alignment explanation
Indices: 56539--56750 Score: 315
Period size: 91 Copynumber: 2.3 Consensus size: 92
56529 GATGTAAAAA
*
56539 AAAAAAGATTTATCC-TTATAGTGGGACTCGAATTCTAATTCTTAAGGATGAAAGGAGATTTTAA
1 AAAAAAGATTTATCCTTTATAGTGGGACTCGAATTCTAATTCTTAAGGATGAAAGGAGAGTTTAA
*
56603 GATATAATTTACTTCTTTCAGGGATTC
66 GATATAATTTACTTCTTTCAGGAATTC
* * *
56630 AAAAAAAATTTATCCTTT-TAGTGGGACTCGAATTCTAGTTCTTGAGGATGAAAGGAGAGTTTAA
1 AAAAAAGATTTATCCTTTATAGTGGGACTCGAATTCTAATTCTTAAGGATGAAAGGAGAGTTTAA
* *
56694 GATGTAATTTACTTCTTTTAGGAATTC
66 GATATAATTTACTTCTTTCAGGAATTC
*
56721 -AAAAAGATTTATCCTTGTATCG-GGGACTCG
1 AAAAAAGATTTATCCTT-TATAGTGGGACTCG
56751 GAACAAGAGG
Statistics
Matches: 109, Mismatches: 9, Indels: 6
0.88 0.07 0.05
Matches are distributed among these distances:
90 15 0.14
91 90 0.83
92 4 0.04
ACGTcount: A:0.33, C:0.11, G:0.19, T:0.36
Consensus pattern (92 bp):
AAAAAAGATTTATCCTTTATAGTGGGACTCGAATTCTAATTCTTAAGGATGAAAGGAGAGTTTAA
GATATAATTTACTTCTTTCAGGAATTC
Found at i:58336 original size:18 final size:18
Alignment explanation
Indices: 58313--58364 Score: 77
Period size: 18 Copynumber: 2.9 Consensus size: 18
58303 GGTATACTCC
*
58313 TTTCACAGCTGACAGAGA
1 TTTCACAGCTGACACAGA
*
58331 TTTCACAGCTGCCACAGA
1 TTTCACAGCTGACACAGA
*
58349 TTTCACCGCTGACACA
1 TTTCACAGCTGACACA
58365 ACACCTTAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.29, C:0.31, G:0.17, T:0.23
Consensus pattern (18 bp):
TTTCACAGCTGACACAGA
Found at i:62714 original size:30 final size:30
Alignment explanation
Indices: 62678--62771 Score: 113
Period size: 30 Copynumber: 3.1 Consensus size: 30
62668 TATGTGCTTG
62678 GGGACTTTAGTATAGATGCCTCTGTGTTTA
1 GGGACTTTAGTATAGATGCCTCTGTGTTTA
* *
62708 GGGACTTTAATATAGATGCC-CTTGTGCTT-
1 GGGACTTTAGTATAGATGCCTC-TGTGTTTA
*
62737 GAGGACTTT-GATGTAGATGCCTCTGTGTTTA
1 G-GGACTTTAG-TATAGATGCCTCTGTGTTTA
62768 GGGA
1 GGGA
62772 TGAATACCCT
Statistics
Matches: 54, Mismatches: 5, Indels: 10
0.78 0.07 0.14
Matches are distributed among these distances:
29 2 0.04
30 50 0.93
31 2 0.04
ACGTcount: A:0.20, C:0.14, G:0.29, T:0.37
Consensus pattern (30 bp):
GGGACTTTAGTATAGATGCCTCTGTGTTTA
Found at i:62848 original size:58 final size:58
Alignment explanation
Indices: 62690--62855 Score: 186
Period size: 58 Copynumber: 2.9 Consensus size: 58
62680 GACTTTAGTA
* *
62690 TAGATGCCTCTGTGTTTAGGGACTTTAATATAGATGCCCTTGTGCTTGAGGAC--TTTGATG
1 TAGATGCCTCTGTGTTTAGGGAC-TT-ATA-A-ATGCCCTTGTGTTTGAAGACTTTTTGATG
* *
62750 TAGATGCCTCTGTGTTTAGGG----ATGAATACCCTTGTGTTTGAAGACTTTTTGA-G
1 TAGATGCCTCTGTGTTTAGGGACTTATAAATGCCCTTGTGTTTGAAGACTTTTTGATG
62803 -AGATGTGCCTCTGTGTTTAGGGACTTATAAATGCCCTTGTGTTTGAAGACTTT
1 TAGA--TGCCTCTGTGTTTAGGGACTTATAAATGCCCTTGTGTTTGAAGACTTT
62856 GATTGTTGGG
Statistics
Matches: 92, Mismatches: 6, Indels: 18
0.79 0.05 0.16
Matches are distributed among these distances:
52 20 0.22
53 2 0.02
54 24 0.26
58 25 0.27
60 21 0.23
ACGTcount: A:0.20, C:0.14, G:0.26, T:0.39
Consensus pattern (58 bp):
TAGATGCCTCTGTGTTTAGGGACTTATAAATGCCCTTGTGTTTGAAGACTTTTTGATG
Done.