Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008893.1 Corchorus capsularis cultivar CVL-1 contig08914, 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: 41576
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.35
Found at i:406 original size:33 final size:33
Alignment explanation
Indices: 360--439 Score: 115
Period size: 33 Copynumber: 2.4 Consensus size: 33
350 AGCACTAGTG
* *
360 ACCGGCCATGCGACTTGCAGAAGTCCGGCCAAC
1 ACCGGCCACGCGACTTGCAGAAGCCCGGCCAAC
* * *
393 ACCGGCCACGCGACTTGGAGATGCCCGGCCATC
1 ACCGGCCACGCGACTTGCAGAAGCCCGGCCAAC
426 ACCGGCCACGCGAC
1 ACCGGCCACGCGAC
440 ATGGACATGT
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 42 1.00
ACGTcount: A:0.21, C:0.40, G:0.29, T:0.10
Consensus pattern (33 bp):
ACCGGCCACGCGACTTGCAGAAGCCCGGCCAAC
Found at i:454 original size:33 final size:33
Alignment explanation
Indices: 382--455 Score: 112
Period size: 33 Copynumber: 2.2 Consensus size: 33
372 ACTTGCAGAA
* *
382 GTCCGGCCAACACCGGCCACGCGACTTGGAGAT
1 GTCCGGCCAACACCGGCCACGCGACATGGACAT
* *
415 GCCCGGCCATCACCGGCCACGCGACATGGACAT
1 GTCCGGCCAACACCGGCCACGCGACATGGACAT
448 GTCCGGCC
1 GTCCGGCC
456 TTTTGATCCT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.19, C:0.41, G:0.30, T:0.11
Consensus pattern (33 bp):
GTCCGGCCAACACCGGCCACGCGACATGGACAT
Found at i:4979 original size:19 final size:19
Alignment explanation
Indices: 4955--4991 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
4945 AGAGGATTCA
4955 GAGAGGTGA-AGAAGAGAGC
1 GAGAGGTGAGAG-AGAGAGC
4974 GAGAGGTGAGAGAGAGAG
1 GAGAGGTGAGAGAGAGAG
4992 GATGAGCGAC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 15 0.88
20 2 0.12
ACGTcount: A:0.41, C:0.03, G:0.51, T:0.05
Consensus pattern (19 bp):
GAGAGGTGAGAGAGAGAGC
Found at i:8545 original size:176 final size:176
Alignment explanation
Indices: 8251--8599 Score: 689
Period size: 176 Copynumber: 2.0 Consensus size: 176
8241 AAAAACTCTA
8251 TTTTCATCTAATTAAATTCAACATTTTATAATTATTTTATTTTTACCATTTTAATTTAAAAGGTT
1 TTTTCATCTAATTAAATTCAACATTTTATAATTATTTTATTTTTACCATTTTAATTTAAAAGGTT
*
8316 ATTGTGATTGACTTGTTTCTATTAGTTTAATGTATATATTTATTATTTCCCTAATGTCCAATTAT
66 ATTGTGATTGACTTGTTTCTATTAGTTTAATGTATATATTTATTATTTCCCTAATGTCCAACTAT
8381 TTTATTTGATTTATAATTAATTTTTTGCTAGATAAATGTAACCCTT
131 TTTATTTGATTTATAATTAATTTTTTGCTAGATAAATGTAACCCTT
8427 TTTTCATCTAATTAAATTCAACATTTTATAATTATTTTATTTTTACCATTTTAATTTAAAAGGTT
1 TTTTCATCTAATTAAATTCAACATTTTATAATTATTTTATTTTTACCATTTTAATTTAAAAGGTT
8492 ATTGTGATTGACTTGTTTCTATTAGTTTAATGTATATATTTATTATTTCCCTAATGTCCAACTAT
66 ATTGTGATTGACTTGTTTCTATTAGTTTAATGTATATATTTATTATTTCCCTAATGTCCAACTAT
8557 TTTATTTGATTTATAATTAATTTTTTGCTAGATAAATGTAACC
131 TTTATTTGATTTATAATTAATTTTTTGCTAGATAAATGTAACC
8600 GATTTTTTTT
Statistics
Matches: 172, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
176 172 1.00
ACGTcount: A:0.30, C:0.10, G:0.07, T:0.52
Consensus pattern (176 bp):
TTTTCATCTAATTAAATTCAACATTTTATAATTATTTTATTTTTACCATTTTAATTTAAAAGGTT
ATTGTGATTGACTTGTTTCTATTAGTTTAATGTATATATTTATTATTTCCCTAATGTCCAACTAT
TTTATTTGATTTATAATTAATTTTTTGCTAGATAAATGTAACCCTT
Found at i:9435 original size:11 final size:11
Alignment explanation
Indices: 9392--9429 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
9382 TTCCTATATA
*
9392 AAATAAATTAT
1 AAATTAATTAT
9403 CAAA-TAATTAT
1 -AAATTAATTAT
9414 AAATTAATTAT
1 AAATTAATTAT
9425 AAATT
1 AAATT
9430 TGTTATGAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
10 3 0.12
11 18 0.75
12 3 0.12
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (11 bp):
AAATTAATTAT
Found at i:18391 original size:15 final size:15
Alignment explanation
Indices: 18366--18402 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
18356 ATAAGATTGA
18366 AGAAA-GAGCAAGAAG
1 AGAAAGGAGCAA-AAG
18381 A-AAAGGAGCAAAAG
1 AGAAAGGAGCAAAAG
18395 AGAAAGGA
1 AGAAAGGA
18403 AAAAGCAGAG
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
14 7 0.35
15 13 0.65
ACGTcount: A:0.62, C:0.05, G:0.32, T:0.00
Consensus pattern (15 bp):
AGAAAGGAGCAAAAG
Found at i:18971 original size:12 final size:11
Alignment explanation
Indices: 18944--18970 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
18934 TTAGCTAGTG
18944 TTTTTGGGTTT
1 TTTTTGGGTTT
18955 TTTTTGGGTTT
1 TTTTTGGGTTT
18966 TTTTT
1 TTTTT
18971 TTTTGGTGGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.00, C:0.00, G:0.22, T:0.78
Consensus pattern (11 bp):
TTTTTGGGTTT
Found at i:32152 original size:27 final size:28
Alignment explanation
Indices: 32114--32187 Score: 123
Period size: 27 Copynumber: 2.7 Consensus size: 28
32104 ATTATTATCC
* *
32114 TGACACCAGAAGTTGTCATGGAAA-TCT
1 TGACACCAGAAGTTGTCATGAAAATTAT
32141 TGACACCAGAAGTTGTCATGAAAATTAT
1 TGACACCAGAAGTTGTCATGAAAATTAT
32169 TGACACCAGAAGTTGTCAT
1 TGACACCAGAAGTTGTCAT
32188 CCTAAGATTG
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
27 23 0.52
28 21 0.48
ACGTcount: A:0.35, C:0.18, G:0.20, T:0.27
Consensus pattern (28 bp):
TGACACCAGAAGTTGTCATGAAAATTAT
Found at i:40009 original size:20 final size:20
Alignment explanation
Indices: 39981--40020 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
39971 AAGTTTCTGG
*
39981 TTGAATTTTTTTTAGTTTTT
1 TTGAATTTTTTTTAATTTTT
*
40001 TTGATTTTTTTTTAATTTTT
1 TTGAATTTTTTTTAATTTTT
40021 CGATATAACT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.15, C:0.00, G:0.07, T:0.78
Consensus pattern (20 bp):
TTGAATTTTTTTTAATTTTT
Done.