Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011823.1 Corchorus capsularis cultivar CVL-1 contig11844, 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: 97493
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:804 original size:20 final size:19
Alignment explanation
Indices: 767--810 Score: 54
Period size: 18 Copynumber: 2.3 Consensus size: 19
757 GGGTCCTTAT
*
767 TATATTCTAAATTCT-AAA
1 TATATTCTAAAATCTAAAA
785 TATATTCTAGTAAATCTAAAA
1 TATATTCTA--AAATCTAAAA
806 TATAT
1 TATAT
811 AAAATATTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 9 0.41
20 5 0.23
21 8 0.36
ACGTcount: A:0.45, C:0.09, G:0.02, T:0.43
Consensus pattern (19 bp):
TATATTCTAAAATCTAAAA
Found at i:10079 original size:19 final size:19
Alignment explanation
Indices: 10055--10092 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
10045 TCCTGTCGGT
10055 TGCTAAT-CTCATTAGATTA
1 TGCTAATGCTCATTA-ATTA
10074 TGCTAATGCTCATTAATTA
1 TGCTAATGCTCATTAATTA
10093 AGGTGAAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.32, C:0.16, G:0.11, T:0.42
Consensus pattern (19 bp):
TGCTAATGCTCATTAATTA
Found at i:15481 original size:12 final size:12
Alignment explanation
Indices: 15464--15489 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
15454 TAAGCCGATC
15464 GATGATGAAGAA
1 GATGATGAAGAA
15476 GATGATGAAGAA
1 GATGATGAAGAA
15488 GA
1 GA
15490 ATCAAGAAGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.35, T:0.15
Consensus pattern (12 bp):
GATGATGAAGAA
Found at i:15836 original size:2 final size:2
Alignment explanation
Indices: 15819--15865 Score: 71
Period size: 2 Copynumber: 24.0 Consensus size: 2
15809 TCGTTGATTA
15819 AT AT AT A- AT -T AGT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT
15860 AT AT AT
1 AT AT AT
15866 GCTTTATTGA
Statistics
Matches: 42, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.05
2 38 0.90
3 2 0.05
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:16815 original size:2 final size:2
Alignment explanation
Indices: 16808--16835 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
16798 CTAATTAGAC
16808 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
16836 GGAGAGAAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:22782 original size:30 final size:29
Alignment explanation
Indices: 22720--22789 Score: 86
Period size: 29 Copynumber: 2.4 Consensus size: 29
22710 ACCGAACCGT
****
22720 CAAATAAGCCCCTGAACTATTATTTCGGC
1 CAAATAAGCCCCTGAACTATTAAAAAGGC
*
22749 CAAATAAGCCCCTGAACTCTTAAAAAAGGC
1 CAAATAAGCCCCTGAACTATT-AAAAAGGC
22779 CAAATAAGCCC
1 CAAATAAGCCC
22790 TGTTGCCAAG
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
29 20 0.57
30 15 0.43
ACGTcount: A:0.39, C:0.29, G:0.13, T:0.20
Consensus pattern (29 bp):
CAAATAAGCCCCTGAACTATTAAAAAGGC
Found at i:28451 original size:42 final size:42
Alignment explanation
Indices: 28392--28471 Score: 151
Period size: 42 Copynumber: 1.9 Consensus size: 42
28382 AGAAACCTAA
28392 GATTGCCCCCAGTGCAGATGCAGAGCCAGAGACTCCTCAGCT
1 GATTGCCCCCAGTGCAGATGCAGAGCCAGAGACTCCTCAGCT
*
28434 GATTGCCCCCAGTGCAGATGCGGAGCCAGAGACTCCTC
1 GATTGCCCCCAGTGCAGATGCAGAGCCAGAGACTCCTC
28472 GTCAGCTAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.23, C:0.34, G:0.28, T:0.16
Consensus pattern (42 bp):
GATTGCCCCCAGTGCAGATGCAGAGCCAGAGACTCCTCAGCT
Found at i:30020 original size:27 final size:28
Alignment explanation
Indices: 29963--30030 Score: 70
Period size: 27 Copynumber: 2.5 Consensus size: 28
29953 TGACACCAAA
*
29963 TTTTATGTAG-AGGCACCAAATTGACA-
1 TTTTTTGTAGTAGGCACCAAATTGACAC
* *
29989 GTTTTTGTAGTAGGGACCAAATTGATC-C
1 TTTTTTGTAGTAGGCACCAAATTGA-CAC
30017 TTTTTTGTAAGTAG
1 TTTTTTGT-AGTAG
30031 AGGGATCTGT
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
26 8 0.24
27 13 0.38
28 8 0.24
29 5 0.15
ACGTcount: A:0.28, C:0.12, G:0.22, T:0.38
Consensus pattern (28 bp):
TTTTTTGTAGTAGGCACCAAATTGACAC
Found at i:42410 original size:1 final size:1
Alignment explanation
Indices: 42404--42431 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
42394 TATTATCATC
42404 AAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAA
42432 CCCCGAAAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:53470 original size:2 final size:2
Alignment explanation
Indices: 53463--53490 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
53453 TTTTGTTCAG
53463 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
53491 TTAGTAATGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:54179 original size:2 final size:2
Alignment explanation
Indices: 54174--54201 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
54164 GCATTGATTC
54174 TA 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 TA
54202 GTCTAAGACC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:67369 original size:25 final size:26
Alignment explanation
Indices: 67332--67382 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 26
67322 GGTTTGTTTC
*
67332 TTTTCTTTCTTTCT-TTTTCCCTTTT
1 TTTTCTTTCTTTCTATTTTCCATTTT
* *
67357 TTTTTTTTTTTTCTATTTTCCATTTT
1 TTTTCTTTCTTTCTATTTTCCATTTT
67383 ACTAATCCGA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
25 12 0.55
26 10 0.45
ACGTcount: A:0.04, C:0.18, G:0.00, T:0.78
Consensus pattern (26 bp):
TTTTCTTTCTTTCTATTTTCCATTTT
Found at i:68054 original size:39 final size:39
Alignment explanation
Indices: 68011--68104 Score: 138
Period size: 39 Copynumber: 2.4 Consensus size: 39
68001 AACCGGAGGC
68011 GGCGGCGGAGGCGGAAGCGGAAGTGGG-AGCGAAGAACAA
1 GGCGGCGGAGGCGGAAGCGGAAG-GGGAAGCGAAGAACAA
* *
68050 GGCGGCGGAGGCGGAAGTGGGAGGGGAAGCGAAGAACAA
1 GGCGGCGGAGGCGGAAGCGGAAGGGGAAGCGAAGAACAA
*
68089 GGGGGCGGAGG-GGAAG
1 GGCGGCGGAGGCGGAAG
68105 GCGAAGGCCA
Statistics
Matches: 51, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
38 8 0.16
39 43 0.84
ACGTcount: A:0.29, C:0.13, G:0.56, T:0.02
Consensus pattern (39 bp):
GGCGGCGGAGGCGGAAGCGGAAGGGGAAGCGAAGAACAA
Found at i:68457 original size:3 final size:3
Alignment explanation
Indices: 68443--68474 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
68433 ATTTTGACAC
68443 TAA TAA -AA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
68475 CTCTGAAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 26 0.93
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:83458 original size:88 final size:89
Alignment explanation
Indices: 83350--83512 Score: 310
Period size: 88 Copynumber: 1.8 Consensus size: 89
83340 AGAAATGGCA
*
83350 GGCCAACTTGAACGACATTGATTTTCTTCGTGGGCACAAGATTTTGATTATTTTATTATTCTTCT
1 GGCCAACTTGAACGACATTGATTTTCTTCGTGGGCACAAAATTTTGATTATTTTATTATTCTTCT
83415 ACTT-TTTTTCTTTTTCATGTTAT
66 ACTTCTTTTTCTTTTTCATGTTAT
83438 GGCCAACTTGAACGACATTGATTTTCTTCGTGGGCACAAAATTTTGATTATTTTATTATTCTTCT
1 GGCCAACTTGAACGACATTGATTTTCTTCGTGGGCACAAAATTTTGATTATTTTATTATTCTTCT
83503 ACTTCTTTTT
66 ACTTCTTTTT
83513 ATTAGTTTTT
Statistics
Matches: 73, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
88 68 0.93
89 5 0.07
ACGTcount: A:0.21, C:0.17, G:0.13, T:0.48
Consensus pattern (89 bp):
GGCCAACTTGAACGACATTGATTTTCTTCGTGGGCACAAAATTTTGATTATTTTATTATTCTTCT
ACTTCTTTTTCTTTTTCATGTTAT
Found at i:83585 original size:17 final size:17
Alignment explanation
Indices: 83547--83588 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
83537 TATTCTCATG
*
83547 TAAAAAGTTTAATATTAC
1 TAAAAA-TTTAATAATAC
83565 TAAAAATTATAATAATA-
1 TAAAAATT-TAATAATAC
83582 TAAAAAT
1 TAAAAAT
83589 AAAGAAAGTG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (17 bp):
TAAAAATTTAATAATAC
Found at i:85329 original size:22 final size:22
Alignment explanation
Indices: 85303--85345 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
85293 TTTATAACTA
85303 GGGGCTAAACCTGGATTTAATG
1 GGGGCTAAACCTGGATTTAATG
*
85325 GGGGCTAAATCTGGATTTAAT
1 GGGGCTAAACCTGGATTTAAT
85346 TTATTTCCTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.28, C:0.12, G:0.30, T:0.30
Consensus pattern (22 bp):
GGGGCTAAACCTGGATTTAATG
Found at i:85382 original size:13 final size:13
Alignment explanation
Indices: 85364--85400 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
85354 TTAATTATTA
*
85364 GGAGGGTCAAGTT
1 GGAGGGTCAAATT
*
85377 GGAGGGACAAATT
1 GGAGGGTCAAATT
85390 GGAGGGTCAAA
1 GGAGGGTCAAA
85401 AAGAATTATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.32, C:0.08, G:0.43, T:0.16
Consensus pattern (13 bp):
GGAGGGTCAAATT
Found at i:89343 original size:37 final size:37
Alignment explanation
Indices: 89298--89368 Score: 124
Period size: 37 Copynumber: 1.9 Consensus size: 37
89288 CTTGATCAAT
* *
89298 ATACATGTCTTTTCATATAGACATAACTTTATGATCA
1 ATACATGTCTTTCCAAATAGACATAACTTTATGATCA
89335 ATACATGTCTTTCCAAATAGACATAACTTTATGA
1 ATACATGTCTTTCCAAATAGACATAACTTTATGA
89369 ATAATAATTA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.37, C:0.17, G:0.08, T:0.38
Consensus pattern (37 bp):
ATACATGTCTTTCCAAATAGACATAACTTTATGATCA
Found at i:94440 original size:24 final size:23
Alignment explanation
Indices: 94396--94440 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
94386 GAACTTAAAT
***
94396 AAAATAAGATTTTTTGGCCAAAA
1 AAAATAAGATTTTTAACCCAAAA
94419 AAAATAAGATTTTTCAACCCAA
1 AAAATAAGATTTTT-AACCCAA
94441 CACTAATTGA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 14 0.78
24 4 0.22
ACGTcount: A:0.49, C:0.13, G:0.09, T:0.29
Consensus pattern (23 bp):
AAAATAAGATTTTTAACCCAAAA
Found at i:97455 original size:2 final size:2
Alignment explanation
Indices: 97450--97493 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
97440 ATATAGTGGG
*
97450 AT AT AT AT AT AT AT AT AT AT AT AT AC 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 AT AT AT
97492 AT
1 AT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.