Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016174.1 Corchorus capsularis cultivar CVL-1 contig16195, 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: 25334
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:2772 original size:335 final size:334
Alignment explanation
Indices: 2148--2774 Score: 1114
Period size: 335 Copynumber: 1.9 Consensus size: 334
2138 TGTTATTTAG
2148 AAATTGAGATTTATGTATATGCTTTGCAAATGCCTGCAGATTGCTTTGGGTTTGAATTACTTGAG
1 AAATTGAGATTTATGTATATGCTTTGCAAATGCCTGCAGATTGCTTTGGGTTTGAATTACTTGAG
*
2213 ATGTTAGATTCTTAACTTTGGTTTTTATGGGTTTTTTTTTCCTCCGTTATTATACTTAATTTAAT
66 ATGTTAGATTCTTAACTTTGGTTTTTATGGGTTTTTTTTTCCTCCATTATTATACTTAATTTAAT
*
2278 TGAAGGCCGATTTTAAAAATTATTTCTTTTAATGAAGGAATCACGAGTGTGCTACGTACCACTTA
131 TGAAGGCCGATTTTAAAAATTAATTCTTTTAATGAAGGAATCACGAGTGTGCTACGTACCACTTA
* *
2343 AATTTAGAATAGAATATATATTGGGTGTTGCTAATCACCGCCCCCTTTTTGCTATTCACCGTCTC
196 AATTTAGAATAGAATATATATTGGGTGTTGCTAATCACCGCCCCCTTTTTGCTATTCACCGCCCC
2408 ACTTTTTACGCTTTTGCCCTTTGCTTCATTTTGCTTCATTTTCTAAGATTTCAAATCCTTTGAAA
261 ACTTTTTACGCTTTTGCCCTTTGCTTCATTTTGCTTCATTTTCTAAGATTTCAAATCCTTTGAAA
2473 TCTTGAAAC
326 TCTTGAAAC
* * *
2482 AAATTGAGATTTATGGTATATGCTTTGCAAATGCCTGTAGATTGCTTTGGG-TT-ACTTCCTTGA
1 AAATTGAGATTTAT-GTATATGCTTTGCAAATGCCTGCAGATTGCTTTGGGTTTGAATTACTTGA
2545 GATGTTAGATTCTTAACTTTGGTTTTTATGGGGTTTTTTTTTTCCTCCATTATTATACTTAATTT
65 GATGTTAGATTCTTAACTTTGGTTTTTAT-GGG-TTTTTTTTTCCTCCATTATTATACTTAATTT
* *
2610 AATTGAAGGCCGATTTTAGAAATTAATTCTTTTAATGAAGGAATCACGAGTGTGTTACGTACCAC
128 AATTGAAGGCCGATTTTAAAAATTAATTCTTTTAATGAAGGAATCACGAGTGTGCTACGTACCAC
* *
2675 TTAAATTTAGAATAGAATATATATTGGGTGTTGCTAATCACCGTCCCCTTTTTGTTATTCACCGC
193 TTAAATTTAGAATAGAATATATATTGGGTGTTGCTAATCACCGCCCCCTTTTTGCTATTCACCGC
2740 CCCACTTTTTACGCTTTTGCCCTTTGCTTCATTTT
258 CCCACTTTTTACGCTTTTGCCCTTTGCTTCATTTT
2775 CTAAGATTTC
Statistics
Matches: 279, Mismatches: 11, Indels: 5
0.95 0.04 0.02
Matches are distributed among these distances:
333 37 0.13
334 19 0.07
335 223 0.80
ACGTcount: A:0.24, C:0.16, G:0.16, T:0.43
Consensus pattern (334 bp):
AAATTGAGATTTATGTATATGCTTTGCAAATGCCTGCAGATTGCTTTGGGTTTGAATTACTTGAG
ATGTTAGATTCTTAACTTTGGTTTTTATGGGTTTTTTTTTCCTCCATTATTATACTTAATTTAAT
TGAAGGCCGATTTTAAAAATTAATTCTTTTAATGAAGGAATCACGAGTGTGCTACGTACCACTTA
AATTTAGAATAGAATATATATTGGGTGTTGCTAATCACCGCCCCCTTTTTGCTATTCACCGCCCC
ACTTTTTACGCTTTTGCCCTTTGCTTCATTTTGCTTCATTTTCTAAGATTTCAAATCCTTTGAAA
TCTTGAAAC
Found at i:5513 original size:21 final size:20
Alignment explanation
Indices: 5474--5521 Score: 69
Period size: 21 Copynumber: 2.4 Consensus size: 20
5464 GTCTCTGAAG
5474 CTCTCTCTCCCTCTAAGCCT
1 CTCTCTCTCCCTCTAAGCCT
* *
5494 CTCTCTGCTCTCTCTGAGCCT
1 CTCTCT-CTCCCTCTAAGCCT
5515 CTCTCTC
1 CTCTCTC
5522 CCTCTGAAGC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 7 0.28
21 18 0.72
ACGTcount: A:0.06, C:0.48, G:0.08, T:0.38
Consensus pattern (20 bp):
CTCTCTCTCCCTCTAAGCCT
Found at i:5970 original size:32 final size:32
Alignment explanation
Indices: 5932--6030 Score: 155
Period size: 32 Copynumber: 3.1 Consensus size: 32
5922 CACAGCCGTT
5932 GCAAGGCCGCCCCAGGTGGGC-AGCTTGCCCTG
1 GCAAGGCCGCCCCAGGTGGGCGA-CTTGCCCTG
*
5964 GCAAGGCCACCCCAGGTGGGCGACTTGCCCTG
1 GCAAGGCCGCCCCAGGTGGGCGACTTGCCCTG
* *
5996 GTAAGGCCGTCCCAGGTGGGCGACTTGCCCTG
1 GCAAGGCCGCCCCAGGTGGGCGACTTGCCCTG
6028 GCA
1 GCA
6031 TAGTCGCCCA
Statistics
Matches: 61, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
32 60 0.98
33 1 0.02
ACGTcount: A:0.14, C:0.35, G:0.36, T:0.14
Consensus pattern (32 bp):
GCAAGGCCGCCCCAGGTGGGCGACTTGCCCTG
Found at i:6120 original size:14 final size:14
Alignment explanation
Indices: 6101--6133 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
6091 TTTACCCTAG
6101 ATCTATTTCTCTAC
1 ATCTATTTCTCTAC
*
6115 ATCTATTTCTCTAG
1 ATCTATTTCTCTAC
6129 ATCTA
1 ATCTA
6134 GATCTGCAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.24, C:0.24, G:0.03, T:0.48
Consensus pattern (14 bp):
ATCTATTTCTCTAC
Found at i:6295 original size:15 final size:15
Alignment explanation
Indices: 6275--6303 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
6265 GATGAAGAAG
6275 TTGTTTGAAGTAAAT
1 TTGTTTGAAGTAAAT
6290 TTGTTTGAAGTAAA
1 TTGTTTGAAGTAAA
6304 GATTTTAATT
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:0.34, C:0.00, G:0.21, T:0.45
Consensus pattern (15 bp):
TTGTTTGAAGTAAAT
Found at i:7436 original size:30 final size:29
Alignment explanation
Indices: 7372--7437 Score: 71
Period size: 30 Copynumber: 2.2 Consensus size: 29
7362 TACTCATTGT
** *
7372 ATATTAAATAAATATTCTAATATTTATTAC
1 ATATT-AATAAATATTCTAATAAATATTAA
7402 ATATTAATAAATATTTCTAATAAA-ATTTAA
1 ATATTAATAAATA-TTCTAATAAATA-TTAA
7432 ATATTA
1 ATATTA
7438 TTTGAAATAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
29 9 0.29
30 22 0.71
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (29 bp):
ATATTAATAAATATTCTAATAAATATTAA
Found at i:8424 original size:2 final size:2
Alignment explanation
Indices: 8417--8448 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
8407 ACACCACAAG
*
8417 AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
8449 GTAATTTACC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:8831 original size:31 final size:31
Alignment explanation
Indices: 8763--8832 Score: 97
Period size: 31 Copynumber: 2.3 Consensus size: 31
8753 GACTCAACTC
* *
8763 AATTGACCCAATATTTTGAGTACATGGACTA
1 AATTGATCCAATATTGTGAGTACATGGACTA
*
8794 AATTGATCCAATATTGTGAGTATA-GAGACTA
1 AATTGATCCAATATTGTGAGTACATG-GACTA
8825 AATTGATC
1 AATTGATC
8833 TTTTTTTAGA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
30 1 0.03
31 34 0.97
ACGTcount: A:0.37, C:0.13, G:0.17, T:0.33
Consensus pattern (31 bp):
AATTGATCCAATATTGTGAGTACATGGACTA
Found at i:10733 original size:29 final size:30
Alignment explanation
Indices: 10701--10760 Score: 77
Period size: 29 Copynumber: 2.0 Consensus size: 30
10691 TTTTGTCTCA
*
10701 TGAACTTCATTTTTGG-ACATTTTACCCCC
1 TGAACTTCAATTTTGGAACATTTTACCCCC
* * *
10730 TGAACTTTAATTTTGGAACCTTTTGCCCCC
1 TGAACTTCAATTTTGGAACATTTTACCCCC
10760 T
1 T
10761 CAACCTAACG
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
29 14 0.54
30 12 0.46
ACGTcount: A:0.20, C:0.27, G:0.12, T:0.42
Consensus pattern (30 bp):
TGAACTTCAATTTTGGAACATTTTACCCCC
Found at i:11020 original size:30 final size:29
Alignment explanation
Indices: 10955--11058 Score: 154
Period size: 29 Copynumber: 3.6 Consensus size: 29
10945 GTAAAACGTC
*
10955 CCAAAATTGAAGTTTAGGGGGCAAAATGA
1 CCAAAATTGAAGTTCAGGGGGCAAAATGA
*
10984 CCAAAATTGAAGTTCAGGGGGCAAAATGTC
1 CCAAAATTGAAGTTCAGGGGGCAAAATG-A
*
11014 CCAAAATTGAAGTTCAGGGTGCAAAATGA
1 CCAAAATTGAAGTTCAGGGGGCAAAATGA
* *
11043 CCAAGATTGAAATTCA
1 CCAAAATTGAAGTTCA
11059 AAGGACAAAA
Statistics
Matches: 68, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
29 41 0.60
30 27 0.40
ACGTcount: A:0.40, C:0.14, G:0.24, T:0.21
Consensus pattern (29 bp):
CCAAAATTGAAGTTCAGGGGGCAAAATGA
Found at i:11026 original size:59 final size:59
Alignment explanation
Indices: 10941--11058 Score: 182
Period size: 59 Copynumber: 2.0 Consensus size: 59
10931 TTAAGTTGAG
* * *
10941 GGGGGTAAAACGTCCCAAAATTGAAGTTTAGGGGGCAAAATGACCAAAATTGAAGTTCA
1 GGGGGCAAAACGTCCCAAAATTGAAGTTCAGGGGGCAAAATGACCAAAATTGAAATTCA
* * *
11000 GGGGGCAAAATGTCCCAAAATTGAAGTTCAGGGTGCAAAATGACCAAGATTGAAATTCA
1 GGGGGCAAAACGTCCCAAAATTGAAGTTCAGGGGGCAAAATGACCAAAATTGAAATTCA
11059 AAGGACAAAA
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
59 53 1.00
ACGTcount: A:0.39, C:0.14, G:0.26, T:0.20
Consensus pattern (59 bp):
GGGGGCAAAACGTCCCAAAATTGAAGTTCAGGGGGCAAAATGACCAAAATTGAAATTCA
Found at i:11780 original size:11 final size:11
Alignment explanation
Indices: 11764--11788 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
11754 AGGTGGCAGT
11764 AACTTAAACAC
1 AACTTAAACAC
11775 AACTTAAACAC
1 AACTTAAACAC
11786 AAC
1 AAC
11789 AACATAACAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.56, C:0.28, G:0.00, T:0.16
Consensus pattern (11 bp):
AACTTAAACAC
Found at i:19546 original size:131 final size:136
Alignment explanation
Indices: 19397--19651 Score: 394
Period size: 132 Copynumber: 1.9 Consensus size: 136
19387 AGAAATATAT
* * *
19397 TTTAAAAATTCTACTATATGCAAG-TTTTTTTAATTAAATTAGTAAAATGGTAAAAATAAAATAG
1 TTTAAAAATTCTAATATATACAAGTTTTTTTTAATTAAAATAGTAAAATGGTAAAAATAAAATAG
*
19461 GTATAAGGATATTAG-A-T-TT-AATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAA
66 GTATAAGGATATTAGAATTATTCAATTAAATAAAAATAGAGTTTTTAGTTGACTAAAACTATAAA
19522 AGTGTA
131 AGTGTA
* * *
19528 TTTAAAAATTCTAATATATATAAGTTTTTTTTAATTAAAATAGTATAATGGTAAAAATAGAATAG
1 TTTAAAAATTCTAATATATACAAGTTTTTTTTAATTAAAATAGTAAAATGGTAAAAATAAAATAG
*
19593 TTATAAGGATATTAGATATTATTCAATTAAATAAAAATAGAGTTTTTAGTTGACTAAAA
66 GTATAAGGATATTAGA-ATTATTCAATTAAATAAAAATAGAGTTTTTAGTTGACTAAAA
19652 ACTAGTATAA
Statistics
Matches: 110, Mismatches: 8, Indels: 6
0.89 0.06 0.05
Matches are distributed among these distances:
131 21 0.19
132 51 0.46
134 1 0.01
135 1 0.01
136 2 0.02
137 34 0.31
ACGTcount: A:0.47, C:0.03, G:0.12, T:0.39
Consensus pattern (136 bp):
TTTAAAAATTCTAATATATACAAGTTTTTTTTAATTAAAATAGTAAAATGGTAAAAATAAAATAG
GTATAAGGATATTAGAATTATTCAATTAAATAAAAATAGAGTTTTTAGTTGACTAAAACTATAAA
AGTGTA
Found at i:20769 original size:17 final size:17
Alignment explanation
Indices: 20747--20780 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
20737 GAAATTTGAA
20747 GAGACAAGAGTCATCGT
1 GAGACAAGAGTCATCGT
20764 GAGACAAGAGTCATCGT
1 GAGACAAGAGTCATCGT
20781 AAAAGATTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.35, C:0.18, G:0.29, T:0.18
Consensus pattern (17 bp):
GAGACAAGAGTCATCGT
Found at i:23601 original size:24 final size:26
Alignment explanation
Indices: 23555--23614 Score: 72
Period size: 25 Copynumber: 2.4 Consensus size: 26
23545 TTTGACCATT
23555 AATTATTAAAAAAATATAATTTT-AAA
1 AATT-TTAAAAAAATATAATTTTGAAA
* *
23581 AATTTTAAAAAAATA-AGTTTTGGAA
1 AATTTTAAAAAAATATAATTTTGAAA
23606 AA-TTTAAAA
1 AATTTTAAAA
23615 CTTAAATTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
24 12 0.39
25 15 0.48
26 4 0.13
ACGTcount: A:0.58, C:0.00, G:0.05, T:0.37
Consensus pattern (26 bp):
AATTTTAAAAAAATATAATTTTGAAA
Found at i:25066 original size:29 final size:31
Alignment explanation
Indices: 25002--25066 Score: 82
Period size: 29 Copynumber: 2.2 Consensus size: 31
24992 CTTACTCAAA
* *
25002 AAAAAAATTAAGTTATAGTAAATCTCTTCCCT
1 AAAAAAA-TAAGTTATAGTAAATCTCTGCACT
25034 -AAAAAA-AAGTTATAGTAAATCTC-GCACT
1 AAAAAAATAAGTTATAGTAAATCTCTGCACT
25062 AAAAA
1 AAAAA
25067 GGGTTATGGA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
28 3 0.10
29 21 0.70
31 6 0.20
ACGTcount: A:0.51, C:0.14, G:0.08, T:0.28
Consensus pattern (31 bp):
AAAAAAATAAGTTATAGTAAATCTCTGCACT
Found at i:25073 original size:27 final size:29
Alignment explanation
Indices: 25011--25066 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
25001 AAAAAAAATT
* *
25011 AAGTTATAGTAAATCTCTTCCCTAAAAAA
1 AAGTTATAGTAAATCTCTGCACTAAAAAA
25040 AAGTTATAGTAAATCTC-GCACTAAAAA
1 AAGTTATAGTAAATCTCTGCACTAAAAA
25067 GGGTTATGGA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 8 0.32
29 17 0.68
ACGTcount: A:0.46, C:0.16, G:0.09, T:0.29
Consensus pattern (29 bp):
AAGTTATAGTAAATCTCTGCACTAAAAAA
Done.