Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011023.1 Corchorus capsularis cultivar CVL-1 contig11044, 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: 36402
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
Found at i:873 original size:31 final size:30
Alignment explanation
Indices: 838--902 Score: 71
Period size: 31 Copynumber: 2.1 Consensus size: 30
828 AGCTAAATAC
*
838 CAAAAAAAT-TCCTTATAT-TTTTCTCTTGGAA
1 CAAAAAAATCT-CTTATATAGTTT-T-TTGGAA
*
869 CAAAATAATCTCTTATATAGTTTTTTGGAA
1 CAAAAAAATCTCTTATATAGTTTTTTGGAA
899 CAAA
1 CAAA
903 TTAATCCTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
30 10 0.33
31 16 0.53
32 4 0.13
ACGTcount: A:0.38, C:0.14, G:0.08, T:0.40
Consensus pattern (30 bp):
CAAAAAAATCTCTTATATAGTTTTTTGGAA
Found at i:3533 original size:9 final size:9
Alignment explanation
Indices: 3519--3557 Score: 51
Period size: 9 Copynumber: 4.3 Consensus size: 9
3509 TTAATTTCTT
*
3519 TTAATTTAA
1 TTAATTAAA
3528 TTAATTAAA
1 TTAATTAAA
**
3537 TTAAAGAAA
1 TTAATTAAA
3546 TTAATTAAA
1 TTAATTAAA
3555 TTA
1 TTA
3558 TATTGAAAAC
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.44
Consensus pattern (9 bp):
TTAATTAAA
Found at i:5329 original size:22 final size:22
Alignment explanation
Indices: 5301--5343 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
5291 ATGATGGATC
* *
5301 AAGTTAGAGGTGACGGTGTTAG
1 AAGTTAGAGGTAACAGTGTTAG
5323 AAGTTAGAGGTAACAGTGTTA
1 AAGTTAGAGGTAACAGTGTTA
5344 AGATTTAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.33, C:0.05, G:0.35, T:0.28
Consensus pattern (22 bp):
AAGTTAGAGGTAACAGTGTTAG
Found at i:7632 original size:2 final size:2
Alignment explanation
Indices: 7621--7664 Score: 54
Period size: 2 Copynumber: 22.0 Consensus size: 2
7611 AGTAAAGTAA
* *
7621 AT AT -T AT AT AT AT AT AT AT AT AT AT AT CT AT AT CT AT ACT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT
7663 AT
1 AT
7665 TAAAAAGTAC
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
1 1 0.03
2 33 0.92
3 2 0.06
ACGTcount: A:0.43, C:0.07, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:8384 original size:2 final size:2
Alignment explanation
Indices: 8377--8412 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
8367 GTCTGTTTTG
8377 TA TA TA TA 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 TA TA TA TA
8413 GGTGGAGTTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:10264 original size:72 final size:73
Alignment explanation
Indices: 10145--10289 Score: 247
Period size: 72 Copynumber: 2.0 Consensus size: 73
10135 TGAAACTTTT
* * *
10145 TTATTCGTCAAAAGATAATCCATAGAAGAAAGTAAAAAGATAATATTTGTTCCTAGATAAAATTC
1 TTATTCGTCAAAAGATAATCCATAGAAGAAAATAAAAAGATAATATTTGTTCCCAGACAAAATTC
10210 TATATTTA
66 TATATTTA
*
10218 TTATTCGTC-AAAGATAATCCATAGAAGAAAATAAAAAGATAGTATTTGTTCCCAGACAAAATTC
1 TTATTCGTCAAAAGATAATCCATAGAAGAAAATAAAAAGATAATATTTGTTCCCAGACAAAATTC
10282 TATATTTA
66 TATATTTA
10290 CTAGACTTCC
Statistics
Matches: 68, Mismatches: 4, Indels: 1
0.93 0.05 0.01
Matches are distributed among these distances:
72 59 0.87
73 9 0.13
ACGTcount: A:0.45, C:0.11, G:0.11, T:0.33
Consensus pattern (73 bp):
TTATTCGTCAAAAGATAATCCATAGAAGAAAATAAAAAGATAATATTTGTTCCCAGACAAAATTC
TATATTTA
Found at i:10454 original size:2 final size:2
Alignment explanation
Indices: 10440--10477 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
10430 AATTATGTTT
*
10440 TA TA TA T- TC TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
10478 TCAATTTCAT
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:11038 original size:109 final size:109
Alignment explanation
Indices: 10903--11121 Score: 350
Period size: 109 Copynumber: 2.0 Consensus size: 109
10893 CTTTATTAAA
* * *
10903 TTTTAATTATGTTCAATTGATTTTGTACTA-TGTTTGTTTGATTAATAATGGTTTTCGGGTCATA
1 TTTTAATTATATTCAATTGATTTTGTACTACT-TTTGTTTGACTAATAATGATTTTCGGGTCATA
* * *
10967 AGAAGTTTCCAGCAAGAAATTAATACCTCACTTTTATGCTTTTTT
65 AAAAGTTTCCAACAAGAAATTAATACCTCACTTTTATGCCTTTTT
* *
11012 TTTTAATTCTATTCAATTGATTTTGTATTACTTTTGTTTGACTAATAATGATTTTCGGGTCATAA
1 TTTTAATTATATTCAATTGATTTTGTACTACTTTTGTTTGACTAATAATGATTTTCGGGTCATAA
11077 AAAGTTTCCAACAAGAAATTAATACCTCACTTTTATGCCTTTTT
66 AAAGTTTCCAACAAGAAATTAATACCTCACTTTTATGCCTTTTT
11121 T
1 T
11122 ATTGCTAGAA
Statistics
Matches: 101, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
109 100 0.99
110 1 0.01
ACGTcount: A:0.28, C:0.12, G:0.12, T:0.47
Consensus pattern (109 bp):
TTTTAATTATATTCAATTGATTTTGTACTACTTTTGTTTGACTAATAATGATTTTCGGGTCATAA
AAAGTTTCCAACAAGAAATTAATACCTCACTTTTATGCCTTTTT
Found at i:12138 original size:31 final size:31
Alignment explanation
Indices: 12103--12176 Score: 105
Period size: 31 Copynumber: 2.4 Consensus size: 31
12093 AGTTTTGAGA
*
12103 AACTTTTGAAT-TGCCTATTGTACCCTTAATT
1 AACTTTT-AATATGCCGATTGTACCCTTAATT
*
12134 AACTTTTAATATTCCGATTGTACCCTTAATT
1 AACTTTTAATATGCCGATTGTACCCTTAATT
*
12165 AACTTGTAATAT
1 AACTTTTAATAT
12177 TCCTATTATC
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
30 3 0.08
31 36 0.92
ACGTcount: A:0.30, C:0.18, G:0.08, T:0.45
Consensus pattern (31 bp):
AACTTTTAATATGCCGATTGTACCCTTAATT
Found at i:12177 original size:31 final size:31
Alignment explanation
Indices: 12119--12179 Score: 113
Period size: 31 Copynumber: 2.0 Consensus size: 31
12109 TGAATTGCCT
*
12119 ATTGTACCCTTAATTAACTTTTAATATTCCG
1 ATTGTACCCTTAATTAACTTGTAATATTCCG
12150 ATTGTACCCTTAATTAACTTGTAATATTCC
1 ATTGTACCCTTAATTAACTTGTAATATTCC
12180 TATTATCCTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.30, C:0.20, G:0.07, T:0.44
Consensus pattern (31 bp):
ATTGTACCCTTAATTAACTTGTAATATTCCG
Found at i:13036 original size:2 final size:2
Alignment explanation
Indices: 13019--13080 Score: 56
Period size: 2 Copynumber: 29.5 Consensus size: 2
13009 TTATAGTTTT
*
13019 TA TA T- TA TA T- TA TA TA TA TA TA TA TA TA TA TA CA CTA TA CTA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA -TA
13061 TA CTA TA CTA TA CTA TA TA T
1 TA -TA TA -TA TA -TA TA TA T
13081 TATTTTTGTC
Statistics
Matches: 51, Mismatches: 2, Indels: 14
0.76 0.03 0.21
Matches are distributed among these distances:
1 2 0.04
2 40 0.78
3 9 0.18
ACGTcount: A:0.44, C:0.10, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:13411 original size:14 final size:13
Alignment explanation
Indices: 13380--13404 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
13370 TTTCCTTCTT
13380 CAGTCCATTTTTC
1 CAGTCCATTTTTC
13393 CAGTCCATTTTT
1 CAGTCCATTTTT
13405 GTTAGTCTGT
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:0.16, C:0.28, G:0.08, T:0.48
Consensus pattern (13 bp):
CAGTCCATTTTTC
Found at i:14554 original size:12 final size:12
Alignment explanation
Indices: 14537--14591 Score: 101
Period size: 12 Copynumber: 4.5 Consensus size: 12
14527 TAAATACAGG
14537 TATCGACGGATA
1 TATCGACGGATA
14549 TATCGAACGGATA
1 TATCG-ACGGATA
14562 TATCGACGGATA
1 TATCGACGGATA
14574 TATCGACGGATA
1 TATCGACGGATA
14586 TATCGA
1 TATCGA
14592 GATATCGATG
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
12 30 0.71
13 12 0.29
ACGTcount: A:0.35, C:0.16, G:0.24, T:0.25
Consensus pattern (12 bp):
TATCGACGGATA
Found at i:14565 original size:25 final size:24
Alignment explanation
Indices: 14537--14591 Score: 101
Period size: 25 Copynumber: 2.2 Consensus size: 24
14527 TAAATACAGG
14537 TATCGACGGATATATCGAACGGATA
1 TATCGACGGATATATCG-ACGGATA
14562 TATCGACGGATATATCGACGGATA
1 TATCGACGGATATATCGACGGATA
14586 TATCGA
1 TATCGA
14592 GATATCGATG
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
24 13 0.43
25 17 0.57
ACGTcount: A:0.35, C:0.16, G:0.24, T:0.25
Consensus pattern (24 bp):
TATCGACGGATATATCGACGGATA
Found at i:14767 original size:10 final size:9
Alignment explanation
Indices: 14751--14775 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
14741 ATATGTAGAC
14751 ATTTTTTTT
1 ATTTTTTTT
14760 ATTTTTTTT
1 ATTTTTTTT
14769 ATTTTTT
1 ATTTTTT
14776 GTACTGCGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (9 bp):
ATTTTTTTT
Found at i:15620 original size:10 final size:10
Alignment explanation
Indices: 15605--15640 Score: 63
Period size: 10 Copynumber: 3.6 Consensus size: 10
15595 AATTTAATAT
15605 GGATATTTAC
1 GGATATTTAC
*
15615 GGATATTTAT
1 GGATATTTAC
15625 GGATATTTAC
1 GGATATTTAC
15635 GGATAT
1 GGATAT
15641 ATCGAGATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 24 1.00
ACGTcount: A:0.31, C:0.06, G:0.22, T:0.42
Consensus pattern (10 bp):
GGATATTTAC
Found at i:15627 original size:20 final size:20
Alignment explanation
Indices: 15602--15640 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
15592 TTTAATTTAA
15602 TATGGATATTTACGGATATT
1 TATGGATATTTACGGATATT
15622 TATGGATATTTACGGATAT
1 TATGGATATTTACGGATAT
15641 ATCGAGATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.31, C:0.05, G:0.21, T:0.44
Consensus pattern (20 bp):
TATGGATATTTACGGATATT
Found at i:21444 original size:6 final size:6
Alignment explanation
Indices: 21421--21458 Score: 60
Period size: 6 Copynumber: 6.5 Consensus size: 6
21411 TTTGGATTAC
*
21421 ATTAAT ATTAA- ATAAAT ATTAAT ATTAAT ATTAAT ATT
1 ATTAAT ATTAAT ATTAAT ATTAAT ATTAAT ATTAAT ATT
21459 GCCAATGCTG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
5 4 0.14
6 25 0.86
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (6 bp):
ATTAAT
Found at i:25167 original size:17 final size:17
Alignment explanation
Indices: 25145--25179 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
25135 TAAACAACAA
25145 TTTAGTTAGTT-GTTAGT
1 TTTAGTTA-TTAGTTAGT
25162 TTTAGTTATTAGTTAGT
1 TTTAGTTATTAGTTAGT
25179 T
1 T
25180 AAGCCTATAG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 2 0.12
17 15 0.88
ACGTcount: A:0.20, C:0.00, G:0.20, T:0.60
Consensus pattern (17 bp):
TTTAGTTATTAGTTAGT
Found at i:29681 original size:109 final size:107
Alignment explanation
Indices: 29481--29678 Score: 330
Period size: 109 Copynumber: 1.9 Consensus size: 107
29471 TTTATTAGTC
* *
29481 AACAAAATAATCCAACTTTACATTATAAATTTTAAGGCTGGGATATTCGGAAAAAAGAAAACAAA
1 AACAAAATAATCCAACTTTACATTATAAATTATAAGGCTGAGATATTCGGAAAAAAGAAAACAAA
29546 AAAATTGATTTAAGGATATTGTTAATTAATTATATTAATTCTTG
66 AAAATTGA-TTAAGGATATTGTTAATT-ATTATATTAATTCTTG
*
29590 AACAAAATAATCCGACTTTACATTATAAATTATAAGGCTGAGATATTC-GAAAAAA-AAAACAAA
1 AACAAAATAATCCAACTTTACATTATAAATTATAAGGCTGAGATATTCGGAAAAAAGAAAACAAA
29653 AAAATTGA-TAAGGATATTGTTAATTA
66 AAAATTGATTAAGGATATTGTTAATTA
29679 ATTTTTATAT
Statistics
Matches: 86, Mismatches: 3, Indels: 5
0.91 0.03 0.05
Matches are distributed among these distances:
104 1 0.01
105 17 0.20
107 16 0.19
108 7 0.08
109 45 0.52
ACGTcount: A:0.48, C:0.09, G:0.12, T:0.31
Consensus pattern (107 bp):
AACAAAATAATCCAACTTTACATTATAAATTATAAGGCTGAGATATTCGGAAAAAAGAAAACAAA
AAAATTGATTAAGGATATTGTTAATTATTATATTAATTCTTG
Found at i:32799 original size:79 final size:79
Alignment explanation
Indices: 32668--32827 Score: 293
Period size: 79 Copynumber: 2.0 Consensus size: 79
32658 TATCTATGTT
32668 TAAGAACTTTAGATTAGTATGGATTATAACTTTTATTTTACCAGATTTGCAGTTTTTATAATCTC
1 TAAGAACTTTAGATTAGTATGGATTATAACTTTTATTTTACCAGATTTGCAGTTTTTATAATCTC
*
32733 TAAGGACTTTCCAG
66 TAAGAACTTTCCAG
* *
32747 TAAGAGCTTTAGATTAGTATGGATTATAACTTTTATTTTAGCAGATTTGCAGTTTTTATAATCTC
1 TAAGAACTTTAGATTAGTATGGATTATAACTTTTATTTTACCAGATTTGCAGTTTTTATAATCTC
32812 TAAGAACTTTCCAG
66 TAAGAACTTTCCAG
32826 TA
1 TA
32828 TTTATGTTCA
Statistics
Matches: 78, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
79 78 1.00
ACGTcount: A:0.31, C:0.12, G:0.14, T:0.43
Consensus pattern (79 bp):
TAAGAACTTTAGATTAGTATGGATTATAACTTTTATTTTACCAGATTTGCAGTTTTTATAATCTC
TAAGAACTTTCCAG
Found at i:33449 original size:29 final size:30
Alignment explanation
Indices: 33392--33468 Score: 95
Period size: 29 Copynumber: 2.6 Consensus size: 30
33382 TACCATACAG
*
33392 GGTCCCTCTACTTACAAAAATGAATCAATTT
1 GGTCCCCCTACTTACAAAAATG-ATCAATTT
33423 GGTCCCCCTA-TTACAAAAACTG-TCAATTT
1 GGTCCCCCTACTTACAAAAA-TGATCAATTT
**
33452 GGTCCCTTTACTTACAA
1 GGTCCCCCTACTTACAA
33469 TTTCTTATCA
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
29 15 0.37
30 15 0.37
31 11 0.27
ACGTcount: A:0.31, C:0.26, G:0.10, T:0.32
Consensus pattern (30 bp):
GGTCCCCCTACTTACAAAAATGATCAATTT
Found at i:33663 original size:2 final size:2
Alignment explanation
Indices: 33656--33682 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
33646 ATTTTAAGAG
33656 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
33683 TCAAAATTTT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:35616 original size:29 final size:31
Alignment explanation
Indices: 35576--35649 Score: 98
Period size: 29 Copynumber: 2.5 Consensus size: 31
35566 CACCAAATTA
35576 TAAGTAGAGGGACCAAATTGA-CAATTTTTG
1 TAAGTAGAGGGACCAAATTGATCAATTTTTG
* * **
35606 T-AGTAGGGGGATCAAATTGATCCCTTTTTG
1 TAAGTAGAGGGACCAAATTGATCAATTTTTG
35636 TAAGTAGAGGGACC
1 TAAGTAGAGGGACC
35650 TATACAGTAT
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
29 17 0.47
30 9 0.25
31 10 0.28
ACGTcount: A:0.31, C:0.12, G:0.27, T:0.30
Consensus pattern (31 bp):
TAAGTAGAGGGACCAAATTGATCAATTTTTG
Done.