Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015952.1 Corchorus capsularis cultivar CVL-1 contig15973, 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: 16974
ACGTcount: A:0.28, C:0.18, G:0.21, T:0.32
Found at i:84 original size:31 final size:30
Alignment explanation
Indices: 23--85 Score: 74
Period size: 31 Copynumber: 2.0 Consensus size: 30
13 TCTTCTGCTT
**
23 AGTTTTTACTTCTATATTTCTTCCAAAAAAA
1 AGTTTTTACTTCTATATTTAAT-CAAAAAAA
54 AGTTTTTACTTCTATATATTAAT-AATAAAAA
1 AGTTTTTACTTCTATAT-TTAATCAA-AAAAA
85 A
1 A
86 CAACTTATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
30 2 0.07
31 23 0.82
32 3 0.11
ACGTcount: A:0.41, C:0.11, G:0.03, T:0.44
Consensus pattern (30 bp):
AGTTTTTACTTCTATATTTAATCAAAAAAA
Found at i:2555 original size:22 final size:21
Alignment explanation
Indices: 2486--2757 Score: 114
Period size: 22 Copynumber: 12.5 Consensus size: 21
2476 TAAAAGTCTC
* * *
2486 AATTTCATA-AGGAGTACCGA
1 AATTTCATAGAGGATTATCAA
*
2506 AATTTAATAGAAGG-TTATC-A
1 AATTTCATAG-AGGATTATCAA
* *
2526 AATCTCATAGAGTGATTATCGA
1 AATTTCATAGAG-GATTATCAA
2548 AATTTCATAGAGATCAGATTATCAA
1 AATTTCATAGAG----GATTATCAA
*
2573 AATTT-ATAGGAAGATTATCAA
1 AATTTCATA-GAGGATTATCAA
*
2594 AATTTCATAGTGTTG-TTATCAA
1 AATTTCATAGAG--GATTATCAA
*
2616 AATCTCA-ACGCGAGG-TTATCAA
1 AATTTCATA---GAGGATTATCAA
* * * *
2638 AATTACATAATATGATTATCAG
1 AATTTCAT-AGAGGATTATCAA
* * *
2660 AATTTCATAGAGGGGTCAACAA
1 AATTTCATAGA-GGATTATCAA
* *
2682 AATTTTATAAAGAGATTATCAA
1 AATTTCATAGAG-GATTATCAA
2704 AATTTCATAAAGAGG-TTATCAA
1 AATTTCAT--AGAGGATTATCAA
* *
2726 ATTTTCA-AAATGTGATTA-CAAA
1 AATTTCATAGA-G-GATTATC-AA
2748 AATTTCATAG
1 AATTTCATAG
2758 TGGTATTTCT
Statistics
Matches: 189, Mismatches: 36, Indels: 51
0.68 0.13 0.18
Matches are distributed among these distances:
19 4 0.02
20 19 0.10
21 31 0.16
22 108 0.57
23 3 0.02
24 9 0.05
25 15 0.08
ACGTcount: A:0.42, C:0.11, G:0.14, T:0.33
Consensus pattern (21 bp):
AATTTCATAGAGGATTATCAA
Found at i:2587 original size:21 final size:24
Alignment explanation
Indices: 2539--2603 Score: 91
Period size: 21 Copynumber: 2.8 Consensus size: 24
2529 CTCATAGAGT
*
2539 GATTATCGAAATTTCATAGAGATCA
1 GATTATCAAAATTTCATAGAGA-CA
2564 GATTATCAAAATTT-ATAG-GA-A
1 GATTATCAAAATTTCATAGAGACA
2585 GATTATCAAAATTTCATAG
1 GATTATCAAAATTTCATAG
2604 TGTTGTTATC
Statistics
Matches: 38, Mismatches: 1, Indels: 5
0.86 0.02 0.11
Matches are distributed among these distances:
21 15 0.39
22 4 0.11
23 2 0.05
24 4 0.11
25 13 0.34
ACGTcount: A:0.43, C:0.09, G:0.14, T:0.34
Consensus pattern (24 bp):
GATTATCAAAATTTCATAGAGACA
Found at i:2743 original size:44 final size:45
Alignment explanation
Indices: 2564--2757 Score: 147
Period size: 44 Copynumber: 4.4 Consensus size: 45
2554 ATAGAGATCA
* *
2564 GATTATCAAAATTT-ATAGGAAGA--TTATCAAAATTTCATAGTGTT
1 GATTATCAAAATTTCATA-GAAGAGGTTATCAAAATTTCAAAATG-T
* * * * *
2608 G-TTATCAAAATCTCA-ACG-CGAGGTTATCAAAATTACATAATAT
1 GATTATCAAAATTTCATA-GAAGAGGTTATCAAAATTTCAAAATGT
* * * * * *
2651 GATTATCAGAATTTCATAG-AGGGGTCAACAAAATTTTATAAA-GA
1 GATTATCAAAATTTCATAGAAGAGGTTATCAAAATTTCA-AAATGT
*
2695 GATTATCAAAATTTCATA-AAGAGGTTATCAAATTTTCAAAATGT
1 GATTATCAAAATTTCATAGAAGAGGTTATCAAAATTTCAAAATGT
2739 GATTA-CAAAAATTTCATAG
1 GATTATC-AAAATTTCATAG
2758 TGGTATTTCT
Statistics
Matches: 116, Mismatches: 24, Indels: 19
0.73 0.15 0.12
Matches are distributed among these distances:
42 2 0.02
43 19 0.16
44 92 0.79
45 3 0.03
ACGTcount: A:0.43, C:0.10, G:0.13, T:0.34
Consensus pattern (45 bp):
GATTATCAAAATTTCATAGAAGAGGTTATCAAAATTTCAAAATGT
Found at i:2965 original size:22 final size:22
Alignment explanation
Indices: 2838--3351 Score: 209
Period size: 22 Copynumber: 23.6 Consensus size: 22
2828 TTATGGAGTA
*
2838 ATCAAAATTT--TAGGGAGGAT
1 ATCAAAATTTCATAGGGAGGTT
**
2858 ATCAAAATTTCATAGTTTA-GTT
1 ATCAAAATTTCATAG-GGAGGTT
* **
2880 TTCAAAATTTCATA-AAAGGGTT
1 ATCAAAATTTCATAGGGA-GGTT
*
2902 ATCAAAATTTCATAGGGAGATT
1 ATCAAAATTTCATAGGGAGGTT
* **
2924 AACAAAATTTCATAATGAGGTT
1 ATCAAAATTTCATAGGGAGGTT
** *
2946 ATCAAAAAATCATAGGGAGGTG
1 ATCAAAATTTCATAGGGAGGTT
* *
2968 ATTAAAA-TT--T--GTA-GTT
1 ATCAAAATTTCATAGGGAGGTT
* * * *
2984 ATCAAGATTTCATAAGAAAGTT
1 ATCAAAATTTCATAGGGAGGTT
*
3006 ATCAAAATTTTATAGGGAGGTTTAT
1 ATCAAAATTTCATAGGGAGG--T-T
* * *
3031 ATCAAAATTTTATAGGAAGATTT
1 ATCAAAATTTCATAGGGAG-GTT
* *
3054 ATTAAAATTTCATAGCGAGGTT
1 ATCAAAATTTCATAGGGAGGTT
* * * *
3076 ATCATAATTTCATAGTGTGATT
1 ATCAAAATTTCATAGGGAGGTT
* * *
3098 ATCAAAATTTCAGAGTGTGGTT
1 ATCAAAATTTCATAGGGAGGTT
3120 A-CTAACAA-TTCATAGGGAGGTT
1 ATC-AA-AATTTCATAGGGAGGTT
* * ** *
3142 -T-ATATTTTCATAACGTGGTT
1 ATCAAAATTTCATAGGGAGGTT
* * *
3162 ATCAATATATCATATGGAGGTT
1 ATCAAAATTTCATAGGGAGGTT
** * **
3184 AT-AGCATCTCATAGTGTTGGTT
1 ATCAAAATTTCATAG-GGAGGTT
**
3206 ATCAAAATTTCATATTGAGGTGT
1 ATCAAAATTTCATAGGGAGGT-T
*
3229 -TCAAAATTTCTTAGGGAGGTT
1 ATCAAAATTTCATAGGGAGGTT
* * *
3250 AACAAAATTTCATAAGAAGGTT
1 ATCAAAATTTCATAGGGAGGTT
* * ***
3272 A-AAAAAGTTTTATAAAAAGGTT
1 ATCAAAA-TTTCATAGGGAGGTT
* * * * * **
3294 CTCGAAATTCCAGA-GTATCATT
1 ATCAAAATTTCATAGGGA-GGTT
* *
3316 ATTAAAATTTCATAGGAAGGTT
1 ATCAAAATTTCATAGGGAGGTT
3338 ATCAAAATTTCATA
1 ATCAAAATTTCATA
3352 ATGGGATCAT
Statistics
Matches: 360, Mismatches: 104, Indels: 58
0.69 0.20 0.11
Matches are distributed among these distances:
16 7 0.02
17 4 0.01
19 3 0.01
20 23 0.06
21 19 0.05
22 249 0.69
23 34 0.09
24 2 0.01
25 19 0.05
ACGTcount: A:0.38, C:0.09, G:0.17, T:0.36
Consensus pattern (22 bp):
ATCAAAATTTCATAGGGAGGTT
Found at i:3033 original size:25 final size:25
Alignment explanation
Indices: 3005--3075 Score: 92
Period size: 25 Copynumber: 2.9 Consensus size: 25
2995 ATAAGAAAGT
3005 TATCAAAATTTTATAGGGAGGTTTA
1 TATCAAAATTTTATAGGGAGGTTTA
* *
3030 TATCAAAATTTTATAGGAAGATTTA
1 TATCAAAATTTTATAGGGAGGTTTA
* *
3055 T-T-AAAATTTCATAGCGAGGTT
1 TATCAAAATTTTATAGGGAGGTT
3076 ATCATAATTT
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
23 15 0.38
24 1 0.03
25 24 0.60
ACGTcount: A:0.38, C:0.06, G:0.17, T:0.39
Consensus pattern (25 bp):
TATCAAAATTTTATAGGGAGGTTTA
Found at i:3068 original size:23 final size:23
Alignment explanation
Indices: 2990--3068 Score: 70
Period size: 25 Copynumber: 3.4 Consensus size: 23
2980 AGTTATCAAG
* * *
2990 ATTTCATAAGAA-AGTTATCAAA
1 ATTTCATAGGAAGATTTATTAAA
* * *
3012 ATTTTATAGGGAGGTTTATATCAAA
1 ATTTCATAGGAAGATTTAT-T-AAA
*
3037 ATTTTATAGGAAGATTTATTAAA
1 ATTTCATAGGAAGATTTATTAAA
3060 ATTTCATAG
1 ATTTCATAG
3069 CGAGGTTATC
Statistics
Matches: 45, Mismatches: 9, Indels: 5
0.76 0.15 0.08
Matches are distributed among these distances:
22 9 0.20
23 15 0.33
24 1 0.02
25 20 0.44
ACGTcount: A:0.42, C:0.05, G:0.14, T:0.39
Consensus pattern (23 bp):
ATTTCATAGGAAGATTTATTAAA
Found at i:5463 original size:30 final size:30
Alignment explanation
Indices: 5427--5528 Score: 95
Period size: 30 Copynumber: 3.4 Consensus size: 30
5417 CTGTGTTATA
*
5427 TGTGTTTGGGGACTTTAGTATAGATGCCTC
1 TGTGTTTAGGGACTTTAGTATAGATGCCTC
* * *
5457 TGTGTTTAGAGACTTTAATATAGGTGCC-C
1 TGTGTTTAGGGACTTTAGTATAGATGCCTC
*
5486 TTGTGCTT-GAGGACTTTGATGTA-A-ATGCCTC
1 -TGTGTTTAG-GGACTTT-A-GTATAGATGCCTC
5517 TGTGTTTAGGGA
1 TGTGTTTAGGGA
5529 TGAATACCCT
Statistics
Matches: 57, Mismatches: 9, Indels: 12
0.73 0.12 0.15
Matches are distributed among these distances:
29 2 0.04
30 49 0.86
31 4 0.07
32 2 0.04
ACGTcount: A:0.20, C:0.13, G:0.28, T:0.39
Consensus pattern (30 bp):
TGTGTTTAGGGACTTTAGTATAGATGCCTC
Found at i:5600 original size:26 final size:26
Alignment explanation
Indices: 5570--5665 Score: 97
Period size: 26 Copynumber: 3.4 Consensus size: 26
5560 GAGTTGCCTC
5570 TGTGTTTAGGGACTTATAAATGCCCT
1 TGTGTTTAGGGACTTATAAATGCCCT
5596 TGTGTTT-GAGGACTTTGATATAGAATTG-CCT
1 TGTGTTTAG-GGAC--T--TATA-AA-TGCCCT
5627 CTGTGTTTAGGGACTTATAAATGCCCT
1 -TGTGTTTAGGGACTTATAAATGCCCT
5654 TGTGTTTGAGGG
1 TGTGTTT-AGGG
5666 CTTTAATTGT
Statistics
Matches: 59, Mismatches: 0, Indels: 21
0.74 0.00 0.26
Matches are distributed among these distances:
25 1 0.02
26 20 0.34
27 9 0.15
28 5 0.08
30 5 0.08
31 5 0.08
32 13 0.22
33 1 0.02
ACGTcount: A:0.21, C:0.12, G:0.27, T:0.40
Consensus pattern (26 bp):
TGTGTTTAGGGACTTATAAATGCCCT
Found at i:5637 original size:58 final size:56
Alignment explanation
Indices: 5427--5670 Score: 241
Period size: 58 Copynumber: 4.3 Consensus size: 56
5417 CTGTGTTATA
* * *
5427 TGTGTTTGGGGACTTTAGTATAG-ATGCCTCTGTGTTTAGAGACTTTAATATAGGTGCCCT
1 TGTGTTTGAGGACTTTA-TATAGAATGCCTCTGTGTTTAGGGAC-TT-ATA-A-ATGCCCT
* * * *
5487 TGTGCTTGAGGACTTTGATGTA-AATGCCTCTGTGTTTAGGG----ATGAATACCCT
1 TGTGTTTGAGGACTTT-ATATAGAATGCCTCTGTGTTTAGGGACTTATAAATGCCCT
* * * *
5539 TGTGTTTAAAGACTTT-TGAGAGAGTTGCCTCTGTGTTTAGGGACTTATAAATGCCCT
1 TGTGTTTGAGGACTTTAT-ATAGA-ATGCCTCTGTGTTTAGGGACTTATAAATGCCCT
5596 TGTGTTTGAGGACTTTGATATAGAATTGCCTCTGTGTTTAGGGACTTATAAATGCCCT
1 TGTGTTTGAGGACTTT-ATATAGAA-TGCCTCTGTGTTTAGGGACTTATAAATGCCCT
*
5654 TGTGTTTGAGGGCTTTA
1 TGTGTTTGAGGACTTTA
5671 ATTGTTGGGT
Statistics
Matches: 152, Mismatches: 20, Indels: 27
0.76 0.10 0.14
Matches are distributed among these distances:
50 1 0.01
51 1 0.01
52 19 0.12
53 18 0.12
54 2 0.01
57 24 0.16
58 51 0.34
59 1 0.01
60 34 0.22
61 1 0.01
ACGTcount: A:0.21, C:0.14, G:0.26, T:0.39
Consensus pattern (56 bp):
TGTGTTTGAGGACTTTATATAGAATGCCTCTGTGTTTAGGGACTTATAAATGCCCT
Found at i:5641 original size:32 final size:29
Alignment explanation
Indices: 5563--5669 Score: 81
Period size: 26 Copynumber: 3.8 Consensus size: 29
5553 TTTGAGAGAG
5563 TTGCCTCTGTGTTTAGGGAC--TTATAAA
1 TTGCCTCTGTGTTTAGGGACTTTTATAAA
5590 -TGCC-CTTGTGTTT-GAGGACTTTGATATAGAA
1 TTGCCTC-TGTGTTTAG-GGACTTT--TATA-AA
5621 TTGCCTCTGTGTTTAGGGAC--TTATAAA
1 TTGCCTCTGTGTTTAGGGACTTTTATAAA
5648 -TGCC-CTTGTGTTTGAGGG-CTTT
1 TTGCCTC-TGTGTTT-AGGGACTTT
5670 AATTGTTGGG
Statistics
Matches: 66, Mismatches: 0, Indels: 27
0.71 0.00 0.29
Matches are distributed among these distances:
25 3 0.05
26 27 0.41
27 6 0.09
28 6 0.09
30 5 0.08
31 2 0.03
32 15 0.23
33 2 0.03
ACGTcount: A:0.19, C:0.15, G:0.25, T:0.41
Consensus pattern (29 bp):
TTGCCTCTGTGTTTAGGGACTTTTATAAA
Found at i:10475 original size:7 final size:7
Alignment explanation
Indices: 10449--10514 Score: 60
Period size: 7 Copynumber: 8.9 Consensus size: 7
10439 ATCTGATGAG
10449 TATTTGAA
1 TATTTG-A
*
10457 TGTTTGGA
1 TATTT-GA
10465 TATTTGA
1 TATTTGA
*
10472 TATTTGG
1 TATTTGA
10479 TATTTGGA
1 TATTT-GA
*
10487 TATTTGG
1 TATTTGA
10494 TATTTGAA
1 TATTTG-A
*
10502 TATTTGG
1 TATTTGA
10509 TATTTG
1 TATTTG
10515 GGTATGTATG
Statistics
Matches: 48, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
7 26 0.54
8 21 0.44
9 1 0.02
ACGTcount: A:0.23, C:0.00, G:0.23, T:0.55
Consensus pattern (7 bp):
TATTTGA
Found at i:10486 original size:22 final size:23
Alignment explanation
Indices: 10449--10514 Score: 91
Period size: 22 Copynumber: 3.0 Consensus size: 23
10439 ATCTGATGAG
*
10449 TATTTGAATGTTTGGATATTTGA
1 TATTTGAATATTTGGATATTTGA
* *
10472 TATTTG-GTATTTGGATATTTGG
1 TATTTGAATATTTGGATATTTGA
10494 TATTTGAATATTTGG-TATTTG
1 TATTTGAATATTTGGATATTTG
10515 GGTATGTATG
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
22 25 0.66
23 13 0.34
ACGTcount: A:0.23, C:0.00, G:0.23, T:0.55
Consensus pattern (23 bp):
TATTTGAATATTTGGATATTTGA
Found at i:10488 original size:15 final size:15
Alignment explanation
Indices: 10448--10515 Score: 93
Period size: 15 Copynumber: 4.5 Consensus size: 15
10438 AATCTGATGA
* *
10448 GTATTTGAATGTTTG
1 GTATTTGGATATTTG
10463 GATATTT-GATATTTG
1 G-TATTTGGATATTTG
10478 GTATTTGGATATTTG
1 GTATTTGGATATTTG
*
10493 GTATTTGAATATTTG
1 GTATTTGGATATTTG
10508 GTATTTGG
1 GTATTTGG
10516 GTATGTATGA
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
14 5 0.11
15 37 0.79
16 5 0.11
ACGTcount: A:0.22, C:0.00, G:0.25, T:0.53
Consensus pattern (15 bp):
GTATTTGGATATTTG
Found at i:10515 original size:7 final size:7
Alignment explanation
Indices: 10459--10515 Score: 69
Period size: 7 Copynumber: 7.7 Consensus size: 7
10449 TATTTGAATG
10459 TTTGGATA
1 TTTGG-TA
*
10467 TTTGATA
1 TTTGGTA
10474 TTTGGTA
1 TTTGGTA
10481 TTTGGATA
1 TTTGG-TA
10489 TTTGGTA
1 TTTGGTA
*
10496 TTTGAATA
1 TTTG-GTA
10504 TTTGGTA
1 TTTGGTA
10511 TTTGG
1 TTTGG
10516 GTATGTATGA
Statistics
Matches: 43, Mismatches: 4, Indels: 5
0.83 0.08 0.10
Matches are distributed among these distances:
7 26 0.60
8 17 0.40
ACGTcount: A:0.21, C:0.00, G:0.25, T:0.54
Consensus pattern (7 bp):
TTTGGTA
Done.