Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007822.1 Corchorus capsularis cultivar CVL-1 contig07843, 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: 40634
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Found at i:18425 original size:51 final size:51
Alignment explanation
Indices: 18365--18569 Score: 189
Period size: 51 Copynumber: 3.8 Consensus size: 51
18355 AAAAACCAAA
18365 TTGGTAATCAACTTAATTCGGTGCAATTAAGTAAATTGGTAATTAAATAAT
1 TTGGTAATCAACTTAATTCGGTGCAATTAAGTAAATTGGTAATTAAATAAT
*
18416 TTGGTAATCAACTTAATTCGGTGCAATTAAGTAAATTGGAAATTAAATTAAGTAT
1 TTGGTAATCAACTTAATTCGGTGCAATTAAGTAAATTGGTAATTAAA-T-A--AT
* * * * * * *
18471 ATTGGTAATTAAATTAAGTAATTTGGT--AATCAACTTAATTCGGTGTAATTAAGTAAT
1 -TTGGTAA-TCAACT---TAATTCGGTGCAATTAAGTAAATT--G-GTAATTAAATAAT
* **
18528 TTGGTAATCAACTTAATTCGGTGTAATTAAGTAGTTTGGTAA
1 TTGGTAATCAACTTAATTCGGTGCAATTAAGTAAATTGGTAA
18570 AGAACTTAAT
Statistics
Matches: 123, Mismatches: 17, Indels: 28
0.73 0.10 0.17
Matches are distributed among these distances:
51 50 0.41
52 10 0.08
53 1 0.01
54 8 0.07
55 6 0.05
56 14 0.11
57 6 0.05
58 10 0.08
59 1 0.01
60 10 0.08
61 7 0.06
ACGTcount: A:0.38, C:0.07, G:0.17, T:0.39
Consensus pattern (51 bp):
TTGGTAATCAACTTAATTCGGTGCAATTAAGTAAATTGGTAATTAAATAAT
Found at i:18444 original size:35 final size:35
Alignment explanation
Indices: 18403--18773 Score: 420
Period size: 35 Copynumber: 10.4 Consensus size: 35
18393 AAGTAAATTG
* *
18403 GTAATTAAATAATTTGGTAATCAACTTAATTCGGT
1 GTAATTAAGTAAATTGGTAATCAACTTAATTCGGT
* * * * *
18438 GCAATTAAGTAAATTGGAAATTAAATTAAGTATATTGGT
1 GTAATTAAGTAAATTGGTAATCAACTT-A--AT-TCGGT
* *
18477 AATTAAATTAAGTAATTTGGTAATCAACTTAATTCGGT
1 --GT-AATTAAGTAAATTGGTAATCAACTTAATTCGGT
*
18515 GTAATTAAGTAATTTGGTAATCAACTTAATTCGGT
1 GTAATTAAGTAAATTGGTAATCAACTTAATTCGGT
** **
18550 GTAATTAAGTAGTTTGGTAAAGAACTTAATTCGGT
1 GTAATTAAGTAAATTGGTAATCAACTTAATTCGGT
* *
18585 GTGATTAAGCAAATTGGTAATCAACTTAATTCGGT
1 GTAATTAAGTAAATTGGTAATCAACTTAATTCGGT
* *
18620 GTAATTAAGTAAATTAGTAATCCACTTAATTCGGT
1 GTAATTAAGTAAATTGGTAATCAACTTAATTCGGT
* *
18655 GTGATTAAGTAAATTGGTAATTAACTTAATTCGGT
1 GTAATTAAGTAAATTGGTAATCAACTTAATTCGGT
* ** *
18690 ATAATTAAGTAAATCAGTAATCAACTTAATTTGGT
1 GTAATTAAGTAAATTGGTAATCAACTTAATTCGGT
** *
18725 GTAATTAAGTAAATCAGTAATTC-GCTTAATTCGGT
1 GTAATTAAGTAAATTGGTAA-TCAACTTAATTCGGT
18760 GTAATTAAGTAAAT
1 GTAATTAAGTAAAT
18774 AAATGGCTTA
Statistics
Matches: 287, Mismatches: 41, Indels: 16
0.83 0.12 0.05
Matches are distributed among these distances:
35 249 0.87
36 4 0.01
38 6 0.02
39 6 0.02
41 1 0.00
42 21 0.07
ACGTcount: A:0.38, C:0.08, G:0.17, T:0.38
Consensus pattern (35 bp):
GTAATTAAGTAAATTGGTAATCAACTTAATTCGGT
Found at i:18497 original size:21 final size:21
Alignment explanation
Indices: 18440--18500 Score: 88
Period size: 21 Copynumber: 2.9 Consensus size: 21
18430 AATTCGGTGC
* *
18440 AATTAAGTAAATTGGAAATTA
1 AATTAAGTAATTTGGTAATTA
18461 AATTAAGT-ATATTGGTAATTA
1 AATTAAGTAAT-TTGGTAATTA
18482 AATTAAGTAATTTGGTAAT
1 AATTAAGTAATTTGGTAAT
18501 CAACTTAATT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
20 1 0.03
21 33 0.92
22 2 0.06
ACGTcount: A:0.46, C:0.00, G:0.15, T:0.39
Consensus pattern (21 bp):
AATTAAGTAATTTGGTAATTA
Found at i:18508 original size:21 final size:21
Alignment explanation
Indices: 18440--18508 Score: 77
Period size: 21 Copynumber: 3.3 Consensus size: 21
18430 AATTCGGTGC
* * *
18440 AATTAAGTAAATTGGAAATTA
1 AATTAAGTAATTTGGTAATCA
*
18461 AATTAAGT-ATATTGGTAATTA
1 AATTAAGTAAT-TTGGTAATCA
18482 AATTAAGTAATTTGGTAATCA
1 AATTAAGTAATTTGGTAATCA
*
18503 ACTTAA
1 AATTAA
18509 TTCGGTGTAA
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
20 1 0.02
21 39 0.93
22 2 0.05
ACGTcount: A:0.46, C:0.03, G:0.13, T:0.38
Consensus pattern (21 bp):
AATTAAGTAATTTGGTAATCA
Found at i:18685 original size:16 final size:17
Alignment explanation
Indices: 18363--18690 Score: 82
Period size: 16 Copynumber: 18.5 Consensus size: 17
18353 AGAAAAACCA
*
18363 AATT-GGTAATCAACTT
1 AATTCGGTAATTAACTT
* *
18379 AATTCGGTGCAATTAAGTA
1 AATTCGGT--AATTAACTT
*
18398 AATT-GGTAATTAA-AT
1 AATTCGGTAATTAACTT
* *
18413 AATTTGGTAATCAACTT
1 AATTCGGTAATTAACTT
* *
18430 AATTCGGTGCAATTAAGTA
1 AATTCGGT--AATTAACTT
* *
18449 AATT-GGAAATTAAATT
1 AATTCGGTAATTAACTT
* *
18465 AAGTATATTGGTAATTAAATTAAGT
1 -A--AT-TCGGTAATT-AACT---T
* *
18490 AATTTGGTAATCAACTT
1 AATTCGGTAATTAACTT
*
18507 AATTCGGTGTAATTAA-GT
1 AATTC-G-GTAATTAACTT
* *
18525 AATTTGGTAATCAACTT
1 AATTCGGTAATTAACTT
*
18542 AATTCGGTGTAATTAA-GT
1 AATTC-G-GTAATTAACTT
* * **
18560 AGTTTGGTAAAGAACTT
1 AATTCGGTAATTAACTT
* *
18577 AATTCGGTGTGATTAAGC-A
1 AATTC-G-GTAATTAA-CTT
*
18596 AATT-GGTAATCAACTT
1 AATTCGGTAATTAACTT
* *
18612 AATTCGGTGTAATTAAGTA
1 AATTC-G-GTAATTAACTT
* **
18631 AATT-AGTAATCCACTT
1 AATTCGGTAATTAACTT
* * *
18647 AATTCGGTGTGATTAAGTA
1 AATTC-G-GTAATTAACTT
18666 AATT-GGTAATTAACTT
1 AATTCGGTAATTAACTT
18682 AATTCGGTA
1 AATTCGGTA
18691 TAATTAAGTA
Statistics
Matches: 221, Mismatches: 58, Indels: 65
0.64 0.17 0.19
Matches are distributed among these distances:
15 5 0.02
16 71 0.32
17 34 0.15
18 18 0.08
19 67 0.30
20 5 0.02
21 14 0.06
22 5 0.02
24 1 0.00
25 1 0.00
ACGTcount: A:0.37, C:0.08, G:0.17, T:0.38
Consensus pattern (17 bp):
AATTCGGTAATTAACTT
Found at i:19215 original size:113 final size:113
Alignment explanation
Indices: 19086--19329 Score: 425
Period size: 113 Copynumber: 2.2 Consensus size: 113
19076 TTTAAGTTTT
*
19086 TGGGAAAGTTCCCATCAAGTTGTCAAAGTTTGAAATTCGGAAAGTTCCCATCGAGTCTTAGTTTT
1 TGGGAAAGTTCCCATCAAGTTGTCAAAGTTTCAAATTCGGAAAGTTCCCATCGAGTCTTAGTTTT
19151 TTCAATTTAGGGAAAGTTCCCGCCAATTTCAGGTTTTAGTTTTCAAAA
66 TTCAATTTAGGGAAAGTTCCCGCCAATTTCAGGTTTTAGTTTTCAAAA
* * *
19199 TGGGAAAGTTCCCATCAAGTTGTCAAAGTTTCAAATTGGGAAAGTTCCCATTGGGTCTTAGTTTT
1 TGGGAAAGTTCCCATCAAGTTGTCAAAGTTTCAAATTCGGAAAGTTCCCATCGAGTCTTAGTTTT
* *
19264 TTCAATTTAGGGAAAGTTCCCGCCAGTTTGAGGTTTTAGTTTTCAAAA
66 TTCAATTTAGGGAAAGTTCCCGCCAATTTCAGGTTTTAGTTTTCAAAA
*
19312 TGGGAAAGTTCCCGTCAA
1 TGGGAAAGTTCCCATCAA
19330 ATAAAAGTTT
Statistics
Matches: 124, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
113 124 1.00
ACGTcount: A:0.27, C:0.16, G:0.21, T:0.35
Consensus pattern (113 bp):
TGGGAAAGTTCCCATCAAGTTGTCAAAGTTTCAAATTCGGAAAGTTCCCATCGAGTCTTAGTTTT
TTCAATTTAGGGAAAGTTCCCGCCAATTTCAGGTTTTAGTTTTCAAAA
Found at i:19239 original size:36 final size:36
Alignment explanation
Indices: 19085--19249 Score: 127
Period size: 36 Copynumber: 4.4 Consensus size: 36
19075 TTTTAAGTTT
*
19085 TTGGGAAAGTTCCCATCAAGTTGTCAAAGTTTGAAA
1 TTGGGAAAGTTCCCATCAAGTTGTCAAAGTTTCAAA
* * *** *
19121 TTCGGAAAGTTCCCATCGAGTCT-T-AGTTTTTTCAAT
1 TTGGGAAAGTTCCCATCAAGT-TGTCA-AAGTTTCAAA
** * ***
19157 TTAGGGAAAGTTCCCGCCAATTTCAGGTTTTAGTTTTCAAA
1 TT-GGGAAAGTTCCCATCAAGTT---GTCAAAG-TTTCAAA
*
19198 ATGGGAAAGTTCCCATCAAGTTGTCAAAGTTTCAAA
1 TTGGGAAAGTTCCCATCAAGTTGTCAAAGTTTCAAA
19234 TTGGGAAAGTTCCCAT
1 TTGGGAAAGTTCCCAT
19250 TGGGTCTTAG
Statistics
Matches: 96, Mismatches: 24, Indels: 18
0.70 0.17 0.13
Matches are distributed among these distances:
35 1 0.01
36 50 0.52
37 19 0.20
40 19 0.20
41 7 0.07
ACGTcount: A:0.29, C:0.17, G:0.20, T:0.34
Consensus pattern (36 bp):
TTGGGAAAGTTCCCATCAAGTTGTCAAAGTTTCAAA
Found at i:22466 original size:2 final size:2
Alignment explanation
Indices: 22459--22484 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
22449 GAACAAAGAC
22459 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
22485 TTGAGTGGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:27371 original size:15 final size:15
Alignment explanation
Indices: 27351--27380 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
27341 GCTTGATATT
27351 TTACCTCTATTTATA
1 TTACCTCTATTTATA
27366 TTACCTCTATTTATA
1 TTACCTCTATTTATA
27381 GAGTGGCGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.20, G:0.00, T:0.53
Consensus pattern (15 bp):
TTACCTCTATTTATA
Found at i:30721 original size:17 final size:18
Alignment explanation
Indices: 30693--30729 Score: 67
Period size: 17 Copynumber: 2.1 Consensus size: 18
30683 CCTCCCCATA
30693 GTACCTAGGTAGTATGAG
1 GTACCTAGGTAGTATGAG
30711 GTACC-AGGTAGTATGAG
1 GTACCTAGGTAGTATGAG
30728 GT
1 GT
30730 GATAGGCTGC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 14 0.74
18 5 0.26
ACGTcount: A:0.27, C:0.11, G:0.35, T:0.27
Consensus pattern (18 bp):
GTACCTAGGTAGTATGAG
Found at i:32274 original size:28 final size:28
Alignment explanation
Indices: 32242--32299 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
32232 ATCCTATATT
32242 ATAAGAAACAATAATAGAAGGAAGTGTA
1 ATAAGAAACAATAATAGAAGGAAGTGTA
32270 ATAAGAAACAATAATAGAAGGAAGTGTA
1 ATAAGAAACAATAATAGAAGGAAGTGTA
32298 AT
1 AT
32300 TGCCTAAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.57, C:0.03, G:0.21, T:0.19
Consensus pattern (28 bp):
ATAAGAAACAATAATAGAAGGAAGTGTA
Found at i:36713 original size:27 final size:27
Alignment explanation
Indices: 36683--36737 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
36673 TTTTTCTTAC
*
36683 TAAACTTTATTAAAATCACTTATAAAA
1 TAAACTTTATTAAAATCACATATAAAA
* * *
36710 TAAATTTTCTTAAAATCACATCTAAAA
1 TAAACTTTATTAAAATCACATATAAAA
36737 T
1 T
36738 CGATTTCTTA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.49, C:0.13, G:0.00, T:0.38
Consensus pattern (27 bp):
TAAACTTTATTAAAATCACATATAAAA
Found at i:36743 original size:27 final size:26
Alignment explanation
Indices: 36683--36750 Score: 73
Period size: 27 Copynumber: 2.5 Consensus size: 26
36673 TTTTTCTTAC
* *
36683 TAAACTTTATTAAAATCACTTATAAAA
1 TAAA-TTTCTTAAAATCACATATAAAA
*
36710 TAAATTTTCTTAAAATCACATCTAAAA
1 TAAA-TTTCTTAAAATCACATATAAAA
**
36737 TCGATTTCTTAAAA
1 TAAATTTCTTAAAA
36751 GGGATGTCTT
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
26 10 0.29
27 25 0.71
ACGTcount: A:0.47, C:0.13, G:0.01, T:0.38
Consensus pattern (26 bp):
TAAATTTCTTAAAATCACATATAAAA
Done.