Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007137.1 Corchorus capsularis cultivar CVL-1 contig07158, 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: 35045
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Found at i:2496 original size:12 final size:12
Alignment explanation
Indices: 2479--2508 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
2469 TTGTGGCCGG
2479 ATGGCCCGTGCA
1 ATGGCCCGTGCA
*
2491 ATGGCCCGTGCG
1 ATGGCCCGTGCA
2503 ATGGCC
1 ATGGCC
2509 GGTTGTGGCC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.13, C:0.33, G:0.37, T:0.17
Consensus pattern (12 bp):
ATGGCCCGTGCA
Found at i:2508 original size:42 final size:42
Alignment explanation
Indices: 2461--2547 Score: 147
Period size: 42 Copynumber: 2.1 Consensus size: 42
2451 AATGGGTCGA
*
2461 ATGGCCGGTTGTGGCCGGATGGCCCGTGCAATGGCCCGTGCG
1 ATGGCCGGTTGTGGCCGGATGGCCCGTGCAATAGCCCGTGCG
* *
2503 ATGGCCGGTTGTGGCCGGATGGCTCGTGCGATAGCCCGTGCG
1 ATGGCCGGTTGTGGCCGGATGGCCCGTGCAATAGCCCGTGCG
2545 ATG
1 ATG
2548 TCCCATGCGT
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.10, C:0.26, G:0.43, T:0.21
Consensus pattern (42 bp):
ATGGCCGGTTGTGGCCGGATGGCCCGTGCAATAGCCCGTGCG
Found at i:2587 original size:54 final size:54
Alignment explanation
Indices: 2482--2588 Score: 126
Period size: 54 Copynumber: 2.0 Consensus size: 54
2472 TGGCCGGATG
* ** *
2482 GCCCGTGCAATGGCCCGTGCGATGGCCGGTTGTGGCCGGATGGCTCGTGCGATA
1 GCCCGTGCAATGGCCCATGCGATGGCCGGTCATGGCCGGATGGCTCATGCGATA
* * * *
2536 GCCCGTGCGATGTCCCATGCGTTGGCCGGTCATGGCCGG-TTGCTCCATGCGAT
1 GCCCGTGCAATGGCCCATGCGATGGCCGGTCATGGCCGGATGGCT-CATGCGAT
2589 GCTGGCCGGT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
53 4 0.09
54 40 0.91
ACGTcount: A:0.10, C:0.30, G:0.37, T:0.22
Consensus pattern (54 bp):
GCCCGTGCAATGGCCCATGCGATGGCCGGTCATGGCCGGATGGCTCATGCGATA
Found at i:13944 original size:21 final size:21
Alignment explanation
Indices: 13905--13944 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
13895 CAAGCACCAA
*
13905 GAAGATGCCATTTGATCCATT
1 GAAGATGCCATTAGATCCATT
*
13926 GAAGATGCCATTAGGTCCA
1 GAAGATGCCATTAGATCCA
13945 ATAACTAGAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.28
Consensus pattern (21 bp):
GAAGATGCCATTAGATCCATT
Found at i:17380 original size:3 final size:3
Alignment explanation
Indices: 17368--17400 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
17358 GCTCACGGAA
17368 GAT G-T GAT GAT GAT GAT GAT GAT GAT GAT GAT G
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT G
17401 GGGGAAATGA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.07
3 27 0.93
ACGTcount: A:0.30, C:0.00, G:0.36, T:0.33
Consensus pattern (3 bp):
GAT
Found at i:18488 original size:12 final size:12
Alignment explanation
Indices: 18471--18538 Score: 91
Period size: 12 Copynumber: 5.5 Consensus size: 12
18461 CATCGATACC
18471 TCGATATATCCG
1 TCGATATATCCG
18483 TCGATATATCCG
1 TCGATATATCCG
*
18495 TTCGATATATCCA
1 -TCGATATATCCG
*
18508 TCGATATATTCG
1 TCGATATATCCG
*
18520 TTCGATGTATCCG
1 -TCGATATATCCG
18533 TCGATA
1 TCGATA
18539 CCTGTATTAA
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
12 27 0.56
13 21 0.44
ACGTcount: A:0.25, C:0.22, G:0.16, T:0.37
Consensus pattern (12 bp):
TCGATATATCCG
Found at i:18499 original size:25 final size:25
Alignment explanation
Indices: 18471--18538 Score: 109
Period size: 25 Copynumber: 2.7 Consensus size: 25
18461 CATCGATACC
18471 TCGATATATCCGTCGATATATCCGT
1 TCGATATATCCGTCGATATATCCGT
* *
18496 TCGATATATCCATCGATATATTCGT
1 TCGATATATCCGTCGATATATCCGT
*
18521 TCGATGTATCCGTCGATA
1 TCGATATATCCGTCGATA
18539 CCTGTATTAA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 39 1.00
ACGTcount: A:0.25, C:0.22, G:0.16, T:0.37
Consensus pattern (25 bp):
TCGATATATCCGTCGATATATCCGT
Found at i:18729 original size:15 final size:15
Alignment explanation
Indices: 18695--18729 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
18685 TCCTTTTGAC
*
18695 CTTTGTCTTTTTTTT
1 CTTTTTCTTTTTTTT
18710 CTTTTTCTTTTTTTT
1 CTTTTTCTTTTTTTT
18725 -TTTTT
1 CTTTTT
18730 GACAACATAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 5 0.26
15 14 0.74
ACGTcount: A:0.00, C:0.11, G:0.03, T:0.86
Consensus pattern (15 bp):
CTTTTTCTTTTTTTT
Found at i:26844 original size:21 final size:22
Alignment explanation
Indices: 26818--26860 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
26808 TAACCCTTGG
26818 AATTA-GAGTAG-TCTTGTAACT
1 AATTAGGAGTAGTTCTT-TAACT
26839 AATTAGGAGTAGTTCTTTAACT
1 AATTAGGAGTAGTTCTTTAACT
26861 TAGCATTTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 5 0.25
22 11 0.55
23 4 0.20
ACGTcount: A:0.33, C:0.09, G:0.19, T:0.40
Consensus pattern (22 bp):
AATTAGGAGTAGTTCTTTAACT
Found at i:28348 original size:76 final size:75
Alignment explanation
Indices: 28211--28350 Score: 174
Period size: 76 Copynumber: 1.9 Consensus size: 75
28201 AGTCCTTATG
* * * *
28211 TACTCAGATCTGCCTCCAACGGTCATTTCCACATTAAATGCAAATCTGTCAAATCTTTCAATTTG
1 TACTCAGATCTGCCTCCAACGATCATTTCCACATCAAATCCAAATCTGTCAAATCTGTCAATTTG
28276 TTTCCTTAAA
66 TTTCCTTAAA
* * ** *
28286 TACTTAGATTTGCCTCCAACGATCATATTCTTCATCAATTCCAAATCCT-TCAAATCTGTCAATT
1 TACTCAGATCTGCCTCCAACGATCAT-TTCCACATCAAATCCAAAT-CTGTCAAATCTGTCAATT
28350 T
64 T
28351 ATGGCGTTGA
Statistics
Matches: 54, Mismatches: 9, Indels: 3
0.82 0.14 0.05
Matches are distributed among these distances:
75 23 0.43
76 29 0.54
77 2 0.04
ACGTcount: A:0.29, C:0.26, G:0.08, T:0.37
Consensus pattern (75 bp):
TACTCAGATCTGCCTCCAACGATCATTTCCACATCAAATCCAAATCTGTCAAATCTGTCAATTTG
TTTCCTTAAA
Found at i:31660 original size:34 final size:35
Alignment explanation
Indices: 31600--31667 Score: 129
Period size: 34 Copynumber: 2.0 Consensus size: 35
31590 AAAACCCTGA
31600 AAATCGTATGAGATGGTGGAGTGGGTAAGAATTGG
1 AAATCGTATGAGATGGTGGAGTGGGTAAGAATTGG
31635 AAATCGTATGAGATGG-GGAGTGGGTAAGAATTG
1 AAATCGTATGAGATGGTGGAGTGGGTAAGAATTG
31668 AAGACCAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
34 17 0.52
35 16 0.48
ACGTcount: A:0.32, C:0.03, G:0.40, T:0.25
Consensus pattern (35 bp):
AAATCGTATGAGATGGTGGAGTGGGTAAGAATTGG
Found at i:31771 original size:16 final size:15
Alignment explanation
Indices: 31746--31779 Score: 59
Period size: 16 Copynumber: 2.2 Consensus size: 15
31736 GCAGCGGTGC
31746 CAAAAGATTAAAATT
1 CAAAAGATTAAAATT
31761 CAAACAGATTAAAATT
1 CAAA-AGATTAAAATT
31777 CAA
1 CAA
31780 GCAGCGTTGC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 4 0.22
16 14 0.78
ACGTcount: A:0.59, C:0.12, G:0.06, T:0.24
Consensus pattern (15 bp):
CAAAAGATTAAAATT
Found at i:32888 original size:38 final size:38
Alignment explanation
Indices: 32837--32914 Score: 131
Period size: 38 Copynumber: 2.1 Consensus size: 38
32827 TTTCAACAAA
*
32837 TTCAACTATCTTACATTCTTACTTAATACTTT-ACATTT
1 TTCAACAATCTTACATTCTTACTTAATACTTTGA-ATTT
32875 TTCAACAATCTTACATTCTTACTTAATACTTTGAATTT
1 TTCAACAATCTTACATTCTTACTTAATACTTTGAATTT
32913 TT
1 TT
32915 GGTAATTTTA
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
38 37 0.97
39 1 0.03
ACGTcount: A:0.29, C:0.19, G:0.01, T:0.50
Consensus pattern (38 bp):
TTCAACAATCTTACATTCTTACTTAATACTTTGAATTT
Found at i:34414 original size:29 final size:29
Alignment explanation
Indices: 34379--34434 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
34369 TAAAATTTCG
*
34379 TCTACCAATACACGTGCTACATAATTCCA
1 TCTACCAATAAACGTGCTACATAATTCCA
*
34408 TCTACCAATAAACGTGTTACATAATTC
1 TCTACCAATAAACGTGCTACATAATTC
34435 TTTAGTTTGT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.36, C:0.27, G:0.07, T:0.30
Consensus pattern (29 bp):
TCTACCAATAAACGTGCTACATAATTCCA
Done.