Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014735.1 Corchorus capsularis cultivar CVL-1 contig14756, 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: 3914
ACGTcount: A:0.31, C:0.20, G:0.16, T:0.33
Found at i:695 original size:10 final size:10
Alignment explanation
Indices: 680--704 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
670 GAGGACTCTA
680 GAATTTTCTG
1 GAATTTTCTG
690 GAATTTTCTG
1 GAATTTTCTG
700 GAATT
1 GAATT
705 GAGCAGGGAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.24, C:0.08, G:0.20, T:0.48
Consensus pattern (10 bp):
GAATTTTCTG
Found at i:2649 original size:382 final size:382
Alignment explanation
Indices: 1943--2707 Score: 1521
Period size: 382 Copynumber: 2.0 Consensus size: 382
1933 TAGAAACCCT
1943 AATCAACCCTAAACTAGTATTCAGTTTGACTCTCTAACCAGTCCCCAGCGGAGTCGCCAAGCTGT
1 AATCAACCCTAAACTAGTATTCAGTTTGACTCTCTAACCAGTCCCCAGCGGAGTCGCCAAGCTGT
2008 CGCAACGTCCGGGTCCGGGGGTACCAAACCCTTACCGTTTAACGACTTAAAGAACTAAAAACTAA
66 CGCAACGTCCGGGTCCGGGGGTACCAAACCCTTACCGTTTAACGACTTAAAGAACTAAAAACTAA
2073 GGGAGTCGCCATTAATCTTTTTTTAACCTAGGTTTGATTAGCCACCTATCAGATTATTAAGCCTA
131 GGGAGTCGCCATTAATCTTTTTTTAACCTAGGTTTGATTAGCCACCTATCAGATTATTAAGCCTA
2138 ATGTTAACCTAAGCTTGGCGAAGGTAACACTAAATCTAATAAACGGTCTTCTAACCAGAGTCCTA
196 ATGTTAACCTAAGCTTGGCGAAGGTAACACTAAATCTAATAAACGGTCTTCTAACCAGAGTCCTA
2203 AAGGTTCGGGAGTCGGGTACGCGTGGGGAAGGATTAGCACCCCCACGACGCCCGTCAAAAGACGG
261 AAGGTTCGGGAGTCGGGTACGCGTGGGGAAGGATTAGCACCCCCACGACGCCCGTCAAAAGACGG
2268 CACTGACTAGTTTAGACTTAATTATGGGTTTCTATTATCGCTTGCTACCATTCTTGA
326 CACTGACTAGTTTAGACTTAATTATGGGTTTCTATTATCGCTTGCTACCATTCTTGA
2325 AATCAACCCTAAACTAGTATTCAGTTTGACTCTCTAACCAGTCCCCAGCGGAGTCGCCAAGCTGT
1 AATCAACCCTAAACTAGTATTCAGTTTGACTCTCTAACCAGTCCCCAGCGGAGTCGCCAAGCTGT
2390 CGCAACGTCCGGGTCCGGGGGTACCAAACCCTTACCGTTTAACGACTTAAAGAACTAAAAACTAA
66 CGCAACGTCCGGGTCCGGGGGTACCAAACCCTTACCGTTTAACGACTTAAAGAACTAAAAACTAA
2455 GGGAGTCGCCATTAATCTTTTTTTAACCTAGGTTTGATTAGCCACCTATCAGATTATTAAGCCTA
131 GGGAGTCGCCATTAATCTTTTTTTAACCTAGGTTTGATTAGCCACCTATCAGATTATTAAGCCTA
*
2520 ATGTTAACCTAAGCTTGGCGAAGGTAACACTAAATCTAATAAACGGTCTTCTAACCAGAGTCTTA
196 ATGTTAACCTAAGCTTGGCGAAGGTAACACTAAATCTAATAAACGGTCTTCTAACCAGAGTCCTA
2585 AAGGTTCGGGAGTCGGGTACGCGTGGGGAAGGATTAGCACCCCCACGACGCCCGTCAAAAGACGG
261 AAGGTTCGGGAGTCGGGTACGCGTGGGGAAGGATTAGCACCCCCACGACGCCCGTCAAAAGACGG
2650 CACTGACTAGTTTAGACTTAATTATGGGTTTCTATTATCGCTTGCTACCATTCTTGA
326 CACTGACTAGTTTAGACTTAATTATGGGTTTCTATTATCGCTTGCTACCATTCTTGA
2707 A
1 A
2708 TATTTTCATG
Statistics
Matches: 382, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
382 382 1.00
ACGTcount: A:0.29, C:0.24, G:0.21, T:0.27
Consensus pattern (382 bp):
AATCAACCCTAAACTAGTATTCAGTTTGACTCTCTAACCAGTCCCCAGCGGAGTCGCCAAGCTGT
CGCAACGTCCGGGTCCGGGGGTACCAAACCCTTACCGTTTAACGACTTAAAGAACTAAAAACTAA
GGGAGTCGCCATTAATCTTTTTTTAACCTAGGTTTGATTAGCCACCTATCAGATTATTAAGCCTA
ATGTTAACCTAAGCTTGGCGAAGGTAACACTAAATCTAATAAACGGTCTTCTAACCAGAGTCCTA
AAGGTTCGGGAGTCGGGTACGCGTGGGGAAGGATTAGCACCCCCACGACGCCCGTCAAAAGACGG
CACTGACTAGTTTAGACTTAATTATGGGTTTCTATTATCGCTTGCTACCATTCTTGA
Found at i:2924 original size:43 final size:42
Alignment explanation
Indices: 2868--3208 Score: 251
Period size: 43 Copynumber: 7.7 Consensus size: 42
2858 CTAATTATTC
* *
2868 TTTACTTTGTACTGATTACTATTTTACACTTGTTGATTACCT
1 TTTACTTTTTACTGATTACTATTTTACTCTTGTTGATTACCT
* * * *
2910 TCTTACTTTTTACTGAATACCATTTTACTCTTATACTGATTACTATTT
1 T-TTACTTTTTACTGATTACTATTTTACTCTTGT--TGATTAC---CT
* * * *
2958 TCTGCTCCTTTTTTTTACTGATTACTCTTTTACT-TTTTACTGATTGCCT
1 T-T--TAC---TTTTTACTGATTACTATTTTACTCTTGT--TGATTACCT
* *
3007 TTTGCTTTTTACTGATTACCT-TTTTACTTCTTGCTGATTAGCCT
1 TTTACTTTTTACTGATTA-CTATTTTAC-TCTTGTTGATTA-CCT
* * * *
3051 TTTACTCTTTACTGATCACCT-TTTTACTCTTACTTAATT-CCT
1 TTTACTTTTTACTGATTA-CTATTTTACTCTT-GTTGATTACCT
* * * * **
3093 TTTACTTCTTATTTATTACTTTTTTACTCTTACTGATTA-CT
1 TTTACTTTTTACTGATTACTATTTTACTCTTGTTGATTACCT
*
3134 ATTTACTTTTTACTGACTACTATTTTACTCTTGTTGATTACCT
1 -TTTACTTTTTACTGATTACTATTTTACTCTTGTTGATTACCT
3177 TCTTACTTTTTACTGATTACTATTTTACTCTT
1 T-TTACTTTTTACTGATTACTATTTTACTCTT
3209 TACTAATTTA
Statistics
Matches: 239, Mismatches: 39, Indels: 41
0.75 0.12 0.13
Matches are distributed among these distances:
41 8 0.03
42 60 0.25
43 86 0.36
44 34 0.14
45 9 0.04
46 2 0.01
48 5 0.02
49 2 0.01
50 2 0.01
52 11 0.05
53 20 0.08
ACGTcount: A:0.19, C:0.20, G:0.06, T:0.55
Consensus pattern (42 bp):
TTTACTTTTTACTGATTACTATTTTACTCTTGTTGATTACCT
Found at i:2930 original size:22 final size:21
Alignment explanation
Indices: 2901--2952 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 21
2891 TTACACTTGT
2901 TGATTACCTTCTTACTTTTTAC
1 TGATTACCTT-TTACTTTTTAC
* *
2923 TGAATACCATTTTACTCTTATAC
1 TGATTACC-TTTTACT-TTTTAC
2946 TGATTAC
1 TGATTAC
2953 TATTTTCTGC
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
22 12 0.48
23 13 0.52
ACGTcount: A:0.25, C:0.21, G:0.06, T:0.48
Consensus pattern (21 bp):
TGATTACCTTTTACTTTTTAC
Found at i:3008 original size:21 final size:21
Alignment explanation
Indices: 2969--3227 Score: 188
Period size: 22 Copynumber: 12.0 Consensus size: 21
2959 CTGCTCCTTT
2969 TTTTTACTGATTACTCTTTTAC
1 TTTTTACTGATTAC-CTTTTAC
* *
2991 TTTTTACTGATTGCCTTTTGC
1 TTTTTACTGATTACCTTTTAC
3012 TTTTTACTGATTACCTTTTTAC
1 TTTTTACTGATTACC-TTTTAC
* *
3034 TTCTTGCTGATTAGCCTTTTAC
1 TTTTTACTGATTA-CCTTTTAC
* *
3056 TCTTTACTGATCACCTTTTTAC
1 TTTTTACTGATTACC-TTTTAC
* *
3078 -TCTTACTTAATT-CCTTTTAC
1 TTTTTAC-TGATTACCTTTTAC
* * * *
3098 TTCTTATTTATTACTTTTTTAC
1 TTTTTACTGATTAC-CTTTTAC
*
3120 -TCTTACTGATTA-CTATTTAC
1 TTTTTACTGATTACCT-TTTAC
* *
3140 TTTTTACTGACTACTATTTTAC
1 TTTTTACTGATTAC-CTTTTAC
*
3162 TCTTGT--TGATTACCTTCTTAC
1 T-TTTTACTGATTACCTT-TTAC
*
3183 TTTTTACTGATTACTATTTTAC
1 TTTTTACTGATTAC-CTTTTAC
* *
3205 TCTTTACTAATTTACCATTTTAC
1 TTTTTACTGA-TTACC-TTTTAC
3228 CCTTTCAGAT
Statistics
Matches: 188, Mismatches: 31, Indels: 35
0.74 0.12 0.14
Matches are distributed among these distances:
19 1 0.01
20 20 0.11
21 65 0.35
22 84 0.45
23 18 0.10
ACGTcount: A:0.19, C:0.20, G:0.05, T:0.56
Consensus pattern (21 bp):
TTTTTACTGATTACCTTTTAC
Found at i:3312 original size:55 final size:55
Alignment explanation
Indices: 3247--3531 Score: 509
Period size: 55 Copynumber: 5.2 Consensus size: 55
3237 TACCTTTTTC
*
3247 CTTTTTACTTAATTACTGATTTACTGATTACTACTACTTTGACTCTGATTAATCT
1 CTTTTTACTTAATTACTGATTTACTGATTACTATTACTTTGACTCTGATTAATCT
3302 CTTTTTACTTAATTACTGATTTACTGATTACTATTACTTTGACTCTGATTAATCT
1 CTTTTTACTTAATTACTGATTTACTGATTACTATTACTTTGACTCTGATTAATCT
3357 CTTTTTACTTAATTACTGATTTACTGATTACTATTACTTTGACTCTGATTAATCT
1 CTTTTTACTTAATTACTGATTTACTGATTACTATTACTTTGACTCTGATTAATCT
* * *
3412 CTTTTTTACTTAATTATTGATTTCCTGATTACTATTACTTTGAATCTGATTAATCT
1 C-TTTTTACTTAATTACTGATTTACTGATTACTATTACTTTGACTCTGATTAATCT
*
3468 CTTTTTACTTAATTACTTA-TTACTGATTACTATTACTTTGACTCTGATTAATCT
1 CTTTTTACTTAATTACTGATTTACTGATTACTATTACTTTGACTCTGATTAATCT
3522 CTTTTTACTT
1 CTTTTTACTT
3532 TTTAGATTTC
Statistics
Matches: 221, Mismatches: 8, Indels: 3
0.95 0.03 0.01
Matches are distributed among these distances:
54 43 0.19
55 126 0.57
56 52 0.24
ACGTcount: A:0.25, C:0.16, G:0.07, T:0.52
Consensus pattern (55 bp):
CTTTTTACTTAATTACTGATTTACTGATTACTATTACTTTGACTCTGATTAATCT
Found at i:3320 original size:26 final size:26
Alignment explanation
Indices: 3291--3377 Score: 79
Period size: 26 Copynumber: 3.2 Consensus size: 26
3281 TACTTTGACT
3291 CTGATTAATCTCTTTTTACTTAATTA
1 CTGATTAATCTCTTTTTACTTAATTA
* * * *
3317 CTGATTTA-CTGATTACTATTACTTTGACT-
1 CTGATTAATCT-CTT--T-TTAC-TTAATTA
3346 CTGATTAATCTCTTTTTACTTAATTA
1 CTGATTAATCTCTTTTTACTTAATTA
3372 CTGATT
1 CTGATT
3378 TACTGATTAC
Statistics
Matches: 46, Mismatches: 8, Indels: 14
0.68 0.12 0.21
Matches are distributed among these distances:
25 6 0.13
26 19 0.41
27 1 0.02
28 1 0.02
29 13 0.28
30 6 0.13
ACGTcount: A:0.25, C:0.16, G:0.07, T:0.52
Consensus pattern (26 bp):
CTGATTAATCTCTTTTTACTTAATTA
Done.