Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008983.1 Corchorus capsularis cultivar CVL-1 contig09004, 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: 7855
ACGTcount: A:0.32, C:0.15, G:0.19, T:0.34
Found at i:206 original size:32 final size:33
Alignment explanation
Indices: 139--207 Score: 113
Period size: 33 Copynumber: 2.1 Consensus size: 33
129 CTTGCTCAAC
*
139 TTGTAAAGGCGTGATGAAGGCCCGTGAACTTCA
1 TTGTAAAGGCGTGATGAAGGCCCGTCAACTTCA
*
172 TTGTAACGGCGTGATGAAGGCCCG-CAACTTCA
1 TTGTAAAGGCGTGATGAAGGCCCGTCAACTTCA
204 TTGT
1 TTGT
208 GTGTAAGAGC
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
32 11 0.32
33 23 0.68
ACGTcount: A:0.25, C:0.20, G:0.29, T:0.26
Consensus pattern (33 bp):
TTGTAAAGGCGTGATGAAGGCCCGTCAACTTCA
Found at i:2508 original size:17 final size:17
Alignment explanation
Indices: 2481--2514 Score: 52
Period size: 16 Copynumber: 2.0 Consensus size: 17
2471 GCAAAATGAA
2481 CCCGAAACCCGAAACCCG
1 CCCGAAACCCG-AACCCG
2499 CCCG-AACCCGAACCCG
1 CCCGAAACCCGAACCCG
2515 AAATTACCCG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.38
17 6 0.38
18 4 0.25
ACGTcount: A:0.29, C:0.53, G:0.18, T:0.00
Consensus pattern (17 bp):
CCCGAAACCCGAACCCG
Found at i:2581 original size:7 final size:6
Alignment explanation
Indices: 2557--2645 Score: 55
Period size: 6 Copynumber: 14.8 Consensus size: 6
2547 CCCGAACTCG
* *
2557 CCCGTA CCCGAA CCCGAA TCCCGAA CCTGAAAATA CCCGAA CCCGAGA
1 CCCGAA CCCGAA CCCGAA -CCCGAA CCCG---A-A CCCGAA CCCGA-A
*
2605 --C-AA CCCGAA CCCAAA CCCG-- CCCGAA CCCG-A CCCGAA CCCGA
1 CCCGAA CCCGAA CCCGAA CCCGAA CCCGAA CCCGAA CCCGAA CCCGA
2646 GATCAAAATA
Statistics
Matches: 66, Mismatches: 5, Indels: 24
0.69 0.05 0.25
Matches are distributed among these distances:
3 1 0.02
4 5 0.08
5 7 0.11
6 40 0.61
7 8 0.12
9 1 0.02
10 4 0.06
ACGTcount: A:0.33, C:0.47, G:0.16, T:0.04
Consensus pattern (6 bp):
CCCGAA
Found at i:2581 original size:13 final size:14
Alignment explanation
Indices: 2561--2616 Score: 51
Period size: 16 Copynumber: 3.8 Consensus size: 14
2551 AACTCGCCCG
2561 TACCCGAACCCGAA
1 TACCCGAACCCGAA
*
2575 T-CCCGAACCTGAAAA
1 TACCCGAACCCG--AA
2590 TACCCGAACCCGAGA
1 TACCCGAACCCGA-A
*
2605 CAACCCGAACCC
1 -TACCCGAACCC
2617 AAACCCGCCC
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
13 9 0.26
14 2 0.06
15 4 0.12
16 19 0.56
ACGTcount: A:0.36, C:0.43, G:0.14, T:0.07
Consensus pattern (14 bp):
TACCCGAACCCGAA
Found at i:2616 original size:22 final size:22
Alignment explanation
Indices: 2591--2647 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
2581 ACCTGAAAAT
2591 ACCCGAACCCGAGAC-AACCCG
1 ACCCGAACCCGAGACGAACCCG
* **
2612 AACCCAAACCCG-CCCGAACCCG
1 -ACCCGAACCCGAGACGAACCCG
2634 ACCCGAACCCGAGA
1 ACCCGAACCCGAGA
2648 TCAAAATAAT
Statistics
Matches: 27, Mismatches: 6, Indels: 4
0.73 0.16 0.11
Matches are distributed among these distances:
21 11 0.41
22 16 0.59
ACGTcount: A:0.33, C:0.49, G:0.18, T:0.00
Consensus pattern (22 bp):
ACCCGAACCCGAGACGAACCCG
Found at i:3410 original size:17 final size:16
Alignment explanation
Indices: 3388--3448 Score: 70
Period size: 17 Copynumber: 3.7 Consensus size: 16
3378 CGAAAGTGAA
3388 CCCGAACCCGACCTGGG
1 CCCGAACCCGACC-GGG
3405 CCCGAACCCGA-CGCGG
1 CCCGAACCCGACCG-GG
* *
3421 CCCGAGCCCGACCCGAG
1 CCCGAACCCGA-CCGGG
3438 CCCGAACCCGA
1 CCCGAACCCGA
3449 AAATACCCGA
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
15 1 0.03
16 13 0.34
17 22 0.58
18 2 0.05
ACGTcount: A:0.20, C:0.51, G:0.28, T:0.02
Consensus pattern (16 bp):
CCCGAACCCGACCGGG
Found at i:3469 original size:15 final size:15
Alignment explanation
Indices: 3438--3509 Score: 117
Period size: 15 Copynumber: 4.7 Consensus size: 15
3428 CCGACCCGAG
3438 CCCGAACCCGAAAATA
1 CCCGAACCCG-AAATA
3454 CCCGAACCCGAAATA
1 CCCGAACCCGAAATA
3469 CCCGAACCCGAAATTA
1 CCCGAACCCGAAA-TA
*
3485 CCCGAACCCGAAGTA
1 CCCGAACCCGAAATA
3500 CCCGAACCCG
1 CCCGAACCCG
3510 CCCAATTGCC
Statistics
Matches: 54, Mismatches: 1, Indels: 3
0.93 0.02 0.05
Matches are distributed among these distances:
15 30 0.56
16 24 0.44
ACGTcount: A:0.36, C:0.42, G:0.15, T:0.07
Consensus pattern (15 bp):
CCCGAACCCGAAATA
Found at i:3476 original size:31 final size:31
Alignment explanation
Indices: 3438--3509 Score: 126
Period size: 31 Copynumber: 2.3 Consensus size: 31
3428 CCGACCCGAG
3438 CCCGAACCCGAAAATACCCGAACCCGAAATA
1 CCCGAACCCGAAAATACCCGAACCCGAAATA
* *
3469 CCCGAACCCGAAATTACCCGAACCCGAAGTA
1 CCCGAACCCGAAAATACCCGAACCCGAAATA
3500 CCCGAACCCG
1 CCCGAACCCG
3510 CCCAATTGCC
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 39 1.00
ACGTcount: A:0.36, C:0.42, G:0.15, T:0.07
Consensus pattern (31 bp):
CCCGAACCCGAAAATACCCGAACCCGAAATA
Found at i:6357 original size:2 final size:2
Alignment explanation
Indices: 6350--6379 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
6340 TTATATTGTT
*
6350 TA TA TA TA TA TA AA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
6380 GTCTCTCGTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Done.