Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009283.1 Corchorus capsularis cultivar CVL-1 contig09304, 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: 13040
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.33
Found at i:3750 original size:17 final size:17
Alignment explanation
Indices: 3728--3764 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
3718 TGTATATTCA
*
3728 CAAGGCAATGCCATTTT
1 CAAGGCAATACCATTTT
3745 CAAGGCAATACCATTTT
1 CAAGGCAATACCATTTT
3762 CAA
1 CAA
3765 AAAGAAAAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.35, C:0.24, G:0.14, T:0.27
Consensus pattern (17 bp):
CAAGGCAATACCATTTT
Found at i:9286 original size:21 final size:21
Alignment explanation
Indices: 9261--9814 Score: 499
Period size: 21 Copynumber: 26.4 Consensus size: 21
9251 GTGTGGTTGA
*
9261 ACTATCAAAATTTGGGATTTG
1 ACTATCAAAATTTGGGGTTTG
* * *
9282 GCTATCAAATTTTGGGGTTTA
1 ACTATCAAAATTTGGGGTTTG
*
9303 ACTATCAAATTTTGGGGTTTG
1 ACTATCAAAATTTGGGGTTTG
*
9324 TCTATCAAAATTTGGGGTTTG
1 ACTATCAAAATTTGGGGTTTG
*
9345 ACTATCAAAATTTGGGATTTG
1 ACTATCAAAATTTGGGGTTTG
* *
9366 TCTATCAAACTTTGGGGTTTG
1 ACTATCAAAATTTGGGGTTTG
* * *
9387 ACTAT-ACAATTTTTGGATTTG
1 ACTATCA-AAATTTGGGGTTTG
* *
9408 ACTTTCAAAATTCGGGGTTTG
1 ACTATCAAAATTTGGGGTTTG
* * *
9429 ACTACCAAACTTTGTGG-TTG
1 ACTATCAAAATTTGGGGTTTG
*
9449 AACTATCAAAATTTGGGATTTG
1 -ACTATCAAAATTTGGGGTTTG
* *
9471 GCTATCAAACTTTGGGGTTTG
1 ACTATCAAAATTTGGGGTTTG
9492 ACTATCAAAATTTGGGGTTTG
1 ACTATCAAAATTTGGGGTTTG
* * *
9513 ACTACCAAATTTTAGGG-TTG
1 ACTATCAAAATTTGGGGTTTG
*
9533 AACTATCAAAATTTGGGATTTG
1 -ACTATCAAAATTTGGGGTTTG
** *
9555 ACTATCAAACCTTGGGGTTTT
1 ACTATCAAAATTTGGGGTTTG
9576 ACTAT-AAACATTTGGGGTTTG
1 ACTATCAAA-ATTTGGGGTTTG
* **
9597 ACTATCAAACTTTGATGTTTG
1 ACTATCAAAATTTGGGGTTTG
* *
9618 AGTATCAAAATTTGGGATTTG
1 ACTATCAAAATTTGGGGTTTG
*
9639 ACTATCAAAACTT-GGGTTTG
1 ACTATCAAAATTTGGGGTTTG
* *
9659 ACTATCAAACTTTGGGGTTTA
1 ACTATCAAAATTTGGGGTTTG
* * * **
9680 ACTACCAAACTTTGTGGTTAA
1 ACTATCAAAATTTGGGGTTTG
* *
9701 ACTATCAAAAATTGGGATTTG
1 ACTATCAAAATTTGGGGTTTG
* * * * *
9722 ATTATTAAACTTTGTGATTTG
1 ACTATCAAAATTTGGGGTTTG
* **
9743 AATAT-AAAATTTTGGACTTTG
1 ACTATCAAAA-TTTGGGGTTTG
* * * *
9764 CCTATCAAACTCTGGAGTTTG
1 ACTATCAAAATTTGGGGTTTG
* * * *
9785 ACTATCAGACTTCGGAGTTTG
1 ACTATCAAAATTTGGGGTTTG
9806 ACTATCAAA
1 ACTATCAAA
9815 GTTTTGAGCT
Statistics
Matches: 428, Mismatches: 94, Indels: 22
0.79 0.17 0.04
Matches are distributed among these distances:
20 30 0.07
21 385 0.90
22 13 0.03
ACGTcount: A:0.29, C:0.12, G:0.20, T:0.39
Consensus pattern (21 bp):
ACTATCAAAATTTGGGGTTTG
Found at i:9981 original size:53 final size:53
Alignment explanation
Indices: 9895--10031 Score: 193
Period size: 53 Copynumber: 2.6 Consensus size: 53
9885 AAAGTATTAA
* * * *
9895 ATCATTGTACATCCATGGTCAAACCCCACAATTCAATAGTCAAATCACAAAAC
1 ATCATTGTACATGCATGGTCAAACCCAAAAATTCAATAGTCAAACCACAAAAC
* *
9948 ATCATTGTACATGCATGGTTAAACCCAAAAATTCAATAGTCAAACCACAAAAT
1 ATCATTGTACATGCATGGTCAAACCCAAAAATTCAATAGTCAAACCACAAAAC
* *
10001 ATCATTGTACATGTATAGTCAAACTCCAAAA
1 ATCATTGTACATGCATGGTCAAAC-CCAAAA
10032 GACGATGGTC
Statistics
Matches: 74, Mismatches: 9, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
53 68 0.92
54 6 0.08
ACGTcount: A:0.43, C:0.23, G:0.09, T:0.25
Consensus pattern (53 bp):
ATCATTGTACATGCATGGTCAAACCCAAAAATTCAATAGTCAAACCACAAAAC
Found at i:10331 original size:7 final size:7
Alignment explanation
Indices: 10319--10351 Score: 50
Period size: 7 Copynumber: 4.7 Consensus size: 7
10309 TAAGGTATTA
10319 GTTTGAG
1 GTTTGAG
10326 GTTTGAG
1 GTTTGAG
10333 GTTTGAAG
1 GTTTG-AG
10341 G-TTGAG
1 GTTTGAG
10347 GTTTG
1 GTTTG
10352 TACATAAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
6 3 0.12
7 18 0.75
8 3 0.12
ACGTcount: A:0.15, C:0.00, G:0.42, T:0.42
Consensus pattern (7 bp):
GTTTGAG
Found at i:10511 original size:35 final size:36
Alignment explanation
Indices: 10451--10522 Score: 110
Period size: 35 Copynumber: 2.0 Consensus size: 36
10441 TTTTAAATTG
* *
10451 TAATTGTCTAACTAGTATTCTCATGTTTAGTTGTTT
1 TAATTGTCTAACTAATATTATCATGTTTAGTTGTTT
*
10487 TAATTTTCT-ACTAATATTATCATGTTTAGTTGTTT
1 TAATTGTCTAACTAATATTATCATGTTTAGTTGTTT
10522 T
1 T
10523 TGTAATTTAT
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
35 25 0.76
36 8 0.24
ACGTcount: A:0.24, C:0.10, G:0.11, T:0.56
Consensus pattern (36 bp):
TAATTGTCTAACTAATATTATCATGTTTAGTTGTTT
Found at i:10696 original size:16 final size:16
Alignment explanation
Indices: 10660--10733 Score: 87
Period size: 16 Copynumber: 4.6 Consensus size: 16
10650 TTTTATTATT
*
10660 AATGACCCGTAACCC-
1 AATGACCCGAAACCCG
*
10675 AGATGACCCGAAACCTG
1 A-ATGACCCGAAACCCG
*
10692 AATGACCCGAGACCCG
1 AATGACCCGAAACCCG
*
10708 TATGACCCGAAACCCG
1 AATGACCCGAAACCCG
*
10724 AATAACCCGA
1 AATGACCCGA
10734 GAAGTTAACT
Statistics
Matches: 49, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
15 1 0.02
16 47 0.96
17 1 0.02
ACGTcount: A:0.35, C:0.35, G:0.19, T:0.11
Consensus pattern (16 bp):
AATGACCCGAAACCCG
Found at i:10713 original size:32 final size:32
Alignment explanation
Indices: 10660--10735 Score: 102
Period size: 32 Copynumber: 2.4 Consensus size: 32
10650 TTTTATTATT
*
10660 AATGACCCGTA-ACCCAGATGACCCGAAACCTG
1 AATGACCCG-AGACCCAGATGACCCGAAACCCG
10692 AATGACCCGAGACCC-GTATGACCCGAAACCCG
1 AATGACCCGAGACCCAG-ATGACCCGAAACCCG
*
10724 AATAACCCGAGA
1 AATGACCCGAGA
10736 AGTTAACTCG
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
31 2 0.05
32 38 0.95
ACGTcount: A:0.36, C:0.34, G:0.20, T:0.11
Consensus pattern (32 bp):
AATGACCCGAGACCCAGATGACCCGAAACCCG
Found at i:11315 original size:42 final size:41
Alignment explanation
Indices: 11251--11331 Score: 126
Period size: 42 Copynumber: 2.0 Consensus size: 41
11241 TGTTGACACA
*
11251 TACCCCACCTGAGAATTAATTATGTATTTAATATTCAAAACC
1 TACCCCACCTGAGAATCAATTATGTATTT-ATATTCAAAACC
* *
11293 TACCTCACCTGATAATCAATTATGTATTTATATTCAAAA
1 TACCCCACCTGAGAATCAATTATGTATTTATATTCAAAA
11332 TTAATATCTA
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
41 10 0.28
42 26 0.72
ACGTcount: A:0.38, C:0.20, G:0.06, T:0.36
Consensus pattern (41 bp):
TACCCCACCTGAGAATCAATTATGTATTTATATTCAAAACC
Found at i:11646 original size:16 final size:16
Alignment explanation
Indices: 11562--11648 Score: 79
Period size: 16 Copynumber: 5.6 Consensus size: 16
11552 CCCAACCCGA
* *
11562 GACCCGGAACCCGTAT
1 GACCCGAAACCCGAAT
*
11578 GACCCGAGACCCGAAT
1 GACCCGAAACCCGAAT
**
11594 GACCCGAAA-CCTTAT
1 GACCCGAAACCCGAAT
* *
11609 AACCCG-AACCCAAAT
1 GACCCGAAACCCGAAT
*
11624 TACCCGAAACCCGAAT
1 GACCCGAAACCCGAAT
*
11640 GATCCGAAA
1 GACCCGAAA
11649 AAGCTGTCTG
Statistics
Matches: 56, Mismatches: 13, Indels: 4
0.77 0.18 0.05
Matches are distributed among these distances:
14 2 0.04
15 18 0.32
16 36 0.64
ACGTcount: A:0.36, C:0.36, G:0.17, T:0.11
Consensus pattern (16 bp):
GACCCGAAACCCGAAT
Found at i:12834 original size:21 final size:21
Alignment explanation
Indices: 12808--12847 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
12798 TTGACAATTT
12808 TTCTCTCTCCACATTTACAAC
1 TTCTCTCTCCACATTTACAAC
*
12829 TTCTCTCTCCAGATTTACA
1 TTCTCTCTCCACATTTACA
12848 TGTAACCGGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.23, C:0.35, G:0.03, T:0.40
Consensus pattern (21 bp):
TTCTCTCTCCACATTTACAAC
Done.