Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008318.1 Corchorus capsularis cultivar CVL-1 contig08339, 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: 31034
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Found at i:3217 original size:22 final size:22
Alignment explanation
Indices: 3187--3228 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
3177 CATGAGAAAC
* *
3187 CAAGCCAAGAAAATGGGTGTTA
1 CAAGACAAGAAAAAGGGTGTTA
3209 CAAGACAAGAAAAAGGGTGT
1 CAAGACAAGAAAAAGGGTGT
3229 CTGAGTTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.45, C:0.12, G:0.29, T:0.14
Consensus pattern (22 bp):
CAAGACAAGAAAAAGGGTGTTA
Found at i:3476 original size:13 final size:13
Alignment explanation
Indices: 3432--3494 Score: 54
Period size: 15 Copynumber: 4.5 Consensus size: 13
3422 TTTTATGCAT
**
3432 TTAATATATTAAA
1 TTAATATAGAAAA
*
3445 TTAATAATGAGAATTA
1 TTAAT-AT-AGAA-AA
3461 TTAATATAGAAAA
1 TTAATATAGAAAA
3474 TTAATTTATAGAAAA
1 TTAA--TATAGAAAA
3489 TTAATA
1 TTAATA
3495 ATGAAAATAC
Statistics
Matches: 41, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
13 12 0.29
14 6 0.15
15 17 0.41
16 6 0.15
ACGTcount: A:0.54, C:0.00, G:0.06, T:0.40
Consensus pattern (13 bp):
TTAATATAGAAAA
Found at i:3486 original size:29 final size:28
Alignment explanation
Indices: 3432--3502 Score: 65
Period size: 29 Copynumber: 2.5 Consensus size: 28
3422 TTTTATGCAT
** *
3432 TTAATATATTAAATTAATAATGAGAATTA
1 TTAATATAGAAAATTAATAATGAGAA-AA
*
3461 TTAATATAGAAAATTAATTTAT-AGAAAA
1 TTAATATAGAAAATTAA-TAATGAGAAAA
3489 TTAATA-ATGAAAAT
1 TTAATATA-GAAAAT
3503 ACCGTTTCTA
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
27 1 0.03
28 13 0.36
29 19 0.53
30 3 0.08
ACGTcount: A:0.55, C:0.00, G:0.07, T:0.38
Consensus pattern (28 bp):
TTAATATAGAAAATTAATAATGAGAAAA
Found at i:3502 original size:13 final size:14
Alignment explanation
Indices: 3442--3502 Score: 63
Period size: 15 Copynumber: 4.3 Consensus size: 14
3432 TTAATATATT
3442 AAATTAATAATGAGA
1 AAATTAATAAT-AGA
*
3457 ATTATTAAT-ATAGA
1 A-AATTAATAATAGA
*
3471 AAATTAATTTATAGA
1 AAATTAA-TAATAGA
3486 AAATTAATAAT-GA
1 AAATTAATAATAGA
3499 AAAT
1 AAAT
3503 ACCGTTTCTA
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
13 11 0.28
14 8 0.20
15 15 0.38
16 6 0.15
ACGTcount: A:0.57, C:0.00, G:0.08, T:0.34
Consensus pattern (14 bp):
AAATTAATAATAGA
Found at i:3909 original size:20 final size:20
Alignment explanation
Indices: 3884--3924 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
3874 AAAGAGGGAT
3884 AATAGGATTGGAAAGCAACA
1 AATAGGATTGGAAAGCAACA
*
3904 AATAGGTTTGGAAAGCAACA
1 AATAGGATTGGAAAGCAACA
3924 A
1 A
3925 GGAATTAGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.49, C:0.10, G:0.24, T:0.17
Consensus pattern (20 bp):
AATAGGATTGGAAAGCAACA
Found at i:4277 original size:29 final size:30
Alignment explanation
Indices: 4244--4303 Score: 104
Period size: 29 Copynumber: 2.0 Consensus size: 30
4234 TTAATTCAAA
*
4244 AAAGTAACGTGTTAGTGGTGTATATA-TAT
1 AAAGTAACGTGTTAGTGGTATATATACTAT
4273 AAAGTAACGTGTTAGTGGTATATATACTAT
1 AAAGTAACGTGTTAGTGGTATATATACTAT
4303 A
1 A
4304 TATTATTTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
29 25 0.86
30 4 0.14
ACGTcount: A:0.37, C:0.05, G:0.22, T:0.37
Consensus pattern (30 bp):
AAAGTAACGTGTTAGTGGTATATATACTAT
Found at i:5295 original size:13 final size:13
Alignment explanation
Indices: 5277--5305 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
5267 TATAGATATA
5277 TATCTATACTAAT
1 TATCTATACTAAT
5290 TATCTATACTAAT
1 TATCTATACTAAT
5303 TAT
1 TAT
5306 AATGTCAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.38, C:0.14, G:0.00, T:0.48
Consensus pattern (13 bp):
TATCTATACTAAT
Found at i:5447 original size:13 final size:13
Alignment explanation
Indices: 5429--5459 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
5419 CATTATAAGA
5429 TAAATATAATATT
1 TAAATATAATATT
5442 TAAATATAATATT
1 TAAATATAATATT
5455 TAAAT
1 TAAAT
5460 TTATTTATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (13 bp):
TAAATATAATATT
Found at i:8723 original size:36 final size:37
Alignment explanation
Indices: 8676--8749 Score: 132
Period size: 37 Copynumber: 2.0 Consensus size: 37
8666 CATACAGAAA
*
8676 CTACATAAACTATCTT-ATCTTTCTCATTCCATATTT
1 CTACAGAAACTATCTTCATCTTTCTCATTCCATATTT
8712 CTACAGAAACTATCTTCATCTTTCTCATTCCATATTT
1 CTACAGAAACTATCTTCATCTTTCTCATTCCATATTT
8749 C
1 C
8750 GTGAAGACAG
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
36 15 0.42
37 21 0.58
ACGTcount: A:0.27, C:0.27, G:0.01, T:0.45
Consensus pattern (37 bp):
CTACAGAAACTATCTTCATCTTTCTCATTCCATATTT
Found at i:14538 original size:27 final size:27
Alignment explanation
Indices: 14508--14562 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
14498 GTTCACACAC
14508 ATTAGTGTATTTTAATGGATCATATTA
1 ATTAGTGTATTTTAATGGATCATATTA
14535 ATTAGTGTATTTTAATGGATCATATTA
1 ATTAGTGTATTTTAATGGATCATATTA
14562 A
1 A
14563 GTGTCAAGGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.35, C:0.04, G:0.15, T:0.47
Consensus pattern (27 bp):
ATTAGTGTATTTTAATGGATCATATTA
Found at i:16720 original size:60 final size:60
Alignment explanation
Indices: 16627--16806 Score: 308
Period size: 60 Copynumber: 3.0 Consensus size: 60
16617 TTCCATGGTT
16627 TGGTGTCAATCCCAAAAGGGATTCAGATTCGACTCTTGCATCCACAAGCTCTCTCGTGGA
1 TGGTGTCAATCCCAAAAGGGATTCAGATTCGACTCTTGCATCCACAAGCTCTCTCGTGGA
*
16687 TGGTGTCAATCCCAGAAGGGATTCAGATTCGACTCTTGCATCCACAAGCTCTCTCGTGGA
1 TGGTGTCAATCCCAAAAGGGATTCAGATTCGACTCTTGCATCCACAAGCTCTCTCGTGGA
** *
16747 TGGTGTCAATATCAAAAGGGATTCAGAATT-GACTCTTGCATCCACAAGCTCTCTCTTGGA
1 TGGTGTCAATCCCAAAAGGGATTCAG-ATTCGACTCTTGCATCCACAAGCTCTCTCGTGGA
16807 GTACCATAAA
Statistics
Matches: 114, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
60 111 0.97
61 3 0.03
ACGTcount: A:0.26, C:0.25, G:0.22, T:0.28
Consensus pattern (60 bp):
TGGTGTCAATCCCAAAAGGGATTCAGATTCGACTCTTGCATCCACAAGCTCTCTCGTGGA
Found at i:17737 original size:12 final size:12
Alignment explanation
Indices: 17720--17744 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
17710 ATCTCTTGTC
17720 CTTCCAGTCATT
1 CTTCCAGTCATT
17732 CTTCCAGTCATT
1 CTTCCAGTCATT
17744 C
1 C
17745 ATGTTGACAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.36, G:0.08, T:0.40
Consensus pattern (12 bp):
CTTCCAGTCATT
Done.