Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011613.1 Corchorus capsularis cultivar CVL-1 contig11634, 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: 20769
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Found at i:3375 original size:3 final size:3
Alignment explanation
Indices: 3360--3411 Score: 95
Period size: 3 Copynumber: 17.0 Consensus size: 3
3350 GTAAATATAT
3360 ATA ATA TATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
3406 ATA ATA
1 ATA ATA
3412 TATATTAAAA
Statistics
Matches: 48, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
3 45 0.94
4 3 0.06
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:4915 original size:13 final size:13
Alignment explanation
Indices: 4897--4926 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
4887 AAACCCAATT
4897 TAGATTTATTCAA
1 TAGATTTATTCAA
*
4910 TAGATTTATTGAA
1 TAGATTTATTCAA
4923 TAGA
1 TAGA
4927 AAGAATGAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.40, C:0.03, G:0.13, T:0.43
Consensus pattern (13 bp):
TAGATTTATTCAA
Found at i:4931 original size:68 final size:68
Alignment explanation
Indices: 4846--4972 Score: 220
Period size: 68 Copynumber: 1.9 Consensus size: 68
4836 AACCCAAAAT
*
4846 TTTATTGAATAGAAAGAATGAAACTAGTACCAACAACTTGA-AAACCCAATTTAGATTTATTCAA
1 TTTATTGAATAGAAAGAATGAAACTAGTACCAACAAC-TCACAAACCCAATTTAGATTTATTCAA
4910 TAGA
65 TAGA
*
4914 TTTATTGAATAGAAAGAATGAAACTAGTACCAGCAACTCACAAACCCAATTTAGATTTA
1 TTTATTGAATAGAAAGAATGAAACTAGTACCAACAACTCACAAACCCAATTTAGATTTA
4973 GCCGCACCTG
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
67 2 0.04
68 54 0.96
ACGTcount: A:0.45, C:0.15, G:0.12, T:0.28
Consensus pattern (68 bp):
TTTATTGAATAGAAAGAATGAAACTAGTACCAACAACTCACAAACCCAATTTAGATTTATTCAAT
AGA
Found at i:6023 original size:27 final size:26
Alignment explanation
Indices: 5993--6045 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
5983 TCCTGAATTG
* *
5993 ACACAACCCGATAACGTTATATCCTGA
1 ACACAA-CAGATAACGGTATATCCTGA
*
6020 ACACAAGAGATAACGGTATATCCTGA
1 ACACAACAGATAACGGTATATCCTGA
6046 GTTGCATTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
26 17 0.74
27 6 0.26
ACGTcount: A:0.40, C:0.25, G:0.15, T:0.21
Consensus pattern (26 bp):
ACACAACAGATAACGGTATATCCTGA
Found at i:8772 original size:21 final size:19
Alignment explanation
Indices: 8728--8778 Score: 59
Period size: 21 Copynumber: 2.6 Consensus size: 19
8718 ATATCAACTA
*
8728 TATT-TTTTTTTCTTGATT
1 TATTATTTTTTTCTTAATT
8746 TATTATTTTTTTCTCTAACTT
1 TATTATTTTTTTCT-TAA-TT
*
8767 TTTTATTTTTTT
1 TATTATTTTTTT
8779 ATCCATTTCT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
18 4 0.14
19 9 0.32
20 2 0.07
21 13 0.46
ACGTcount: A:0.14, C:0.08, G:0.02, T:0.76
Consensus pattern (19 bp):
TATTATTTTTTTCTTAATT
Found at i:11497 original size:16 final size:16
Alignment explanation
Indices: 11476--11509 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
11466 AATTAATCTT
11476 AGGGAGTTGGGAAGGG
1 AGGGAGTTGGGAAGGG
11492 AGGGAGTTGGGAAGGG
1 AGGGAGTTGGGAAGGG
11508 AG
1 AG
11510 AGAAGATAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.26, C:0.00, G:0.62, T:0.12
Consensus pattern (16 bp):
AGGGAGTTGGGAAGGG
Found at i:13549 original size:14 final size:14
Alignment explanation
Indices: 13530--13562 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
13520 ATGATTTGAT
13530 GAAAATGGTCTTTG
1 GAAAATGGTCTTTG
*
13544 GAAAATGGTTTTTG
1 GAAAATGGTCTTTG
13558 GAAAA
1 GAAAA
13563 CATCTGTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.36, C:0.03, G:0.27, T:0.33
Consensus pattern (14 bp):
GAAAATGGTCTTTG
Found at i:18737 original size:42 final size:43
Alignment explanation
Indices: 18690--18779 Score: 146
Period size: 45 Copynumber: 2.1 Consensus size: 43
18680 CATTACTTAA
*
18690 ATTCTA-CTCCATCTCTAGGTAATTCATCAAAATAAAACTAAT
1 ATTCTACCTCCATCTCTAGATAATTCATCAAAATAAAACTAAT
18732 ATTCTACTCCTCCATCTCTAGATAATTCATCAAAATAAAACTAAT
1 ATTCTA--CCTCCATCTCTAGATAATTCATCAAAATAAAACTAAT
18777 ATT
1 ATT
18780 AATTGTTGTT
Statistics
Matches: 44, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
42 6 0.14
45 38 0.86
ACGTcount: A:0.40, C:0.22, G:0.03, T:0.34
Consensus pattern (43 bp):
ATTCTACCTCCATCTCTAGATAATTCATCAAAATAAAACTAAT
Found at i:19763 original size:22 final size:22
Alignment explanation
Indices: 19695--19760 Score: 78
Period size: 23 Copynumber: 2.9 Consensus size: 22
19685 ATAATATGAT
* *
19695 TAATTATAAAAAAAACAAAACATA
1 TAATTATATATAAAAC-AAA-ATA
*
19719 TAATTATATATATAACAAAATA
1 TAATTATATATAAAACAAAATA
19741 TAATTATATTATAAAACAAA
1 TAATTATA-TATAAAACAAA
19761 TATTACATAT
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
22 11 0.30
23 13 0.35
24 13 0.35
ACGTcount: A:0.64, C:0.06, G:0.00, T:0.30
Consensus pattern (22 bp):
TAATTATATATAAAACAAAATA
Found at i:20159 original size:33 final size:33
Alignment explanation
Indices: 20113--20175 Score: 108
Period size: 33 Copynumber: 1.9 Consensus size: 33
20103 CTAAGATACT
*
20113 GAGTGTGTGTCATTATAAATTTTGGAGTGATCC
1 GAGTGTGTATCATTATAAATTTTGGAGTGATCC
*
20146 GAGTGTGTATCATTATAGATTTTGGAGTGA
1 GAGTGTGTATCATTATAAATTTTGGAGTGA
20176 CCACCCCACA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.25, C:0.06, G:0.29, T:0.40
Consensus pattern (33 bp):
GAGTGTGTATCATTATAAATTTTGGAGTGATCC
Done.