Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007243.1 Corchorus capsularis cultivar CVL-1 contig07264, 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: 18011
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:5502 original size:31 final size:32
Alignment explanation
Indices: 5457--5518 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 32
5447 GCAATTTTTG
* * *
5457 AGAGCAAGGCCGATTGGAGGAG-AAGTCGACT
1 AGAGCAAAGCCGATTGAAGAAGCAAGTCGACT
*
5488 AGAGCAAAGTCGATTGAAGAAGCAAGTCGAC
1 AGAGCAAAGCCGATTGAAGAAGCAAGTCGAC
5519 AAGGAAGTCG
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
31 18 0.69
32 8 0.31
ACGTcount: A:0.37, C:0.16, G:0.34, T:0.13
Consensus pattern (32 bp):
AGAGCAAAGCCGATTGAAGAAGCAAGTCGACT
Found at i:6604 original size:29 final size:29
Alignment explanation
Indices: 6547--6605 Score: 68
Period size: 29 Copynumber: 2.0 Consensus size: 29
6537 AGTTATTTAG
* *
6547 TTTATGCTTTATCTTTAATTTTCCTTTAA
1 TTTATGCTTTATCTTTAAGTTTCCATTAA
6576 TTTATGTCTTTAT-TTTCAAGTTT-CATTAA
1 TTTATG-CTTTATCTTT-AAGTTTCCATTAA
6605 T
1 T
6606 AAACTGTTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
29 15 0.58
30 11 0.42
ACGTcount: A:0.22, C:0.12, G:0.05, T:0.61
Consensus pattern (29 bp):
TTTATGCTTTATCTTTAAGTTTCCATTAA
Found at i:9703 original size:135 final size:133
Alignment explanation
Indices: 9458--9718 Score: 432
Period size: 135 Copynumber: 1.9 Consensus size: 133
9448 TCTTTAAATC
** * * *
9458 CTCTTTATTAATTTGTTTTGTTTGAGAAAAGGAAGTGTCGATCTCTCTGTGGGTTCGACCCCTAC
1 CTCTTTATTAATTTGTTTTGCCTAAGAAAAGGAAGTGCCAATCTCTCTGTGGGTTCGACCCCTAC
9523 TTGCCCTAGCTAGTTTAGTTAGTAATTGTTGGGATAATTACTTTTATGATTGCTGACGACCGATC
66 TTGCCCTAGCTAGTTTAGTTAGTAATTGTTGGGATAATTACTTTTATGATTGCTGACGACCGATC
9588 ATT
131 ATT
*
9591 CTCTTTATTATTTTGTTTTGACCTAAGAAAAAGGAAGTGCCAATCTCTCTGTGGGTTCGACCCCT
1 CTCTTTATTAATTTGTTTTG-CCTAAG-AAAAGGAAGTGCCAATCTCTCTGTGGGTTCGACCCCT
* *
9656 ACTTGCCCTAGCTAGTTTAGTTAGTAATTGTTGGGATATTTATTTTTATGATTGCTGACGACC
64 ACTTGCCCTAGCTAGTTTAGTTAGTAATTGTTGGGATAATTACTTTTATGATTGCTGACGACC
9719 TTTCAGTGGC
Statistics
Matches: 118, Mismatches: 8, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
133 19 0.16
134 3 0.03
135 96 0.81
ACGTcount: A:0.22, C:0.17, G:0.20, T:0.40
Consensus pattern (133 bp):
CTCTTTATTAATTTGTTTTGCCTAAGAAAAGGAAGTGCCAATCTCTCTGTGGGTTCGACCCCTAC
TTGCCCTAGCTAGTTTAGTTAGTAATTGTTGGGATAATTACTTTTATGATTGCTGACGACCGATC
ATT
Found at i:10347 original size:15 final size:16
Alignment explanation
Indices: 10315--10348 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
10305 AAGAAGAATT
*
10315 TAAAATTAAATCTAAC
1 TAAAAGTAAATCTAAC
10331 TAAAAGTAAAT-TAAC
1 TAAAAGTAAATCTAAC
10346 TAA
1 TAA
10349 GAGAGCAATC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.59, C:0.09, G:0.03, T:0.29
Consensus pattern (16 bp):
TAAAAGTAAATCTAAC
Found at i:11706 original size:20 final size:21
Alignment explanation
Indices: 11668--11706 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
11658 TAGAAAATAA
*
11668 GGTAAAAATGCATATAAAAGT
1 GGTAAAAATGCATAGAAAAGT
*
11689 GGTAAAAA-GTATAGAAAA
1 GGTAAAAATGCATAGAAAA
11707 ATAGCCATAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 8 0.50
21 8 0.50
ACGTcount: A:0.56, C:0.03, G:0.21, T:0.21
Consensus pattern (21 bp):
GGTAAAAATGCATAGAAAAGT
Found at i:11915 original size:12 final size:14
Alignment explanation
Indices: 11887--11919 Score: 52
Period size: 12 Copynumber: 2.5 Consensus size: 14
11877 AGCAAAGAAC
11887 ATCAATAATACTTA
1 ATCAATAATACTTA
11901 ATCAA-AATA-TTA
1 ATCAATAATACTTA
11913 ATCAATA
1 ATCAATA
11920 GCAAGCATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 8 0.44
13 5 0.28
14 5 0.28
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (14 bp):
ATCAATAATACTTA
Found at i:12894 original size:6 final size:6
Alignment explanation
Indices: 12883--12909 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
12873 AAAGCAAAGC
12883 AAATCT AAATCT AAATCT AAATCT AAA
1 AAATCT AAATCT AAATCT AAATCT AAA
12910 GTAGATTAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.56, C:0.15, G:0.00, T:0.30
Consensus pattern (6 bp):
AAATCT
Found at i:12930 original size:13 final size:13
Alignment explanation
Indices: 12914--12940 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
12904 TCTAAAGTAG
12914 ATTAATAAAGCAA
1 ATTAATAAAGCAA
12927 ATTAATAAAGCAA
1 ATTAATAAAGCAA
12940 A
1 A
12941 CAATAATTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.63, C:0.07, G:0.07, T:0.22
Consensus pattern (13 bp):
ATTAATAAAGCAA
Done.