Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005460.1 Corchorus capsularis cultivar CVL-1 contig05478, 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: 10848
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.34
Found at i:2534 original size:12 final size:12
Alignment explanation
Indices: 2517--2542 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
2507 TATTCCTTTA
2517 TATATATATATG
1 TATATATATATG
2529 TATATATATATG
1 TATATATATATG
2541 TA
1 TA
2543 CTAAACGAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.50
Consensus pattern (12 bp):
TATATATATATG
Found at i:4611 original size:25 final size:24
Alignment explanation
Indices: 4564--4642 Score: 77
Period size: 25 Copynumber: 3.1 Consensus size: 24
4554 AAAAATATAT
*
4564 TAAATAAGTATAATATATATTAATAAA
1 TAAATAA-TA-AATATATTTTAA-AAA
4591 TAAATAATAAATATATTTTAAATAA
1 TAAATAATAAATATATTTTAAA-AA
* * * *
4616 TAAAAAATATATTTTTTTTAAAAA
1 TAAATAATAAATATATTTTAAAAA
4640 TAA
1 TAA
4643 TGAGTTAAAA
Statistics
Matches: 46, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
24 6 0.13
25 31 0.67
26 2 0.04
27 7 0.15
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (24 bp):
TAAATAATAAATATATTTTAAAAA
Found at i:4617 original size:21 final size:21
Alignment explanation
Indices: 4551--4630 Score: 76
Period size: 21 Copynumber: 3.8 Consensus size: 21
4541 AATTATTTTG
*
4551 ATAA-AAA-ATATATTAAATA
1 ATAATAAATATATTTTAAATA
*
4570 AGT-ATAATATATATTAATAAATAA
1 A-TAATAA-ATATATT-TTAAAT-A
4594 ATAATAAATATATTTTAAATA
1 ATAATAAATATATTTTAAATA
*
4615 ATAAAAAATATATTTT
1 ATAATAAATATATTTT
4631 TTTTAAAAAT
Statistics
Matches: 50, Mismatches: 4, Indels: 12
0.76 0.06 0.18
Matches are distributed among these distances:
19 2 0.04
20 3 0.06
21 17 0.34
22 9 0.18
23 13 0.26
24 6 0.12
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.39
Consensus pattern (21 bp):
ATAATAAATATATTTTAAATA
Found at i:5110 original size:22 final size:23
Alignment explanation
Indices: 5058--5110 Score: 58
Period size: 22 Copynumber: 2.3 Consensus size: 23
5048 CAATTATTTA
*
5058 AAATAAAATTTGAAAAGTAAAAT
1 AAATATAATTTGAAAAGTAAAAT
5081 ACAA-ATAATTT-AATAA-TAAAAT
1 A-AATATAATTTGAA-AAGTAAAAT
5103 AAATATAA
1 AAATATAA
5111 ATAAGTTTTG
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 2 0.08
22 13 0.50
23 9 0.35
24 2 0.08
ACGTcount: A:0.66, C:0.02, G:0.04, T:0.28
Consensus pattern (23 bp):
AAATATAATTTGAAAAGTAAAAT
Found at i:5134 original size:25 final size:25
Alignment explanation
Indices: 5106--5157 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
5096 ATAAAATAAA
5106 TATAAATAAGTTTTGATAAAGAAAT
1 TATAAATAAGTTTTGATAAAGAAAT
5131 TATAAATAAGTTTTGATAAAGAAAT
1 TATAAATAAGTTTTGATAAAGAAAT
5156 TA
1 TA
5158 GATATGATTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.12, T:0.37
Consensus pattern (25 bp):
TATAAATAAGTTTTGATAAAGAAAT
Found at i:7796 original size:149 final size:153
Alignment explanation
Indices: 7628--7910 Score: 457
Period size: 149 Copynumber: 1.9 Consensus size: 153
7618 AATAACCTTA
**
7628 TAAATTAAAATGTTAAAAATAAAATAATTATAAAAATATTGAATTTAATTAAATGAAAATAGAGT
1 TAAATTAAAATGGCAAAAATAAAATAATTATAAAAATATTGAATTTAATTAAATGAAAATAGAGT
* * * *
7693 TTTTA-TTAGAATCAAACTATATATTAAAA-ATTATAATATAT-C-AAGTTTTAATGAAAAATAG
66 TTTTAGATAAAATAAAACTATATATTAAAATATTATAATATATCCAAAGTTTTAACGAAAAATAG
7754 TAAACAGGTAAAAATAAACTTTT
131 TAAACAGGTAAAAATAAACTTTT
7777 TAAATTAAAATGGCAAAAATAAAATAATTATAAAAATATTGAATTTAATTAAATGAAAATAGAGT
1 TAAATTAAAATGGCAAAAATAAAATAATTATAAAAATATTGAATTTAATTAAATGAAAATAGAGT
* * *
7842 TTTTAGATAAAATAAAACTATATATTAAAATTTTTTAATATATCCAAATTTTTAACGAAAAATAG
66 TTTTAGATAAAATAAAACTATATATTAAAATATTATAATATATCCAAAGTTTTAACGAAAAATAG
7907 TAAA
131 TAAA
7911 ATAATAAAAA
Statistics
Matches: 121, Mismatches: 9, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
149 68 0.56
150 21 0.17
151 10 0.08
152 1 0.01
153 21 0.17
ACGTcount: A:0.54, C:0.04, G:0.07, T:0.35
Consensus pattern (153 bp):
TAAATTAAAATGGCAAAAATAAAATAATTATAAAAATATTGAATTTAATTAAATGAAAATAGAGT
TTTTAGATAAAATAAAACTATATATTAAAATATTATAATATATCCAAAGTTTTAACGAAAAATAG
TAAACAGGTAAAAATAAACTTTT
Found at i:8939 original size:23 final size:23
Alignment explanation
Indices: 8889--8939 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
8879 AAGACAATAG
8889 AAAAAGCTCTCACAAAGGAGATC
1 AAAAAGCTCTCACAAAGGAGATC
* * * *
8912 TAAAAGCTCTTACTAAGGAGTTC
1 AAAAAGCTCTCACAAAGGAGATC
8935 AAAAA
1 AAAAA
8940 AAAAAATTTG
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.47, C:0.18, G:0.16, T:0.20
Consensus pattern (23 bp):
AAAAAGCTCTCACAAAGGAGATC
Done.