Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009344.1 Corchorus capsularis cultivar CVL-1 contig09365, 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: 30046
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:48 original size:34 final size:32
Alignment explanation
Indices: 1--86 Score: 113
Period size: 34 Copynumber: 2.6 Consensus size: 32
1 AGCCGCCTCAGTGGGGCGGCCTGCCCAATGGTGA
1 AGCCGCCTCAGTGGGGCGGCCTGCCC-ATGGT-A
35 AGCCGCC-CAAGTGGGGCGGCCTGCCCATGGTA
1 AGCCGCCTC-AGTGGGGCGGCCTGCCCATGGTA
*
67 AGCCGCCATC-TTGGGGCGGC
1 AGCCGCC-TCAGTGGGGCGGC
87 ACGGGTCATC
Statistics
Matches: 48, Mismatches: 1, Indels: 8
0.84 0.02 0.14
Matches are distributed among these distances:
32 17 0.35
33 6 0.12
34 25 0.52
ACGTcount: A:0.14, C:0.34, G:0.38, T:0.14
Consensus pattern (32 bp):
AGCCGCCTCAGTGGGGCGGCCTGCCCATGGTA
Found at i:86 original size:32 final size:34
Alignment explanation
Indices: 1--73 Score: 116
Period size: 34 Copynumber: 2.2 Consensus size: 34
1 AGCCGCCTC-AGTGGGGCGGCCTGCCCAATGGTGA
1 AGCCGCC-CAAGTGGGGCGGCCTGCCCAATGGTGA
35 AGCCGCCCAAGTGGGGCGGCCTGCCC-ATGGT-A
1 AGCCGCCCAAGTGGGGCGGCCTGCCCAATGGTGA
67 AGCCGCC
1 AGCCGCC
74 ATCTTGGGGC
Statistics
Matches: 38, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
32 8 0.21
33 6 0.16
34 24 0.63
ACGTcount: A:0.15, C:0.36, G:0.37, T:0.12
Consensus pattern (34 bp):
AGCCGCCCAAGTGGGGCGGCCTGCCCAATGGTGA
Found at i:1412 original size:38 final size:38
Alignment explanation
Indices: 1361--1437 Score: 154
Period size: 38 Copynumber: 2.0 Consensus size: 38
1351 ACACGTTGAC
1361 AAATCAGCATTTCTAACAGCTTCAAATTGTACCTTTAA
1 AAATCAGCATTTCTAACAGCTTCAAATTGTACCTTTAA
1399 AAATCAGCATTTCTAACAGCTTCAAATTGTACCTTTAA
1 AAATCAGCATTTCTAACAGCTTCAAATTGTACCTTTAA
1437 A
1 A
1438 GATGTCTTTC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.38, C:0.21, G:0.08, T:0.34
Consensus pattern (38 bp):
AAATCAGCATTTCTAACAGCTTCAAATTGTACCTTTAA
Found at i:14072 original size:18 final size:18
Alignment explanation
Indices: 14046--14103 Score: 80
Period size: 18 Copynumber: 3.2 Consensus size: 18
14036 GGTTCTCCTA
*
14046 CTCGTCGCAGCCCTAGTC
1 CTCGCCGCAGCCCTAGTC
**
14064 CTCGCCGCAGCTATAGTC
1 CTCGCCGCAGCCCTAGTC
*
14082 CTCGCCGCAGCCCTAGTT
1 CTCGCCGCAGCCCTAGTC
14100 CTCG
1 CTCG
14104 GAAAAGTCCT
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 34 1.00
ACGTcount: A:0.12, C:0.43, G:0.22, T:0.22
Consensus pattern (18 bp):
CTCGCCGCAGCCCTAGTC
Found at i:21687 original size:7 final size:7
Alignment explanation
Indices: 21671--21700 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
21661 CTTCAAATCC
21671 TTTT-TT
1 TTTTCTT
21677 TTTTCTT
1 TTTTCTT
21684 TTTTCTT
1 TTTTCTT
21691 TTTTCTT
1 TTTTCTT
21698 TTT
1 TTT
21701 AAATAGAAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 4 0.17
7 19 0.83
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (7 bp):
TTTTCTT
Found at i:26409 original size:24 final size:24
Alignment explanation
Indices: 26377--26427 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
26367 CCTGCCTTCC
*
26377 TTTTTAATTGTCCATTTTAATTAA
1 TTTTTAATTATCCATTTTAATTAA
*
26401 TTTTTAATTATCCGTTTTAATTAA
1 TTTTTAATTATCCATTTTAATTAA
26425 TTT
1 TTT
26428 ATTTGTTTAG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.27, C:0.08, G:0.04, T:0.61
Consensus pattern (24 bp):
TTTTTAATTATCCATTTTAATTAA
Found at i:26761 original size:40 final size:40
Alignment explanation
Indices: 26706--26781 Score: 125
Period size: 40 Copynumber: 1.9 Consensus size: 40
26696 AACTATGGGT
*
26706 TAAATCTGAACTTAATTTATTACCTTAATTATTAGGGGGC
1 TAAATCTGAACTTAATTTATTACCTTAAATATTAGGGGGC
* *
26746 TAAATCTGAATTTAATTTGTTACCTTAAATATTAGG
1 TAAATCTGAACTTAATTTATTACCTTAAATATTAGG
26782 AGGGTCAAGT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 33 1.00
ACGTcount: A:0.34, C:0.11, G:0.13, T:0.42
Consensus pattern (40 bp):
TAAATCTGAACTTAATTTATTACCTTAAATATTAGGGGGC
Found at i:28656 original size:18 final size:18
Alignment explanation
Indices: 28635--28675 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
28625 TTTGAAAAAA
28635 ATTTAATATATCTAATTT
1 ATTTAATATATCTAATTT
*
28653 ATTTAATATATTTAATTT
1 ATTTAATATATCTAATTT
28671 -TTTAA
1 ATTTAA
28676 ATTAAAATAG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 5 0.23
18 17 0.77
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (18 bp):
ATTTAATATATCTAATTT
Found at i:28659 original size:9 final size:9
Alignment explanation
Indices: 28635--28668 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
28625 TTTGAAAAAA
28635 ATTTAATAT
1 ATTTAATAT
* *
28644 ATCTAATTT
1 ATTTAATAT
28653 ATTTAATAT
1 ATTTAATAT
28662 ATTTAAT
1 ATTTAAT
28669 TTTTTAAATT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (9 bp):
ATTTAATAT
Done.