Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008709.1 Corchorus capsularis cultivar CVL-1 contig08730, 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: 29460
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.35
Found at i:1628 original size:28 final size:29
Alignment explanation
Indices: 1588--1645 Score: 109
Period size: 28 Copynumber: 2.0 Consensus size: 29
1578 AATACTGTGT
1588 TCATTGACTTATCCAAG-AAAAAAAATAC
1 TCATTGACTTATCCAAGAAAAAAAAATAC
1616 TCATTGACTTATCCAAGAAAAAAAAATAC
1 TCATTGACTTATCCAAGAAAAAAAAATAC
1645 T
1 T
1646 GTGTTCATTG
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
28 17 0.59
29 12 0.41
ACGTcount: A:0.50, C:0.17, G:0.07, T:0.26
Consensus pattern (29 bp):
TCATTGACTTATCCAAGAAAAAAAAATAC
Found at i:5631 original size:6 final size:6
Alignment explanation
Indices: 5620--5644 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
5610 ACAAAGTAAC
5620 TTGAAA TTGAAA TTGAAA TTGAAA T
1 TTGAAA TTGAAA TTGAAA TTGAAA T
5645 GAACATATGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.16, T:0.36
Consensus pattern (6 bp):
TTGAAA
Found at i:8314 original size:32 final size:31
Alignment explanation
Indices: 8249--8354 Score: 131
Period size: 32 Copynumber: 3.4 Consensus size: 31
8239 CGAGCTTAAG
* *
8249 TCGGGTTCGGGTTAAATTTAGTCGGGTTGAT
1 TCGGGTTCGGGTTAAATTTGGTCAGGTTGAT
*
8280 TCGGATTCGGGTTAAATTTGGATCAGGTTGAT
1 TCGGGTTCGGGTTAAATTTGG-TCAGGTTGAT
* * * *
8312 TCGGGTTTGGGTCAATTTTGGGTCAGGTTAAT
1 TCGGGTTCGGGTTAAATTT-GGTCAGGTTGAT
8344 TCGGGTTCGGG
1 TCGGGTTCGGG
8355 CTCGGATTGG
Statistics
Matches: 64, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
31 19 0.30
32 43 0.67
33 2 0.03
ACGTcount: A:0.16, C:0.10, G:0.36, T:0.38
Consensus pattern (31 bp):
TCGGGTTCGGGTTAAATTTGGTCAGGTTGAT
Found at i:8555 original size:21 final size:22
Alignment explanation
Indices: 8531--8571 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
8521 TAAATATTAG
8531 TATT-GAATTCAGGTTTTTTCA
1 TATTCGAATTCAGGTTTTTTCA
* *
8552 TATTCGGATTCGGGTTTTTT
1 TATTCGAATTCAGGTTTTTT
8572 TGGGTTCGGG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 4 0.24
22 13 0.76
ACGTcount: A:0.17, C:0.10, G:0.20, T:0.54
Consensus pattern (22 bp):
TATTCGAATTCAGGTTTTTTCA
Found at i:8607 original size:15 final size:16
Alignment explanation
Indices: 8576--8626 Score: 61
Period size: 15 Copynumber: 3.2 Consensus size: 16
8566 TTTTTTTGGG
*
8576 TTCGGGTTTCAGATTTT
1 TTCGGGTTT-TGATTTT
8593 TT-GGGTTTTGATTTT
1 TTCGGGTTTTGATTTT
*
8608 TTCGGG-TTTGAGTTT
1 TTCGGGTTTTGATTTT
8623 TTCG
1 TTCG
8627 AGTTCGGGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
15 20 0.65
16 9 0.29
17 2 0.06
ACGTcount: A:0.08, C:0.08, G:0.27, T:0.57
Consensus pattern (16 bp):
TTCGGGTTTTGATTTT
Found at i:8825 original size:35 final size:35
Alignment explanation
Indices: 8779--8845 Score: 109
Period size: 35 Copynumber: 1.9 Consensus size: 35
8769 AGTCACATGA
8779 ACAACCAATAACTTTAT-TGCCAACAAAAAAAAAGG
1 ACAACCAATAACTTTATGTGCCAA-AAAAAAAAAGG
*
8814 ACAACCAATAACTTTTTGTGCCAAAAAAAAAA
1 ACAACCAATAACTTTATGTGCCAAAAAAAAAA
8846 CAGCCAATAA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
35 24 0.80
36 6 0.20
ACGTcount: A:0.54, C:0.19, G:0.07, T:0.19
Consensus pattern (35 bp):
ACAACCAATAACTTTATGTGCCAAAAAAAAAAAGG
Found at i:15354 original size:25 final size:25
Alignment explanation
Indices: 15320--15370 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
15310 ATATCAATGG
15320 TTGGAATAAAAAAGGTGTAAAAATC
1 TTGGAATAAAAAAGGTGTAAAAATC
*
15345 TTGGAATAAAAAAGGTGTGAAAATC
1 TTGGAATAAAAAAGGTGTAAAAATC
15370 T
1 T
15371 ATCACGAGGA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.49, C:0.04, G:0.22, T:0.25
Consensus pattern (25 bp):
TTGGAATAAAAAAGGTGTAAAAATC
Found at i:27912 original size:11 final size:11
Alignment explanation
Indices: 27886--27920 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
27876 TATTGATCAT
*
27886 ATATATATATAT
1 ATATA-ATATAA
27898 ATATAATATAA
1 ATATAATATAA
27909 ATATAATATAA
1 ATATAATATAA
27920 A
1 A
27921 GTTTGGACCA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 17 0.77
12 5 0.23
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (11 bp):
ATATAATATAA
Done.