Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01001285.1 Corchorus capsularis cultivar CVL-1 contig01285, 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: 8236
ACGTcount: A:0.30, C:0.14, G:0.19, T:0.36
Found at i:513 original size:39 final size:41
Alignment explanation
Indices: 424--518 Score: 126
Period size: 39 Copynumber: 2.4 Consensus size: 41
414 CAGGAGTACT
424 AAACTAAATAGCTTCTTAATGTATATAAAAAAAGAAAATAA
1 AAACTAAATAGCTTCTTAATGTATATAAAAAAAGAAAATAA
**
465 AAACTAAATAGCTTCTTGTTG-A-A-AAAAATAA-ATAAATAA
1 AAACTAAATAGCTTCTTAATGTATATAAAAA-AAGA-AAATAA
504 AAACTAAATAGCTTC
1 AAACTAAATAGCTTC
519 AGAATTGAAA
Statistics
Matches: 50, Mismatches: 2, Indels: 6
0.86 0.03 0.10
Matches are distributed among these distances:
38 6 0.12
39 24 0.48
40 1 0.02
41 19 0.38
ACGTcount: A:0.56, C:0.09, G:0.07, T:0.27
Consensus pattern (41 bp):
AAACTAAATAGCTTCTTAATGTATATAAAAAAAGAAAATAA
Found at i:907 original size:17 final size:17
Alignment explanation
Indices: 863--913 Score: 59
Period size: 17 Copynumber: 2.9 Consensus size: 17
853 ATATATATAT
863 ATTAATTATAATTATAATA
1 ATTAATTA-AATTA-AATA
* *
882 A-TAAATAAATTAATTA
1 ATTAATTAAATTAAATA
898 ATTAATTAAATTAAAT
1 ATTAATTAAATTAAAT
914 CTATAAAATG
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
16 4 0.15
17 17 0.63
18 5 0.19
19 1 0.04
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
ATTAATTAAATTAAATA
Found at i:1141 original size:39 final size:39
Alignment explanation
Indices: 1087--1166 Score: 142
Period size: 39 Copynumber: 2.1 Consensus size: 39
1077 GATTCATTAG
* *
1087 GGCAGCTGTTGATTTGTGGCATGAAGAGGTGATGATTCA
1 GGCAGCTGTTAATTTGTGACATGAAGAGGTGATGATTCA
1126 GGCAGCTGTTAATTTGTGACATGAAGAGGTGATGATTCA
1 GGCAGCTGTTAATTTGTGACATGAAGAGGTGATGATTCA
1165 GG
1 GG
1167 TGATTTTGGG
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.25, C:0.10, G:0.35, T:0.30
Consensus pattern (39 bp):
GGCAGCTGTTAATTTGTGACATGAAGAGGTGATGATTCA
Found at i:4319 original size:19 final size:21
Alignment explanation
Indices: 4294--4338 Score: 76
Period size: 20 Copynumber: 2.2 Consensus size: 21
4284 TTTCTATTCT
4294 GCTATGGG-GTGAAGCAGGGA
1 GCTATGGGAGTGAAGCAGGGA
4314 -CTATGGGAGTGAAGCAGGGA
1 GCTATGGGAGTGAAGCAGGGA
4334 GCTAT
1 GCTAT
4339 TGTTGAGAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 7 0.30
20 12 0.52
21 4 0.17
ACGTcount: A:0.27, C:0.11, G:0.44, T:0.18
Consensus pattern (21 bp):
GCTATGGGAGTGAAGCAGGGA
Found at i:4617 original size:12 final size:12
Alignment explanation
Indices: 4600--4624 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
4590 TTCTTTTTAT
4600 GGTCTTCTACAC
1 GGTCTTCTACAC
4612 GGTCTTCTACAC
1 GGTCTTCTACAC
4624 G
1 G
4625 TGTTTAATTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.32, G:0.20, T:0.32
Consensus pattern (12 bp):
GGTCTTCTACAC
Found at i:8201 original size:163 final size:163
Alignment explanation
Indices: 7931--8236 Score: 612
Period size: 163 Copynumber: 1.9 Consensus size: 163
7921 GCTTTTATTT
7931 TTGTATTTTTTTCTATTTATCTGTTTAAGGTGATTCAAGTGTCTATTGAAAGGTAATTTCATGAT
1 TTGTATTTTTTTCTATTTATCTGTTTAAGGTGATTCAAGTGTCTATTGAAAGGTAATTTCATGAT
7996 CTACAATTTTCATGAAGAACTCAAAAGTCAATTTTTATGTTTTGATTCTAAAAAGTGCTTCCGAA
66 CTACAATTTTCATGAAGAACTCAAAAGTCAATTTTTATGTTTTGATTCTAAAAAGTGCTTCCGAA
8061 ATTTTGTGGTTTTGATTGCCGGTCAATTTAATA
131 ATTTTGTGGTTTTGATTGCCGGTCAATTTAATA
8094 TTGTATTTTTTTCTATTTATCTGTTTAAGGTGATTCAAGTGTCTATTGAAAGGTAATTTCATGAT
1 TTGTATTTTTTTCTATTTATCTGTTTAAGGTGATTCAAGTGTCTATTGAAAGGTAATTTCATGAT
8159 CTACAATTTTCATGAAGAACTCAAAAGTCAATTTTTATGTTTTGATTCTAAAAAGTGCTTCCGAA
66 CTACAATTTTCATGAAGAACTCAAAAGTCAATTTTTATGTTTTGATTCTAAAAAGTGCTTCCGAA
8224 ATTTTGTGGTTTT
131 ATTTTGTGGTTTT
Statistics
Matches: 143, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
163 143 1.00
ACGTcount: A:0.28, C:0.11, G:0.16, T:0.45
Consensus pattern (163 bp):
TTGTATTTTTTTCTATTTATCTGTTTAAGGTGATTCAAGTGTCTATTGAAAGGTAATTTCATGAT
CTACAATTTTCATGAAGAACTCAAAAGTCAATTTTTATGTTTTGATTCTAAAAAGTGCTTCCGAA
ATTTTGTGGTTTTGATTGCCGGTCAATTTAATA
Done.