Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021306.1 Corchorus olitorius cultivar O-4 contig21339, 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: 12435
ACGTcount: A:0.31, C:0.20, G:0.20, T:0.30
Found at i:1731 original size:20 final size:20
Alignment explanation
Indices: 1699--1744 Score: 51
Period size: 20 Copynumber: 2.3 Consensus size: 20
1689 TTTATATTTT
1699 TATAAATACTAAACA-TAATA
1 TATAAATACTAAACACTAA-A
*
1719 TATAAATTA-TAAATACTAAA
1 TATAAA-TACTAAACACTAAA
1739 TATAAA
1 TATAAA
1745 AAATATTAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
20 18 0.78
21 5 0.22
ACGTcount: A:0.61, C:0.07, G:0.00, T:0.33
Consensus pattern (20 bp):
TATAAATACTAAACACTAAA
Found at i:4170 original size:29 final size:30
Alignment explanation
Indices: 4096--4168 Score: 123
Period size: 29 Copynumber: 2.5 Consensus size: 30
4086 TTTTGGCGCC
4096 GTTGCCGGGGAAGGGAACTTTTTCTGGTTT
1 GTTGCCGGGGAAGGGAACTTTTTCTGGTTT
4126 GTT-CCGGGGAAGGGAACTTTTTCTGGTTT
1 GTTGCCGGGGAAGGGAACTTTTTCTGGTTT
4155 -TTGCCAGGGGAAGG
1 GTTGCC-GGGGAAGG
4169 AAAATAGACT
Statistics
Matches: 41, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
28 2 0.05
29 28 0.68
30 11 0.27
ACGTcount: A:0.15, C:0.14, G:0.38, T:0.33
Consensus pattern (30 bp):
GTTGCCGGGGAAGGGAACTTTTTCTGGTTT
Found at i:4355 original size:29 final size:31
Alignment explanation
Indices: 4294--4351 Score: 86
Period size: 28 Copynumber: 2.0 Consensus size: 31
4284 TTTTTAATTT
4294 TGTTTCTGCGTCATAAAAAAGAAAAGTTTTG
1 TGTTTCTGCGTCATAAAAAAGAAAAGTTTTG
*
4325 TGTTT-TGCGTCA-AGAAAA-AAAAGTTTT
1 TGTTTCTGCGTCATAAAAAAGAAAAGTTTT
4352 TGTGCCATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
28 9 0.35
29 5 0.19
30 7 0.27
31 5 0.19
ACGTcount: A:0.36, C:0.09, G:0.19, T:0.36
Consensus pattern (31 bp):
TGTTTCTGCGTCATAAAAAAGAAAAGTTTTG
Found at i:4380 original size:27 final size:27
Alignment explanation
Indices: 4347--4405 Score: 73
Period size: 27 Copynumber: 2.2 Consensus size: 27
4337 AGAAAAAAAA
* * *
4347 GTTTTTGTGCCATAAAAATTTTTTTTT
1 GTTTTTGCGCCATAAAAAATATTTTTT
*
4374 GTTTTTGCGTCATAAAAAATATTTTTT
1 GTTTTTGCGCCATAAAAAATATTTTTT
*
4401 CTTTT
1 GTTTT
4406 ATTTTCTGTT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.24, C:0.08, G:0.10, T:0.58
Consensus pattern (27 bp):
GTTTTTGCGCCATAAAAAATATTTTTT
Found at i:7258 original size:15 final size:16
Alignment explanation
Indices: 7225--7264 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
7215 TTACTTTGCT
7225 TTGTTTTCTAGTATAA
1 TTGTTTTCTAGTATAA
*
7241 TTGTTTTCTA-TTTAA
1 TTGTTTTCTAGTATAA
*
7256 TTGCTTTCT
1 TTGTTTTCT
7265 TTCAACCTCT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 12 0.55
16 10 0.45
ACGTcount: A:0.17, C:0.10, G:0.10, T:0.62
Consensus pattern (16 bp):
TTGTTTTCTAGTATAA
Found at i:10357 original size:30 final size:30
Alignment explanation
Indices: 10323--10382 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
10313 GAAGTTCGTG
* *
10323 TTTGAAGACTTATTGAAG-ATAATTTGAAGA
1 TTTGAAGAC-CATTGAAGAATAATTTCAAGA
10353 TTTGAAGACCATTGAAGAATAATTTCAAGA
1 TTTGAAGACCATTGAAGAATAATTTCAAGA
10383 GCAAGAATTG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 7 0.26
30 20 0.74
ACGTcount: A:0.42, C:0.07, G:0.18, T:0.33
Consensus pattern (30 bp):
TTTGAAGACCATTGAAGAATAATTTCAAGA
Done.