Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021194.1 Corchorus olitorius cultivar O-4 contig21227, 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: 32481
ACGTcount: A:0.31, C:0.22, G:0.18, T:0.29
Found at i:1293 original size:16 final size:16
Alignment explanation
Indices: 1268--1326 Score: 73
Period size: 16 Copynumber: 3.6 Consensus size: 16
1258 CGGGTTGATC
1268 GGGTTCGGGTCATTTT
1 GGGTTCGGGTCATTTT
*
1284 GGGTTTGGGTCATTTT
1 GGGTTCGGGTCATTTT
* * *
1300 CGGCTTCGGGTAATTTC
1 -GGGTTCGGGTCATTTT
1317 GGGTTCGGGT
1 GGGTTCGGGT
1327 ACCCAAAATT
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
16 24 0.67
17 12 0.33
ACGTcount: A:0.07, C:0.14, G:0.39, T:0.41
Consensus pattern (16 bp):
GGGTTCGGGTCATTTT
Found at i:6792 original size:395 final size:397
Alignment explanation
Indices: 6018--6811 Score: 1414
Period size: 395 Copynumber: 2.0 Consensus size: 397
6008 GATCTGCCAT
**
6018 CACGAACTTGCCAGAAGAAATTCTCTTTAATAAGGTCTCTCCCTTCTAACAGACTACTCCAACCC
1 CACGAACTTGCCAGAAGAAATTCTCCATAATAAGGTCTCTCCCTTCTAACAGACTACTCCAACCC
* * * *
6083 CAAGAGGCATGTGGTCCTTTTTTTGCTTATAGGGGGGAGGTATTTGGGAAATACATTCCTTTTCA
66 CAAGAGGCATGTGGTCCTTTTATTGCTTATAGCGGGGAGGTATTTGGGAAATACAATCCTTTTAA
* *
6148 AACCTGAGTTCCATAACTGATCCTCATTCTGCAAAAGCCTCCAATATTGATTTGCTAACAGAGCA
131 AACCTGAGTCCCATAACTGATCCTCATTCTGCAAAAGCCTCCAATACTGATTTGCTAACAGAGCA
6213 GTGTTGAATAAGCATAAATCCTTAAAACCCAAACCTCCATCTTTCTTGCATTTTGTCAAACTGGA
196 GTGTTGAATAAGCATAAATCCTTAAAACCCAAACCTCCATCTTTCTTGCATTTTGTCAAACTGGA
6278 CCAGCTCTTCCAATGGATCTTTCCTTCAGATTCTTTTTGACCCCACCAAAAGTTTGCTACTGCTG
261 CCAGCTCTTCCAATGGATCTTTCCTTCAGATTCTTTTTGACCCCACCAAAAGTTTGCTACTGCTG
*
6343 AATTCATATCTTTATACACCCCTTTAGGAATCTTGAAGCAAGCCATTGTATAAGTAGAAATGGCC
326 AATTAATATCTTTATACACCCCTTTAGGAATCTTGAAGCAAGCCATTGTATAAGTAGAAATGGCC
6408 ATAGCAA
391 ATAGCAA
** *
6415 CACGAACTTGCCAGAAGATTTTCTCCATAATAAGGTCTCT-CTTTCTAACAGACTACTCCAACCC
1 CACGAACTTGCCAGAAGAAATTCTCCATAATAAGGTCTCTCCCTTCTAACAGACTACTCCAACCC
6479 CAAGAGGCATGTGGTCCTTTTATTGCTTATAGCGGGGAGGTATTTGGGAAATACAATCCTTTTAA
66 CAAGAGGCATGTGGTCCTTTTATTGCTTATAGCGGGGAGGTATTTGGGAAATACAATCCTTTTAA
*
6544 AACCTGAG-CCCATAACTGATCCTCATTCTGCAAAAGCCTCCAATACTGATTTGCTAGCAGAGCA
131 AACCTGAGTCCCATAACTGATCCTCATTCTGCAAAAGCCTCCAATACTGATTTGCTAACAGAGCA
*
6608 GTGTTGAATAAGCATAAATCCTTAAAACCCAAACCTCCATCTTTCTTGCGTTTTGTCAAACTGGA
196 GTGTTGAATAAGCATAAATCCTTAAAACCCAAACCTCCATCTTTCTTGCATTTTGTCAAACTGGA
*
6673 CCAGCTCTTCCAATGGATCTTTCCTTCCA-ATTCTTTTTGACCCCACCAAAAGTTTGCTATTGCT
261 CCAGCTCTTCCAATGGATCTTTCCTT-CAGATTCTTTTTGACCCCACCAAAAGTTTGCTACTGCT
*
6737 GAATTAATATCTTTATACACCCCTTTAGGAATCTTGAAGCAAGCCATTGTATAAGTAGGAATGGC
325 GAATTAATATCTTTATACACCCCTTTAGGAATCTTGAAGCAAGCCATTGTATAAGTAGAAATGGC
6802 CATAGCAA
390 CATAGCAA
6810 CA
1 CA
6812 GCTTTAATCA
Statistics
Matches: 380, Mismatches: 16, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
395 250 0.66
396 94 0.25
397 36 0.09
ACGTcount: A:0.29, C:0.24, G:0.16, T:0.31
Consensus pattern (397 bp):
CACGAACTTGCCAGAAGAAATTCTCCATAATAAGGTCTCTCCCTTCTAACAGACTACTCCAACCC
CAAGAGGCATGTGGTCCTTTTATTGCTTATAGCGGGGAGGTATTTGGGAAATACAATCCTTTTAA
AACCTGAGTCCCATAACTGATCCTCATTCTGCAAAAGCCTCCAATACTGATTTGCTAACAGAGCA
GTGTTGAATAAGCATAAATCCTTAAAACCCAAACCTCCATCTTTCTTGCATTTTGTCAAACTGGA
CCAGCTCTTCCAATGGATCTTTCCTTCAGATTCTTTTTGACCCCACCAAAAGTTTGCTACTGCTG
AATTAATATCTTTATACACCCCTTTAGGAATCTTGAAGCAAGCCATTGTATAAGTAGAAATGGCC
ATAGCAA
Found at i:16484 original size:30 final size:30
Alignment explanation
Indices: 16448--16521 Score: 121
Period size: 30 Copynumber: 2.5 Consensus size: 30
16438 TCGGTGTCGA
* *
16448 GTCGAGCTTGAGCCTCAAAAATGAGGCTCG
1 GTCGAGCTCGAGCCTAAAAAATGAGGCTCG
*
16478 GTCGAGCTCGAGCCTAAAAAATGAGGCTTG
1 GTCGAGCTCGAGCCTAAAAAATGAGGCTCG
16508 GTCGAGCTCGAGCC
1 GTCGAGCTCGAGCC
16522 AAGCTTCGAG
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 41 1.00
ACGTcount: A:0.26, C:0.24, G:0.31, T:0.19
Consensus pattern (30 bp):
GTCGAGCTCGAGCCTAAAAAATGAGGCTCG
Done.