Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021517.1 Corchorus olitorius cultivar O-4 contig21550, 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: 5001
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:470 original size:52 final size:51
Alignment explanation
Indices: 402--806 Score: 567
Period size: 52 Copynumber: 7.8 Consensus size: 51
392 CAATTTAAGT
* * *
402 TTTTCAAATTGGGAAAGTTCCCATCAGTTTTCAATGTATTCAATTTAGCTC
1 TTTTCAAATCGGGAAAGTTCCCACCAGTTTTCAAAGTATTCAATTTAGCTC
* *
453 TTTTACAAATCGAGAAAGGTCCCACCAGTTTTCAAAGTATTCAATTTAGCTC
1 TTTT-CAAATCGGGAAAGTTCCCACCAGTTTTCAAAGTATTCAATTTAGCTC
* * * *
505 TTTTTAAATTGGGAAAGTTCCCACCAGTTTTCAAAGTATTCAATTTAGGTT
1 TTTTCAAATCGGGAAAGTTCCCACCAGTTTTCAAAGTATTCAATTTAGCTC
* * * *
556 TTTTCAAATTGGGAAAGTTCCCATCAATTTTCAAAGTATTCAATTTAGCAC
1 TTTTCAAATCGGGAAAGTTCCCACCAGTTTTCAAAGTATTCAATTTAGCTC
607 TTTTTCAAATCGGGAAAGTTCCCACCAGTTTTCAAAGTATTCAATTTAGCTC
1 -TTTTCAAATCGGGAAAGTTCCCACCAGTTTTCAAAGTATTCAATTTAGCTC
* * * * *
659 TTTTTAAATTGGGAAAGTTTCCACCAGTTTTCAAAGTATTCAATCTGGCTC
1 TTTTCAAATCGGGAAAGTTCCCACCAGTTTTCAAAGTATTCAATTTAGCTC
* * *
710 GTTTTCAAATCGGGAAAGTTCCCACCAGTTTTCAAAGAATTCAATCTGGCTC
1 -TTTTCAAATCGGGAAAGTTCCCACCAGTTTTCAAAGTATTCAATTTAGCTC
*
762 TTTTTCAAATCGGGAAAGTTCCCACCAAGTTTTCAAAGTTTTCAA
1 -TTTTCAAATCGGGAAAGTTCCCACC-AGTTTTCAAAGTATTCAA
807 ATTGGGAAAG
Statistics
Matches: 317, Mismatches: 33, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
51 136 0.43
52 165 0.52
53 16 0.05
ACGTcount: A:0.30, C:0.19, G:0.14, T:0.37
Consensus pattern (51 bp):
TTTTCAAATCGGGAAAGTTCCCACCAGTTTTCAAAGTATTCAATTTAGCTC
Found at i:526 original size:103 final size:104
Alignment explanation
Indices: 401--806 Score: 593
Period size: 103 Copynumber: 3.9 Consensus size: 104
391 TCAATTTAAG
* * * * *
401 TTTTTCAAATTGGGAAAGTTCCCATCAGTTTTCAATGTATTCAATTTAGCTCTTTTACAAATCGA
1 TTTTTCAAATCGGGAAAGTTCCCACCAGTTTTCAAAGTATTCAATTTAGCTCTTTTTCAAATCGG
*
466 GAAAGGTCCCACCAGTTTTCAAAGTATTCAATTTAGCTC
66 GAAAGTTCCCACCAGTTTTCAAAGTATTCAATTTAGCTC
* * *
505 TTTTT-AAATTGGGAAAGTTCCCACCAGTTTTCAAAGTATTCAATTTAGGT-TTTTTCAAATTGG
1 TTTTTCAAATCGGGAAAGTTCCCACCAGTTTTCAAAGTATTCAATTTAGCTCTTTTTCAAATCGG
* * *
568 GAAAGTTCCCATCAATTTTCAAAGTATTCAATTTAGCAC
66 GAAAGTTCCCACCAGTTTTCAAAGTATTCAATTTAGCTC
*
607 TTTTTCAAATCGGGAAAGTTCCCACCAGTTTTCAAAGTATTCAATTTAGCTCTTTTT-AAATTGG
1 TTTTTCAAATCGGGAAAGTTCCCACCAGTTTTCAAAGTATTCAATTTAGCTCTTTTTCAAATCGG
* * *
671 GAAAGTTTCCACCAGTTTTCAAAGTATTCAATCTGGCTC
66 GAAAGTTCCCACCAGTTTTCAAAGTATTCAATTTAGCTC
* * * *
710 GTTTTCAAATCGGGAAAGTTCCCACCAGTTTTCAAAGAATTCAATCTGGCTCTTTTTCAAATCGG
1 TTTTTCAAATCGGGAAAGTTCCCACCAGTTTTCAAAGTATTCAATTTAGCTCTTTTTCAAATCGG
*
775 GAAAGTTCCCACCAAGTTTTCAAAGTTTTCAA
66 GAAAGTTCCCACC-AGTTTTCAAAGTATTCAA
807 ATTGGGAAAG
Statistics
Matches: 273, Mismatches: 25, Indels: 7
0.90 0.08 0.02
Matches are distributed among these distances:
102 50 0.18
103 178 0.65
104 28 0.10
105 17 0.06
ACGTcount: A:0.30, C:0.19, G:0.14, T:0.37
Consensus pattern (104 bp):
TTTTTCAAATCGGGAAAGTTCCCACCAGTTTTCAAAGTATTCAATTTAGCTCTTTTTCAAATCGG
GAAAGTTCCCACCAGTTTTCAAAGTATTCAATTTAGCTC
Found at i:683 original size:154 final size:154
Alignment explanation
Indices: 391--806 Score: 647
Period size: 154 Copynumber: 2.7 Consensus size: 154
381 AAGAATTTTA
* *
391 TCAATTTAAG-TTTTTCAAATTGGGAAAGTTCCCATCAGTTTTCAATGTATTCAATTTAGCTCTT
1 TCAATTTAGGTTTTTTCAAATTGGGAAAGTTCCCATCAGTTTTCAAAGTATTCAATTTAGCTCTT
* * *
455 TTACAAATCGAGAAAGGTCCCACCAGTTTTCAAAGTATTCAATTTAGCTCTTTTTAAATTGGGAA
66 TTTCAAATCGGGAAAGTTCCCACCAGTTTTCAAAGTATTCAATTTAGCTCTTTTTAAATTGGGAA
520 AGTTCCCACCAGTTTTCAAAGTAT
131 AGTTCCCACCAGTTTTCAAAGTAT
* *
544 TCAATTTAGGTTTTTTCAAATTGGGAAAGTTCCCATCAATTTTCAAAGTATTCAATTTAGCACTT
1 TCAATTTAGGTTTTTTCAAATTGGGAAAGTTCCCATCAGTTTTCAAAGTATTCAATTTAGCTCTT
609 TTTCAAATCGGGAAAGTTCCCACCAGTTTTCAAAGTATTCAATTTAGCTCTTTTTAAATTGGGAA
66 TTTCAAATCGGGAAAGTTCCCACCAGTTTTCAAAGTATTCAATTTAGCTCTTTTTAAATTGGGAA
*
674 AGTTTCCACCAGTTTTCAAAGTAT
131 AGTTCCCACCAGTTTTCAAAGTAT
* * * * * * *
698 TCAATCT-GGCTCGTTTTCAAATCGGGAAAGTTCCCACCAGTTTTCAAAGAATTCAATCTGGCTC
1 TCAATTTAGG-T-TTTTTCAAATTGGGAAAGTTCCCATCAGTTTTCAAAGTATTCAATTTAGCTC
*
762 TTTTTCAAATCGGGAAAGTTCCCACCAAGTTTTCAAAGTTTTCAA
64 TTTTTCAAATCGGGAAAGTTCCCACC-AGTTTTCAAAGTATTCAA
807 ATTGGGAAAG
Statistics
Matches: 241, Mismatches: 18, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
153 11 0.05
154 143 0.59
155 70 0.29
156 17 0.07
ACGTcount: A:0.30, C:0.19, G:0.14, T:0.37
Consensus pattern (154 bp):
TCAATTTAGGTTTTTTCAAATTGGGAAAGTTCCCATCAGTTTTCAAAGTATTCAATTTAGCTCTT
TTTCAAATCGGGAAAGTTCCCACCAGTTTTCAAAGTATTCAATTTAGCTCTTTTTAAATTGGGAA
AGTTCCCACCAGTTTTCAAAGTAT
Found at i:1903 original size:32 final size:32
Alignment explanation
Indices: 1866--1935 Score: 88
Period size: 32 Copynumber: 2.2 Consensus size: 32
1856 CCTTTATTCC
*
1866 TTGATTTGAATTATTTGTTATG-TTTCTATGCT
1 TTGATTTGAA-TATTTATTATGATTTCTATGCT
* *
1898 TTGATTTGGATCTTTATTATGATTTCTATGCT
1 TTGATTTGAATATTTATTATGATTTCTATGCT
*
1930 ATGATT
1 TTGATT
1936 GTTATGATTG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
31 9 0.27
32 24 0.73
ACGTcount: A:0.20, C:0.07, G:0.16, T:0.57
Consensus pattern (32 bp):
TTGATTTGAATATTTATTATGATTTCTATGCT
Found at i:3989 original size:31 final size:31
Alignment explanation
Indices: 3951--4010 Score: 111
Period size: 31 Copynumber: 1.9 Consensus size: 31
3941 CTAATGTCTC
*
3951 TCATGGATTTTTCGAAATCCATGAGTAGCTA
1 TCATGGATTTTTCAAAATCCATGAGTAGCTA
3982 TCATGGATTTTTCAAAATCCATGAGTAGC
1 TCATGGATTTTTCAAAATCCATGAGTAGC
4011 CAAATTCTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.35
Consensus pattern (31 bp):
TCATGGATTTTTCAAAATCCATGAGTAGCTA
Done.