Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012125.1 Corchorus olitorius cultivar O-4 contig12158, 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: 28482
ACGTcount: A:0.30, C:0.20, G:0.19, T:0.31
Found at i:123 original size:17 final size:18
Alignment explanation
Indices: 93--127 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
83 TAAAAAGGTT
93 TTCAAAAATCCAAAAAAA
1 TTCAAAAATCCAAAAAAA
*
111 TTCAAAACT-CAAAAAAA
1 TTCAAAAATCCAAAAAAA
128 AAAAAGAAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.66, C:0.17, G:0.00, T:0.17
Consensus pattern (18 bp):
TTCAAAAATCCAAAAAAA
Found at i:128 original size:18 final size:18
Alignment explanation
Indices: 93--128 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
83 TAAAAAGGTT
*
93 TTCAAAAATCCAAAAAAA
1 TTCAAAAATCAAAAAAAA
*
111 TTCAAAACTCAAAAAAAA
1 TTCAAAAATCAAAAAAAA
129 AAAAGAAGAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.67, C:0.17, G:0.00, T:0.17
Consensus pattern (18 bp):
TTCAAAAATCAAAAAAAA
Found at i:185 original size:43 final size:43
Alignment explanation
Indices: 137--222 Score: 163
Period size: 43 Copynumber: 2.0 Consensus size: 43
127 AAAAAAGAAG
137 AAGTATTCAATTTAAATTTTTCAAATTGGGAAAGTTCCCATCA
1 AAGTATTCAATTTAAATTTTTCAAATTGGGAAAGTTCCCATCA
*
180 AAGTATTCAATTTAAGTTTTTCAAATTGGGAAAGTTCCCATCA
1 AAGTATTCAATTTAAATTTTTCAAATTGGGAAAGTTCCCATCA
223 GTTTTCAAAG
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.36, C:0.14, G:0.13, T:0.37
Consensus pattern (43 bp):
AAGTATTCAATTTAAATTTTTCAAATTGGGAAAGTTCCCATCA
Found at i:239 original size:50 final size:51
Alignment explanation
Indices: 177--280 Score: 140
Period size: 52 Copynumber: 2.0 Consensus size: 51
167 AAAGTTCCCA
*
177 TCAAAGTATTCAATTTAAG-T-TTTTCAAATTGGGAAAGTTCCCATCAGTTT
1 TCAAAGTATTCAATTT-AGCTGTTTTCAAATTGGGAAAGTTCCCATCAGGTT
* * *
227 TCAAAGTGTTCAATTTAGCTGGTTTTTAAATTGGGAAGGTTCCCATCAGGTT
1 TCAAAGTATTCAATTTAGCT-GTTTTCAAATTGGGAAAGTTCCCATCAGGTT
279 TC
1 TC
281 GGTTTTCAAT
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
49 2 0.04
50 16 0.34
52 29 0.62
ACGTcount: A:0.28, C:0.14, G:0.18, T:0.39
Consensus pattern (51 bp):
TCAAAGTATTCAATTTAGCTGTTTTCAAATTGGGAAAGTTCCCATCAGGTT
Found at i:4925 original size:6 final size:5
Alignment explanation
Indices: 4892--4932 Score: 64
Period size: 5 Copynumber: 7.8 Consensus size: 5
4882 CAAAGAAACA
4892 AAAAT AAAAT AAAAT AAAAT AAAAT AATAAT AATAAT AAAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AA-AAT AA-AAT AAAA
4933 CTAGGCCTAA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
5 24 0.69
6 11 0.31
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (5 bp):
AAAAT
Found at i:5076 original size:13 final size:14
Alignment explanation
Indices: 5039--5077 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
5029 GCTTTTAAAG
*
5039 GATTTTTCAAAAAT
1 GATTTCTCAAAAAT
5053 GATTTCTCAAAAAT
1 GATTTCTCAAAAAT
*
5067 GGTTTC-CAAAA
1 GATTTCTCAAAA
5078 TTTGTTTTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 5 0.22
14 18 0.78
ACGTcount: A:0.41, C:0.13, G:0.10, T:0.36
Consensus pattern (14 bp):
GATTTCTCAAAAAT
Found at i:6932 original size:107 final size:107
Alignment explanation
Indices: 6738--7537 Score: 663
Period size: 107 Copynumber: 7.5 Consensus size: 107
6728 TGTTCAGCTG
*
6738 TTCTTCAGTTTATTTCAGTTGACCCAGGGTGGTCTTTTCTTCAGTTTATGTCAGAATGATCGAGG
1 TTCTTCAGTTTATTGCAGTTGACCCAGGGTGGTCTTTTCTTCAGTTTATGTCAGAATGATCGAGG
* * *
6803 GTGGTCGTTCTTCAGTTTATTTC-GATTGACCAAGGGCGGTCT
66 GTGGTCGTTCTTCAATTTATTTCAG-TTGACCCAGGGTGGTCT
6845 TTCTTCAGTTTATTGCAGTTGACCCAGGGTGGTCTTTTCTTCAGTTTATGTCAGAATGATCGAGG
1 TTCTTCAGTTTATTGCAGTTGACCCAGGGTGGTCTTTTCTTCAGTTTATGTCAGAATGATCGAGG
* *
6910 GTGGTCGTTCTTCAATTCATTTCAGTTGACCCAGGGAGGTCT
66 GTGGTCGTTCTTCAATTTATTTCAGTTGACCCAGGGTGGTCT
* *
6952 TTCTTCAATTTATTTCAGTTGACCCAGGGTGGTCTTTTCTTCAGTTTATGTCAGAATGATCGAGG
1 TTCTTCAGTTTATTGCAGTTGACCCAGGGTGGTCTTTTCTTCAGTTTATGTCAGAATGATCGAGG
*
7017 GTGGTCGTTCTTCAGTTTATTTC-GATTGACCCAGGGTGGTCTT
66 GTGGTCGTTCTTCAATTTATTTCAG-TTGACCCAGGGTGGTC-T
* * * * * * * * *
7060 TTCTTCAGTTTA-TGTCAGAATGATCGAGGGGGGTC-GTTCTTCAGTTTATTTC-GATTGACCCA
1 TTCTTCAGTTTATTG-CAG-TTGACCCAGGGTGGTCTTTTCTTCAGTTTATGTCAGAATGATCGA
*
7122 GGGCGGT-GTTTCTTCAATTTATTTCAGTTGACCCAGGGTGGTCCT
64 GGGTGGTCG-TTCTTCAATTTATTTCAGTTGACCCAGGGTGGT-CT
* ** * * * * * * *
7167 TTCTTCAGTTTA-TGTCGGAAAGATCGA-GG-GGTC-GTTCTTCAGTTTATTTC-GATTGACCCA
1 TTCTTCAGTTTATTG-CAG-TTGACCCAGGGTGGTCTTTTCTTCAGTTTATGTCAGAATGATCGA
* * ** * *
7227 GGGCGGTCTTTCTTCTGTTTATTGCAGTTGACCCAGGGTGGTTTT
64 GGGTGGTCGTTCTTCAATTTATTTCAGTTGACCCAGGGTGG-TCT
* * * * * * * * *
7272 TTCTTCAGTTTA-TGTCAGAATGATCGA-GATGGGTC-GTTCTTCAGTTTATTTC-GATTGACCA
1 TTCTTCAGTTTATTG-CAG-TTGACCCAGGGT-GGTCTTTTCTTCAGTTTATGTCAGAATGATCG
* * *
7333 AGGGTGGTCTTTCTTCAGTTTATTGCAGTTGACCCAGGGTGGTCTT
63 AGGGTGGTCGTTCTTCAATTTATTTCAGTTGACCCAGGGTGGTC-T
* * * * * * * * *
7379 TTCTTCAGTTTA-TGTCAGAATGATCGAGGGTGGTC-GTTCTTCAGCTTATTTCAG-TTGACCCA
1 TTCTTCAGTTTATTG-CAG-TTGACCCAGGGTGGTCTTTTCTTCAGTTTATGTCAGAATGATCGA
* * * * * * * * ** *
7441 AGGCGGTCTTTCTTCAATTCATCTCAGTTGGCCAAAGACGGTCC
64 GGGTGGTCGTTCTTCAATTTATTTCAGTTGACCCAGGGTGGTCT
*
7485 TTCTTCAGTCATT-TT-C-GATTGACCCAGGGTGGT-TTTTCTTCAGTTTATTTCAG
1 TTCTTCAGT--TTATTGCAG-TTGACCCAGGGTGGTCTTTTCTTCAGTTTATGTCAG
7538 TCGGTCCAGG
Statistics
Matches: 617, Mismatches: 57, Indels: 40
0.86 0.08 0.06
Matches are distributed among these distances:
105 125 0.20
106 16 0.03
107 425 0.69
108 39 0.06
109 12 0.02
ACGTcount: A:0.17, C:0.19, G:0.25, T:0.40
Consensus pattern (107 bp):
TTCTTCAGTTTATTGCAGTTGACCCAGGGTGGTCTTTTCTTCAGTTTATGTCAGAATGATCGAGG
GTGGTCGTTCTTCAATTTATTTCAGTTGACCCAGGGTGGTCT
Found at i:6937 original size:72 final size:72
Alignment explanation
Indices: 6738--7537 Score: 765
Period size: 72 Copynumber: 11.2 Consensus size: 72
6728 TGTTCAGCTG
* * * *
6738 TTCTTCAGTTTATTTCAG-TTGACCCAGGGTGGTCTTTTCTTCAGTTTATGTCAGAATGATCGAG
1 TTCTTCAGTTTATTTCAGATTGACCCAGGGTGGTC-TTTCTTCAGTTTATTTCAGATTGACCCAG
*
6802 GGTGGTCG
65 GGTGGTCT
* * *
6810 TTCTTCAGTTTATTTC-GATTGACCAAGGGCGGTCTTTCTTCAGTTTATTGCAG-TTGACCCAGG
1 TTCTTCAGTTTATTTCAGATTGACCCAGGGTGGTCTTTCTTCAGTTTATTTCAGATTGACCCAGG
6873 GTGGTCTT
66 GTGGTC-T
* * * * * * *
6881 TTCTTCAGTTTATGTCAGAATGATCGAGGGTGGTCGTTCTTCAATTCATTTCAG-TTGACCCAGG
1 TTCTTCAGTTTATTTCAGATTGACCCAGGGTGGTCTTTCTTCAGTTTATTTCAGATTGACCCAGG
*
6945 GAGGTCT
66 GTGGTCT
* * * * *
6952 TTCTTCAATTTATTTCAG-TTGACCCAGGGTGGTCTTTTCTTCAGTTTATGTCAGAATGATCGAG
1 TTCTTCAGTTTATTTCAGATTGACCCAGGGTGGTC-TTTCTTCAGTTTATTTCAGATTGACCCAG
*
7016 GGTGGTCG
65 GGTGGTCT
* * * *
7024 TTCTTCAGTTTATTTC-GATTGACCCAGGGTGGTCTTTTCTTCAGTTTATGTCAGAATGATCGAG
1 TTCTTCAGTTTATTTCAGATTGACCCAGGGTGGTC-TTTCTTCAGTTTATTTCAGATTGACCCAG
* *
7088 GGGGGTCG
65 GGTGGTCT
* * *
7096 TTCTTCAGTTTATTTC-GATTGACCCAGGGCGGTGTTTCTTCAATTTATTTCAG-TTGACCCAGG
1 TTCTTCAGTTTATTTCAGATTGACCCAGGGTGGTCTTTCTTCAGTTTATTTCAGATTGACCCAGG
7159 GTGGTCCT
66 GTGGT-CT
* * ** * * *
7167 TTCTTCAGTTTATGTCGGAAAGATCGA-GG-GGTCGTTCTTCAGTTTATTTC-GATTGACCCAGG
1 TTCTTCAGTTTATTTCAGATTGACCCAGGGTGGTCTTTCTTCAGTTTATTTCAGATTGACCCAGG
*
7229 GCGGTCT
66 GTGGTCT
* * * * * * *
7236 TTCTTCTGTTTATTGCAG-TTGACCCAGGGTGGTTTTTTCTTCAGTTTATGTCAGAATGATCGA-
1 TTCTTCAGTTTATTTCAGATTGACCCAGGGTGG-TCTTTCTTCAGTTTATTTCAGATTGACCCAG
* *
7299 GATGGGTCG
65 GGT-GGTCT
* *
7308 TTCTTCAGTTTATTTC-GATTGACCAAGGGTGGTCTTTCTTCAGTTTATTGCAG-TTGACCCAGG
1 TTCTTCAGTTTATTTCAGATTGACCCAGGGTGGTCTTTCTTCAGTTTATTTCAGATTGACCCAGG
7371 GTGGTCTT
66 GTGGTC-T
* * * * * * *
7379 TTCTTCAGTTTATGTCAGAATGATCGAGGGTGGTCGTTCTTCAGCTTATTTCAG-TTGACCCAAG
1 TTCTTCAGTTTATTTCAGATTGACCCAGGGTGGTCTTTCTTCAGTTTATTTCAGATTGACCCAGG
*
7443 GCGGTCT
66 GTGGTCT
* * * * * * ** * *
7450 TTCTTCAATTCATCTCAG-TTGGCCAAAGACGGTCCTTCTTCAG-TCATTTTC-GATTGACCCAG
1 TTCTTCAGTTTATTTCAGATTGACCCAGGGTGGTCTTTCTTCAGTTTA-TTTCAGATTGACCCAG
*
7512 GGTGGTTT
65 GGTGGTCT
7520 TTCTTCAGTTTATTTCAG
1 TTCTTCAGTTTATTTCAG
7538 TCGGTCCAGG
Statistics
Matches: 601, Mismatches: 107, Indels: 42
0.80 0.14 0.06
Matches are distributed among these distances:
68 4 0.01
69 22 0.04
70 130 0.22
71 170 0.28
72 275 0.46
ACGTcount: A:0.17, C:0.19, G:0.25, T:0.40
Consensus pattern (72 bp):
TTCTTCAGTTTATTTCAGATTGACCCAGGGTGGTCTTTCTTCAGTTTATTTCAGATTGACCCAGG
GTGGTCT
Found at i:7550 original size:35 final size:36
Alignment explanation
Indices: 6738--7537 Score: 765
Period size: 35 Copynumber: 22.5 Consensus size: 36
6728 TGTTCAGCTG
6738 TTCTTCAGTTTATTTCAG-TTGACCCAGGGTGGTCTT
1 TTCTTCAGTTTATTTCAGATTGACCCAGGGTGGTC-T
* * * * *
6774 TTCTTCAGTTTATGTCAGAATGATCGAGGGTGGTCG
1 TTCTTCAGTTTATTTCAGATTGACCCAGGGTGGTCT
* *
6810 TTCTTCAGTTTATTTC-GATTGACCAAGGGCGGTCT
1 TTCTTCAGTTTATTTCAGATTGACCCAGGGTGGTCT
*
6845 TTCTTCAGTTTATTGCAG-TTGACCCAGGGTGGTCTT
1 TTCTTCAGTTTATTTCAGATTGACCCAGGGTGGTC-T
* * * * *
6881 TTCTTCAGTTTATGTCAGAATGATCGAGGGTGGTCG
1 TTCTTCAGTTTATTTCAGATTGACCCAGGGTGGTCT
* * *
6917 TTCTTCAATTCATTTCAG-TTGACCCAGGGAGGTCT
1 TTCTTCAGTTTATTTCAGATTGACCCAGGGTGGTCT
*
6952 TTCTTCAATTTATTTCAG-TTGACCCAGGGTGGTCTT
1 TTCTTCAGTTTATTTCAGATTGACCCAGGGTGGTC-T
* * * * *
6988 TTCTTCAGTTTATGTCAGAATGATCGAGGGTGGTCG
1 TTCTTCAGTTTATTTCAGATTGACCCAGGGTGGTCT
7024 TTCTTCAGTTTATTTC-GATTGACCCAGGGTGGTCTT
1 TTCTTCAGTTTATTTCAGATTGACCCAGGGTGGTC-T
* * * * * *
7060 TTCTTCAGTTTATGTCAGAATGATCGAGGGGGGTCG
1 TTCTTCAGTTTATTTCAGATTGACCCAGGGTGGTCT
* *
7096 TTCTTCAGTTTATTTC-GATTGACCCAGGGCGGTGT
1 TTCTTCAGTTTATTTCAGATTGACCCAGGGTGGTCT
*
7131 TTCTTCAATTTATTTCAG-TTGACCCAGGGTGGTCCT
1 TTCTTCAGTTTATTTCAGATTGACCCAGGGTGGT-CT
* * ** * * *
7167 TTCTTCAGTTTATGTCGGAAAGATCGA-GG-GGTCG
1 TTCTTCAGTTTATTTCAGATTGACCCAGGGTGGTCT
*
7201 TTCTTCAGTTTATTTC-GATTGACCCAGGGCGGTCT
1 TTCTTCAGTTTATTTCAGATTGACCCAGGGTGGTCT
* * *
7236 TTCTTCTGTTTATTGCAG-TTGACCCAGGGTGGTTTT
1 TTCTTCAGTTTATTTCAGATTGACCCAGGGTGG-TCT
* * * * * *
7272 TTCTTCAGTTTATGTCAGAATGATCGA-GATGGGTCG
1 TTCTTCAGTTTATTTCAGATTGACCCAGGGT-GGTCT
*
7308 TTCTTCAGTTTATTTC-GATTGACCAAGGGTGGTCT
1 TTCTTCAGTTTATTTCAGATTGACCCAGGGTGGTCT
*
7343 TTCTTCAGTTTATTGCAG-TTGACCCAGGGTGGTCTT
1 TTCTTCAGTTTATTTCAGATTGACCCAGGGTGGTC-T
* * * * *
7379 TTCTTCAGTTTATGTCAGAATGATCGAGGGTGGTCG
1 TTCTTCAGTTTATTTCAGATTGACCCAGGGTGGTCT
* * *
7415 TTCTTCAGCTTATTTCAG-TTGACCCAAGGCGGTCT
1 TTCTTCAGTTTATTTCAGATTGACCCAGGGTGGTCT
* * * * * * ** *
7450 TTCTTCAATTCATCTCAG-TTGGCCAAAGACGGTCC
1 TTCTTCAGTTTATTTCAGATTGACCCAGGGTGGTCT
* *
7485 TTCTTCAG-TCATTTTC-GATTGACCCAGGGTGGTTT
1 TTCTTCAGTTTA-TTTCAGATTGACCCAGGGTGGTCT
7520 TTCTTCAGTTTATTTCAG
1 TTCTTCAGTTTATTTCAG
7538 TCGGTCCAGG
Statistics
Matches: 615, Mismatches: 124, Indels: 50
0.78 0.16 0.06
Matches are distributed among these distances:
33 6 0.01
34 22 0.04
35 289 0.47
36 221 0.36
37 77 0.13
ACGTcount: A:0.17, C:0.19, G:0.25, T:0.40
Consensus pattern (36 bp):
TTCTTCAGTTTATTTCAGATTGACCCAGGGTGGTCT
Found at i:11552 original size:43 final size:43
Alignment explanation
Indices: 11505--11590 Score: 154
Period size: 43 Copynumber: 2.0 Consensus size: 43
11495 AAAAAAGAAG
*
11505 AAGTATTCAATTTAAATTTTTCAAATTGGGAAAGTTCCCATCA
1 AAGTATTCAATTTAAATTTTTCAAATTGGAAAAGTTCCCATCA
*
11548 AAGTATTCAATTTAAGTTTTTCAAATTGGAAAAGTTCCCATCA
1 AAGTATTCAATTTAAATTTTTCAAATTGGAAAAGTTCCCATCA
11591 GTTTTCAAAG
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 41 1.00
ACGTcount: A:0.37, C:0.14, G:0.12, T:0.37
Consensus pattern (43 bp):
AAGTATTCAATTTAAATTTTTCAAATTGGAAAAGTTCCCATCA
Found at i:11607 original size:50 final size:51
Alignment explanation
Indices: 11545--11648 Score: 131
Period size: 52 Copynumber: 2.0 Consensus size: 51
11535 AAAGTTCCCA
*
11545 TCAAAGTATTCAATTTAAG-T-TTTTCAAATTGGAAAAGTTCCCATCAGTTT
1 TCAAAGTATTCAATTT-AGCTGTTTTCAAATTGGAAAAGTTCCCATCAGGTT
* * * *
11595 TCAAAGTGTTCAATTTAGCTGGTTTTTAAATTGGGAAGGTTCCCATCAGGTT
1 TCAAAGTATTCAATTTAGCT-GTTTTCAAATTGGAAAAGTTCCCATCAGGTT
11647 TC
1 TC
11649 GGTTTTCAAT
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
49 2 0.04
50 16 0.35
52 28 0.61
ACGTcount: A:0.29, C:0.14, G:0.17, T:0.39
Consensus pattern (51 bp):
TCAAAGTATTCAATTTAGCTGTTTTCAAATTGGAAAAGTTCCCATCAGGTT
Found at i:25549 original size:15 final size:16
Alignment explanation
Indices: 25531--25560 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
25521 GAAAGAAAGC
25531 AATTAAAC-AGAAAAA
1 AATTAAACTAGAAAAA
25546 AATTAAACTAGAAAA
1 AATTAAACTAGAAAA
25561 CAAAGCAAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.70, C:0.07, G:0.07, T:0.17
Consensus pattern (16 bp):
AATTAAACTAGAAAAA
Done.