Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024132.1 Corchorus olitorius cultivar O-4 contig24165, 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: 30765
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.31
Found at i:2763 original size:12 final size:13
Alignment explanation
Indices: 2744--2775 Score: 57
Period size: 12 Copynumber: 2.5 Consensus size: 13
2734 GCAGCTTCCT
2744 AGAAAAACTCAAA
1 AGAAAAACTCAAA
2757 A-AAAAACTCAAA
1 AGAAAAACTCAAA
2769 AGAAAAA
1 AGAAAAA
2776 TTGTTAGTAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 12 0.67
13 6 0.33
ACGTcount: A:0.75, C:0.12, G:0.06, T:0.06
Consensus pattern (13 bp):
AGAAAAACTCAAA
Found at i:3377 original size:15 final size:16
Alignment explanation
Indices: 3353--3392 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
3343 AGAGGTTGAA
*
3353 AGAAAGCAATTAAAC-
1 AGAAAACAATTAAACT
*
3368 AGAAAACAATTATACT
1 AGAAAACAATTAAACT
3384 AGAAAACAA
1 AGAAAACAA
3393 AGCAAAGTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 13 0.59
16 9 0.41
ACGTcount: A:0.62, C:0.12, G:0.10, T:0.15
Consensus pattern (16 bp):
AGAAAACAATTAAACT
Found at i:6718 original size:34 final size:34
Alignment explanation
Indices: 6675--6744 Score: 140
Period size: 34 Copynumber: 2.1 Consensus size: 34
6665 TATGAGTCCA
6675 AATGCCCAAGAGAGCACGTAACCACGTACGCCCG
1 AATGCCCAAGAGAGCACGTAACCACGTACGCCCG
6709 AATGCCCAAGAGAGCACGTAACCACGTACGCCCG
1 AATGCCCAAGAGAGCACGTAACCACGTACGCCCG
6743 AA
1 AA
6745 AAATGAAGCC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.34, C:0.34, G:0.23, T:0.09
Consensus pattern (34 bp):
AATGCCCAAGAGAGCACGTAACCACGTACGCCCG
Found at i:15385 original size:116 final size:117
Alignment explanation
Indices: 15169--15463 Score: 408
Period size: 116 Copynumber: 2.5 Consensus size: 117
15159 TCTTTCAAGC
* *
15169 GTTGGCATCGGTTGGCCTTCTTGAAATGAAAAAGCAAAGCTTTCAAATGTTGGCATCGATTGGCC
1 GTTGGCATCGGTTGGCCTTCTTG-AA-G---AA--AAAGCTTTCAAAAGTTGGCATCGGTTGGCC
* *
15234 TTCTAAATTGTTTTCAAAGTTGGCATCGATGGGCCTTCTTGAAG-AAAAGTTTCCAAAA
59 TTCTAAATTGTTTTCAAAATTGGCATCGATCGGCCTTCTTGAAGAAAAAGTTTCCAAAA
15292 GTTGGCATCGGTTGGCCTTCTTGAAGAAAAAGCTTTCAAAAGTTGGCATCGGTTGGCCTTCTAAA
1 GTTGGCATCGGTTGGCCTTCTTGAAGAAAAAGCTTTCAAAAGTTGGCATCGGTTGGCCTTCTAAA
*
15357 TTGTTTTCAAAATTGGCATCGGTCGGCCTTCTTGAAGAAAAAGTTTCCAAAA
66 TTGTTTTCAAAATTGGCATCGATCGGCCTTCTTGAAGAAAAAGTTTCCAAAA
* *
15409 ATTGGCATCGGTTGGCCTTC-T----AAAAA-TTTTC-AAAGTTGGCATCGGTTGGCCTTCT
1 GTTGGCATCGGTTGGCCTTCTTGAAGAAAAAGCTTTCAAAAGTTGGCATCGGTTGGCCTTCT
15464 TGAAAGGAAG
Statistics
Matches: 164, Mismatches: 7, Indels: 15
0.88 0.04 0.08
Matches are distributed among these distances:
110 24 0.15
111 4 0.02
112 5 0.03
116 70 0.43
117 33 0.20
118 2 0.01
121 1 0.01
122 2 0.01
123 23 0.14
ACGTcount: A:0.26, C:0.18, G:0.23, T:0.33
Consensus pattern (117 bp):
GTTGGCATCGGTTGGCCTTCTTGAAGAAAAAGCTTTCAAAAGTTGGCATCGGTTGGCCTTCTAAA
TTGTTTTCAAAATTGGCATCGATCGGCCTTCTTGAAGAAAAAGTTTCCAAAA
Found at i:15390 original size:76 final size:74
Alignment explanation
Indices: 15278--15499 Score: 304
Period size: 76 Copynumber: 3.0 Consensus size: 74
15268 CTTCTTGAAG
* *
15278 AAAAGTTTCCAAAAGTTGGCATCGGTTGGCCTTCTTGAAGAAAAAGCTTTCAAAAGTTGGCATCG
1 AAAAGTTTTCAAAA-TTGGCATCGGTTGGCCTTCTTGAAGAAAAAG-TTTCAAAAATTGGCATCG
15343 GTTGGCCTTCT
64 GTTGGCCTTCT
* *
15354 AAATTGTTTTCAAAATTGGCATCGGTCGGCCTTCTTGAAGAAAAAGTTTCCAAAAATTGGCATCG
1 AAA-AGTTTTCAAAATTGGCATCGGTTGGCCTTCTTGAAGAAAAAGTTT-CAAAAATTGGCATCG
15419 GTTGGCCTTCT
64 GTTGGCCTTCT
* * ** * *
15430 AAAAATTTTCAAAGTTGGCATCGGTTGGCCTTCTTGAA-AGGAAGTTTC-CAATTTGGCATCGGT
1 AAAAGTTTTCAAAATTGGCATCGGTTGGCCTTCTTGAAGAAAAAGTTTCAAAAATTGGCATCGGT
15493 TGGCCTT
66 TGGCCTT
15500 ATTGTAACGA
Statistics
Matches: 132, Mismatches: 12, Indels: 8
0.87 0.08 0.05
Matches are distributed among these distances:
72 20 0.15
73 1 0.01
74 7 0.05
75 34 0.26
76 61 0.46
77 9 0.07
ACGTcount: A:0.27, C:0.18, G:0.23, T:0.32
Consensus pattern (74 bp):
AAAAGTTTTCAAAATTGGCATCGGTTGGCCTTCTTGAAGAAAAAGTTTCAAAAATTGGCATCGGT
TGGCCTTCT
Found at i:17474 original size:20 final size:21
Alignment explanation
Indices: 17449--17487 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
17439 AGTTAGATTA
*
17449 AATTAGGAT-CTTTCATAATT
1 AATTAGGATACATTCATAATT
17469 AATTAGGATACATTCATAA
1 AATTAGGATACATTCATAA
17488 CATGCATCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.41, C:0.10, G:0.10, T:0.38
Consensus pattern (21 bp):
AATTAGGATACATTCATAATT
Found at i:19502 original size:24 final size:24
Alignment explanation
Indices: 19475--19529 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 24
19465 TTAATGATGT
*
19475 GGTGACAATTTACTTTATTTCTTG
1 GGTGACAATTTACTCTATTTCTTG
* * *
19499 GGTGACATTTTGCTCTATTTGTTG
1 GGTGACAATTTACTCTATTTCTTG
*
19523 GTTGACA
1 GGTGACA
19530 TCTGGTATGG
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.18, C:0.13, G:0.22, T:0.47
Consensus pattern (24 bp):
GGTGACAATTTACTCTATTTCTTG
Found at i:19616 original size:47 final size:49
Alignment explanation
Indices: 19545--19638 Score: 138
Period size: 49 Copynumber: 2.0 Consensus size: 49
19535 TATGGTTGTC
*
19545 TTCCCAAATCAAGCCAAG-TGTT-TCTTCTTATGTGTGGCACCTGTCCT
1 TTCCCAAATCAAGCCAAGTTGTTCTCTTCTTATGTGTGACACCTGTCCT
* * *
19592 TTCCCACATCATGCCAAGTTTTTCTCTTCTTATGTGTGACACCTGTC
1 TTCCCAAATCAAGCCAAGTTGTTCTCTTCTTATGTGTGACACCTGTC
19639 TTTTAATTTG
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
47 16 0.39
48 3 0.07
49 22 0.54
ACGTcount: A:0.18, C:0.29, G:0.15, T:0.38
Consensus pattern (49 bp):
TTCCCAAATCAAGCCAAGTTGTTCTCTTCTTATGTGTGACACCTGTCCT
Found at i:19713 original size:19 final size:19
Alignment explanation
Indices: 19674--19718 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 19
19664 TCTTCATGCA
* *
19674 TTGGGCCATTTAAATTATC
1 TTGGGCTATTCAAATTATC
19693 TTTGGGCTATTCAAA-TATC
1 -TTGGGCTATTCAAATTATC
19712 TTGGGCT
1 TTGGGCT
19719 TTTTTTTACC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 7 0.30
19 4 0.17
20 12 0.52
ACGTcount: A:0.22, C:0.16, G:0.20, T:0.42
Consensus pattern (19 bp):
TTGGGCTATTCAAATTATC
Done.