Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020317.1 Corchorus olitorius cultivar O-4 contig20350, 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: 23634
ACGTcount: A:0.31, C:0.16, G:0.21, T:0.32
Found at i:10735 original size:27 final size:28
Alignment explanation
Indices: 10712--10768 Score: 84
Period size: 27 Copynumber: 2.1 Consensus size: 28
10702 TGAGAAACAT
*
10712 TTTTCAAAAAT-TGTTTTCAGGAAAAGG
1 TTTTCAAAAATGAGTTTTCAGGAAAAGG
10739 TTTTCAAAAATGAGTTTTCA--AAAAGG
1 TTTTCAAAAATGAGTTTTCAGGAAAAGG
10765 TTTT
1 TTTT
10769 GAGTTTGTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
26 10 0.36
27 11 0.39
28 7 0.25
ACGTcount: A:0.37, C:0.07, G:0.16, T:0.40
Consensus pattern (28 bp):
TTTTCAAAAATGAGTTTTCAGGAAAAGG
Found at i:10741 original size:14 final size:12
Alignment explanation
Indices: 10712--10768 Score: 60
Period size: 14 Copynumber: 4.3 Consensus size: 12
10702 TGAGAAACAT
*
10712 TTTTCAAAAATTG
1 TTTTCAAAAA-GG
10725 TTTTCAGGAAAAGG
1 TTTTCA--AAAAGG
10739 TTTTCAAAAATGAG
1 TTTTCAAAAA-G-G
10753 TTTTCAAAAAGG
1 TTTTCAAAAAGG
10765 TTTT
1 TTTT
10769 GAGTTTGTAA
Statistics
Matches: 39, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
12 9 0.23
13 8 0.21
14 18 0.46
15 4 0.10
ACGTcount: A:0.37, C:0.07, G:0.16, T:0.40
Consensus pattern (12 bp):
TTTTCAAAAAGG
Found at i:11437 original size:17 final size:17
Alignment explanation
Indices: 11415--11455 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
11405 CATTCAACTC
11415 AAAGAAAAAAAGAAAGA
1 AAAGAAAAAAAGAAAGA
* *
11432 AAAG-AAAGAAGGAAGA
1 AAAGAAAAAAAGAAAGA
11448 AAA-AAAAA
1 AAAGAAAAA
11456 CTTGGCCTAA
Statistics
Matches: 20, Mismatches: 3, Indels: 3
0.77 0.12 0.12
Matches are distributed among these distances:
16 16 0.80
17 4 0.20
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (17 bp):
AAAGAAAAAAAGAAAGA
Found at i:11678 original size:16 final size:15
Alignment explanation
Indices: 11637--11686 Score: 55
Period size: 16 Copynumber: 3.2 Consensus size: 15
11627 GTCTTGATAA
*
11637 GAAAGAGACAAGAAG
1 GAAAGAGAAAAGAAG
*
11652 GAAAAATGAAAAGAAG
1 GAAAGA-GAAAAGAAG
*
11668 GAAAGGAGAAAAGAGG
1 GAAA-GAGAAAAGAAG
11684 GAA
1 GAA
11687 TAAAAAAGAA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
15 5 0.17
16 23 0.79
17 1 0.03
ACGTcount: A:0.62, C:0.02, G:0.34, T:0.02
Consensus pattern (15 bp):
GAAAGAGAAAAGAAG
Found at i:11976 original size:20 final size:21
Alignment explanation
Indices: 11929--11977 Score: 57
Period size: 19 Copynumber: 2.4 Consensus size: 21
11919 GAAGAGATTG
* *
11929 TTCTTAAAATGAAAATTGTTT
1 TTCTCAAAATGAAAAGTGTTT
*
11950 TT-GCAAAA-GAAAAGTGTTT
1 TTCTCAAAATGAAAAGTGTTT
11969 TTCTCAAAA
1 TTCTCAAAA
11978 AGGTTTTAGA
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
19 12 0.52
20 9 0.39
21 2 0.09
ACGTcount: A:0.41, C:0.08, G:0.12, T:0.39
Consensus pattern (21 bp):
TTCTCAAAATGAAAAGTGTTT
Found at i:12080 original size:22 final size:21
Alignment explanation
Indices: 12034--12083 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
12024 ATGGCGGAAA
*
12034 AAAAGAAAAAAAAAGAGAGGC
1 AAAAGAAAAAAAAAGAGAAGC
* *
12055 AAAATAAAAAATAAAGAAGAAGA
1 AAAAGAAAAAA-AAAG-AGAAGC
12078 AAAAGA
1 AAAAGA
12084 GGGATACATC
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 10 0.43
22 4 0.17
23 9 0.39
ACGTcount: A:0.76, C:0.02, G:0.18, T:0.04
Consensus pattern (21 bp):
AAAAGAAAAAAAAAGAGAAGC
Found at i:13451 original size:50 final size:50
Alignment explanation
Indices: 13339--13562 Score: 344
Period size: 50 Copynumber: 4.5 Consensus size: 50
13329 GCTAAATTTA
* *
13339 AAGTGATCTAGTGCGATCAATCAAGTTTATAGTGG-TTAAGTTTTTCTTC
1 AAGTGATCCAGTGCGATCAATCAAGTTTACAGTGGTTTAAGTTTTTCTTC
*
13388 AAGTGATCTAGTGCGATCAATCAAGTTTACAGTGGTTTAAGTTTTTCTTC
1 AAGTGATCCAGTGCGATCAATCAAGTTTACAGTGGTTTAAGTTTTTCTTC
*
13438 AAGTGATCCAGTGCGATCAATCAAGTTTACAGTGGTTTAAGTTTTTCCTC
1 AAGTGATCCAGTGCGATCAATCAAGTTTACAGTGGTTTAAGTTTTTCTTC
* * **
13488 AAGTGATCCAGTGCGATCAATCAAGTTTGCAGTGGTTTAAG-TTTCCTAA
1 AAGTGATCCAGTGCGATCAATCAAGTTTACAGTGGTTTAAGTTTTTCTTC
*
13537 AAGTGATCCAAGTGCGGTCAATCAAG
1 AAGTGATCC-AGTGCGATCAATCAAG
13563 AAAGTTTCCT
Statistics
Matches: 164, Mismatches: 9, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
49 47 0.29
50 117 0.71
ACGTcount: A:0.28, C:0.16, G:0.21, T:0.35
Consensus pattern (50 bp):
AAGTGATCCAGTGCGATCAATCAAGTTTACAGTGGTTTAAGTTTTTCTTC
Found at i:13597 original size:37 final size:38
Alignment explanation
Indices: 13526--13602 Score: 138
Period size: 37 Copynumber: 2.1 Consensus size: 38
13516 GCAGTGGTTT
13526 AAGTTTCCTAAAAGTGATCCAAGTGCGGTCAATCAAGA
1 AAGTTTCCTAAAAGTGATCCAAGTGCGGTCAATCAAGA
*
13564 AAGTTTCCTAAAGGTGATCC-AGTGCGGTCAATCAAGA
1 AAGTTTCCTAAAAGTGATCCAAGTGCGGTCAATCAAGA
13601 AA
1 AA
13603 ATTTACAGTG
Statistics
Matches: 38, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
37 19 0.50
38 19 0.50
ACGTcount: A:0.36, C:0.18, G:0.22, T:0.23
Consensus pattern (38 bp):
AAGTTTCCTAAAAGTGATCCAAGTGCGGTCAATCAAGA
Found at i:13653 original size:54 final size:54
Alignment explanation
Indices: 13577--13685 Score: 137
Period size: 54 Copynumber: 2.0 Consensus size: 54
13567 TTTCCTAAAG
* * *
13577 GTGATCCAGTGCGGTCAATCAAGAAAATTTACAGTGGTTTAAGTTTATCTTCAA
1 GTGATCCAGTACAGTCAATCAAGAAAATTTACAGTGATTTAAGTTTATCTTCAA
* * * * **
13631 GTGATCCAGTACAGTCAGTCAAGGAAGTTTTCAGTGATTTGGGTTTATCTTCAA
1 GTGATCCAGTACAGTCAATCAAGAAAATTTACAGTGATTTAAGTTTATCTTCAA
13685 G
1 G
13686 CGGGATTCGG
Statistics
Matches: 46, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
54 46 1.00
ACGTcount: A:0.28, C:0.15, G:0.23, T:0.34
Consensus pattern (54 bp):
GTGATCCAGTACAGTCAATCAAGAAAATTTACAGTGATTTAAGTTTATCTTCAA
Found at i:13653 original size:91 final size:86
Alignment explanation
Indices: 13481--13660 Score: 209
Period size: 91 Copynumber: 2.0 Consensus size: 86
13471 GGTTTAAGTT
* *
13481 TTTCCTCAAGTGATCCAGTGCGATCAATCAAGTTTGCAGTGGTTTAAGTTTCCTAAAAGTGATCC
1 TTTCCTAAAGTGATCCAGTGCGATCAATCAAGTTTACAGTGGTTTAAGTTTCCTAAAAGTGATCC
* *
13546 AAGTGCGGTCAATCAAGAAAG
66 AAGTACAGTCAATCAAGAAAG
* * **
13567 TTTCCTAAAGGTGATCCAGTGCGGTCAATCAAGAAAATTTACAGTGGTTTAAGTTTATCTTCAAG
1 TTTCCTAAA-GTGATCCAGTGCGATCAATCAAG----TTTACAGTGGTTTAAGTTT-CCTAAAAG
* *
13632 TGATCC-AGTACAGTCAGTCAAGGAAG
60 TGATCCAAGTACAGTCAATCAAGAAAG
13658 TTT
1 TTT
13661 TCAGTGATTT
Statistics
Matches: 78, Mismatches: 10, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
86 8 0.10
87 22 0.28
91 37 0.47
92 11 0.14
ACGTcount: A:0.31, C:0.17, G:0.22, T:0.31
Consensus pattern (86 bp):
TTTCCTAAAGTGATCCAGTGCGATCAATCAAGTTTACAGTGGTTTAAGTTTCCTAAAAGTGATCC
AAGTACAGTCAATCAAGAAAG
Found at i:14217 original size:19 final size:19
Alignment explanation
Indices: 14178--14228 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 19
14168 TTATATTAGA
* *
14178 TGCACTTAGG-TTTGGGTT
1 TGCACTTAGGCATTGGGCT
*
14196 TGCACTTGGGCATTGGGCT
1 TGCACTTAGGCATTGGGCT
*
14215 TGCATTTAGGCATT
1 TGCACTTAGGCATT
14229 TTAACTTTAG
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
18 9 0.33
19 18 0.67
ACGTcount: A:0.14, C:0.16, G:0.31, T:0.39
Consensus pattern (19 bp):
TGCACTTAGGCATTGGGCT
Found at i:16510 original size:41 final size:41
Alignment explanation
Indices: 16462--16572 Score: 143
Period size: 41 Copynumber: 2.7 Consensus size: 41
16452 TTTCAATACA
* * *
16462 GTCCCTGATTTAGGGTAATATTTGTTAATTGATTCAATTTT
1 GTCCCTGATTTAGGATAATATTTATTAATTGATTCAATTTC
*
16503 GTCCCTGATTTAGGATAATATTTATTAATTGGTTCAATTTC
1 GTCCCTGATTTAGGATAATATTTATTAATTGATTCAATTTC
* * **
16544 GCCCCTGATTTGGGATTTTATTT-TTAATT
1 GTCCCTGATTTAGGATAATATTTATTAATT
16573 TATACGACCT
Statistics
Matches: 62, Mismatches: 8, Indels: 1
0.87 0.11 0.01
Matches are distributed among these distances:
40 6 0.10
41 56 0.90
ACGTcount: A:0.23, C:0.12, G:0.16, T:0.49
Consensus pattern (41 bp):
GTCCCTGATTTAGGATAATATTTATTAATTGATTCAATTTC
Found at i:18680 original size:89 final size:88
Alignment explanation
Indices: 18528--18698 Score: 234
Period size: 89 Copynumber: 1.9 Consensus size: 88
18518 CGGTGTAGCA
* * * *
18528 TCTTCAAGATTGGAATTCGGTGAGCTCGATGCAGCACATTTTCAGATAGATCAGGGTGATTCGGT
1 TCTTCAAGATTGGAATTCGGTGAGCTCGATGCAGCACATTTTAAAAAAGATCAGGATGATTCGGT
18593 GAATCAAGTTAATGCGGCGCATC
66 GAATCAAGTTAATGCGGCGCATC
* * * * *
18616 TCTTCAAAGATTGGAATTCGGTGAGCTCGGTGCAGCATATTTTAAAAAAGTTGAGGATGTTTCGG
1 TCTTC-AAGATTGGAATTCGGTGAGCTCGATGCAGCACATTTTAAAAAAGATCAGGATGATTCGG
* *
18681 TGAATTAAGTTACTGCGG
65 TGAATCAAGTTAATGCGG
18699 TGCAGTATTT
Statistics
Matches: 71, Mismatches: 11, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
88 5 0.07
89 66 0.93
ACGTcount: A:0.27, C:0.15, G:0.27, T:0.30
Consensus pattern (88 bp):
TCTTCAAGATTGGAATTCGGTGAGCTCGATGCAGCACATTTTAAAAAAGATCAGGATGATTCGGT
GAATCAAGTTAATGCGGCGCATC
Done.