Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023198.1 Corchorus olitorius cultivar O-4 contig23231, 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: 16303
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35
Found at i:96 original size:13 final size:14
Alignment explanation
Indices: 76--109 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
66 CGCGACCCGC
*
76 TATTTTTTCTGGGT
1 TATTTTTTCTGCGT
90 T-TTTTTTCTGCGT
1 TATTTTTTCTGCGT
103 TATTTTT
1 TATTTTT
110 ATCTTTTTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
13 12 0.67
14 6 0.33
ACGTcount: A:0.06, C:0.09, G:0.15, T:0.71
Consensus pattern (14 bp):
TATTTTTTCTGCGT
Found at i:2763 original size:23 final size:23
Alignment explanation
Indices: 2737--2784 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
2727 AAAATTTAGT
* *
2737 TTTATAGAGTTGATTGTTTAAAC
1 TTTATAGAGATGATTATTTAAAC
2760 TTTATAGAGATGATTATTTAAAC
1 TTTATAGAGATGATTATTTAAAC
2783 TT
1 TT
2785 AGAAATTTAG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.33, C:0.04, G:0.15, T:0.48
Consensus pattern (23 bp):
TTTATAGAGATGATTATTTAAAC
Found at i:10080 original size:31 final size:31
Alignment explanation
Indices: 10022--10098 Score: 86
Period size: 31 Copynumber: 2.5 Consensus size: 31
10012 ATAGAACAAT
* *
10022 CAAGCCTTAAATTG-AAGCAAATCAACATAAA
1 CAAGCCTCAAATTGCAAGCAAATAAACAT-AA
* *
10053 CAAGCCTCAAATTGCAA-CAATTAAACATGA
1 CAAGCCTCAAATTGCAAGCAAATAAACATAA
*
10083 CAAGTCTCAAATTGCA
1 CAAGCCTCAAATTGCA
10099 GTAATCAAGT
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
30 16 0.40
31 22 0.55
32 2 0.05
ACGTcount: A:0.47, C:0.22, G:0.10, T:0.21
Consensus pattern (31 bp):
CAAGCCTCAAATTGCAAGCAAATAAACATAA
Found at i:11514 original size:19 final size:19
Alignment explanation
Indices: 11490--11548 Score: 54
Period size: 19 Copynumber: 3.3 Consensus size: 19
11480 TTTCAGTTCT
11490 TTTCTTGCTACAATGTGTG
1 TTTCTTGCTACAATGTGTG
* * *
11509 TTTCTT--TTCTAT-TCT-
1 TTTCTTGCTACAATGTGTG
*
11524 TTTCTTGCTGCAATGTGTG
1 TTTCTTGCTACAATGTGTG
11543 TTTCTT
1 TTTCTT
11549 TTCTGTTCTT
Statistics
Matches: 30, Mismatches: 6, Indels: 8
0.68 0.14 0.18
Matches are distributed among these distances:
15 6 0.20
16 2 0.07
17 8 0.27
18 2 0.07
19 12 0.40
ACGTcount: A:0.10, C:0.17, G:0.15, T:0.58
Consensus pattern (19 bp):
TTTCTTGCTACAATGTGTG
Found at i:11576 original size:34 final size:34
Alignment explanation
Indices: 11473--11564 Score: 148
Period size: 34 Copynumber: 2.7 Consensus size: 34
11463 GATCAATGCT
* * *
11473 TGTTTCATTTCAGTTCTTTTCTTGCTACAATGTG
1 TGTTTCTTTTCTGTTCTTTTCTTGCTGCAATGTG
*
11507 TGTTTCTTTTCTATTCTTTTCTTGCTGCAATGTG
1 TGTTTCTTTTCTGTTCTTTTCTTGCTGCAATGTG
11541 TGTTTCTTTTCTGTTCTTTTCTTG
1 TGTTTCTTTTCTGTTCTTTTCTTG
11565 TTGTAGTGTG
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 53 1.00
ACGTcount: A:0.09, C:0.17, G:0.14, T:0.60
Consensus pattern (34 bp):
TGTTTCTTTTCTGTTCTTTTCTTGCTGCAATGTG
Found at i:12830 original size:27 final size:27
Alignment explanation
Indices: 12762--12836 Score: 89
Period size: 27 Copynumber: 2.8 Consensus size: 27
12752 GAATCAAGAG
* *
12762 TGGACTTG-AAATGACCAAAATGCCCC
1 TGGACATGCAAATGATCAAAATGCCCC
* *
12788 TGGACGTGCAAATGATTAAAATGCCCC
1 TGGACATGCAAATGATCAAAATGCCCC
* *
12815 TGGACATGTAACTGATCAAAAT
1 TGGACATGCAAATGATCAAAAT
12837 AAGAGGTAAA
Statistics
Matches: 41, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
26 7 0.17
27 34 0.83
ACGTcount: A:0.36, C:0.21, G:0.20, T:0.23
Consensus pattern (27 bp):
TGGACATGCAAATGATCAAAATGCCCC
Found at i:14053 original size:201 final size:199
Alignment explanation
Indices: 13667--14278 Score: 858
Period size: 201 Copynumber: 3.1 Consensus size: 199
13657 AGGGCGTGAC
*
13667 AGTATTAATATT-AA-ATATTTAATTAATTATAAAATGGGGTA-GTGTCAACCTCTTAACCCGCT
1 AGTATTAATATTAAATATATTTAATTAATTATGAAATGGGGTATGTGTCAA-CTCTTAACCCGCT
* * * * *
13729 TATGGAG-TCTAAAATTTACAATGACAGTGAATTGTATAATAATCCTATAAGAAAAAGTATATAA
65 TATGAAGTTC-AAAATTTACACTGACAGTGTATTGTATAATAATCCTATAAGAAAAATTATACAA
*
13793 TACACCGTCAGTGGAATTTAGCAGACTGCACGTGCGGGGTTTAAGGGTTGACATGTGTCCCCTTA
129 TACACCGTCAGTGGAGTTTAGCAGACTGCACGTGCGGGGTTTAAGGGTTGACATGTGTCCCCTTA
13858 GGGAAT
194 GGGAAT
* ** *
13864 ATGTATTGATATTAAATATATTTTCTTAATTATGAAATGGGGTATGTGTCAACTACTTAACCCAC
1 A-GTATTAATATTAAATATATTTAATTAATTATGAAATGGGGTATGTGTCAACT-CTTAACCCGC
13929 TTATGAAGTTCAAAATTTACACTGACAGTGTATTGTATAATAATCCTATAAGAAAAATTATACAA
64 TTATGAAGTTCAAAATTTACACTGACAGTGTATTGTATAATAATCCTATAAGAAAAATTATACAA
* *
13994 TACACCGTCAGTGGAGTTTAGCATACTGCACGTGCGGGGTTTAAGGGTCGACATGTGT-CCCTTA
129 TACACCGTCAGTGGAGTTTAGCAGACTGCACGTGCGGGGTTTAAGGGTTGACATGTGTCCCCTTA
14058 GGGGAAT
194 -GGGAAT
* * * *
14065 ACATATTAATATTAAATATATTTAATTAATTATGAAATAGTGTATGTGTCAACTTCTTAACTCGC
1 A-GTATTAATATTAAATATATTTAATTAATTATGAAATGGGGTATGTGTCAAC-TCTTAACCCGC
* * * *
14130 TTATGAAGTTCAAAATTTACACTAACAATGTATTGTATAATAAT-CTTTAAAAAAAATTATACAA
64 TTATGAAGTTCAAAATTTACACTGACAGTGTATTGTATAATAATCCTATAAGAAAAATTATACAA
* * * * * *
14194 TACACCGTCAGTGAAGTTTAGCAGACTGCATGCGCGAGGTTCAAGGGTTGACATGTTTCCCCTTA
129 TACACCGTCAGTGGAGTTTAGCAGACTGCACGTGCGGGGTTTAAGGGTTGACATGTGTCCCCTTA
14259 GGGAAT
194 GGGAAT
*
14265 AGTTTTGAATATTA
1 AGTATT-AATATTA
14279 GAGTTTAGAG
Statistics
Matches: 369, Mismatches: 36, Indels: 17
0.87 0.09 0.04
Matches are distributed among these distances:
197 1 0.00
198 10 0.03
199 5 0.01
200 114 0.31
201 236 0.64
202 3 0.01
ACGTcount: A:0.35, C:0.14, G:0.18, T:0.33
Consensus pattern (199 bp):
AGTATTAATATTAAATATATTTAATTAATTATGAAATGGGGTATGTGTCAACTCTTAACCCGCTT
ATGAAGTTCAAAATTTACACTGACAGTGTATTGTATAATAATCCTATAAGAAAAATTATACAATA
CACCGTCAGTGGAGTTTAGCAGACTGCACGTGCGGGGTTTAAGGGTTGACATGTGTCCCCTTAGG
GAAT
Found at i:15283 original size:22 final size:22
Alignment explanation
Indices: 15258--15301 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
15248 TGATAATGTT
* *
15258 AAAATAATTGATAATGTTACTA
1 AAAAGAATTGATAAAGTTACTA
**
15280 AAAAGGTTTGATAAAGTTACTA
1 AAAAGAATTGATAAAGTTACTA
15302 CAATATTAAT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.48, C:0.05, G:0.14, T:0.34
Consensus pattern (22 bp):
AAAAGAATTGATAAAGTTACTA
Found at i:15319 original size:20 final size:18
Alignment explanation
Indices: 15290--15357 Score: 73
Period size: 18 Copynumber: 3.6 Consensus size: 18
15280 AAAAGGTTTG
*
15290 ATAAAGTTACTACAATATT
1 ATAAAATTACTACAA-ATT
*
15309 AATAACATTACTACAAATT
1 -ATAAAATTACTACAAATT
*
15328 ATAAAATTACTAAAAATCT
1 ATAAAATTACTACAAAT-T
*
15347 CTAAAATTACT
1 ATAAAATTACT
15358 GAAAAACCTA
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
18 15 0.36
19 14 0.33
20 13 0.31
ACGTcount: A:0.51, C:0.13, G:0.01, T:0.34
Consensus pattern (18 bp):
ATAAAATTACTACAAATT
Found at i:15353 original size:19 final size:19
Alignment explanation
Indices: 15310--15382 Score: 76
Period size: 19 Copynumber: 3.8 Consensus size: 19
15300 TACAATATTA
* *
15310 ATAACATTACTACAAAT-T
1 ATAAAATTACTAAAAATCT
15328 ATAAAATTACTAAAAATCT
1 ATAAAATTACTAAAAATCT
* *
15347 CTAAAATTACTGAAAAACCT
1 ATAAAATTACT-AAAAATCT
* *
15367 ATAAAGTTATTAAAAA
1 ATAAAATTACTAAAAA
15383 AGCTTAATAA
Statistics
Matches: 46, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
18 15 0.33
19 16 0.35
20 15 0.33
ACGTcount: A:0.55, C:0.12, G:0.03, T:0.30
Consensus pattern (19 bp):
ATAAAATTACTAAAAATCT
Found at i:15449 original size:21 final size:22
Alignment explanation
Indices: 15423--15471 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
15413 TGAAATTCAC
*
15423 AATAAGATTA-CTAAAAATCTT
1 AATAAGATTAGCTAAAAAACTT
* *
15444 AATAAGGTTAGGTAAAAAACTT
1 AATAAGATTAGCTAAAAAACTT
15466 AATAAG
1 AATAAG
15472 GTGACCAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 9 0.38
22 15 0.62
ACGTcount: A:0.53, C:0.06, G:0.12, T:0.29
Consensus pattern (22 bp):
AATAAGATTAGCTAAAAAACTT
Done.