Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01010139.1 Corchorus olitorius cultivar O-4 contig10171, 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: 14076
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:10041 original size:35 final size:35
Alignment explanation
Indices: 9976--10043 Score: 84
Period size: 35 Copynumber: 1.9 Consensus size: 35
9966 TTTATTTCAT
* **
9976 TTTTTTTAAATTTTAGAAAATATAGGATAATTTAA
1 TTTTTTTAAATTATAGAAAATATAAAATAATTTAA
*
10011 TTTTTTTAAATTATA-AAAATGTAAAAATAATTT
1 TTTTTTTAAATTATAGAAAATAT-AAAATAATTT
10044 TTTTATTGTA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
34 6 0.21
35 22 0.79
ACGTcount: A:0.46, C:0.00, G:0.06, T:0.49
Consensus pattern (35 bp):
TTTTTTTAAATTATAGAAAATATAAAATAATTTAA
Found at i:13116 original size:36 final size:35
Alignment explanation
Indices: 13003--13133 Score: 99
Period size: 36 Copynumber: 3.7 Consensus size: 35
12993 TGAAAATGAC
* * *
13003 GGGAACTTTCCCTAAATTGAAAAC-TAAAACCT-GAT
1 GGGAACTTTTCC-AATTTGAAAACTTAAAAACTAG-T
* * * *
13038 GGGAACTTTTCCAA-CTAAAAACTTTGAAAACTGAAT
1 GGGAACTTTTCCAATTTGAAAAC-TTAAAAACT-AGT
*
13074 GAGAAC-TTTCCTAATTTGAAAACTTAAAAAACTAGT
1 GGGAACTTTTCC-AATTTGAAAACTT-AAAAACTAGT
*
13110 GGGAACTTTTACAATTTGAAAACT
1 GGGAACTTTTCCAATTTGAAAACT
13134 GGCTAAATTA
Statistics
Matches: 75, Mismatches: 13, Indels: 15
0.73 0.13 0.15
Matches are distributed among these distances:
33 6 0.08
34 2 0.03
35 22 0.29
36 29 0.39
37 16 0.21
ACGTcount: A:0.41, C:0.16, G:0.14, T:0.29
Consensus pattern (35 bp):
GGGAACTTTTCCAATTTGAAAACTTAAAAACTAGT
Found at i:13209 original size:89 final size:89
Alignment explanation
Indices: 13053--13262 Score: 368
Period size: 89 Copynumber: 2.4 Consensus size: 89
13043 CTTTTCCAAC
* * *
13053 TAAAAACTTTGAAAACTGAATGAGAACTTTCCTAATTTGAAAACTTAAAAAACTAGTGGGAACTT
1 TAAATACTTTGAAAACTGAATGAGAACTTTCCCAATTTAAAAACTTAAAAAACTAGTGGGAACTT
13118 TTACAATTTGAAAACTGGCTAAAT
66 TTACAATTTGAAAACTGGCTAAAT
13142 TAAATACTTTGAAAACTGAATGAGAACTTTCCCAATTTAAAAACTTAAAAAACTAGTGGGAACTT
1 TAAATACTTTGAAAACTGAATGAGAACTTTCCCAATTTAAAAACTTAAAAAACTAGTGGGAACTT
13207 TTACAATTTGAAAACTGGCTAAAT
66 TTACAATTTGAAAACTGGCTAAAT
* *
13231 TAAATACTTTGAAAACT-TATGGGAACTTTCCC
1 TAAATACTTTGAAAACTGAATGAGAACTTTCCC
13263 GACTTGAAAA
Statistics
Matches: 116, Mismatches: 5, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
88 13 0.11
89 103 0.89
ACGTcount: A:0.42, C:0.14, G:0.13, T:0.31
Consensus pattern (89 bp):
TAAATACTTTGAAAACTGAATGAGAACTTTCCCAATTTAAAAACTTAAAAAACTAGTGGGAACTT
TTACAATTTGAAAACTGGCTAAAT
Found at i:13373 original size:53 final size:52
Alignment explanation
Indices: 13190--13477 Score: 325
Period size: 52 Copynumber: 5.5 Consensus size: 52
13180 AAAAACTTAA
** * *
13190 AAAACT-AGTGGGAACTTTTACAATTTGAAAACTG-GCTAAATTAAATACTTTG
1 AAAACTGA-TGGGAACTTTCCCAATTTGAAAA-AGAGCTAAATTGAATACTTTG
* * *
13242 AAAACTTATGGGAACTTTCCCGACTTGAAAAAGAGCTAAATTGAATA-TTGTG
1 AAAACTGATGGGAACTTTCCCAATTTGAAAAAGAGCTAAATTGAATACTT-TG
* * * *
13294 AAAACTGGTGGGAACTTTCCCAATTTGAAAAAGAGATAGATTGAATACTTCG
1 AAAACTGATGGGAACTTTCCCAATTTGAAAAAGAGCTAAATTGAATACTTTG
** *
13346 AAGATTTGATGGGAACTTTCCCAATTTGAAAAAGGGCTAAATTGAATACTTTG
1 AA-AACTGATGGGAACTTTCCCAATTTGAAAAAGAGCTAAATTGAATACTTTG
* * *
13399 AAAACTGGTGGGAAC--TCTCAATTTGAAAAAGAGCTAGATTGAATACTTTG
1 AAAACTGATGGGAACTTTCCCAATTTGAAAAAGAGCTAAATTGAATACTTTG
**
13449 AAGATTTGATGGGAACTTTCCCAATTTGA
1 AA-AACTGATGGGAACTTTCCCAATTTGA
13478 GAACTTAAAA
Statistics
Matches: 198, Mismatches: 30, Indels: 15
0.81 0.12 0.06
Matches are distributed among these distances:
50 34 0.17
51 13 0.07
52 93 0.47
53 58 0.29
ACGTcount: A:0.38, C:0.12, G:0.20, T:0.30
Consensus pattern (52 bp):
AAAACTGATGGGAACTTTCCCAATTTGAAAAAGAGCTAAATTGAATACTTTG
Found at i:13472 original size:103 final size:104
Alignment explanation
Indices: 13190--13477 Score: 395
Period size: 103 Copynumber: 2.8 Consensus size: 104
13180 AAAAACTTAA
* * * * * * *
13190 AAAACTAGTGGGAACTTTTACAATTTGAAAACTG-GCTAAATTAAATACTTTGAAAACTT-ATGG
1 AAAACTGGTGGGAACTTCT-CAATTTGAAAA-AGAGCTAGATTGAATACTTTGAAGATTTGATGG
* *
13253 GAACTTTCCCGACTTGAAAAAGAGCTAAATTGAATATTGTG
64 GAACTTTCCCAATTTGAAAAAGAGCTAAATTGAATATTGTG
* * *
13294 AAAACTGGTGGGAACTTTCCCAATTTGAAAAAGAGATAGATTGAATACTTCGAAGATTTGATGGG
1 AAAACTGGTGGGAAC-TTCTCAATTTGAAAAAGAGCTAGATTGAATACTTTGAAGATTTGATGGG
*
13359 AACTTTCCCAATTTGAAAAAGGGCTAAATTGAATACTT-TG
65 AACTTTCCCAATTTGAAAAAGAGCTAAATTGAATA-TTGTG
13399 AAAACTGGTGGGAAC-TCTCAATTTGAAAAAGAGCTAGATTGAATACTTTGAAGATTTGATGGGA
1 AAAACTGGTGGGAACTTCTCAATTTGAAAAAGAGCTAGATTGAATACTTTGAAGATTTGATGGGA
13463 ACTTTCCCAATTTGA
66 ACTTTCCCAATTTGA
13478 GAACTTAAAA
Statistics
Matches: 164, Mismatches: 16, Indels: 9
0.87 0.08 0.05
Matches are distributed among these distances:
103 62 0.38
104 44 0.27
105 56 0.34
106 2 0.01
ACGTcount: A:0.38, C:0.12, G:0.20, T:0.30
Consensus pattern (104 bp):
AAAACTGGTGGGAACTTCTCAATTTGAAAAAGAGCTAGATTGAATACTTTGAAGATTTGATGGGA
ACTTTCCCAATTTGAAAAAGAGCTAAATTGAATATTGTG
Done.