Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017703.1 Corchorus olitorius cultivar O-4 contig17736, 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: 33220
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:4969 original size:14 final size:14
Alignment explanation
Indices: 4952--4980 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
4942 TTATTTTTAT
4952 ATTTATTACTATTA
1 ATTTATTACTATTA
4966 ATTTATTACTATTA
1 ATTTATTACTATTA
4980 A
1 A
4981 CTACTAATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.38, C:0.07, G:0.00, T:0.55
Consensus pattern (14 bp):
ATTTATTACTATTA
Found at i:5404 original size:5 final size:5
Alignment explanation
Indices: 5382--5438 Score: 53
Period size: 5 Copynumber: 10.8 Consensus size: 5
5372 AAATTTATTG
* *
5382 ATAAT AT-AT GATATT ATAAT ATAAT ATAAT ATTATT ATCAAT ATAAT
1 ATAAT ATAAT -ATAAT ATAAT ATAAT ATAAT A-TAAT AT-AAT ATAAT
5429 ATATAT ATAA
1 ATA-AT ATAA
5439 AGATTGAGTA
Statistics
Matches: 43, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
4 2 0.05
5 27 0.63
6 14 0.33
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.44
Consensus pattern (5 bp):
ATAAT
Found at i:6900 original size:31 final size:31
Alignment explanation
Indices: 6865--6937 Score: 80
Period size: 31 Copynumber: 2.4 Consensus size: 31
6855 TAAATTATTG
*
6865 CAAATTAAAACAAAT-TAAG-CATTAAATTAAA
1 CAAATTAAAA-AAATGAAAGTC-TTAAATTAAA
*
6896 CAAA-TAATTAAAATGAAAGTCTTAAATTAAA
1 CAAATTAA-AAAAATGAAAGTCTTAAATTAAA
6927 CAAATTAAAAA
1 CAAATTAAAAA
6938 CTGATAGACC
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
30 7 0.20
31 24 0.69
32 4 0.11
ACGTcount: A:0.62, C:0.08, G:0.04, T:0.26
Consensus pattern (31 bp):
CAAATTAAAAAAATGAAAGTCTTAAATTAAA
Found at i:7898 original size:17 final size:18
Alignment explanation
Indices: 7878--7919 Score: 59
Period size: 17 Copynumber: 2.4 Consensus size: 18
7868 AAGAGATCAC
*
7878 AAATATTCAATTAA-AAT
1 AAATATTCAAATAATAAT
*
7895 AAATATTTAAATAATAAT
1 AAATATTCAAATAATAAT
7913 AAATATT
1 AAATATT
7920 AAACATTGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 12 0.55
18 10 0.45
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (18 bp):
AAATATTCAAATAATAAT
Found at i:10667 original size:26 final size:26
Alignment explanation
Indices: 10635--10686 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 26
10625 TACGTTTAAT
10635 AAAGGAGTCTAGTAAA-TTATATCAAA
1 AAAGGAGTCTAGTAAATTTA-ATCAAA
10661 AAAGGAGTCTAGTAAATTTAATCAAA
1 AAAGGAGTCTAGTAAATTTAATCAAA
10687 TCCAAAGTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
26 22 0.88
27 3 0.12
ACGTcount: A:0.50, C:0.08, G:0.15, T:0.27
Consensus pattern (26 bp):
AAAGGAGTCTAGTAAATTTAATCAAA
Found at i:10731 original size:28 final size:25
Alignment explanation
Indices: 10672--10743 Score: 76
Period size: 23 Copynumber: 2.8 Consensus size: 25
10662 AAGGAGTCTA
10672 GTAAATTTAATCAAATCCAAAGTTT
1 GTAAATTTAATCAAATCCAAAGTTT
**
10697 -T-TTTTTAATCAAATCCAAAGTCTCT
1 GTAAATTTAATCAAATCCAAAGT-T-T
*
10722 GGTAAATTTAATTAAATCCAAA
1 -GTAAATTTAATCAAATCCAAA
10744 TTAATTGTAC
Statistics
Matches: 37, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
23 18 0.49
24 2 0.05
25 1 0.03
27 1 0.03
28 15 0.41
ACGTcount: A:0.42, C:0.14, G:0.07, T:0.38
Consensus pattern (25 bp):
GTAAATTTAATCAAATCCAAAGTTT
Found at i:15525 original size:51 final size:50
Alignment explanation
Indices: 15424--15525 Score: 111
Period size: 51 Copynumber: 2.0 Consensus size: 50
15414 GTTCTTCATA
* **
15424 TTTTCCTTGTTTAGATCTTGTCTCAGGACAATCAAACACTCTTTTAGTGT
1 TTTTCCTTGTTTAGATCTTGTCTCAGGACAATCAAACACTCGTACAGTGT
*
15474 TTTTCTCTTGTTTCA-ATCTTGTCTCCGGAC-ATACAAACACT-GTACACGTGT
1 TTTTC-CTTGTTT-AGATCTTGTCTCAGGACAAT-CAAACACTCGTACA-GTGT
15525 T
1 T
15526 CTTCATTCAG
Statistics
Matches: 44, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
50 9 0.20
51 34 0.77
52 1 0.02
ACGTcount: A:0.22, C:0.23, G:0.14, T:0.42
Consensus pattern (50 bp):
TTTTCCTTGTTTAGATCTTGTCTCAGGACAATCAAACACTCGTACAGTGT
Found at i:17675 original size:35 final size:39
Alignment explanation
Indices: 17562--17696 Score: 143
Period size: 41 Copynumber: 3.4 Consensus size: 39
17552 CTTTCCCACT
* * *
17562 TTGAAAACTTTAAAAAAAAAACTGGATTGGATCTTACCCTAAA
1 TTGAAAACTTT--GAAAAGAACTGGA--GGATCTTTCCCTAAA
17605 TTGAAAACTTTGAAAAGAACTGGACAGGATCTTTCCCTAAA
1 TTGAAAACTTTGAAAAGAACTGG--AGGATCTTTCCCTAAA
*
17646 TTGAAAACCTTGAAAAG-A-TGG-GG-TCTTTCCCTAAA
1 TTGAAAACTTTGAAAAGAACTGGAGGATCTTTCCCTAAA
*
17681 TTAAAAACTTTGAAAA
1 TTGAAAACTTTGAAAA
17697 ACTTGGATTG
Statistics
Matches: 84, Mismatches: 6, Indels: 12
0.82 0.06 0.12
Matches are distributed among these distances:
35 26 0.31
36 2 0.02
39 3 0.04
40 1 0.01
41 40 0.48
43 12 0.14
ACGTcount: A:0.42, C:0.15, G:0.15, T:0.28
Consensus pattern (39 bp):
TTGAAAACTTTGAAAAGAACTGGAGGATCTTTCCCTAAA
Found at i:18406 original size:2 final size:2
Alignment explanation
Indices: 18399--18434 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
18389 TATCATGGTA
18399 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
18435 CACAAGAAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:20516 original size:3 final size:3
Alignment explanation
Indices: 20510--20538 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
20500 TATAGTATAT
20510 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
20539 TGTAACTCCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:27373 original size:21 final size:21
Alignment explanation
Indices: 27349--27389 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
27339 TCATGAGTGC
27349 TCAACAACAACAAATATGTGT
1 TCAACAACAACAAATATGTGT
* * *
27370 TCAATAACAGCAAATGTGTG
1 TCAACAACAACAAATATGTG
27390 CACAATAGCA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.44, C:0.17, G:0.15, T:0.24
Consensus pattern (21 bp):
TCAACAACAACAAATATGTGT
Found at i:27976 original size:69 final size:69
Alignment explanation
Indices: 27865--28003 Score: 251
Period size: 69 Copynumber: 2.0 Consensus size: 69
27855 TAAAAGCGTT
*
27865 AGTTTTCCTGGCATCCCATCAGCTAAGAAAAATACAGCCGCCGTCGAACTAATTTGGAAGACTAA
1 AGTTTTCCTGGCATCCCATCAGCTAAGAAAAATACAGCCGCCGTCAAACTAATTTGGAAGACTAA
27930 CCGC
66 CCGC
* *
27934 AGTTTTCCTGGCATCCCATTAGCTAAGAAAAATATAGCCGCCGTCAAACTAATTTGGAAGACTAA
1 AGTTTTCCTGGCATCCCATCAGCTAAGAAAAATACAGCCGCCGTCAAACTAATTTGGAAGACTAA
27999 CCGC
66 CCGC
28003 A
1 A
28004 AAGACTCAAG
Statistics
Matches: 67, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
69 67 1.00
ACGTcount: A:0.33, C:0.26, G:0.18, T:0.23
Consensus pattern (69 bp):
AGTTTTCCTGGCATCCCATCAGCTAAGAAAAATACAGCCGCCGTCAAACTAATTTGGAAGACTAA
CCGC
Found at i:29959 original size:2 final size:2
Alignment explanation
Indices: 29947--29981 Score: 61
Period size: 2 Copynumber: 17.0 Consensus size: 2
29937 AATTAAATGG
29947 TA TA CTA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
29982 ATAAAAATAA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 30 0.94
3 2 0.06
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:31296 original size:50 final size:50
Alignment explanation
Indices: 31224--31329 Score: 144
Period size: 50 Copynumber: 2.1 Consensus size: 50
31214 TATTTCTGAA
* * *
31224 AAGAAAAACACGTGTACAGTGTT-TGTATGTCCGAAGACAAGATTGAAAGC
1 AAGAAAAACACGTGAAAAGTGTTCT-TATGTCCGAAAACAAGATTGAAAGC
*
31274 AAGAAAAACACGT-AAAAGGTGTTCTTTTGTCCGAAAACAAGATTGAAAGC
1 AAGAAAAACACGTGAAAA-GTGTTCTTATGTCCGAAAACAAGATTGAAAGC
31324 AAGAAA
1 AAGAAA
31330 TATTGAAGAA
Statistics
Matches: 50, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
49 2 0.04
50 47 0.94
51 1 0.02
ACGTcount: A:0.44, C:0.13, G:0.22, T:0.21
Consensus pattern (50 bp):
AAGAAAAACACGTGAAAAGTGTTCTTATGTCCGAAAACAAGATTGAAAGC
Done.