Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015531.1 Corchorus olitorius cultivar O-4 contig15564, 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: 20972
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.32
Found at i:1581 original size:15 final size:15
Alignment explanation
Indices: 1548--1590 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
1538 TACATACCAC
*
1548 TAATAATAATTATTA
1 TAATAATAATAATTA
1563 TAATAATAATAAGTT-
1 TAATAATAATAA-TTA
*
1578 TAATAATTATAAT
1 TAATAATAATAAT
1591 ATTAAGATGT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 1 0.04
15 22 0.88
16 2 0.08
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (15 bp):
TAATAATAATAATTA
Found at i:1590 original size:9 final size:9
Alignment explanation
Indices: 1550--1591 Score: 50
Period size: 9 Copynumber: 4.7 Consensus size: 9
1540 CATACCACTA
1550 ATAATAATT
1 ATAATAATT
* *
1559 ATTATAATA
1 ATAATAATT
1568 ATAATAAGTT
1 ATAATAA-TT
1578 -TAATAATT
1 ATAATAATT
1586 ATAATA
1 ATAATA
1592 TTAAGATGTT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
8 2 0.07
9 24 0.89
10 1 0.04
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (9 bp):
ATAATAATT
Found at i:1602 original size:24 final size:24
Alignment explanation
Indices: 1554--1604 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
1544 CCACTAATAA
* *
1554 TAATTATTATAATAATAATAAGTT
1 TAATAATTATAATAATAAGAAGTT
* *
1578 TAATAATTATAATATTAAGATGTT
1 TAATAATTATAATAATAAGAAGTT
1602 TAA
1 TAA
1605 CGTAAAAAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.49, C:0.00, G:0.06, T:0.45
Consensus pattern (24 bp):
TAATAATTATAATAATAAGAAGTT
Found at i:10581 original size:72 final size:72
Alignment explanation
Indices: 10497--10633 Score: 231
Period size: 72 Copynumber: 1.9 Consensus size: 72
10487 CACCCTACGG
* **
10497 GATATCCAATGATCTCATAGCATTGTTCTTTTGTGTGCCCCATCTTTTGACAATG-TCTACACCT
1 GATATCCAATGATCTCATAGCATTGATCTTTCATGTGCCCCATCTTTTGACAATGTTC-ACACCT
10561 TACAGCAC
65 TACAGCAC
10569 GATATCCAATGATCTCATAGCATTGATCTTTCATGTGCCCCATCTTTTGACAATGTTCACACCTT
1 GATATCCAATGATCTCATAGCATTGATCTTTCATGTGCCCCATCTTTTGACAATGTTCACACCTT
10634 GGCTTGTCTT
Statistics
Matches: 61, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
72 59 0.97
73 2 0.03
ACGTcount: A:0.24, C:0.26, G:0.13, T:0.36
Consensus pattern (72 bp):
GATATCCAATGATCTCATAGCATTGATCTTTCATGTGCCCCATCTTTTGACAATGTTCACACCTT
ACAGCAC
Found at i:11736 original size:30 final size:30
Alignment explanation
Indices: 11700--11765 Score: 96
Period size: 30 Copynumber: 2.2 Consensus size: 30
11690 TTGGATCCTA
*
11700 CTGTAAACAAACTGTTGACTTTGAATCCCG
1 CTGTAAACAAACTGTTGACTTTAAATCCCG
* * *
11730 CTGTAAATACATTGTTGACTTTAAATCCCG
1 CTGTAAACAAACTGTTGACTTTAAATCCCG
11760 CTGTAA
1 CTGTAA
11766 GAACATTGTT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.30, C:0.21, G:0.15, T:0.33
Consensus pattern (30 bp):
CTGTAAACAAACTGTTGACTTTAAATCCCG
Found at i:11772 original size:30 final size:30
Alignment explanation
Indices: 11712--11779 Score: 111
Period size: 30 Copynumber: 2.3 Consensus size: 30
11702 GTAAACAAAC
*
11712 TGTTGACTTTGAATCCCGCTGTAAATACAT
1 TGTTGACTTTAAATCCCGCTGTAAATACAT
11742 TGTTGACTTTAAATCCCGCTGTAAGA-ACAT
1 TGTTGACTTTAAATCCCGCTGTAA-ATACAT
11772 TGTTGACT
1 TGTTGACT
11780 GATTTCATCA
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
30 35 0.97
31 1 0.03
ACGTcount: A:0.26, C:0.19, G:0.18, T:0.37
Consensus pattern (30 bp):
TGTTGACTTTAAATCCCGCTGTAAATACAT
Found at i:12487 original size:71 final size:71
Alignment explanation
Indices: 12313--12600 Score: 452
Period size: 71 Copynumber: 4.0 Consensus size: 71
12303 ATTTTTTTTC
* * * *
12313 TTTTTTCCTACTCAAAAATATGATATTGAAATGGATTACACAATAGGAGATAGCCCTCTCC-TTT
1 TTTTTTACTACTCAAAAACATGATATTGAAATGGACTACACAATAGGAGGTAGCCCTCTCCTTTT
12377 CCCTTT
66 CCCTTT
12383 TTTTTTACTACTCAAAAACATGATATTGAAATGGACTACACAATAGGAGGTAGCCCTCTCCTTTT
1 TTTTTTACTACTCAAAAACATGATATTGAAATGGACTACACAATAGGAGGTAGCCCTCTCCTTTT
12448 CCCTTT
66 CCCTTT
*
12454 TTTTTAACTACTCAAAAACATGATATTGAAATGGACTACACAATAGGAGGTAGCCCTCTCCTTTT
1 TTTTTTACTACTCAAAAACATGATATTGAAATGGACTACACAATAGGAGGTAGCCCTCTCC--TT
12519 CCCATAATCCCTTT
64 ----T--TCCCTTT
12533 TTTTTTACTACTCAAAAACATGATATTGAAATGGACTACACAATAGGAGGTAGCCCTCTCCTTTT
1 TTTTTTACTACTCAAAAACATGATATTGAAATGGACTACACAATAGGAGGTAGCCCTCTCCTTTT
12598 CCC
66 CCC
12601 ATAATCCCAC
Statistics
Matches: 203, Mismatches: 6, Indels: 17
0.90 0.03 0.08
Matches are distributed among these distances:
70 57 0.28
71 73 0.36
73 3 0.01
77 3 0.01
79 67 0.33
ACGTcount: A:0.31, C:0.23, G:0.12, T:0.34
Consensus pattern (71 bp):
TTTTTTACTACTCAAAAACATGATATTGAAATGGACTACACAATAGGAGGTAGCCCTCTCCTTTT
CCCTTT
Found at i:12578 original size:79 final size:79
Alignment explanation
Indices: 12447--12608 Score: 315
Period size: 79 Copynumber: 2.1 Consensus size: 79
12437 CCTCTCCTTT
12447 TCCCTTTTTTTTAACTACTCAAAAACATGATATTGAAATGGACTACACAATAGGAGGTAGCCCTC
1 TCCCTTTTTTTTAACTACTCAAAAACATGATATTGAAATGGACTACACAATAGGAGGTAGCCCTC
12512 TCCTTTTCCCATAA
66 TCCTTTTCCCATAA
*
12526 TCCCTTTTTTTTTACTACTCAAAAACATGATATTGAAATGGACTACACAATAGGAGGTAGCCCTC
1 TCCCTTTTTTTTAACTACTCAAAAACATGATATTGAAATGGACTACACAATAGGAGGTAGCCCTC
12591 TCCTTTTCCCATAA
66 TCCTTTTCCCATAA
12605 TCCC
1 TCCC
12609 ACCCCGTATC
Statistics
Matches: 82, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
79 82 1.00
ACGTcount: A:0.30, C:0.25, G:0.11, T:0.33
Consensus pattern (79 bp):
TCCCTTTTTTTTAACTACTCAAAAACATGATATTGAAATGGACTACACAATAGGAGGTAGCCCTC
TCCTTTTCCCATAA
Found at i:12647 original size:150 final size:150
Alignment explanation
Indices: 12376--12679 Score: 418
Period size: 150 Copynumber: 2.0 Consensus size: 150
12366 CCCTCTCCTT
12376 TCCCTTTTTTTTTACTACTCAAAAACATGATATTGAAATGGACTACACAATAGGAGGTAGCCCTC
1 TCCCTTTTTTTTTACTACTCAAAAACATGATATTGAAATGGACTACACAATAGGAGGTAGCCCTC
* ** *** ***
12441 TCCTTTTCCCTTTTTTTTAACTACTCAAAAACATGATATTGAAATGGACTACACAATAGGAGGTA
66 TCCTTTTCCCATAATCCCAACTACTCAAAAACATGATACCCAAATGGACTACACAATAGGAGGTA
12506 GCCCTCTCCTTTTCCCATAA
131 GCCCTCTCCTTTTCCCATAA
12526 TCCCTTTTTTTTTACTACTCAAAAACATGATATTGAAATGGACTACACAATAGGAGGTAGCCCTC
1 TCCCTTTTTTTTTACTACTCAAAAACATGATATTGAAATGGACTACACAATAGGAGGTAGCCCTC
* *** *
12591 TCCTTTTCCCATAATCCCACCCCGTA-TC-ATCCCATGAT-CCCAAGCT-GACTACACAATAGGA
66 TCCTTTTCCCATAATCCCA--AC-TACTCAAAAACATGATACCCAA-ATGGACTACACAATAGGA
12652 GGTAGCCCTCTCCTTTTCCCATAA
127 GGTAGCCCTCTCCTTTTCCCATAA
12676 TCCC
1 TCCC
12680 ACCCCGATCA
Statistics
Matches: 136, Mismatches: 14, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
150 123 0.90
151 8 0.06
152 3 0.02
153 2 0.01
ACGTcount: A:0.29, C:0.28, G:0.12, T:0.32
Consensus pattern (150 bp):
TCCCTTTTTTTTTACTACTCAAAAACATGATATTGAAATGGACTACACAATAGGAGGTAGCCCTC
TCCTTTTCCCATAATCCCAACTACTCAAAAACATGATACCCAAATGGACTACACAATAGGAGGTA
GCCCTCTCCTTTTCCCATAA
Found at i:12682 original size:71 final size:70
Alignment explanation
Indices: 12566--12702 Score: 256
Period size: 71 Copynumber: 1.9 Consensus size: 70
12556 TATTGAAATG
*
12566 GACTACACAATAGGAGGTAGCCCTCTCCTTTTCCCATAATCCCACCCCGTATCATCCCATGATCC
1 GACTACACAATAGGAGGTAGCCCTCTCCTTTTCCCATAATCCCACCCCG-ATCATCCCAGGATCC
12631 CAAGCT
65 CAAGCT
12637 GACTACACAATAGGAGGTAGCCCTCTCCTTTTCCCATAATCCCACCCCGATCATCCCAGGATCCC
1 GACTACACAATAGGAGGTAGCCCTCTCCTTTTCCCATAATCCCACCCCGATCATCCCAGGATCCC
12702 A
66 A
12703 CAATTGTATT
Statistics
Matches: 65, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
70 16 0.25
71 49 0.75
ACGTcount: A:0.26, C:0.39, G:0.13, T:0.23
Consensus pattern (70 bp):
GACTACACAATAGGAGGTAGCCCTCTCCTTTTCCCATAATCCCACCCCGATCATCCCAGGATCCC
AAGCT
Found at i:12722 original size:58 final size:58
Alignment explanation
Indices: 12659--12993 Score: 554
Period size: 58 Copynumber: 5.8 Consensus size: 58
12649 GGAGGTAGCC
12659 CTCTCCTTTTCCCATA-ATCCCACCCCGATCATCCCAGGATCCCACAATTGTATTCGAT
1 CTCTCCTTTTCCCA-AGATCCCACCCCGATCATCCCAGGATCCCACAATTGTATTCGAT
12717 CTCTCCTTTTCCCAAGATCCCACCCCGATCATCCCAGGATCCCACAATTGTATTCGAT
1 CTCTCCTTTTCCCAAGATCCCACCCCGATCATCCCAGGATCCCACAATTGTATTCGAT
12775 CTCTCCTTTTCCCAAGATCCCACCCCGATCATCCCAGGATCCCACAATTGTATTCGAT
1 CTCTCCTTTTCCCAAGATCCCACCCCGATCATCCCAGGATCCCACAATTGTATTCGAT
12833 CTCTCCTTTTCCCAAGATCCCACCCCGATCATCCCAGGATCCCACAATTGTATTCGAT
1 CTCTCCTTTTCCCAAGATCCCACCCCGATCATCCCAGGATCCCACAATTGTATTCGAT
*
12891 CTCTCCTTTTCCCATA-ATCCCACCCCGATCATCCCAGGATCCCACAATTGTATCCGAT
1 CTCTCCTTTTCCCA-AGATCCCACCCCGATCATCCCAGGATCCCACAATTGTATTCGAT
**
12949 CATC-CCATGATCCCATA-ATCCCACCCCGATCATCCCATGG-TCCCA
1 C-TCTCC-TTTTCCCA-AGATCCCACCCCGATCATCCCA-GGATCCCA
12994 AGCTTACTAC
Statistics
Matches: 269, Mismatches: 3, Indels: 9
0.96 0.01 0.03
Matches are distributed among these distances:
57 1 0.00
58 230 0.86
59 36 0.13
60 2 0.01
ACGTcount: A:0.23, C:0.41, G:0.10, T:0.27
Consensus pattern (58 bp):
CTCTCCTTTTCCCAAGATCCCACCCCGATCATCCCAGGATCCCACAATTGTATTCGAT
Found at i:12890 original size:29 final size:29
Alignment explanation
Indices: 12857--12963 Score: 92
Period size: 29 Copynumber: 3.7 Consensus size: 29
12847 AGATCCCACC
12857 CCGATCATCCCAGGATCCCACAATTGTAT
1 CCGATCATCCCAGGATCCCACAATTGTAT
* *** * *** *
12886 TCGATC-TCTCC-TTTTCCCATAATCCCACC
1 CCGATCATC-CCAGGATCCCACAATTGTA-T
12915 CCGATCATCCCAGGATCCCACAATTGTAT
1 CCGATCATCCCAGGATCCCACAATTGTAT
*
12944 CCGATCATCCCATGATCCCA
1 CCGATCATCCCAGGATCCCA
12964 TAATCCCACC
Statistics
Matches: 55, Mismatches: 19, Indels: 8
0.67 0.23 0.10
Matches are distributed among these distances:
28 11 0.20
29 33 0.60
30 11 0.20
ACGTcount: A:0.24, C:0.39, G:0.10, T:0.26
Consensus pattern (29 bp):
CCGATCATCCCAGGATCCCACAATTGTAT
Found at i:12934 original size:30 final size:30
Alignment explanation
Indices: 12900--12993 Score: 111
Period size: 30 Copynumber: 3.2 Consensus size: 30
12890 TCTCTCCTTT
12900 TCCCATAATCCCACCCCGATCATCCCAGGA
1 TCCCATAATCCCACCCCGATCATCCCAGGA
* *** * *
12930 TCCCACAATTGTA-TCCGATCATCCCATGA
1 TCCCATAATCCCACCCCGATCATCCCAGGA
12959 TCCCATAATCCCACCCCGATCATCCCATGG-
1 TCCCATAATCCCACCCCGATCATCCCA-GGA
12989 TCCCA
1 TCCCA
12994 AGCTTACTAC
Statistics
Matches: 50, Mismatches: 12, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
29 23 0.46
30 26 0.52
31 1 0.02
ACGTcount: A:0.26, C:0.44, G:0.10, T:0.21
Consensus pattern (30 bp):
TCCCATAATCCCACCCCGATCATCCCAGGA
Found at i:13075 original size:21 final size:21
Alignment explanation
Indices: 13051--13090 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
13041 CATAATCACA
13051 ATAGGAGGTAGCCCTCTCCAC
1 ATAGGAGGTAGCCCTCTCCAC
13072 ATAGGAGGTAGCCCTCTCC
1 ATAGGAGGTAGCCCTCTCC
13091 TCTTCCCATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.23, C:0.33, G:0.25, T:0.20
Consensus pattern (21 bp):
ATAGGAGGTAGCCCTCTCCAC
Found at i:13083 original size:65 final size:65
Alignment explanation
Indices: 13007--13133 Score: 236
Period size: 65 Copynumber: 2.0 Consensus size: 65
12997 TTACTACACA
*
13007 ATAGGAGGTAGCCATCTCCTTTTCCCATAATCCCCATAATCACAATAGGAGGTAGCCCTCTCCAC
1 ATAGGAGGTAGCCATCTCCTCTTCCCATAATCCCCATAATCACAATAGGAGGTAGCCCTCTCCAC
*
13072 ATAGGAGGTAGCCCTCTCCTCTTCCCATAATCCCCATAATCACAATAGGAGGTAGCCCTCTC
1 ATAGGAGGTAGCCATCTCCTCTTCCCATAATCCCCATAATCACAATAGGAGGTAGCCCTCTC
13134 TACCCCCATA
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
65 60 1.00
ACGTcount: A:0.27, C:0.33, G:0.16, T:0.24
Consensus pattern (65 bp):
ATAGGAGGTAGCCATCTCCTCTTCCCATAATCCCCATAATCACAATAGGAGGTAGCCCTCTCCAC
Found at i:13146 original size:34 final size:34
Alignment explanation
Indices: 13103--13173 Score: 142
Period size: 34 Copynumber: 2.1 Consensus size: 34
13093 TTCCCATAAT
13103 CCCCATAATCACAATAGGAGGTAGCCCTCTCTAC
1 CCCCATAATCACAATAGGAGGTAGCCCTCTCTAC
13137 CCCCATAATCACAATAGGAGGTAGCCCTCTCTAC
1 CCCCATAATCACAATAGGAGGTAGCCCTCTCTAC
13171 CCC
1 CCC
13174 GATCAGCCCT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 37 1.00
ACGTcount: A:0.28, C:0.38, G:0.14, T:0.20
Consensus pattern (34 bp):
CCCCATAATCACAATAGGAGGTAGCCCTCTCTAC
Found at i:16903 original size:15 final size:15
Alignment explanation
Indices: 16883--16927 Score: 56
Period size: 15 Copynumber: 3.0 Consensus size: 15
16873 TAGGGCTAGG
16883 AAATGGACTATGATC
1 AAATGGACTATGATC
*
16898 AAATGGACTAT-ATGG
1 AAATGGACTATGAT-C
*
16913 AAATGGCCTATGATC
1 AAATGGACTATGATC
16928 TTGTGATGGA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
14 2 0.08
15 21 0.84
16 2 0.08
ACGTcount: A:0.38, C:0.13, G:0.22, T:0.27
Consensus pattern (15 bp):
AAATGGACTATGATC
Found at i:18257 original size:12 final size:12
Alignment explanation
Indices: 18240--18265 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
18230 GCCTTTGTTT
18240 ATTATTAGAATA
1 ATTATTAGAATA
18252 ATTATTAGAATA
1 ATTATTAGAATA
18264 AT
1 AT
18266 AAAAACATTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.08, T:0.42
Consensus pattern (12 bp):
ATTATTAGAATA
Found at i:20536 original size:23 final size:22
Alignment explanation
Indices: 20497--20647 Score: 69
Period size: 22 Copynumber: 6.8 Consensus size: 22
20487 TGAATATTTT
*
20497 TATGAAATTTTGATAACTATAC
1 TATGAAATTTTGATAACCATAC
* * *
20519 TATTAAATTTTTACTAACCATGC
1 TATGAAATTTTGA-TAACCATAC
* **
20542 TATGAAATTTTAATAA-TTTACC
1 TATGAAATTTTGATAACCATA-C
* * *
20564 TATAAAATTGTGATAA--ATTCC
1 TATGAAATTTTGATAACCA-TAC
* * *
20585 ATATGAAACTTTAATAACC-TAAT
1 -TATGAAATTTTGATAACCAT-AC
* * *
20608 TATGAAATTTTAATAAACCTTCC
1 TATGAAATTTTGAT-AACCATAC
20631 TATGAAATTTTG-TAACC
1 TATGAAATTTTGATAACC
20648 TTCCTATATA
Statistics
Matches: 96, Mismatches: 24, Indels: 19
0.69 0.17 0.14
Matches are distributed among these distances:
21 6 0.06
22 56 0.58
23 33 0.34
24 1 0.01
ACGTcount: A:0.40, C:0.13, G:0.07, T:0.40
Consensus pattern (22 bp):
TATGAAATTTTGATAACCATAC
Found at i:20649 original size:21 final size:23
Alignment explanation
Indices: 20541--20654 Score: 80
Period size: 22 Copynumber: 5.2 Consensus size: 23
20531 ACTAACCATG
*
20541 CTATGAAATTTTAAT-AA-TTTAC
1 CTATGAAATTTTAATAAACCTT-C
* * *
20563 CTATAAAATTGTGATAAA--TTC
1 CTATGAAATTTTAATAAACCTTC
* **
20584 CATATGAAACTTTAAT-AACCTAA
1 C-TATGAAATTTTAATAAACCTTC
*
20607 TTATGAAATTTTAATAAACCTTC
1 CTATGAAATTTTAATAAACCTTC
*
20630 CTATGAAATTTT-GT-AACCTTC
1 CTATGAAATTTTAATAAACCTTC
20651 CTAT
1 CTAT
20655 ATATGATTTT
Statistics
Matches: 72, Mismatches: 15, Indels: 11
0.73 0.15 0.11
Matches are distributed among these distances:
21 15 0.21
22 38 0.53
23 19 0.26
ACGTcount: A:0.39, C:0.14, G:0.06, T:0.40
Consensus pattern (23 bp):
CTATGAAATTTTAATAAACCTTC
Done.