Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007178.1 Corchorus capsularis cultivar CVL-1 contig07199, 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: 38494
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:6376 original size:2 final size:2
Alignment explanation
Indices: 6371--6410 Score: 57
Period size: 2 Copynumber: 20.5 Consensus size: 2
6361 AGCAAAAAAT
6371 TA TA TA -A TA GTA TA -A TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
6411 TTGATAATTG
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
1 2 0.06
2 31 0.89
3 2 0.06
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
TA
Found at i:6570 original size:14 final size:14
Alignment explanation
Indices: 6526--6575 Score: 55
Period size: 14 Copynumber: 3.4 Consensus size: 14
6516 GGAATATAAA
*
6526 ATATAATTATATAT
1 ATATAATTATATTT
* *
6540 ATTAATATTTATGTTT
1 A-T-ATAATTATATTT
6556 ATATAATTATATTT
1 ATATAATTATATTT
6570 ATATAA
1 ATATAA
6576 ATAAAAATAT
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
14 17 0.59
15 2 0.07
16 10 0.34
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (14 bp):
ATATAATTATATTT
Found at i:6637 original size:11 final size:11
Alignment explanation
Indices: 6610--6673 Score: 51
Period size: 11 Copynumber: 5.8 Consensus size: 11
6600 TGATATATAA
6610 TATAAACGAAC
1 TATAAACGAAC
*
6621 -ATAAACGAGC
1 TATAAACGAAC
*
6631 TATAAACGATC
1 TATAAACGAAC
**
6642 TATTAAATAAAC
1 TA-TAAACGAAC
*
6654 AATAAACGAAC
1 TATAAACGAAC
6665 -ACTAAACGA
1 TA-TAAACGA
6674 GCATTAATCG
Statistics
Matches: 42, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
10 10 0.24
11 25 0.60
12 7 0.17
ACGTcount: A:0.55, C:0.17, G:0.09, T:0.19
Consensus pattern (11 bp):
TATAAACGAAC
Found at i:8866 original size:11 final size:11
Alignment explanation
Indices: 8850--8882 Score: 66
Period size: 11 Copynumber: 3.0 Consensus size: 11
8840 AATTAGCATG
8850 CTAACCTCCTA
1 CTAACCTCCTA
8861 CTAACCTCCTA
1 CTAACCTCCTA
8872 CTAACCTCCTA
1 CTAACCTCCTA
8883 TCTGCTTAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.27, C:0.45, G:0.00, T:0.27
Consensus pattern (11 bp):
CTAACCTCCTA
Found at i:11286 original size:2 final size:2
Alignment explanation
Indices: 11279--11310 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
11269 CTACTAGTTA
11279 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
11311 GCATTAAATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:16894 original size:167 final size:163
Alignment explanation
Indices: 16607--17044 Score: 642
Period size: 167 Copynumber: 2.6 Consensus size: 163
16597 ATGAGGAGCG
* ** *
16607 AGAGAACTAATTGTTTTCGTCTTTTCACACTTCACCGATTACTTAAATGTCCTAACTTTTGATTC
1 AGAGAACTAATTTTTTTCGTCTTTTC-CACTTGGCAGATTACTTAAATGTCCTAACTTTTGATTC
* * * *
16672 TTGAGGTGATTAAATAACTAGACTTTTTGGTCATTTTTCAATTGACTTTAATAGAGTAGTGGAAT
65 TTGAGGGGATTAAATAACTA-ACTTTTTGGTCATTTCTCAATGGACTTGAATAGAGTAGTGGAAT
* * * **
16737 TAATAAAAGATTCCTACCAAGGCTTGCTTTTGGAGTT
129 TAATAAAAGA-TCCCACCAAGGATTGATGAT-GAGTT
*
16774 AGAGAACTTATTTTTTTCGTCTTTTCCTACTTGGCAGATTACTTAAATGTCCTAACTTTTGATTC
1 AGAGAACTAATTTTTTTCGTCTTTTCC-ACTTGGCAGATTACTTAAATGTCCTAACTTTTGATTC
*
16839 TTGAGGGGATTAAATAAGTAATCTTTTTGGTCATTTCTCAATGGACTTGAATAGAGTAGTGGAAT
65 TTGAGGGGATTAAATAACTAA-CTTTTTGGTCATTTCTCAATGGACTTGAATAGAGTAGTGGAAT
*
16904 TAATAAAAGATCCCATCAAGGATTGATGATGAGTT
129 TAATAAAAGATCCCACCAAGGATTGATGATGAGTT
* * *
16939 AGAGAACTAATCTTTTTCGTCTTTACGACTTGGCAGATTACTTAAATGTCCTAACTTTTGATTCT
1 AGAGAACTAATTTTTTTCGTCTTTTCCACTTGGCAGATTACTTAAATGTCCTAACTTTTGATTCT
17004 TGAGGGGATTAAATAACTAAACTTTTTGGTCATTTCTCAAT
66 TGAGGGGATTAAATAACT-AACTTTTTGGTCATTTCTCAAT
17045 TGAAAAATGA
Statistics
Matches: 247, Mismatches: 21, Indels: 9
0.89 0.08 0.03
Matches are distributed among these distances:
164 75 0.30
165 30 0.12
166 16 0.06
167 126 0.51
ACGTcount: A:0.29, C:0.14, G:0.17, T:0.40
Consensus pattern (163 bp):
AGAGAACTAATTTTTTTCGTCTTTTCCACTTGGCAGATTACTTAAATGTCCTAACTTTTGATTCT
TGAGGGGATTAAATAACTAACTTTTTGGTCATTTCTCAATGGACTTGAATAGAGTAGTGGAATTA
ATAAAAGATCCCACCAAGGATTGATGATGAGTT
Found at i:19062 original size:11 final size:11
Alignment explanation
Indices: 19019--19056 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
19009 TTCCTATATA
*
19019 AAATAAATTAT
1 AAATTAATTAT
19030 CAAA-TAATTAT
1 -AAATTAATTAT
19041 AAATTAATTAT
1 AAATTAATTAT
19052 AAATT
1 AAATT
19057 TGTTATGAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
10 3 0.12
11 18 0.75
12 3 0.12
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (11 bp):
AAATTAATTAT
Found at i:19439 original size:14 final size:14
Alignment explanation
Indices: 19370--19441 Score: 58
Period size: 14 Copynumber: 5.1 Consensus size: 14
19360 CAAAATTTCA
**
19370 TTTCTTAACTGAATT
1 TTTCTTAAAAGAA-T
19385 TTTCTTAAAAGAA-
1 TTTCTTAAAAGAAT
* *
19398 TTT-ATAAAATAAAT
1 TTTCTTAAAA-GAAT
**
19412 TTTCTTAACTGAAT
1 TTTCTTAAAAGAAT
19426 TTTCTTAAAAGAAT
1 TTTCTTAAAAGAAT
19440 TT
1 TT
19442 ATAAAATAAA
Statistics
Matches: 44, Mismatches: 10, Indels: 7
0.72 0.16 0.11
Matches are distributed among these distances:
12 5 0.11
13 5 0.11
14 20 0.45
15 14 0.32
ACGTcount: A:0.39, C:0.08, G:0.06, T:0.47
Consensus pattern (14 bp):
TTTCTTAAAAGAAT
Found at i:19441 original size:41 final size:42
Alignment explanation
Indices: 19370--19451 Score: 157
Period size: 41 Copynumber: 2.0 Consensus size: 42
19360 CAAAATTTCA
19370 TTTCTTAACTGAATTTTTCTTAAAAGAATTTATAAAATAAAT
1 TTTCTTAACTGAATTTTTCTTAAAAGAATTTATAAAATAAAT
19412 TTTCTTAACTGAA-TTTTCTTAAAAGAATTTATAAAATAAA
1 TTTCTTAACTGAATTTTTCTTAAAAGAATTTATAAAATAAA
19452 ACAGCCGCAC
Statistics
Matches: 40, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
41 27 0.68
42 13 0.32
ACGTcount: A:0.44, C:0.07, G:0.05, T:0.44
Consensus pattern (42 bp):
TTTCTTAACTGAATTTTTCTTAAAAGAATTTATAAAATAAAT
Found at i:20255 original size:15 final size:15
Alignment explanation
Indices: 20237--20283 Score: 53
Period size: 14 Copynumber: 3.3 Consensus size: 15
20227 GTGCTTCTAA
20237 ACTTCTCTTGAACAC
1 ACTTCTCTTGAACAC
** *
20252 ACTT-AATTAAACA-
1 ACTTCTCTTGAACAC
20265 ACTTCTCTTGAACAC
1 ACTTCTCTTGAACAC
20280 ACTT
1 ACTT
20284 AAACTTGATC
Statistics
Matches: 24, Mismatches: 6, Indels: 4
0.71 0.18 0.12
Matches are distributed among these distances:
13 4 0.17
14 12 0.50
15 8 0.33
ACGTcount: A:0.34, C:0.28, G:0.04, T:0.34
Consensus pattern (15 bp):
ACTTCTCTTGAACAC
Found at i:21049 original size:20 final size:20
Alignment explanation
Indices: 21011--21051 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
21001 CACAATTCTA
* *
21011 CACAATCTTTCTCTCTCTCT
1 CACAATCTTTATCTATCTCT
*
21031 CACAATCTTTATTTATCTCT
1 CACAATCTTTATCTATCTCT
21051 C
1 C
21052 TTCTACTCTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.20, C:0.34, G:0.00, T:0.46
Consensus pattern (20 bp):
CACAATCTTTATCTATCTCT
Found at i:23029 original size:87 final size:87
Alignment explanation
Indices: 22916--23102 Score: 238
Period size: 87 Copynumber: 2.1 Consensus size: 87
22906 TGGAGAATAA
* * *
22916 TTTGAATTC-AATTGATTGTGATCTTCCTAATGGAGTTATGAG-TGGTTATGGTGCAAAATCTTT
1 TTTGAATTCAAATT-ATTGTGATCTTCCTAATGGAGTTATG-GTTAGTAATGATGCAAAATCTTT
*
22979 GGAAAAT-ATTATGTTAGAGGATAG
64 GGAAAATGATT-TGGTAGAGGATAG
23003 TTTGAATTCAAATT-TTAGTGATCTTCCTAATGGAGTTATGGTTAGTAATGATGCAAAATCTTTG
1 TTTGAATTCAAATTATT-GTGATCTTCCTAATGGAGTTATGGTTAGTAATGATGCAAAATCTTTG
* * * *
23067 GAAACTGATTTGGTGGTGGATAT
65 GAAAATGATTTGGTAGAGGATAG
23090 TTTGAATTCAAAT
1 TTTGAATTCAAAT
23103 CGGAGTGGTC
Statistics
Matches: 88, Mismatches: 8, Indels: 8
0.85 0.08 0.08
Matches are distributed among these distances:
86 3 0.03
87 78 0.89
88 7 0.08
ACGTcount: A:0.30, C:0.07, G:0.22, T:0.40
Consensus pattern (87 bp):
TTTGAATTCAAATTATTGTGATCTTCCTAATGGAGTTATGGTTAGTAATGATGCAAAATCTTTGG
AAAATGATTTGGTAGAGGATAG
Found at i:23120 original size:87 final size:87
Alignment explanation
Indices: 22933--23122 Score: 231
Period size: 87 Copynumber: 2.2 Consensus size: 87
22923 TCAATTGATT
* * * *
22933 GTGATCTTCCTAATGGAGTTATGAGTGGTTATGGTGCAAAATCTTTGGAAAATATTATGTTAGAG
1 GTGATCTTCCTAATGGAGTTATGAGTAGTAATGATGCAAAATCTTTGGAAAATATTATGGTAGAG
***
22998 GATAGTTTGAATTCAAATTTTA
66 GATAGTTTGAATTCAAATCGGA
* *
23020 GTGATCTTCCTAATGGAGTTATG-GTTAGTAATGATGCAAAATCTTTGGAAACTGATT-TGGTGG
1 GTGATCTTCCTAATGGAGTTATGAG-TAGTAATGATGCAAAATCTTTGGAAAAT-ATTATGGTAG
* *
23083 TGGATATTTTGAATTCAAATCGGA
64 AGGATAGTTTGAATTCAAATCGGA
* *
23107 GTGGTCTTGCTAATGG
1 GTGATCTTCCTAATGG
23123 GAATATGGCA
Statistics
Matches: 88, Mismatches: 13, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
86 1 0.01
87 84 0.95
88 3 0.03
ACGTcount: A:0.28, C:0.08, G:0.25, T:0.38
Consensus pattern (87 bp):
GTGATCTTCCTAATGGAGTTATGAGTAGTAATGATGCAAAATCTTTGGAAAATATTATGGTAGAG
GATAGTTTGAATTCAAATCGGA
Found at i:25737 original size:7 final size:7
Alignment explanation
Indices: 25725--25758 Score: 68
Period size: 7 Copynumber: 4.9 Consensus size: 7
25715 TTTTTACACT
25725 TTTGCCC
1 TTTGCCC
25732 TTTGCCC
1 TTTGCCC
25739 TTTGCCC
1 TTTGCCC
25746 TTTGCCC
1 TTTGCCC
25753 TTTGCC
1 TTTGCC
25759 ATTTTTTACA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.00, C:0.41, G:0.15, T:0.44
Consensus pattern (7 bp):
TTTGCCC
Found at i:25822 original size:33 final size:33
Alignment explanation
Indices: 25780--25877 Score: 160
Period size: 33 Copynumber: 3.0 Consensus size: 33
25770 TTTTGCCCTT
*
25780 AGCCACGGCGGAGCCTCCCCACTAGGGCGGCTC
1 AGCCACGGCGGAGCCGCCCCACTAGGGCGGCTC
*
25813 AGCCACGGCGGAGCCGCCCCACTAGGGCAGCTC
1 AGCCACGGCGGAGCCGCCCCACTAGGGCGGCTC
* *
25846 AGCCACAGCGGAACCGCCCCACTAGGGCGGCT
1 AGCCACGGCGGAGCCGCCCCACTAGGGCGGCT
25878 AGACTATTAT
Statistics
Matches: 60, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 60 1.00
ACGTcount: A:0.18, C:0.42, G:0.33, T:0.07
Consensus pattern (33 bp):
AGCCACGGCGGAGCCGCCCCACTAGGGCGGCTC
Found at i:26640 original size:26 final size:28
Alignment explanation
Indices: 26590--26647 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
26580 TTCTAACTCA
26590 ACCTCTTTTTTATTGCAATTATATATGC
1 ACCTCTTTTTTATTGCAATTATATATGC
26618 ACCTCTTTTTTATTGCAATTATATATGC
1 ACCTCTTTTTTATTGCAATTATATATGC
26646 AC
1 AC
26648 TATACACACC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.26, C:0.19, G:0.07, T:0.48
Consensus pattern (28 bp):
ACCTCTTTTTTATTGCAATTATATATGC
Found at i:31004 original size:22 final size:20
Alignment explanation
Indices: 30960--31007 Score: 60
Period size: 22 Copynumber: 2.3 Consensus size: 20
30950 TTTAGGAAAA
*
30960 TATTCTTTTAAATTATTTAT
1 TATTTTTTTAAATTATTTAT
*
30980 TATTTTTTATAAATTTTATTAT
1 TATTTTTT-TAAATTAT-TTAT
31002 TATTTT
1 TATTTT
31008 AGATGAAACC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 7 0.29
21 7 0.29
22 10 0.42
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (20 bp):
TATTTTTTTAAATTATTTAT
Found at i:31679 original size:151 final size:151
Alignment explanation
Indices: 31498--31805 Score: 519
Period size: 151 Copynumber: 2.0 Consensus size: 151
31488 TTATAATTAC
*
31498 TTTATTTTTACCATTTTACTATTTTTCATTAAAAACTTGGATATATTAAAAAATTTTAATATATA
1 TTTATTTTTACCATTTTACTATTTTCCATTAAAAACTTGGATATATTAAAAAATTTTAATATATA
* *
31563 GTTTGATTCTACTAAAAGCTCTATGTTCATTTAATTAAATTCAATATTTTTATAATTATTTTATT
66 GTTTAATTCTACTAAAAACTCTATGTTCATTTAATTAAATTCAATATTTTTATAATTATTTTATT
31628 GTTACCATTTTAAT-TTAAAAG
131 GTTACCATTTT-ATGTTAAAAG
***
31649 TTTATTTTTACCATTTTACTATTTTCCATTAAAAACTTGGATATATTAAATTTTTTTAATATATA
1 TTTATTTTTACCATTTTACTATTTTCCATTAAAAACTTGGATATATTAAAAAATTTTAATATATA
*
31714 GTTTAATTCTACTAAAAACTCTATTTTCATTTAATTAAATTCAATATTTTTATAATTATTTTATT
66 GTTTAATTCTACTAAAAACTCTATGTTCATTTAATTAAATTCAATATTTTTATAATTATTTTATT
*
31779 TTTACCATTTTATGTTAAAAG
131 GTTACCATTTTATGTTAAAAG
*
31800 GTTATT
1 TTTATT
31806 GTGATTGATA
Statistics
Matches: 147, Mismatches: 9, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
150 2 0.01
151 145 0.99
ACGTcount: A:0.35, C:0.09, G:0.05, T:0.52
Consensus pattern (151 bp):
TTTATTTTTACCATTTTACTATTTTCCATTAAAAACTTGGATATATTAAAAAATTTTAATATATA
GTTTAATTCTACTAAAAACTCTATGTTCATTTAATTAAATTCAATATTTTTATAATTATTTTATT
GTTACCATTTTATGTTAAAAG
Found at i:32729 original size:78 final size:78
Alignment explanation
Indices: 32600--32760 Score: 304
Period size: 78 Copynumber: 2.1 Consensus size: 78
32590 ACTTTGTTAA
32600 TATTTTTCTTTACGTGGAATTATTTATTTTGTTCCAATGGTAGTAAAACTCTATGTATATACAAA
1 TATTTTTCTTTACGTGGAATTATTTATTTTGTTCCAATGGTAGTAAAACTCTATGTATATACAAA
*
32665 TGGACGAGTCGGG
66 TGGACGAGTCGAG
*
32678 TATTTTTCTTTATGTGGAATTATTTATTTTGTTCCAATGGTAGTAAAACTCTATGTATATACAAA
1 TATTTTTCTTTACGTGGAATTATTTATTTTGTTCCAATGGTAGTAAAACTCTATGTATATACAAA
32743 TGGACGAGTCGAG
66 TGGACGAGTCGAG
32756 TATTT
1 TATTT
32761 GGGTTTAATT
Statistics
Matches: 81, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
78 81 1.00
ACGTcount: A:0.29, C:0.11, G:0.18, T:0.43
Consensus pattern (78 bp):
TATTTTTCTTTACGTGGAATTATTTATTTTGTTCCAATGGTAGTAAAACTCTATGTATATACAAA
TGGACGAGTCGAG
Found at i:35379 original size:36 final size:36
Alignment explanation
Indices: 35332--35406 Score: 141
Period size: 36 Copynumber: 2.1 Consensus size: 36
35322 AATAACAAAT
*
35332 AACAAACCATAATAAGGAAAAGTGTAATTACTATAA
1 AACAAACCATAATAAGGAAAAGTGTAATTACTACAA
35368 AACAAACCATAATAAGGAAAAGTGTAATTACTACAA
1 AACAAACCATAATAAGGAAAAGTGTAATTACTACAA
35404 AAC
1 AAC
35407 CAAGCTAAAG
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.56, C:0.13, G:0.11, T:0.20
Consensus pattern (36 bp):
AACAAACCATAATAAGGAAAAGTGTAATTACTACAA
Done.