Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007527.1 Corchorus capsularis cultivar CVL-1 contig07548, 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: 49772
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:1049 original size:63 final size:64
Alignment explanation
Indices: 961--1086 Score: 175
Period size: 66 Copynumber: 1.9 Consensus size: 64
951 GCATGCTTTA
* *
961 AAATAAAACTAACAAGAAACTTAAACCATGCATA-ATATGGTCTCCAAAATGAGCATCAACTAGG
1 AAATAAAACTAACAAAAAACTTAAACCA-GAATACATATGGTCTCCAAAATGAGCATCAACTAGG
*
1025 AAATAAAACT-TCAAAAAACTTAAACCAGAATATGCCATATGGTCTCCAAAATGAGCATCAAC
1 AAATAAAACTAACAAAAAACTTAAACCAGAATA---CATATGGTCTCCAAAATGAGCATCAAC
1087 GTCTAGCTGC
Statistics
Matches: 55, Mismatches: 3, Indels: 6
0.86 0.05 0.09
Matches are distributed among these distances:
62 4 0.07
63 15 0.27
64 10 0.18
66 26 0.47
ACGTcount: A:0.48, C:0.20, G:0.11, T:0.21
Consensus pattern (64 bp):
AAATAAAACTAACAAAAAACTTAAACCAGAATACATATGGTCTCCAAAATGAGCATCAACTAGG
Found at i:3592 original size:15 final size:15
Alignment explanation
Indices: 3551--3606 Score: 51
Period size: 15 Copynumber: 3.6 Consensus size: 15
3541 CGCACAAATA
*
3551 TCGGGTCATTTGGGT
1 TCGGGTCATTTTGGT
3566 T-GGGTCAATTTTGGT
1 TCGGGTC-ATTTTGGT
* *
3581 TCGGGTCTTTTTCAGTT
1 TCGGGTCATTTT--GGT
3598 TCGGGTCAT
1 TCGGGTCAT
3607 ATGGTTCAGA
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
14 5 0.15
15 13 0.39
16 5 0.15
17 10 0.30
ACGTcount: A:0.09, C:0.14, G:0.32, T:0.45
Consensus pattern (15 bp):
TCGGGTCATTTTGGT
Found at i:5061 original size:10 final size:10
Alignment explanation
Indices: 5048--5075 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
5038 GTGAGGAGTA
5048 GTGTGTATGT
1 GTGTGTATGT
5058 GTGTGTATGT
1 GTGTGTATGT
5068 GTGTGTAT
1 GTGTGTAT
5076 ATATATATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.11, C:0.00, G:0.39, T:0.50
Consensus pattern (10 bp):
GTGTGTATGT
Found at i:5078 original size:2 final size:2
Alignment explanation
Indices: 5073--5127 Score: 51
Period size: 2 Copynumber: 28.0 Consensus size: 2
5063 TATGTGTGTG
* * *
5073 TA TA TA TA TA TA TA T- TC TA TG TA T- TA TA TA TC TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
5113 TC TA TA CTA TA TA TA
1 TA TA TA -TA TA TA TA
5128 AAAGCACAGG
Statistics
Matches: 43, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
1 2 0.05
2 39 0.91
3 2 0.05
ACGTcount: A:0.40, C:0.07, G:0.02, T:0.51
Consensus pattern (2 bp):
TA
Found at i:6032 original size:349 final size:350
Alignment explanation
Indices: 5390--6180 Score: 1040
Period size: 349 Copynumber: 2.2 Consensus size: 350
5380 TCCAAAATAT
* * *
5390 TCTCCAAGTCGGTTTAGGAGAAGATCAATTCTATTCA-AAACTTTCAAGGGCAAAATTGTCCACT
1 TCTCCAAGTCGGTTTAGGAGAAGATCAATTAT-TTCAGAAA-TTTCAAGGGCAAAATCGTCCACC
* * * *
5454 GGAAC-GACAGAACTAGGTCTCTAGAACAACATAAAAGTTGTAGATCTTGGAATCCTCTTTCCAA
64 AGAACTG-CAGAATTAGGTCTC--GAGCAACATAAAAGTTGTAGATATTGGAATCCTCTTTCCAA
* *
5518 CGGTACCTCATTTGCATTTTTCTGAGCTCTAGATCAAAAGTTATGAATTTTTTTTCCAAAACTGC
126 CGGTACCTCATTTGCATTTTTCTGAGCTCTAGATAAAAAGTTATGAATTTTTCTTCCAAAACTGC
* * *
5583 TCTTATGAAGTCCTCTTTTGAATAGGATTTAACAATACTACATCAGGGTTGAATCATTACTGCAT
191 TCTTATGAAGACCTCTTTTGAACAGGATTTAACAATACTACATCAGGGCTGAATCATTACTGCAT
* * * *
5648 CATGATTATTGATTGGACTTGAACTCCTTCTTTGGGCTTTCATA-ATAACAAAGTGG-GTCTAAG
256 CATAATTACTGATTGGACTTGAACTCCTTCTTTGGGCTTCCATATA-AACAAAGTGGAG-CTAAA
*
5711 AATATCATATTTA-GACTTCAAGACATCTGGC
319 AATATCAGATTTAGGACTTCAAGACATCTGGC
* *
5742 TCTCCAAGTCGGTTTAGGAGAAGATCAATTATGTTCAGAAATTTCAAGGGAAAAATCGTCTACCA
1 TCTCCAAGTCGGTTTAGGAGAAGATCAATTAT-TTCAGAAATTTCAAGGGCAAAATCGTCCACCA
** *
5807 GAACTGCAGAATTAGGTCTCGAGGTACATAAAAGTTGTAGATATTGGAATTCTCTTTCCAACGGT
65 GAACTGCAGAATTAGGTCTCGAGCAACATAAAAGTTGTAGATATTGGAATCCTCTTTCCAACGGT
* * * * *
5872 ACCTTATTTGCATTTTTCTGAGTTTTGGATAAAAAGTTATGAA-TTTTCTTCCAAAATTGCTCTT
130 ACCTCATTTGCATTTTTCTGAGCTCTAGATAAAAAGTTATGAATTTTTCTTCCAAAACTGCTCTT
* * ** * ** *
5936 GTGAAGACCTCTTTTGAACATGATTTAACAATGTTGCATCATTGCTGAATCATTATTGCATCATA
195 ATGAAGACCTCTTTTGAACAGGATTTAACAATACTACATCAGGGCTGAATCATTACTGCATCATA
* * * *
6001 ATTACTGGTTGGACTT-AGACTCCTTCTTTGGGCTTCCATGTAAACGAATTGGAGCTAAAAATAT
260 ATTACTGATTGGACTTGA-ACTCCTTCTTTGGGCTTCCATATAAACAAAGTGGAGCTAAAAATAT
**
6065 CAGATTTAGGGTTTCAAGACATCTGGC
324 CAGATTTAGGACTTCAAGACATCTGGC
*
6092 TCTCCAAGTCGGTTTAGGAGAAGATCAATTATATCTAGAAAATTTCATA-GGCAAAATCGTCCAC
1 TCTCCAAGTCGGTTTAGGAGAAGATCAATTATTTC-AG-AAATTTCA-AGGGCAAAATCGTCCAC
6156 CAGAACTGCAGAATTAGGTCTCGAG
63 CAGAACTGCAGAATTAGGTCTCGAG
6181 ATGAACATAA
Statistics
Matches: 385, Mismatches: 45, Indels: 19
0.86 0.10 0.04
Matches are distributed among these distances:
348 1 0.00
349 132 0.34
350 130 0.34
351 46 0.12
352 72 0.19
353 4 0.01
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Consensus pattern (350 bp):
TCTCCAAGTCGGTTTAGGAGAAGATCAATTATTTCAGAAATTTCAAGGGCAAAATCGTCCACCAG
AACTGCAGAATTAGGTCTCGAGCAACATAAAAGTTGTAGATATTGGAATCCTCTTTCCAACGGTA
CCTCATTTGCATTTTTCTGAGCTCTAGATAAAAAGTTATGAATTTTTCTTCCAAAACTGCTCTTA
TGAAGACCTCTTTTGAACAGGATTTAACAATACTACATCAGGGCTGAATCATTACTGCATCATAA
TTACTGATTGGACTTGAACTCCTTCTTTGGGCTTCCATATAAACAAAGTGGAGCTAAAAATATCA
GATTTAGGACTTCAAGACATCTGGC
Found at i:8131 original size:22 final size:22
Alignment explanation
Indices: 8105--8149 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
8095 TTTTGGACTA
8105 TTTAATAATATCTAATTCTAAT
1 TTTAATAATATCTAATTCTAAT
*
8127 TTTAATAATATCTAATTTTAAT
1 TTTAATAATATCTAATTCTAAT
8149 T
1 T
8150 GTGATATGTG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.40, C:0.07, G:0.00, T:0.53
Consensus pattern (22 bp):
TTTAATAATATCTAATTCTAAT
Found at i:8140 original size:16 final size:15
Alignment explanation
Indices: 8117--8148 Score: 55
Period size: 16 Copynumber: 2.1 Consensus size: 15
8107 TAATAATATC
8117 TAATTCTAATTTTAA
1 TAATTCTAATTTTAA
8132 TAATATCTAATTTTAA
1 TAAT-TCTAATTTTAA
8148 T
1 T
8149 TGTGATATGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.25
16 12 0.75
ACGTcount: A:0.41, C:0.06, G:0.00, T:0.53
Consensus pattern (15 bp):
TAATTCTAATTTTAA
Found at i:12010 original size:21 final size:20
Alignment explanation
Indices: 11971--12012 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
11961 ACATGTGGGG
* *
11971 AATTTCTTTTTGGCTTGTTC
1 AATTTCTTTTTGACATGTTC
11991 AATTTCTTTTTGCACATGTTC
1 AATTTCTTTTTG-ACATGTTC
12012 A
1 A
12013 TATGGTTGTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 12 0.63
21 7 0.37
ACGTcount: A:0.17, C:0.17, G:0.12, T:0.55
Consensus pattern (20 bp):
AATTTCTTTTTGACATGTTC
Found at i:14749 original size:10 final size:11
Alignment explanation
Indices: 14730--14779 Score: 50
Period size: 10 Copynumber: 4.5 Consensus size: 11
14720 TCTTTAAATG
14730 TATTTATATTT
1 TATTTATATTT
14741 TATTT-TATTT
1 TATTTATATTT
**
14751 TATACA-ATTT
1 TATTTATATTT
14761 TATTTACTATTT
1 TATTTA-TATTT
14773 ATATTTA
1 -TATTTA
14780 GAATAAATTA
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
10 16 0.52
11 5 0.16
12 4 0.13
13 6 0.19
ACGTcount: A:0.30, C:0.04, G:0.00, T:0.66
Consensus pattern (11 bp):
TATTTATATTT
Found at i:17561 original size:33 final size:33
Alignment explanation
Indices: 17524--17605 Score: 137
Period size: 33 Copynumber: 2.5 Consensus size: 33
17514 TTCTTTTCAC
*
17524 CCAAAACAGAATTATTTTCAATGCTATGATCAA
1 CCAAAACAGAATTATTTGCAATGCTATGATCAA
*
17557 CCAAAACATAATTATTTGCAATGCTATGATCAA
1 CCAAAACAGAATTATTTGCAATGCTATGATCAA
*
17590 CCAAAACAGATTTATT
1 CCAAAACAGAATTATT
17606 ATCATCACAA
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.43, C:0.18, G:0.09, T:0.30
Consensus pattern (33 bp):
CCAAAACAGAATTATTTGCAATGCTATGATCAA
Found at i:17629 original size:33 final size:33
Alignment explanation
Indices: 17592--17696 Score: 122
Period size: 33 Copynumber: 3.2 Consensus size: 33
17582 ATGATCAACC
* *
17592 AAAACAGATTTATTATCATCACAAACAACACTT
1 AAAACAGATTTAGTATCATCGCAAACAACACTT
* * *
17625 AAAACAGATTTAGTGTCATTGCAAACAACACTC
1 AAAACAGATTTAGTATCATCGCAAACAACACTT
** *
17658 AAATTAGGTTTAGTATCATCGCAAACAACA-TCT
1 AAAACAGATTTAGTATCATCGCAAACAACACT-T
17691 AAAACA
1 AAAACA
17697 CTCTTTACAA
Statistics
Matches: 58, Mismatches: 13, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
32 1 0.02
33 57 0.98
ACGTcount: A:0.46, C:0.20, G:0.09, T:0.26
Consensus pattern (33 bp):
AAAACAGATTTAGTATCATCGCAAACAACACTT
Found at i:30241 original size:26 final size:26
Alignment explanation
Indices: 30197--30246 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
30187 ATGATTTAGG
* *
30197 GGTTACTAACGCCCTTTTTCTTTTGA
1 GGTTACTAACACCCATTTTCTTTTGA
* *
30223 GGTTACTAACACTCATTTTTTTTT
1 GGTTACTAACACCCATTTTCTTTT
30247 TCAAGAGGGA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 20 1.00
ACGTcount: A:0.18, C:0.20, G:0.12, T:0.50
Consensus pattern (26 bp):
GGTTACTAACACCCATTTTCTTTTGA
Found at i:36351 original size:22 final size:23
Alignment explanation
Indices: 36332--36384 Score: 74
Period size: 22 Copynumber: 2.3 Consensus size: 23
36322 AAACAAAAGA
36332 AACGAAAAA-TTAAAAGAAAAAT
1 AACGAAAAATTTAAAAGAAAAAT
36354 AACGAAAAATTTAAAAGATAAAAGT
1 AACGAAAAATTTAAAAGA-AAAA-T
36379 AA-GAAA
1 AACGAAA
36385 TTCTTAGGTA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
22 9 0.32
23 8 0.29
24 8 0.29
25 3 0.11
ACGTcount: A:0.70, C:0.04, G:0.11, T:0.15
Consensus pattern (23 bp):
AACGAAAAATTTAAAAGAAAAAT
Found at i:37339 original size:476 final size:476
Alignment explanation
Indices: 36447--37398 Score: 1771
Period size: 476 Copynumber: 2.0 Consensus size: 476
36437 CAACGGCGCC
36447 AAAATTGTGATCGGTCATTGAACAAACCACAAGATAAATCCCCAAAAACAAATAACTACTAGCTA
1 AAAATTGTGATCGGTCATTGAACAAACCACAAGATAAATCCCCAAAAACAAATAACTACTAGCTA
*
36512 GGGCAAGTAGGGGTTGAATCCACACAGAAGGTAAGAGCAAATCAAAGGCAAATTGTACTAAAGAA
66 GGGCAAGTAGGGGTCGAATCCACACAGAAGGTAAGAGCAAATCAAAGGCAAATTGTACTAAAGAA
36577 AAGCTTACTAAAAAGGGATTTTTAGGATTTTTCAAAATAGATTAATTAAACTAGAAAACAATTAA
131 AAGCTTACTAAAAAGGGATTTTTAGGATTTTTCAAAATAGATTAATTAAACTAGAAAACAATTAA
* *
36642 AAGAAATCTGAACTAAAGATTTAAAAGAGAGTTTGAGAAAATCAATGAGTAAAAACATATTTCTT
196 AAGAAATCTAAACTAAAGATTTAAAAGAGAGTTTGAGAAAATCAATGAGTAAAAACATACTTCTT
* *
36707 CTCCTTTAGGCAACTATTTTGATCAAGTGAATCATGAATCATAGACACTAAACATAAATTTGGCT
261 CTCCTTTAGGCAACTATTTTGATCAAATGAATCATGAATCATAGACACTAAACATAAATTTGGCC
*
36772 TAAATTGCAATCAATTAAGAATCATAAATTATGCCAAATCGGTATATAGCCTAAGACGTAGACAT
326 TAAATTGCAATCAATTAAGAATCATAAATTATCCCAAATCGGTATATAGCCTAAGACGTAGACAT
36837 CAACTTCCATTGAAACAAAGTAATCCTCTTAATATCTTAAACAACTCCATTTGAATAATTGGTAT
391 CAACTTCCATTGAAACAAAGTAATCCTCTTAATATCTTAAACAACTCCATTTGAATAATTGGTAT
36902 AGGAGAGGAATACTCGACCCT
456 AGGAGAGGAATACTCGACCCT
* * * *
36923 AAAATTGTGATTGGTCTTTGAACAAACCACAAGATAAATCCCCACAAACCAATAACTACTAGCTA
1 AAAATTGTGATCGGTCATTGAACAAACCACAAGATAAATCCCCAAAAACAAATAACTACTAGCTA
*
36988 GGGCAAGTAGGGGTCGAATCCACAGAGAAGGTAAGAGCAAATCAAAGGCAAATTGTACTAAAGAA
66 GGGCAAGTAGGGGTCGAATCCACACAGAAGGTAAGAGCAAATCAAAGGCAAATTGTACTAAAGAA
37053 AAGCTTACTAAAAAGGGATTTTTAGGATTTTTCAAAATAGATTAATTAAACTAGAAAACAATTAA
131 AAGCTTACTAAAAAGGGATTTTTAGGATTTTTCAAAATAGATTAATTAAACTAGAAAACAATTAA
37118 AAGAAATCTAAACTAAAGATTTAAAAGAGAGTTTGAGAAAATCAATGAGTAAAAACATACTTCTT
196 AAGAAATCTAAACTAAAGATTTAAAAGAGAGTTTGAGAAAATCAATGAGTAAAAACATACTTCTT
*
37183 CTCCTTTAGGCAATTATTTTGATCAAATGAATCATGAATCATAGACACTAAACATAAATTTGGCC
261 CTCCTTTAGGCAACTATTTTGATCAAATGAATCATGAATCATAGACACTAAACATAAATTTGGCC
37248 TAAATTGCAATCAATTAAGAATCATAAATTA-CCCAAAATCGGTATATAGCCTAAGACGTAGACA
326 TAAATTGCAATCAATTAAGAATCATAAATTATCCC-AAATCGGTATATAGCCTAAGACGTAGACA
37312 TCAACTTCCATTGAAACAAAGTAATCCTCTTAATATCTTAAACAACTCCATTTGAATAATTGGTA
390 TCAACTTCCATTGAAACAAAGTAATCCTCTTAATATCTTAAACAACTCCATTTGAATAATTGGTA
*
37377 TAGGAGAGGAATATTCGACCCT
455 TAGGAGAGGAATACTCGACCCT
37399 CCAACATGCT
Statistics
Matches: 462, Mismatches: 13, Indels: 2
0.97 0.03 0.00
Matches are distributed among these distances:
475 2 0.00
476 460 1.00
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.26
Consensus pattern (476 bp):
AAAATTGTGATCGGTCATTGAACAAACCACAAGATAAATCCCCAAAAACAAATAACTACTAGCTA
GGGCAAGTAGGGGTCGAATCCACACAGAAGGTAAGAGCAAATCAAAGGCAAATTGTACTAAAGAA
AAGCTTACTAAAAAGGGATTTTTAGGATTTTTCAAAATAGATTAATTAAACTAGAAAACAATTAA
AAGAAATCTAAACTAAAGATTTAAAAGAGAGTTTGAGAAAATCAATGAGTAAAAACATACTTCTT
CTCCTTTAGGCAACTATTTTGATCAAATGAATCATGAATCATAGACACTAAACATAAATTTGGCC
TAAATTGCAATCAATTAAGAATCATAAATTATCCCAAATCGGTATATAGCCTAAGACGTAGACAT
CAACTTCCATTGAAACAAAGTAATCCTCTTAATATCTTAAACAACTCCATTTGAATAATTGGTAT
AGGAGAGGAATACTCGACCCT
Found at i:45044 original size:34 final size:34
Alignment explanation
Indices: 45000--45070 Score: 106
Period size: 34 Copynumber: 2.1 Consensus size: 34
44990 TGTTTCTTTC
*
45000 TTTTACTTGTTTCAAAATTCCATGCTAAGCACTA
1 TTTTACTTGTTTCAAAATTCCATACTAAGCACTA
* * *
45034 TTTTATTTGTTTCAAAATTCCGTATTAAGCACTA
1 TTTTACTTGTTTCAAAATTCCATACTAAGCACTA
45068 TTT
1 TTT
45071 AATAGTATTT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.28, C:0.17, G:0.08, T:0.46
Consensus pattern (34 bp):
TTTTACTTGTTTCAAAATTCCATACTAAGCACTA
Found at i:47415 original size:29 final size:29
Alignment explanation
Indices: 47378--47451 Score: 98
Period size: 29 Copynumber: 2.6 Consensus size: 29
47368 GGGTCATCCA
47378 GGGGCATTTTGGTCATTTTCACATCTAGG
1 GGGGCATTTTGGTCATTTTCACATCTAGG
** *
47407 GGGGCATTTTGGTCATTTTTGCATTTAGG
1 GGGGCATTTTGGTCATTTTCACATCTAGG
47436 GGGTG--TTTTGGTCATT
1 GGG-GCATTTTGGTCATT
47452 CTTAATCTAC
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
28 11 0.27
29 29 0.71
30 1 0.02
ACGTcount: A:0.14, C:0.12, G:0.31, T:0.43
Consensus pattern (29 bp):
GGGGCATTTTGGTCATTTTCACATCTAGG
Done.