Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005539.1 Corchorus capsularis cultivar CVL-1 contig05557, 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: 18041
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.34
Found at i:5214 original size:54 final size:53
Alignment explanation
Indices: 5171--5359 Score: 229
Period size: 54 Copynumber: 3.5 Consensus size: 53
5161 TGTGATCGTA
* *
5171 ACTGGAGATCAAATTTCTAGAAGGGAATCAATCATCACCTCTGATAGGATCATT
1 ACTGGAAATCAAATTTCTAGAAAGGAATCAA-CATCACCTCTGATAGGATCATT
* * * *
5225 ACTGGAAATCAGAA-TTCTAGAAAGGAATCAAGCAACACCCCCGATAGGGTCATT
1 ACTGGAAATCA-AATTTCTAGAAAGGAATCAA-CATCACCTCTGATAGGATCATT
* * *
5279 ACTGGAAATCAGATTTCTATAAAGGAATCAACTTC-CACTCCTGATAGGATCATT
1 ACTGGAAATCAAATTTCTAGAAAGGAATCAACATCAC-CT-CTGATAGGATCATT
*
5333 ACTGGAAATCAAATTTCTAGAAGGGAA
1 ACTGGAAATCAAATTTCTAGAAAGGAA
5360 CCAAGCTCTG
Statistics
Matches: 114, Mismatches: 17, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
52 1 0.01
53 4 0.04
54 107 0.94
55 2 0.02
ACGTcount: A:0.38, C:0.19, G:0.19, T:0.25
Consensus pattern (53 bp):
ACTGGAAATCAAATTTCTAGAAAGGAATCAACATCACCTCTGATAGGATCATT
Found at i:5283 original size:108 final size:108
Alignment explanation
Indices: 5171--5365 Score: 279
Period size: 108 Copynumber: 1.8 Consensus size: 108
5161 TGTGATCGTA
* *
5171 ACTGGAGATCAAATTTCTAGAAGGGAATCAATCAT-CAC-CTCTGATAGGATCATTACTGGAAAT
1 ACTGGAAATCAAATTTCTAGAAAGGAATCAA-CATCCACTC-CTGATAGGATCATTACTGGAAAT
*
5234 CAGAA-TTCTAGAAAGGAATCAAGCAACACCCCCGATAGGGTCATT
64 CA-AATTTCTAGAAAGGAACCAAGCAACACCCCCGATAGGGTCATT
* * *
5279 ACTGGAAATCAGATTTCTATAAAGGAATCAACTTCCACTCCTGATAGGATCATTACTGGAAATCA
1 ACTGGAAATCAAATTTCTAGAAAGGAATCAACATCCACTCCTGATAGGATCATTACTGGAAATCA
*
5344 AATTTCTAGAAGGGAACCAAGC
66 AATTTCTAGAAAGGAACCAAGC
5366 TCTGCATCTG
Statistics
Matches: 77, Mismatches: 7, Indels: 6
0.86 0.08 0.07
Matches are distributed among these distances:
107 4 0.05
108 72 0.94
109 1 0.01
ACGTcount: A:0.37, C:0.20, G:0.18, T:0.24
Consensus pattern (108 bp):
ACTGGAAATCAAATTTCTAGAAAGGAATCAACATCCACTCCTGATAGGATCATTACTGGAAATCA
AATTTCTAGAAAGGAACCAAGCAACACCCCCGATAGGGTCATT
Found at i:5580 original size:54 final size:54
Alignment explanation
Indices: 5472--5672 Score: 192
Period size: 54 Copynumber: 3.7 Consensus size: 54
5462 TCTTCTGATG
* ** * * * * * *
5472 GGATCGTTACTGGGGATCAAATTTCTAGAAGGGAATCAATTATCAC-CTCTGATA
1 GGATCATTACTGGAAATCAGATTTCTAGAAAGGAACCAACTAACACTC-CCGATA
* *
5526 GGATCATTACTGGAAATCAGAATTCTAGAAAGGAATCAAGC-AACA-TGCCCGATA
1 GGATCATTACTGGAAATCAGATTTCTAGAAAGGAACCAA-CTAACACT-CCCGATA
* ** **
5580 GGGTCATTACTGGAAATCAGATTTCTAGAAAGGAACCAACTTCCACTCCTAATA
1 GGATCATTACTGGAAATCAGATTTCTAGAAAGGAACCAACTAACACTCCCGATA
* *
5634 GGATCATTACTGGAAATCAGATTTCTAGGAGGGAACCAA
1 GGATCATTACTGGAAATCAGATTTCTAGAAAGGAACCAA
5673 GCTATGCATC
Statistics
Matches: 123, Mismatches: 19, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
53 1 0.01
54 120 0.98
55 2 0.02
ACGTcount: A:0.36, C:0.18, G:0.21, T:0.25
Consensus pattern (54 bp):
GGATCATTACTGGAAATCAGATTTCTAGAAAGGAACCAACTAACACTCCCGATA
Found at i:5641 original size:309 final size:309
Alignment explanation
Indices: 5082--5702 Score: 1107
Period size: 309 Copynumber: 2.0 Consensus size: 309
5072 CCAATTTCTA
* *
5082 GAACAGAATCAACTTCTGGTTATGAGGGAAGCATTACTAGCAGTCAGGTTTCTAGAAGCGAGTCA
1 GAACAGAATCAACTTCTGATTATGAGGGAAGCATTACTAGAAGTCAGGTTTCTAGAAGCGAGTCA
*
5147 ACCCCCTCTTCTGATGTGATCGTAACTGGAGATCAAATTTCTAGAAGGGAATCAATCATCACCTC
66 ACCCCCTCTTCTGATGGGATCGTAACTGGAGATCAAATTTCTAGAAGGGAATCAATCATCACCTC
5212 TGATAGGATCATTACTGGAAATCAGAATTCTAGAAAGGAATCAAGCAACACCCCCGATAGGGTCA
131 TGATAGGATCATTACTGGAAATCAGAATTCTAGAAAGGAATCAAGCAACACCCCCGATAGGGTCA
* * *
5277 TTACTGGAAATCAGATTTCTATAAAGGAATCAACTTCCACTCCTGATAGGATCATTACTGGAAAT
196 TTACTGGAAATCAGATTTCTAGAAAGGAACCAACTTCCACTCCTAATAGGATCATTACTGGAAAT
* *
5342 CAAATTTCTAGAAGGGAACCAAGCTCTGCATCTGGTGGCATCGTTGCTG
261 CAAATTTCTAGAAGGGAACCAAGCTATGCATCTGGTGGCATCATTGCTG
5391 GAACAGAATCAACTTCTGATTATGAGGGAAGCATTACTAGAAGTCAGGTTTCTAGAAGCGAGTCA
1 GAACAGAATCAACTTCTGATTATGAGGGAAGCATTACTAGAAGTCAGGTTTCTAGAAGCGAGTCA
* * *
5456 ACCCCCTCTTCTGATGGGATCGTTACTGGGGATCAAATTTCTAGAAGGGAATCAATTATCACCTC
66 ACCCCCTCTTCTGATGGGATCGTAACTGGAGATCAAATTTCTAGAAGGGAATCAATCATCACCTC
**
5521 TGATAGGATCATTACTGGAAATCAGAATTCTAGAAAGGAATCAAGCAACATGCCCGATAGGGTCA
131 TGATAGGATCATTACTGGAAATCAGAATTCTAGAAAGGAATCAAGCAACACCCCCGATAGGGTCA
5586 TTACTGGAAATCAGATTTCTAGAAAGGAACCAACTTCCACTCCTAATAGGATCATTACTGGAAAT
196 TTACTGGAAATCAGATTTCTAGAAAGGAACCAACTTCCACTCCTAATAGGATCATTACTGGAAAT
* *
5651 CAGATTTCTAGGAGGGAACCAAGCTATGCATCTGGTGGCATCATTGCTG
261 CAAATTTCTAGAAGGGAACCAAGCTATGCATCTGGTGGCATCATTGCTG
5700 GAA
1 GAA
5703 ATCAAATCTC
Statistics
Matches: 297, Mismatches: 15, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
309 297 1.00
ACGTcount: A:0.33, C:0.20, G:0.22, T:0.26
Consensus pattern (309 bp):
GAACAGAATCAACTTCTGATTATGAGGGAAGCATTACTAGAAGTCAGGTTTCTAGAAGCGAGTCA
ACCCCCTCTTCTGATGGGATCGTAACTGGAGATCAAATTTCTAGAAGGGAATCAATCATCACCTC
TGATAGGATCATTACTGGAAATCAGAATTCTAGAAAGGAATCAAGCAACACCCCCGATAGGGTCA
TTACTGGAAATCAGATTTCTAGAAAGGAACCAACTTCCACTCCTAATAGGATCATTACTGGAAAT
CAAATTTCTAGAAGGGAACCAAGCTATGCATCTGGTGGCATCATTGCTG
Found at i:5694 original size:54 final size:53
Alignment explanation
Indices: 5583--5835 Score: 179
Period size: 54 Copynumber: 4.7 Consensus size: 53
5573 CCCGATAGGG
* * **
5583 TCATTACTGGAAATCAGATTTCTAGAAAGGAACCAA-CTTCCACTCCTAATAGG-A
1 TCATTACTGGAAATCAGATTTCTAGAAGGGAACCAAGCTTGCA-T-CTGGT-GGCA
*
5637 TCATTACTGGAAATCAGATTTCTAGGAGGGAACCAAGCTATGCATCTGGTGGCA
1 TCATTACTGGAAATCAGATTTCTAGAAGGGAACCAAGCT-TGCATCTGGTGGCA
* * * * * * *
5691 TCATTGCTGGAAATCAAATCTCTAGAAGGGAATCAAGATCTGCATTTGGTGGCG
1 TCATTACTGGAAATCAGATTTCTAGAAGGGAACCAAGCT-TGCATCTGGTGGCA
** ** * * * * * * *
5745 TTGTTACCAGAAATCCA-ATCTCTAGAAGGGAATCAACCTCTCCTTCTGATGGTA
1 TCATTACTGGAAAT-CAGATTTCTAGAAGGGAACCAAGCT-TGCATCTGGTGGCA
* * * *
5799 TCATTACTGGAAACCAAATTTCTCGAAGGGAATCAAG
1 TCATTACTGGAAATCAGATTTCTAGAAGGGAACCAAG
5836 TTCTGTTTCT
Statistics
Matches: 159, Mismatches: 35, Indels: 10
0.78 0.17 0.05
Matches are distributed among these distances:
53 4 0.03
54 147 0.92
55 5 0.03
56 3 0.02
ACGTcount: A:0.32, C:0.20, G:0.21, T:0.27
Consensus pattern (53 bp):
TCATTACTGGAAATCAGATTTCTAGAAGGGAACCAAGCTTGCATCTGGTGGCA
Found at i:5695 original size:108 final size:107
Alignment explanation
Indices: 5523--5722 Score: 242
Period size: 108 Copynumber: 1.9 Consensus size: 107
5513 ATCACCTCTG
* *
5523 ATAGGATCATTACTGGAAATCAGAATTCTAGAAAGGAATCAAGCAACATGCCCGATAGGGTCATT
1 ATAGGATCATTACTGGAAATCAGAATTCTAGAAAGGAACCAAGCAACAT-CCCGATAGGATCATT
* *
5588 ACTGGAAATCAGATTTCTAGAAAGGAACCAACTTCCACTCCTA
65 ACTGGAAATCAAATCTCTAGAAAGGAACCAACTTCCACTCCTA
* * * * * *
5631 ATAGGATCATTACTGGAAATCAGATTTCTAGGAGGGAACCAAGCTATGCAT-CTGGT-GGCATCA
1 ATAGGATCATTACTGGAAATCAGAATTCTAGAAAGGAACCAAGC-A-ACATCCCGATAGG-ATCA
* *
5694 TTGCTGGAAATCAAATCTCTAGAAGGGAA
63 TTACTGGAAATCAAATCTCTAGAAAGGAA
5723 TCAAGATCTG
Statistics
Matches: 77, Mismatches: 12, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
107 2 0.03
108 71 0.92
109 1 0.01
110 3 0.04
ACGTcount: A:0.36, C:0.18, G:0.21, T:0.24
Consensus pattern (107 bp):
ATAGGATCATTACTGGAAATCAGAATTCTAGAAAGGAACCAAGCAACATCCCGATAGGATCATTA
CTGGAAATCAAATCTCTAGAAAGGAACCAACTTCCACTCCTA
Found at i:12929 original size:81 final size:81
Alignment explanation
Indices: 12698--12936 Score: 388
Period size: 81 Copynumber: 3.0 Consensus size: 81
12688 CGGGAATGCT
* * * * *
12698 AATGCTAGTAAAAAGACAGCTAATGCTGGTTCTCCTCTCTCGGTGGAATCATTACCAGCAACAAA
1 AATGCTAGTAAAAAGACAGCTAATGCCGGTTCTCCTCCCTCAGTGGAATCCTCACCAGCAACAAA
** *
12763 GAAGAATTCTGCCGCT
66 GAAGGGTTCTGCCGCC
*
12779 AATGCTAGTAAAAAGGCAGCTAATGCCGGTTCTCCTCCCTCAGTGGAATCCTCACCAGCAACAAA
1 AATGCTAGTAAAAAGACAGCTAATGCCGGTTCTCCTCCCTCAGTGGAATCCTCACCAGCAACAAA
12844 GAAGGGTTCTGCCGCC
66 GAAGGGTTCTGCCGCC
*
12860 AATGCTAGTAAAAAGACAGCTATTGCCGGTTCTCCTCCCTCAGTGGAATCCTCACCAGCAACAAA
1 AATGCTAGTAAAAAGACAGCTAATGCCGGTTCTCCTCCCTCAGTGGAATCCTCACCAGCAACAAA
12925 GAAGGGTTCTGC
66 GAAGGGTTCTGC
12937 TCGGCAAAAG
Statistics
Matches: 147, Mismatches: 11, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
81 147 1.00
ACGTcount: A:0.30, C:0.27, G:0.21, T:0.22
Consensus pattern (81 bp):
AATGCTAGTAAAAAGACAGCTAATGCCGGTTCTCCTCCCTCAGTGGAATCCTCACCAGCAACAAA
GAAGGGTTCTGCCGCC
Found at i:16007 original size:6 final size:6
Alignment explanation
Indices: 15996--16021 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
15986 ACCTCAAACA
15996 AGTTTT AGTTTT AGTTTT AGTTTT AG
1 AGTTTT AGTTTT AGTTTT AGTTTT AG
16022 GTGAGTTTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.19, C:0.00, G:0.19, T:0.62
Consensus pattern (6 bp):
AGTTTT
Found at i:17113 original size:29 final size:29
Alignment explanation
Indices: 17071--17144 Score: 148
Period size: 29 Copynumber: 2.6 Consensus size: 29
17061 GAACATTGTA
17071 TCGCAACATAGTATATTTTTTTGAAATCT
1 TCGCAACATAGTATATTTTTTTGAAATCT
17100 TCGCAACATAGTATATTTTTTTGAAATCT
1 TCGCAACATAGTATATTTTTTTGAAATCT
17129 TCGCAACATAGTATAT
1 TCGCAACATAGTATAT
17145 GTAATTAACT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 45 1.00
ACGTcount: A:0.32, C:0.15, G:0.11, T:0.42
Consensus pattern (29 bp):
TCGCAACATAGTATATTTTTTTGAAATCT
Done.