Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012830.1 Corchorus capsularis cultivar CVL-1 contig12851, 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: 11784
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Found at i:66 original size:14 final size:13
Alignment explanation
Indices: 50--74 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
40 AACTTAAGAA
50 AAAAATTGGGGAT
1 AAAAATTGGGGAT
63 AAAAATTGGGGA
1 AAAAATTGGGGA
75 AAATATACGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.00, G:0.32, T:0.20
Consensus pattern (13 bp):
AAAAATTGGGGAT
Found at i:3409 original size:15 final size:15
Alignment explanation
Indices: 3389--3417 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
3379 AGCAATGACC
3389 ACAACAACAGCAACG
1 ACAACAACAGCAACG
3404 ACAACAACAGCAAC
1 ACAACAACAGCAAC
3418 AACTGGATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.55, C:0.34, G:0.10, T:0.00
Consensus pattern (15 bp):
ACAACAACAGCAACG
Found at i:3420 original size:18 final size:18
Alignment explanation
Indices: 3375--3420 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 18
3365 CTACCACCAT
* *
3375 CAGCAGCAATGACCACAA
1 CAGCAGCAACGACAACAA
*
3393 CAACAGCAACGACAACAA
1 CAGCAGCAACGACAACAA
*
3411 CAGCAACAAC
1 CAGCAGCAAC
3421 TGGATTAGTG
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.50, C:0.35, G:0.13, T:0.02
Consensus pattern (18 bp):
CAGCAGCAACGACAACAA
Found at i:6006 original size:12 final size:12
Alignment explanation
Indices: 5991--6015 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5981 AGCTGCTGCC
5991 GAGGAGAAGAAA
1 GAGGAGAAGAAA
6003 GAGGAGAAGAAA
1 GAGGAGAAGAAA
6015 G
1 G
6016 TGAGTATAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.56, C:0.00, G:0.44, T:0.00
Consensus pattern (12 bp):
GAGGAGAAGAAA
Found at i:7308 original size:22 final size:24
Alignment explanation
Indices: 7280--7333 Score: 71
Period size: 22 Copynumber: 2.4 Consensus size: 24
7270 ATTTCAATCC
7280 AAATTTCATAAAGG-A-GTTACCA
1 AAATTTCATAAAGGTAGGTTACCA
*
7302 AAATTTC--ACAGGTAGGTTACCA
1 AAATTTCATAAAGGTAGGTTACCA
7324 AAATTTCATA
1 AAATTTCATA
7334 GGTTACAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
20 4 0.15
21 1 0.04
22 21 0.78
24 1 0.04
ACGTcount: A:0.43, C:0.15, G:0.13, T:0.30
Consensus pattern (24 bp):
AAATTTCATAAAGGTAGGTTACCA
Found at i:7336 original size:22 final size:22
Alignment explanation
Indices: 7295--7336 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
7285 TCATAAAGGA
7295 GTTACCAAAATTTCACAGGTAG
1 GTTACCAAAATTTCACAGGTAG
*
7317 GTTACCAAAATTTCATAGGT
1 GTTACCAAAATTTCACAGGT
7337 TACAAAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.36, C:0.17, G:0.17, T:0.31
Consensus pattern (22 bp):
GTTACCAAAATTTCACAGGTAG
Found at i:7337 original size:18 final size:18
Alignment explanation
Indices: 7295--7351 Score: 69
Period size: 18 Copynumber: 2.9 Consensus size: 18
7285 TCATAAAGGA
7295 GTTACCAAAATTTCACAGGTAG
1 GTTACCAAAATTT--CA--TAG
7317 GTTACCAAAATTTCATAG
1 GTTACCAAAATTTCATAG
*
7335 GTTACAAAAATTTCATA
1 GTTACCAAAATTTCATA
7352 TCCATCAAGG
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
18 19 0.56
20 2 0.06
22 13 0.38
ACGTcount: A:0.40, C:0.16, G:0.12, T:0.32
Consensus pattern (18 bp):
GTTACCAAAATTTCATAG
Found at i:7461 original size:48 final size:47
Alignment explanation
Indices: 7404--7562 Score: 149
Period size: 48 Copynumber: 3.3 Consensus size: 47
7394 TGATCATAGG
*
7404 TCACAGCCATCGAGGGCCAGAACTCGCCCAGAAGGCAAAGGTTATCCA
1 TCACGGCCATCGAGGGCCAGAACT-GCCCAGAAGGCAAAGGTTATCCA
* * * * * * * *
7452 CCAAGGCCATCGAGGGCCAAAAATGACCATGACGCCAAAGGCTATCCA
1 TCACGGCCATCGAGGGCCAGAACTGCCCA-GAAGGCAAAGGTTATCCA
* * * * *
7500 TCACGACCATCGAGGG-TAGAAACGGCCAAGAAGGAAAAGGTTATCCA
1 TCACGGCCATCGAGGGCCAG-AACTGCCCAGAAGGCAAAGGTTATCCA
*
7547 TCACGGTCATCGAGGG
1 TCACGGCCATCGAGGG
7563 ACAAAAATGT
Statistics
Matches: 85, Mismatches: 24, Indels: 5
0.75 0.21 0.04
Matches are distributed among these distances:
47 33 0.39
48 52 0.61
ACGTcount: A:0.33, C:0.28, G:0.26, T:0.13
Consensus pattern (47 bp):
TCACGGCCATCGAGGGCCAGAACTGCCCAGAAGGCAAAGGTTATCCA
Found at i:8125 original size:44 final size:44
Alignment explanation
Indices: 8061--8146 Score: 136
Period size: 44 Copynumber: 2.0 Consensus size: 44
8051 AAATTTTGCC
8061 AAAATTTCATAGCCAAGTTACCAAAATTTCATAGGCAGGTTACT
1 AAAATTTCATAGCCAAGTTACCAAAATTTCATAGGCAGGTTACT
*** *
8105 AAAATTTCATAGCGTGGTTACCAAAATTTCATAGGGAGGTTA
1 AAAATTTCATAGCCAAGTTACCAAAATTTCATAGGCAGGTTA
8147 AGGATTTGAA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
44 38 1.00
ACGTcount: A:0.37, C:0.15, G:0.17, T:0.30
Consensus pattern (44 bp):
AAAATTTCATAGCCAAGTTACCAAAATTTCATAGGCAGGTTACT
Found at i:8146 original size:22 final size:22
Alignment explanation
Indices: 8059--8138 Score: 115
Period size: 22 Copynumber: 3.6 Consensus size: 22
8049 TAAAATTTTG
*
8059 CCAAAATTTCATAGCCAAGTTA
1 CCAAAATTTCATAGCCAGGTTA
*
8081 CCAAAATTTCATAGGCAGGTTA
1 CCAAAATTTCATAGCCAGGTTA
* **
8103 CTAAAATTTCATAGCGTGGTTA
1 CCAAAATTTCATAGCCAGGTTA
8125 CCAAAATTTCATAG
1 CCAAAATTTCATAG
8139 GGAGGTTAAG
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 51 1.00
ACGTcount: A:0.38, C:0.19, G:0.14, T:0.30
Consensus pattern (22 bp):
CCAAAATTTCATAGCCAGGTTA
Found at i:11355 original size:317 final size:319
Alignment explanation
Indices: 10291--11784 Score: 1854
Period size: 326 Copynumber: 4.6 Consensus size: 319
10281 GTTGAATTAT
* * *
10291 TATTAACCATCATGGTTTTTGGATAAAAACGCGTTCTAGAGCCCTGACTTAGTTTTGCATGATTT
1 TATTAACCATCACGG-TTTTGGCTAAAAACGCGTTCTGGAGCCCTGACTTAGTTTTGCATGATTT
* *
10356 TTGGCGTAAAGACTCCTTGAAATATCTATATTCATGCAATGAAATCAT-AGCCATATTGAATTTA
65 TTGGCGTAAAGGCTCCTTGAAATATCTATATTCATCCAATGAAATC-TCAGCCATATTGAATTTA
* * *
10420 AGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATCCAATTAAAAATTAAATCGTAAAAAAG
129 AGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTCAATTAAAAATTAAATCGAAAAAAAA
* * *
10485 GGAAAAACAATATTA-AAAGCGTGAAAACCCGTTTAATCTTTTTGGCGTTGAATTATATATTTTT
194 GG-AAAACGATATTAGAAA-CGTGAAAACCCATTTAATCTTTTTGGCATTGAATTATATATTTTT
* *
10549 TCTGATTATTGTGGCAAAAATTTGAGGGAAAAAAAATTTTCGGGTCAGTTTTTAGCCGAAATCGT
257 TCTGAATATTGTGGCAAAAATTTGA-GG--AAAAAATTTTCGGGTCAGTTTTTAGCCAAAATC--
10614 GTG
317 GTG
* * * * * * * *
10617 TATTAATCATCACGATTTTTTGTTAAAAACGTGTTCTGGAG-TCTCGACTCATTTTTGCATGATT
1 TATTAACCATCACG-GTTTTGGCTAAAAACGCGTTCTGGAGCCCT-GACTTAGTTTTGCATGATT
* * *
10681 TTTGGCGTAAAGGCTCCTCGAAATATATATATTCATCTAATGAAATCTCAGCCATATTGAATTTA
64 TTTGGCGTAAAGGCTCCTTGAAATATCTATATTCATCCAATGAAATCTCAGCCATATTGAATTTA
* * * *
10746 AGGATTTGTTTTTACGAGTATGTGCATCTTTTTTCGATTCAATTAAAAATTAAATCGAAAAAAAA
129 AGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTCAATTAAAAATTAAATCG-AAAAAAA
* * * * * *
10811 AGAAAAATGATATTAGAAGCGTGAAAAGCCATTTAATCTCTTTGGCATTGAATTATATGTTTTTT
193 AGGAAAACGATATTAGAAACGTGAAAACCCATTTAATCTTTTTGGCATTGAATTATATATTTTTT
* *
10876 CTTAATATTGTGGCAAAAATTTGAGGAAAAAATTTTCGGGTCAATTTTTAGCCAAAATCGTG
258 CTGAATATTGTGGCAAAAATTTGAGGAAAAAATTTTCGGGTCAGTTTTTAGCCAAAATCGTG
* * *
10938 TATTAACCATCACGATTTTGGCTAAAAACGCATTCTGGAGCCCTGACTTAGTTTTGCATGAGTTT
1 TATTAACCATCACGGTTTTGGCTAAAAACGCGTTCTGGAGCCCTGACTTAGTTTTGCATGATTTT
* * *
11003 TAGCGTAAAGGCTCCTTCAAATATTTATATTCATCCAATGAAATCTCAGCCATATTGAATTTAAG
66 TGGCGTAAAGGCTCCTTGAAATATCTATATTCATCCAATGAAATCTCAGCCATATTGAATTTAAG
* * * *
11068 GATTTGTTTTTACCAGCATCTAAATCTTGTTTCAATTCAATTAAAAATTAAATTGAAAAAAAAGG
131 GATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTCAATTAAAAATTAAATCGAAAAAAAAGG
* * * * * * * * *
11133 GAAACGATAATACAAACATGACAAGCCATTTAAT-TTTTTTGCGTTGAATTATATATTTTTTATG
196 AAAACGATATTAGAAACGTGAAAACCCATTTAATCTTTTTGGCATTGAATTATATATTTTTTCTG
* *
11197 AAAATTGTGGCAAAAATTTGAGGAAAAAATTTT-GGGTCAGTTTTTAGCCAAGATCGTG
261 AATATTGTGGCAAAAATTTGAGGAAAAAATTTTCGGGTCAGTTTTTAGCCAAAATCGTG
* * * *
11255 TATGTTA-CATCACGGTTTTGGCTAAAAACGCATTCTGGAGCCTTGTCTTAGTTTTGCATGATTT
1 TAT-TAACCATCACGGTTTTGGCTAAAAACGCGTTCTGGAGCCCTGACTTAGTTTTGCATGATTT
* * * *
11319 CTGGCATAAAGACTCCTTAAAATATCTATATTCATCCAATGAAATCTCAGCCATATTGAATTTAA
65 TTGGCGTAAAGGCTCCTTGAAATATCTATATTCATCCAATGAAATCTCAGCCATATTGAATTTAA
*
11384 GGATTTGTTTTTACGAGCATCTAAATCTTGTTTCGATTCAATTAAAAATTAAATCGAAAAAAAAG
130 GGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTCAATTAAAAATTAAATCGAAAAAAAAG
* * * * ** *
11449 AAAAACGATATTGGAAACGTGAAAACCCCTTCAATCTTTTTAACATTGAATTATATATTTTCTCT
195 GAAAACGATATTAGAAACGTGAAAACCCATTTAATCTTTTTGGCATTGAATTATATATTTTTTCT
* * *
11514 -AAGTATTGTGGTAAAAAAATTGAGGAAAAAATTTTCGGGTCACTTTTTGCAAAATTTTAGCCAA
260 GAA-TATTGTGG-CAAAAATTTGAGGAAAAAATTTTCGGGTCA------G----TTTTTAGCCAA
11578 AATCGTG
313 AATCGTG
* * * * * *
11585 TAATAAACATCACGGTTTTTGGTTAAAAAGGCGTT-TCGG-GTCCCCGACTTAGATTTGCATGAT
1 TATTAACCATCACGG-TTTTGGCTAAAAACGCGTTCT-GGAG-CCCTGACTTAGTTTTGCATGAT
* * * * * *
11648 TTTTGGCGTAATGGTTCCTTGAAATATCTATATTCATCTAACGAAATCTCACCCATATTGGATTT
63 TTTTGGCGTAAAGGCTCCTTGAAATATCTATATTCATCCAATGAAATCTCAGCCATATTGAATTT
* * *
11713 AAGGATTTGTTTTTACGAGCATCTGAATCATGTTTAGATTCAATTAAAAATAAAATCGAAAAAAA
128 AAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTCAATTAAAAATTAAATCGAAAAAAA
11778 AGGAAAA
193 AGGAAAA
Statistics
Matches: 1010, Mismatches: 133, Indels: 45
0.85 0.11 0.04
Matches are distributed among these distances:
317 227 0.22
318 89 0.09
319 57 0.06
320 152 0.15
321 18 0.02
323 31 0.03
325 5 0.00
326 234 0.23
327 9 0.01
329 2 0.00
330 28 0.03
331 158 0.16
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.36
Consensus pattern (319 bp):
TATTAACCATCACGGTTTTGGCTAAAAACGCGTTCTGGAGCCCTGACTTAGTTTTGCATGATTTT
TGGCGTAAAGGCTCCTTGAAATATCTATATTCATCCAATGAAATCTCAGCCATATTGAATTTAAG
GATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTCAATTAAAAATTAAATCGAAAAAAAAGG
AAAACGATATTAGAAACGTGAAAACCCATTTAATCTTTTTGGCATTGAATTATATATTTTTTCTG
AATATTGTGGCAAAAATTTGAGGAAAAAATTTTCGGGTCAGTTTTTAGCCAAAATCGTG
Done.