Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009131.1 Corchorus capsularis cultivar CVL-1 contig09152, 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: 13186
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.35
Found at i:1695 original size:1 final size:1
Alignment explanation
Indices: 1689--1727 Score: 78
Period size: 1 Copynumber: 39.0 Consensus size: 1
1679 TGCTCTGTGC
1689 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1728 CTAAGATCCG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 38 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:4129 original size:16 final size:17
Alignment explanation
Indices: 4110--4148 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
4100 ATATCAGGCT
4110 GGGTTCAAATCA-TTTC
1 GGGTTCAAATCATTTTC
**
4126 GGGTTCAGGTCATTTTC
1 GGGTTCAAATCATTTTC
4143 GGGTTC
1 GGGTTC
4149 GGGCTTGAGT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 10 0.50
17 10 0.50
ACGTcount: A:0.15, C:0.18, G:0.28, T:0.38
Consensus pattern (17 bp):
GGGTTCAAATCATTTTC
Found at i:4216 original size:32 final size:32
Alignment explanation
Indices: 4168--4263 Score: 138
Period size: 32 Copynumber: 3.0 Consensus size: 32
4158 TTAGGTCAAA
*
4168 TTAAATTTGGGACAGGTTGATTCGGGTTCGGG
1 TTAAATTTGGGTCAGGTTGATTCGGGTTCGGG
* *
4200 TTAACTTTGGGTCAGGTTGATTCGGATTCGGG
1 TTAAATTTGGGTCAGGTTGATTCGGGTTCGGG
* * *
4232 TTAATTTTGGGTCAAGTTAATTCGGGTTCGGG
1 TTAAATTTGGGTCAGGTTGATTCGGGTTCGGG
4264 CTGGGTTTTG
Statistics
Matches: 57, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
32 57 1.00
ACGTcount: A:0.18, C:0.10, G:0.34, T:0.38
Consensus pattern (32 bp):
TTAAATTTGGGTCAGGTTGATTCGGGTTCGGG
Found at i:5188 original size:16 final size:16
Alignment explanation
Indices: 5153--5200 Score: 51
Period size: 16 Copynumber: 3.0 Consensus size: 16
5143 CGAAATCTGA
* * *
5153 TTTTTCGGGTTTGAGC
1 TTTTTCGGGTTCGGGT
5169 TTTTTCGGGTTCGGGT
1 TTTTTCGGGTTCGGGT
* *
5185 TTTTTAGGATTCGGGT
1 TTTTTCGGGTTCGGGT
5201 ATTTGACTTT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.06, C:0.10, G:0.33, T:0.50
Consensus pattern (16 bp):
TTTTTCGGGTTCGGGT
Found at i:5477 original size:17 final size:17
Alignment explanation
Indices: 5455--5492 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
5445 TATGTTTTAT
*
5455 ATATTAT-GTTAATAATA
1 ATATTATAGTT-ATAAAA
5472 ATATTATAGTTATAAAA
1 ATATTATAGTTATAAAA
5489 ATAT
1 ATAT
5493 AGATGATTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 16 0.84
18 3 0.16
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (17 bp):
ATATTATAGTTATAAAA
Found at i:7544 original size:386 final size:385
Alignment explanation
Indices: 6836--7554 Score: 1032
Period size: 385 Copynumber: 1.9 Consensus size: 385
6826 TGCTTTGACT
* * *
6836 TTGCGTTTGGAGATAAAAAAGTTGCTTTTGAACCCAAATGCAATACCAAATAAATCACGTTTGTG
1 TTGCGTTTGAAGAAAAAAAAGTTGCTTTTGAACCCAAACGCAATACCAAATAAATCACGTTTGTG
*
6901 TCAAAAACTAATTTTGAACGCAAAAACCAAGCCAACCCGAGAAACTAATCTTTAGGTGCTTTTGC
66 TCAAAAACTAATTTTGAACGCAAAAACCAAGCCAACCCGAAAAACTAATCTTTAGGTGCTTTTGC
* * * *
6966 GTTTCAAAAGTGCTTTTGGACATTAAATGACTAAAATCCCCTAATTATTTTTCTCTTTCCTTTTT
131 ATTTCAAAAGTACTTTTGGACATTAAATGACTAAAATCCCCTAATTATTTCTCTCTATCCTTTTT
* * *
7031 AACTAGCATATCCCTTTTAGACAATTTATCCTTCAACCCCATTTTTTCACAGCAATATCAAACAT
196 AACTAACATATCCATTTTAGACAATTTATCCTTCAACCACATTTTTTCACAGCAATATCAAACAT
* * *
7096 TATTTACATTTTTCTACCGCAATTCAAAAAAGCACTTATCAAAAGCACTTTTTCCAAACCAAGCT
261 TATTTACATTTTTCTACCACAATTCAAAAAAGCACTTATCAAAAGCAATTCTTCCAAACCAAGCT
7161 TTTTCAAATTGCAACCTCAATACCAAACCAAACCTTAGTCTATTTAGGCCTAATTTATCA
326 TTTTCAAATTGCAACCTCAATACCAAACCAAACCTTAGTCTATTTAGGCCTAATTTATCA
** * **
7221 TTGCGTTTGAAGAAAAAAAAGTTG-TTTTTCACCTCAAACGCAATACCAAATAACTCTTGGTTTG
1 TTGCGTTTGAAGAAAAAAAAGTTGCTTTTGAACC-CAAACGCAATACCAAATAAATC-ACGTTTG
* * * ** * *
7285 TGTCAAGAGCTGATTTTGAACGCAAAAGTCAAGCCAA-CCTAAAAAGGTAATCTTTAGGTGCTTT
64 TGTCAAAAACTAATTTTGAACGCAAAAACCAAGCCAACCCGAAAAA-CTAATCTTTAGGTGCTTT
***
7349 TGCATTTCAAAAGTACTTTTGGACATTAAATGACTAAAATTTTCTAATTATTTCTCTCTAT-CTT
128 TGCATTTCAAAAGTACTTTTGGACATTAAATGACTAAAATCCCCTAATTATTTCTCTCTATCCTT
* * ** *
7413 TTTAACTAATATATCCATTTTAGACATTTTATTTTTCTACCACATTTTTTCACAGCAATATCAAA
193 TTTAACTAACATATCCATTTTAGACAATTTATCCTTCAACCACATTTTTTCACAGCAATATCAAA
* * *
7478 CATTATTTACATTTTTCTACTACAATTCGAAAAAGCACTTTTTCAAAAGCAATTCTT-CATAACC
258 CATTATTTACATTTTTCTACCACAATTCAAAAAAGCAC-TTATCAAAAGCAATTCTTCCA-AACC
7542 AAGCTTTTTCAAA
321 AAGCTTTTTCAAA
7555 CATTAACCTC
Statistics
Matches: 292, Mismatches: 37, Indels: 9
0.86 0.11 0.03
Matches are distributed among these distances:
384 7 0.02
385 145 0.50
386 140 0.48
ACGTcount: A:0.34, C:0.20, G:0.10, T:0.35
Consensus pattern (385 bp):
TTGCGTTTGAAGAAAAAAAAGTTGCTTTTGAACCCAAACGCAATACCAAATAAATCACGTTTGTG
TCAAAAACTAATTTTGAACGCAAAAACCAAGCCAACCCGAAAAACTAATCTTTAGGTGCTTTTGC
ATTTCAAAAGTACTTTTGGACATTAAATGACTAAAATCCCCTAATTATTTCTCTCTATCCTTTTT
AACTAACATATCCATTTTAGACAATTTATCCTTCAACCACATTTTTTCACAGCAATATCAAACAT
TATTTACATTTTTCTACCACAATTCAAAAAAGCACTTATCAAAAGCAATTCTTCCAAACCAAGCT
TTTTCAAATTGCAACCTCAATACCAAACCAAACCTTAGTCTATTTAGGCCTAATTTATCA
Found at i:7572 original size:386 final size:384
Alignment explanation
Indices: 6836--7573 Score: 1027
Period size: 386 Copynumber: 1.9 Consensus size: 384
6826 TGCTTTGACT
* * *
6836 TTGCGTTTGGAGATAAAAAAGTTGCTTTTGAACCCAAATGCAATACCAAATAAATCACGTTTGTG
1 TTGCGTTTGAAGAAAAAAAAGTTGCTTTTGAACCCAAACGCAATACCAAATAAATCACGTTTGTG
*
6901 TCAAAAACTAATTTTGAACGCAAAAACCAAGCCAACCCGAGAAACTAATCTTTAGGTGCTTTTGC
66 TCAAAAACTAATTTTGAACGCAAAAACCAAGCCAACCCGAAAAACTAATCTTTAGGTGCTTTTGC
* * * *
6966 GTTTCAAAAGTGCTTTTGGACATTAAATGACTAAAATCCCCTAATTATTTTTCTCTTTCCTTTTT
131 ATTTCAAAAGTACTTTTGGACATTAAATGACTAAAATCCCCTAATTATTTCTCTCTATCCTTTTT
* * *
7031 AACTAGCATATCCCTTTTAGACAATTTATCCTTCAACCCCATTTTTTCACAGCAATATCAAACAT
196 AACTAACATATCCATTTTAGACAATTTATCCTTCAACCACATTTTTTCACAGCAATATCAAACAT
* * *
7096 TATTTACATTTTTCTACCGCAATTCAAAAAAGCACTTATCAAAAGCACTTTTTCCAAACCAAGCT
261 TATTTACATTTTTCTACCACAATTCAAAAAAGCACTTATCAAAAGCAATTCTTCCAAACCAAGCT
7161 TTTTCAAATTGCAACCTCAATACCAAACCAAACCTTAGTCTATTTAGGCCTAATTTATCA
326 TTTTCAAATT-CAACCTCAATACCAAACCAAACCTTAGTCTATTTAGGCCTAATTTATCA
** * **
7221 TTGCGTTTGAAGAAAAAAAAGTTG-TTTTTCACCTCAAACGCAATACCAAATAACTCTTGGTTTG
1 TTGCGTTTGAAGAAAAAAAAGTTGCTTTTGAACC-CAAACGCAATACCAAATAAATC-ACGTTTG
* * * ** * *
7285 TGTCAAGAGCTGATTTTGAACGCAAAAGTCAAGCCAA-CCTAAAAAGGTAATCTTTAGGTGCTTT
64 TGTCAAAAACTAATTTTGAACGCAAAAACCAAGCCAACCCGAAAAA-CTAATCTTTAGGTGCTTT
***
7349 TGCATTTCAAAAGTACTTTTGGACATTAAATGACTAAAATTTTCTAATTATTTCTCTCTAT-CTT
128 TGCATTTCAAAAGTACTTTTGGACATTAAATGACTAAAATCCCCTAATTATTTCTCTCTATCCTT
* * ** *
7413 TTTAACTAATATATCCATTTTAGACATTTTATTTTTCTACCACATTTTTTCACAGCAATATCAAA
193 TTTAACTAACATATCCATTTTAGACAATTTATCCTTCAACCACATTTTTTCACAGCAATATCAAA
* * *
7478 CATTATTTACATTTTTCTACTACAATTCGAAAAAGCACTTTTTCAAAAGCAATTCTT-CATAACC
258 CATTATTTACATTTTTCTACCACAATTCAAAAAAGCAC-TTATCAAAAGCAATTCTTCCA-AACC
*
7542 AAGCTTTTTCAAACATT-AACCTCGATACCAAA
321 AAGCTTTTTC-AA-ATTCAACCTCAATACCAAA
7574 ATAAGTTTTA
Statistics
Matches: 308, Mismatches: 38, Indels: 13
0.86 0.11 0.04
Matches are distributed among these distances:
384 7 0.02
385 145 0.47
386 151 0.49
387 2 0.01
388 3 0.01
ACGTcount: A:0.34, C:0.21, G:0.10, T:0.35
Consensus pattern (384 bp):
TTGCGTTTGAAGAAAAAAAAGTTGCTTTTGAACCCAAACGCAATACCAAATAAATCACGTTTGTG
TCAAAAACTAATTTTGAACGCAAAAACCAAGCCAACCCGAAAAACTAATCTTTAGGTGCTTTTGC
ATTTCAAAAGTACTTTTGGACATTAAATGACTAAAATCCCCTAATTATTTCTCTCTATCCTTTTT
AACTAACATATCCATTTTAGACAATTTATCCTTCAACCACATTTTTTCACAGCAATATCAAACAT
TATTTACATTTTTCTACCACAATTCAAAAAAGCACTTATCAAAAGCAATTCTTCCAAACCAAGCT
TTTTCAAATTCAACCTCAATACCAAACCAAACCTTAGTCTATTTAGGCCTAATTTATCA
Found at i:12269 original size:16 final size:16
Alignment explanation
Indices: 12238--12292 Score: 60
Period size: 16 Copynumber: 3.4 Consensus size: 16
12228 CTCAAATGTC
*
12238 GGGTCA-TTTGGGTTT
1 GGGTCATTTTTGGTTT
12253 GGGTCATTTTTGGTTT
1 GGGTCATTTTTGGTTT
*
12269 GGGT-GTTTTTCGGTTTT
1 GGGTCATTTTT-GG-TTT
12286 GGGTCAT
1 GGGTCAT
12293 ATGGTTCCAA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
15 11 0.33
16 14 0.42
17 7 0.21
18 1 0.03
ACGTcount: A:0.05, C:0.07, G:0.36, T:0.51
Consensus pattern (16 bp):
GGGTCATTTTTGGTTT
Done.