Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024460.1 Corchorus olitorius cultivar O-4 contig24493, 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: 20332
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Found at i:4582 original size:50 final size:50
Alignment explanation
Indices: 4405--4582 Score: 214
Period size: 51 Copynumber: 3.6 Consensus size: 50
4395 TTTTTGGACA
* * *
4405 TTTGAGTAACTTGTAAATAAAAATGTGATTTTTGAGT-AAAGATTGAACT
1 TTTGAGTAATTTGTAAATAAAAATGAGATTTTTAAGTAAAAGATTGAACT
* * *** *
4454 TTTAAGCAATTTGTAAATAAAAATGAGAAGATTAAGTAAAAGATTGAAGAT
1 TTTGAGTAATTTGTAAATAAAAATGAGATTTTTAAGTAAAAGATTGAA-CT
* * * *
4505 TTTGATTAATTTGTCAATAAAAGTGAGATTTTTAAGTAAAAGATTGACCT
1 TTTGAGTAATTTGTAAATAAAAATGAGATTTTTAAGTAAAAGATTGAACT
*
4555 TTTGATTAATTTGTAAATAAAAATGAGA
1 TTTGAGTAATTTGTAAATAAAAATGAGA
4583 CCTTTGGACT
Statistics
Matches: 106, Mismatches: 21, Indels: 3
0.82 0.16 0.02
Matches are distributed among these distances:
49 29 0.27
50 37 0.35
51 40 0.38
ACGTcount: A:0.43, C:0.03, G:0.17, T:0.37
Consensus pattern (50 bp):
TTTGAGTAATTTGTAAATAAAAATGAGATTTTTAAGTAAAAGATTGAACT
Found at i:4609 original size:101 final size:99
Alignment explanation
Indices: 4405--4627 Score: 243
Period size: 101 Copynumber: 2.2 Consensus size: 99
4395 TTTTTGGACA
* * * *
4405 TTTGAGTAACTTGTAAATAAAAATGTGATTTTTGAGTAAAGATTGAACTTTTAAGCAATTTGTAA
1 TTTGATTAATTTGT-AATAAAAATGAGATTTTTAAGTAAAGATTGAACTTTTAAGCAATTTGTAA
* *
4470 ATAAAAATGAGAAGATTAAGTAAAAGATTGAAGAT
65 ATAAAAATGAGAACATTAACTAAAAGATTGAAGAT
* * * **
4505 TTTGATTAATTTGTCAATAAAAGTGAGATTTTTAAGTAAAAGATTGACCTTTTGATTAATTTGTA
1 TTTGATTAATTTGT-AATAAAAATGAGATTTTTAAGT-AAAGATTGAACTTTTAAGCAATTTGTA
* * * *
4570 AATAAAAATGAGACCTTTGGACTAAAGGATT-AA-ATT
64 AATAAAAATGAGAACATT-AACTAAAAGATTGAAGA-T
*
4606 TTTGATTAGTTTGTAATAAAAA
1 TTTGATTAATTTGTAATAAAAA
4628 AGAAATCCTT
Statistics
Matches: 102, Mismatches: 18, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
100 39 0.38
101 54 0.53
102 9 0.09
ACGTcount: A:0.42, C:0.04, G:0.17, T:0.37
Consensus pattern (99 bp):
TTTGATTAATTTGTAATAAAAATGAGATTTTTAAGTAAAGATTGAACTTTTAAGCAATTTGTAAA
TAAAAATGAGAACATTAACTAAAAGATTGAAGAT
Found at i:5318 original size:40 final size:40
Alignment explanation
Indices: 5273--5607 Score: 347
Period size: 40 Copynumber: 8.3 Consensus size: 40
5263 TTCCATGCCG
* ****
5273 GAAGGTGTTGTTTAAATTCCTATTTTGCCCTTATGAACCA
1 GAAGGTGTTGTTTAAATTCCTGTTTTGCCCTTCCCCACCA
* *
5313 GAAGGTGTTATTTAAATTCCTGTTTTGCCCTTCCCCAATC-
1 GAAGGTGTTGTTTAAATTCCTGTTTTGCCCTTCCCC-ACCA
* * *
5353 GAAGCTGTTGTTTAAATTCTTGTTTT-CCCTTCCCCACCG
1 GAAGGTGTTGTTTAAATTCCTGTTTTGCCCTTCCCCACCA
*
5392 GAAGGTGTTGTTTGAAA-TCCTGTTTTGCCCTTCCCCATCA
1 GAAGGTGTTGTTT-AAATTCCTGTTTTGCCCTTCCCCACCA
* *
5432 CAAGGTGTTGTTTAAATTCCCTGTTTTGTCCTTCCCCACCA
1 GAAGGTGTTGTTTAAATT-CCTGTTTTGCCCTTCCCCACCA
* *
5473 GGAGGTGTTGTTTAAATTCCTGTTTTAG-CCTTCCCCACCG
1 GAAGGTGTTGTTTAAATTCCTGTTTT-GCCCTTCCCCACCA
* *** * *
5513 GAATGTGTTGTTTAAATTCCCAATTTGCCATTCCCCACCG
1 GAAGGTGTTGTTTAAATTCCTGTTTTGCCCTTCCCCACCA
** * * *
5553 GAAGGTGTTGTTTACTTTTCCCAG-TTTGCCCTTTCCCACCG
1 GAAGGTGTTGTTTA-AATT-CCTGTTTTGCCCTTCCCCACCA
5594 GAAGGTGTTGTTTA
1 GAAGGTGTTGTTTA
5608 CTTTTTCCAG
Statistics
Matches: 251, Mismatches: 34, Indels: 19
0.83 0.11 0.06
Matches are distributed among these distances:
38 2 0.01
39 33 0.13
40 144 0.57
41 70 0.28
42 2 0.01
ACGTcount: A:0.18, C:0.25, G:0.18, T:0.39
Consensus pattern (40 bp):
GAAGGTGTTGTTTAAATTCCTGTTTTGCCCTTCCCCACCA
Found at i:5524 original size:160 final size:160
Alignment explanation
Indices: 5274--5565 Score: 394
Period size: 160 Copynumber: 1.8 Consensus size: 160
5264 TCCATGCCGG
**
5274 AAGGTGTTGTTTAAATTCCTATTTTGCCCTTATGAACCAGAAGGTGTTATTTAAATTCCTGTTTT
1 AAGGTGTTGTTTAAATTCCTATTTTGCCCTTACCAACCAGAAGGTGTTATTTAAATTCCTGTTTT
* *** * *
5339 GCCCTTCCCCAATCGAAGCTGTTGTTTAAATT-CTTGTTTTCCCTTCCCCACCGGAAGGTGTTGT
66 GCCCTTCCCCAACCGAAGCTGTTGTTTAAATTCCCAATTTGCCATTCCCCACCGGAAGGTGTTGT
5403 TTGAAATCCTGTTTTGCCCTTCCCCATCAC
131 TTGAAATCCTGTTTTGCCCTTCCCCATCAC
* * * * * *
5433 AAGGTGTTGTTTAAATTCCCTGTTTTGTCCTTCCCCACCAGGAGGTGTTGTTTAAATTCCTGTTT
1 AAGGTGTTGTTTAAATT-CCTATTTTGCCCTTACCAACCAGAAGGTGTTATTTAAATTCCTGTTT
5498 TAG-CCTTCCCC-ACCGGAATG-TGTTGTTTAAATTCCCAATTTGCCATTCCCCACCGGAAGGTG
65 T-GCCCTTCCCCAACC-GAA-GCTGTTGTTTAAATTCCCAATTTGCCATTCCCCACCGGAAGGTG
5560 TTGTTT
127 TTGTTT
5566 ACTTTTCCCA
Statistics
Matches: 114, Mismatches: 14, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
159 19 0.17
160 64 0.56
161 31 0.27
ACGTcount: A:0.19, C:0.24, G:0.18, T:0.39
Consensus pattern (160 bp):
AAGGTGTTGTTTAAATTCCTATTTTGCCCTTACCAACCAGAAGGTGTTATTTAAATTCCTGTTTT
GCCCTTCCCCAACCGAAGCTGTTGTTTAAATTCCCAATTTGCCATTCCCCACCGGAAGGTGTTGT
TTGAAATCCTGTTTTGCCCTTCCCCATCAC
Found at i:5558 original size:121 final size:119
Alignment explanation
Indices: 5270--5761 Score: 396
Period size: 121 Copynumber: 4.1 Consensus size: 119
5260 TCCTTCCATG
**** *
5270 CCGGAAGGTGTTGTTTAAATTCCTATTTTGCCCTTATGAACCAGAAGGTGTTATTTAAATT-CCT
1 CCGGAAGGTGTTGTTTAAATTCCTATTTTGCCCTTCCCCACCAGAAGGTGTTGTTTAAATTCCCT
* * * *
5334 GTTTTGCCCTTCCCCAATCGAAGCTGTTGTTTAAATTCTTGTTTTCCCTTCCCCA
66 GTTTTGCCCTTCCCC-ACCGGAGGTGTTGTTTAAATTCCTGTTTTCCCTTCCCCA
* * *
5389 CCGGAAGGTGTTGTTTGAAA-TCCTGTTTTGCCCTTCCCCATCACAAGGTGTTGTTTAAATTCCC
1 CCGGAAGGTGTTGTTT-AAATTCCTATTTTGCCCTTCCCCACCAGAAGGTGTTGTTTAAATTCCC
* *
5453 TGTTTTGTCCTTCCCCACCAGGAGGTGTTGTTTAAATTCCTGTTTTAGCCTTCCCCA
65 TGTTTTGCCCTTCCCCACC-GGAGGTGTTGTTTAAATTCCTGTTTT-CCCTTCCCCA
* * * * * **
5510 CCGGAATGTGTTGTTTAAATTCCCAATTTGCCATTCCCCACCGGAAGGTGTTGTTTACTTTTCCC
1 CCGGAAGGTGTTGTTTAAATTCCTATTTTGCCCTTCCCCACCAGAAGGTGTTGTTTA-AATTCCC
* * ** * * *
5575 AG-TTTGCCCTTTCCCACCGGAAGGTGTTGTTTACTTTTTCCAGTTTGCCCTTTCCCA
65 TGTTTTGCCCTTCCCCACCGG-AGGTGTTGTTTA--AATTCCTGTTTTCCCTTCCCCA
** ** ** * * ** **
5632 -C-TTA--T-TTACTT---TTCC-CGTTTGCCCTTCCCCACCAAAAGGTGTTTTTTACTTTTACT
1 CCGGAAGGTGTTGTTTAAATTCCTATTTTGCCCTTCCCCACCAGAAGGTGTTGTTTAAATTCCCT
* ** *
5688 GCTTTGCCCTTCCCCACCGGAAGGTGTTGTTTACTTTTCCTGCTTTGCCCTTCCCCA
66 GTTTTGCCCTTCCCCACCGG-AGGTGTTGTTTA-AATTCCTG-TTTTCCCTTCCCCA
*
5745 CCGGAATGTGTTGTTTA
1 CCGGAAGGTGTTGTTTA
5762 CTTTTCCGTT
Statistics
Matches: 301, Mismatches: 55, Indels: 34
0.77 0.14 0.09
Matches are distributed among these distances:
112 12 0.04
113 70 0.23
114 5 0.02
115 1 0.00
117 5 0.02
118 5 0.02
119 51 0.17
120 49 0.16
121 81 0.27
122 14 0.05
123 8 0.03
ACGTcount: A:0.16, C:0.27, G:0.17, T:0.40
Consensus pattern (119 bp):
CCGGAAGGTGTTGTTTAAATTCCTATTTTGCCCTTCCCCACCAGAAGGTGTTGTTTAAATTCCCT
GTTTTGCCCTTCCCCACCGGAGGTGTTGTTTAAATTCCTGTTTTCCCTTCCCCA
Found at i:5591 original size:41 final size:41
Alignment explanation
Indices: 5374--5768 Score: 301
Period size: 41 Copynumber: 10.0 Consensus size: 41
5364 TTAAATTCTT
* ** *
5374 GTTTTCCCTTCCCCACCGGAAGGTGTTGTTTGA--AAT-CCT
1 GTTTGCCCTTCCCCACCGGAAGGTGTTGTTT-ACTTTTCCCA
* ** ** *
5413 GTTTTGCCCTTCCCCATCACAAGGTGTTGTTTA-AATTCCCT
1 G-TTTGCCCTTCCCCACCGGAAGGTGTTGTTTACTTTTCCCA
* ** *
5454 GTTTTGTCCTTCCCCACCAGG-AGGTGTTGTTTA-AATT-CCT
1 G-TTTGCCCTTCCCCACC-GGAAGGTGTTGTTTACTTTTCCCA
* **
5494 GTTTTAG-CCTTCCCCACCGGAATGTGTTGTTTA-AATTCCCA
1 G-TTT-GCCCTTCCCCACCGGAAGGTGTTGTTTACTTTTCCCA
* *
5535 ATTTGCCATTCCCCACCGGAAGGTGTTGTTTACTTTTCCCA
1 GTTTGCCCTTCCCCACCGGAAGGTGTTGTTTACTTTTCCCA
* *
5576 GTTTGCCCTTTCCCACCGGAAGGTGTTGTTTACTTTTTCCA
1 GTTTGCCCTTCCCCACCGGAAGGTGTTGTTTACTTTTCCCA
* *
5617 GTTTGCCCTTTCCCA-C--------TTATTTACTTTTCCC-
1 GTTTGCCCTTCCCCACCGGAAGGTGTTGTTTACTTTTCCCA
** * * *
5648 GTTTGCCCTTCCCCACCAAAAGGTGTTTTTTACTTTT-ACT
1 GTTTGCCCTTCCCCACCGGAAGGTGTTGTTTACTTTTCCCA
*
5688 GCTTTGCCCTTCCCCACCGGAAGGTGTTGTTTACTTTT-CCT
1 G-TTTGCCCTTCCCCACCGGAAGGTGTTGTTTACTTTTCCCA
*
5729 GCTTTGCCCTTCCCCACCGGAATGTGTTGTTTACTTTTCC
1 G-TTTGCCCTTCCCCACCGGAAGGTGTTGTTTACTTTTCC
5769 GTTTTACCCT
Statistics
Matches: 305, Mismatches: 30, Indels: 39
0.82 0.08 0.10
Matches are distributed among these distances:
31 14 0.05
32 14 0.05
39 6 0.02
40 102 0.33
41 168 0.55
42 1 0.00
ACGTcount: A:0.14, C:0.29, G:0.17, T:0.40
Consensus pattern (41 bp):
GTTTGCCCTTCCCCACCGGAAGGTGTTGTTTACTTTTCCCA
Found at i:5652 original size:31 final size:32
Alignment explanation
Indices: 5604--5663 Score: 95
Period size: 31 Copynumber: 1.9 Consensus size: 32
5594 GAAGGTGTTG
*
5604 TTTACTTTTTCCAGTTTGCCCTTTCCCACTTA
1 TTTACTTTTTCCAGTTTGCCCTTCCCCACTTA
*
5636 TTTAC-TTTTCCCGTTTGCCCTTCCCCAC
1 TTTACTTTTTCCAGTTTGCCCTTCCCCAC
5664 CAAAAGGTGT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
31 21 0.81
32 5 0.19
ACGTcount: A:0.10, C:0.37, G:0.07, T:0.47
Consensus pattern (32 bp):
TTTACTTTTTCCAGTTTGCCCTTCCCCACTTA
Found at i:5694 original size:72 final size:73
Alignment explanation
Indices: 5563--5704 Score: 198
Period size: 72 Copynumber: 2.0 Consensus size: 73
5553 GAAGGTGTTG
* ** * *
5563 TTTACTTTTCCCAGTTTGCCCTTTCCCACCGGAAGGTGTTGTTTACTTTTTCCAGTTTGCCCTTT
1 TTTACTTTTCCCAGTTTGCCCTTCCCCACCAAAAGGTGTTGTTTACTTTTTACAGTTTGCCCTTC
5628 CCCACTTA
66 CCCACTTA
* *
5636 TTTACTTTTCCC-GTTTGCCCTTCCCCACCAAAAGGTGTTTTTTAC-TTTTACTGCTTTGCCCTT
1 TTTACTTTTCCCAGTTTGCCCTTCCCCACCAAAAGGTGTTGTTTACTTTTTACAG-TTTGCCCTT
5699 CCCCAC
65 CCCCAC
5705 CGGAAGGTGT
Statistics
Matches: 61, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
71 6 0.10
72 43 0.70
73 12 0.20
ACGTcount: A:0.13, C:0.32, G:0.12, T:0.43
Consensus pattern (73 bp):
TTTACTTTTCCCAGTTTGCCCTTCCCCACCAAAAGGTGTTGTTTACTTTTTACAGTTTGCCCTTC
CCCACTTA
Found at i:5735 original size:113 final size:113
Alignment explanation
Indices: 5536--5745 Score: 307
Period size: 113 Copynumber: 1.9 Consensus size: 113
5526 AAATTCCCAA
** * *
5536 TTTGCCATTCCCCACCGGAAGGTGTTGTTTACTTTTCCCAGTTTGCCCTTTCCCACCGGAAGGTG
1 TTTGCCATTCCCCACCAAAAGGTGTTGTTTACTTTTCACAGTTTGCCCTTCCCCACCGGAAGGTG
*
5601 TTGTTTACTTTTTCCAGTTTGCCCTTTCCCACTTATTTACTTTTCCCG
66 TTGTTTACTTTTTCCAGTTTGCCCTTCCCCACTTATTTACTTTTCCCG
* * *
5649 TTTGCCCTTCCCCACCAAAAGGTGTTTTTTACTTTT-ACTGCTTTGCCCTTCCCCACCGGAAGGT
1 TTTGCCATTCCCCACCAAAAGGTGTTGTTTACTTTTCACAG-TTTGCCCTTCCCCACCGGAAGGT
*
5713 GTTGTTTAC-TTTTCCTGCTTTGCCCTTCCCCAC
65 GTTGTTTACTTTTTCCAG-TTTGCCCTTCCCCAC
5746 CGGAATGTGT
Statistics
Matches: 86, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
112 9 0.10
113 77 0.90
ACGTcount: A:0.12, C:0.32, G:0.15, T:0.40
Consensus pattern (113 bp):
TTTGCCATTCCCCACCAAAAGGTGTTGTTTACTTTTCACAGTTTGCCCTTCCCCACCGGAAGGTG
TTGTTTACTTTTTCCAGTTTGCCCTTCCCCACTTATTTACTTTTCCCG
Found at i:8291 original size:17 final size:18
Alignment explanation
Indices: 8258--8293 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
8248 CTCCTCTTGC
8258 ATGAAAACACTTCTTTTT
1 ATGAAAACACTTCTTTTT
*
8276 ATGAAAACA-TTTTTTTT
1 ATGAAAACACTTCTTTTT
8293 A
1 A
8294 ACTACCCTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.36, C:0.11, G:0.06, T:0.47
Consensus pattern (18 bp):
ATGAAAACACTTCTTTTT
Found at i:9113 original size:10 final size:10
Alignment explanation
Indices: 9085--9135 Score: 57
Period size: 11 Copynumber: 4.8 Consensus size: 10
9075 GAAAAGCATT
*
9085 TGGCCGGTAA
1 TGGCCGGTGA
9095 TGGCACGGTGA
1 TGGC-CGGTGA
*
9106 TGGCCGGTGG
1 TGGCCGGTGA
9116 TGGCTCGGTGGA
1 TGGC-CGGT-GA
9128 TGGCCGGT
1 TGGCCGGT
9136 AGTGGCTTGA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
10 13 0.37
11 17 0.49
12 5 0.14
ACGTcount: A:0.10, C:0.20, G:0.49, T:0.22
Consensus pattern (10 bp):
TGGCCGGTGA
Found at i:9132 original size:22 final size:21
Alignment explanation
Indices: 9085--9142 Score: 80
Period size: 21 Copynumber: 2.7 Consensus size: 21
9075 GAAAAGCATT
* *
9085 TGGCCGGTAATGGCACGGTGA
1 TGGCCGGTAGTGGCTCGGTGA
*
9106 TGGCCGGTGGTGGCTCGGTGGA
1 TGGCCGGTAGTGGCTCGGT-GA
9128 TGGCCGGTAGTGGCT
1 TGGCCGGTAGTGGCT
9143 TGATGGTGGC
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
21 16 0.50
22 16 0.50
ACGTcount: A:0.10, C:0.19, G:0.48, T:0.22
Consensus pattern (21 bp):
TGGCCGGTAGTGGCTCGGTGA
Done.