Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017168.1 Corchorus olitorius cultivar O-4 contig17201, 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: 22349
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:245 original size:22 final size:23
Alignment explanation
Indices: 209--279 Score: 69
Period size: 22 Copynumber: 3.2 Consensus size: 23
199 ATATATATTA
*
209 TTAAACTAAAT-AATAAATATAT
1 TTAAAATAAATAAATAAATATAT
*
231 TTGAAAT-AATAAAT-AATGA-AT
1 TTAAAATAAATAAATAAAT-ATAT
*
252 TCAAAATAAATAAATAATATATAT
1 TTAAAATAAATAAATAA-ATATAT
276 TTAA
1 TTAA
280 TTACTAAACG
Statistics
Matches: 38, Mismatches: 5, Indels: 10
0.72 0.09 0.19
Matches are distributed among these distances:
21 13 0.34
22 16 0.42
23 2 0.05
24 7 0.18
ACGTcount: A:0.59, C:0.03, G:0.03, T:0.35
Consensus pattern (23 bp):
TTAAAATAAATAAATAAATATAT
Found at i:435 original size:16 final size:16
Alignment explanation
Indices: 414--530 Score: 234
Period size: 16 Copynumber: 7.3 Consensus size: 16
404 TTAAAGCTTG
414 GGCCCGGCCCGAACCC
1 GGCCCGGCCCGAACCC
430 GGCCCGGCCCGAACCC
1 GGCCCGGCCCGAACCC
446 GGCCCGGCCCGAACCC
1 GGCCCGGCCCGAACCC
462 GGCCCGGCCCGAACCC
1 GGCCCGGCCCGAACCC
478 GGCCCGGCCCGAACCC
1 GGCCCGGCCCGAACCC
494 GGCCCGGCCCGAACCC
1 GGCCCGGCCCGAACCC
510 GGCCCGGCCCGAACCC
1 GGCCCGGCCCGAACCC
526 GGCCC
1 GGCCC
531 ATGAACAGGT
Statistics
Matches: 101, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 101 1.00
ACGTcount: A:0.12, C:0.56, G:0.32, T:0.00
Consensus pattern (16 bp):
GGCCCGGCCCGAACCC
Found at i:2376 original size:19 final size:19
Alignment explanation
Indices: 2352--2410 Score: 82
Period size: 19 Copynumber: 3.0 Consensus size: 19
2342 CTGTTTGATA
2352 ATTGTACAGATGAGATTAT
1 ATTGTACAGATGAGATTAT
*
2371 ATTGTACAGATTAGATTATGT
1 ATTGTACAGATGAGATTA--T
*
2392 ATTGTACATATGAGATTAT
1 ATTGTACAGATGAGATTAT
2411 TAGAGCAGCG
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
19 18 0.51
21 17 0.49
ACGTcount: A:0.36, C:0.05, G:0.19, T:0.41
Consensus pattern (19 bp):
ATTGTACAGATGAGATTAT
Found at i:2396 original size:21 final size:20
Alignment explanation
Indices: 2352--2412 Score: 88
Period size: 21 Copynumber: 3.0 Consensus size: 20
2342 CTGTTTGATA
2352 ATTGTACAGATGAGATTA-T
1 ATTGTACAGATGAGATTATT
*
2371 ATTGTACAGATTAGATTATGT
1 ATTGTACAGATGAGATTAT-T
*
2392 ATTGTACATATGAGATTATT
1 ATTGTACAGATGAGATTATT
2412 A
1 A
2413 GAGCAGCGAT
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
19 17 0.46
20 2 0.05
21 18 0.49
ACGTcount: A:0.36, C:0.05, G:0.18, T:0.41
Consensus pattern (20 bp):
ATTGTACAGATGAGATTATT
Found at i:2935 original size:21 final size:19
Alignment explanation
Indices: 2891--2949 Score: 73
Period size: 19 Copynumber: 3.0 Consensus size: 19
2881 CTGTTTAGCA
*
2891 ACTGTACAGATGAGATTAT
1 ACTGTACAAATGAGATTAT
* *
2910 ACTGTACATATTAGATTAGGT
1 ACTGTACAAATGAGATTA--T
2931 ACTGTACAAATGAGATTAT
1 ACTGTACAAATGAGATTAT
2950 TAGAGCAGCG
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
19 17 0.50
21 17 0.50
ACGTcount: A:0.37, C:0.10, G:0.19, T:0.34
Consensus pattern (19 bp):
ACTGTACAAATGAGATTAT
Found at i:4181 original size:13 final size:13
Alignment explanation
Indices: 4165--4190 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
4155 TTTGTAAAGG
4165 TATTATTATTATT
1 TATTATTATTATT
4178 TATTATTATTATT
1 TATTATTATTATT
4191 GTAATATAGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (13 bp):
TATTATTATTATT
Found at i:4865 original size:96 final size:96
Alignment explanation
Indices: 4696--4883 Score: 340
Period size: 96 Copynumber: 2.0 Consensus size: 96
4686 GGCTATCTTT
*
4696 GATCCGGTTATCAATGGAGATCGTGTCTAGAAATGAAACAATATCTCCATGTTTTGTTCAGAAAT
1 GATCCGGTTATCAATGGAGATCGTGTCTAGAAATGAAACAATATCTCCATGTTTGGTTCAGAAAT
4761 ATTTTTAGGATTTATCTAGAGAATGAATGGA
66 ATTTTTAGGATTTATCTAGAGAATGAATGGA
* *
4792 GATCTGGTTATCAATGGAGATCGTGTCTAGGAATGAAACAATATCTCCATGTTTGGTTCAGAAAT
1 GATCCGGTTATCAATGGAGATCGTGTCTAGAAATGAAACAATATCTCCATGTTTGGTTCAGAAAT
*
4857 ATTTTTAGGGTTTATCTAGAGAATGAA
66 ATTTTTAGGATTTATCTAGAGAATGAA
4884 ATTACGTTCA
Statistics
Matches: 88, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
96 88 1.00
ACGTcount: A:0.32, C:0.11, G:0.22, T:0.35
Consensus pattern (96 bp):
GATCCGGTTATCAATGGAGATCGTGTCTAGAAATGAAACAATATCTCCATGTTTGGTTCAGAAAT
ATTTTTAGGATTTATCTAGAGAATGAATGGA
Found at i:6098 original size:15 final size:15
Alignment explanation
Indices: 6055--6099 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
6045 TATCATCCAT
*
6055 AATATATCCTTCAAA
1 AATATATCCTTAAAA
*
6070 AATAAATCCTTTAAAA
1 AATATATCC-TTAAAA
*
6086 AATATATTCTTAAA
1 AATATATCCTTAAA
6100 TATCATTCAA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
15 13 0.52
16 12 0.48
ACGTcount: A:0.51, C:0.13, G:0.00, T:0.36
Consensus pattern (15 bp):
AATATATCCTTAAAA
Found at i:6320 original size:20 final size:20
Alignment explanation
Indices: 6301--6337 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
6291 TATTAATTAT
*
6301 TTTA-ATATTATATTTTTTA
1 TTTATATATTACATTTTTTA
6320 TTTATATATTACATTTTT
1 TTTATATATTACATTTTT
6338 AATTAAAAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 4 0.25
20 12 0.75
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.68
Consensus pattern (20 bp):
TTTATATATTACATTTTTTA
Found at i:6478 original size:13 final size:13
Alignment explanation
Indices: 6460--6484 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
6450 ATATAATAAG
6460 TATGATTTATGAA
1 TATGATTTATGAA
6473 TATGATTTATGA
1 TATGATTTATGA
6485 GGTTATAGAG
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:0.36, C:0.00, G:0.16, T:0.48
Consensus pattern (13 bp):
TATGATTTATGAA
Found at i:19070 original size:89 final size:89
Alignment explanation
Indices: 18919--19096 Score: 347
Period size: 89 Copynumber: 2.0 Consensus size: 89
18909 ATTCATTAAT
*
18919 ACTCTAAGCTGCCTTCGAATATTTGCGAATTGATGTTGATTAATTGCAGTGGTTAATTTAGCTCC
1 ACTCTAAGCTGCCTTCGAATATTTGCGAATTGATGTTGATTAACTGCAGTGGTTAATTTAGCTCC
18984 AAATTGCAGCGTTGAGGTCTCAAA
66 AAATTGCAGCGTTGAGGTCTCAAA
19008 ACTCTAAGCTGCCTTCGAATATTTGCGAATTGATGTTGATTAACTGCAGTGGTTAATTTAGCTCC
1 ACTCTAAGCTGCCTTCGAATATTTGCGAATTGATGTTGATTAACTGCAGTGGTTAATTTAGCTCC
19073 AAATTGCAGCGTTGAGGTCTCAAA
66 AAATTGCAGCGTTGAGGTCTCAAA
19097 CTGGGTATTC
Statistics
Matches: 88, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
89 88 1.00
ACGTcount: A:0.27, C:0.17, G:0.21, T:0.34
Consensus pattern (89 bp):
ACTCTAAGCTGCCTTCGAATATTTGCGAATTGATGTTGATTAACTGCAGTGGTTAATTTAGCTCC
AAATTGCAGCGTTGAGGTCTCAAA
Done.