Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016686.1 Corchorus olitorius cultivar O-4 contig16719, 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: 9791
ACGTcount: A:0.31, C:0.14, G:0.18, T:0.37
Found at i:1742 original size:57 final size:57
Alignment explanation
Indices: 1659--1774 Score: 189
Period size: 57 Copynumber: 2.0 Consensus size: 57
1649 TTTATTTTGT
* *
1659 AGAATAATTAAGTAGAGATAGGGGGGATAGGGTTTATTATAACATTTATTATGTGAA
1 AGAATAATTAAGTAGAAATAGGGGGGATAGGATTTATTATAACATTTATTATGTGAA
*
1716 AGAATAATTAAGTAGAAAT-GGTGGGGATAGGATTTATTATAACATTTATTGTGTGAA
1 AGAATAATTAAGTAGAAATAGG-GGGGATAGGATTTATTATAACATTTATTATGTGAA
1773 AG
1 AG
1775 GAAATGGATA
Statistics
Matches: 55, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
56 2 0.04
57 53 0.96
ACGTcount: A:0.39, C:0.02, G:0.26, T:0.34
Consensus pattern (57 bp):
AGAATAATTAAGTAGAAATAGGGGGGATAGGATTTATTATAACATTTATTATGTGAA
Found at i:2420 original size:31 final size:31
Alignment explanation
Indices: 2378--2439 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
2368 GAGTTTTGTA
*
2378 AAACTTTTGAATCGCCTATTACACCCTTATT
1 AAACTTCTGAATCGCCTATTACACCCTTATT
* *
2409 AAACTTCTGAATCGCCTATTATATCCTTATT
1 AAACTTCTGAATCGCCTATTACACCCTTATT
2440 TTTTAATATA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.29, C:0.24, G:0.06, T:0.40
Consensus pattern (31 bp):
AAACTTCTGAATCGCCTATTACACCCTTATT
Found at i:2585 original size:93 final size:93
Alignment explanation
Indices: 2474--2642 Score: 302
Period size: 93 Copynumber: 1.8 Consensus size: 93
2464 TTGTTTAAAT
*
2474 TTTTATAGTTTTAGTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATAACTA
1 TTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATAACTA
*
2539 TTTTGTTTTTAGCATTTTACTATTTTAC
66 TTTTATTTTTAGCATTTTACTATTTTAC
* *
2567 TTTTATAGTTTTACTCAACTAAAAACTCTGTTTTTATTTAATTAAATCTAATATCCTTATACCTA
1 TTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATAACTA
2632 TTTTATTTTTA
66 TTTTATTTTTA
2643 CGATATTACT
Statistics
Matches: 72, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 72 1.00
ACGTcount: A:0.31, C:0.12, G:0.04, T:0.53
Consensus pattern (93 bp):
TTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATAACTA
TTTTATTTTTAGCATTTTACTATTTTAC
Found at i:3318 original size:9 final size:9
Alignment explanation
Indices: 3304--3351 Score: 68
Period size: 9 Copynumber: 5.8 Consensus size: 9
3294 TCACTCGGGT
3304 TTTGGGTCA
1 TTTGGGTCA
3313 TTTGGGT--
1 TTTGGGTCA
3320 TTTGGGTCA
1 TTTGGGTCA
3329 TTTGGGT--
1 TTTGGGTCA
3336 TTTGGGTCA
1 TTTGGGTCA
3345 TTTGGGT
1 TTTGGGT
3352 TTTGGGTTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
7 14 0.40
9 21 0.60
ACGTcount: A:0.06, C:0.06, G:0.38, T:0.50
Consensus pattern (9 bp):
TTTGGGTCA
Found at i:3319 original size:16 final size:16
Alignment explanation
Indices: 3300--3358 Score: 118
Period size: 16 Copynumber: 3.7 Consensus size: 16
3290 CAGGTCACTC
3300 GGGTTTTGGGTCATTT
1 GGGTTTTGGGTCATTT
3316 GGGTTTTGGGTCATTT
1 GGGTTTTGGGTCATTT
3332 GGGTTTTGGGTCATTT
1 GGGTTTTGGGTCATTT
3348 GGGTTTTGGGT
1 GGGTTTTGGGT
3359 TTTTTTGGCT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 43 1.00
ACGTcount: A:0.05, C:0.05, G:0.41, T:0.49
Consensus pattern (16 bp):
GGGTTTTGGGTCATTT
Found at i:3323 original size:7 final size:7
Alignment explanation
Indices: 3300--3361 Score: 70
Period size: 7 Copynumber: 8.0 Consensus size: 7
3290 CAGGTCACTC
3300 GGGTTTT
1 GGGTTTT
3307 GGGTCATTT
1 GGGT--TTT
3316 GGGTTTT
1 GGGTTTT
3323 GGGTCATTT
1 GGGT--TTT
3332 GGGTTTT
1 GGGTTTT
3339 GGGTCATTT
1 GGGT--TTT
3348 GGGTTTT
1 GGGTTTT
3355 GGGTTTT
1 GGGTTTT
3362 TTTGGCTCTA
Statistics
Matches: 49, Mismatches: 0, Indels: 12
0.80 0.00 0.20
Matches are distributed among these distances:
7 28 0.57
9 21 0.43
ACGTcount: A:0.05, C:0.05, G:0.39, T:0.52
Consensus pattern (7 bp):
GGGTTTT
Found at i:4147 original size:19 final size:18
Alignment explanation
Indices: 4123--4162 Score: 71
Period size: 19 Copynumber: 2.2 Consensus size: 18
4113 GCCCATAAGG
4123 AAGAAGAAAAGAGAAAAGA
1 AAGAAGAAAAGA-AAAAGA
4142 AAGAAGAAAAGAAAAAGA
1 AAGAAGAAAAGAAAAAGA
4160 AAG
1 AAG
4163 GGAAAAAGGA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 9 0.43
19 12 0.57
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (18 bp):
AAGAAGAAAAGAAAAAGA
Found at i:4180 original size:19 final size:18
Alignment explanation
Indices: 4129--4188 Score: 59
Period size: 19 Copynumber: 3.2 Consensus size: 18
4119 AAGGAAGAAG
*
4129 AAAAGAGAAAAG-AAAGAA
1 AAAAGA-AAAAGAAAAGGA
*
4147 GAAAAGAAAAAGAAAGGGA
1 -AAAAGAAAAAGAAAAGGA
*
4166 AAAAGGAAAAGGAAAAGGA
1 AAAA-GAAAAAGAAAAGGA
4185 AAAA
1 AAAA
4189 AATTAATTAA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
18 9 0.26
19 26 0.74
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (18 bp):
AAAAGAAAAAGAAAAGGA
Found at i:4188 original size:7 final size:6
Alignment explanation
Indices: 4119--4187 Score: 54
Period size: 6 Copynumber: 11.3 Consensus size: 6
4109 CTTGGCCCAT
* * *
4119 AAGGAA GAA-GAA AAGAGAA AA-GAA AGAAGAA AA-GAA AAAGAA AGGGAAA
1 AAGGAA -AAGGAA AAG-GAA AAGGAA A-AGGAA AAGGAA AAGGAA AAGG-AA
4168 AAGGAA AAGGAA AAGGAA AA
1 AAGGAA AAGGAA AAGGAA AA
4188 AAATTAATTA
Statistics
Matches: 53, Mismatches: 3, Indels: 13
0.77 0.04 0.19
Matches are distributed among these distances:
5 11 0.21
6 26 0.49
7 16 0.30
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (6 bp):
AAGGAA
Found at i:5648 original size:12 final size:11
Alignment explanation
Indices: 5591--5647 Score: 51
Period size: 12 Copynumber: 4.8 Consensus size: 11
5581 TCCTTTGAGG
5591 AAATGTTTTAT
1 AAATGTTTTAT
* *
5602 TACTGTTTTACAT
1 AAATGTTTT--AT
*
5615 AAATGATTTAT
1 AAATGTTTTAT
5626 AAAATGTTTTGAT
1 -AAATGTTTT-AT
5639 AAATGTTTT
1 AAATGTTTT
5648 GGGTGCATAA
Statistics
Matches: 36, Mismatches: 6, Indels: 7
0.73 0.12 0.14
Matches are distributed among these distances:
11 9 0.25
12 17 0.47
13 10 0.28
ACGTcount: A:0.35, C:0.04, G:0.11, T:0.51
Consensus pattern (11 bp):
AAATGTTTTAT
Found at i:7528 original size:155 final size:151
Alignment explanation
Indices: 7242--7532 Score: 456
Period size: 155 Copynumber: 1.9 Consensus size: 151
7232 TCTTTTTACT
* *
7242 ATTTTAATATTTTTCATTAAAAACTAGGATATATAAAATTTTTTAATATACAGTTTTATTCTACT
1 ATTTTAATATTTTTCATTAAAAACTAGGATATATAAAATTTTTTAATATAAAGTTTTATTCTACA
* * *
7307 AAAAATTATATTTTCATATAATTAAATTCAATATTTTATAATTATTTTATTTTTACCATTTTAAT
66 AAAAACTATATTTTCATATAATCAAATTCAATATTTTATAATTATTTTATTTTTACCATTTGAAT
7372 TTAAAATTTTATATTTCTACC
131 TTAAAATTTTATATTTCTACC
* * *
7393 ATTTTACTATTTTTCATTAAAAACTTGGATATATTAAAATTTTTTAATATAAAGTTTTATTTTAC
1 ATTTTAATATTTTTCATTAAAAACTAGGATATA-TAAAATTTTTTAATATAAAGTTTTATTCTAC
* *
7458 AAAAGAAACTCTATTTTCATTTAATCAAATTCAATATTTTTATAATTATTTTATTTTTACCATTT
65 -AAA-AAACTATATTTTCATATAATCAAATTCAATA-TTTTATAATTATTTTATTTTTACCATTT
7523 GAATTTAAAA
127 GAATTTAAAA
7533 GGTGATTGTG
Statistics
Matches: 126, Mismatches: 10, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
151 31 0.25
152 29 0.23
153 2 0.02
154 27 0.21
155 37 0.29
ACGTcount: A:0.38, C:0.08, G:0.03, T:0.51
Consensus pattern (151 bp):
ATTTTAATATTTTTCATTAAAAACTAGGATATATAAAATTTTTTAATATAAAGTTTTATTCTACA
AAAAACTATATTTTCATATAATCAAATTCAATATTTTATAATTATTTTATTTTTACCATTTGAAT
TTAAAATTTTATATTTCTACC
Done.