Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017513.1 Corchorus olitorius cultivar O-4 contig17546, 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: 51643
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.32
Found at i:183 original size:21 final size:21
Alignment explanation
Indices: 159--202 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
149 TAATTATAAC
159 TTCACTTATCAAATCAATATA
1 TTCACTTATCAAATCAATATA
* * *
180 TTCACTTATGAAATTAATTTA
1 TTCACTTATCAAATCAATATA
201 TT
1 TT
203 AATTTATCTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.39, C:0.14, G:0.02, T:0.45
Consensus pattern (21 bp):
TTCACTTATCAAATCAATATA
Found at i:860 original size:22 final size:21
Alignment explanation
Indices: 827--870 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 21
817 ATAACTTCAC
*
827 TTATGAAATTAATATATTAAT
1 TTATGAAATTAAAATATTAAT
848 TTATGTAAATTAAAATATTAAT
1 TTATG-AAATTAAAATATTAAT
870 T
1 T
871 ATTCCAATTG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 5 0.24
22 16 0.76
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.48
Consensus pattern (21 bp):
TTATGAAATTAAAATATTAAT
Found at i:13297 original size:35 final size:35
Alignment explanation
Indices: 13246--14364 Score: 1534
Period size: 35 Copynumber: 32.4 Consensus size: 35
13236 TCCAGTGCGG
* *
13246 TCCTTTCAAGATGTTTTCGATGATCAGAGTTGATC
1 TCCTTTCAAGAAGTTTTTGATGATCAGAGTTGATC
* *
13281 TCGTTTCAAGAAGTTTTTTATGATCAGAGTTGATC
1 TCCTTTCAAGAAGTTTTTGATGATCAGAGTTGATC
* * *
13316 TCCTTTCAAAAAGTTTTCGATGATCAGAGTTTATC
1 TCCTTTCAAGAAGTTTTTGATGATCAGAGTTGATC
* *
13351 TCCTTTCAAGAAGTTTTTTATGATCAAAGTTGATC
1 TCCTTTCAAGAAGTTTTTGATGATCAGAGTTGATC
* *
13386 TCCTTTCAAGAAGTTTTCGATGATCAGAGCTGATC
1 TCCTTTCAAGAAGTTTTTGATGATCAGAGTTGATC
*
13421 TCCTTTCAAGAAGTTTTCGATGATCAGAGTTGATC
1 TCCTTTCAAGAAGTTTTTGATGATCAGAGTTGATC
*
13456 TCCTTTCAAGAAGTTTTCGATGATCAGAGTTGATC
1 TCCTTTCAAGAAGTTTTTGATGATCAGAGTTGATC
* * *
13491 TCGTTTCAAGAAGTTTTCGATGATCAAAGTTGATC
1 TCCTTTCAAGAAGTTTTTGATGATCAGAGTTGATC
* *
13526 TCCTTTCAAGAAGTTTTCGATGATCAAAGTTGATC
1 TCCTTTCAAGAAGTTTTTGATGATCAGAGTTGATC
*
13561 TCCTTTCAAAAAGTGTTTT-ATGATCAGAGTTGATC
1 TCCTTTCAAGAAGT-TTTTGATGATCAGAGTTGATC
* *
13596 TTCTTTCAAGAAGTTTTTGATGATCAGAATTGATC
1 TCCTTTCAAGAAGTTTTTGATGATCAGAGTTGATC
* *
13631 TCCTTTCAAGAAGTTTTCGATGATCGGAGTTGATC
1 TCCTTTCAAGAAGTTTTTGATGATCAGAGTTGATC
*
13666 TCGTTTC---AA-------ATGATCAGAGTTGATC
1 TCCTTTCAAGAAGTTTTTGATGATCAGAGTTGATC
* *
13691 TCATTTCAAGAAGTTTTTTATGATCAGAGTTGATC
1 TCCTTTCAAGAAGTTTTTGATGATCAGAGTTGATC
* *
13726 TCATTTCAAGAAGTTTTCGATGATCAGAGTTGATC
1 TCCTTTCAAGAAGTTTTTGATGATCAGAGTTGATC
*
13761 TCCTTTCAAGAAGTTTTTTATGATCAGAGTTGATC
1 TCCTTTCAAGAAGTTTTTGATGATCAGAGTTGATC
* *
13796 TCCTTTCAAGAAGTTTTTTATGATCAGAGTTGATT
1 TCCTTTCAAGAAGTTTTTGATGATCAGAGTTGATC
*
13831 TCCTTTCAAGAAGTTTTTTATGATCAGAGTTGATC
1 TCCTTTCAAGAAGTTTTTGATGATCAGAGTTGATC
*
13866 TCCTTTCAAGAAGTTTTCGATGATCAGAGTTGATC
1 TCCTTTCAAGAAGTTTTTGATGATCAGAGTTGATC
* * *
13901 TCGTTTCAAGAAGTTTTTTATGATCAGAGCTGATC
1 TCCTTTCAAGAAGTTTTTGATGATCAGAGTTGATC
* * * *
13936 TCATTTCAAGAAG-TTTTG-TTATTAGAGTTGATA
1 TCCTTTCAAGAAGTTTTTGATGATCAGAGTTGATC
*
13969 TCATTTCAAGAAGTTTTTGATGATCAGAGTTGATC
1 TCCTTTCAAGAAGTTTTTGATGATCAGAGTTGATC
* * *
14004 TCGTTTCAAGAAGTTTTTTATGATTAGAGTTGATC
1 TCCTTTCAAGAAGTTTTTGATGATCAGAGTTGATC
14039 TCCTTTCAAGAAGTTTTTGATGATCAGAGTTGATC
1 TCCTTTCAAGAAGTTTTTGATGATCAGAGTTGATC
*
14074 TCCTTTCAAGAAGTTTTCGATGATCAGAGTTGATC
1 TCCTTTCAAGAAGTTTTTGATGATCAGAGTTGATC
* *
14109 TCGTTTCAAGAAGTTTTTTATGATCAGAGTTGATC
1 TCCTTTCAAGAAGTTTTTGATGATCAGAGTTGATC
* * * *
14144 TCATTTCAATAAGTTTTT-ATGATTAGAGTTGATT
1 TCCTTTCAAGAAGTTTTTGATGATCAGAGTTGATC
*
14178 TCATTTCAAGAAGTTTTTGATGATCAGAGTTGATC
1 TCCTTTCAAGAAGTTTTTGATGATCAGAGTTGATC
* * *
14213 TCTTTTCAAGAAGTTTTT-TTTATCAGAGTTGATC
1 TCCTTTCAAGAAGTTTTTGATGATCAGAGTTGATC
* * *
14247 TCATTTCAAGAAGTTTTT-TTTATCAGAGTTGATC
1 TCCTTTCAAGAAGTTTTTGATGATCAGAGTTGATC
* *
14281 TCATTTCAAGACGTTTTT-ATGATCAGAGTTGATC
1 TCCTTTCAAGAAGTTTTTGATGATCAGAGTTGATC
*
14315 TCCTTTCAAGAAGTTTTCGATGATCAGAGTTGATC
1 TCCTTTCAAGAAGTTTTTGATGATCAGAGTTGATC
** *
14350 TTGTTTTAAGAAGTT
1 TCCTTTCAAGAAGTT
14365 CAAGGTTGAA
Statistics
Matches: 981, Mismatches: 87, Indels: 32
0.89 0.08 0.03
Matches are distributed among these distances:
25 21 0.02
28 2 0.00
32 2 0.00
33 24 0.02
34 137 0.14
35 792 0.81
36 3 0.00
ACGTcount: A:0.27, C:0.14, G:0.18, T:0.41
Consensus pattern (35 bp):
TCCTTTCAAGAAGTTTTTGATGATCAGAGTTGATC
Found at i:13671 original size:25 final size:25
Alignment explanation
Indices: 13650--13699 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
13640 GAAGTTTTCG
*
13650 ATGATCGGAGTTGATCTCGTTTCAA
1 ATGATCAGAGTTGATCTCGTTTCAA
*
13675 ATGATCAGAGTTGATCTCATTTCAA
1 ATGATCAGAGTTGATCTCGTTTCAA
13700 GAAGTTTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.28, C:0.16, G:0.20, T:0.36
Consensus pattern (25 bp):
ATGATCAGAGTTGATCTCGTTTCAA
Found at i:20475 original size:97 final size:97
Alignment explanation
Indices: 20363--20566 Score: 248
Period size: 97 Copynumber: 2.1 Consensus size: 97
20353 AATAGCATAT
* * * ** *
20363 TTATTATCATTTGGAAGCAAATTTAAACACGGATATTTAGTTTTCGTGGTAAATTCCGTTTCCAA
1 TTATTAT-ATCTGGAAGCAAATTTAAACACAGATATGTAAATTACGTGGTAAATTCCGTTTCCAA
* *
20428 ATGAAATAAAAGTTTGTTTATAGAAT-TATTTTA
65 ATAAAAT-AAAGTTTATTTATAGAATATATTTTA
* * * * *
20461 TTATTATATCTGGAATCAGATTTACACACAGATATGTAAATTACGTGTTAAGTTCCGTTTCCAAA
1 TTATTATATCTGGAAGCAAATTTAAACACAGATATGTAAATTACGTGGTAAATTCCGTTTCCAAA
*
20526 TAAAATAAATTTTATTTATAGAATATATTTTA
66 TAAAATAAAGTTTATTTATAGAATATATTTTA
*
20558 TTAATATAT
1 TTATTATAT
20567 TCACTTCTTG
Statistics
Matches: 90, Mismatches: 15, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
96 16 0.18
97 67 0.74
98 7 0.08
ACGTcount: A:0.37, C:0.09, G:0.12, T:0.42
Consensus pattern (97 bp):
TTATTATATCTGGAAGCAAATTTAAACACAGATATGTAAATTACGTGGTAAATTCCGTTTCCAAA
TAAAATAAAGTTTATTTATAGAATATATTTTA
Found at i:31194 original size:30 final size:30
Alignment explanation
Indices: 31158--31305 Score: 172
Period size: 30 Copynumber: 4.9 Consensus size: 30
31148 TTTCGGATGA
*
31158 CGATATTGTCTGATTTTTAGATGTAGGTGT
1 CGATATTGTCTGATTTTCAGATGTAGGTGT
* *
31188 CGATATTGTCGGATTTTCAGATGTAGTTGT
1 CGATATTGTCTGATTTTCAGATGTAGGTGT
* * * *
31218 CGACATTTTTTGATTTTCAGATGTAGTTG-
1 CGATATTGTCTGATTTTCAGATGTAGGTGT
* * * *
31247 CTGACATTGTCTTATTTTTAGATGTAGGTGC
1 C-GATATTGTCTGATTTTCAGATGTAGGTGT
*
31278 CGATATTTTCTGATTTTCAGATGTAGGT
1 CGATATTGTCTGATTTTCAGATGTAGGT
31306 AGTGCCAGAT
Statistics
Matches: 100, Mismatches: 16, Indels: 4
0.83 0.13 0.03
Matches are distributed among these distances:
29 1 0.01
30 98 0.98
31 1 0.01
ACGTcount: A:0.20, C:0.10, G:0.24, T:0.46
Consensus pattern (30 bp):
CGATATTGTCTGATTTTCAGATGTAGGTGT
Found at i:31347 original size:30 final size:29
Alignment explanation
Indices: 31311--31411 Score: 121
Period size: 30 Copynumber: 3.4 Consensus size: 29
31301 TAGGTAGTGC
*
31311 CAGATGTAGGTGCCATCATTGTCTTATTTT
1 CAGATGTAGTTGCCA-CATTGTCTTATTTT
* * *
31341 CAGATGTACTTGCCGACATTTTCTAATTTT
1 CAGATGTAGTTGCC-ACATTGTCTTATTTT
* *
31371 TAGATGTAGTTGCAAACATTGTCTTATTTT
1 CAGATGTAGTTGC-CACATTGTCTTATTTT
31401 CAGATGTAGTT
1 CAGATGTAGTT
31412 TCTGATGATA
Statistics
Matches: 59, Mismatches: 10, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
30 58 0.98
31 1 0.02
ACGTcount: A:0.24, C:0.15, G:0.18, T:0.44
Consensus pattern (29 bp):
CAGATGTAGTTGCCACATTGTCTTATTTT
Found at i:34533 original size:7 final size:7
Alignment explanation
Indices: 34521--34571 Score: 68
Period size: 7 Copynumber: 7.4 Consensus size: 7
34511 ATGTCCCTTA
34521 TAGGGTT
1 TAGGGTT
34528 TAGGGTT
1 TAGGGTT
*
34535 TATGGTT
1 TAGGGTT
34542 TAGGG-T
1 TAGGGTT
*
34548 TGGGGTT
1 TAGGGTT
34555 TAGGGTT
1 TAGGGTT
*
34562 TTGGGTT
1 TAGGGTT
34569 TAG
1 TAG
34572 AGCATCTTTC
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
6 5 0.14
7 32 0.86
ACGTcount: A:0.12, C:0.00, G:0.43, T:0.45
Consensus pattern (7 bp):
TAGGGTT
Found at i:34555 original size:20 final size:20
Alignment explanation
Indices: 34530--34568 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
34520 ATAGGGTTTA
*
34530 GGGTTTATGGTTTAGGGTTG
1 GGGTTTAGGGTTTAGGGTTG
*
34550 GGGTTTAGGGTTTTGGGTT
1 GGGTTTAGGGTTTAGGGTT
34569 TAGAGCATCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.08, C:0.00, G:0.46, T:0.46
Consensus pattern (20 bp):
GGGTTTAGGGTTTAGGGTTG
Found at i:34722 original size:2 final size:2
Alignment explanation
Indices: 34715--34752 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
34705 ATGGATGAAT
34715 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
34753 CATGGCAAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:34798 original size:25 final size:25
Alignment explanation
Indices: 34770--34819 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
34760 AATTTAAACT
*
34770 ACTATGGGCCGCTTAAATGTTACAA
1 ACTATAGGCCGCTTAAATGTTACAA
*
34795 ACTATAGGCCGCTTAATTGTTACAA
1 ACTATAGGCCGCTTAAATGTTACAA
34820 TTATTTGTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.30
Consensus pattern (25 bp):
ACTATAGGCCGCTTAAATGTTACAA
Found at i:39054 original size:29 final size:28
Alignment explanation
Indices: 38981--39067 Score: 120
Period size: 28 Copynumber: 3.1 Consensus size: 28
38971 AATTTAGTTG
*
38981 TTTGCACCTCCAGGGGCATTTTGGTCAT
1 TTTGCACGTCCAGGGGCATTTTGGTCAT
*
39009 TTTGCATGTCCAGGGGCATTTTGGTCAT
1 TTTGCACGTCCAGGGGCATTTTGGTCAT
* * *
39037 TCTTGCACGTCCAAGGGCTTTTTAGTCAT
1 T-TTGCACGTCCAGGGGCATTTTGGTCAT
39066 TT
1 TT
39068 CAAGTACATT
Statistics
Matches: 52, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
28 28 0.54
29 24 0.46
ACGTcount: A:0.15, C:0.22, G:0.24, T:0.39
Consensus pattern (28 bp):
TTTGCACGTCCAGGGGCATTTTGGTCAT
Found at i:39647 original size:25 final size:25
Alignment explanation
Indices: 39596--39647 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
39586 TGGTGGTTTT
* *
39596 ACTCTACATTTACATTTCGTTTTGC
1 ACTCCACATTTACATTTCGTTTGGC
39621 ACTCCACATTTACATTTTC-TTTGGC
1 ACTCCACATTTACA-TTTCGTTTGGC
39646 AC
1 AC
39648 CAAATGATGT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 20 0.83
26 4 0.17
ACGTcount: A:0.21, C:0.27, G:0.08, T:0.44
Consensus pattern (25 bp):
ACTCCACATTTACATTTCGTTTGGC
Found at i:46193 original size:26 final size:26
Alignment explanation
Indices: 46141--46198 Score: 107
Period size: 26 Copynumber: 2.2 Consensus size: 26
46131 AAAAAAAAAA
*
46141 TTTTGCGTTTTTGAAAAAAAAATTGT
1 TTTTGCGTTTTTGAAAAAAAAAGTGT
46167 TTTTGCGTTTTTGAAAAAAAAAGTGT
1 TTTTGCGTTTTTGAAAAAAAAAGTGT
46193 TTTTGC
1 TTTTGC
46199 ATATAAAAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.31, C:0.05, G:0.17, T:0.47
Consensus pattern (26 bp):
TTTTGCGTTTTTGAAAAAAAAAGTGT
Found at i:46195 original size:25 final size:24
Alignment explanation
Indices: 46115--46195 Score: 90
Period size: 26 Copynumber: 3.2 Consensus size: 24
46105 AATTTTTCTT
* **
46115 TTTTGCGTTTTTTCTAAAAAAAAAAA
1 TTTTGCG-TTTTT-GAAAAAAAAATG
46141 TTTTGCGTTTTTGAAAAAAAAATTG
1 TTTTGCGTTTTTGAAAAAAAAA-TG
46166 TTTTTGCGTTTTTGAAAAAAAAAGTG
1 -TTTTGCGTTTTTGAAAAAAAAA-TG
46192 TTTT
1 TTTT
46196 TGCATATAAA
Statistics
Matches: 49, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
24 9 0.18
25 9 0.18
26 31 0.63
ACGTcount: A:0.36, C:0.05, G:0.14, T:0.46
Consensus pattern (24 bp):
TTTTGCGTTTTTGAAAAAAAAATG
Found at i:50028 original size:24 final size:24
Alignment explanation
Indices: 49949--50031 Score: 75
Period size: 24 Copynumber: 3.5 Consensus size: 24
49939 GCTGCTGGTA
49949 CACTTGAAATCTAGCTAGACTCAT
1 CACTTGAAATCTAGCTAGACTCAT
** **
49973 CACTTTG-GCTGCT-GCT-G-CTGGT
1 CAC-TTGAAAT-CTAGCTAGACTCAT
49995 ACACTTGAAATCTAGCTAGACTCAT
1 -CACTTGAAATCTAGCTAGACTCAT
50020 CACTTGAAATCT
1 CACTTGAAATCT
50032 GCTTGGTTAC
Statistics
Matches: 44, Mismatches: 8, Indels: 14
0.67 0.12 0.21
Matches are distributed among these distances:
22 8 0.18
23 8 0.18
24 20 0.45
25 8 0.18
ACGTcount: A:0.27, C:0.25, G:0.17, T:0.31
Consensus pattern (24 bp):
CACTTGAAATCTAGCTAGACTCAT
Found at i:50283 original size:24 final size:24
Alignment explanation
Indices: 50230--50288 Score: 73
Period size: 24 Copynumber: 2.5 Consensus size: 24
50220 AATCAAGTAG
*
50230 AGGATTCCAACCTCAGTCAAATCC
1 AGGATTCCAACCTCAATCAAATCC
* * *
50254 AAGATTGCAACCTCAATCAAATCT
1 AGGATTCCAACCTCAATCAAATCC
*
50278 AGGATTTCAAC
1 AGGATTCCAAC
50289 GACAGCCAAG
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.37, C:0.27, G:0.12, T:0.24
Consensus pattern (24 bp):
AGGATTCCAACCTCAATCAAATCC
Done.