Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015807.1 Corchorus capsularis cultivar CVL-1 contig15828, 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: 22466
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:564 original size:21 final size:21
Alignment explanation
Indices: 547--586 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
537 GCCTTGTTCT
547 TGCCTCATCTCTTCTTGTGAA
1 TGCCTCATCTCTTCTTGTGAA
*
568 TGCCTCATTTCTTCTTGTG
1 TGCCTCATCTCTTCTTGTG
587 CTGTCTCAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.10, C:0.28, G:0.15, T:0.47
Consensus pattern (21 bp):
TGCCTCATCTCTTCTTGTGAA
Found at i:4313 original size:67 final size:67
Alignment explanation
Indices: 4221--4470 Score: 232
Period size: 67 Copynumber: 3.5 Consensus size: 67
4211 TCTAAATTTC
*
4221 CCACAATTTGGCAAGATTTAGAAAATATTCTCATTATTATTAAATCTAAAAATATCTCCTAAACC
1 CCACAATTTGGCAAGATTCAGAAAATATTCTCATTATTATTAAATCTAAAAATATCTCCTAAACC
4286 TT
66 TT
* ** * *
4288 CCACAATTTGGCAAGATTCAGAAAATATTCTCTTTACAAATTAAATCTTTATAATTTTTATTTCT
1 CCACAATTTGGCAAGATTCAGAAAATATTCTCATTA-TTATTAAATC--TA-AA----AATATC-
* *
4353 TAAAATATCTTCTAAATCTC
57 -------TC--CTAAACCTT
4373 CCACAATTTGGCAAGAATT-AGAAAATATTCTCATTATTATTAAATCTAAAAATATCTCCTAAAC
1 CCACAATTTGGCAAG-ATTCAGAAAATATTCTCATTATTATTAAATCTAAAAATATCTCCTAAAC
4437 CTT
65 CTT
* *
4440 CCACAATTTGACAAGATTCAAAAAATATTCT
1 CCACAATTTGGCAAGATTCAGAAAATATTCT
4471 ATTTACAAAT
Statistics
Matches: 146, Mismatches: 17, Indels: 40
0.72 0.08 0.20
Matches are distributed among these distances:
66 3 0.02
67 66 0.45
68 8 0.05
69 2 0.01
70 2 0.01
71 2 0.01
75 4 0.03
77 4 0.03
81 2 0.01
82 2 0.01
83 2 0.01
84 8 0.05
85 38 0.26
86 3 0.02
ACGTcount: A:0.40, C:0.18, G:0.06, T:0.37
Consensus pattern (67 bp):
CCACAATTTGGCAAGATTCAGAAAATATTCTCATTATTATTAAATCTAAAAATATCTCCTAAACC
TT
Found at i:4481 original size:152 final size:151
Alignment explanation
Indices: 4205--4555 Score: 596
Period size: 152 Copynumber: 2.3 Consensus size: 151
4195 TTCCTTTTTT
*
4205 ATATCTTCTAAATTTCCCACAATTTGGCAAGATTTAGAAAATATTCTCATTATTATTAAATCTAA
1 ATATCTTCTAAATCTCCCACAATTTGGCAAGATTTAGAAAATATTCTCATTATTATTAAATCTAA
* * *
4270 AAATATCTCCTAAACCTTCCACAATTTGGCAAGATTCAGAAAATATTCTCTTTACAAATTAAATC
66 AAATATCTCCTAAACCTTCCACAATTTGACAAGATTCAAAAAATATTCTATTTACAAATTAAATC
*
4335 TTTATAATTTTTATTTCTTAAA
131 TTTATAA-TTTTATTTATTAAA
*
4357 ATATCTTCTAAATCTCCCACAATTTGGCAAGAATTAGAAAATATTCTCATTATTATTAAATCTAA
1 ATATCTTCTAAATCTCCCACAATTTGGCAAGATTTAGAAAATATTCTCATTATTATTAAATCTAA
4422 AAATATCTCCTAAACCTTCCACAATTTGACAAGATTCAAAAAATATTCTATTTACAAATTAAATC
66 AAATATCTCCTAAACCTTCCACAATTTGACAAGATTCAAAAAATATTCTATTTACAAATTAAATC
4487 TTTATAATTTTATTTATTAAA
131 TTTATAATTTTATTTATTAAA
* * *
4508 ATAT-TTCCTAAACCTTCCACAATTTGGCAAGATTTAGAAAATGTTCTC
1 ATATCTT-CTAAATCTCCCACAATTTGGCAAGATTTAGAAAATATTCTC
4556 TTTACAAATT
Statistics
Matches: 188, Mismatches: 10, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
150 2 0.01
151 54 0.29
152 132 0.70
ACGTcount: A:0.39, C:0.17, G:0.05, T:0.39
Consensus pattern (151 bp):
ATATCTTCTAAATCTCCCACAATTTGGCAAGATTTAGAAAATATTCTCATTATTATTAAATCTAA
AAATATCTCCTAAACCTTCCACAATTTGACAAGATTCAAAAAATATTCTATTTACAAATTAAATC
TTTATAATTTTATTTATTAAA
Found at i:6696 original size:49 final size:50
Alignment explanation
Indices: 6605--6706 Score: 179
Period size: 49 Copynumber: 2.0 Consensus size: 50
6595 GATTTGAAGA
6605 CTATTGAAGAATTAATTCAAGAAGATAAAATTGAAGATTTAGAGCTTATTTG
1 CTATTGAAGAATTAATTC-A-AAGATAAAATTGAAGATTTAGAGCTTATTTG
6657 CTATTGAAGAATTAATTC-AAGATAAAATTGAAGATTTAGAGCTTATTTG
1 CTATTGAAGAATTAATTCAAAGATAAAATTGAAGATTTAGAGCTTATTTG
6706 C
1 C
6707 AAAGGATTGA
Statistics
Matches: 50, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
49 32 0.64
52 18 0.36
ACGTcount: A:0.41, C:0.07, G:0.17, T:0.35
Consensus pattern (50 bp):
CTATTGAAGAATTAATTCAAAGATAAAATTGAAGATTTAGAGCTTATTTG
Found at i:8630 original size:21 final size:21
Alignment explanation
Indices: 8605--8680 Score: 107
Period size: 21 Copynumber: 3.6 Consensus size: 21
8595 TAATCCTATG
* *
8605 TTGGAGGTCTCTTAATTATAT
1 TTGGAGGTTTCTTATTTATAT
8626 TTGGAGGTTTCTTATTTATAT
1 TTGGAGGTTTCTTATTTATAT
*
8647 TTAGAGGTTTCTTATTTATAT
1 TTGGAGGTTTCTTATTTATAT
* *
8668 TTGAAAGTTTCTT
1 TTGGAGGTTTCTT
8681 TCATATATTT
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 49 1.00
ACGTcount: A:0.22, C:0.07, G:0.17, T:0.54
Consensus pattern (21 bp):
TTGGAGGTTTCTTATTTATAT
Found at i:8688 original size:42 final size:42
Alignment explanation
Indices: 8608--8700 Score: 109
Period size: 42 Copynumber: 2.2 Consensus size: 42
8598 TCCTATGTTG
* * * *
8608 GAGGTCTCTTAATTATATTTGGAGGTTTCTTATTTATATTTA
1 GAGGTTTCTTAATTATATTTGAAAGTTTCTTATATATATTTA
*
8650 GAGGTTTCTTATTTATATTTGAAAGTTTCTT-TCATATATTTA
1 GAGGTTTCTTAATTATATTTGAAAGTTTCTTAT-ATATATTTA
*
8692 G-GTTTTCTT
1 GAGGTTTCTT
8701 TATAATTTAT
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
41 8 0.18
42 36 0.82
ACGTcount: A:0.23, C:0.08, G:0.15, T:0.55
Consensus pattern (42 bp):
GAGGTTTCTTAATTATATTTGAAAGTTTCTTATATATATTTA
Found at i:9196 original size:33 final size:33
Alignment explanation
Indices: 9154--9227 Score: 96
Period size: 33 Copynumber: 2.2 Consensus size: 33
9144 GTGTTTTAGA
* *
9154 TGTTGTTTGCAATGATACTAAACCTAATTTGA-G
1 TGTTGTTTGCAATGACAATAAACCT-ATTTGAGG
* *
9187 TGTTGTTTGCAATGACAATAAATCTATTTTAGG
1 TGTTGTTTGCAATGACAATAAACCTATTTGAGG
9220 TGTTGTTT
1 TGTTGTTT
9228 CTGATGAAAC
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
32 5 0.14
33 31 0.86
ACGTcount: A:0.27, C:0.09, G:0.19, T:0.45
Consensus pattern (33 bp):
TGTTGTTTGCAATGACAATAAACCTATTTGAGG
Found at i:9710 original size:30 final size:30
Alignment explanation
Indices: 9674--9736 Score: 101
Period size: 30 Copynumber: 2.1 Consensus size: 30
9664 TCTTCAAGGG
*
9674 GGAGGGAATGATGCGCCCAAGG-CTTATCAT
1 GGAGGGAATGATGC-ACCAAGGACTTATCAT
9704 GGAGGGAATGATGCACCAAGGACTTATCAT
1 GGAGGGAATGATGCACCAAGGACTTATCAT
9734 GGA
1 GGA
9737 CTTGAAAACA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
29 6 0.19
30 25 0.81
ACGTcount: A:0.30, C:0.17, G:0.33, T:0.19
Consensus pattern (30 bp):
GGAGGGAATGATGCACCAAGGACTTATCAT
Found at i:12261 original size:32 final size:31
Alignment explanation
Indices: 12214--12291 Score: 120
Period size: 32 Copynumber: 2.5 Consensus size: 31
12204 AAACAAGAAG
* *
12214 AACAAGTAAGAACTTATATGAAAAAGTGAAA
1 AACAACTAAGAACTTATATGAAAAACTGAAA
12245 AACAACATAAGAACTTATATGAAAAACTGAAA
1 AACAAC-TAAGAACTTATATGAAAAACTGAAA
*
12277 AACAACGAAGAACTT
1 AACAACTAAGAACTT
12292 TCAGAGAAAA
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
31 13 0.30
32 30 0.70
ACGTcount: A:0.58, C:0.12, G:0.13, T:0.18
Consensus pattern (31 bp):
AACAACTAAGAACTTATATGAAAAACTGAAA
Found at i:14348 original size:107 final size:110
Alignment explanation
Indices: 14160--14374 Score: 364
Period size: 107 Copynumber: 2.0 Consensus size: 110
14150 ACCATGGTGC
* *
14160 GGGTCACGATCCGCACGCGACCCATGCCATGGCTCGGGCCGCGGGCGGGTCGCGACCAGTTTTCT
1 GGGTCACGATCCGCACGCGACCCATGCCATGGCTCGAGCCGCGCGCGGGTCGCGACCAGTTTTCT
14225 TCTTCTTAAGA-TTTTTTTTTTTAGATTTTCCTATAATTTCTTGT
66 TCTTCTTAAGATTTTTTTTTTTTAGATTTTCCTATAATTTCTTGT
* * *
14269 GGGTCGCGATCCGCGCGCGACCCA-GCCATGGC-CGAGTCGCGCGCGGGTCGCGACCAGTTTTCT
1 GGGTCACGATCCGCACGCGACCCATGCCATGGCTCGAGCCGCGCGCGGGTCGCGACCAGTTTTCT
14332 TCTTCTTAAGATTTTTTTTTTTTAGATTTTCCTATAATTTCTT
66 TCTTCTTAAGATTTTTTTTTTTTAGATTTTCCTATAATTTCTT
14375 TTTATCCTTT
Statistics
Matches: 100, Mismatches: 5, Indels: 3
0.93 0.05 0.03
Matches are distributed among these distances:
107 39 0.39
108 39 0.39
109 22 0.22
ACGTcount: A:0.14, C:0.26, G:0.24, T:0.36
Consensus pattern (110 bp):
GGGTCACGATCCGCACGCGACCCATGCCATGGCTCGAGCCGCGCGCGGGTCGCGACCAGTTTTCT
TCTTCTTAAGATTTTTTTTTTTTAGATTTTCCTATAATTTCTTGT
Found at i:15943 original size:6 final size:6
Alignment explanation
Indices: 15928--15959 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
15918 AAAGCAAAGC
15928 AAAT-T AAATCT AAATCT AAATCT AAATCT AAA
1 AAATCT AAATCT AAATCT AAATCT AAATCT AAA
15960 GCAAATTAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 4 0.15
6 22 0.85
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.31
Consensus pattern (6 bp):
AAATCT
Done.