Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008138.1 Corchorus capsularis cultivar CVL-1 contig08159, 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: 47521
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.32
Found at i:4828 original size:29 final size:31
Alignment explanation
Indices: 4795--4863 Score: 106
Period size: 29 Copynumber: 2.3 Consensus size: 31
4785 TTTTACAACG
4795 TAAGGGATTAATTTGT-CCAAAA-AAAAACA
1 TAAGGGATTAATTTGTCCCAAAAGAAAAACA
* *
4824 TAAGGGATTATTTTGTCCCAAAAGTAAAACA
1 TAAGGGATTAATTTGTCCCAAAAGAAAAACA
4855 TAAGGGATT
1 TAAGGGATT
4864 TTTTTGGGTA
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
29 15 0.42
30 6 0.17
31 15 0.42
ACGTcount: A:0.45, C:0.10, G:0.17, T:0.28
Consensus pattern (31 bp):
TAAGGGATTAATTTGTCCCAAAAGAAAAACA
Found at i:4856 original size:31 final size:29
Alignment explanation
Indices: 4795--4869 Score: 105
Period size: 31 Copynumber: 2.5 Consensus size: 29
4785 TTTTACAACG
*
4795 TAAGGGATTAATTTGTCCAAAAAAAAACA
1 TAAGGGATTATTTTGTCCAAAAAAAAACA
*
4824 TAAGGGATTATTTTGTCCCAAAAGTAAAACA
1 TAAGGGATTATTTTGT-CCAAAA-AAAAACA
*
4855 TAAGGGATTTTTTTG
1 TAAGGGATTATTTTG
4870 GGTATTTAGC
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
29 15 0.37
30 6 0.15
31 20 0.49
ACGTcount: A:0.41, C:0.09, G:0.17, T:0.32
Consensus pattern (29 bp):
TAAGGGATTATTTTGTCCAAAAAAAAACA
Found at i:9735 original size:226 final size:235
Alignment explanation
Indices: 9314--9777 Score: 775
Period size: 226 Copynumber: 2.0 Consensus size: 235
9304 GATGAGTTCA
*
9314 TATACTTTTACTAAATCCAAAAAGCTTTTTTTTTATCAGAAAATTTTGTTGAAGTCCTAATTTTT
1 TATACTTTTACTAAATCC-AAAA-CTTTTTTTTTACCAGAAAATTTTGTTGAAGTCCTAATTTTT
*
9379 TTTAATTATTATTGCATATAGATTTTGTTGATAAATATCTTATACTTTTTGTATTCTCTAGTTGG
64 TTTAATTATTATTGCATATAAATTTTGTTGATAAATATCTTATACTTTTTGTATTCTCTAGTTGG
*
9444 TTATGATGTCCTCAGGTTGTGAAATTGCTTATAGTTCATACTCGACATTACTTGATACATTTAGT
129 TTATGATGTCCTCAGGTTGTGAAATTACTTATAGTTCATACTCGACATTACTTGATACATTTAGT
9509 AAAAT-A-AT-AT-T-TAGGACAAAGGGAGATGTATTTGTAT
194 AAAATAATATAATATCTAGGACAAAGGGAGATGTATTTGTAT
* *
9546 TATACTTTTATTAAATCC-AAA-TTTTTTTTTACCAGAAAATTTTGTTGAAGTCTTAA-TTTTTT
1 TATACTTTTACTAAATCCAAAACTTTTTTTTTACCAGAAAATTTTGTTGAAGTCCTAATTTTTTT
9608 TAATTATTATTGCATATAAATTTTGTTGATAAATATCTTATA-TTTTTGTATTCTCTAGTTGGTT
66 TAATTATTATTGCATATAAATTTTGTTGATAAATATCTTATACTTTTTGTATTCTCTAGTTGGTT
* * *
9672 ATGATGTCCTCAGGTTGTGAAATTACTTATAGTTCATTCTCGACCTTACTTGATACTTTTAGTAA
131 ATGATGTCCTCAGGTTGTGAAATTACTTATAGTTCATACTCGACATTACTTGATACATTTAGTAA
9737 AATAATATAATATCTAGGACAAAGGGAGATGTATTTGTAT
196 AATAATATAATATCTAGGACAAAGGGAGATGTATTTGTAT
9777 T
1 T
9778 TAAACCCGCC
Statistics
Matches: 219, Mismatches: 8, Indels: 11
0.92 0.03 0.05
Matches are distributed among these distances:
226 86 0.39
227 48 0.22
228 35 0.16
229 2 0.01
230 4 0.02
231 27 0.12
232 17 0.08
ACGTcount: A:0.31, C:0.10, G:0.13, T:0.46
Consensus pattern (235 bp):
TATACTTTTACTAAATCCAAAACTTTTTTTTTACCAGAAAATTTTGTTGAAGTCCTAATTTTTTT
TAATTATTATTGCATATAAATTTTGTTGATAAATATCTTATACTTTTTGTATTCTCTAGTTGGTT
ATGATGTCCTCAGGTTGTGAAATTACTTATAGTTCATACTCGACATTACTTGATACATTTAGTAA
AATAATATAATATCTAGGACAAAGGGAGATGTATTTGTAT
Found at i:16032 original size:21 final size:20
Alignment explanation
Indices: 15993--16034 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
15983 TCCTTTGCTT
*
15993 ATTGTCTTCAATGCTCTTCA
1 ATTGTCTTCAATGCACTTCA
*
16013 ATTGATCTTCAATGGACTTCA
1 ATTG-TCTTCAATGCACTTCA
16034 A
1 A
16035 ACCTTCAAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.26, C:0.21, G:0.12, T:0.40
Consensus pattern (20 bp):
ATTGTCTTCAATGCACTTCA
Found at i:17203 original size:21 final size:20
Alignment explanation
Indices: 17164--17205 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
17154 TCCTTTGCTT
*
17164 ATTGTCTTCAATGCTCTTCA
1 ATTGTCTTCAATGCACTTCA
*
17184 ATTGATCTTCAATGGACTTCA
1 ATTG-TCTTCAATGCACTTCA
17205 A
1 A
17206 ACCTTCAAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.26, C:0.21, G:0.12, T:0.40
Consensus pattern (20 bp):
ATTGTCTTCAATGCACTTCA
Found at i:18706 original size:30 final size:31
Alignment explanation
Indices: 18672--18746 Score: 91
Period size: 30 Copynumber: 2.5 Consensus size: 31
18662 CCGGTTGTGC
** *
18672 CCGGTCTTGTGCGATTGGC-CCATGCCATGG
1 CCGGTCTTGTGCGATTCCCTCCATGCAATGG
*
18702 CCGGTCATGTGCGA-TCCCTCCATGCAATGG
1 CCGGTCTTGTGCGATTCCCTCCATGCAATGG
*
18732 TCGGTCTTGTGCGAT
1 CCGGTCTTGTGCGAT
18747 GGCATCCTCT
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
29 2 0.05
30 35 0.95
ACGTcount: A:0.12, C:0.29, G:0.31, T:0.28
Consensus pattern (31 bp):
CCGGTCTTGTGCGATTCCCTCCATGCAATGG
Found at i:19772 original size:48 final size:48
Alignment explanation
Indices: 19715--20118 Score: 347
Period size: 48 Copynumber: 8.6 Consensus size: 48
19705 CGAAAATTGG
* *
19715 CCTTTCCGGTCGGAAGGCGCAAGTTTTCTTCATTTATTCCCAAAATGC
1 CCTTCCCGGTCGGAAGGTGCAAGTTTTCTTCATTTATTCCCAAAATGC
* *
19763 CCTTCCCGGTCGGAAGGTGCAAG-TTT-TTCATCCCTAGT-CCAAACATGC
1 CCTTCCCGGTCGGAAGGTGCAAGTTTTCTTCAT--TTATTCCCAAA-ATGC
*
19811 CCTTCCCGGTCGGAAGGTGCAAG-TTT-TTCATCCCTATT-CCAAACATGC
1 CCTTCCCGGTCGGAAGGTGCAAGTTTTCTTCAT--TTATTCCCAAA-ATGC
* * *
19859 CCTTCCTGGTCGGAAGGTGCAAGTTTTCTTTATTTATTCCCAAAATAC
1 CCTTCCCGGTCGGAAGGTGCAAGTTTTCTTCATTTATTCCCAAAATGC
* *
19907 CCTTCCCGGTCGGAAGGTGCAAATTTTCTTCATTTACTCCCAAAATGC
1 CCTTCCCGGTCGGAAGGTGCAAGTTTTCTTCATTTATTCCCAAAATGC
* * ** * * * *
19955 CCTTCCTGGTCGGAAGATGCAAACTTACTTCACTTGTTCCAAAAATGC
1 CCTTCCCGGTCGGAAGGTGCAAGTTTTCTTCATTTATTCCCAAAATGC
* * * *
20003 CCTTCCTGGTCGGAAGGTGTAA---------A--TGTTCCAAAAATGC
1 CCTTCCCGGTCGGAAGGTGCAAGTTTTCTTCATTTATTCCCAAAATGC
* * * * * *
20040 CCTTCCCGGTCGGAAGGTGTAAATTTCCTTCACTTGTTCCAAAAATGC
1 CCTTCCCGGTCGGAAGGTGCAAGTTTTCTTCATTTATTCCCAAAATGC
* * **
20088 CCTTCCCGATTGGAAGGCACAAGTTTTCTTC
1 CCTTCCCGGTCGGAAGGTGCAAGTTTTCTTC
20119 TTTTTCTTCT
Statistics
Matches: 307, Mismatches: 32, Indels: 34
0.82 0.09 0.09
Matches are distributed among these distances:
37 35 0.11
39 1 0.00
46 6 0.02
47 8 0.03
48 245 0.80
49 8 0.03
50 4 0.01
ACGTcount: A:0.23, C:0.27, G:0.19, T:0.31
Consensus pattern (48 bp):
CCTTCCCGGTCGGAAGGTGCAAGTTTTCTTCATTTATTCCCAAAATGC
Found at i:19955 original size:144 final size:143
Alignment explanation
Indices: 19718--20021 Score: 402
Period size: 144 Copynumber: 2.1 Consensus size: 143
19708 AAATTGGCCT
* *
19718 TTCC-GGTCGGAAGGCGCAAGTTTTCTTCATTTATTCCCAAAATGCCCTTCCCGGTCGGAAGGTG
1 TTCCTGGTCGGAAGGTGCAAGTTTTCTTCATTTATTCCCAAAATACCCTTCCCGGTCGGAAGGTG
* * * *
19782 CAAGTTTTTCATCCCTAGTCCAAACATGCCCTTCCCGGTCGGAAGGTGC-AAGTT-TTTCATCCC
66 CAAGTTTTTCAT-CCTACTCCAAACATGCCCTTCCCGGTCGGAAGATGCAAACTTACTTCA--CC
*
19845 TATTCCAAACATGCCC
128 TATTCCAAAAATGCCC
*
19861 TTCCTGGTCGGAAGGTGCAAGTTTTCTTTATTTATTCCCAAAATACCCTTCCCGGTCGGAAGGTG
1 TTCCTGGTCGGAAGGTGCAAGTTTTCTTCATTTATTCCCAAAATACCCTTCCCGGTCGGAAGGTG
* * * *
19926 CAAATTTTCTTCAT-TTACTCCCAAA-ATGCCCTTCCTGGTCGGAAGATGCAAACTTACTTCACT
66 C-AAGTTT-TTCATCCTACT-CCAAACATGCCCTTCCCGGTCGGAAGATGCAAACTTACTTCACC
*
19989 TGTTCCAAAAATGCCC
128 TATTCCAAAAATGCCC
20005 TTCCTGGTCGGAAGGTG
1 TTCCTGGTCGGAAGGTG
20022 TAAATGTTCC
Statistics
Matches: 142, Mismatches: 13, Indels: 11
0.86 0.08 0.07
Matches are distributed among these distances:
143 4 0.03
144 115 0.81
145 14 0.10
146 9 0.06
ACGTcount: A:0.22, C:0.28, G:0.19, T:0.31
Consensus pattern (143 bp):
TTCCTGGTCGGAAGGTGCAAGTTTTCTTCATTTATTCCCAAAATACCCTTCCCGGTCGGAAGGTG
CAAGTTTTTCATCCTACTCCAAACATGCCCTTCCCGGTCGGAAGATGCAAACTTACTTCACCTAT
TCCAAAAATGCCC
Found at i:20039 original size:37 final size:37
Alignment explanation
Indices: 19989--20067 Score: 142
Period size: 37 Copynumber: 2.2 Consensus size: 37
19979 TTACTTCACT
*
19989 TGTTCCAAAAATGCCCTTCCTGGTCGGAAGGTGTAAA
1 TGTTCCAAAAATGCCCTTCCCGGTCGGAAGGTGTAAA
20026 TGTTCCAAAAATGCCCTTCCCGGTCGGAAGGTGTAAA
1 TGTTCCAAAAATGCCCTTCCCGGTCGGAAGGTGTAAA
20063 T-TTCC
1 TGTTCC
20068 TTCACTTGTT
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
36 4 0.10
37 37 0.90
ACGTcount: A:0.25, C:0.24, G:0.23, T:0.28
Consensus pattern (37 bp):
TGTTCCAAAAATGCCCTTCCCGGTCGGAAGGTGTAAA
Found at i:20103 original size:85 final size:85
Alignment explanation
Indices: 19948--20104 Score: 242
Period size: 85 Copynumber: 1.8 Consensus size: 85
19938 ATTTACTCCC
* * *
19948 AAAATGCCCTTCCTGGTCGGAAGATGCAAACTTACTTCACTTGTTCCAAAAATGCCCTTCCTGGT
1 AAAATGCCCTTCCCGGTCGGAAGATGCAAACTTACTTCACTTGTTCCAAAAATGCCCTTCCCGAT
20013 CGGAAGGTGTAAATGTTCCA
66 CGGAAGGTGTAAATGTTCCA
* * * *
20033 AAAATGCCCTTCCCGGTCGGAAGGTGTAAATTTCCTTCACTTGTTCCAAAAATGCCCTTCCCGAT
1 AAAATGCCCTTCCCGGTCGGAAGATGCAAACTTACTTCACTTGTTCCAAAAATGCCCTTCCCGAT
*
20098 TGGAAGG
66 CGGAAGG
20105 CACAAGTTTT
Statistics
Matches: 64, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
85 64 1.00
ACGTcount: A:0.26, C:0.25, G:0.20, T:0.28
Consensus pattern (85 bp):
AAAATGCCCTTCCCGGTCGGAAGATGCAAACTTACTTCACTTGTTCCAAAAATGCCCTTCCCGAT
CGGAAGGTGTAAATGTTCCA
Found at i:22773 original size:24 final size:23
Alignment explanation
Indices: 22746--22792 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
22736 GCCACCTTAA
*
22746 CGTGAATGGGAAGGACCCCCTTGC
1 CGTGAACGGGAAGG-CCCCCTTGC
* *
22770 CGTGAGCGGGAAGGTCCCCTTGC
1 CGTGAACGGGAAGGCCCCCTTGC
22793 TGCGCATGGT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 8 0.40
24 12 0.60
ACGTcount: A:0.17, C:0.30, G:0.36, T:0.17
Consensus pattern (23 bp):
CGTGAACGGGAAGGCCCCCTTGC
Found at i:24203 original size:33 final size:33
Alignment explanation
Indices: 24153--24277 Score: 153
Period size: 33 Copynumber: 3.7 Consensus size: 33
24143 CCGCGCAACA
*
24153 CCGGCCACAAGACCGGCCACGCGACATGGACATGT
1 CCGGCCAC-A-ACCGGCCACGCGACATGGACATGC
*
24188 CCGGCCATC-ACCGGCCACGCGACATGGACATGG
1 CCGGCCA-CAACCGGCCACGCGACATGGACATGC
* ** * *
24221 CCGGCTACAACCGGCCAAACGACTTGGCCATGC
1 CCGGCCACAACCGGCCACGCGACATGGACATGC
24254 CCGGCCACAACCGGCCACGCGACA
1 CCGGCCACAACCGGCCACGCGACA
24278 ATTTGTCTAT
Statistics
Matches: 77, Mismatches: 11, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
32 1 0.01
33 68 0.88
35 7 0.09
36 1 0.01
ACGTcount: A:0.24, C:0.41, G:0.27, T:0.08
Consensus pattern (33 bp):
CCGGCCACAACCGGCCACGCGACATGGACATGC
Found at i:30535 original size:33 final size:33
Alignment explanation
Indices: 30465--30578 Score: 108
Period size: 33 Copynumber: 3.5 Consensus size: 33
30455 CGGCCACAAG
* * *
30465 ACCGGCCACGCGACATGGACATGTCCGGCCATC-
1 ACCGGCCACACGACATGGACATGGCCCGCCA-CA
* *
30498 ACCGGCCACACGACATGGACATGGCCTGCTACA
1 ACCGGCCACACGACATGGACATGGCCCGCCACA
* *
30531 ACCGGCCAAACGAC-TCGGCCAT-GCCCGACCACA
1 ACCGGCCACACGACAT-GGACATGGCCCG-CCACA
*
30564 ACCGGCCACGCGACA
1 ACCGGCCACACGACA
30579 ATTTGTCTAT
Statistics
Matches: 67, Mismatches: 10, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
32 6 0.09
33 61 0.91
ACGTcount: A:0.25, C:0.41, G:0.25, T:0.09
Consensus pattern (33 bp):
ACCGGCCACACGACATGGACATGGCCCGCCACA
Found at i:33623 original size:21 final size:21
Alignment explanation
Indices: 33599--33640 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
33589 TAGACATAAT
*
33599 AATATAGAAATATTTGATATG
1 AATATAGAAATATTTAATATG
*
33620 AATATAGACATATTTAATATG
1 AATATAGAAATATTTAATATG
33641 TATAGTAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.48, C:0.02, G:0.12, T:0.38
Consensus pattern (21 bp):
AATATAGAAATATTTAATATG
Found at i:36420 original size:21 final size:21
Alignment explanation
Indices: 36394--36453 Score: 111
Period size: 21 Copynumber: 2.9 Consensus size: 21
36384 GATGGTGAAA
36394 GTTTGTATGAATACTAGGATC
1 GTTTGTATGAATACTAGGATC
36415 GTTTGTATGAATACTAGGATC
1 GTTTGTATGAATACTAGGATC
*
36436 GTTTGTATGAATATTAGG
1 GTTTGTATGAATACTAGG
36454 TTCGGATCAA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.28, C:0.07, G:0.25, T:0.40
Consensus pattern (21 bp):
GTTTGTATGAATACTAGGATC
Found at i:36554 original size:5 final size:5
Alignment explanation
Indices: 36537--36603 Score: 82
Period size: 5 Copynumber: 13.4 Consensus size: 5
36527 TAAGGAGATT
* * *
36537 TTTTG TTTT- TTTGG TTTGG TTTGG TTTTG TTTTG TTTTG TTTTG TTTTG
1 TTTTG TTTTG TTTTG TTTTG TTTTG TTTTG TTTTG TTTTG TTTTG TTTTG
*
36586 TTTTTG TTTTT TTTTG TT
1 -TTTTG TTTTG TTTTG TT
36604 GGAAAAGCGA
Statistics
Matches: 56, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
4 3 0.05
5 48 0.86
6 5 0.09
ACGTcount: A:0.00, C:0.00, G:0.21, T:0.79
Consensus pattern (5 bp):
TTTTG
Found at i:40424 original size:130 final size:130
Alignment explanation
Indices: 40191--40441 Score: 466
Period size: 130 Copynumber: 1.9 Consensus size: 130
40181 ATATGATTTT
* *
40191 TTGAAATTGAAGATAGCGGCGTCTATATATCAGACGCCACTATTTAGTGGCGTTTAAATAAGAAG
1 TTGAAATTGAAGATAGCGGCGTCTATATATCAGACGCCACTATTTAGAGGCGTTAAAATAAGAAG
* *
40256 ACGCCGCCATATTAATATGTGGAGGGAGAGATTTTTTTTTCTTTTTTTGGAGGGAATTTCTGAAA
66 ACGCCGCCATATTAATATGTGGAGGGAGAGATTATTTTTCCTTTTTTTGGAGGGAATTTCTGAAA
40321 TTGAAATTGAAGATAGCGGCGTCTATATATCAGACGCCACTATTTAGAGGCGTTAAAATAAGAAG
1 TTGAAATTGAAGATAGCGGCGTCTATATATCAGACGCCACTATTTAGAGGCGTTAAAATAAGAAG
40386 ACGCCGCCATATTAATATGTGGAGGGAGAGATTATTTTTCCTTTTTTTGGAGGGAA
66 ACGCCGCCATATTAATATGTGGAGGGAGAGATTATTTTTCCTTTTTTTGGAGGGAA
40442 AAATTCCCTC
Statistics
Matches: 117, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
130 117 1.00
ACGTcount: A:0.30, C:0.13, G:0.24, T:0.33
Consensus pattern (130 bp):
TTGAAATTGAAGATAGCGGCGTCTATATATCAGACGCCACTATTTAGAGGCGTTAAAATAAGAAG
ACGCCGCCATATTAATATGTGGAGGGAGAGATTATTTTTCCTTTTTTTGGAGGGAATTTCTGAAA
Found at i:45572 original size:27 final size:27
Alignment explanation
Indices: 45542--45626 Score: 161
Period size: 27 Copynumber: 3.1 Consensus size: 27
45532 CCCCTAAAAT
45542 TTCGACCCCAGCAGTGGATCCTCCCAC
1 TTCGACCCCAGCAGTGGATCCTCCCAC
45569 TTCGACCCCAGCAGTGGATCCTCCCAC
1 TTCGACCCCAGCAGTGGATCCTCCCAC
*
45596 TTCGACCCTAGCAGTGGATCCTCCCAC
1 TTCGACCCCAGCAGTGGATCCTCCCAC
45623 TTCG
1 TTCG
45627 CCTCGGGTCG
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
27 57 1.00
ACGTcount: A:0.18, C:0.42, G:0.19, T:0.21
Consensus pattern (27 bp):
TTCGACCCCAGCAGTGGATCCTCCCAC
Done.