Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013039.1 Corchorus capsularis cultivar CVL-1 contig13060, 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: 45753
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:2013 original size:29 final size:30
Alignment explanation
Indices: 1978--2037 Score: 88
Period size: 29 Copynumber: 2.0 Consensus size: 30
1968 ACTTGTAGCG
*
1978 TTTGGACGTTTTGTCCCC-TGAACT-TCAAT
1 TTTGGACATTTTG-CCCCATGAACTCTCAAT
2007 TTTGGACATTTTGCCCCATGAACTCTCAAT
1 TTTGGACATTTTGCCCCATGAACTCTCAAT
2037 T
1 T
2038 AGGCTCTGTT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
28 4 0.14
29 18 0.64
30 6 0.21
ACGTcount: A:0.20, C:0.25, G:0.15, T:0.40
Consensus pattern (30 bp):
TTTGGACATTTTGCCCCATGAACTCTCAAT
Found at i:2521 original size:32 final size:32
Alignment explanation
Indices: 2480--2544 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
2470 AGTGGAGAAG
2480 TTTCTGTATTTATAAATACTGAAAGGTTATCT
1 TTTCTGTATTTATAAATACTGAAAGGTTATCT
2512 TTTCTGTATTTATAAATACTGAAAGGTTATCT
1 TTTCTGTATTTATAAATACTGAAAGGTTATCT
2544 T
1 T
2545 GAATGGTTAC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.31, C:0.09, G:0.12, T:0.48
Consensus pattern (32 bp):
TTTCTGTATTTATAAATACTGAAAGGTTATCT
Found at i:4264 original size:20 final size:20
Alignment explanation
Indices: 4239--4278 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
4229 TACAACACTG
4239 GTTTTAGGGTGAAGTAATTT
1 GTTTTAGGGTGAAGTAATTT
4259 GTTTTAGGGTGAAGTAATTT
1 GTTTTAGGGTGAAGTAATTT
4279 TGCCTAAGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.25, C:0.00, G:0.30, T:0.45
Consensus pattern (20 bp):
GTTTTAGGGTGAAGTAATTT
Found at i:10362 original size:24 final size:24
Alignment explanation
Indices: 10330--10377 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
10320 TGGAGCGGCG
*
10330 GAGGGAAAAGGGGAAAACACGTAT
1 GAGGGAAAAGAGGAAAACACGTAT
*
10354 GAGGGAAAAGAGGAAGACACGTAT
1 GAGGGAAAAGAGGAAAACACGTAT
10378 ACACAGTCCA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.46, C:0.08, G:0.38, T:0.08
Consensus pattern (24 bp):
GAGGGAAAAGAGGAAAACACGTAT
Found at i:11651 original size:35 final size:35
Alignment explanation
Indices: 11612--11679 Score: 136
Period size: 35 Copynumber: 1.9 Consensus size: 35
11602 AATAAATTTT
11612 TTATGTTAAATATAAACATAGGGTTTTAGTTCCAA
1 TTATGTTAAATATAAACATAGGGTTTTAGTTCCAA
11647 TTATGTTAAATATAAACATAGGGTTTTAGTTCC
1 TTATGTTAAATATAAACATAGGGTTTTAGTTCC
11680 GATCCCTCCG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.35, C:0.09, G:0.15, T:0.41
Consensus pattern (35 bp):
TTATGTTAAATATAAACATAGGGTTTTAGTTCCAA
Found at i:11857 original size:17 final size:17
Alignment explanation
Indices: 11837--11901 Score: 85
Period size: 17 Copynumber: 3.6 Consensus size: 17
11827 CGGACCATTT
11837 TCGGGTTCGGGCTTGAG
1 TCGGGTTCGGGCTTGAG
* *
11854 TCGGGTTCGGGCTCGGG
1 TCGGGTTCGGGCTTGAG
11871 TTATCGGGTTCGGGCTTGAG
1 ---TCGGGTTCGGGCTTGAG
11891 TCGGGTTCGGG
1 TCGGGTTCGGG
11902 TTGGATTTGG
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
17 26 0.63
20 15 0.37
ACGTcount: A:0.05, C:0.18, G:0.48, T:0.29
Consensus pattern (17 bp):
TCGGGTTCGGGCTTGAG
Found at i:11960 original size:15 final size:15
Alignment explanation
Indices: 11910--11960 Score: 57
Period size: 15 Copynumber: 3.3 Consensus size: 15
11900 GGTTGGATTT
11910 GGGTCAGGTTAATTC
1 GGGTCAGGTTAATTC
* *
11925 GGGTTCGGGTTGAATTT
1 GGG-TCAGGTT-AATTC
*
11942 GGGTCAAGTTAATTC
1 GGGTCAGGTTAATTC
11957 GGGT
1 GGGT
11961 TCGGGTTCTG
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
15 11 0.38
16 11 0.38
17 7 0.24
ACGTcount: A:0.18, C:0.10, G:0.37, T:0.35
Consensus pattern (15 bp):
GGGTCAGGTTAATTC
Found at i:11968 original size:38 final size:32
Alignment explanation
Indices: 11891--11967 Score: 136
Period size: 32 Copynumber: 2.4 Consensus size: 32
11881 CGGGCTTGAG
* *
11891 TCGGGTTCGGGTTGGATTTGGGTCAGGTTAAT
1 TCGGGTTCGGGTTGAATTTGGGTCAAGTTAAT
11923 TCGGGTTCGGGTTGAATTTGGGTCAAGTTAAT
1 TCGGGTTCGGGTTGAATTTGGGTCAAGTTAAT
11955 TCGGGTTCGGGTT
1 TCGGGTTCGGGTT
11968 CTGTTTGGGT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
32 43 1.00
ACGTcount: A:0.13, C:0.10, G:0.39, T:0.38
Consensus pattern (32 bp):
TCGGGTTCGGGTTGAATTTGGGTCAAGTTAAT
Found at i:11975 original size:32 final size:31
Alignment explanation
Indices: 11891--11977 Score: 111
Period size: 32 Copynumber: 2.7 Consensus size: 31
11881 CGGGCTTGAG
* *
11891 TCGGGTTCGGGTTGGATTTGGGTCAGGTTAAT
1 TCGGGTTCGGGTTAG-TTTGGGTCAAGTTAAT
*
11923 TCGGGTTCGGGTTGAATTTGGGTCAAGTTAAT
1 TCGGGTTCGGGTT-AGTTTGGGTCAAGTTAAT
*
11955 TCGGGTTCGGGTTCTGTTTGGGT
1 TCGGGTTCGGGTT-AGTTTGGGT
11978 TTTGGCCAGA
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
32 48 1.00
ACGTcount: A:0.11, C:0.10, G:0.39, T:0.39
Consensus pattern (31 bp):
TCGGGTTCGGGTTAGTTTGGGTCAAGTTAAT
Found at i:12136 original size:16 final size:16
Alignment explanation
Indices: 12115--12178 Score: 83
Period size: 16 Copynumber: 4.0 Consensus size: 16
12105 TTTTCATAAA
*
12115 TTTTCGGATTCGGGTT
1 TTTTCGGGTTCGGGTT
* * *
12131 TTTTCGGGTTTGAGCT
1 TTTTCGGGTTCGGGTT
12147 TTTTCGGGTTCGGGTT
1 TTTTCGGGTTCGGGTT
*
12163 TTTTCGGGTTCAGGTT
1 TTTTCGGGTTCGGGTT
12179 CAGGCGGGTT
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 40 1.00
ACGTcount: A:0.05, C:0.12, G:0.33, T:0.50
Consensus pattern (16 bp):
TTTTCGGGTTCGGGTT
Found at i:12262 original size:15 final size:16
Alignment explanation
Indices: 12242--12271 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
12232 GGAGATCAGG
12242 TTTTCGGA-CGGGTTT
1 TTTTCGGATCGGGTTT
12257 TTTTCGGATCGGGTT
1 TTTTCGGATCGGGTT
12272 CACTTTGCCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.07, C:0.13, G:0.33, T:0.47
Consensus pattern (16 bp):
TTTTCGGATCGGGTTT
Found at i:12479 original size:6 final size:6
Alignment explanation
Indices: 12468--12492 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
12458 GCTGAGGAAA
12468 TCTTAT TCTTAT TCTTAT TCTTAT T
1 TCTTAT TCTTAT TCTTAT TCTTAT T
12493 TTTTAGGCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.16, G:0.00, T:0.68
Consensus pattern (6 bp):
TCTTAT
Found at i:23227 original size:33 final size:33
Alignment explanation
Indices: 23185--23250 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
23175 GAGAGAGAGA
23185 TTAGATTTAGAGGAAGAAGCTTCTGACGATATG
1 TTAGATTTAGAGGAAGAAGCTTCTGACGATATG
23218 TTAGATTTAGAGGAAGAAGCTTCTGACGATATG
1 TTAGATTTAGAGGAAGAAGCTTCTGACGATATG
23251 CTCCAAATCC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.33, C:0.09, G:0.27, T:0.30
Consensus pattern (33 bp):
TTAGATTTAGAGGAAGAAGCTTCTGACGATATG
Found at i:28924 original size:32 final size:32
Alignment explanation
Indices: 28887--28963 Score: 118
Period size: 32 Copynumber: 2.4 Consensus size: 32
28877 TAAAAAGTTA
* **
28887 GGAACATCATTAATCATGCATTTAAAATGGTG
1 GGAACACCATTAATCAAACATTTAAAATGGTG
*
28919 TGAACACCATTAATCAAACATTTAAAATGGTG
1 GGAACACCATTAATCAAACATTTAAAATGGTG
28951 GGAACACCATTAA
1 GGAACACCATTAA
28964 AGCCATTTGA
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
32 40 1.00
ACGTcount: A:0.42, C:0.16, G:0.16, T:0.27
Consensus pattern (32 bp):
GGAACACCATTAATCAAACATTTAAAATGGTG
Found at i:30983 original size:11 final size:11
Alignment explanation
Indices: 30967--30991 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
30957 TCCACGTTTC
30967 ATACCTATCCT
1 ATACCTATCCT
30978 ATACCTATCCT
1 ATACCTATCCT
30989 ATA
1 ATA
30992 TATAGCCAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.32, C:0.32, G:0.00, T:0.36
Consensus pattern (11 bp):
ATACCTATCCT
Found at i:33649 original size:31 final size:31
Alignment explanation
Indices: 33609--33750 Score: 185
Period size: 31 Copynumber: 4.5 Consensus size: 31
33599 ACGGTGTCCG
*
33609 ACGTGGCATGCCCCGTGTACCAAAAAGTGAC
1 ACGTGGCATGCCACGTGTACCAAAAAGTGAC
*
33640 ATGTGGCATGCCACGTGTACCAAAAAAGTGAC
1 ACGTGGCATGCCACGTGTACC-AAAAAGTGAC
* * * *
33672 ACATGTCACGCCACGTATACCAAAAAGTGAC
1 ACGTGGCATGCCACGTGTACCAAAAAGTGAC
* **
33703 ATGTGGCATGCCACGTGTTTCAAAAAGTGAC
1 ACGTGGCATGCCACGTGTACCAAAAAGTGAC
*
33734 ACGTGGTATGCCACGTG
1 ACGTGGCATGCCACGTG
33751 CACAAAAGGA
Statistics
Matches: 94, Mismatches: 16, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
31 68 0.72
32 26 0.28
ACGTcount: A:0.31, C:0.25, G:0.25, T:0.20
Consensus pattern (31 bp):
ACGTGGCATGCCACGTGTACCAAAAAGTGAC
Found at i:44522 original size:34 final size:34
Alignment explanation
Indices: 44474--44543 Score: 122
Period size: 34 Copynumber: 2.1 Consensus size: 34
44464 TCAGTTCGAG
*
44474 ACTTCAAGTCTTGCGAATGTCAGAATTCCATGAT
1 ACTTCAAGTCTTGCGAATGTCAGAATTCCAGGAT
*
44508 ACTTTAAGTCTTGCGAATGTCAGAATTCCAGGAT
1 ACTTCAAGTCTTGCGAATGTCAGAATTCCAGGAT
44542 AC
1 AC
44544 AGAACTCGAT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.30, C:0.20, G:0.19, T:0.31
Consensus pattern (34 bp):
ACTTCAAGTCTTGCGAATGTCAGAATTCCAGGAT
Done.