Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009885.1 Corchorus capsularis cultivar CVL-1 contig09906, 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: 29676
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:3291 original size:13 final size:12
Alignment explanation
Indices: 3268--3310 Score: 77
Period size: 12 Copynumber: 3.5 Consensus size: 12
3258 TTAATATAGG
3268 TATCGACGGATA
1 TATCGACGGATA
3280 TATCGAACGGATA
1 TATCG-ACGGATA
3293 TATCGACGGATA
1 TATCGACGGATA
3305 TATCGA
1 TATCGA
3311 GGTATCGATG
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
12 18 0.60
13 12 0.40
ACGTcount: A:0.35, C:0.16, G:0.23, T:0.26
Consensus pattern (12 bp):
TATCGACGGATA
Found at i:12474 original size:329 final size:329
Alignment explanation
Indices: 11869--12526 Score: 1246
Period size: 329 Copynumber: 2.0 Consensus size: 329
11859 GTTGGTTTTG
11869 TTTTTCTTTGGTGTACCTTGTAATTTACGGGTGGGTTTACTCTTTTTCCTTCTTGAGGATTTTTT
1 TTTTTCTTTGGTGTACCTTGTAATTTACGGGTGGGTTTACTCTTTTTCCTTCTTGAGGATTTTTT
*
11934 CCATTGGGTTTTCCCTCTTGAAGGTTTTAACGAGGCACCCCTATGTCCCCCTCTTTTTTTTTCAA
66 CCATTGGGTTTTCCCTCTTGAAGGTTTTAACGAGGCACCCCTATGTCCCCCTCTTTTTTTCTCAA
* *
11999 TAATATCTCACCTTTTAAAAAAAGTTAGATATCCATTGAAGCCAAGGATGAAATCCTTTTATCCC
131 TAATACCTCACCTTTGAAAAAAAGTTAGATATCCATTGAAGCCAAGGATGAAATCCTTTTATCCC
12064 AAGAGTGTGATTGTCTTGGAATTGAAATATTTATTGAATTGTTTCTTTAATCTCACTAGTATTTT
196 AAGAGTGTGATTGTCTTGGAATTGAAATATTTATTGAATTGTTTCTTTAATCTCACTAGTATTTT
12129 TGTTATTTATTTAGTTCAATTAATTTCTCCATAAAACCTCCAATTTAGTTTAATTCACAACTTTA
261 TGTTATTTATTTAGTTCAATTAATTTCTCCATAAAACCTCCAATTTAGTTTAATTCACAACTTTA
12194 GAAA
326 GAAA
12198 TTTTTCTTTGGTGTACCTTGTAATTTACGGGTGGGTTTACTCTTTTTCCTTCTTGAGGATTTTTT
1 TTTTTCTTTGGTGTACCTTGTAATTTACGGGTGGGTTTACTCTTTTTCCTTCTTGAGGATTTTTT
* *
12263 TCATTGGGTTTTCCCTTTTGAAGGTTTTAACGAGGCACCCCTATGTCCCCCTCTTTTTTTCTCAA
66 CCATTGGGTTTTCCCTCTTGAAGGTTTTAACGAGGCACCCCTATGTCCCCCTCTTTTTTTCTCAA
12328 TAATACCTCACCTTTCGAAAAAAAGTTAGATATCCATTGAAGCCAAGGATGAAATCCTTTTATCC
131 TAATACCTCACCTTT-GAAAAAAAGTTAGATATCCATTGAAGCCAAGGATGAAATCCTTTTATCC
12393 CAAGAGTGTGATTGTCTTGGAATTGAAATATTTATTGAATTGTTTCTTTAATCTCACTAGTATTT
195 CAAGAGTGTGATTGTCTTGGAATTGAAATATTTATTGAATTGTTTCTTTAATCTCACTAGTATTT
*
12458 TTGTTATTTA-TTAGTTCAATTAATTTCTTCATAAAACCTCCAATTTAGTTTAATTCACAACTTT
260 TTGTTATTTATTTAGTTCAATTAATTTCTCCATAAAACCTCCAATTTAGTTTAATTCACAACTTT
12522 AGAAA
325 AGAAA
12527 AGTAATTAAA
Statistics
Matches: 322, Mismatches: 6, Indels: 2
0.98 0.02 0.01
Matches are distributed among these distances:
329 199 0.62
330 123 0.38
ACGTcount: A:0.25, C:0.17, G:0.14, T:0.44
Consensus pattern (329 bp):
TTTTTCTTTGGTGTACCTTGTAATTTACGGGTGGGTTTACTCTTTTTCCTTCTTGAGGATTTTTT
CCATTGGGTTTTCCCTCTTGAAGGTTTTAACGAGGCACCCCTATGTCCCCCTCTTTTTTTCTCAA
TAATACCTCACCTTTGAAAAAAAGTTAGATATCCATTGAAGCCAAGGATGAAATCCTTTTATCCC
AAGAGTGTGATTGTCTTGGAATTGAAATATTTATTGAATTGTTTCTTTAATCTCACTAGTATTTT
TGTTATTTATTTAGTTCAATTAATTTCTCCATAAAACCTCCAATTTAGTTTAATTCACAACTTTA
GAAA
Found at i:12728 original size:53 final size:53
Alignment explanation
Indices: 12628--12733 Score: 194
Period size: 53 Copynumber: 2.0 Consensus size: 53
12618 CTTATCAGAC
12628 TCATTAATTATGAACCAATGGGAAAATAAAAAAAATAAATGTAAAAAACTCTA
1 TCATTAATTATGAACCAATGGGAAAATAAAAAAAATAAATGTAAAAAACTCTA
*
12681 TCATTAATTATGAACCAATGGGAAAATTAAGAAAAATAAATGTAAAAAACTCT
1 TCATTAATTATGAACCAATGGGAAAA-TAAAAAAAATAAATGTAAAAAACTCT
12734 CATCCTAATT
Statistics
Matches: 51, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
53 26 0.51
54 25 0.49
ACGTcount: A:0.55, C:0.09, G:0.10, T:0.25
Consensus pattern (53 bp):
TCATTAATTATGAACCAATGGGAAAATAAAAAAAATAAATGTAAAAAACTCTA
Found at i:12743 original size:54 final size:53
Alignment explanation
Indices: 12632--12743 Score: 181
Period size: 54 Copynumber: 2.1 Consensus size: 53
12622 TCAGACTCAT
*
12632 TAATTATGAACCAATGGGAAAATAAAAAAAATAAATGTAAAAAACTCTATCAT
1 TAATTATGAACCAATGGGAAAATAAAAAAAATAAATGTAAAAAACTCTATCAC
*
12685 TAATTATGAACCAATGGGAAAATTAAGAAAAATAAATGTAAAAAACTCTCATC-C
1 TAATTATGAACCAATGGGAAAA-TAAAAAAAATAAATGTAAAAAACTCT-ATCAC
12739 TAATT
1 TAATT
12744 TAAACTAGGG
Statistics
Matches: 55, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
53 22 0.40
54 30 0.55
55 3 0.05
ACGTcount: A:0.54, C:0.11, G:0.10, T:0.26
Consensus pattern (53 bp):
TAATTATGAACCAATGGGAAAATAAAAAAAATAAATGTAAAAAACTCTATCAC
Found at i:14121 original size:2 final size:2
Alignment explanation
Indices: 14114--14146 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
14104 TTGTCTGATT
14114 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
14147 TAAAGGAAGG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:16129 original size:11 final size:11
Alignment explanation
Indices: 16097--16130 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
16087 TCCCCCAATT
*
16097 TTTGTGCCCCT
1 TTTGTGCCCCA
16108 TTTGTGCCCCA
1 TTTGTGCCCCA
*
16119 TTTGTACCCCA
1 TTTGTGCCCCA
16130 T
1 T
16131 CCACCAAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.09, C:0.35, G:0.15, T:0.41
Consensus pattern (11 bp):
TTTGTGCCCCA
Found at i:20820 original size:31 final size:31
Alignment explanation
Indices: 20784--20848 Score: 112
Period size: 31 Copynumber: 2.1 Consensus size: 31
20774 AACTGAACTA
20784 ACTCAAACATCCAAGATCTAAAGAACTGGAG
1 ACTCAAACATCCAAGATCTAAAGAACTGGAG
**
20815 ACTCAAACATCCAAGATCTAAAGATTTGGAG
1 ACTCAAACATCCAAGATCTAAAGAACTGGAG
20846 ACT
1 ACT
20849 GATAACTCAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.43, C:0.22, G:0.15, T:0.20
Consensus pattern (31 bp):
ACTCAAACATCCAAGATCTAAAGAACTGGAG
Found at i:21001 original size:19 final size:19
Alignment explanation
Indices: 20977--21014 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
20967 CAAGGAGGAG
20977 GAGCGAAAAGAAAACAAAA
1 GAGCGAAAAGAAAACAAAA
*
20996 GAGCGAAAAGAGAACAAAA
1 GAGCGAAAAGAAAACAAAA
21015 CAAGAAAAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.66, C:0.11, G:0.24, T:0.00
Consensus pattern (19 bp):
GAGCGAAAAGAAAACAAAA
Found at i:21661 original size:30 final size:32
Alignment explanation
Indices: 21622--21697 Score: 77
Period size: 30 Copynumber: 2.5 Consensus size: 32
21612 TGTAGTGTTT
*
21622 GGACGTTTTGCCCCCCTAAACT-TCAATTTTA
1 GGACATTTTGCCCCCCTAAACTCTCAATTTTA
* * *
21653 -GACATTTTG-TCTCCTGAACTCTCAATTTTA
1 GGACATTTTGCCCCCCTAAACTCTCAATTTTA
* *
21683 GGACGTTTTACCCCC
1 GGACATTTTGCCCCC
21698 TCTCAAACGA
Statistics
Matches: 34, Mismatches: 8, Indels: 5
0.72 0.17 0.11
Matches are distributed among these distances:
29 8 0.24
30 17 0.50
31 7 0.21
32 2 0.06
ACGTcount: A:0.21, C:0.29, G:0.13, T:0.37
Consensus pattern (32 bp):
GGACATTTTGCCCCCCTAAACTCTCAATTTTA
Found at i:23188 original size:29 final size:30
Alignment explanation
Indices: 23107--23188 Score: 107
Period size: 29 Copynumber: 2.8 Consensus size: 30
23097 ACAGAGGCTC
*
23107 AAATTGAGAGTTCAGAAGGTAAAATATTCA
1 AAATTGAGAGTTCAGAGGGTAAAATATTCA
* *
23137 AATTTGAGAGTTCAGAGGG-AAAATGTTCA
1 AAATTGAGAGTTCAGAGGGTAAAATATTCA
23166 AAATTGA-AGTTCAG-GGGTCAAAA
1 AAATTGAGAGTTCAGAGGGT-AAAA
23189 CGTTTTAAAC
Statistics
Matches: 46, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
27 3 0.07
28 7 0.15
29 19 0.41
30 17 0.37
ACGTcount: A:0.43, C:0.07, G:0.24, T:0.26
Consensus pattern (30 bp):
AAATTGAGAGTTCAGAGGGTAAAATATTCA
Done.