Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007494.1 Corchorus capsularis cultivar CVL-1 contig07515, 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: 28884
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Found at i:4609 original size:38 final size:38
Alignment explanation
Indices: 4543--4807 Score: 408
Period size: 38 Copynumber: 7.0 Consensus size: 38
4533 TCACTCACAA
*
4543 TCTTGCCAACAG-TTAA-CCCCTGAGGCACGGGTCCAC
1 TCTTACCAACAGTTTAACCCCCTGAGGCACGGGTCCAC
*
4579 TCTTACCAACAGTTTAACCCCCTGAAGCACGGGTCCAC
1 TCTTACCAACAGTTTAACCCCCTGAGGCACGGGTCCAC
4617 TCTTACCAACAGTTTAACCCCCTGAGGCACGGGTCCAC
1 TCTTACCAACAGTTTAACCCCCTGAGGCACGGGTCCAC
* *
4655 TCTTACCATCAGTTTAACCCCCTGAGGCGCGGGTCCAC
1 TCTTACCAACAGTTTAACCCCCTGAGGCACGGGTCCAC
* *
4693 TCTTACCAACAGTTTTACCCCCTGAGGCACGAGTCCAC
1 TCTTACCAACAGTTTAACCCCCTGAGGCACGGGTCCAC
* * * *
4731 TCTTACCATCAGTTTAACCTCCTGAGTCACAGGTCCAC
1 TCTTACCAACAGTTTAACCCCCTGAGGCACGGGTCCAC
* *
4769 TCTTACCATCAGTTTAACCCCCTGAGGCGCGGGTCCAC
1 TCTTACCAACAGTTTAACCCCCTGAGGCACGGGTCCAC
4807 T
1 T
4808 ATGCACAGCC
Statistics
Matches: 208, Mismatches: 19, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
36 11 0.05
37 4 0.02
38 193 0.93
ACGTcount: A:0.22, C:0.36, G:0.18, T:0.23
Consensus pattern (38 bp):
TCTTACCAACAGTTTAACCCCCTGAGGCACGGGTCCAC
Found at i:13573 original size:51 final size:51
Alignment explanation
Indices: 13469--13594 Score: 166
Period size: 51 Copynumber: 2.5 Consensus size: 51
13459 AGTTAGTGTC
*
13469 AAAAATATGATCTTTAGTT-AAAAAGATTAGATCTTGGTAAAATTTAAAAT
1 AAAAATATGATCTTTATTTAAAAAAGATTAGATCTTGGTAAAATTTAAAAT
* ** *
13519 AAAAATATGATCTTTATTTAAAAAAGATT-GAGTCTTGGTAAATTTTGGAGT
1 AAAAATATGATCTTTATTTAAAAAAGATTAGA-TCTTGGTAAAATTTAAAAT
* *
13570 AAAAATGTGATTTTTATTTAAAAAA
1 AAAAATATGATCTTTATTTAAAAAA
13595 AAAAGGTTAG
Statistics
Matches: 67, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
50 20 0.30
51 47 0.70
ACGTcount: A:0.45, C:0.03, G:0.13, T:0.38
Consensus pattern (51 bp):
AAAAATATGATCTTTATTTAAAAAAGATTAGATCTTGGTAAAATTTAAAAT
Found at i:14150 original size:35 final size:34
Alignment explanation
Indices: 14100--14334 Score: 263
Period size: 35 Copynumber: 6.7 Consensus size: 34
14090 CAGTAATAGG
* *
14100 TAACTTAATTCAGGGTAATTAAGTAGGTTAGTGAA
1 TAACTTAATTCAGGGTAATTAAGTAAGTCAGT-AA
* *
14135 TAATTTAATTCAGGGTAATTAATTAAGTCAGTAA
1 TAACTTAATTCAGGGTAATTAAGTAAGTCAGTAA
* * * *
14169 GTAGCTTAATTCAGTGTAATTAAGTAAAGTCAATTAG
1 -TAACTTAATTCAGGGTAATTAAGT-AAGTC-AGTAA
* *
14206 TAACTTAATTCAGGGAAATTAAGTAATTCAGTAA
1 TAACTTAATTCAGGGTAATTAAGTAAGTCAGTAA
* * *
14240 TCAACTTAATCCAGGGTAGTTAAGTAAGTCAATAA
1 T-AACTTAATTCAGGGTAATTAAGTAAGTCAGTAA
* *
14275 GTAACTTAATTCAGGGTAATTAAGTAAGTCATTGA
1 -TAACTTAATTCAGGGTAATTAAGTAAGTCAGTAA
*
14310 TCGACTTAATTCAGGGTAATTAAGT
1 T-AACTTAATTCAGGGTAATTAAGT
14335 TTAGTACGAA
Statistics
Matches: 168, Mismatches: 26, Indels: 12
0.82 0.13 0.06
Matches are distributed among these distances:
34 7 0.04
35 131 0.78
36 27 0.16
37 3 0.02
ACGTcount: A:0.39, C:0.09, G:0.18, T:0.34
Consensus pattern (34 bp):
TAACTTAATTCAGGGTAATTAAGTAAGTCAGTAA
Found at i:14249 original size:106 final size:103
Alignment explanation
Indices: 14099--14334 Score: 305
Period size: 106 Copynumber: 2.2 Consensus size: 103
14089 TCAGTAATAG
* * * *
14099 GTAACTTAATTCAGGGTAATTAAGTAGGTTAGTGAATAATTTAATTCAGGGTAATTAATTAAGTC
1 GTAACTTAATTCAGGGTAATTAAGTAGATTAGTGAATAACTTAATCCAGGGTAATTAAGTAAGTC
* * *
14164 AGTAAGTAGCTTAATTCAGTGTAATTAAGTAAAGTCAATT
66 AATAAGTAACTTAATTCAGGGTAATTAAGT-AAGTC-ATT
* *
14204 AGTAACTTAATTCAGGGAAATTAAGTA-ATTCAGT-AATCAACTTAATCCAGGGTAGTTAAGTAA
1 -GTAACTTAATTCAGGGTAATTAAGTAGATT-AGTGAAT-AACTTAATCCAGGGTAATTAAGTAA
14267 GTCAATAAGTAACTTAATTCAGGGTAATTAAGTAAGTCATT
63 GTCAATAAGTAACTTAATTCAGGGTAATTAAGTAAGTCATT
*
14308 GATCGACTTAATTCAGGGTAATTAAGT
1 G-T-AACTTAATTCAGGGTAATTAAGT
14335 TTAGTACGAA
Statistics
Matches: 115, Mismatches: 11, Indels: 9
0.85 0.08 0.07
Matches are distributed among these distances:
103 1 0.01
104 4 0.03
105 31 0.27
106 79 0.69
ACGTcount: A:0.39, C:0.09, G:0.19, T:0.34
Consensus pattern (103 bp):
GTAACTTAATTCAGGGTAATTAAGTAGATTAGTGAATAACTTAATCCAGGGTAATTAAGTAAGTC
AATAAGTAACTTAATTCAGGGTAATTAAGTAAGTCATT
Found at i:17231 original size:35 final size:33
Alignment explanation
Indices: 17167--17231 Score: 85
Period size: 35 Copynumber: 1.9 Consensus size: 33
17157 GGTTGCATCG
* *
17167 ATAAAAAAAATCTTTTCTGTTTTTCCTTTTAAA
1 ATAAAAAAAATATTTTCTGTTTCTCCTTTTAAA
*
17200 ATAAAAAAAACTTATTTTCTGTTTCTGCTTTT
1 ATAAAAAAAA--TATTTTCTGTTTCTCCTTTT
17232 TAATTTTTAG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
33 10 0.37
35 17 0.63
ACGTcount: A:0.34, C:0.12, G:0.05, T:0.49
Consensus pattern (33 bp):
ATAAAAAAAATATTTTCTGTTTCTCCTTTTAAA
Found at i:24153 original size:42 final size:42
Alignment explanation
Indices: 24106--24192 Score: 138
Period size: 42 Copynumber: 2.1 Consensus size: 42
24096 AAGGGATCGT
* *
24106 ACATGACTGGCCATTACATGGAGCAATCGCACAAGACCGGGC
1 ACATGACCGGCCATGACATGGAGCAATCGCACAAGACCGGGC
* *
24148 ACATGACCGGCCATGGCATGGAGCAATCGCACATGACCGGGC
1 ACATGACCGGCCATGACATGGAGCAATCGCACAAGACCGGGC
24190 ACA
1 ACA
24193 ACCTGGGCAC
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.30, C:0.30, G:0.28, T:0.13
Consensus pattern (42 bp):
ACATGACCGGCCATGACATGGAGCAATCGCACAAGACCGGGC
Done.