Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013345.1 Corchorus capsularis cultivar CVL-1 contig13366, 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: 8395
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Found at i:180 original size:17 final size:17
Alignment explanation
Indices: 158--193 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
148 CTTCGAACAA
158 AACTATCCACAATGTAG
1 AACTATCCACAATGTAG
175 AACTATCCACAATGTAG
1 AACTATCCACAATGTAG
192 AA
1 AA
194 TTGGTGTTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.44, C:0.22, G:0.11, T:0.22
Consensus pattern (17 bp):
AACTATCCACAATGTAG
Found at i:644 original size:31 final size:31
Alignment explanation
Indices: 594--756 Score: 137
Period size: 31 Copynumber: 5.5 Consensus size: 31
584 ACGGTGTCCG
*
594 ACGTGGCACGCCACGTGTACCAAAAAGTGAC
1 ACGTGGCACGCCACATGTACCAAAAAGTGAC
* *
625 ATGTGGCACACCACATGTACCAAAAAGT---
1 ACGTGGCACGCCACATGTACCAAAAAGTGAC
*
653 -CGT-----GCCACATGTACCAAAAATTGAC
1 ACGTGGCACGCCACATGTACCAAAAAGTGAC
* * *
678 ACATGTCACGCCACGTGTACCAAAAAGTGAC
1 ACGTGGCACGCCACATGTACCAAAAAGTGAC
* ** ** *
709 ACGTGGCATGCCACATGTTTCAAAAAAAGGC
1 ACGTGGCACGCCACATGTACCAAAAAGTGAC
*
740 ACGTGGCATGCCACATG
1 ACGTGGCACGCCACATG
757 CATAAAAGGA
Statistics
Matches: 105, Mismatches: 18, Indels: 18
0.74 0.13 0.13
Matches are distributed among these distances:
22 17 0.16
26 2 0.02
27 2 0.02
31 84 0.80
ACGTcount: A:0.34, C:0.27, G:0.21, T:0.17
Consensus pattern (31 bp):
ACGTGGCACGCCACATGTACCAAAAAGTGAC
Found at i:682 original size:19 final size:21
Alignment explanation
Indices: 636--683 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 21
626 TGTGGCACAC
*
636 CACATGTACCAAAAAGTCGTGC
1 CACATGTACCAAAAAGTC-TGA
658 CACATGTACCAAAAA-T-TGA
1 CACATGTACCAAAAAGTCTGA
677 CACATGT
1 CACATGT
684 CACGCCACGT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
19 9 0.36
21 1 0.04
22 15 0.60
ACGTcount: A:0.40, C:0.25, G:0.15, T:0.21
Consensus pattern (21 bp):
CACATGTACCAAAAAGTCTGA
Found at i:697 original size:53 final size:53
Alignment explanation
Indices: 603--705 Score: 143
Period size: 53 Copynumber: 1.9 Consensus size: 53
593 GACGTGGCAC
* **
603 GCCACGTGTACCAAAAAGTGACATGTGGCACACCACATGTACCAAAAAGTCGT
1 GCCACATGTACCAAAAAGTGACACATGGCACACCACATGTACCAAAAAGTCGT
* * * *
656 GCCACATGTACCAAAAATTGACACATGTCACGCCACGTGTACCAAAAAGT
1 GCCACATGTACCAAAAAGTGACACATGGCACACCACATGTACCAAAAAGT
706 GACACGTGGC
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
53 43 1.00
ACGTcount: A:0.37, C:0.27, G:0.18, T:0.17
Consensus pattern (53 bp):
GCCACATGTACCAAAAAGTGACACATGGCACACCACATGTACCAAAAAGTCGT
Found at i:2229 original size:55 final size:55
Alignment explanation
Indices: 2163--2275 Score: 190
Period size: 55 Copynumber: 2.1 Consensus size: 55
2153 TTAAATCCTC
* *
2163 TGATTCAATCTCCTAGAAAAGTTTTCGAGGACTTGACAGCTTGATCTCGATGATT
1 TGATTCAATCTCCTAGAAAAGTTTTCAAGGACTTGACAGCTTGATCGCGATGATT
* *
2218 TGATTCGATCTCCTGGAAAAGTTTTCAAGGACTTGACAGCTTGATCGCGATGATT
1 TGATTCAATCTCCTAGAAAAGTTTTCAAGGACTTGACAGCTTGATCGCGATGATT
2273 TGA
1 TGA
2276 AAGGAATGGC
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
55 54 1.00
ACGTcount: A:0.27, C:0.18, G:0.22, T:0.34
Consensus pattern (55 bp):
TGATTCAATCTCCTAGAAAAGTTTTCAAGGACTTGACAGCTTGATCGCGATGATT
Found at i:5966 original size:31 final size:31
Alignment explanation
Indices: 5931--5998 Score: 100
Period size: 31 Copynumber: 2.2 Consensus size: 31
5921 TTTATCATAA
* * *
5931 AAACATAAATATGCCTCCAATTGAAACAATC
1 AAACATAAACAAGCCTCAAATTGAAACAATC
*
5962 AAACATAAACAAGCTTCAAATTGAAACAATC
1 AAACATAAACAAGCCTCAAATTGAAACAATC
5993 AAACAT
1 AAACAT
5999 GACCAGTCCC
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.53, C:0.21, G:0.06, T:0.21
Consensus pattern (31 bp):
AAACATAAACAAGCCTCAAATTGAAACAATC
Found at i:6546 original size:15 final size:15
Alignment explanation
Indices: 6528--6556 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
6518 AGAAAGGAGA
6528 GAATGAAGAGAGAGT
1 GAATGAAGAGAGAGT
6543 GAATGAAGAGAGAG
1 GAATGAAGAGAGAG
6557 AGAAAAATCG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.48, C:0.00, G:0.41, T:0.10
Consensus pattern (15 bp):
GAATGAAGAGAGAGT
Done.