Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009792.1 Corchorus capsularis cultivar CVL-1 contig09813, 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: 19198
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:1434 original size:11 final size:10
Alignment explanation
Indices: 1416--1449 Score: 50
Period size: 11 Copynumber: 3.2 Consensus size: 10
1406 GAAGTTCGTG
1416 TTTTGAAGAT
1 TTTTGAAGAT
1426 TTCTTGAAGAT
1 TT-TTGAAGAT
1437 ATTTTGAAGAT
1 -TTTTGAAGAT
1448 TT
1 TT
1450 GAAGACAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
10 4 0.18
11 16 0.73
12 2 0.09
ACGTcount: A:0.29, C:0.03, G:0.18, T:0.50
Consensus pattern (10 bp):
TTTTGAAGAT
Found at i:6435 original size:21 final size:21
Alignment explanation
Indices: 6402--6450 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
6392 AAGAATTGTA
**
6402 GCTT-CTTGGAAATGGCTCTT
1 GCTTCCTTGGAAATCCCTCTT
*
6422 GCTTCCTTTGAAATCCCTCTT
1 GCTTCCTTGGAAATCCCTCTT
6443 GCATTCCT
1 GC-TTCCT
6451 AAAGCATTGA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 4 0.17
21 15 0.62
22 5 0.21
ACGTcount: A:0.14, C:0.29, G:0.16, T:0.41
Consensus pattern (21 bp):
GCTTCCTTGGAAATCCCTCTT
Found at i:12240 original size:15 final size:15
Alignment explanation
Indices: 12220--12249 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
12210 ATACTAAAAG
12220 AAATAAACAAATAAT
1 AAATAAACAAATAAT
*
12235 AAATAAATAAATAAT
1 AAATAAACAAATAAT
12250 TAGATACAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.73, C:0.03, G:0.00, T:0.23
Consensus pattern (15 bp):
AAATAAACAAATAAT
Found at i:13583 original size:56 final size:55
Alignment explanation
Indices: 13522--13630 Score: 173
Period size: 55 Copynumber: 2.0 Consensus size: 55
13512 AGTCAAATTA
*
13522 TCATCAATTCGAGATCAAGTCATCAAGACCCTCGAATCAAATCAAATCAAACTCCC
1 TCATCAATTCAAGATCAAGTCAT-AAGACCCTCGAATCAAATCAAATCAAACTCCC
** *
13578 TCATCAATTCAAGATCAAGTCATTTGACCCTTGAATCAAATCAAATCAAACTC
1 TCATCAATTCAAGATCAAGTCATAAGACCCTCGAATCAAATCAAATCAAACTC
13631 TCAAATTATC
Statistics
Matches: 49, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
55 27 0.55
56 22 0.45
ACGTcount: A:0.39, C:0.28, G:0.08, T:0.25
Consensus pattern (55 bp):
TCATCAATTCAAGATCAAGTCATAAGACCCTCGAATCAAATCAAATCAAACTCCC
Found at i:13645 original size:50 final size:53
Alignment explanation
Indices: 13548--13647 Score: 134
Period size: 55 Copynumber: 1.9 Consensus size: 53
13538 AAGTCATCAA
*
13548 GACCCTCGAATCAAATCAAATCAAACTCCCTCATCAATTCAAGATCAAGTCATTT
1 GACCCTCGAATCAAATCAAATCAAACT-CCTCA-CAATTCAACATCAAGTCATTT
* *
13603 GACCCTTGAATCAAATCAAATCAAACT-CTCA-AATT-ATCATCAAGT
1 GACCCTCGAATCAAATCAAATCAAACTCCTCACAATTCAACATCAAGT
13648 TCAAGATCAA
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
50 8 0.19
51 4 0.10
53 4 0.10
55 26 0.62
ACGTcount: A:0.40, C:0.27, G:0.07, T:0.26
Consensus pattern (53 bp):
GACCCTCGAATCAAATCAAATCAAACTCCTCACAATTCAACATCAAGTCATTT
Found at i:14260 original size:1 final size:1
Alignment explanation
Indices: 14250--14279 Score: 51
Period size: 1 Copynumber: 30.0 Consensus size: 1
14240 CACACCTAAT
*
14250 AAAAATAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
14280 GATTGATGGC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.97, C:0.00, G:0.00, T:0.03
Consensus pattern (1 bp):
A
Done.