Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013822.1 Corchorus capsularis cultivar CVL-1 contig13843, 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: 28875
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Found at i:4608 original size:10 final size:10
Alignment explanation
Indices: 4583--4615 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
4573 GTCCATTGTT
4583 ATCTCCATG-
1 ATCTCCATGC
*
4592 TTCTCCATGC
1 ATCTCCATGC
4602 ATCTCCATGC
1 ATCTCCATGC
4612 ATCT
1 ATCT
4616 ATGCAGCCCA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
9 8 0.38
10 13 0.62
ACGTcount: A:0.18, C:0.36, G:0.09, T:0.36
Consensus pattern (10 bp):
ATCTCCATGC
Found at i:7779 original size:24 final size:25
Alignment explanation
Indices: 7752--7807 Score: 62
Period size: 24 Copynumber: 2.3 Consensus size: 25
7742 TCTAATAGTA
*
7752 TTTTCTTTTTCCTGTTGCTCA-TCC
1 TTTTCTTTCTCCTGTTGCTCACTCC
* *
7776 TTTT-TCTTCTGCTGTTGCTCACTCT
1 TTTTCT-TTCTCCTGTTGCTCACTCC
7801 TTTTCTT
1 TTTTCTT
7808 CTTCTACTGC
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
23 1 0.04
24 17 0.65
25 7 0.27
26 1 0.04
ACGTcount: A:0.04, C:0.27, G:0.09, T:0.61
Consensus pattern (25 bp):
TTTTCTTTCTCCTGTTGCTCACTCC
Found at i:7808 original size:24 final size:24
Alignment explanation
Indices: 7763--7809 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
7753 TTTCTTTTTC
7763 CTGTTGCTCATCCTTTTTCTTCTG
1 CTGTTGCTCATCCTTTTTCTTCTG
7787 CTGTTGCTCA-CTCTTTTTCTTCT
1 CTGTTGCTCATC-CTTTTTCTTCT
7810 TCTACTGCTC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
23 1 0.05
24 21 0.95
ACGTcount: A:0.04, C:0.30, G:0.11, T:0.55
Consensus pattern (24 bp):
CTGTTGCTCATCCTTTTTCTTCTG
Found at i:7818 original size:24 final size:24
Alignment explanation
Indices: 7767--7819 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
7757 TTTTTCCTGT
**
7767 TGCTCATCCTTTTTCTTCTGCTGT
1 TGCTCATCCTTTTTCTTCTGCTAC
*
7791 TGCTCA-CTCTTTTTCTTCTTCTAC
1 TGCTCATC-CTTTTTCTTCTGCTAC
7815 TGCTC
1 TGCTC
7820 TTTTGCTTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 1 0.04
24 24 0.96
ACGTcount: A:0.06, C:0.32, G:0.09, T:0.53
Consensus pattern (24 bp):
TGCTCATCCTTTTTCTTCTGCTAC
Found at i:10902 original size:10 final size:10
Alignment explanation
Indices: 10887--10912 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
10877 AGTTGCTGCC
10887 AAATTCCAGA
1 AAATTCCAGA
10897 AAATTCCAGA
1 AAATTCCAGA
10907 AAATTC
1 AAATTC
10913 TAGAGTTCTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.50, C:0.19, G:0.08, T:0.23
Consensus pattern (10 bp):
AAATTCCAGA
Found at i:17605 original size:11 final size:11
Alignment explanation
Indices: 17589--17618 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
17579 AAATTCGTGA
17589 TTGAAGATATT
1 TTGAAGATATT
17600 TTGAAGATATT
1 TTGAAGATATT
17611 TTGAAGAT
1 TTGAAGAT
17619 TTGAAGATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.37, C:0.00, G:0.20, T:0.43
Consensus pattern (11 bp):
TTGAAGATATT
Found at i:18040 original size:10 final size:10
Alignment explanation
Indices: 18025--18050 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
18015 AGTTGCTGCC
18025 AAATTCCAGA
1 AAATTCCAGA
18035 AAATTCCAGA
1 AAATTCCAGA
18045 AAATTC
1 AAATTC
18051 TAGAGTCCTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.50, C:0.19, G:0.08, T:0.23
Consensus pattern (10 bp):
AAATTCCAGA
Done.