Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011626.1 Corchorus capsularis cultivar CVL-1 contig11647, 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: 14264
ACGTcount: A:0.30, C:0.21, G:0.17, T:0.32
Found at i:6104 original size:13 final size:13
Alignment explanation
Indices: 6086--6113 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
6076 AGGACAATTA
6086 TTGGGTTGCATTG
1 TTGGGTTGCATTG
6099 TTGGGTTGCATTG
1 TTGGGTTGCATTG
6112 TT
1 TT
6114 TCGTTTCAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.07, C:0.07, G:0.36, T:0.50
Consensus pattern (13 bp):
TTGGGTTGCATTG
Found at i:8942 original size:21 final size:21
Alignment explanation
Indices: 8918--8966 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
8908 CAGCTGGGGG
* * *
8918 CCCATGTGGTATGCTTGGCGC
1 CCCATGTGGTATGCCTCGCGA
*
8939 CCCATGTGGTTTGCCTCGCGA
1 CCCATGTGGTATGCCTCGCGA
8960 CCCATGT
1 CCCATGT
8967 CCTCCAGTGC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.10, C:0.33, G:0.29, T:0.29
Consensus pattern (21 bp):
CCCATGTGGTATGCCTCGCGA
Found at i:10072 original size:24 final size:24
Alignment explanation
Indices: 10040--10092 Score: 88
Period size: 24 Copynumber: 2.2 Consensus size: 24
10030 CGCTCCGAAA
* *
10040 CCAATAAATGTTTTGGGACCGCTT
1 CCAATAAATATTGTGGGACCGCTT
10064 CCAATAAATATTGTGGGACCGCTT
1 CCAATAAATATTGTGGGACCGCTT
10088 CCAAT
1 CCAAT
10093 CACGTGCAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.28, C:0.23, G:0.19, T:0.30
Consensus pattern (24 bp):
CCAATAAATATTGTGGGACCGCTT
Found at i:10726 original size:24 final size:24
Alignment explanation
Indices: 10694--10746 Score: 88
Period size: 24 Copynumber: 2.2 Consensus size: 24
10684 CGCTCCGAAA
* *
10694 CCAATAAATGTTTTGGGACCGCTT
1 CCAATAAATATTGTGGGACCGCTT
10718 CCAATAAATATTGTGGGACCGCTT
1 CCAATAAATATTGTGGGACCGCTT
10742 CCAAT
1 CCAAT
10747 CACGTGCAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.28, C:0.23, G:0.19, T:0.30
Consensus pattern (24 bp):
CCAATAAATATTGTGGGACCGCTT
Found at i:11714 original size:10 final size:10
Alignment explanation
Indices: 11697--11732 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
11687 TTTGTGACTA
11697 TAACCCATTC
1 TAACCCATTC
*
11707 TGACCCATTC
1 TAACCCATTC
*
11717 TAACTCATTC
1 TAACCCATTC
11727 TAACCC
1 TAACCC
11733 CAAAACCCTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.28, C:0.39, G:0.03, T:0.31
Consensus pattern (10 bp):
TAACCCATTC
Found at i:13641 original size:35 final size:35
Alignment explanation
Indices: 12768--13636 Score: 1294
Period size: 35 Copynumber: 24.7 Consensus size: 35
12758 CTTAATTACC
* * *
12768 CTTACTTAGTTACCATGCATTAAGTTGATTACTGA
1 CTTACTTAATTACCCTGAATTAAGTTGATTACTGA
*
12803 CTCACTTAATTATCCC-GAATTAAGTTGATTACTGA
1 CTTACTTAATTA-CCCTGAATTAAGTTGATTACTGA
* * * *
12838 ATTACTTAATTACCTTTAATTAAGTTTATTACTGA
1 CTTACTTAATTACCCTGAATTAAGTTGATTACTGA
* *
12873 CTAACGTAATTACCCTGAATTAAGTTGATTACTGA
1 CTTACTTAATTACCCTGAATTAAGTTGATTACTGA
* *
12908 CTTACTTAATTACCCTAAAATAAGTTGATTACTGA
1 CTTACTTAATTACCCTGAATTAAGTTGATTACTGA
*
12943 CTTACTTAATTACCCTGAATTAAGTTGATTACTGC
1 CTTACTTAATTACCCTGAATTAAGTTGATTACTGA
* *
12978 CTCACTTAATTACCCTAAATTAAGTTGATTACTGA
1 CTTACTTAATTACCCTGAATTAAGTTGATTACTGA
* * *
13013 ATTACTTAATTACCCTTAATTAAGTTTATTACTGA
1 CTTACTTAATTACCCTGAATTAAGTTGATTACTGA
*
13048 CTGACTTAATTACCCTGAATTAAGTTGATTACTGA
1 CTTACTTAATTACCCTGAATTAAGTTGATTACTGA
13083 CTTACTTAATTACCCTGAATTAAGTTGATTACTGA
1 CTTACTTAATTACCCTGAATTAAGTTGATTACTGA
13118 CTTACTTAATTACCCTGAATTAAGTTGATTACTGA
1 CTTACTTAATTACCCTGAATTAAGTTGATTACTGA
*
13153 CTTACTTAATTACCCTGAATTAAGTTGATTATTGA
1 CTTACTTAATTACCCTGAATTAAGTTGATTACTGA
*
13188 ATTACTTAATTACCCTGAATTAAGTTGATTACTGA
1 CTTACTTAATTACCCTGAATTAAGTTGATTACTGA
*
13223 C--ACCTTAATTACCCTGAATTAAGTTGAATACTGA
1 CTTA-CTTAATTACCCTGAATTAAGTTGATTACTGA
* *
13257 CTCACTTAATTATCCTGAATTAAGTTGATTACTGA
1 CTTACTTAATTACCCTGAATTAAGTTGATTACTGA
* *
13292 CTCACTTAATTACCCTGAATTAAGTTGATTATTGA
1 CTTACTTAATTACCCTGAATTAAGTTGATTACTGA
*
13327 ATTACTTAATTACCCTGAATTAAGTTGATTACTGA
1 CTTACTTAATTACCCTGAATTAAGTTGATTACTGA
* *
13362 CTCACTTAATTACCCTGAATTAAGTTGATTATTGA
1 CTTACTTAATTACCCTGAATTAAGTTGATTACTGA
*
13397 ATTACTTAATTACCCTGAATTAAGTTGATTACTGA
1 CTTACTTAATTACCCTGAATTAAGTTGATTACTGA
**
13432 CACACTTAATTACCCTGAATTAAGTTGATTACTGA
1 CTTACTTAATTACCCTGAATTAAGTTGATTACTGA
**
13467 CACACTTAATTACCCTGAATTAAGTTGATTACTGA
1 CTTACTTAATTACCCTGAATTAAGTTGATTACTGA
**
13502 CACACTTAATTACCCTGAATTAAGTTGATTACTGA
1 CTTACTTAATTACCCTGAATTAAGTTGATTACTGA
* *
13537 CTTACTGAATTACCCTGAATTAAGTTGATTATTGA
1 CTTACTTAATTACCCTGAATTAAGTTGATTACTGA
* * *
13572 ATTACTTAATTACCCTGAATTAAGTTACTAACTTACTAA
1 CTTACTTAATTACCCTGAATTAAG-T--TGA-TTACTGA
13611 CTTACTTAATTACCCTGAATTAAGTT
1 CTTACTTAATTACCCTGAATTAAGTT
13637 ACTTATTACT
Statistics
Matches: 760, Mismatches: 65, Indels: 17
0.90 0.08 0.02
Matches are distributed among these distances:
33 1 0.00
34 33 0.04
35 690 0.91
36 5 0.01
38 3 0.00
39 28 0.04
ACGTcount: A:0.33, C:0.17, G:0.11, T:0.39
Consensus pattern (35 bp):
CTTACTTAATTACCCTGAATTAAGTTGATTACTGA
Done.