Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021732.1 Corchorus olitorius cultivar O-4 contig21765, 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: 24036
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.31
Found at i:8614 original size:13 final size:13
Alignment explanation
Indices: 8596--8621 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
8586 CTTGGCATGA
8596 GTGATGATTTTTG
1 GTGATGATTTTTG
8609 GTGATGATTTTTG
1 GTGATGATTTTTG
8622 TTGTTACCTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.00, G:0.31, T:0.54
Consensus pattern (13 bp):
GTGATGATTTTTG
Found at i:12111 original size:20 final size:22
Alignment explanation
Indices: 12081--12122 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
12071 AGGTTGCTAA
12081 ATTTATAAGTAAAC-ATATAAG
1 ATTTATAAGTAAACTATATAAG
12102 ATTT-TAAGTAAACTATATAAG
1 ATTTATAAGTAAACTATATAAG
12123 CCTTTTTAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 9 0.45
21 11 0.55
ACGTcount: A:0.50, C:0.05, G:0.10, T:0.36
Consensus pattern (22 bp):
ATTTATAAGTAAACTATATAAG
Found at i:12141 original size:21 final size:22
Alignment explanation
Indices: 12086--12147 Score: 76
Period size: 21 Copynumber: 3.0 Consensus size: 22
12076 GCTAAATTTA
*
12086 TAAGTAAAC-ATATAAG-ATTT
1 TAAGTAAACTATATAAGCCTTT
12106 TAAGTAAACTATATAAGCCTTT
1 TAAGTAAACTATATAAGCCTTT
* *
12128 TTAGTAATCT-TATAAGCCTT
1 TAAGTAAACTATATAAGCCTT
12148 ATTTTTTTAG
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
20 9 0.24
21 17 0.46
22 11 0.30
ACGTcount: A:0.40, C:0.11, G:0.10, T:0.39
Consensus pattern (22 bp):
TAAGTAAACTATATAAGCCTTT
Found at i:12152 original size:23 final size:24
Alignment explanation
Indices: 12081--12152 Score: 68
Period size: 21 Copynumber: 3.2 Consensus size: 24
12071 AGGTTGCTAA
12081 ATTTATAAGTAAAC-ATATAAG---
1 ATTT-TAAGTAAACTATATAAGCCT
12102 ATTTTAAGTAAACTATATAAGCCT
1 ATTTTAAGTAAACTATATAAGCCT
*
12126 -TTTT-AGTAATCT-TATAAGCCTT
1 ATTTTAAGTAAACTATATAAGCC-T
12148 ATTTT
1 ATTTT
12153 TTTAGTAACC
Statistics
Matches: 44, Mismatches: 1, Indels: 10
0.80 0.02 0.18
Matches are distributed among these distances:
20 9 0.20
21 19 0.43
22 8 0.18
23 8 0.18
ACGTcount: A:0.39, C:0.10, G:0.08, T:0.43
Consensus pattern (24 bp):
ATTTTAAGTAAACTATATAAGCCT
Found at i:12445 original size:21 final size:21
Alignment explanation
Indices: 12398--12446 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 21
12388 AACATATAAG
*
12398 ATTTCTTTAATAACTCTTATA
1 ATTTTTTTAATAACTCTTATA
*
12419 AGTTTTTTTAATAA-TCTTTTGA
1 A-TTTTTTTAATAACTCTTAT-A
12441 ATTTTT
1 ATTTTT
12447 AGTAAACTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
21 11 0.46
22 13 0.54
ACGTcount: A:0.29, C:0.08, G:0.04, T:0.59
Consensus pattern (21 bp):
ATTTTTTTAATAACTCTTATA
Found at i:12446 original size:22 final size:22
Alignment explanation
Indices: 12392--12436 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
12382 TTTAGTAACA
*
12392 TATAAGATTTCTTTAATAACTCT
1 TATAAG-TTTTTTTAATAACTCT
12415 TATAAGTTTTTTTAATAA-TCT
1 TATAAGTTTTTTTAATAACTCT
12436 T
1 T
12437 TTGAATTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 4 0.19
22 11 0.52
23 6 0.29
ACGTcount: A:0.33, C:0.09, G:0.04, T:0.53
Consensus pattern (22 bp):
TATAAGTTTTTTTAATAACTCT
Found at i:15684 original size:28 final size:28
Alignment explanation
Indices: 15610--15684 Score: 91
Period size: 28 Copynumber: 2.7 Consensus size: 28
15600 TATAGGCCTA
*
15610 AAATTACCGTTTTACCCTAAGAATGAGT
1 AAATTACCGTTTTACCCTTAGAATGAGT
*
15638 AAATTACCGTTTTATCCTTAGAA-G-GTT
1 AAATTACCGTTTTACCCTTAGAATGAG-T
*
15665 AAATTTACAGTTTTACCCTT
1 AAA-TTACCGTTTTACCCTT
15685 TTTAACCTTG
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
26 1 0.02
27 5 0.12
28 35 0.85
ACGTcount: A:0.32, C:0.17, G:0.12, T:0.39
Consensus pattern (28 bp):
AAATTACCGTTTTACCCTTAGAATGAGT
Found at i:17265 original size:2 final size:2
Alignment explanation
Indices: 17258--17298 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
17248 TGACAACTAG
17258 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
17299 CATTACTTAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:18855 original size:18 final size:18
Alignment explanation
Indices: 18832--18873 Score: 84
Period size: 18 Copynumber: 2.3 Consensus size: 18
18822 AAAAACTTAT
18832 CATGGACTTGAAGATATG
1 CATGGACTTGAAGATATG
18850 CATGGACTTGAAGATATG
1 CATGGACTTGAAGATATG
18868 CATGGA
1 CATGGA
18874 AAGCAAGGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.33, C:0.12, G:0.29, T:0.26
Consensus pattern (18 bp):
CATGGACTTGAAGATATG
Done.