Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009523.1 Corchorus capsularis cultivar CVL-1 contig09544, 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: 20205
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.36
Found at i:1420 original size:2 final size:2
Alignment explanation
Indices: 1413--1444 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
1403 ATTATATTGT
1413 TA TA TA TA TA -A TA -A TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1445 AATGTTCTCT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 26 0.93
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:6467 original size:156 final size:155
Alignment explanation
Indices: 6171--6484 Score: 474
Period size: 156 Copynumber: 2.0 Consensus size: 155
6161 CCTTGGAACC
** *
6171 ATAATTGGGCTCTCCTTAACTCCTTCTCACCAAGAGGTTTATACTTTATTGTTTGTTTTAACAAA
1 ATAATTGGGCTCTCCTTAACTCCTTCTCACCAAGAGGTAAATACTTTAGTGTTTGTTTTAACAAA
*
6236 TTAAACAACAATACTTTATAATTTTTATTTTTATAACTCTTTGTGGGTATATTATGTAGGGAAAG
66 TTAAAAAACAATACTTTATAATTTTTATTTTTATAACTCTTTGTGGGTATATTATGTAGGGAAAG
6301 AGAGTTACCTTTGATGGTTCCTGCA
131 AGAGTTACCTTTGATGGTTCCTGCA
* * *
6326 ATAATTTGGCTCTCCTTAACTCCTTCTCACCCAAGAGGTAAATAGTTTAGTGTTT-TATCTTGAC
1 ATAATTGGGCTCTCCTTAACTCCTTCTCA-CCAAGAGGTAAATACTTTAGTGTTTGT-T-TTAAC
*
6390 AAA-TAAAAAAGCAGTACTTTAT-ATTTTTCATTTTTATAACTCTTTGTGGGTATATT-TGTAGG
63 AAATTAAAAAA-CAATACTTTATAATTTTT-ATTTTTATAACTCTTTGTGGGTATATTATGTAGG
*
6452 GAAAGAGAGTTACCTTTGATGGTTGCTGCA
126 GAAAGAGAGTTACCTTTGATGGTTCCTGCA
6482 ATA
1 ATA
6485 TCTATTCCGG
Statistics
Matches: 145, Mismatches: 9, Indels: 9
0.89 0.06 0.06
Matches are distributed among these distances:
155 29 0.20
156 72 0.50
157 44 0.30
ACGTcount: A:0.29, C:0.15, G:0.16, T:0.41
Consensus pattern (155 bp):
ATAATTGGGCTCTCCTTAACTCCTTCTCACCAAGAGGTAAATACTTTAGTGTTTGTTTTAACAAA
TTAAAAAACAATACTTTATAATTTTTATTTTTATAACTCTTTGTGGGTATATTATGTAGGGAAAG
AGAGTTACCTTTGATGGTTCCTGCA
Found at i:7365 original size:167 final size:166
Alignment explanation
Indices: 7089--7425 Score: 638
Period size: 167 Copynumber: 2.0 Consensus size: 166
7079 GTCTTTGACA
* *
7089 TCATGTTGTAATATGAAGCAATTGAATTTCCAAGATAAAAAAGCAAAAAGTCAAGTGCATTTCAA
1 TCATGTTGTAATATGAAGCAACTGAATTTCCAAGATAAAAAAACAAAAAGTCAAGTGCATTTCAA
7154 CCTTGATGTTATCTTTGCAATCATAATATTGCAAGTTAAATCATGGTTTAAGCTACTCAGGATAA
66 CCTTGATGTTATCTTTGCAATCATAATATTGCAAGTTAAATCATGGTTTAAGCTACTCAGGATAA
*
7219 GTCGGTGGCAAATAAAAGCTTTATTCATGCTTAATGC
131 GTCGATGG-AAATAAAAGCTTTATTCATGCTTAATGC
7256 TCATGTTGTAATATGAAGCAACTGAATTTCCAAGATAAAAAAACAAAAAGTCAAGTGCATTTCAA
1 TCATGTTGTAATATGAAGCAACTGAATTTCCAAGATAAAAAAACAAAAAGTCAAGTGCATTTCAA
7321 CCTTGATGTTATCTTTGCAATCATAATATTGCAAGTTAAATCATGGTTTAAGCTACTCAGGATAA
66 CCTTGATGTTATCTTTGCAATCATAATATTGCAAGTTAAATCATGGTTTAAGCTACTCAGGATAA
7386 GTCGATGGAAATAAAAGCTTTATTCATGCTTAATGC
131 GTCGATGGAAATAAAAGCTTTATTCATGCTTAATGC
7422 TCAT
1 TCAT
7426 TTGATTTCAA
Statistics
Matches: 167, Mismatches: 3, Indels: 1
0.98 0.02 0.01
Matches are distributed among these distances:
166 32 0.19
167 135 0.81
ACGTcount: A:0.37, C:0.15, G:0.16, T:0.32
Consensus pattern (166 bp):
TCATGTTGTAATATGAAGCAACTGAATTTCCAAGATAAAAAAACAAAAAGTCAAGTGCATTTCAA
CCTTGATGTTATCTTTGCAATCATAATATTGCAAGTTAAATCATGGTTTAAGCTACTCAGGATAA
GTCGATGGAAATAAAAGCTTTATTCATGCTTAATGC
Found at i:9632 original size:14 final size:14
Alignment explanation
Indices: 9613--9640 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
9603 CATCATCTGA
9613 TTTTTTTTTGTTAT
1 TTTTTTTTTGTTAT
9627 TTTTTTTTTGTTAT
1 TTTTTTTTTGTTAT
9641 GGATTATTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.07, C:0.00, G:0.07, T:0.86
Consensus pattern (14 bp):
TTTTTTTTTGTTAT
Found at i:9986 original size:7 final size:7
Alignment explanation
Indices: 9974--9999 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
9964 AAATACTAAG
9974 TCACTTA
1 TCACTTA
9981 TCACTTA
1 TCACTTA
9988 TCACTTA
1 TCACTTA
9995 TCACT
1 TCACT
10000 CAACACACAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.27, C:0.31, G:0.00, T:0.42
Consensus pattern (7 bp):
TCACTTA
Found at i:12852 original size:10 final size:9
Alignment explanation
Indices: 12822--12872 Score: 50
Period size: 10 Copynumber: 5.3 Consensus size: 9
12812 GTATTGCTTT
12822 TCTGTCTTC
1 TCTGTCTTC
12831 TTCT-TCTCTC
1 -TCTGTCT-TC
12841 TCTGTCTGTC
1 TCTGTCT-TC
12851 TCTGTCTCTC
1 TCTGTCT-TC
*
12861 TCTCTCTTC
1 TCTGTCTTC
12870 TCT
1 TCT
12873 AATGCCTGTT
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
9 11 0.31
10 25 0.69
ACGTcount: A:0.00, C:0.37, G:0.08, T:0.55
Consensus pattern (9 bp):
TCTGTCTTC
Found at i:13663 original size:53 final size:53
Alignment explanation
Indices: 13480--13768 Score: 319
Period size: 53 Copynumber: 5.2 Consensus size: 53
13470 CTCTCTCGTT
*
13480 TACCTTCGTGTCTGCGAGCCTCGCCCACTGCGGAGAGCCGCTGTCTTGTCTTCTCGTG
1 TACCTTCGTGTCTGCGAGCCTCGCCCACTGCGGAGA---GCTG-C-TGTCTTCTCATG
* * * * *
13538 TACCTTCATGTCTGCGAGCCTCGCCCCTCACCGCGGTGAGCCGCTGTCTTCTCATT
1 TACCTTCGTGTCTGCGAGCCTCG--CC-CACTGCGGAGAGCTGCTGTCTTCTCATG
* *
13594 TACCTTTGTGTCTGCGAGCCTCGCCCACTGCGAAGAGCTGCTGTCTTCTCATG
1 TACCTTCGTGTCTGCGAGCCTCGCCCACTGCGGAGAGCTGCTGTCTTCTCATG
* *
13647 TACCTTCGTGTATGCGAGCCTTGCCCACTGCGGAGAGCCTG-TGTCTTCTCATG
1 TACCTTCGTGTCTGCGAGCCTCGCCCACTGCGGAGAG-CTGCTGTCTTCTCATG
* * * * *
13700 TGCTTTCGTGTCTGCGAGCCTCGCGCCTCACTGCGGAGAGCTGTTGTCTTCTCGTA
1 TACCTTCGTGTCTGCGAGCCT--CGCC-CACTGCGGAGAGCTGCTGTCTTCTCATG
*
13756 TACCTTTGTGTCT
1 TACCTTCGTGTCT
13769 TAGCGTGTTG
Statistics
Matches: 197, Mismatches: 26, Indels: 18
0.82 0.11 0.07
Matches are distributed among these distances:
53 86 0.44
54 5 0.03
55 6 0.03
56 63 0.32
57 1 0.01
58 25 0.13
60 2 0.01
61 9 0.05
ACGTcount: A:0.11, C:0.33, G:0.25, T:0.31
Consensus pattern (53 bp):
TACCTTCGTGTCTGCGAGCCTCGCCCACTGCGGAGAGCTGCTGTCTTCTCATG
Found at i:13740 original size:109 final size:109
Alignment explanation
Indices: 13480--13766 Score: 334
Period size: 109 Copynumber: 2.6 Consensus size: 109
13470 CTCTCTCGTT
13480 TACC-TTCGTGTCTGCGAGCCTCGCCCACTGCGGAGAGCCGCTGTCTTGTCTTCTCGTGTACCTT
1 TACCTTTCGTGTCTGCGAGCCTCGCCCACTGCGGAGA---GCTG-C-TGTCTTCTCGTGTACCTT
* * * *
13544 CATGTCTGCGAGCCTCGCCCCTCACCGCGGTGAGCCGCTGTCTTCTCATT
61 CGTGTATGCGAGCCTCG-CCCTCACCGCGGAGAGCCGCTGTCTTCTCATG
* *
13594 TACCTTT-GTGTCTGCGAGCCTCGCCCACTGCGAAGAGCTGCTGTCTTCTCATGTACCTTCGTGT
1 TACCTTTCGTGTCTGCGAGCCTCGCCCACTGCGGAGAGCTGCTGTCTTCTCGTGTACCTTCGTGT
* *
13658 ATGCGAGCCTTG-CC-CACTGCGGAGAGCCTG-TGTCTTCTCATG
66 ATGCGAGCCTCGCCCTCACCGCGGAGAGCC-GCTGTCTTCTCATG
* * * *
13700 T-GCTTTCGTGTCTGCGAGCCTCGCGCCTCACTGCGGAGAGCTGTTGTCTTCTCGTATACCTTTG
1 TACCTTTCGTGTCTGCGAGCCT--CGCC-CACTGCGGAGAGCTGCTGTCTTCTCGTGTACCTTCG
13764 TGT
63 TGT
13767 CTTAGCGTGT
Statistics
Matches: 153, Mismatches: 14, Indels: 17
0.83 0.08 0.09
Matches are distributed among these distances:
105 4 0.03
106 38 0.25
107 3 0.02
108 4 0.03
109 65 0.42
110 1 0.01
111 4 0.03
114 32 0.21
115 2 0.01
ACGTcount: A:0.11, C:0.33, G:0.25, T:0.31
Consensus pattern (109 bp):
TACCTTTCGTGTCTGCGAGCCTCGCCCACTGCGGAGAGCTGCTGTCTTCTCGTGTACCTTCGTGT
ATGCGAGCCTCGCCCTCACCGCGGAGAGCCGCTGTCTTCTCATG
Found at i:13906 original size:14 final size:14
Alignment explanation
Indices: 13887--13914 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
13877 TTTAGAATTA
13887 ATTAAAGTGTTTTG
1 ATTAAAGTGTTTTG
13901 ATTAAAGTGTTTTG
1 ATTAAAGTGTTTTG
13915 CTTTTGTGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.00, G:0.21, T:0.50
Consensus pattern (14 bp):
ATTAAAGTGTTTTG
Found at i:16913 original size:16 final size:17
Alignment explanation
Indices: 16886--16917 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
16876 AAGTCCATCT
16886 AATTCTAAAAATTTCCA
1 AATTCTAAAAATTTCCA
16903 AATTC-AAAAATTTCC
1 AATTCTAAAAATTTCC
16918 TTAATCTTAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.47, C:0.19, G:0.00, T:0.34
Consensus pattern (17 bp):
AATTCTAAAAATTTCCA
Found at i:18138 original size:19 final size:20
Alignment explanation
Indices: 18116--18156 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
18106 AAAAAGACCC
18116 TGAG-AAACTTAAAATTTGT
1 TGAGAAAACTTAAAATTTGT
* *
18135 TGAGAAAACTTGAGATTTGT
1 TGAGAAAACTTAAAATTTGT
18155 TG
1 TG
18157 CTAGAGAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 4 0.21
20 15 0.79
ACGTcount: A:0.37, C:0.05, G:0.22, T:0.37
Consensus pattern (20 bp):
TGAGAAAACTTAAAATTTGT
Done.