Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010740.1 Corchorus capsularis cultivar CVL-1 contig10761, 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: 35556
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Found at i:109 original size:19 final size:18
Alignment explanation
Indices: 85--120 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
75 TGAAGATTTC
85 TTGAAGATAATTTGAAGAT
1 TTGAAGATAA-TTGAAGAT
*
104 TTGAAGATCATTGAAGA
1 TTGAAGATAATTGAAGA
121 ATTATTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.03, G:0.22, T:0.33
Consensus pattern (18 bp):
TTGAAGATAATTGAAGAT
Found at i:1918 original size:21 final size:21
Alignment explanation
Indices: 1894--1935 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
1884 TGTATTTTTT
1894 ATTTTCATACAAAAATATCAA
1 ATTTTCATACAAAAATATCAA
*
1915 ATTTTCATATAAAAATATCAA
1 ATTTTCATACAAAAATATCAA
1936 GTCATATCTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.52, C:0.12, G:0.00, T:0.36
Consensus pattern (21 bp):
ATTTTCATACAAAAATATCAA
Found at i:3029 original size:35 final size:35
Alignment explanation
Indices: 2930--3031 Score: 114
Period size: 37 Copynumber: 2.9 Consensus size: 35
2920 TTTTGGTAGC
*
2930 AATTGTGGTTTTGCTTGCTGCTAGTACTTAGGTTT
1 AATTGTGGTTTTGCTTGCTGCTAGTACATAGGTTT
* * *** * *
2965 AAGATGTTTGTTTAATTTCCTGCTGGTACATAGGTTT
1 AA-TTG-TGGTTTTGCTTGCTGCTAGTACATAGGTTT
3002 AATTGTGGTTTTGCTTGCTGCTAGTACATA
1 AATTGTGGTTTTGCTTGCTGCTAGTACATA
3032 TGTTGCATTT
Statistics
Matches: 50, Mismatches: 15, Indels: 4
0.72 0.22 0.06
Matches are distributed among these distances:
35 21 0.42
36 4 0.08
37 25 0.50
ACGTcount: A:0.19, C:0.12, G:0.24, T:0.46
Consensus pattern (35 bp):
AATTGTGGTTTTGCTTGCTGCTAGTACATAGGTTT
Found at i:3739 original size:17 final size:17
Alignment explanation
Indices: 3719--3753 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
3709 ATAGAAGAGA
*
3719 GATGGAAATGGTTTAAG
1 GATGGAAATAGTTTAAG
3736 GATGGAAATAGTTTAAG
1 GATGGAAATAGTTTAAG
3753 G
1 G
3754 TAATGACATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.37, C:0.00, G:0.34, T:0.29
Consensus pattern (17 bp):
GATGGAAATAGTTTAAG
Found at i:9165 original size:26 final size:27
Alignment explanation
Indices: 9105--9166 Score: 74
Period size: 26 Copynumber: 2.3 Consensus size: 27
9095 GGTAAAAAAA
*
9105 ATTGCATTTTTGTTTATGTTTGCATAT
1 ATTGCATTTTTGTTTATGTTTGCATAC
* *
9132 ATTTCATTTTCT-TTT-TGTTTGCATGC
1 ATTGCATTTT-TGTTTATGTTTGCATAC
9158 ATTGCATTT
1 ATTGCATTT
9167 GTATTAAGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
26 17 0.57
27 12 0.40
28 1 0.03
ACGTcount: A:0.16, C:0.11, G:0.13, T:0.60
Consensus pattern (27 bp):
ATTGCATTTTTGTTTATGTTTGCATAC
Found at i:14660 original size:14 final size:14
Alignment explanation
Indices: 14628--14661 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
14618 GAAAATTCTA
* *
14628 AAAAGAAAATAAAG
1 AAAATAAAACAAAG
14642 AAAATAAAACAAAG
1 AAAATAAAACAAAG
14656 AAAATA
1 AAAATA
14662 TTAAGGGTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.79, C:0.03, G:0.09, T:0.09
Consensus pattern (14 bp):
AAAATAAAACAAAG
Found at i:18216 original size:32 final size:32
Alignment explanation
Indices: 18170--18230 Score: 81
Period size: 32 Copynumber: 1.9 Consensus size: 32
18160 AAATACTAAC
18170 AAAATATGGTAAAAACA-CATATAAAAATAGCA
1 AAAATATGGTAAAAACAGC-TATAAAAATAGCA
*
18202 AAAAGTAT-GTAAAAATAGCTATAAAAATA
1 AAAA-TATGGTAAAAACAGCTATAAAAATA
18231 TGCATAATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
32 22 0.85
33 4 0.15
ACGTcount: A:0.62, C:0.07, G:0.10, T:0.21
Consensus pattern (32 bp):
AAAATATGGTAAAAACAGCTATAAAAATAGCA
Found at i:20403 original size:17 final size:17
Alignment explanation
Indices: 20372--20427 Score: 67
Period size: 17 Copynumber: 3.3 Consensus size: 17
20362 CAGCGCCTGA
* *
20372 CTGCGGCGGCACGGCTG
1 CTGCGGCGACGCGGCTG
*
20389 CTGTGGCGACGCGGCTG
1 CTGCGGCGACGCGGCTG
* *
20406 CTGCGGTGATGCGGCTG
1 CTGCGGCGACGCGGCTG
20423 CTGCG
1 CTGCG
20428 TGGCAGCGAT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
17 33 1.00
ACGTcount: A:0.05, C:0.30, G:0.46, T:0.18
Consensus pattern (17 bp):
CTGCGGCGACGCGGCTG
Found at i:20603 original size:9 final size:9
Alignment explanation
Indices: 20587--20634 Score: 60
Period size: 9 Copynumber: 5.3 Consensus size: 9
20577 AGGGACACTT
20587 GGGTAAGGA
1 GGGTAAGGA
*
20596 GTGTAAGGA
1 GGGTAAGGA
20605 GGGTAAGGA
1 GGGTAAGGA
* *
20614 GGGAAATGA
1 GGGTAAGGA
*
20623 GCGTAAGGA
1 GGGTAAGGA
20632 GGG
1 GGG
20635 AAATGAGTGA
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
9 31 1.00
ACGTcount: A:0.33, C:0.02, G:0.52, T:0.12
Consensus pattern (9 bp):
GGGTAAGGA
Found at i:20628 original size:18 final size:18
Alignment explanation
Indices: 20607--20653 Score: 76
Period size: 18 Copynumber: 2.6 Consensus size: 18
20597 TGTAAGGAGG
20607 GTAAGGAGGGAAATGAGC
1 GTAAGGAGGGAAATGAGC
*
20625 GTAAGGAGGGAAATGAGT
1 GTAAGGAGGGAAATGAGC
*
20643 GAAAGGAGGGA
1 GTAAGGAGGGA
20654 CACTAGTCAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.40, C:0.02, G:0.47, T:0.11
Consensus pattern (18 bp):
GTAAGGAGGGAAATGAGC
Found at i:30754 original size:18 final size:18
Alignment explanation
Indices: 30731--30769 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
30721 GTTTTTTCTA
30731 AAAAAAAAATTTGCGTCG
1 AAAAAAAAATTTGCGTCG
*
30749 AAAAAAAAATTTGTGTCG
1 AAAAAAAAATTTGCGTCG
30767 AAA
1 AAA
30770 TAAATTTAGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.54, C:0.08, G:0.15, T:0.23
Consensus pattern (18 bp):
AAAAAAAAATTTGCGTCG
Done.