Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021717.1 Corchorus olitorius cultivar O-4 contig21750, 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: 10234
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.35
Found at i:234 original size:18 final size:18
Alignment explanation
Indices: 207--241 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
197 AAAAAAATAG
* *
207 TTCAATTCCAATTCCAAT
1 TTCAAATCCAAATCCAAT
225 TTCAAATCCAAATCCAA
1 TTCAAATCCAAATCCAA
242 ATATTAGTCA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.40, C:0.29, G:0.00, T:0.31
Consensus pattern (18 bp):
TTCAAATCCAAATCCAAT
Found at i:755 original size:20 final size:19
Alignment explanation
Indices: 714--761 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 19
704 AGAAGAATTT
*
714 AAAAAAATAAAAGGAAATG
1 AAAAAAATAAAAGGAAAAG
733 AAAAAAA-AAAAGAGAAAA-
1 AAAAAAATAAAAG-GAAAAG
*
751 AGAAAAATAAA
1 AAAAAAATAAA
762 GAAGTTTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
18 11 0.44
19 14 0.56
ACGTcount: A:0.81, C:0.00, G:0.12, T:0.06
Consensus pattern (19 bp):
AAAAAAATAAAAGGAAAAG
Found at i:973 original size:31 final size:29
Alignment explanation
Indices: 899--973 Score: 89
Period size: 31 Copynumber: 2.6 Consensus size: 29
889 AGACTAACCG
*
899 ATAAA-GATTAATTTGTCCCAAAGAAAAC
1 ATAAAGGATTATTTTGTCCCAAAGAAAAC
* *
927 ATAAGGGATTATTTTGTCCCAAAAGAAAAAT
1 ATAAAGGATTATTTTGTCCC-AAAG-AAAAC
*
958 ATAAAGGATTTTTTTG
1 ATAAAGGATTATTTTG
974 AATTTTAACC
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
28 4 0.10
29 13 0.33
30 4 0.10
31 18 0.46
ACGTcount: A:0.44, C:0.09, G:0.15, T:0.32
Consensus pattern (29 bp):
ATAAAGGATTATTTTGTCCCAAAGAAAAC
Found at i:5804 original size:27 final size:27
Alignment explanation
Indices: 5755--5806 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
5745 AAATCAATTA
*
5755 GAAATCATAAAAACATAAAATAAATCT
1 GAAATCATAAAAACACAAAATAAATCT
*
5782 GAAATCATAAAATAC-CAAGATAAAT
1 GAAATCATAAAA-ACACAAAATAAAT
5807 AATCAGATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
27 20 0.91
28 2 0.09
ACGTcount: A:0.62, C:0.12, G:0.06, T:0.21
Consensus pattern (27 bp):
GAAATCATAAAAACACAAAATAAATCT
Found at i:7677 original size:8 final size:8
Alignment explanation
Indices: 7646--7679 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
7636 TTGTGACACA
*
7646 TATATATA
1 TATATATG
7654 TATATATG
1 TATATATG
*
7662 TATGTATG
1 TATATATG
7670 TATATATG
1 TATATATG
7678 TA
1 TA
7680 CCAGATAAAC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.38, C:0.00, G:0.12, T:0.50
Consensus pattern (8 bp):
TATATATG
Found at i:7765 original size:16 final size:17
Alignment explanation
Indices: 7744--7777 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
7734 TGATACTTTG
7744 AAGAATAAT-AAAAGTA
1 AAGAATAATAAAAAGTA
7760 AAGAATAATAAAAAGTA
1 AAGAATAATAAAAAGTA
7777 A
1 A
7778 GAAAATTGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.53
17 8 0.47
ACGTcount: A:0.71, C:0.00, G:0.12, T:0.18
Consensus pattern (17 bp):
AAGAATAATAAAAAGTA
Found at i:8019 original size:22 final size:22
Alignment explanation
Indices: 7989--8130 Score: 115
Period size: 22 Copynumber: 6.2 Consensus size: 22
7979 CCAGAGATTC
*
7989 TTTCTACTTTGCAGAGCATTAT
1 TTTCCACTTTGCAGAGCATTAT
*
8011 TTTCCACTTTGCTGAGCATTAT
1 TTTCCACTTTGCAGAGCATTAT
* *** *
8033 TTTCTTCAACTTCAGCTTTGCACTAT
1 TTTC--C-ACTT-TGCAGAGCATTAT
*** *
8059 TGGAAACATCTGTGCAGAG-ATTAT
1 T--TTCCA-CTTTGCAGAGCATTAT
8083 TTTCCACTTTGCAGAGCATTAT
1 TTTCCACTTTGCAGAGCATTAT
8105 TTTCCACTTTGCAGAGCATTAT
1 TTTCCACTTTGCAGAGCATTAT
8127 TTTC
1 TTTC
8131 TTCAACTTCA
Statistics
Matches: 93, Mismatches: 19, Indels: 16
0.73 0.15 0.12
Matches are distributed among these distances:
21 9 0.10
22 57 0.61
24 6 0.06
25 8 0.09
26 13 0.14
ACGTcount: A:0.23, C:0.21, G:0.14, T:0.42
Consensus pattern (22 bp):
TTTCCACTTTGCAGAGCATTAT
Found at i:8124 original size:94 final size:93
Alignment explanation
Indices: 7964--8212 Score: 444
Period size: 94 Copynumber: 2.7 Consensus size: 93
7954 TATTGACATA
* *
7964 ATTGGAAACATCTTTCCAGAGATTCTTTCTACTTTGCAGAGCATTATTTTCCACTTTGCTGAGCA
1 ATTGGAAACATCTTTGCAGAGATTCTTTCTACTTTGCAGAGCATTATTTTCCACTTTGCAGAGCA
8029 TTATTTTCTTCAACTTCAGCTTTGCACT
66 TTATTTTCTTCAACTTCAGCTTTGCACT
* * *
8057 ATTGGAAACATCTGTGCAGAGATTATTTTCCACTTTGCAGAGCATTATTTTCCACTTTGCAGAGC
1 ATTGGAAACATCTTTGCAGAGATT-CTTTCTACTTTGCAGAGCATTATTTTCCACTTTGCAGAGC
8122 ATTATTTTCTTCAACTTCAGCTTTGCACT
65 ATTATTTTCTTCAACTTCAGCTTTGCACT
8151 ATTGGAAACATCTTTGCAGAGATTCTTTCTACTTTGCAGAGCATTATTTTCCACTTTGCAGA
1 ATTGGAAACATCTTTGCAGAGATTCTTTCTACTTTGCAGAGCATTATTTTCCACTTTGCAGA
8213 ACACTTCTTG
Statistics
Matches: 147, Mismatches: 8, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
93 58 0.39
94 89 0.61
ACGTcount: A:0.24, C:0.21, G:0.14, T:0.40
Consensus pattern (93 bp):
ATTGGAAACATCTTTGCAGAGATTCTTTCTACTTTGCAGAGCATTATTTTCCACTTTGCAGAGCA
TTATTTTCTTCAACTTCAGCTTTGCACT
Found at i:8185 original size:20 final size:22
Alignment explanation
Indices: 8162--8212 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
8152 TTGGAAACAT
*
8162 CTTTGCAGAG-ATT-CTTTCTA
1 CTTTGCAGAGCATTACTTTCCA
*
8182 CTTTGCAGAGCATTATTTTCCA
1 CTTTGCAGAGCATTACTTTCCA
8204 CTTTGCAGA
1 CTTTGCAGA
8213 ACACTTCTTG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
20 10 0.37
21 3 0.11
22 14 0.52
ACGTcount: A:0.22, C:0.22, G:0.16, T:0.41
Consensus pattern (22 bp):
CTTTGCAGAGCATTACTTTCCA
Done.