Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014603.1 Corchorus capsularis cultivar CVL-1 contig14624, 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: 7076
ACGTcount: A:0.33, C:0.17, G:0.21, T:0.29
Found at i:4702 original size:7 final size:7
Alignment explanation
Indices: 4686--4735 Score: 66
Period size: 7 Copynumber: 6.9 Consensus size: 7
4676 TTCCCATTCT
4686 AAAAAA-
1 AAAAAAG
4692 AAAAAAG
1 AAAAAAG
4699 AAAAGGAAAG
1 -AAA--AAAG
4709 AAAAAAG
1 AAAAAAG
4716 AAAAAAG
1 AAAAAAG
4723 AAAAAAG
1 AAAAAAG
4730 AAAAAA
1 AAAAAA
4736 CTTGGCCTAA
Statistics
Matches: 40, Mismatches: 0, Indels: 7
0.85 0.00 0.15
Matches are distributed among these distances:
6 6 0.15
7 24 0.60
8 3 0.08
9 3 0.08
10 4 0.10
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:4803 original size:15 final size:14
Alignment explanation
Indices: 4783--4827 Score: 58
Period size: 15 Copynumber: 3.3 Consensus size: 14
4773 GATAAGTGGA
4783 AAAATGAAAAAAATG
1 AAAATGAAAAAAA-G
4798 AAAATGAAAAAAAG
1 AAAATGAAAAAAAG
*
4812 -AAA-GAAAAAGAG
1 AAAATGAAAAAAAG
4824 AAAA
1 AAAA
4828 AGCAACGATG
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
12 8 0.29
13 6 0.21
14 1 0.04
15 13 0.46
ACGTcount: A:0.78, C:0.00, G:0.16, T:0.07
Consensus pattern (14 bp):
AAAATGAAAAAAAG
Found at i:4921 original size:75 final size:74
Alignment explanation
Indices: 4837--4991 Score: 231
Period size: 75 Copynumber: 2.1 Consensus size: 74
4827 AAGCAACGAT
* *
4837 GGTTTTCAAAAAGAGTCGTGGTTTTCAAAAGGTTTTGATAAAATGG-TTTTAAAAAAAAGTCATG
1 GGTTTTCAAAAAGAGTCATGATTTTCAAAAGGTTTTGATAAAA-GGATTTTAAAAAAAAGTCATG
4901 GTCTTCAAAAA
65 GTCTTC-AAAA
* * *
4912 GGTTTTCAAAAAGAGTCATGATTTTCAAAAGGTTTTGATAAAAGGATTTTCAAAAAGAGTCTTGG
1 GGTTTTCAAAAAGAGTCATGATTTTCAAAAGGTTTTGATAAAAGGATTTTAAAAAAAAGTCATGG
*
4977 TTTTCAAAA
66 TCTTCAAAA
4986 GGTTTT
1 GGTTTT
4992 GATAAAATGA
Statistics
Matches: 73, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
74 12 0.16
75 61 0.84
ACGTcount: A:0.37, C:0.08, G:0.20, T:0.35
Consensus pattern (74 bp):
GGTTTTCAAAAAGAGTCATGATTTTCAAAAGGTTTTGATAAAAGGATTTTAAAAAAAAGTCATGG
TCTTCAAAA
Found at i:4942 original size:30 final size:31
Alignment explanation
Indices: 4876--4947 Score: 92
Period size: 31 Copynumber: 2.4 Consensus size: 31
4866 AGGTTTTGAT
* *
4876 AAAATGGTTTTAAAAAAAAGTCATGGTCTTC
1 AAAAAGGTTTTAAAAAAAAGTCATGATCTTC
* * *
4907 AAAAAGGTTTTCAAAAAGAGTCATGATTTTC
1 AAAAAGGTTTTAAAAAAAAGTCATGATCTTC
4938 -AAAAGGTTTT
1 AAAAAGGTTTT
4948 GATAAAAGGA
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
30 10 0.28
31 26 0.72
ACGTcount: A:0.42, C:0.08, G:0.17, T:0.33
Consensus pattern (31 bp):
AAAAAGGTTTTAAAAAAAAGTCATGATCTTC
Found at i:5027 original size:45 final size:44
Alignment explanation
Indices: 4908--5058 Score: 214
Period size: 44 Copynumber: 3.4 Consensus size: 44
4898 ATGGTCTTCA
*
4908 AAAAGG-TTTTCAAAAAGAGTCATGATTTTCAAAAGGTTTTGAT
1 AAAAGGATTTTCAAAAAGAGTCATGGTTTTCAAAAGGTTTTGAT
*
4951 AAAAGGATTTTCAAAAAGAGTCTTGGTTTTCAAAAGGTTTTGAT
1 AAAAGGATTTTCAAAAAGAGTCATGGTTTTCAAAAGGTTTTGAT
* * *
4995 AAAATGATTTTCAAAAAATAGTCATGGTTTTCAAGAGGGTTTTGAT
1 AAAAGGATTTTC-AAAAAGAGTCATGGTTTTCAA-AAGGTTTTGAT
*
5041 AAAAGGGTTTTCCAAAAA
1 AAAAGGATTTT-CAAAAA
5059 TGATTTCTAA
Statistics
Matches: 96, Mismatches: 8, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
43 6 0.06
44 46 0.48
45 19 0.20
46 24 0.25
47 1 0.01
ACGTcount: A:0.39, C:0.07, G:0.19, T:0.34
Consensus pattern (44 bp):
AAAAGGATTTTCAAAAAGAGTCATGGTTTTCAAAAGGTTTTGAT
Found at i:5804 original size:15 final size:15
Alignment explanation
Indices: 5781--5824 Score: 61
Period size: 16 Copynumber: 2.8 Consensus size: 15
5771 AAAAAAAAGG
5781 AAGAGAAAGAAAAGAA
1 AAGA-AAAGAAAAGAA
5797 AAGAAAAGAAAAGAA
1 AAGAAAAGAAAAGAA
*
5812 AGAAAAAAGAAAA
1 A-AGAAAAGAAAA
5825 ATGAATGATG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
15 12 0.46
16 14 0.54
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (15 bp):
AAGAAAAGAAAAGAA
Found at i:5843 original size:5 final size:5
Alignment explanation
Indices: 5781--5824 Score: 61
Period size: 5 Copynumber: 8.4 Consensus size: 5
5771 AAAAAAAAGG
*
5781 AAGAGA AAGAA AAGAA AAGAA AAGAA AAGAA AGAAAA AAGAA AA
1 AAGA-A AAGAA AAGAA AAGAA AAGAA AAGAA A-AGAA AAGAA AA
5825 ATGAATGATG
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
5 27 0.77
6 8 0.23
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (5 bp):
AAGAA
Found at i:6995 original size:36 final size:36
Alignment explanation
Indices: 6949--7052 Score: 102
Period size: 35 Copynumber: 2.9 Consensus size: 36
6939 TGACCCATGA
*
6949 TGGTTTTTCTTCAGTTTATGTCGGAATGATCGAGGG
1 TGGTCTTTCTTCAGTTTATGTCGGAATGATCGAGGG
** * * * *
6985 TGGTCTTTCTTTGGTTTATTTCGG-TTGACCTAGGG
1 TGGTCTTTCTTCAGTTTATGTCGGAATGATCGAGGG
* * **
7020 CGGCCTTTCTTCAGTTTATGTTAGAATGATCGA
1 TGGTCTTTCTTCAGTTTATGTCGGAATGATCGA
7053 TTCAGTCGAC
Statistics
Matches: 50, Mismatches: 17, Indels: 2
0.72 0.25 0.03
Matches are distributed among these distances:
35 25 0.50
36 25 0.50
ACGTcount: A:0.15, C:0.14, G:0.27, T:0.43
Consensus pattern (36 bp):
TGGTCTTTCTTCAGTTTATGTCGGAATGATCGAGGG
Done.