Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017918.1 Corchorus olitorius cultivar O-4 contig17951, 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: 19355
ACGTcount: A:0.26, C:0.22, G:0.21, T:0.31
Found at i:3786 original size:19 final size:19
Alignment explanation
Indices: 3762--3806 Score: 76
Period size: 17 Copynumber: 2.5 Consensus size: 19
3752 TGTGTGTGGA
3762 ATGTGTGTGGAATATTCAT
1 ATGTGTGTGGAATATTCAT
3781 A--TGTGTGGAATATTCAT
1 ATGTGTGTGGAATATTCAT
3798 ATGTGTGTG
1 ATGTGTGTG
3807 TTAGGTGCAG
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
17 17 0.71
19 7 0.29
ACGTcount: A:0.24, C:0.04, G:0.29, T:0.42
Consensus pattern (19 bp):
ATGTGTGTGGAATATTCAT
Found at i:3787 original size:17 final size:17
Alignment explanation
Indices: 3765--3804 Score: 80
Period size: 17 Copynumber: 2.4 Consensus size: 17
3755 GTGTGGAATG
3765 TGTGTGGAATATTCATA
1 TGTGTGGAATATTCATA
3782 TGTGTGGAATATTCATA
1 TGTGTGGAATATTCATA
3799 TGTGTG
1 TGTGTG
3805 TGTTAGGTGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.25, C:0.05, G:0.28, T:0.42
Consensus pattern (17 bp):
TGTGTGGAATATTCATA
Found at i:3788 original size:28 final size:29
Alignment explanation
Indices: 3733--3791 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 29
3723 AATGCTCATG
* *
3733 TGTGTGTGGATTATTCACATGTGTGTGGAA
1 TGTGTGTGGAATATT-ACATATGTGTGGAA
3763 TGTGTGTGGAATATT-CATATGTGTGGAA
1 TGTGTGTGGAATATTACATATGTGTGGAA
3791 T
1 T
3792 ATTCATATGT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
28 13 0.48
30 14 0.52
ACGTcount: A:0.22, C:0.05, G:0.32, T:0.41
Consensus pattern (29 bp):
TGTGTGTGGAATATTACATATGTGTGGAA
Found at i:16512 original size:33 final size:33
Alignment explanation
Indices: 16470--16544 Score: 150
Period size: 33 Copynumber: 2.3 Consensus size: 33
16460 TGTGGAGAAG
16470 CTAACTCTGGCTACCACAAGCTTCGCCTGTTTC
1 CTAACTCTGGCTACCACAAGCTTCGCCTGTTTC
16503 CTAACTCTGGCTACCACAAGCTTCGCCTGTTTC
1 CTAACTCTGGCTACCACAAGCTTCGCCTGTTTC
16536 CTAACTCTG
1 CTAACTCTG
16545 TCACAGGAGC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 42 1.00
ACGTcount: A:0.19, C:0.36, G:0.15, T:0.31
Consensus pattern (33 bp):
CTAACTCTGGCTACCACAAGCTTCGCCTGTTTC
Found at i:18807 original size:46 final size:47
Alignment explanation
Indices: 18717--18833 Score: 125
Period size: 46 Copynumber: 2.5 Consensus size: 47
18707 TTTAATTTTA
* **
18717 ATTTTAAAGCCCATTTCCTCA-TTAGTTTCATTCAAAGTCCATTCC-C
1 ATTTTAAAGCCCATTTCCTTATTTAG-TAAATTCAAAGTCCATTCCTC
*
18763 ATTTTAAAGCCCATTTCCTTATTTAG-AAATTCAAGGTCCAATTCCTTC
1 ATTTTAAAGCCCATTTCCTTATTTAGTAAATTCAAAGTCC-ATTCC-TC
*
18811 -TTTTTAAGACCCATTTCCTTATT
1 ATTTTAAAG-CCCATTTCCTTATT
18834 AGTTTCTCAA
Statistics
Matches: 61, Mismatches: 5, Indels: 8
0.82 0.07 0.11
Matches are distributed among these distances:
45 10 0.16
46 25 0.41
47 11 0.18
48 15 0.25
ACGTcount: A:0.26, C:0.25, G:0.07, T:0.42
Consensus pattern (47 bp):
ATTTTAAAGCCCATTTCCTTATTTAGTAAATTCAAAGTCCATTCCTC
Found at i:18887 original size:13 final size:13
Alignment explanation
Indices: 18869--18898 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
18859 ATGCATTTGG
18869 TCTTCTTCCTTTT
1 TCTTCTTCCTTTT
*
18882 TCTTCTTTCTTTT
1 TCTTCTTCCTTTT
18895 TCTT
1 TCTT
18899 TTTCTTTTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (13 bp):
TCTTCTTCCTTTT
Found at i:18906 original size:5 final size:6
Alignment explanation
Indices: 18877--18911 Score: 54
Period size: 6 Copynumber: 5.8 Consensus size: 6
18867 GGTCTTCTTC
18877 CTTTTT CTTCTTT CTTTTT CTTTTT C-TTTT CTTTT
1 CTTTTT CTT-TTT CTTTTT CTTTTT CTTTTT CTTTT
18912 GGGTCCGGTC
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
5 5 0.19
6 16 0.59
7 6 0.22
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (6 bp):
CTTTTT
Found at i:18908 original size:11 final size:12
Alignment explanation
Indices: 18877--18911 Score: 54
Period size: 11 Copynumber: 2.9 Consensus size: 12
18867 GGTCTTCTTC
18877 CTTTTTCTTCTTT
1 CTTTTTCTT-TTT
18890 CTTTTTCTTTTT
1 CTTTTTCTTTTT
18902 C-TTTTCTTTT
1 CTTTTTCTTTT
18912 GGGTCCGGTC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 9 0.41
12 4 0.18
13 9 0.41
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (12 bp):
CTTTTTCTTTTT
Done.