Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007315.1 Corchorus capsularis cultivar CVL-1 contig07336, 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: 21388
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Found at i:6878 original size:13 final size:13
Alignment explanation
Indices: 6860--6900 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
6850 AATCTAAATC
* *
6860 TAAAGCAGATTAA
1 TAAAGCAAACTAA
6873 TAAAGCAAACTAA
1 TAAAGCAAACTAA
6886 TAAAGCAAAC-AA
1 TAAAGCAAACTAA
6898 TAA
1 TAA
6901 TTATAAAGCA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
12 5 0.19
13 21 0.81
ACGTcount: A:0.61, C:0.12, G:0.10, T:0.17
Consensus pattern (13 bp):
TAAAGCAAACTAA
Found at i:9066 original size:30 final size:30
Alignment explanation
Indices: 9030--9097 Score: 95
Period size: 30 Copynumber: 2.3 Consensus size: 30
9020 AAGGGTCCAT
*
9030 TGGCCGGTTGT-GCGCGG-ATGGCCCATGCGA
1 TGGCCGGTTGTGGC-CGGTA-GCCCCATGCGA
9060 TGGCCGGTTGTGGCCGGTAGCCCCATGCGA
1 TGGCCGGTTGTGGCCGGTAGCCCCATGCGA
9090 TGGCCGGT
1 TGGCCGGT
9098 CAAGTGGCCG
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
30 32 0.91
31 3 0.09
ACGTcount: A:0.09, C:0.28, G:0.43, T:0.21
Consensus pattern (30 bp):
TGGCCGGTTGTGGCCGGTAGCCCCATGCGA
Found at i:12972 original size:18 final size:17
Alignment explanation
Indices: 12945--12980 Score: 63
Period size: 18 Copynumber: 2.1 Consensus size: 17
12935 TTTCTCTTCA
12945 TCTATTTTTCTTCTAGT
1 TCTATTTTTCTTCTAGT
12962 TCTAGTTTTTCTTCTAGT
1 TCTA-TTTTTCTTCTAGT
12980 T
1 T
12981 TTAGGTTGAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.11, C:0.17, G:0.08, T:0.64
Consensus pattern (17 bp):
TCTATTTTTCTTCTAGT
Found at i:15691 original size:9 final size:9
Alignment explanation
Indices: 15677--15703 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
15667 AACATATCTC
15677 TTCAAAGAT
1 TTCAAAGAT
15686 TTCAAAGAT
1 TTCAAAGAT
15695 TTCAAAGAT
1 TTCAAAGAT
15704 GATAATATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.44, C:0.11, G:0.11, T:0.33
Consensus pattern (9 bp):
TTCAAAGAT
Found at i:15822 original size:2 final size:2
Alignment explanation
Indices: 15815--15844 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
15805 AAATGCTTAG
15815 AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
15845 ACAATGTTGA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:19541 original size:2 final size:2
Alignment explanation
Indices: 19536--19564 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
19526 CACGTGTGTG
19536 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
19565 CTGATACCAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:19912 original size:55 final size:55
Alignment explanation
Indices: 19828--19937 Score: 211
Period size: 55 Copynumber: 2.0 Consensus size: 55
19818 ATTGAAAACA
19828 TTTTGCAGACATTCCCTCCATGATGAGGATAACTTTGCAGAGCATTATTTTCTTC
1 TTTTGCAGACATTCCCTCCATGATGAGGATAACTTTGCAGAGCATTATTTTCTTC
*
19883 TTTTGCAGAGATTCCCTCCATGATGAGGATAACTTTGCAGAGCATTATTTTCTTC
1 TTTTGCAGACATTCCCTCCATGATGAGGATAACTTTGCAGAGCATTATTTTCTTC
19938 AACTTTGCAG
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
55 54 1.00
ACGTcount: A:0.24, C:0.21, G:0.17, T:0.38
Consensus pattern (55 bp):
TTTTGCAGACATTCCCTCCATGATGAGGATAACTTTGCAGAGCATTATTTTCTTC
Found at i:19947 original size:25 final size:25
Alignment explanation
Indices: 19913--19967 Score: 101
Period size: 25 Copynumber: 2.2 Consensus size: 25
19903 TGATGAGGAT
*
19913 AACTTTGCAGAGCATTATTTTCTTC
1 AACTTTGCAGAGCATTATCTTCTTC
19938 AACTTTGCAGAGCATTATCTTCTTC
1 AACTTTGCAGAGCATTATCTTCTTC
19963 AACTT
1 AACTT
19968 CTGACTCTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.25, C:0.22, G:0.11, T:0.42
Consensus pattern (25 bp):
AACTTTGCAGAGCATTATCTTCTTC
Done.