Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009543.1 Corchorus capsularis cultivar CVL-1 contig09564, 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: 39964
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Found at i:10878 original size:13 final size:13
Alignment explanation
Indices: 10860--10885 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
10850 AATTCTCGAT
10860 TTTTTTTTCTTAA
1 TTTTTTTTCTTAA
10873 TTTTTTTTCTTAA
1 TTTTTTTTCTTAA
10886 ATATTTTTAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.08, G:0.00, T:0.77
Consensus pattern (13 bp):
TTTTTTTTCTTAA
Found at i:15786 original size:12 final size:12
Alignment explanation
Indices: 15769--15798 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
15759 CCTAAGCTCA
15769 TCATCATCATCT
1 TCATCATCATCT
*
15781 TCATCATCTTCT
1 TCATCATCATCT
15793 TCATCA
1 TCATCA
15799 GTATTTACGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.23, C:0.33, G:0.00, T:0.43
Consensus pattern (12 bp):
TCATCATCATCT
Found at i:29969 original size:26 final size:25
Alignment explanation
Indices: 29940--29988 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
29930 AGATTTGAAG
* *
29940 AGATCAAAATCATAAAGAAACAAAGA
1 AGATCAAAA-AATAAAAAAACAAAGA
29966 AGATCAAAAAATAAAAAAACAAA
1 AGATCAAAAAATAAAAAAACAAA
29989 TAATGGTTGC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 12 0.57
26 9 0.43
ACGTcount: A:0.71, C:0.10, G:0.08, T:0.10
Consensus pattern (25 bp):
AGATCAAAAAATAAAAAAACAAAGA
Found at i:33611 original size:16 final size:15
Alignment explanation
Indices: 33582--33626 Score: 72
Period size: 16 Copynumber: 2.9 Consensus size: 15
33572 ATGAAGTTTT
*
33582 TATACTATTATTATA
1 TATATTATTATTATA
33597 TATATTATATATTATA
1 TATATTAT-TATTATA
33613 TATATTATTATTAT
1 TATATTATTATTAT
33627 TACAAAGAGG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
15 13 0.46
16 15 0.54
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (15 bp):
TATATTATTATTATA
Found at i:33627 original size:9 final size:10
Alignment explanation
Indices: 33581--33628 Score: 66
Period size: 9 Copynumber: 5.0 Consensus size: 10
33571 TATGAAGTTT
33581 TTATACTATTA
1 TTATA-TATTA
33592 TTATATA-TA
1 TTATATATTA
33601 TTATATATTA
1 TTATATATTA
33611 -TATATATTA
1 TTATATATTA
33620 TTAT-TATTA
1 TTATATATTA
33629 CAAAGAGGCA
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
9 23 0.66
10 7 0.20
11 5 0.14
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (10 bp):
TTATATATTA
Found at i:34099 original size:12 final size:12
Alignment explanation
Indices: 34084--34117 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
34074 TCTCCTTCCA
*
34084 TTTTCTTTTTCT
1 TTTTCTTTCTCT
34096 TTTTCTTTCTCT
1 TTTTCTTTCTCT
*
34108 TTCTCTTTCT
1 TTTTCTTTCT
34118 TTCCTCCCTC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (12 bp):
TTTTCTTTCTCT
Found at i:34110 original size:16 final size:16
Alignment explanation
Indices: 34085--34120 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
34075 CTCCTTCCAT
* *
34085 TTTCTTTTTCTTTTTC
1 TTTCTCTTTCTCTTTC
34101 TTTCTCTTTCTCTTTC
1 TTTCTCTTTCTCTTTC
34117 TTTC
1 TTTC
34121 CTCCCTCATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (16 bp):
TTTCTCTTTCTCTTTC
Done.