Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013812.1 Corchorus capsularis cultivar CVL-1 contig13833, 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: 24479
ACGTcount: A:0.34, C:0.19, G:0.18, T:0.30
Found at i:912 original size:2 final size:2
Alignment explanation
Indices: 905--938 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
895 GGAGCCAAGA
905 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
939 TGTAAATACC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2143 original size:12 final size:12
Alignment explanation
Indices: 2126--2156 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
2116 GTTGAAACAT
*
2126 GGAGAAATCGAC
1 GGAGAAATCAAC
2138 GGAGAAATCAAC
1 GGAGAAATCAAC
2150 GGAGAAA
1 GGAGAAA
2157 ATTCTGGGGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.48, C:0.13, G:0.32, T:0.06
Consensus pattern (12 bp):
GGAGAAATCAAC
Found at i:7702 original size:11 final size:11
Alignment explanation
Indices: 7686--7710 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
7676 ATAATCATCC
7686 AAAAAGGCACA
1 AAAAAGGCACA
7697 AAAAAGGCACA
1 AAAAAGGCACA
7708 AAA
1 AAA
7711 TTGGTGATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.68, C:0.16, G:0.16, T:0.00
Consensus pattern (11 bp):
AAAAAGGCACA
Found at i:14939 original size:20 final size:20
Alignment explanation
Indices: 14914--14953 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
14904 GTACTTAGGG
14914 TTTGACTAAGAAAATTACTC
1 TTTGACTAAGAAAATTACTC
14934 TTTGACTAAGAAAATTACTC
1 TTTGACTAAGAAAATTACTC
14954 CATCTGTCCC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.40, C:0.15, G:0.10, T:0.35
Consensus pattern (20 bp):
TTTGACTAAGAAAATTACTC
Found at i:15768 original size:25 final size:25
Alignment explanation
Indices: 15739--15794 Score: 78
Period size: 25 Copynumber: 2.2 Consensus size: 25
15729 TTTATTATTA
15739 ATTTAATTTACTAATT-GTAAAATTT
1 ATTTAATTTACTAATTGGT-AAATTT
*
15764 ATTTAATTTATTAATTGGTAAATTT
1 ATTTAATTTACTAATTGGTAAATTT
*
15789 AATTAA
1 ATTTAA
15795 CGTTAAGAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
25 26 0.93
26 2 0.07
ACGTcount: A:0.41, C:0.02, G:0.05, T:0.52
Consensus pattern (25 bp):
ATTTAATTTACTAATTGGTAAATTT
Found at i:23052 original size:29 final size:30
Alignment explanation
Indices: 23020--23076 Score: 73
Period size: 29 Copynumber: 1.9 Consensus size: 30
23010 AAGCAATTTC
*
23020 AAAATATTTTATCC-CAAATCA-ATCAAATT
1 AAAAGATTTTA-CCTCAAATCAGATCAAATT
*
23049 AAAAGATTTTACCTCAAATTAGATCAAA
1 AAAAGATTTTACCTCAAATCAGATCAAA
23077 ACTGAAACTG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 2 0.08
29 16 0.67
30 6 0.25
ACGTcount: A:0.49, C:0.16, G:0.04, T:0.32
Consensus pattern (30 bp):
AAAAGATTTTACCTCAAATCAGATCAAATT
Found at i:23142 original size:27 final size:27
Alignment explanation
Indices: 23104--23161 Score: 116
Period size: 27 Copynumber: 2.1 Consensus size: 27
23094 TTACCCTTAA
23104 TTGAGTAATTAGCCTATTGGAGAAAAG
1 TTGAGTAATTAGCCTATTGGAGAAAAG
23131 TTGAGTAATTAGCCTATTGGAGAAAAG
1 TTGAGTAATTAGCCTATTGGAGAAAAG
23158 TTGA
1 TTGA
23162 TGCAAGAGTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.36, C:0.07, G:0.26, T:0.31
Consensus pattern (27 bp):
TTGAGTAATTAGCCTATTGGAGAAAAG
Done.