Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011780.1 Corchorus capsularis cultivar CVL-1 contig11801, 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: 53109
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Found at i:14 original size:2 final size:2
Alignment explanation
Indices: 8--33 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1 TCCCCTC
8 CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT
34 ACACTACGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:21563 original size:21 final size:21
Alignment explanation
Indices: 21539--21602 Score: 69
Period size: 21 Copynumber: 3.1 Consensus size: 21
21529 TCTGCTCTAA
21539 TAATCTCATCTGTACAGTACC
1 TAATCTCATCTGTACAGTACC
* * * *
21560 TAATTTGATATGTACAATA--
1 TAATCTCATCTGTACAGTACC
*
21579 TAATCTCATCTATACAGTACC
1 TAATCTCATCTGTACAGTACC
21600 TAA
1 TAA
21603 ACAATGTCAA
Statistics
Matches: 32, Mismatches: 9, Indels: 4
0.71 0.20 0.09
Matches are distributed among these distances:
19 14 0.44
21 18 0.56
ACGTcount: A:0.36, C:0.20, G:0.08, T:0.36
Consensus pattern (21 bp):
TAATCTCATCTGTACAGTACC
Found at i:30452 original size:3 final size:3
Alignment explanation
Indices: 30444--30475 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
30434 ATAAACCCCA
30444 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
30476 ATGCTTGTCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:33694 original size:16 final size:16
Alignment explanation
Indices: 33673--33707 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
33663 GGATGGAGGA
33673 AGTGCCAGACTAACTC
1 AGTGCCAGACTAACTC
33689 AGTGCCAGACTAACTC
1 AGTGCCAGACTAACTC
33705 AGT
1 AGT
33708 TTTGGAAGCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.31, C:0.29, G:0.20, T:0.20
Consensus pattern (16 bp):
AGTGCCAGACTAACTC
Found at i:34257 original size:24 final size:24
Alignment explanation
Indices: 34225--34272 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
34215 AGCCAGAGAT
*
34225 TGCCATGTGTCAAGCAATTAGGAC
1 TGCCATGTGTCAAACAATTAGGAC
*
34249 TGCCATGTGTCAAACTATTAGGAC
1 TGCCATGTGTCAAACAATTAGGAC
34273 ACTTAGCTAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.27
Consensus pattern (24 bp):
TGCCATGTGTCAAACAATTAGGAC
Found at i:41698 original size:1 final size:1
Alignment explanation
Indices: 41692--41721 Score: 60
Period size: 1 Copynumber: 30.0 Consensus size: 1
41682 TGATTTCCGG
41692 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
41722 GATGGGAAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:47733 original size:21 final size:20
Alignment explanation
Indices: 47699--47737 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
47689 CAATGGCAAA
47699 CAAGTCATTGCATTGCTTAAC
1 CAAGTCATTGCATT-CTTAAC
47720 CAAGCTCATT-CATTCTTA
1 CAAG-TCATTGCATTCTTA
47738 CACTGGTATG
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 4 0.24
21 8 0.47
22 5 0.29
ACGTcount: A:0.28, C:0.26, G:0.10, T:0.36
Consensus pattern (20 bp):
CAAGTCATTGCATTCTTAAC
Done.