Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012314.1 Corchorus olitorius cultivar O-4 contig12347, 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: 25560
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Found at i:159 original size:12 final size:12
Alignment explanation
Indices: 144--168 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
134 AGGCGTCATG
144 TGTTATATATAA
1 TGTTATATATAA
156 TGTTATATATAA
1 TGTTATATATAA
168 T
1 T
169 TATACACTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.00, G:0.08, T:0.52
Consensus pattern (12 bp):
TGTTATATATAA
Found at i:4903 original size:42 final size:43
Alignment explanation
Indices: 4852--4945 Score: 122
Period size: 45 Copynumber: 2.2 Consensus size: 43
4842 AGTGCATTAC
4852 CTAA-ATTCTA-CTCCATCTCTACG-TAATTAATCAAAATAAAG
1 CTAATATTCTACCTCCATCTCTA-GATAATTAATCAAAATAAAG
* *
4893 CTAATATTCTACTCCTCCATCTCTAGATAATTCATCAAAATAAAT
1 CTAATATTCTA--CCTCCATCTCTAGATAATTAATCAAAATAAAG
4938 CTAATATT
1 CTAATATT
4946 AATTGTTGCT
Statistics
Matches: 46, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
41 4 0.09
42 6 0.13
44 1 0.02
45 35 0.76
ACGTcount: A:0.39, C:0.22, G:0.03, T:0.35
Consensus pattern (43 bp):
CTAATATTCTACCTCCATCTCTAGATAATTAATCAAAATAAAG
Found at i:6953 original size:66 final size:67
Alignment explanation
Indices: 6832--6963 Score: 239
Period size: 66 Copynumber: 2.0 Consensus size: 67
6822 CTTAGCATTA
*
6832 GCTAACTGTGCTTTTGGAAATGTGAAAAATATACTAAATATAAGCAACTAATAGAAACCTTAATA
1 GCTAACTGTGCTTTTGGAAATGTGAAAAATATACTAAATATAAGCAACTAATAGAAACCTCAATA
6897 AT
66 AT
*
6899 GCTAACTGTGCTTTTGGAAATGTG-AAAATATACTAAATATAAGCAACTATTAGAAACCTCAATA
1 GCTAACTGTGCTTTTGGAAATGTGAAAAATATACTAAATATAAGCAACTAATAGAAACCTCAATA
6963 A
66 A
6964 AAAGGAAGTC
Statistics
Matches: 63, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
66 39 0.62
67 24 0.38
ACGTcount: A:0.44, C:0.13, G:0.14, T:0.30
Consensus pattern (67 bp):
GCTAACTGTGCTTTTGGAAATGTGAAAAATATACTAAATATAAGCAACTAATAGAAACCTCAATA
AT
Found at i:14906 original size:4 final size:4
Alignment explanation
Indices: 14897--14963 Score: 62
Period size: 4 Copynumber: 16.8 Consensus size: 4
14887 AAAGTGTATA
** * * *
14897 TGTG TGTG TGTG TGTG TGTG TGTG CATG TGTG CGTG TGTG TTTG TATG
1 TGTG TGTG TGTG TGTG TGTG TGTG TGTG TGTG TGTG TGTG TGTG TGTG
* * *
14945 TGTG TATG TATG TATG TGT
1 TGTG TGTG TGTG TGTG TGT
14964 ATCTATGTAT
Statistics
Matches: 52, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
4 52 1.00
ACGTcount: A:0.07, C:0.03, G:0.40, T:0.49
Consensus pattern (4 bp):
TGTG
Found at i:14916 original size:16 final size:16
Alignment explanation
Indices: 14891--14963 Score: 74
Period size: 16 Copynumber: 4.6 Consensus size: 16
14881 AATAAAAAAG
* *
14891 TGTATATGTGTGTGTG
1 TGTATGTGTGTGTGTA
* *
14907 TGTGTGTGTGTGTGCA
1 TGTATGTGTGTGTGTA
* * *
14923 TGTGTGCGTGTGTGTT
1 TGTATGTGTGTGTGTA
*
14939 TGTATGTGTGTATGTA
1 TGTATGTGTGTGTGTA
14955 TGTATGTGT
1 TGTATGTGT
14964 ATCTATGTAT
Statistics
Matches: 46, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 46 1.00
ACGTcount: A:0.10, C:0.03, G:0.38, T:0.49
Consensus pattern (16 bp):
TGTATGTGTGTGTGTA
Found at i:14964 original size:14 final size:14
Alignment explanation
Indices: 14933--14975 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 14
14923 TGTGTGCGTG
*
14933 TGTGTTTGTATG--
1 TGTGTATGTATGTA
14945 TGTGTATGTATGTA
1 TGTGTATGTATGTA
*
14959 TGTGTATCTATGTA
1 TGTGTATGTATGTA
14973 TGT
1 TGT
14976 AAAATATAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
12 11 0.41
14 16 0.59
ACGTcount: A:0.16, C:0.02, G:0.28, T:0.53
Consensus pattern (14 bp):
TGTGTATGTATGTA
Found at i:17949 original size:3 final size:3
Alignment explanation
Indices: 17941--17965 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
17931 AGAGAGAGAG
17941 GAA GAA GAA GAA GAA GAA GAA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA G
17966 CTCAATATGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:24809 original size:30 final size:30
Alignment explanation
Indices: 24746--24807 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 30
24736 TATTCTGTCA
24746 TTATTTTTTATTTAGGTTAGTATTAGGCTT
1 TTATTTTTTATTTAGGTTAGTATTAGGCTT
*
24776 TTATTTTCTTATTTTA-GTTAGTATTGGGCTT
1 TTATTTT-TTA-TTTAGGTTAGTATTAGGCTT
24807 T
1 T
24808 ATGGGCTGTT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
30 7 0.24
31 18 0.62
32 4 0.14
ACGTcount: A:0.18, C:0.05, G:0.16, T:0.61
Consensus pattern (30 bp):
TTATTTTTTATTTAGGTTAGTATTAGGCTT
Done.