Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006899.1 Corchorus capsularis cultivar CVL-1 contig06920, 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: 32604
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.31
Found at i:916 original size:32 final size:32
Alignment explanation
Indices: 855--916 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 32
845 AATTGACATG
* * *
855 ACATGAAATCTAAATCCTAAGTAAGATAAAAT
1 ACATGAAATATAAACCCTAAGTAACATAAAAT
* *
887 ACATGATATATAAACCCTAAGTGACATAAA
1 ACATGAAATATAAACCCTAAGTAACATAAA
917 GAAATGCCCC
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 25 1.00
ACGTcount: A:0.52, C:0.15, G:0.10, T:0.24
Consensus pattern (32 bp):
ACATGAAATATAAACCCTAAGTAACATAAAAT
Found at i:1093 original size:32 final size:32
Alignment explanation
Indices: 1047--1108 Score: 106
Period size: 32 Copynumber: 1.9 Consensus size: 32
1037 AAATGACATG
*
1047 ACATGAAATCTAAACCCTAAGTGAGATAAAAT
1 ACATGAAATATAAACCCTAAGTGAGATAAAAT
*
1079 ACATGATATATAAACCCTAAGTGAGATAAA
1 ACATGAAATATAAACCCTAAGTGAGATAAA
1109 GAAATGCCCC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.50, C:0.15, G:0.13, T:0.23
Consensus pattern (32 bp):
ACATGAAATATAAACCCTAAGTGAGATAAAAT
Found at i:1110 original size:192 final size:191
Alignment explanation
Indices: 809--1205 Score: 631
Period size: 192 Copynumber: 2.1 Consensus size: 191
799 AACCCTAATG
*
809 AAATTTAAAAAAAAAAAGGCTATGAGAGACAAAAAAAATTGACATGACATGAAATCTAAATCCTA
1 AAATTTAAAAAAAAAAAGGCTATGAGAGAC--AAAAAATTGACATGACATGAAATCTAAACCCTA
874 AGTAAGATAAAATACATGATATATAAACCCTAAGTGACATAAAGAAATGCCCCAAAACTATATTA
64 AGTAAGATAAAATACATGATATATAAACCCTAAGTGACATAAAGAAATGCCCCAAAACTATATTA
*
939 AACCCTAAATGAGATAGAT-TAAATTTCAAC-ATTCTATGTCATAAAAAGTGGTGGAAGAGTCT
129 AACCCTAAATGAGATAG-TCTAAATTTCAACAATTCTATGTCATAAAAAGTGGTGGAAGAGTCA
1001 AAATTTGAAATAAAAAAAGATGGCTATGAGAGAC-AAAAA-TGACATGACATGAAATCTAAACCC
1 AAATTT-AAA-AAAAAAA-A-GGCTATGAGAGACAAAAAATTGACATGACATGAAATCTAAACCC
* *
1064 TAAGTGAGATAAAATACATGATATATAAACCCTAAGTGAGATAAAGAAATGCCCCAAAACTATAT
62 TAAGTAAGATAAAATACATGATATATAAACCCTAAGTGACATAAAGAAATGCCCCAAAACTATAT
* *
1129 TAAACCCTAAGTGAGATAGTCTAAATTTCAACATATTCTATGTCATAAAAATTGGTGGAAGAGTC
127 TAAACCCTAAATGAGATAGTCTAAATTTCAACA-ATTCTATGTCATAAAAAGTGGTGGAAGAGTC
1194 A
191 A
*
1195 AAATTTCAAAA
1 AAATTTAAAAA
1206 GTTGTGACAT
Statistics
Matches: 191, Mismatches: 7, Indels: 14
0.90 0.03 0.07
Matches are distributed among these distances:
191 1 0.01
192 123 0.64
193 10 0.05
194 43 0.23
195 1 0.01
196 13 0.07
ACGTcount: A:0.49, C:0.13, G:0.14, T:0.24
Consensus pattern (191 bp):
AAATTTAAAAAAAAAAAGGCTATGAGAGACAAAAAATTGACATGACATGAAATCTAAACCCTAAG
TAAGATAAAATACATGATATATAAACCCTAAGTGACATAAAGAAATGCCCCAAAACTATATTAAA
CCCTAAATGAGATAGTCTAAATTTCAACAATTCTATGTCATAAAAAGTGGTGGAAGAGTCA
Found at i:2060 original size:38 final size:37
Alignment explanation
Indices: 2014--2087 Score: 121
Period size: 38 Copynumber: 2.0 Consensus size: 37
2004 TTGTTATCAT
2014 TTAGGCTTTGGTTATCAACTTTCCTCTTAGACTAATG
1 TTAGGCTTTGGTTATCAACTTTCCTCTTAGACTAATG
* *
2051 TTAGCGCTTTGGTTATCAATTTTTCTCTTAGACTAAT
1 TTAG-GCTTTGGTTATCAACTTTCCTCTTAGACTAAT
2088 TATCAAAATT
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
37 4 0.12
38 30 0.88
ACGTcount: A:0.22, C:0.18, G:0.15, T:0.46
Consensus pattern (37 bp):
TTAGGCTTTGGTTATCAACTTTCCTCTTAGACTAATG
Found at i:6330 original size:2 final size:2
Alignment explanation
Indices: 6323--6350 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
6313 GGACTAAACC
6323 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
6351 CTTAAAGGGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6553 original size:14 final size:14
Alignment explanation
Indices: 6534--6561 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
6524 TACACAACTA
6534 GAAGAAAAAAAAAG
1 GAAGAAAAAAAAAG
6548 GAAGAAAAAAAAAG
1 GAAGAAAAAAAAAG
6562 CTGTACTGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (14 bp):
GAAGAAAAAAAAAG
Found at i:13399 original size:39 final size:40
Alignment explanation
Indices: 13321--13402 Score: 130
Period size: 40 Copynumber: 2.1 Consensus size: 40
13311 TCACTGAATA
*
13321 AAAAAAGGGAAATCTAAGATTTAGGTCAGCTTAGACCCAT
1 AAAAAAGGGAAATCTAAGATTTAGGTCAGCTCAGACCCAT
* *
13361 AAAAAAGGGAAATTTGAGATTTAGGTCAGCTCAG-CCCAT
1 AAAAAAGGGAAATCTAAGATTTAGGTCAGCTCAGACCCAT
13400 AAA
1 AAA
13403 TACCTAGTAC
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
39 8 0.21
40 31 0.79
ACGTcount: A:0.43, C:0.15, G:0.21, T:0.22
Consensus pattern (40 bp):
AAAAAAGGGAAATCTAAGATTTAGGTCAGCTCAGACCCAT
Done.