Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01001923.1 Corchorus capsularis cultivar CVL-1 contig01925, 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, 600
Length: 1001
ACGTcount: A:0.37, C:0.15, G:0.17, T:0.31
Found at i:113 original size:70 final size:70
Alignment explanation
Indices: 25--245 Score: 299
Period size: 70 Copynumber: 3.2 Consensus size: 70
15 ACATAGAATG
25 AAATTATGTAATACCATATAATGAACATAGAAAATTATGTAATACCATATAATGAAATAGAATGA
1 AAATTATGTAATACCATATAATGAACATAGAAAATTATGTAATACCATATAATGAAATAGAATGA
90 AATCA
66 AATCA
* * ** * * *
95 AAATTATGTAATACCATATAATGAACATAGAATGAA--AT-CAAAATTACATAAT-ACCATATAA
1 AAATTATGTAATACCATATAATGAACATAGAA--AATTATGTAATACCATATAATGA-AATAGAA
*
156 TGAAATAGA
63 TGAAAT-CA
165 AAATTATGTAATACCATATAATGAA-ATAGAAAATTATGTAATACCATATAATGAAATAGAATGA
1 AAATTATGTAATACCATATAATGAACATAGAAAATTATGTAATACCATATAATGAAATAGAATGA
229 AATCA
66 AATCA
234 AAATTATGTAAT
1 AAATTATGTAAT
246 TGTAATTATG
Statistics
Matches: 127, Mismatches: 16, Indels: 17
0.79 0.10 0.11
Matches are distributed among these distances:
67 2 0.02
68 1 0.01
69 41 0.32
70 80 0.63
71 1 0.01
72 2 0.02
ACGTcount: A:0.53, C:0.08, G:0.10, T:0.29
Consensus pattern (70 bp):
AAATTATGTAATACCATATAATGAACATAGAAAATTATGTAATACCATATAATGAAATAGAATGA
AATCA
Found at i:136 original size:40 final size:39
Alignment explanation
Indices: 55--245 Score: 229
Period size: 30 Copynumber: 5.3 Consensus size: 39
45 ATGAACATAG
55 AAAATTATGTAATACCATATAATGAAATAGAATGAAATC
1 AAAATTATGTAATACCATATAATGAAATAGAATGAAATC
94 AAAATTATGTAATACCATATAATGAACATAGAATGAAATC
1 AAAATTATGTAATACCATATAATGAA-ATAGAATGAAATC
**
134 AAAATTACATAATACCATATAATGAAAT---A-G-----
1 AAAATTATGTAATACCATATAATGAAATAGAATGAAATC
164 AAAATTATGTAATACCATATAATGAAAT---A-G-----
1 AAAATTATGTAATACCATATAATGAAATAGAATGAAATC
194 AAAATTATGTAATACCATATAATGAAATAGAATGAAATC
1 AAAATTATGTAATACCATATAATGAAATAGAATGAAATC
233 AAAATTATGTAAT
1 AAAATTATGTAAT
246 TGTAATTATG
Statistics
Matches: 138, Mismatches: 4, Indels: 20
0.85 0.02 0.12
Matches are distributed among these distances:
30 56 0.41
33 1 0.01
34 1 0.01
35 1 0.01
36 1 0.01
39 41 0.30
40 37 0.27
ACGTcount: A:0.54, C:0.08, G:0.09, T:0.29
Consensus pattern (39 bp):
AAAATTATGTAATACCATATAATGAAATAGAATGAAATC
Found at i:222 original size:15 final size:15
Alignment explanation
Indices: 144--222 Score: 68
Period size: 15 Copynumber: 5.3 Consensus size: 15
134 AAAATTACAT
144 AATACCATATAATGA
1 AATACCATATAATGA
** * * *
159 AATAGAAAATTATGT
1 AATACCATATAATGA
174 AATACCATATAATGA
1 AATACCATATAATGA
** * * *
189 AATAGAAAATTATGT
1 AATACCATATAATGA
204 AATACCATATAATGA
1 AATACCATATAATGA
219 AATA
1 AATA
223 GAATGAAATC
Statistics
Matches: 44, Mismatches: 20, Indels: 0
0.69 0.31 0.00
Matches are distributed among these distances:
15 44 1.00
ACGTcount: A:0.54, C:0.08, G:0.09, T:0.29
Consensus pattern (15 bp):
AATACCATATAATGA
Done.