Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01004605.1 Corchorus capsularis cultivar CVL-1 contig04617, 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, 613
Length: 1022
ACGTcount: A:0.38, C:0.15, G:0.17, T:0.31
Found at i:199 original size:70 final size:70
Alignment explanation
Indices: 70--325 Score: 309
Period size: 70 Copynumber: 3.7 Consensus size: 70
60 GAATGAAATC
*
70 AAAATTATGTAATATCATATAATGAACATAGAATG------AAATTATGTAATACCATATAATGA
1 AAAATTATGTAATACCATATAATGAA-ATAGAATGAAATCAAAATTATGTAATACCATATAATGA
129 ACATAG
65 ACATAG
135 AAAATTATGTAATACCATATAATGAAATAGAATGAAATCAAAATTATGTAATACCATATAATGAA
1 AAAATTATGTAATACCATATAATGAAATAGAATGAAATCAAAATTATGTAATACCATATAATGAA
200 CATAG
66 CATAG
* * ** * * * *
205 AATGAA--AT-CAAAATTACATAAT-ACCATATAATGAAATAGAAAATTATGTAATACCATATAA
1 AA--AATTATGTAATACCATATAATGA-AATAGAATGAAAT-CAAAATTATGTAATACCATATAA
266 TGAA-ATAG
62 TGAACATAG
274 AAAATTATGTAATACCATATAATGAAATAGAATGAAATCAAAATTATGTAAT
1 AAAATTATGTAATACCATATAATGAAATAGAATGAAATCAAAATTATGTAAT
326 TGTAATTATG
Statistics
Matches: 160, Mismatches: 17, Indels: 24
0.80 0.08 0.12
Matches are distributed among these distances:
64 8 0.05
65 25 0.16
67 2 0.01
68 1 0.01
69 41 0.26
70 80 0.50
71 1 0.01
72 2 0.01
ACGTcount: A:0.53, C:0.08, G:0.10, T:0.29
Consensus pattern (70 bp):
AAAATTATGTAATACCATATAATGAAATAGAATGAAATCAAAATTATGTAATACCATATAATGAA
CATAG
Found at i:248 original size:30 final size:30
Alignment explanation
Indices: 200--305 Score: 169
Period size: 30 Copynumber: 3.6 Consensus size: 30
190 ATATAATGAA
* * **
200 CATAGAATGAAAT-CAAAATTACATAATAC
1 CATATAATGAAATAGAAAATTATGTAATAC
229 CATATAATGAAATAGAAAATTATGTAATAC
1 CATATAATGAAATAGAAAATTATGTAATAC
259 CATATAATGAAATAGAAAATTATGTAATAC
1 CATATAATGAAATAGAAAATTATGTAATAC
289 CATATAATGAAATAGAA
1 CATATAATGAAATAGAA
306 TGAAATCAAA
Statistics
Matches: 72, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
29 12 0.17
30 60 0.83
ACGTcount: A:0.55, C:0.08, G:0.09, T:0.27
Consensus pattern (30 bp):
CATATAATGAAATAGAAAATTATGTAATAC
Found at i:302 original size:15 final size:15
Alignment explanation
Indices: 224--302 Score: 68
Period size: 15 Copynumber: 5.3 Consensus size: 15
214 AAAATTACAT
224 AATACCATATAATGA
1 AATACCATATAATGA
** * * *
239 AATAGAAAATTATGT
1 AATACCATATAATGA
254 AATACCATATAATGA
1 AATACCATATAATGA
** * * *
269 AATAGAAAATTATGT
1 AATACCATATAATGA
284 AATACCATATAATGA
1 AATACCATATAATGA
299 AATA
1 AATA
303 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
Found at i:305 original size:139 final size:142
Alignment explanation
Indices: 41--325 Score: 497
Period size: 139 Copynumber: 2.0 Consensus size: 142
31 GCCAATTCAA
** *
41 AATACCATATAATGAAATAGAATGAAATCAAAATTATGTAATATCATATAATGAACATAGAATGA
1 AATACCATATAATGAAATAGAATGAAATCAAAATTACATAATACCATATAATGAACATAGAA-GA
106 AATTATGTAATACCATATAATGAACATAGAAAATTATGTAATACCATATAATGAAATAGAATGAA
65 AATTATGTAATACCATATAATGAACATAGAAAATTATGTAATACCATATAATGAAATAGAATGAA
171 ATCAAAATTATGT
130 ATCAAAATTATGT
184 AATACCATATAATGAACATAGAATGAAATCAAAATTACATAATACCATATAATGAA-ATAG-A-A
1 AATACCATATAATGAA-ATAGAATGAAATCAAAATTACATAATACCATATAATGAACATAGAAGA
246 AATTATGTAATACCATATAATGAA-ATAGAAAATTATGTAATACCATATAATGAAATAGAATGAA
65 AATTATGTAATACCATATAATGAACATAGAAAATTATGTAATACCATATAATGAAATAGAATGAA
310 ATCAAAATTATGT
130 ATCAAAATTATGT
323 AAT
1 AAT
326 TGTAATTATG
Statistics
Matches: 138, Mismatches: 3, Indels: 6
0.94 0.02 0.04
Matches are distributed among these distances:
139 56 0.41
140 25 0.18
142 1 0.01
143 20 0.14
144 36 0.26
ACGTcount: A:0.53, C:0.08, G:0.10, T:0.29
Consensus pattern (142 bp):
AATACCATATAATGAAATAGAATGAAATCAAAATTACATAATACCATATAATGAACATAGAAGAA
ATTATGTAATACCATATAATGAACATAGAAAATTATGTAATACCATATAATGAAATAGAATGAAA
TCAAAATTATGT
Done.