Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018798.1 Corchorus olitorius cultivar O-4 contig18831, 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: 2905
ACGTcount: A:0.36, C:0.18, G:0.17, T:0.29
Found at i:2214 original size:30 final size:30
Alignment explanation
Indices: 2212--2596 Score: 490
Period size: 30 Copynumber: 13.2 Consensus size: 30
2202 AAAATAAAGC
*
2212 AATAAAGCAATGATCCTAAACCAGGATTAA
1 AATAAAGCAATGATCCTCAACCAGGATTAA
*
2242 AATAAAGCAATGATCCTCGACCAGG-----
1 AATAAAGCAATGATCCTCAACCAGGATTAA
2267 -ATAAAGCAATGATCCTCAACCAGG-----
1 AATAAAGCAATGATCCTCAACCAGGATTAA
2291 -ATAAAGCAATGATCCTCAACCAGGATTAA
1 AATAAAGCAATGATCCTCAACCAGGATTAA
* * *
2320 AATAAAGCAGT-ATTCCTAAACCAGGATTAG
1 AATAAAGCAATGA-TCCTCAACCAGGATTAA
*
2350 AATAAAGCAATGATTCTCAACCAGGATTAA
1 AATAAAGCAATGATCCTCAACCAGGATTAA
** *
2380 AATGCAGTAATGATCCTCAACCAGGATTAA
1 AATAAAGCAATGATCCTCAACCAGGATTAA
* * *
2410 AATAAAGCAATGATCCTAAATCAGGACTAA
1 AATAAAGCAATGATCCTCAACCAGGATTAA
2440 AATAAAGCAATGATCCTCAACCAGGATTAA
1 AATAAAGCAATGATCCTCAACCAGGATTAA
* * *
2470 AATAAAGCAATGACCCTAAACCAGGGTTAA
1 AATAAAGCAATGATCCTCAACCAGGATTAA
*
2500 AATAAAGCAATGATCCTAAACCAGGATTAA
1 AATAAAGCAATGATCCTCAACCAGGATTAA
*
2530 AATAAAGCAATGATCCTCAAACAGGATTAA
1 AATAAAGCAATGATCCTCAACCAGGATTAA
* * *
2560 CATAAAGCGACGATCCTCAACCAGGATTAA
1 AATAAAGCAATGATCCTCAACCAGGATTAA
2590 AATAAAG
1 AATAAAG
2597 TTGATAAAGC
Statistics
Matches: 312, Mismatches: 35, Indels: 16
0.86 0.10 0.04
Matches are distributed among these distances:
24 47 0.15
29 1 0.00
30 263 0.84
31 1 0.00
ACGTcount: A:0.46, C:0.19, G:0.15, T:0.20
Consensus pattern (30 bp):
AATAAAGCAATGATCCTCAACCAGGATTAA
Found at i:2229 original size:38 final size:38
Alignment explanation
Indices: 2178--2252 Score: 141
Period size: 38 Copynumber: 2.0 Consensus size: 38
2168 TTAACTGATG
2178 AAGCAATGATCCTAAACCAAGATTAAAATAAAGCAATA
1 AAGCAATGATCCTAAACCAAGATTAAAATAAAGCAATA
*
2216 AAGCAATGATCCTAAACCAGGATTAAAATAAAGCAAT
1 AAGCAATGATCCTAAACCAAGATTAAAATAAAGCAAT
2253 GATCCTCGAC
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.53, C:0.16, G:0.12, T:0.19
Consensus pattern (38 bp):
AAGCAATGATCCTAAACCAAGATTAAAATAAAGCAATA
Found at i:2275 original size:24 final size:24
Alignment explanation
Indices: 2243--2316 Score: 139
Period size: 24 Copynumber: 3.1 Consensus size: 24
2233 CAGGATTAAA
*
2243 ATAAAGCAATGATCCTCGACCAGG
1 ATAAAGCAATGATCCTCAACCAGG
2267 ATAAAGCAATGATCCTCAACCAGG
1 ATAAAGCAATGATCCTCAACCAGG
2291 ATAAAGCAATGATCCTCAACCAGG
1 ATAAAGCAATGATCCTCAACCAGG
2315 AT
1 AT
2317 TAAAATAAAG
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
24 49 1.00
ACGTcount: A:0.41, C:0.24, G:0.18, T:0.18
Consensus pattern (24 bp):
ATAAAGCAATGATCCTCAACCAGG
Done.