Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_169 ID=scaffold_169-JGI_221_v2.0
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: 12568
ACGTcount: A:0.31, C:0.15, G:0.14, T:0.21
Warning! 2372 characters in sequence are not A, C, G, or T
Found at i:6351 original size:14 final size:14
Alignment explanation
Indices: 6332--6365 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
6322 ATTTCATTTT
**
6332 ATATTAATTGTATA
1 ATATTAATTAAATA
6346 ATATTAATTAAATA
1 ATATTAATTAAATA
6360 ATATTA
1 ATATTA
6366 TAATTGCTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (14 bp):
ATATTAATTAAATA
Found at i:8455 original size:21 final size:21
Alignment explanation
Indices: 8429--8470 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
8419 GTCCTGCAGC
8429 ATAAAA-AATCTGAACCGGACA
1 ATAAAAGAA-CTGAACCGGACA
8450 ATAAAAGAACTGAACCGGACA
1 ATAAAAGAACTGAACCGGACA
8471 GGGGAAAACC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 18 0.90
22 2 0.10
ACGTcount: A:0.52, C:0.19, G:0.17, T:0.12
Consensus pattern (21 bp):
ATAAAAGAACTGAACCGGACA
Found at i:9411 original size:40 final size:40
Alignment explanation
Indices: 9353--9436 Score: 159
Period size: 40 Copynumber: 2.1 Consensus size: 40
9343 CTACGTGCGT
*
9353 CACAACTCCCACCGGGTTCCTAGAACCAAAATCAAGCCAA
1 CACAACTCCCACCAGGTTCCTAGAACCAAAATCAAGCCAA
9393 CACAACTCCCACCAGGTTCCTAGAACCAAAATCAAGCCAA
1 CACAACTCCCACCAGGTTCCTAGAACCAAAATCAAGCCAA
9433 CACA
1 CACA
9437 GNNNNNNNNN
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 43 1.00
ACGTcount: A:0.39, C:0.38, G:0.11, T:0.12
Consensus pattern (40 bp):
CACAACTCCCACCAGGTTCCTAGAACCAAAATCAAGCCAA
Found at i:12227 original size:230 final size:229
Alignment explanation
Indices: 11819--12343 Score: 734
Period size: 230 Copynumber: 2.3 Consensus size: 229
11809 CATATTAGCA
* * * *
11819 AAAAGAAGCATATGTCAACTAAAAACAGAGAGGAATAGTATTCTGCTAAGCAGAA-ATTACAAAA
1 AAAAGAAGAATATATCAACTAAAAACAGAGAGGAAAAGTATTCTGCTCAGC-GAATATTACAAAA
* *
11883 ATATTATAAAGATACTATCCTGAGTTCTGAGAGCAAAGGAACTAGTGTAATGTTATTTGGAAAAT
65 ATATTATAAAGATACTATCCTCAGTTCTGAGAGCAAAGGAACTAGTGTAATGTTAATTGGAAAAT
* * **
11948 GAACTATAATGACAAAAATATAAATGATAAGCCGAAATCTAAGCGTGATTTGGGCCCAAAAAAAC
130 GAACTATAATGACAAAAATATAAATGAAAAGCCAAAATCTAAGCGTGATTCAGGCCCAAAAAAAC
*
12013 CAAACCACAAAATTATTCTACTAAGCAAAAACAAG
195 CAAACCACAAAATTACTCTACTAAGCAAAAACAAG
* * *
12048 AAAAGAAGAATATATTAACTAAAAACAGAGAGGAAAATTATTCTGCTCAGCGAATATTAAAAAAA
1 AAAAGAAGAATATATCAACTAAAAACAGAGAGGAAAAGTATTCTGCTCAGCGAATATTACAAAAA
* * * * * * *
12113 TCTTATTATAGATATTTTCTTCAGTGT-TGGGAGCAATA-GAACTAGTGTCATGTTAATTGGAAA
66 TATTA-TAAAGATACTATCCTCAGT-TCTGAGAGCAA-AGGAACTAGTGTAATGTTAATTGGAAA
* *
12176 A-GTAACTATAATGACAAAAATATAAATGAAAAGCCAAAATCTAATCGTGATTCAGGCTCAAAAA
128 ATG-AACTATAATGACAAAAATATAAATGAAAAGCCAAAATCTAAGCGTGATTCAGGCCCAAAAA
* * *
12240 CACCAAACCCCAAAATTACTCTGCTAAGCAAAAACAAG
192 AACCAAACCACAAAATTACTCTACTAAGCAAAAACAAG
*
12278 AAAAGAAGAATATATCAACTAAAAACAGAGAGGAAAAGTATTCTGCTCAGCGGATATTACAAAAA
1 AAAAGAAGAATATATCAACTAAAAACAGAGAGGAAAAGTATTCTGCTCAGCGAATATTACAAAAA
12343 T
66 T
12344 TATTCTGCTA
Statistics
Matches: 261, Mismatches: 30, Indels: 9
0.87 0.10 0.03
Matches are distributed among these distances:
228 3 0.01
229 59 0.23
230 197 0.75
231 2 0.01
ACGTcount: A:0.47, C:0.14, G:0.15, T:0.23
Consensus pattern (229 bp):
AAAAGAAGAATATATCAACTAAAAACAGAGAGGAAAAGTATTCTGCTCAGCGAATATTACAAAAA
TATTATAAAGATACTATCCTCAGTTCTGAGAGCAAAGGAACTAGTGTAATGTTAATTGGAAAATG
AACTATAATGACAAAAATATAAATGAAAAGCCAAAATCTAAGCGTGATTCAGGCCCAAAAAAACC
AAACCACAAAATTACTCTACTAAGCAAAAACAAG
Done.