Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_127 ID=scaffold_127-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: 11812
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:208 original size:17 final size:18
Alignment explanation
Indices: 181--215 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
171 CCAATTTAAT
181 TAAATAAAATATTAAAAA
1 TAAATAAAATATTAAAAA
199 TAAA-AAAATATTAAAAA
1 TAAATAAAATATTAAAAA
216 AATCTGTTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 13 0.76
18 4 0.24
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (18 bp):
TAAATAAAATATTAAAAA
Found at i:317 original size:10 final size:9
Alignment explanation
Indices: 305--510 Score: 59
Period size: 9 Copynumber: 21.7 Consensus size: 9
295 TCAGTTCAAG
305 TTTTTATAA
1 TTTTTATAA
*
314 GTTTATATCAA
1 -TTTTTAT-AA
*
325 TTTTAAT-A
1 TTTTTATAA
333 TTTTTATAA
1 TTTTTATAA
*
342 CTTTTATAGA
1 TTTTTATA-A
*
352 TTTTTAATAT
1 TTTTT-ATAA
362 TTTTTATAAA
1 TTTTTAT-AA
*
372 ATTTTA-AA
1 TTTTTATAA
*
380 TATTTTAATGA
1 T-TTTT-ATAA
391 TTTCTT-TAA
1 TTT-TTATAA
**
400 GTTCATATAAA
1 -TTTTTAT-AA
*
411 TTTTCAT-A
1 TTTTTATAA
419 TATTTT-TAA
1 T-TTTTATAA
*
428 TATTTA-ACA
1 TTTTTATA-A
*
437 TTTTGA-ATA
1 TTTTTATA-A
446 TTTTTATAA
1 TTTTTATAA
* *
455 TTTTTTCTTA
1 -TTTTTATAA
465 TTTTATATATA
1 TTTT-TATA-A
*
476 TATATATTAT-T
1 T-T-T-TTATAA
487 TTTTTATAA
1 TTTTTATAA
496 TTTTTATAA
1 TTTTTATAA
505 TTTTTA
1 TTTTTA
511 GGGAAAAAAT
Statistics
Matches: 143, Mismatches: 29, Indels: 49
0.65 0.13 0.22
Matches are distributed among these distances:
8 20 0.14
9 55 0.38
10 48 0.34
11 14 0.10
12 1 0.01
13 4 0.03
14 1 0.01
ACGTcount: A:0.33, C:0.03, G:0.02, T:0.61
Consensus pattern (9 bp):
TTTTTATAA
Found at i:366 original size:20 final size:21
Alignment explanation
Indices: 343--385 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
333 TTTTTATAAC
* *
343 TTTTAT-AGATTTTTAATATT
1 TTTTATAAAATTTTAAATATT
363 TTTTATAAAATTTTAAATATT
1 TTTTATAAAATTTTAAATATT
384 TT
1 TT
386 AATGATTTCT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (21 bp):
TTTTATAAAATTTTAAATATT
Found at i:385 original size:29 final size:30
Alignment explanation
Indices: 324--398 Score: 86
Period size: 29 Copynumber: 2.5 Consensus size: 30
314 GTTTATATCA
*
324 ATTTTAATA-TTTTTATAACTTTTATAGAT
1 ATTTTAATATTTTTTATAAATTTTATAGAT
353 -TTTTAATATTTTTTATAAAATTTTA-A-AT
1 ATTTTAATATTTTTTAT-AAATTTTATAGAT
381 ATTTTAATGATTTCTTTA
1 ATTTTAAT-ATTT-TTTA
399 AGTTCATATA
Statistics
Matches: 40, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
28 10 0.25
29 15 0.38
30 11 0.28
31 4 0.10
ACGTcount: A:0.35, C:0.03, G:0.03, T:0.60
Consensus pattern (30 bp):
ATTTTAATATTTTTTATAAATTTTATAGAT
Found at i:1428 original size:17 final size:18
Alignment explanation
Indices: 1389--1437 Score: 66
Period size: 17 Copynumber: 2.7 Consensus size: 18
1379 ATTGGACTTG
1389 AGTTTTCAATTTCAATTTT
1 AGTTTTC-ATTTCAATTTT
1408 -GTTTTCATTT-AATTTT
1 AGTTTTCATTTCAATTTT
1424 AGTTTTCAATTTCA
1 AGTTTTC-ATTTCA
1438 TAAAAGAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
16 6 0.22
17 10 0.37
18 10 0.37
19 1 0.04
ACGTcount: A:0.24, C:0.10, G:0.06, T:0.59
Consensus pattern (18 bp):
AGTTTTCATTTCAATTTT
Done.