Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010696.1 Kokia drynarioides strain JFW-HI SEQ_125643, 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: 3787
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.31
Found at i:238 original size:29 final size:29
Alignment explanation
Indices: 182--593 Score: 377
Period size: 29 Copynumber: 14.0 Consensus size: 29
172 CCTTGAAGGT
*
182 CCCTAAACTATCCAAAAATTCCAATTTTAC
1 CCCTAAACT-TCCAAAAATTCCATTTTTAC
* * *
212 CCCTGAACTTTCAAAAATCCCATTTTTGAC
1 CCCTAAACTTCCAAAAATTCCATTTTT-AC
* * *
242 ACCAAAACTTTCAAAAATTCCATTTTTAC
1 CCCTAAACTTCCAAAAATTCCATTTTTAC
*
271 CCCTAAACTTCCAAAAATCCCATTTTTGA-
1 CCCTAAACTTCCAAAAATTCCATTTTT-AC
*
300 CCCTAAAACTTCCAAAAATTCCTTTTTTAC
1 CCCT-AAACTTCCAAAAATTCCATTTTTAC
* *
330 CCCTAAACTTCCAAAAATGCTATTTTTGAC
1 CCCTAAACTTCCAAAAATTCCATTTTT-AC
* * *
360 CTCGAAACTTCCAAAAA-TCCAATTTTTAA
1 CCCTAAACTTCCAAAAATTCC-ATTTTTAC
389 CCCTAAAACTTCCAAAAATTCCATTTTTA-
1 CCCT-AAACTTCCAAAAATTCCATTTTTAC
* * *
418 GCCTCGAACTTCCAAAAATCCCATTTTTA-
1 CCCT-AAACTTCCAAAAATTCCATTTTTAC
* ** *
447 CACTCAAACTTTTAAAAATCCCATTTTTAAC
1 CCCT-AAACTTCCAAAAATTCCATTTTT-AC
* * *
478 CCCAAAACTTCCAAAAAATCAATTTTTAC
1 CCCTAAACTTCCAAAAATTCCATTTTTAC
* *
507 CACC-AAACTTCCAAAAATACCATTTTTTAT
1 C-CCTAAACTTCCAAAAATTCCA-TTTTTAC
* * *
537 CCCGAAATTTCCAAAAATTCCATTTTTGC
1 CCCTAAACTTCCAAAAATTCCATTTTTAC
* * *
566 CGCTGAA-TGTCTAAAAATTCCATTTTTA
1 CCCTAAACT-TCCAAAAATTCCATTTTTA
594 AATCCTGAAT
Statistics
Matches: 315, Mismatches: 53, Indels: 29
0.79 0.13 0.07
Matches are distributed among these distances:
28 1 0.00
29 163 0.52
30 146 0.46
31 5 0.02
ACGTcount: A:0.36, C:0.27, G:0.03, T:0.33
Consensus pattern (29 bp):
CCCTAAACTTCCAAAAATTCCATTTTTAC
Found at i:253 original size:30 final size:28
Alignment explanation
Indices: 186--563 Score: 312
Period size: 30 Copynumber: 12.8 Consensus size: 28
176 GAAGGTCCCT
* * *
186 AAACTATCCAAAAATTCCAATTTTACCCCT
1 AAACT-TCCAAAAATCCCATTTTTA-CCCA
* *
216 GAACTTTCAAAAATCCCATTTTTGACACCA
1 AAACTTCCAAAAATCCCATTTTT-AC-CCA
* * *
246 AAACTTTCAAAAATTCCATTTTTACCCCT
1 AAACTTCCAAAAATCCCATTTTTA-CCCA
275 AAACTTCCAAAAATCCCATTTTTGACCCTA
1 AAACTTCCAAAAATCCCATTTTT-ACCC-A
* * *
305 AAACTTCCAAAAATTCCTTTTTTACCCCT
1 AAACTTCCAAAAATCCCATTTTTA-CCCA
* * *
334 AAACTTCCAAAAATGCTATTTTTGACCTCG
1 AAACTTCCAAAAATCCCATTTTT-ACC-CA
*
364 AAACTTCCAAAAATCCAATTTTTAACCCTA
1 AAACTTCCAAAAATCCCATTTTT-ACCC-A
*
394 AAACTTCCAAAAATTCCATTTTTAGCCTC-
1 AAACTTCCAAAAATCCCATTTTTA-CC-CA
*
423 GAACTTCCAAAAATCCCATTTTTACACTC-
1 AAACTTCCAAAAATCCCATTTTTAC-C-CA
**
452 AAACTTTTAAAAATCCCATTTTTAACCCCA
1 AAACTTCCAAAAATCCCATTTTT-A-CCCA
* *
482 AAACTTCCAAAAAAT-CAATTTTTACCACC
1 AAACTTCC-AAAAATCCCATTTTTACC-CA
* *
511 AAACTTCCAAAAATACCATTTTTTATCCCG
1 AAACTTCCAAAAATCCCA-TTTTTA-CCCA
* *
541 AAATTTCCAAAAATTCCATTTTT
1 AAACTTCCAAAAATCCCATTTTT
564 GCCGCTGAAT
Statistics
Matches: 291, Mismatches: 37, Indels: 41
0.79 0.10 0.11
Matches are distributed among these distances:
28 9 0.03
29 131 0.45
30 141 0.48
31 10 0.03
ACGTcount: A:0.37, C:0.27, G:0.02, T:0.33
Consensus pattern (28 bp):
AAACTTCCAAAAATCCCATTTTTACCCA
Found at i:286 original size:59 final size:58
Alignment explanation
Indices: 186--563 Score: 415
Period size: 59 Copynumber: 6.4 Consensus size: 58
176 GAAGGTCCCT
* * *
186 AAACTATCCAAAAATTCCAATTTTACCCCTGAACTTTCAAAAATCCCATTTTTGACACCA
1 AAACT-TCCAAAAATTCCATTTTTACCCCTAAACTTCCAAAAATCCCATTTTTGAC-CCA
*
246 AAACTTTCAAAAATTCCATTTTTACCCCTAAACTTCCAAAAATCCCATTTTTGACCCTA
1 AAACTTCCAAAAATTCCATTTTTACCCCTAAACTTCCAAAAATCCCATTTTTGACCC-A
* * * *
305 AAACTTCCAAAAATTCCTTTTTTACCCCTAAACTTCCAAAAATGCTATTTTTGACCTCG
1 AAACTTCCAAAAATTCCATTTTTACCCCTAAACTTCCAAAAATCCCATTTTTGACC-CA
* *
364 AAACTTCCAAAAA-TCCAATTTTTAACCCTAAAACTTCCAAAAATTCCATTTTT-AGCCTC-
1 AAACTTCCAAAAATTCC-ATTTTTACCCCT-AAACTTCCAAAAATCCCATTTTTGA-CC-CA
* * * ** *
423 GAACTTCCAAAAATCCCATTTTTA-CACTCAAACTTTTAAAAATCCCATTTTTAACCCCA
1 AAACTTCCAAAAATTCCATTTTTACCCCT-AAACTTCCAAAAATCCCATTTTTGA-CCCA
* * * * *
482 AAACTTCCAAAAAATCAATTTTTACCACC-AAACTTCCAAAAATACCATTTTTTATCCCG
1 AAACTTCCAAAAATTCCATTTTTACC-CCTAAACTTCCAAAAATCCCATTTTTGA-CCCA
*
541 AAATTTCCAAAAATTCCATTTTT
1 AAACTTCCAAAAATTCCATTTTT
564 GCCGCTGAAT
Statistics
Matches: 273, Mismatches: 35, Indels: 21
0.83 0.11 0.06
Matches are distributed among these distances:
58 29 0.11
59 209 0.77
60 34 0.12
61 1 0.00
ACGTcount: A:0.37, C:0.27, G:0.02, T:0.33
Consensus pattern (58 bp):
AAACTTCCAAAAATTCCATTTTTACCCCTAAACTTCCAAAAATCCCATTTTTGACCCA
Done.