Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01000136.1 Kokia drynarioides strain JFW-HI SEQ_110786, 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, 622
Length: 1038
ACGTcount: A:0.30, C:0.20, G:0.10, T:0.40
Found at i:165 original size:29 final size:29
Alignment explanation
Indices: 123--371 Score: 147
Period size: 29 Copynumber: 8.6 Consensus size: 29
113 CACAATTCTC
*
123 CAAAAATTATATTTTTACCCCTAAACTTTT
1 CAAAAATTACATTTTTACCCCTAAA-TTTT
* * **
153 C-AAAATTCCATTTTAACATC-AAATTTT
1 CAAAAATTACATTTTTACCCCTAAATTTT
* * *
180 CCAAAAATTACA-TTTTACACCAAAAATTT
1 -CAAAAATTACATTTTTACCCCTAAATTTT
* * * *
209 CCAAAATTCCATTTTTGA-CACTGAATTTT
1 CAAAAATTACATTTTT-ACCCCTAAATTTT
* *
238 CCAAAAATTACATTTTTA-CCCTCGAACTTT
1 -CAAAAATTACATTTTTACCCCT-AAATTTT
* * * *
268 CTAAAATCT-CATTTTTA-ACCTCGAGTTTT
1 CAAAAAT-TACATTTTTACCCCT-AAATTTT
* * *
297 CAAAAAATACATTTTTGCCCCCAAACTTTT
1 CAAAAATTACATTTTTACCCCTAAA-TTTT
*
327 C-AAAATTTCATTTTTGACCCC-AAATTTT
1 CAAAAATTACATTTTT-ACCCCTAAATTTT
355 CCAAAAATTACATTTTT
1 -CAAAAATTACATTTTT
372 TTCCACGAAC
Statistics
Matches: 170, Mismatches: 35, Indels: 28
0.73 0.15 0.12
Matches are distributed among these distances:
27 4 0.02
28 25 0.15
29 94 0.55
30 47 0.28
ACGTcount: A:0.36, C:0.22, G:0.03, T:0.39
Consensus pattern (29 bp):
CAAAAATTACATTTTTACCCCTAAATTTT
Found at i:195 original size:58 final size:59
Alignment explanation
Indices: 116--371 Score: 256
Period size: 58 Copynumber: 4.4 Consensus size: 59
106 TTTGACCCAC
* *
116 AATTCTCCAAAAATTATATTTTTACCCCTAAACTTTTCAAAATTCCA-TTTTAACATCA
1 AATTTTCCAAAAATTACATTTTTACCCCTAAACTTTTCAAAATTCCATTTTTAACATCA
* * * * * *
174 AATTTTCCAAAAATTACA-TTTTACACCAAAAATTTCCAAAATTCCATTTTTGACA-CTG
1 AATTTTCCAAAAATTACATTTTTACCCCTAAACTTTTCAAAATTCCATTTTTAACATC-A
* * *
232 AATTTTCCAAAAATTACATTTTTA-CCCTCGAAC-TTTCTAAAA-TCTCATTTTTAACCTCG
1 AATTTTCCAAAAATTACATTTTTACCCCT-AAACTTTTC-AAAATTC-CATTTTTAACATCA
* * * * * * **
291 AGTTTT-CAAAAAATACATTTTTGCCCCCAAACTTTTCAAAATTTCATTTTTGACCCCA
1 AATTTTCCAAAAATTACATTTTTACCCCTAAACTTTTCAAAATTCCATTTTTAACATCA
349 AATTTTCCAAAAATTACATTTTT
1 AATTTTCCAAAAATTACATTTTT
372 TTCCACGAAC
Statistics
Matches: 161, Mismatches: 26, Indels: 21
0.77 0.12 0.10
Matches are distributed among these distances:
57 25 0.16
58 86 0.53
59 49 0.30
60 1 0.01
ACGTcount: A:0.36, C:0.22, G:0.03, T:0.39
Consensus pattern (59 bp):
AATTTTCCAAAAATTACATTTTTACCCCTAAACTTTTCAAAATTCCATTTTTAACATCA
Found at i:409 original size:29 final size:29
Alignment explanation
Indices: 236--517 Score: 150
Period size: 29 Copynumber: 9.6 Consensus size: 29
226 ACACTGAATT
*
236 TTCCAAAAATTACATTTTTACCCTCGAAC
1 TTCCAAAAATTACATTTTTACCCCCGAAC
* * * * **
265 TTTCTAAAATCT-CATTTTTAACCTCGAGT
1 TTCCAAAAAT-TACATTTTTACCCCCGAAC
* * * *
294 TTTCAAAAAATACATTTTTGCCCCCAAAC
1 TTCCAAAAATTACATTTTTACCCCCGAAC
* * * *
323 TTTTC-AAAATTTCATTTTTGA-CCCCAAATT
1 -TTCCAAAAATTACATTTTT-ACCCCCGAA-C
** *
353 TTCCAAAAATTACATTTTTTTCCACGAAC
1 TTCCAAAAATTACATTTTTACCCCCGAAC
*
382 TTCCAAAAATTACAATTTTACCCCCGAA-
1 TTCCAAAAATTACATTTTTACCCCCGAAC
* * *
410 TGTCTAAAAA-TACCATTTTTGA-TCCCGAGCC
1 T-TCCAAAAATTA-CATTTTT-ACCCCCGA-AC
*
441 TTCCAAAAATTTCCA-TTTTACCCCCGAA-
1 TTCCAAAAA-TTACATTTTTACCCCCGAAC
* * * *
469 TATCTAAAAATT-CCTTTTTAAACCTCGAACC
1 T-TCCAAAAATTACATTTTT-ACCCCCGAA-C
500 TTCCAAAAATTACATTTT
1 TTCCAAAAATTACATTTT
518 ATTCCTGAAG
Statistics
Matches: 191, Mismatches: 41, Indels: 40
0.70 0.15 0.15
Matches are distributed among these distances:
27 1 0.01
28 11 0.06
29 120 0.63
30 49 0.26
31 9 0.05
32 1 0.01
ACGTcount: A:0.34, C:0.25, G:0.05, T:0.37
Consensus pattern (29 bp):
TTCCAAAAATTACATTTTTACCCCCGAAC
Found at i:460 original size:59 final size:59
Alignment explanation
Indices: 377--518 Score: 182
Period size: 59 Copynumber: 2.4 Consensus size: 59
367 TTTTTTTCCA
* * * * *
377 CGAA-CTTCCAAAAATTACAATTTTACCCCCGAATGTCTAAAAATACCATTTTTGATCC-
1 CGAACCTTCCAAAAATTTCCATTTTACCCCCGAATATCTAAAAATACC-TTTTTAAACCT
* *
435 CGAGCCTTCCAAAAATTTCCATTTTACCCCCGAATATCTAAAAATTCCTTTTTAAACCT
1 CGAACCTTCCAAAAATTTCCATTTTACCCCCGAATATCTAAAAATACCTTTTTAAACCT
*
494 CGAACCTTCCAAAAA-TTACATTTTA
1 CGAACCTTCCAAAAATTTCCATTTTA
519 TTCCTGAAGC
Statistics
Matches: 73, Mismatches: 9, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
58 20 0.27
59 53 0.73
ACGTcount: A:0.35, C:0.27, G:0.06, T:0.32
Consensus pattern (59 bp):
CGAACCTTCCAAAAATTTCCATTTTACCCCCGAATATCTAAAAATACCTTTTTAAACCT
Done.