Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009864.1 Kokia drynarioides strain JFW-HI SEQ_124598, 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, 706
Length: 1177
ACGTcount: A:0.37, C:0.15, G:0.16, T:0.26
Warning! 73 characters in sequence are not A, C, G, or T
Found at i:716 original size:216 final size:214
Alignment explanation
Indices: 332--1177 Score: 957
Period size: 216 Copynumber: 3.9 Consensus size: 214
322 NNNNNNNNNN
*
332 ATGTAAAAGAGTTTTTAATTCAAAGATCAAAACTTGTTTGCAAAATTTA-AAACTATTTAGACCA
1 ATGTAAAA-AGTTTTTAATTCAAAGATCAAAACTTGTTTGCAAAA-TAACAAACTATTTAGACCA
* * * * *
396 AATGATGCAATCTTCCTCGCTTGGAATGTTCGGAAAATTACTCGAAGGAATGGATCGCCTTGAAT
64 AATGATGCGAT-TTCCTCGCATGAAATGTTCAGAAAAATACTCGAAGGAATGGATCGCCTTGAAT
* * * * * * *
461 ATTTTAAGGAACCGGATTTAAAAAAGAACTCA-AAAAAGTTCGACAAGTTCGGAAGGTCGTCCAA
128 ACTTTAAGGAACTGAAGTTATAAAAGAACTCATTAAAAGTTCGACAAGTT-GGAAGGTAGTCCAA
525 GAACCAAGAGAGACACAATTCTC
192 GAACCAAGAGAGACACAATTCTC
*
548 ATGTAAATAAGTTTTTAATTCAAAGATCAAAACTTGTTTGCAAAATAACAAACTTTTTAGACCAA
1 ATGTAAA-AAGTTTTTAATTCAAAGATCAAAACTTGTTTGCAAAATAACAAACTATTTAGACCAA
* *
613 ATGATGCGATTTCCCTCGCATGAAATGTTCAGAAAAATGCTCGAAGGATTGGATCGCCTTGAATA
65 ATGATGCGATTT-CCTCGCATGAAATGTTCAGAAAAATACTCGAAGGAATGGATCGCCTTGAATA
* * *
678 CTTTAAGGAACTGAAGTTATAAAGGAAC-CATTAAAAGTTCGACAAGTTTGCAGGTTAGTCCAAG
129 CTTTAAGGAACTGAAGTTATAAAAGAACTCATTAAAAGTTCGACAAGTTGGAAGG-TAGTCCAAG
*
742 AACCAAGAGAGACACAGTTCTC
193 AACCAAGAGAGACACAATTCTC
* * *
764 ATGTAAGAAAGTTTTTAATTCAAAGATCAAAACTAGTTTACAAAATGACAAACTATTTAGACCAA
1 ATGTAA-AAAGTTTTTAATTCAAAGATCAAAACTTGTTTGCAAAATAACAAACTATTTAGACCAA
* * * * * * ** *
829 ATGATACGATTTCTTGAGAATGGATTGTTC-GAAAAATTACAAGAAGGAATGGATCGTCTTGAAT
65 ATGATGCGATTTCCT-CGCATGAAATGTTCAGAAAAA-TACTCGAAGGAATGGATCGCCTTGAAT
* * * **********************
893 ACTTTAATGAACTGAAGCTATAAAAGAACTC-GTAAANNNNNNNNNNNNNNNNNNNNNNNTCCAA
128 ACTTTAAGGAACTGAAGTTATAAAAGAACTCATTAAA-AGTTCGACAAGTTGGAAGGTAGTCCAA
957 GAACCAAGAGAGACACAATTCTC
192 GAACCAAGAGAGACACAATTCTC
*
980 ATGTAAATAAGTTTTTAATTCAAAGATCAAAACTTGTTTGCAAAATAACAAACTTTTTAGACCAA
1 ATGTAAA-AAGTTTTTAATTCAAAGATCAAAACTTGTTTGCAAAATAACAAACTATTTAGACCAA
* * *
1045 ACGATGCGATTTCCCTCGCATGAAATGTTCAGAAAATTGCTCGAAGGAATGGATCGCCTTGAATA
65 ATGATGCGATTT-CCTCGCATGAAATGTTCAGAAAAATACTCGAAGGAATGGATCGCCTTGAATA
* *
1110 CTTTAAGGAACTGAAGTTATAAAAGAAC-CATTAAAAGTTCGACAAGTTTGCAAGTTAGTCCAAG
129 CTTTAAGGAACTGAAGTTATAAAAGAACTCATTAAAAGTTCGACAAG-TTGGAAGGTAGTCCAAG
1174 AACC
193 AACC
Statistics
Matches: 512, Mismatches: 103, Indels: 30
0.79 0.16 0.05
Matches are distributed among these distances:
215 20 0.04
216 482 0.94
217 10 0.02
ACGTcount: A:0.39, C:0.15, G:0.17, T:0.27
Consensus pattern (214 bp):
ATGTAAAAAGTTTTTAATTCAAAGATCAAAACTTGTTTGCAAAATAACAAACTATTTAGACCAAA
TGATGCGATTTCCTCGCATGAAATGTTCAGAAAAATACTCGAAGGAATGGATCGCCTTGAATACT
TTAAGGAACTGAAGTTATAAAAGAACTCATTAAAAGTTCGACAAGTTGGAAGGTAGTCCAAGAAC
CAAGAGAGACACAATTCTC
Done.