Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013961.1 Kokia drynarioides strain JFW-HI SEQ_128992, 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, 841
Length: 1403
ACGTcount: A:0.38, C:0.15, G:0.18, T:0.29
Found at i:437 original size:216 final size:217
Alignment explanation
Indices: 1--1403 Score: 1410
Period size: 216 Copynumber: 6.5 Consensus size: 217
** * ** * * * * *
1 ATGATGC-GATTTCTTGAGCAAGGAATGTTTGGAAAACTGCTCGACGTAATGGATCGCCTTGAAT
1 ATGATGCAGATTTCCCGAGCATGGAATGTTCAGAAAAATGCTCTAAGGAATGGATCGTCTTGAAT
* * * * * * *
65 GCTTTAAGGAACAGAAGGTACAAAAGAAGTCGTAAAAGTTTGACACGTTCGAAAGTTCTTCCAAG
66 ACTTTAAGGAACCGAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCGAAAGTTCGTCCAAG
* * ** * **
130 AAGAAATAGAGAAACAATTCTCACACAAATAAG-TTTTAATTCCAAGACCAAAACTTGTTTAGGA
131 AACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTACAA
* *
194 AATGATATACTATTTAGACCAA
196 AATGACAAACTATTTAGACCAA
* *
216 ATGATGCAG-TTTCCCGAGCATGGAATGTTCAGAAAAATGCTCAAAGGAAT-GAGTCATCTTGAA
1 ATGATGCAGATTTCCCGAGCATGGAATGTTCAGAAAAATGCTCTAAGGAATGGA-TCGTCTTGAA
*** * * * * * ** *
279 TACTTTAAGGAAGTTAAGCTATAAAAGATCTCCTCAAAGTTGGACAAGTTCGGGAGTTCGTCCAT
65 TACTTTAAGGAACCGAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCGAAAGTTCGTCCAA
* * * * * * *
344 GGACCAAGAGTGATACAATTCTCTCGTAAATAGGTTTTTAATTCAAAGACTAAAACTTGTTTACA
130 GAACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTACA
409 AAATGACAAACTATTTAGACCAA
195 AAATGACAAACTATTTAGACCAA
* * * *
432 ATGATGC-GATTTCTCGAGCATGGAATGTTCAGAAAATTGCTCTAAGGAATGGATCTTGTTGAAT
1 ATGATGCAGATTTCCCGAGCATGGAATGTTCAGAAAAATGCTCTAAGGAATGGATCGTCTTGAAT
* * * * * *
496 ACTTTAGGGAACCGAAGTTAAAAAATAACTCGTAAAAGTTTGACAAGTTCAAAAGTTTGTACAA-
66 ACTTTAAGGAACCGAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCGAAAGTTCGTCCAAG
* * * * * *
560 AGACAAAGTGAGAAACAATTCTCACCTAAATAATTTTTTAATTCAAAGAGCAAAACTTTTTTGCA
131 A-ACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTACA
625 AAATGACAAACTATTTAGACCAA
195 AAATGACAAACTATTTAGACCAA
* * * *
648 ATGATG-TGATTTCCCGAGCAAGGAATGTT-TGAAAAATTGCTCGTAA-GAATGGATCGTCTCGA
1 ATGATGCAGATTTCCCGAGCATGGAATGTTCAGAAAAA-TGCTC-TAAGGAATGGATCGTCTTGA
* * * * * * *
710 ATACTTTGAGGATCCGAAGTTATCAACGAACTAGTAAAAGTTTGACAAGCTCGTAAGTTCGTCCA
64 ATACTTTAAGGAACCGAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCGAAAGTTCGTCCA
* *
775 AGAACAAAGAGAGAAATAATTCTCACGTAAATAAGTTTTTAATTCAAAGATCAAAACTTGTTTAC
129 AGAACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTAC
*
840 AAAATGAC--A-TATTTAGATCAA
194 AAAATGACAAACTATTTAGACCAA
* * * * ** *
861 ATGATGCA-ATTTTCCGAGCATGGAATGTTCA-AAAAATTACTTTATGGAATGGATTTTGTTGAA
1 ATGATGCAGATTTCCCGAGCATGGAATGTTCAGAAAAA-TGCTCTAAGGAATGGATCGTCTTGAA
* * * * * * * * *
924 TGCTTTAGGGAACCAAAGTTAAAAAATAACTCGTAAAAGTTTGACCAGTTTGGAAGTTTGTCCAA
65 TACTTTAAGGAACCGAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCGAAAGTTCGTCCAA
*
989 GAAGAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAACA-ACCAAAACTTGTTTAC
130 GAACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAA-AGACCAAAACTTGTTTAC
* * *
1053 AAAATAACAATCTATTTTGACCAA
194 AAAATGACAAACTATTTAGACCAA
*** * * ** * * *
1077 ATGATGC-GATTTCTTTTTTATCAAGGAATGTTTGGAAAACTGCTCGAAGGAATGGATCGCCTTG
1 ATGATGCAGATTTC---CCGAGCATGGAATGTTCAGAAAAATGCTCTAAGGAATGGATCGTCTTG
* * * * *
1141 AATGCTTTAAGGAACAGAAGTTATAAAAGAAGTCGTAAAAGTTTGACACGTTCGAAAGTTCTTCC
63 AATACTTTAAGGAACCGAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCGAAAGTTCGTCC
* ** *
1206 AAGAAGAAAGAGAGAAACAATTCTCACACAAATAAGTTTTTAATTCCAAGACCAAAACTTGTTTA
128 AAGAACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTA
** * *
1271 GGAAATGACATACTATATAGACCAA
193 CAAAATGACAAACTATTTAGACCAA
* *
1296 ATGATGCAG-TTTCCCGAG-AT----TGTTCAGAAAAATGCTCAAAGGAATGGGTCGTCTTGAAT
1 ATGATGCAGATTTCCCGAGCATGGAATGTTCAGAAAAATGCTCTAAGGAATGGATCGTCTTGAAT
*** * * * * *
1355 ACTTTAAGGAAGTTAAGCTATAAAAGATCTCCTTAAAGTTGGACAAGTT
66 ACTTTAAGGAACCGAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTT
Statistics
Matches: 964, Mismatches: 200, Indels: 52
0.79 0.16 0.04
Matches are distributed among these distances:
211 71 0.07
212 2 0.00
213 174 0.18
214 4 0.00
215 127 0.13
216 405 0.42
217 6 0.01
218 1 0.00
219 169 0.18
220 5 0.01
ACGTcount: A:0.38, C:0.15, G:0.18, T:0.29
Consensus pattern (217 bp):
ATGATGCAGATTTCCCGAGCATGGAATGTTCAGAAAAATGCTCTAAGGAATGGATCGTCTTGAAT
ACTTTAAGGAACCGAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCGAAAGTTCGTCCAAG
AACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTACAA
AATGACAAACTATTTAGACCAA
Done.