Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009438.1 Kokia drynarioides strain JFW-HI SEQ_124145, 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, 984
Length: 1641
ACGTcount: A:0.40, C:0.13, G:0.18, T:0.29
Found at i:634 original size:216 final size:216
Alignment explanation
Indices: 210--1641 Score: 1492
Period size: 216 Copynumber: 6.6 Consensus size: 216
200 TAACAATTCA
* * * * * * *
210 AAAAAATGCTCTAAGGAATGGATCTTATTGAATACTTTAGGGAAT-CGAAGTTAAAAAATAACTC
1 AAAAATTGCTCGAAGGAATGGATCGTGTTGAATACTTTAAGG-ATCCGAAGTTATAAAATAACTA
* * * ** *
274 GTAAAAGTTTGGCAAGTTCAAAAGTTCGCCCAAG-ATTAA-AGAGAAACAATTTTCACGTAAATA
65 GTAAAAGTTTGACAAGTTCAGAAGTTCGTCCAAGAACAAAGAGAGAAACAATTCTCACGTAAATA
* *
337 AGTTTTTAATTTAAAGACCAAGACTTG-TTAGCAAAATGACAAACTATTTAGACCAAATGATGCG
130 AGTTTTTAATTCAAAGACCAAAACTTGTTTA-CAAAATGACAAACTATTTAGACCAAATGATGCG
* *
401 ATTTCCCGAGAATGGAATGTTTG
194 ATTTCCCGAGCATGGAATGTTCG
* * *
424 AAAAATTACTAGAAGGAATGGATCGTCTTGAATACTTTAAGGATCCGAAGTTATAAAATAACTAG
1 AAAAATTGCTCGAAGGAATGGATCGTGTTGAATACTTTAAGGATCCGAAGTTATAAAATAACTAG
* * * * * *
489 TAAAAGTTTGACAAGCTT-AGACGTTCATCTAAGAAGAAAGAGAGATACCATTCTCACGTAAATA
66 TAAAAGTTTGACAAG-TTCAGAAGTTCGTCCAAGAACAAAGAGAGAAACAATTCTCACGTAAATA
* * * *
553 AGTTTTGAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAACTAATTAGACAAAATGATGCGA
130 AGTTTTTAATTCAAAGACCAAAACTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGA
* *
618 TTTCCCAAGGATGGAATGTTC-
195 TTTCCCGAGCATGGAATGTTCG
* * * * *
639 AGAAAATTGCTCTAA-AAATTGGATCTTGTTGAATAC-TTAATGGAACCAAAGTTA-AAAATTAA
1 A-AAAATTGCTCGAAGGAA-TGGATCGTGTTGAATACTTTAA-GGATCCGAAGTTATAAAA-TAA
* * * * * *
701 CTTGTAAAAGTTTGACAAGTTCAAAAGTTCGTCCATGAACAAAGAGAGAAATAGTTCTCAAGT-A
62 CTAGTAAAAGTTTGACAAGTTCAGAAGTTCGTCCAAGAACAAAGAGAGAAACAATTCTCACGTAA
* ** * *
765 ATAAGTTTTTAACTCAAAGACTGAAACTTGTTTGCAAAAAGACAAACTATTTAGACCAAATGATG
127 ATAAGTTTTTAATTCAAAGACCAAAACTTGTTTACAAAATGACAAACTATTTAGACCAAATGATG
* * * *
830 TGATTTGCCGAGTATGAAATGTTCG
192 CGATTTCCCGAGCATGGAATGTTCG
* * * * * * *
855 GAATATTGCTC-AGAGGAATGGATC-TGTTGAATACTTTAAGGAACCCAATTTATAAAA-GATTC
1 AAAAATTGCTCGA-AGGAATGGATCGTGTTGAATACTTTAAGGATCCGAAGTTATAAAATAACT-
* * * * *
917 AGTAAAAGTTTGACAAGTTCGGATGTTCGTCCAACAAGAAAGAGAGAAATAATTCTCACGTAAAT
64 AGTAAAAGTTTGACAAGTTCAGAAGTTCGTCCAAGAACAAAGAGAGAAACAATTCTCACGTAAAT
* * * **
982 AAGTTTTTATTTCAAAGACCAAAACTTGTTTGCAAAATGACAAACTTTTTAGACCAAATGATGTA
129 AAGTTTTTAATTCAAAGACCAAAACTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCG
* *
1047 ATTTACCGAGCATGGAATGTTCA
194 ATTTCCCGAGCATGGAATGTTCG
* * * * * * * * **
1070 AAAAATTACTTGAAGAAATGGATCGTGTTGGAGT-CTTTAAGGATTCAAATTTATAAAAGATTTA
1 AAAAATTGCTCGAAGGAATGGATCGTGTT-GAATACTTTAAGGATCCGAAGTTATAAAATAACTA
* * * * * * * *
1134 GAAAAAGTTTGATAAGATCGGAAGTTCGTCCAAGAACAAAGTGGGAAACTATTCTCACGTCAATA
65 GTAAAAGTTTGACAAGTTCAGAAGTTCGTCCAAGAACAAAGAGAGAAACAATTCTCACGTAAATA
* ** **
1199 AGTTTTTAATTCAAAGACCAAAACATGTTCGCAACGTGACAAACTATTTAGACCAAATGATGCGA
130 AGTTTTTAATTCAAAGACCAAAACTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGA
* * *
1264 TTTCTCGAGCGTTGAATGTTC-
195 TTTCCCGAGCATGGAATGTTCG
* * * * * * *
1285 AGAAAATTGCTCGAAAGAATAGATCGTCTGGAATACTTTACGGATCCGAAGTTATAAAAGAACTT
1 A-AAAATTGCTCGAAGGAATGGATCGTGTTGAATACTTTAAGGATCCGAAGTTATAAAATAACTA
* * *
1350 GTAATAGTTTGACAAGTTCGGAAGTTCTTCCAAGAACAAAGAGAGAAACAATTCTCACGTAAATA
65 GTAAAAGTTTGACAAGTTCAGAAGTTCGTCCAAGAACAAAGAGAGAAACAATTCTCACGTAAATA
* ** * *
1415 AGTTTTTAATTCAAAGACAAAAACTTGTTTACAAAATGACAAGTTATTTAGACCAAATTATGTGA
130 AGTTTTTAATTCAAAGACCAAAACTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGA
*
1480 TTTCTCGAGCATGGAATGTTCG
195 TTTCCCGAGCATGGAATGTTCG
* * * * * * ** * *
1502 AAAAATTGCTCTAAGCAATGGATCTTGTTTAATAGTTTAGGGAAACGAAGTTAAAAAATAACTCG
1 AAAAATTGCTCGAAGGAATGGATCGTGTTGAATACTTTAAGGATCCGAAGTTATAAAATAACTAG
* * * * *
1567 AAAAAGTTTGGCAAGTTC-GAAAGTTCATCCAAAAACAAAGAGAGAAACAATTTTCACGTAAATA
66 TAAAAGTTTGACAAGTTCAG-AAGTTCGTCCAAGAACAAAGAGAGAAACAATTCTCACGTAAATA
1631 AGTTTTTAATT
130 AGTTTTTAATT
Statistics
Matches: 1012, Mismatches: 181, Indels: 48
0.82 0.15 0.04
Matches are distributed among these distances:
213 4 0.00
214 151 0.15
215 220 0.22
216 628 0.62
217 9 0.01
ACGTcount: A:0.40, C:0.13, G:0.18, T:0.29
Consensus pattern (216 bp):
AAAAATTGCTCGAAGGAATGGATCGTGTTGAATACTTTAAGGATCCGAAGTTATAAAATAACTAG
TAAAAGTTTGACAAGTTCAGAAGTTCGTCCAAGAACAAAGAGAGAAACAATTCTCACGTAAATAA
GTTTTTAATTCAAAGACCAAAACTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGAT
TTCCCGAGCATGGAATGTTCG
Done.