Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008132.1 Kokia drynarioides strain JFW-HI SEQ_122790, 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: 2068
ACGTcount: A:0.41, C:0.14, G:0.17, T:0.28
Found at i:390 original size:216 final size:216
Alignment explanation
Indices: 1--2048 Score: 2376
Period size: 216 Copynumber: 9.5 Consensus size: 216
* *
1 GTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTATACAAAATGACAAACTATTTAGACCAAAT
1 GTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTGCAAAATGACAAACTATTTAGACCAAAT
* * * * * *
66 GATGCGATTTCCCAAGGATAGCATGTTCGGAAAATTGCTCAAAGGAATGGATCTTGTTGAATACT
66 GATGCGATTTCCCGAGCATGGAATGTTCGGAAAATTGCTCAAAGGAATGGATCGTCTTGAATACT
* * * * * * * *
131 TTAGGGAACTAAAGTTAAAAAATAACTCGTAAAAGTTTGACAAGTTTGGAAGTTCGTCGAAGAAC
131 TTAAGGATCCAAAGTTATAAAAGAACTAGTAAAAGTTTGACAAGTTCGGAAGTTCGTCCAAGAAC
*
196 AGAGAGAGAAACAATTCTCAC
196 AAAGAGAGAAACAATTCTCAC
** *
217 GTAAATAAGTTTTTAATTCAACA-ACCAAAACTTGTTTGCAAAACAACAAACTATTTAGTCCAAA
1 GTAAATAAGTTTTTAATTCAA-AGACCAAAACTTGTTTGCAAAATGACAAACTATTTAGACCAAA
** ** * * *
281 TGATATGATTTGTCGAGCATGGAATATTCGGAAAATTACTTAAAGGAATGGATCGTCTTGAATAC
65 TGATGCGATTTCCCGAGCATGGAATGTTCGGAAAATTGCTCAAAGGAATGGATCGTCTTGAATAC
* *
346 TTTAAGGATCCAAAGTTATAAAAGAACTAGTATAAGTCTGACAAGTTCGGAAGTTCGTCCAAGAA
130 TTTAAGGATCCAAAGTTATAAAAGAACTAGTAAAAGTTTGACAAGTTCGGAAGTTCGTCCAAGAA
* *
411 CAAAGACAAAAACAATTCTCAC
195 CAAAGAGAGAAACAATTCTCAC
* * * *
433 GTAAATAAGTTTTGAATTCAAAGACCAAAACTTTTTTACAAAATGACAAACTATTTAGATCAAAT
1 GTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTGCAAAATGACAAACTATTTAGACCAAAT
* * * * * * * *
498 GATCCGACTTCCCAAGGATGGAATGTTCGGAAAATAGCTCTAAA-AAATGGATCATGTTGAATAC
66 GATGCGATTTCCCGAGCATGGAATGTTCGGAAAATTGCTC-AAAGGAATGGATCGTCTTGAATAC
* * ** * * * * *
562 TTTAGGGAACTGAAGTTAAAAAATAACTCGTAAAAGTTTGACAAGTTCGAAAGTTTGTCCAAGAA
130 TTTAAGGATCCAAAGTTATAAAAGAACTAGTAAAAGTTTGACAAGTTCGGAAGTTCGTCCAAGAA
* *
627 CAATGACTAG-AACAATTCTCAC
195 CAAAGA-GAGAAACAATTCTCAC
* * *
649 AT-AATAAGTTTTTAATTTAAAGACCAAAACTTGTTTGCAAAATGACAAATTATTTAGACCAAAT
1 GTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTGCAAAATGACAAACTATTTAGACCAAAT
* * * * * * *
713 GATGCGATTTCCCAAGTACGGAATGTTCAGAAAATTGCTCGGAA-GAATAGATCG--TTGAATAA
66 GATGCGATTTCCCGAGCATGGAATGTTCGGAAAATTGCTC-AAAGGAATGGATCGTCTTGAATAC
* * *
775 TTTAAGGATCAAAAGTTATAAAAGAACTAGTAAAAGTTTGACAGGTTTGGAAGTTCGTCCAAGAA
130 TTTAAGGATCCAAAGTTATAAAAGAACTAGTAAAAGTTTGACAAGTTCGGAAGTTCGTCCAAGAA
*
840 CAAAGAGAGAAATAATTCTCAC
195 CAAAGAGAGAAACAATTCTCAC
* *
862 GTAAATAAGTTTTAAATTCGAAGACCAAAACTTGTTTGCAAAATGACAAACTA--T-G-CCAAAT
1 GTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTGCAAAATGACAAACTATTTAGACCAAAT
* * * * * * * * *
923 GATGCAATTTGCAGAGCATGAAATATTCAGAAAATTGCTCGAAGGAATGGATCGTCTTTAATATT
66 GATGCGATTTCCCGAGCATGGAATGTTCGGAAAATTGCTCAAAGGAATGGATCGTCTTGAATACT
* * * *
988 TTAAGGAAT-CGAAGTTATAAAAGAACTAGTAAAAGTTTGACAAATTCGAAAGTTCGTCCATGAA
131 TTAAGG-ATCCAAAGTTATAAAAGAACTAGTAAAAGTTTGACAAGTTCGGAAGTTCGTCCAAGAA
1052 CAAAGAGAGAAACAATTCTCAC
195 CAAAGAGAGAAACAATTCTCAC
* * * * *
1074 GTAAAT-ATTTTTTAATTCAAAGACCAAAACTGGTATACAAAATGACAAACTATTTATACCAAAT
1 GTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTGCAAAATGACAAACTATTTAGACCAAAT
* * * *
1138 GATGTGATTTCCCAAGGATGGAATGTTCGGAAAATTGCTCAAAGGAATGGATCTTCTTGAATACT
66 GATGCGATTTCCCGAGCATGGAATGTTCGGAAAATTGCTCAAAGGAATGGATCGTCTTGAATACT
* * ** * * * * * * *
1203 TTAGGGAACTGAAGCTAAAAAATAACTCGTAAAAGTTTTACAAGTTTGGAAGTTCGTCCAAGAAT
131 TTAAGGATCCAAAGTTATAAAAGAACTAGTAAAAGTTTGACAAGTTCGGAAGTTCGTCCAAGAAC
* *
1268 AAAGGGAGAAACAATTGTCAC
196 AAAGAGAGAAACAATTCTCAC
* **
1289 GTAAATAAGTTTTTAATTCAATGACCAAAACTTGTTTGCAAAACAACAAACTATTTAGACCAAAT
1 GTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTGCAAAATGACAAACTATTTAGACCAAAT
* * * ** * * *
1354 GATACGATTTGCTGAGCATGGAATAATCGAAAAATTGCTGAAAGGAATGGTTCGTCTTGAATACT
66 GATGCGATTTCCCGAGCATGGAATGTTCGGAAAATTGCTCAAAGGAATGGATCGTCTTGAATACT
* * *
1419 TTAAGGATCCGAAA-TTATAAAAAAACTAGTATAAGTTTGACAAGTTCGAAAGTTCGTCCAAGAA
131 TTAAGGATCC-AAAGTTATAAAAGAACTAGTAAAAGTTTGACAAGTTCGGAAGTTCGTCCAAGAA
* *
1483 TAAAGAGAGAAACAATTCTCAT
195 CAAAGAGAGAAACAATTCTCAC
** * * * * *
1505 GTAAATAAAATTTTAAGTAAAAGACCAAAACTTGTTTACATAATGACAAACTATTTAAACCAAAT
1 GTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTGCAAAATGACAAACTATTTAGACCAAAT
* * * * *
1570 GATGTGATTTCCCGAGCATTGG-ATGTTCGGAAAATTACTCTAAGGAAT-GAGTCCTGTTGAATA
66 GATGCGATTTCCCGAGCA-TGGAATGTTCGGAAAATTGCTCAAAGGAATGGA-TCGTCTTGAATA
* * * * * * *
1633 CTTTAGGGAACCAAAGTTAAAAAATAACCCT-GTAAAAGTTTGACAATTTCGAAAGTTCATCCAA
129 CTTTAAGGATCCAAAGTTATAAAAGAA--CTAGTAAAAGTTTGACAAGTTCGGAAGTTCGTCCAA
* *
1697 GAACAAAAAGAGAAACAATTTTCAC
192 GAACAAAGAGAGAAACAATTCTCAC
* * *
1722 GTAAATAAGTTTTTAATTCTAAGACCAAAACTTGTTTGCAAAATGATAAACAATTTAGACCAAAT
1 GTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTGCAAAATGACAAACTATTTAGACCAAAT
** * * * *
1787 GATGCGATTTCAAGATCATGGAATGTTCGAAAAATTGCTCGAAA-GAATTGATCGGCTTGAATAC
66 GATGCGATTTCCCGAGCATGGAATGTTCGGAAAATTGCTC-AAAGGAATGGATCGTCTTGAATAC
* * * * *
1851 TTTGAGGATCCGAAGTTATCAAAGAACTAGTAAAAGTTTGACAAGCTCGGAAGTTTGTCCAAGAA
130 TTTAAGGATCCAAAGTTATAAAAGAACTAGTAAAAGTTTGACAAGTTCGGAAGTTCGTCCAAGAA
1916 CAAAGAGAGAAACAATTCTCAC
195 CAAAGAGAGAAACAATTCTCAC
* *** *
1938 GTAAATAAGTTTTTAATTCAAAGATCAAAACTTGTGCACAAAATGAC--A-TATTTAGATCAAAT
1 GTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTGCAAAATGACAAACTATTTAGACCAAAT
*
2000 GATGCGATTTCCCGAGCATGGAATGTTC-GAAAATTTGCTCTAAGGAATG
66 GATGCGATTTCCCGAGCATGGAATGTTCGGAAAA-TTGCTCAAAGGAATG
2049 TATTTTGTTG
Statistics
Matches: 1529, Mismatches: 275, Indels: 59
0.82 0.15 0.03
Matches are distributed among these distances:
209 3 0.00
210 47 0.03
211 41 0.03
212 97 0.06
213 128 0.08
214 48 0.03
215 239 0.16
216 741 0.48
217 179 0.12
218 6 0.00
ACGTcount: A:0.41, C:0.14, G:0.17, T:0.28
Consensus pattern (216 bp):
GTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTGCAAAATGACAAACTATTTAGACCAAAT
GATGCGATTTCCCGAGCATGGAATGTTCGGAAAATTGCTCAAAGGAATGGATCGTCTTGAATACT
TTAAGGATCCAAAGTTATAAAAGAACTAGTAAAAGTTTGACAAGTTCGGAAGTTCGTCCAAGAAC
AAAGAGAGAAACAATTCTCAC
Done.