Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014262.1 Kokia drynarioides strain JFW-HI SEQ_129295, 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: 3757
ACGTcount: A:0.40, C:0.14, G:0.17, T:0.28
Found at i:708 original size:215 final size:217
Alignment explanation
Indices: 1--3742 Score: 3469
Period size: 216 Copynumber: 17.5 Consensus size: 217
* * * *
1 ATGCGATTTCCCAAGCATGAAATGTTTGAAAAATTGCTCGAAGGAATGGATCGTCATGAATACTT
1 ATGCGATTTCCCGAGCATGGAATGTTCGAAAAATTGCTCGAAGGAATGGATTGTCATGAATACTT
* * * * * * *
66 TATGGAACTG-AAGTTATAAAAGAACTCGTAAACGTTTGCCAAGTTCGAAAGTTCATCCAAGAAC
66 TAAGGAACTGAAAGTTATAGAAGAACTCGTAAAAGTTCGTCAAGTTCGGAAGTTCGTCCAAGAAC
* * * * * *
130 CAAGATAAAAACAACTCTCA--TAAATAAGTATTTCATTCAAAGACCAAAAGTAGTTTAGAAAAT
131 CAAGAGAGAAACAACTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAAT
*
193 GACAAAGTATTTAGACCAAATG
196 GACAAACTATTTAGACCAAATG
** * * * * *
215 ATGCGCCTTCCCGAGCATGGAATGTTCAAAAAACTGCTCTAAGGAATGGATTGTCCTTAATACTT
1 ATGCGATTTCCCGAGCATGGAATGTTCGAAAAATTGCTCGAAGGAATGGATTGTCATGAATACTT
* * * * * *
280 TAAGAAAC-CAAAGTTATTGAAGAACTCATAAAAGTTCGTCAAGTTCGGAAGTTCATCTAAGAAC
66 TAAGGAACTGAAAGTTATAGAAGAACTCGTAAAAGTTCGTCAAGTTCGGAAGTTCGTCCAAGAAC
* * * * *
344 CAAAAGAAAAACAACTCTCATGTAAATAGGTTTTTAATTTCAAAGACCAAAAGTTGTTTA-GAAA
131 CAAGAGAGAAACAACTCTCACGTAAATAAGTTTTTAA-TTCAAAGACCAAAAGTTGTTTACAAAA
*
408 TGACAAACTATTTAGACAAAATG
195 TGACAAACTATTTAGACCAAATG
* * * * * * * **
431 ATGCGATTTCTCGTGCATGGAATGTTTGGAAAATTGCTAGAAGGAATTGATCGTTTTGAATACTT
1 ATGCGATTTCCCGAGCATGGAATGTTCGAAAAATTGCTCGAAGGAATGGATTGTCATGAATACTT
* * * * ** * * *
496 TATGGAACTGAAGGTT-TAAAAGAACTTGCGAAACTTCATCAAGTTCAGAAGTTCGTCCAAGAAC
66 TAAGGAACTGAAAGTTATAGAAGAACTCGTAAAAGTTCGTCAAGTTCGGAAGTTCGTCCAAGAAC
* * * * * *
560 AAAGAGAGAAACAATTCTCATGTAAATAAGATTTTAATTTAAATACCAAAAGTTGTTTA-AAAAT
131 CAAGAGAGAAACAACTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAAT
*
624 GGCAAACTATTTAGACCAAATG
196 GACAAACTATTTAGACCAAATG
** * * *
646 ATATGATTTCCTGAGCATGCAATGTTCGAAAAATTGCTTGAAGGAATGGATTGTCATGAATACTT
1 ATGCGATTTCCCGAGCATGGAATGTTCGAAAAATTGCTCGAAGGAATGGATTGTCATGAATACTT
* * * * *
711 TAAGGAAC-GAAAGTGATAGATGAACTGGTAAAAGTT-TTCCAAGTTCAGAAGTTCGTCCAAGAA
66 TAAGGAACTGAAAGTTATAGAAGAACTCGTAAAAGTTCGT-CAAGTTCGGAAGTTCGTCCAAGAA
* * * ** *
774 CCAAGAGAGAAACACCTCTCATGTAAATAAGTTTTTCATTCAAAGACCAAAAGTCATTTAGAAAA
130 CCAAGAGAGAAACAACTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAA
*
839 TGAC--AGTATTTAGACCAAATG
195 TGACAAACTATTTAGACCAAATG
* * * * * * * *
860 ATGCGATTTCTCGAGCATGAAATGTTCAAAAAATTACTCTTAAGTAATGGATTATCTTGAATACT
1 ATGCGATTTCCCGAGCATGGAATGTTCGAAAAATTGCTC-GAAGGAATGGATTGTCATGAATACT
* * * *
925 TTAA-GAAATCG-AAGTTATAGAAGAACTC--ATAA------CAAGTTTGGAAGTTCGTCTAAGA
65 TTAAGGAACT-GAAAGTTATAGAAGAACTCGTAAAAGTTCGTCAAGTTCGGAAGTTCGTCCAAGA
* * * *
980 GCCAAGAGAGAAA-AACCTCTCACGTAAATAGGTTTTTAATTCAAAGACCAAAAGTTGTATACCA
129 ACCAAGAGAGAAACAA-CTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAA
*
1044 AATGACAAACTATGTATAGA--AAATA
193 AATGACAAACTAT-T-TAGACCAAATG
* *
1069 ATGTGATTTCCCAAGCATGGAATGTTC-AGAAAATTGCTCGAAGGAATGGATTGT-ATGAATACT
1 ATGCGATTTCCCGAGCATGGAATGTTCGA-AAAATTGCTCGAAGGAATGGATTGTCATGAATACT
* * * * * * ** * ***
1132 TTAAAGAA-TCAAAGTTATAGAAGAACTCATTAAAGTTTGTCAGGTTTAGAAGTTCATCCAATTT
65 TTAAGGAACTGAAAGTTATAGAAGAACTCGTAAAAGTTCGTCAAGTTCGGAAGTTCGTCCAAGAA
* * * * * *
1196 CCAAGAGAG--AGAATTCTCAAGTAAATAAGTTTTTCATTCAAGGACCAAAAGTTGTTTACCAAA
130 CCAAGAGAGAAACAACTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAA
** *
1259 TGACAAA-TAGTTTAGAAAAAATT
195 TGACAAACTA-TTTAGACCAAATG
* ** * * * *
1282 ATGCGATTTTCAAAGCATGAAATGTTCGAAAAATTGCTCGAAGGAATGGATCGCCATTAATACTT
1 ATGCGATTTCCCGAGCATGGAATGTTCGAAAAATTGCTCGAAGGAATGGATTGTCATGAATACTT
* * * * * * *
1347 TATGGAACTG-AAGTTATAAAAGAACTCGTAAACGTTTGCCAAGTTCGAAAGTTCATCCAAGAAC
66 TAAGGAACTGAAAGTTATAGAAGAACTCGTAAAAGTTCGTCAAGTTCGGAAGTTCGTCCAAGAAC
* * * * * * *
1411 CAAGATAAAAACAACTCTCA--TAAATAAGTATTTCATTCAAAGACCAAAACTAGTTTAGAAAAT
131 CAAGAGAGAAACAACTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAAT
*
1474 GACAAAATATTTAGACCAAATG
196 GACAAACTATTTAGACCAAATG
* ** * * * * * * *
1496 ATGTGCCTTCCTGAGCATGTAATGTTCAAAAAACTGCTCTAAGGAGTGGATTGTCTTGAATACTT
1 ATGCGATTTCCCGAGCATGGAATGTTCGAAAAATTGCTCGAAGGAATGGATTGTCATGAATACTT
* * * * * * * *
1561 TAAGAAAC-CAAAGTTATTGAAGAACTCATAAAAGTTCGTTAAGTTTGGAAGTTCATCTAAGAAC
66 TAAGGAACTGAAAGTTATAGAAGAACTCGTAAAAGTTCGTCAAGTTCGGAAGTTCGTCCAAGAAC
* * * * *
1625 CAATAGAAAAACAACTCTCACGTAAATAGGTTTTTAATTCAAGGACCAAAAGTTGTTTA-GAAAT
131 CAAGAGAGAAACAACTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAAT
**
1689 GACAAACTATTTAGAAAAAATG
196 GACAAACTATTTAGACCAAATG
** * * * * * ** *
1711 ATATGATTTCCCGTGCATGGAATGTTTGGAAAATTGCTAGAAGGAATTGATCATTATGAATACTT
1 ATGCGATTTCCCGAGCATGGAATGTTCGAAAAATTGCTCGAAGGAATGGATTGTCATGAATACTT
** * * * * * *
1776 TTTGGAACTGAAGGTT-TAAAAGAACTTGTGAAACTTCATCAAGTTCGGAAG-T--T------A-
66 TAAGGAACTGAAAGTTATAGAAGAACTCGTAAAAGTTCGTCAAGTTCGGAAGTTCGTCCAAGAAC
* * * * *
1830 -AA-AGAGAAACAATTCTTAAGTAAATAAGATTTTAATTTAAAGACCAAAAGTTGTTTACAAAAT
131 CAAGAGAGAAACAACTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAAT
*
1893 GGCAAACTATTTAGACCAAATG
196 GACAAACTATTTAGACCAAATG
* * * *
1915 ATGCGATTTCCCGAGCATGAAACGTTC-AGAAAATTGCTTGAAGGAATGGATTATCATGAATACT
1 ATGCGATTTCCCGAGCATGGAATGTTCGA-AAAATTGCTCGAAGGAATGGATTGTCATGAATACT
* * * * **
1979 TTAAGGAAC-GAAAGTTATTGATGAACTGGTAAAAGTT-TTACAAGTTCAAAAGTTCGTCCAAGA
65 TTAAGGAACTGAAAGTTATAGAAGAACTCGTAAAAGTTCGT-CAAGTTCGGAAGTTCGTCCAAGA
* * *
2042 ACCAGGAGAGAAACAACTCTCACGTAAATAAGTTTTTCATTCAAAGACCAAAA-TTCGTTTAGAA
129 ACCAAGAGAGAAACAACTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAAGTT-GTTTACAA
*
2106 AATGAC--AGTATTTAGACCAAATG
193 AATGACAAACTATTTAGACCAAATG
* * * *
2129 ATGCGATTTCTCGAGCATGGAATGTTCAAAAAATTGCTCTAAGGAATGGATTGTCTTGAATACTT
1 ATGCGATTTCCCGAGCATGGAATGTTCGAAAAATTGCTCGAAGGAATGGATTGTCATGAATACTT
* * * * * * * *
2194 GAA-GAAATCAAAGTTATAGAAGAACTCATAAAAGTAT-GTCTAGTTTGGAAGTTCGTCTAAGAG
66 TAAGGAACTGAAAGTTATAGAAGAACTCGTAAAAGT-TCGTCAAGTTCGGAAGTTCGTCCAAGAA
* * * * * *
2257 CCAAAAGAGAAACAACTCTCACATAAATAGGTTTTAAATTCAAGGACCAAAAGTTGTTTAGAAAA
130 CCAAGAGAGAAACAACTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAA
2322 TGACAAACTATTTAGA-CATAATG
195 TGACAAACTATTTAGACCA-AATG
* * * * * *
2345 ATGCGATTTCCCGTGCTTGGAATGTTGGGAAAATTCCTCGAAGGAATGTATCT-TCATGAATACT
1 ATGCGATTTCCCGAGCATGGAATGTTCGAAAAATTGCTCGAAGGAATGGAT-TGTCATGAATACT
* * * * *
2409 TTAAGGAACTG-AAGTTTTAAAAGAACTCGTAAAACTTCATCATGTTCGGAAGTTCGTCCAAG-A
65 TTAAGGAACTGAAAGTTATAGAAGAACTCGTAAAAGTTCGTCAAGTTCGGAAGTTCGTCCAAGAA
* * * * *
2472 CCAAAGAGAGAAAAAACTCTCACATAAATAACTTTTTAATTTATAA-AGCAAAAGTTGTTTACAA
130 CC-AAGAGAGAAACAACTCTCACGTAAATAAGTTTTTAATTCA-AAGACCAAAAGTTGTTTACAA
2536 AATGACAAACTATTTAGACCAAATG
193 AATGACAAACTATTTAGACCAAATG
* * * *
2561 ATGCGATTTCTCGAGCATGGAATGTTCAAAAAATTACTCGAAGGAGTGGATTGTCATGAATACTT
1 ATGCGATTTCCCGAGCATGGAATGTTCGAAAAATTGCTCGAAGGAATGGATTGTCATGAATACTT
* * * * * * * * * * * * *
2626 TAATGAA-TCAAAGTTACAAAACAACTGGTAAAATTTTGTGAAGTTAGGAAGTTTGTCCATGATC
66 TAAGGAACTGAAAGTTATAGAAGAACTCGTAAAAGTTCGTCAAGTTCGGAAGTTCGTCCAAGAAC
* * * *
2690 CAAGAGATAATA-AATTCTCACGTAAATAAGTTTTTAATT-AAATGACCAAAAGTTGTATACCAA
131 CAAGAGAGAA-ACAACTCTCACGTAAATAAGTTTTTAATTCAAA-GACCAAAAGTTGTTTACAAA
** *
2753 ATGACAAACTAAGTAGACAAAATG
194 ATGACAAACTATTTAGACCAAATG
* * * *
2777 ATGTGATTTCCCTAGCATGGAATGTTC-AGAAAATTGCTCGAAGGAATGGATCGTCATGAAAACT
1 ATGCGATTTCCCGAGCATGGAATGTTCGA-AAAATTGCTCGAAGGAATGGATTGTCATGAATACT
* * * * ** ** * *
2841 TTAAAGAA-TCG-AAGTTATAGAAGAAGTCCTCAAAGTTTATCAAGTTTAGAAGTTCATCCAATA
65 TTAAGGAACT-GAAAGTTATAGAAGAACTCGTAAAAGTTCGTCAAGTTCGGAAGTTCGTCCAAGA
* * * * * * * *
2904 TCCAAGAGAGAAACAATTCTCATGTAAATAACTTTTTCATTCAAAGCCCAAAAGTTGCTTACCAA
129 ACCAAGAGAGAAACAACTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAA
* **
2969 ATGAC-AAGTAGTTTAGAAAAAAAATG
194 ATGACAAACTA-TTTAG--ACCAAATG
* * ** * * * **
2995 GTGCGATTTCCCAAGCATTAAATTTTCGAAAAATTTCTCGAAGGAATGAATCATCATGAATACTT
1 ATGCGATTTCCCGAGCATGGAATGTTCGAAAAATTGCTCGAAGGAATGGATTGTCATGAATACTT
** * * * *
3060 TATTGAACTG-AAGTTATAAAATAACTCGTAAAAGCTT-GCCAAGTTCGGAAGTTCGTCCATGAA
66 TAAGGAACTGAAAGTTATAGAAGAACTCGTAAAAG-TTCGTCAAGTTCGGAAGTTCGTCCAAGAA
* * * * *
3123 CCAAGATAGAAACAACTCTCACGTAAGA-AAGTTTTTCATTCAGAGACCAAAAGTAGTTTAGAAA
130 CCAAGAGAGAAACAACTCTCACGTAA-ATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAA
*
3187 ATGACAAAATATTTAGACCAAATG
194 ATGACAAACTATTTAGACCAAATG
* * * * * * * * *
3211 ATGTGATTTCCCGAGTATGTAATCTTCAAAAAATTGCTCTAA-GAATGGGTTGTAATTAATACTT
1 ATGCGATTTCCCGAGCATGGAATGTTCGAAAAATTGCTCGAAGGAATGGATTGTCATGAATACTT
* * * * ** *
3275 TAAGAAACCG-AAGTTATTGAAGAACTCGTAAAAGTTCGTCAAGTTTGGAAGTTTATCTAAGAAC
66 TAAGGAACTGAAAGTTATAGAAGAACTCGTAAAAGTTCGTCAAGTTCGGAAGTTCGTCCAAGAAC
* * * * *
3339 CAAGAGAAAAAAAACTCTCACGTAAATAGGTTTTTAATTCAAAGACCAAAAGTTGTTTACCAAGT
131 CAAGAGAGAAACAACTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAAT
*
3404 GACAAACTATTTAGACAAAATG
196 GACAAACTATTTAGACCAAATG
* * * * * * *
3426 ATGCAATTTACTGTGCATGGAATGCTCGAAAAATTGCTCGAAGGAATGGATCGTCATCAATACTT
1 ATGCGATTTCCCGAGCATGGAATGTTCGAAAAATTGCTCGAAGGAATGGATTGTCATGAATACTT
* * * * * *
3491 TAAGGAACTG-AAGTTTTAAAAGAACTTC-CAAAACTTCATCAAGTTCGAAAGTTCGTCCAAGAA
66 TAAGGAACTGAAAGTTATAGAAGAAC-TCGTAAAAGTTCGTCAAGTTCGGAAGTTCGTCCAAGAA
* * * * * *
3554 CAAAGAGAGAAACAATTCTCACATAAATAAGATTTTAATTTAAATACCAAAAGTTGTTTACAAAA
130 CCAAGAGAGAAACAACTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAA
* *
3619 TGGCAAACTATTTAGACCAAATT
195 TGACAAACTATTTAGACCAAATG
* * * * * * *
3642 ATGTGATTTCCCAAGCATGCACTATTCGGAAAATTGCTTGAAGGAATGGATTGTCATGAATACTT
1 ATGCGATTTCCCGAGCATGGAATGTTCGAAAAATTGCTCGAAGGAATGGATTGTCATGAATACTT
* *
3707 TAAGGAAC-GAAAGTTATAGATGAACTGGTAAAAGTT
66 TAAGGAACTGAAAGTTATAGAAGAACTCGTAAAAGTT
3743 TTCCAAGTTC
Statistics
Matches: 2845, Mismatches: 588, Indels: 188
0.79 0.16 0.05
Matches are distributed among these distances:
203 54 0.02
204 108 0.04
205 1 0.00
206 2 0.00
207 109 0.04
208 16 0.01
209 42 0.01
210 1 0.00
211 8 0.00
212 4 0.00
213 110 0.04
214 595 0.21
215 553 0.19
216 1026 0.36
217 42 0.01
218 165 0.06
219 9 0.00
ACGTcount: A:0.40, C:0.14, G:0.17, T:0.28
Consensus pattern (217 bp):
ATGCGATTTCCCGAGCATGGAATGTTCGAAAAATTGCTCGAAGGAATGGATTGTCATGAATACTT
TAAGGAACTGAAAGTTATAGAAGAACTCGTAAAAGTTCGTCAAGTTCGGAAGTTCGTCCAAGAAC
CAAGAGAGAAACAACTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAAT
GACAAACTATTTAGACCAAATG
Done.