Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01000069.1 Kokia drynarioides strain JFW-HI SEQ_110621, 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, 623
Length: 1039
ACGTcount: A:0.40, C:0.15, G:0.17, T:0.28
Found at i:377 original size:215 final size:214
Alignment explanation
Indices: 1--986 Score: 1241
Period size: 215 Copynumber: 4.6 Consensus size: 214
*
1 AACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAACCTGTTTACAA
1 AACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTACAA
* * *
66 AATGACAAACTATTTAGACTAAATGATTCGATTTCCCGAGCATGGAATGTTCA-GAAATTTGCTC
66 AATGACAAACTATTTAGACCAAATGATGCGATTTCCC-AGCATGGAATGTT-AGGAAAATTGCTC
* * *
130 TAAGGAATGAATCTTGTTGAATTCTTTAGGGAACCAAAGTTAAAAATAACTCGTAAAAGTTTGAC
129 TAAGGAATGGATCTTGTTAAATACTTTAGGGAACCAAAGTTAAAAATAACTCGTAAAAGTTTGAC
* *
195 AAGTTTGAAAGTTCGTCCAAG
194 AAGTTCGAAAGTTCCTCCAAG
* **
216 AACAAAGAGAGGAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTCGCAA
1 AACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTACAA
* * *
281 AATGACGAACTATTTAGACCAAATGATGCGATTTCCCACGCGTGGAATGTTAGGAAAATTGCTTT
66 AATGACAAACTATTTAGACCAAATGATGCGATTTCCCA-GCATGGAATGTTAGGAAAATTGCTCT
* * * ** *
346 AAGGATTGGATCTCGTTAAATACTGTAGGGAACCGTATTTAAAATATAACTCGTAAAAGTTT-AC
130 AAGGAATGGATCTTGTTAAATACTTTAGGGAACCAAAGTTAAAA-ATAACTCGTAAAAGTTTGA-
* *
410 CAAGTTCGGAAGTTCCTCTAAG
193 CAAGTTCGAAAGTTCCTCCAAG
* * * *
432 AACAAAGAGAGAAATAATTCTCACGTCAATAAGTTTTTAACTCAAAGAACAAAACTTGTTTACAA
1 AACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTACAA
* * * * *
497 AATGAC--ACTATTTAGATCAAATGATGCGATTTCCTGAGCATGGAGTGTTCGGAAAATAGCTCT
66 AATGACAAACTATTTAGACCAAATGATGCGATTTCC-CAGCATGGAATGTTAGGAAAATTGCTCT
* *
560 AAGGAATGGATCTTGTTGAAA-ACTTTAGGGAGCCGAAGTTAAAAATAACTCGTAAAAGTTTTG-
130 AAGGAATGGATCTTGTT-AAATACTTTAGGGAACCAAAGTTAAAAATAACTCGTAAAAG-TTTGA
*
623 CAA-TTCGAAAGTTCGTCCAAG
193 CAAGTTCGAAAGTTCCTCCAAG
* *
644 AACAAAGAGAGAAACAATTCTGACGTAAATAAGTTTTTAATTCAAAGACCAAAATTTGTTTACAA
1 AACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTACAA
** * *
709 AATGACAAACTATTTAGACCAAATGATTTGATTTCCCAAGCATGGAATGTT-CGAAAATTTGCTG
66 AATGACAAACTATTTAGACCAAATGATGCGATTTCCC-AGCATGGAATGTTAGGAAAA-TTGCTC
* * * * * *
773 TAAGGAATGGATCTTGTTGAATACTTTACGGAGCCAAAGTTAAAAAATAGCTCTTAAAATTTTGA
129 TAAGGAATGGATCTTGTTAAATACTTTAGGGAACCAAAGTT-AAAAATAACTCGTAAAAGTTTGA
* * *
838 CAAGTTTGAAAGTTCCTCTAAAA
193 CAAGTTCGAAAGTTCCTC-CAAG
* * * * *
861 AACAAAGAGAGAAACAATTCTCACGTAAATAAGGTTTTAATACAAAGTCCAAAGCTTGTTTGCAA
1 AACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTACAA
* * ** * * *
926 AATGATAAACAATACAGACCAAATGATGCAATTTCCCAAGCATGGAATGTTCGAAAAATTG
66 AATGACAAACTATTTAGACCAAATGATGCGATTTCCC-AGCATGGAATGTTAGGAAAATTG
987 TTCGGAAGAA
Statistics
Matches: 667, Mismatches: 86, Indels: 34
0.85 0.11 0.04
Matches are distributed among these distances:
212 80 0.12
213 24 0.04
214 167 0.25
215 174 0.26
216 111 0.17
217 107 0.16
218 4 0.01
ACGTcount: A:0.40, C:0.15, G:0.17, T:0.28
Consensus pattern (214 bp):
AACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTACAA
AATGACAAACTATTTAGACCAAATGATGCGATTTCCCAGCATGGAATGTTAGGAAAATTGCTCTA
AGGAATGGATCTTGTTAAATACTTTAGGGAACCAAAGTTAAAAATAACTCGTAAAAGTTTGACAA
GTTCGAAAGTTCCTCCAAG
Found at i:853 original size:428 final size:428
Alignment explanation
Indices: 1--984 Score: 1321
Period size: 428 Copynumber: 2.3 Consensus size: 428
*
1 AACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAACCTGTTTACAA
1 AACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAA-TCAAAGACCAAAACTTGTTTACAA
* * * *
66 AATGACAAACTATTTAGACTAAATGATTCGATTTCCCGAGCATGGAATGTTCAGAAATTTGCTCT
65 AATGAC--ACTATTTAGAC-AAATGATGCGATTTCCCGAGCATGGAATGTTCGGAAAATAGCTCT
**
131 AAGGAATGAATCTTGTTGAATTCTTTAGGGAACCAAAGTTAAAAATAACTCGTAAAAGTTTGACA
127 AAGGAATGAATCTTGTTGAAAACTTTAGGGAACCAAAGTTAAAAATAACTCGTAAAAGTTTGACA
* *
196 AGTTTGAAAGTTCGTCCAAGAACAAAGAGAGGAACAATTCTCACGTAAATAAGTTTTTAATTCAA
192 AGTTCGAAAGTTCGTCCAAGAACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAA
* * * *
261 AGACCAAAACTTGTTCGCAAAATGACGAACTATTTAGACCAAATGATGCGATTTCCCACGCGTGG
257 AGACCAAAACTTGTTCACAAAATGACAAACTATTTAGACCAAATGATGCGATTTCCCAAGCATGG
* * * * ** * *
326 AATGTTAGGAAAATTGCTTTAAGGATTGGATCTCGTTAAATACTGTAGGGAACCGTATTTAAAAT
322 AATGTTACGAAAATTGCTGTAAGGAATGGATCTCGTTAAATACTGTACGGAACCAAAGTTAAAAA
* *
391 ATAACTCGTAAAAGTTTACCAAGTTCGGAAGTTCCTCT-AAG
387 ATAACTCGTAAAAGTTTACCAAGTTCGAAAGTTCCTCTAAAA
* * *
432 AACAAAGAGAGAAATAATTCTCACGTCAATAAGTTTTTAACTCAAAGAACAAAACTTGTTTACAA
1 AACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAA-TCAAAGACCAAAACTTGTTTACAA
* *
497 AATGACACTATTTAGATCAAATGATGCGATTTCCTGAGCATGGAGTGTTCGGAAAATAGCTCTAA
65 AATGACACTATTTAGA-CAAATGATGCGATTTCCCGAGCATGGAATGTTCGGAAAATAGCTCTAA
* * *
562 GGAATGGATCTTGTTGAAAACTTTAGGGAGCCGAAGTTAAAAATAACTCGTAAAAGTTTTG-CAA
129 GGAATGAATCTTGTTGAAAACTTTAGGGAACCAAAGTTAAAAATAACTCGTAAAAG-TTTGACAA
*
626 -TTCGAAAGTTCGTCCAAGAACAAAGAGAGAAACAATTCTGACGTAAATAAGTTTTTAATTCAAA
193 GTTCGAAAGTTCGTCCAAGAACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAA
* * **
690 GACCAAAATTTGTTTACAAAATGACAAACTATTTAGACCAAATGATTTGATTTCCCAAGCATGGA
258 GACCAAAACTTGTTCACAAAATGACAAACTATTTAGACCAAATGATGCGATTTCCCAAGCATGGA
* * * *
755 ATGTT-CGAAAATTTGCTGTAAGGAATGGATCTTGTTGAATACTTTACGGAGCCAAAGTTAAAAA
323 ATGTTACGAAAA-TTGCTGTAAGGAATGGATCTCGTTAAATACTGTACGGAACCAAAGTTAAAAA
* * * *
819 ATAGCTCTTAAAATTTTGA-CAAGTTTGAAAGTTCCTCTAAAA
387 ATAACTCGTAAAAGTTT-ACCAAGTTCGAAAGTTCCTCTAAAA
* * * *
861 AACAAAGAGAGAAACAATTCTCACGTAAATAAGGTTTTAATACAAAGTCCAAAGCTTGTTTGCAA
1 AACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAAT-CAAAGACCAAAACTTGTTTACAA
* * ** * * *
926 AATGATAAACAATACAGACCAAATGATGCAATTTCCCAAGCATGGAATGTTCGAAAAAT
65 AATG--ACACTATTTAGA-CAAATGATGCGATTTCCCGAGCATGGAATGTTCGGAAAAT
985 TGTTCGGAAG
Statistics
Matches: 483, Mismatches: 62, Indels: 16
0.86 0.11 0.03
Matches are distributed among these distances:
427 5 0.01
428 196 0.41
429 168 0.35
430 5 0.01
431 109 0.23
ACGTcount: A:0.40, C:0.15, G:0.17, T:0.28
Consensus pattern (428 bp):
AACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATCAAAGACCAAAACTTGTTTACAAA
ATGACACTATTTAGACAAATGATGCGATTTCCCGAGCATGGAATGTTCGGAAAATAGCTCTAAGG
AATGAATCTTGTTGAAAACTTTAGGGAACCAAAGTTAAAAATAACTCGTAAAAGTTTGACAAGTT
CGAAAGTTCGTCCAAGAACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGAC
CAAAACTTGTTCACAAAATGACAAACTATTTAGACCAAATGATGCGATTTCCCAAGCATGGAATG
TTACGAAAATTGCTGTAAGGAATGGATCTCGTTAAATACTGTACGGAACCAAAGTTAAAAAATAA
CTCGTAAAAGTTTACCAAGTTCGAAAGTTCCTCTAAAA
Done.