Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004461.1 Kokia drynarioides strain JFW-HI SEQ_117873, 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, 780
Length: 1301
ACGTcount: A:0.41, C:0.14, G:0.18, T:0.27
Found at i:399 original size:216 final size:218
Alignment explanation
Indices: 4--1301 Score: 1332
Period size: 216 Copynumber: 6.0 Consensus size: 218
1 AAC
* * * * * * * * *
4 GACAATCTATTCAGACCAAATGATGCGATTTCTTGAGCAAGGAATGTTTGGAAAACTACTCGAAG
1 GACAAACTATTTAGACCAAATGATGCAATTTCTCGAGCATGGAATGTTCGGAAAATTGCTCAAAG
*** * * *
69 GAATGGATAACCTTGAATGCTTTAAGGAACGGAAGTTATAAAAGAAGTCGTAAAAGTTTGACATG
66 GAATGGATCGTCTTGAATACTTTAAGGAACTGAAGTTATAAAAGAAGTCGTAAAAGTTTGACAAG
*
134 TTCGAAAGTTCGTCCAAGAAG--AAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCCA
131 TTCGAAAGTTCGTCCAAGAAGACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAA
*
197 AGACCAAAACTTGTGTACGAAAT
196 AGACCAAAACTTGTATACGAAAT
* *
220 GACAAACTCTTTAGACCAAATGATGAAATTTCTCGAGCATGGAATGTTCAGGAAAA-TGCTCAAA
1 GACAAACTATTTAGACCAAATGATGCAATTTCTCGAGCATGGAATGTTC-GGAAAATTGCTCAAA
* * * * * * *
284 GGAATGGGTCGTCTTCAATACTTTAAGGAAGTTAAGTTATAAAAGATGTC-CAATAAGTTTGAAA
65 GGAATGGATCGTCTTGAATACTTTAAGGAACTGAAGTTATAAAAGAAGTCGTAA-AAGTTTGACA
* * * * * * * * *
348 AGTTCGAGAGTTCGTTCATGAA-AC-GAGAGTGATACAATTCTCTCATAAATAAGTTTTTAATTG
129 AGTTCGAAAGTTCGTCCAAGAAGACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTC
*
411 AAAGACCAAAACATG-AT-CAGAAAAT
194 AAAGACCAAAACTTGTATAC-G-AAAT
* * *
436 GACACACTATTTAGACCAAATGATACAATTT-TCCGAGCATGGAATGTTCGGAAAATTGCTCTAA
1 GACAAACTATTTAGACCAAATGATGCAATTTCT-CGAGCATGGAATGTTCGGAAAATTGCTCAAA
* * * ** * * * *
500 GGAATGGATCTTGTTGAATATTTTTGGGAACCGAAGTTAAAAAATAACTCGTAAAAGTTTGACAA
65 GGAATGGATCGTCTTGAATACTTTAAGGAACTGAAGTTATAAAAGAAGTCGTAAAAGTTTGACAA
* * *
565 GCTCGAAAGTTCATAC-A-AAGACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCA
130 GTTCGAAAGTTCGTCCAAGAAGACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCA
* ***
628 AAGACCAAAACTTGTTTGTAAAAT
195 AAGACCAAAACTTGTATACGAAAT
* * * * * * *
652 GACAAACTAATTAGGCCAAATTATGCAATTTGC-CGAGCATGGAATATTCGAAAAATTGCTCGAT
1 GACAAACTATTTAGACCAAATGATGCAATTT-CTCGAGCATGGAATGTTCGGAAAATTGCTCAAA
* * * * *
716 GCAATGTATCGTCTTGAATACTTTAAGGATCTGAAGTTATAAAAGAACTAGTAAAAGTTTGACAA
65 GGAATGGATCGTCTTGAATACTTTAAGGAACTGAAGTTATAAAAGAAGTCGTAAAAGTTTGACAA
*
781 GTTCGAAAGTTCCTCCAAG-A-ACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCA
130 GTTCGAAAGTTCGTCCAAGAAGACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCA
*
844 AAGACCAAAACTTGTATACAAAAT
195 AAGACCAAAACTTGTATACGAAAT
* * * * * *
868 GACAAACTATTTAGACCAAATGATGCGATTTCCCAAGGATGGAATGTTAGAAAAATTGCTCAAAG
1 GACAAACTATTTAGACCAAATGATGCAATTTCTCGAGCATGGAATGTTCGGAAAATTGCTCAAAG
* * ** * * * * * * *
933 GAGTGTATTTTGTTGATTACTTTATGGAACTGAAGTTAAAAAATAACTCGTAAAAGTTTGACAGG
66 GAATGGATCGTCTTGAATACTTTAAGGAACTGAAGTTATAAAAGAAGTCGTAAAAGTTTGACAAG
* * * * *
998 TTTGAAAGTTCAT--ACGAAGACAAACAGAGAAGCAATTCTCACGTAAATAAGTTTTTAATTCAA
131 TTCGAAAGTTCGTCCAAGAAGACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAA
* * **
1061 AGAACAAATCTTGT-TTGGAAAAT
196 AGACCAAAACTTGTATACG-AAAT
* * * * * * *
1084 GACAAACTATTTAGGA-TAAATGATACGATTTAC-CGAGCATGAAATATTCAGAAAATTGCTCGA
1 GACAAACTATTTA-GACCAAATGATGCAATTT-CTCGAGCATGGAATGTTCGGAAAATTGCTCAA
* * * * * *
1147 A-GCA---ATCGTCTTGAATACTTTAAGGATCCGAAGTTATAAAAGAACTAGTAAAAATTTGACA
64 AGGAATGGATCGTCTTGAATACTTTAAGGAACTGAAGTTATAAAAGAAGTCGTAAAAGTTTGACA
* * *
1208 GGTTCGAAAGTTCGTCCAAG-A-ACAAAGAGAGAAAAAATTCTCACGTAAATAAGTTTTTAATAC
129 AGTTCGAAAGTTCGTCCAAGAAGACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTC
*
1271 AAAGACCAAAACTTGTATACAAAAT
194 AAAGACCAAAACTTGTATACGAAAT
1296 GACAAA
1 GACAAA
Statistics
Matches: 891, Mismatches: 165, Indels: 56
0.80 0.15 0.05
Matches are distributed among these distances:
212 121 0.14
213 2 0.00
214 7 0.01
215 17 0.02
216 730 0.82
217 14 0.02
ACGTcount: A:0.41, C:0.14, G:0.18, T:0.27
Consensus pattern (218 bp):
GACAAACTATTTAGACCAAATGATGCAATTTCTCGAGCATGGAATGTTCGGAAAATTGCTCAAAG
GAATGGATCGTCTTGAATACTTTAAGGAACTGAAGTTATAAAAGAAGTCGTAAAAGTTTGACAAG
TTCGAAAGTTCGTCCAAGAAGACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAA
AGACCAAAACTTGTATACGAAAT
Found at i:819 original size:432 final size:430
Alignment explanation
Indices: 4--1301 Score: 1544
Period size: 432 Copynumber: 3.0 Consensus size: 430
1 AAC
* * * * *** * * * * * *
4 GACAATCTATTCAGACCAAATGATGCGATTTCTTGAGCAAGGAATGTTTGGAAAACTACTCGAAG
1 GACAAACTATTTAGACCAAATGATACAATTTCCCAAGCATGGAATGTTAGAAAAATTGCTCAAAG
**** * * * * * * *
69 GAATGGATAACCTTGAATGCTTTAAGGAACGGAAGTTATAAAAGAAGTCGTAAAAGTTTGACATG
66 GAATGGATCTTGTTGAATACTTTATGGAACCGAAGTTAAAAAATAACTCGTAAAAGTTTGACAAG
* * * *
134 TTCGAAAGTTCGT-CCAAGAAGAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCCAA
131 TTCGAAAGTTCATACAAAG-ACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAA
* * *
198 GACCAAAACTTG--TGTACGAAATGACAAACTCTTTAGACCAAATGATGAAATTTCTCGAGCATG
195 GACCAAAACTTGTTTGTA--AAATGACAAACTATTTAGGCCAAATGATGCAATTTC-CGAGCATG
* * * * * * ** *
261 GAATGTTCAGGAAAA-TGCTCAAAGGAATGGGTCGTCTTCAATACTTTAAGGAAGTTAAGTTATA
257 GAATATTC-GAAAAATTGCTCGAAGCAAT-GATCGTCTTGAATACTTTAAGGATCTGAAGTTATA
* * * * * * *
325 AAAG-A-T-GTCCAATAAGTTTGAAAAGTTCGAGAGTTCGTTCATGAA-ACGAGAGTGATACAAT
320 AAAGAACTAGT--AA-AAGTTTGACAAGTTCGAAAGTTCGTCCAAGAACA-AAGAGAGAAACAAT
* * * * *
386 TCTCTCATAAATAAGTTTTTAATTGAAAGACCAAAACATG-ATCAGAAAAT
381 TCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTAT-ACAAAAT
* * * * * *
436 GACACACTATTTAGACCAAATGATACAATTTTCCGAGCATGGAATGTTCGGAAAATTGCTCTAAG
1 GACAAACTATTTAGACCAAATGATACAATTTCCCAAGCATGGAATGTTAGAAAAATTGCTCAAAG
*
501 GAATGGATCTTGTTGAATA-TTTTTGGGAACCGAAGTTAAAAAATAACTCGTAAAAGTTTGACAA
66 GAATGGATCTTGTTGAATACTTTAT-GGAACCGAAGTTAAAAAATAACTCGTAAAAGTTTGACAA
*
565 GCTCGAAAGTTCATACAAAGACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAA
130 GTTCGAAAGTTCATACAAAGACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAA
* *
630 GACCAAAACTTGTTTGTAAAATGACAAACTAATTAGGCCAAATTATGCAATTTGCCGAGCATGGA
195 GACCAAAACTTGTTTGTAAAATGACAAACTATTTAGGCCAAATGATGCAATTT-CCGAGCATGGA
*
695 ATATTCGAAAAATTGCTCGATGCAATGTATCGTCTTGAATACTTTAAGGATCTGAAGTTATAAAA
259 ATATTCGAAAAATTGCTCGAAGCAATG-ATCGTCTTGAATACTTTAAGGATCTGAAGTTATAAAA
*
760 GAACTAGTAAAAGTTTGACAAGTTCGAAAGTTCCTCCAAGAACAAAGAGAGAAACAATTCTCACG
323 GAACTAGTAAAAGTTTGACAAGTTCGAAAGTTCGTCCAAGAACAAAGAGAGAAACAATTCTCACG
825 TAAATAAGTTTTTAATTCAAAGACCAAAACTTGTATACAAAAT
388 TAAATAAGTTTTTAATTCAAAGACCAAAACTTGTATACAAAAT
* * *
868 GACAAACTATTTAGACCAAATGATGCGATTTCCCAAGGATGGAATGTTAGAAAAATTGCTCAAAG
1 GACAAACTATTTAGACCAAATGATACAATTTCCCAAGCATGGAATGTTAGAAAAATTGCTCAAAG
* * * * * *
933 GAGTGTATTTTGTTGATTACTTTATGGAACTGAAGTTAAAAAATAACTCGTAAAAGTTTGACAGG
66 GAATGGATCTTGTTGAATACTTTATGGAACCGAAGTTAAAAAATAACTCGTAAAAGTTTGACAAG
* * * *
998 TTTGAAAGTTCATACGAAGACAAACAGAGAAGCAATTCTCACGTAAATAAGTTTTTAATTCAAAG
131 TTCGAAAGTTCATACAAAGACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAG
* * * ** * * *
1063 AACAAATCTTGTTTGGAAAATGACAAACTATTTAGGATAAATGATACGATTTACCGAGCATGAAA
196 ACCAAAACTTGTTTGTAAAATGACAAACTATTTAGGCCAAATGATGCAATTT-CCGAGCATGGAA
*
1128 TATTC-AGAAAATTGCTCGAAGC-A--ATCGTCTTGAATACTTTAAGGATCCGAAGTTATAAAAG
260 TATTCGA-AAAATTGCTCGAAGCAATGATCGTCTTGAATACTTTAAGGATCTGAAGTTATAAAAG
* * *
1189 AACTAGTAAAAATTTGACAGGTTCGAAAGTTCGTCCAAGAACAAAGAGAGAAAAAATTCTCACGT
324 AACTAGTAAAAGTTTGACAAGTTCGAAAGTTCGTCCAAGAACAAAGAGAGAAACAATTCTCACGT
*
1254 AAATAAGTTTTTAATACAAAGACCAAAACTTGTATACAAAAT
389 AAATAAGTTTTTAATTCAAAGACCAAAACTTGTATACAAAAT
1296 GACAAA
1 GACAAA
Statistics
Matches: 755, Mismatches: 97, Indels: 32
0.85 0.11 0.04
Matches are distributed among these distances:
428 145 0.19
431 11 0.01
432 577 0.76
433 15 0.02
434 5 0.01
435 2 0.00
ACGTcount: A:0.41, C:0.14, G:0.18, T:0.27
Consensus pattern (430 bp):
GACAAACTATTTAGACCAAATGATACAATTTCCCAAGCATGGAATGTTAGAAAAATTGCTCAAAG
GAATGGATCTTGTTGAATACTTTATGGAACCGAAGTTAAAAAATAACTCGTAAAAGTTTGACAAG
TTCGAAAGTTCATACAAAGACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAG
ACCAAAACTTGTTTGTAAAATGACAAACTATTTAGGCCAAATGATGCAATTTCCGAGCATGGAAT
ATTCGAAAAATTGCTCGAAGCAATGATCGTCTTGAATACTTTAAGGATCTGAAGTTATAAAAGAA
CTAGTAAAAGTTTGACAAGTTCGAAAGTTCGTCCAAGAACAAAGAGAGAAACAATTCTCACGTAA
ATAAGTTTTTAATTCAAAGACCAAAACTTGTATACAAAAT
Done.