Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004642.1 Kokia drynarioides strain JFW-HI SEQ_118172, 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, 821
Length: 1369
ACGTcount: A:0.38, C:0.15, G:0.16, T:0.31
Found at i:456 original size:216 final size:216
Alignment explanation
Indices: 1--1047 Score: 1147
Period size: 216 Copynumber: 4.8 Consensus size: 216
*
1 TAAATAAGTTTTTAATTCAAAGATCAAAACTTGTTTACAAAATGAAAAACTATTTAGACCAAATG
1 TAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTACAAAATGAAAAACTATTTAGACCAAATG
* ** * * * *
66 ATGCAATTTCCCTCGCATGTAATGTGCAAAAAATTGCTCAAAGGATTGGATCGTGTT-AGATACG
66 ATGCGATTTCCCGAGCATGGAATGTTCGAAAAATTGCTCAAAGGATTGGATCGTCTTGA-ATACG
* * * * * * ** *
130 TAAAGGAACCGAAGTTGTAAAAGAACTC-GAAAAGTTAGTCATTTTCAAAAGTTCGTCTAAGAAC
130 TTAAGGAACAGAAGTTATAAAAGAACTCATAAAAGTTCGACAAGTTCAAAAGTTCGTCCAAGAAC
* * *
194 CAAGAGAGAATCTATTCTCATG
195 CAAGAGAGAAACAATTCTCACG
* * *
216 TAAATAAGTTTTTAATTCAAAGACCAAAACATGTTTACAAAATGAAAAGCTATTTAGACCGAATG
1 TAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTACAAAATGAAAAACTATTTAGACCAAATG
* * * * * *
281 ATGCGATTTCCCGAGCATGGAATGTTCGAAAAACTACTAAAAGGAATGGA-CTATCTTGAATACT
66 ATGCGATTTCCCGAGCATGGAATGTTCGAAAAATTGCTCAAAGGATTGGATC-GTCTTGAATACG
* * * *
345 TTAAGGAACAGAAGTTAAAAAAGAACTCATAAAAGTTTGACAAGTTCAAAAGTTCGCCCAACAAC
130 TTAAGGAACAGAAGTTATAAAAGAACTCATAAAAGTTCGACAAGTTCAAAAGTTCGTCCAAGAAC
410 CAAGAGAGAAACAATTCTCACG
195 CAAGAGAGAAACAATTCTCACG
* * * * * *
432 TAAATAAGTTTTTAATTAAAAGACCAAAACTTGTTTTCAAAATGACAAACTTTTTGGACCAATTG
1 TAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTACAAAATGAAAAACTATTTAGACCAAATG
* * * * *
497 ATGCAACTTCCCAAGCATGGAATGTTCGGAAAATTGCTCAAAGGATTGGATCGTCTTGAATACTT
66 ATGCGATTTCCCGAGCATGGAATGTTCGAAAAATTGCTCAAAGGATTGGATCGTCTTGAATACGT
* * *
562 TAAGGAACCA-TAGTTATAAAAGAACTCATAAAAGTTCGACAAGTTCAGAAGTTCGTTCAAGAAC
131 TAAGGAA-CAGAAGTTATAAAAGAACTCATAAAAGTTCGACAAGTTCAAAAGTTCGTCCAAGAAC
*
626 CAAGAGAGACACAATTCTCATGTAAACTTATG
195 CAAGAGAGAAACAATTCTC------AC----G
* * *
658 TAAATAAG-TTTTAATTCAAAGATCAAAACTTGTTTA-AAAATTGAAAAACTA-CTAGGCCAAAT
1 TAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTACAAAA-TGAAAAACTATTTAGACCAAAT
* ** * * * *
720 GATGCGATTTCTCTCGCATGGAATGTTCGGAAAATTGCTCAAAGGATTTGATCGTCTTTAATACA
65 GATGCGATTTCCCGAGCATGGAATGTTCGAAAAATTGCTCAAAGGATTGGATCGTCTTGAATACG
* * * * * *
785 TTAAGTAACCGAAGTTATAGAAGAACTCGTAAAAATTCG---A---C--AAGTTCGTCCAAGATC
130 TTAAGGAACAGAAGTTATAAAAGAACTCATAAAAGTTCGACAAGTTCAAAAGTTCGTCCAAGAAC
* *
842 CAAGAGAGAAACAATTCTTACA
195 CAAGAGAGAAACAATTCTCACG
* *
864 TAAATAAGTTTTAAATTCAAAGACC-AAACTTGTTTCACAAAATGAAAAACTATTTAGACCGAAT
1 TAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTT-ACAAAATGAAAAACTATTTAGACCAAAT
* * * *
928 GATGCGATTTCCCGAGCATGGAATGTTCGAAAATTTTCTCAAAGGATTGGATTGTCTTGAATAAG
65 GATGCGATTTCCCGAGCATGGAATGTTCGAAAAATTGCTCAAAGGATTGGATCGTCTTGAATACG
* * *
993 TTAAGGAATCA-AAGTTAATAAAAGAACTCGTAAAAGTTCAACAAGTTCGAAAGTT
130 TTAAGGAA-CAGAAGTT-ATAAAAGAACTCATAAAAGTTCGACAAGTTCAAAAGTT
1048 TCATGCATTT
Statistics
Matches: 694, Mismatches: 107, Indels: 60
0.81 0.12 0.07
Matches are distributed among these distances:
206 18 0.03
207 25 0.04
208 78 0.11
209 21 0.03
210 2 0.00
212 1 0.00
214 1 0.00
215 133 0.19
216 261 0.38
217 8 0.01
218 1 0.00
221 1 0.00
222 2 0.00
223 1 0.00
224 99 0.14
225 33 0.05
226 9 0.01
ACGTcount: A:0.41, C:0.15, G:0.16, T:0.28
Consensus pattern (216 bp):
TAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTACAAAATGAAAAACTATTTAGACCAAATG
ATGCGATTTCCCGAGCATGGAATGTTCGAAAAATTGCTCAAAGGATTGGATCGTCTTGAATACGT
TAAGGAACAGAAGTTATAAAAGAACTCATAAAAGTTCGACAAGTTCAAAAGTTCGTCCAAGAACC
AAGAGAGAAACAATTCTCACG
Done.