Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012170.1 Kokia drynarioides strain JFW-HI SEQ_127171, 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: 1675
ACGTcount: A:0.40, C:0.15, G:0.17, T:0.28
Found at i:379 original size:215 final size:216
Alignment explanation
Indices: 1--1675 Score: 2028
Period size: 215 Copynumber: 7.7 Consensus size: 216
* *
1 ACAAGTTCGAAAGTTCATCCAAGAACAAAGCGAGAAACAATTCTCACGTAAATAAGTTTTTAATT
1 ACAAGTTCGAAAGTTCGTCCAAGAACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATT
* * * * *
66 CAACGACCAAAACTTGTTTCCAAAACGACAAACTATTTAGACCAAATGATGCGATTTCCC-ATGG
66 TAAAGACCAAAACTTGTTTGCAAAATGACAAACTATTTAGACCAAATGATGCGATTTCCCGA-GC
* * * *
130 ATGGAATGTTCGAAAAATTGTTCTAAAAAATGGATCTTGTTGAATACTTTAGGGAACTGAAGTTA
130 ATGGAATGTTCGAAAAATTGCTCGAAAGAATGGATCTTGTTGAATACTTTAAGGAACTGAAGTTA
195 AAAAATAACTCGTAAAAGTTCG
195 AAAAATAACTCGTAAAAGTTCG
217 ACAAGTTCGAAAGTTCGTCCAAGAACAAAGAGAGAAACAATTCTCACGT-AATAAGTTTTTAATT
1 ACAAGTTCGAAAGTTCGTCCAAGAACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATT
* * * * **
281 TAAAGACCAAAACTTGTTTGCAAAATAACAAATTATTTAGGA-TAAATGATTCGATTTTTCGAGC
66 TAAAGACCAAAACTTGTTTGCAAAATGACAAACTATTTA-GACCAAATGATGCGATTTCCCGAGC
* * * * * * * *
345 ATGGAATATTCAAAAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGATCTGGAG-CA
130 ATGGAATGTTCGAAAAATTGCTCGAAAGAATGGATCTTGTTGAATACTTTAAGGAACTGAAGTTA
* * *
409 ATAAAAGAACTAGTAAAAGTTTG
195 A-AAAATAACTCGTAAAAGTTCG
432 ACAAGTTCGAAAGTTCGTCCAAGAACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATT
1 ACAAGTTCGAAAGTTCGTCCAAGAACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATT
* * * * *
497 CAACGACCAAAACTTGTTTGCAAAACGACAAACTATTTAGACCAAATGATGCGATTTCTCGAGCT
66 TAAAGACCAAAACTTGTTTGCAAAATGACAAACTATTTAGACCAAATGATGCGATTTCCCGAGCA
* ** * * * ** *
562 TGAAAAATTCGGAAAATTGCT-GAAATGAATGGATCGTCTTGAATACTTTAAGG-TTTCAAAGTT
131 TGGAATGTTCGAAAAATTGCTCGAAA-GAATGGATCTTGTTGAATACTTTAAGGAACT-GAAGTT
* * *
625 ATAAAAGAACTAGTAAAAGGTT-G
194 AAAAAATAACTCGTAAAA-GTTCG
* * *
648 ACAAGTTCGAAATTTTGTCCAAGAACAAAGAGAGAATCAATTCTCACGTAAATAAGTTTTTAATT
1 ACAAGTTCGAAAGTTCGTCCAAGAACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATT
* * * * * *
713 CAACGACCAGAAGTTGTTTGCAAAACGACAAACTATTTAGACCAAATGATGCGATTTCCC-ATGG
66 TAAAGACCAAAACTTGTTTGCAAAATGACAAACTATTTAGACCAAATGATGCGATTTCCCGA-GC
* *
777 ATGGAATGTTCGAAAAATTGCTCTAAAAAATGGATCTTGTTGAATACTTT-AGCGAACTGAAGTT
130 ATGGAATGTTCGAAAAATTGCTCGAAAGAATGGATCTTGTTGAATACTTTAAG-GAACTGAAGTT
841 AAAAAATAACTCGTAAAAGTTCG
194 AAAAAATAACTCGTAAAAGTTCG
* * *
864 ACAAGTTCGAAAGTTCGTCCAAGAAAAAAGAGGGAAACAATTCTCACGT-AATAAGTTTTTAGTT
1 ACAAGTTCGAAAGTTCGTCCAAGAACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATT
* * *
928 TAAAGACCAAAACTTGTTTGCAGAATGACAAATTATTTAGACCAAATGGTGCGATTTCCCGAGCA
66 TAAAGACCAAAACTTGTTTGCAAAATGACAAACTATTTAGACCAAATGATGCGATTTCCCGAGCA
** * * * * * **
993 TGGAATAATC-AGCAAATTGCTCGAAAGAATAGATCGTCTTGAATACTTTAAGGATCCAAAGTTA
131 TGGAATGTTCGA-AAAATTGCTCGAAAGAATGGATCTTGTTGAATACTTTAAGGAACTGAAGTTA
* * * *
1057 TAAAAGAACTAGTAAAAGTTTG
195 AAAAATAACTCGTAAAAGTTCG
* * * *
1079 ACAGGTTCGAAACTTCATCCAAGAACAAAGAGAGAAACAATTCTCAAGTAAATAAGTTTTTAATT
1 ACAAGTTCGAAAGTTCGTCCAAGAACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATT
* * *
1144 CAAAGGCCAAAACTTGCACCAAAACTTGTTTGCAAAATGACAAACTATTTAGGCCAAATGTTGCG
66 --------TAAA---G-ACCAAAACTTGTTTGCAAAATGACAAACTATTTAGACCAAATGATGCG
* * *
1209 ATTTACCGAGCATGGAATGTTCGAAAAATTGCTCGAAGGAATGGATCTTGTTGAATACTTTAGGG
119 ATTTCCCGAGCATGGAATGTTCGAAAAATTGCTCGAAAGAATGGATCTTGTTGAATACTTTAAGG
* * **
1274 AACTGAAGTTAAAAAATAACACATAAAAGTTTT
184 AACTGAAGTTAAAAAATAACTCGTAAAAGTTCG
* * * *
1307 AAAATTTCGAAAGTTCGTTCAAGAACAAAGAGGGAAACAATTCTCACGT-AATAAGTTTTTAATT
1 ACAAGTTCGAAAGTTCGTCCAAGAACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATT
* * * * ** *
1371 TAAAGATCAAAACTTGTTTGCAGAATAACAAATTATTTAGACCAAATGATGCGATTTCCCTTGGA
66 TAAAGACCAAAACTTGTTTGCAAAATGACAAACTATTTAGACCAAATGATGCGATTTCCCGAGCA
* * * * * * *
1436 TGGAATGTTTGAAAAATTGCTCTAAAAAATGTATCTTGTTGTATACTTTATGGAACTGATGTTAA
131 TGGAATGTTCGAAAAATTGCTCGAAAGAATGGATCTTGTTGAATACTTTAAGGAACTGAAGTTAA
1501 AAAATAACTCGTAAAAGTTCG
196 AAAATAACTCGTAAAAGTTCG
* *
1522 ACAAGTTCGAAAGGTT-GTCCAAGAACAAAGAGGGAAACAATACTCACGT-AATAAGTTTTTAAT
1 ACAAGTTCGAAA-GTTCGTCCAAGAACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAAT
* * * *
1585 TTAAAGGCCAAAACTTGTTTGCAGAATGACAAATTATTTAGACCAAATGGTGCGATTTCCCGAGC
65 TTAAAGACCAAAACTTGTTTGCAAAATGACAAACTATTTAGACCAAATGATGCGATTTCCCGAGC
*
1650 ATGGAATGTTCAAAAAATTGCTCGAA
130 ATGGAATGTTCGAAAAATTGCTCGAA
Statistics
Matches: 1253, Mismatches: 174, Indels: 65
0.84 0.12 0.04
Matches are distributed among these distances:
214 3 0.00
215 631 0.50
216 425 0.34
217 8 0.01
219 3 0.00
224 3 0.00
227 16 0.01
228 163 0.13
229 1 0.00
ACGTcount: A:0.40, C:0.15, G:0.17, T:0.28
Consensus pattern (216 bp):
ACAAGTTCGAAAGTTCGTCCAAGAACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATT
TAAAGACCAAAACTTGTTTGCAAAATGACAAACTATTTAGACCAAATGATGCGATTTCCCGAGCA
TGGAATGTTCGAAAAATTGCTCGAAAGAATGGATCTTGTTGAATACTTTAAGGAACTGAAGTTAA
AAAATAACTCGTAAAAGTTCG
Done.