Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01006776.1 Kokia drynarioides strain JFW-HI SEQ_121375, 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, 829
Length: 1383
ACGTcount: A:0.40, C:0.14, G:0.18, T:0.28
Found at i:416 original size:216 final size:215
Alignment explanation
Indices: 5--1383 Score: 1564
Period size: 216 Copynumber: 6.5 Consensus size: 215
1 ACCT
** *
5 AATGATGCGATTTCTTGAGCATGGAATGTTC-GAAAAATTACTCGAAGGAATGGATCGTCTTGAA
1 AATGATGCGATTTCCCGAGCATGGAATGTTCAG-AAAATTGCTCGAAGGAATGGATCGTCTTGAA
* * * * * * *
69 TACTTTTAGGAAAAAAAGTTATAAAAAATTCGTATAAGTTTGACATGTTCGAAAGTTCTGCCAAG
65 TACTTTAAGGAACAAAAGTTATAAAAAACTCGTAAAAGTTTGACAAGTTCGGAAGTTCGGCCAAG
* * *
134 AACCAATAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCTAAAGTTGTGTACAA
130 AACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAA
199 AATGACAAACTATTTAGACCA
195 AATGACAAACTATTTAGACCA
* *** * * *
220 AATGATGTGATTTATTGAGCATGGAATGTTCAGAAAATTGGTAGAAGGAATGGATCGCCTTGAAT
1 AATGATGCGATTTCCCGAGCATGGAATGTTCAGAAAATTGCTCGAAGGAATGGATCGTCTTGAAT
285 ACTTTAAGGAACAAAAGTT-TAAAAACAACTCGTAAAAGTTTGACAAGTTCGGAAGTTCGGCCAA
66 ACTTTAAGGAACAAAAGTTAT-AAAA-AACTCGTAAAAGTTTGACAAGTTCGGAAGTTCGGCCAA
* * * * **
349 GAACAAAGAGAGAAATAATTGTCACGAAAATAAGTTTTTAATTCAAAGATAAAAAGTTGTTTACA
129 GAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACA
* *
414 AAATGAAAAACTATTTACACCA
194 AAATGACAAACTATTTAGACCA
* * * * ** *
436 AAAGATGTGATCTCCCGAGCATTGAATGTTTGGAAAATTGCTCGAAGGAATGGATCATCTTGAAT
1 AATGATGCGATTTCCCGAGCATGGAATGTTCAGAAAATTGCTCGAAGGAATGGATCGTCTTGAAT
* * * *
501 ACTTTAAGAAACAAAAGTTATGGAAGAACTCGTAAAAGTTTG---A---C--AAGTTCGGCCAAT
66 ACTTTAAGGAACAAAAGTTAT-AAAAAACTCGTAAAAGTTTGACAAGTTCGGAAGTTCGGCCAAG
**
558 AACCAAGAGAGAAATGATTCTCACGTAAATAAG----T--TTCAAAGACCAAAAGTTGTTTACAA
130 AACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAA
617 AATGACAAACTATTTAGACCA
195 AATGACAAACTATTTAGACCA
* * * * * *
638 AATGATGCAATTTCCCAAGCATTGAATGTTCGGAAAATTGCTCGAAGGAATTGATCATCTTGAAT
1 AATGATGCGATTTCCCGAGCATGGAATGTTCAGAAAATTGCTCGAAGGAATGGATCGTCTTGAAT
* * * * * * *
703 ACTGTAAGGAACAAATGTTATAAAAGAACTTGTAAATGTTTGAAAAGTTTGGAAGTTCAGCCAAG
66 ACTTTAAGGAACAAAAGTTATAAAA-AACTCGTAAAAGTTTGACAAGTTCGGAAGTTCGGCCAAG
* * * * * * *
768 ATCCAACAGAGAAACAATTTTCAAGTAAA-AAGTTTTTAATTCAAAGGCCAAATGTTTTTTACAA
130 AACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAA
* *
832 AATGA-AAACCTTTTTAGACCG
195 AATGACAAA-CTATTTAGACCA
** * *
853 AATGATGCGATTTCTTGAGCATGGAATGTTCGAAAAAAATT--TTGAAGGAATGGATCGTCTTGA
1 AATGATGCGATTTCCCGAGCATGGAATGTTC--AGAAAATTGCTCGAAGGAATGGATCGTCTTGA
* * * **
916 ATACCTTT-AGGAA-ACAAAGTTATAAAAAACTCTTAAAAGTTTGACATGTTCGGAAGTTTGGTG
64 ATA-CTTTAAGGAACA-AAAGTTATAAAAAACTCGTAAAAGTTTGACAAGTTCGGAAGTTCGGCC
* * * * *
979 AAGAACCAATAGAGAAACATTTCTCAGGTAAATAAGTTTTTATTTCAAAGAGCAAAAGTTGTTTA
127 AAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTA
* *
1044 TAAAATGACAAACTATTTGGACCA
192 CAAAATGACAAACTATTTAGACCA
* * * * * *
1068 AATGATGCGATTTCCCAAGCATGGAATGTTCAAAAAATTGTTTGACGGAATGGATTGTCTTGAAT
1 AATGATGCGATTTCCCGAGCATGGAATGTTCAGAAAATTGCTCGAAGGAATGGATCGTCTTGAAT
* * *
1133 ACTTTAAGGAATC-GAAGTTATAAAATAACTCGTAAAAGTTTGACAACTTCGTAAGTTCGGCCAA
66 ACTTTAAGGAA-CAAAAGTTATAAAA-AACTCGTAAAAGTTTGACAAGTTCGGAAGTTCGGCCAA
* ** *
1197 GAACCAAGAGAGAAACAATTCTCACCTAAGGAAGTTTTTAATTCAAAGACCCAAAGTTGTTTACA
129 GAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACA
*
1262 AAATGACAAACTATTTGGACCA
194 AAATGACAAACTATTTAGACCA
* * * *
1284 GATGATGCGATTTCCCGAGCCA-GGAATGTTCAAAAAATTGCTCGAAGGAATCGATCATCTTGAA
1 AATGATGCGATTTCCCGAG-CATGGAATGTTCAGAAAATTGCTCGAAGGAATGGATCGTCTTGAA
** *
1348 TACTTTAAGGAACCGATGTTATAAAAGAACTCGTAA
65 TACTTTAAGGAACAAAAGTTATAAAA-AACTCGTAA
Statistics
Matches: 984, Mismatches: 146, Indels: 67
0.82 0.12 0.06
Matches are distributed among these distances:
201 2 0.00
202 132 0.13
204 1 0.00
205 1 0.00
208 41 0.04
209 3 0.00
210 35 0.04
213 10 0.01
214 62 0.06
215 290 0.29
216 396 0.40
217 11 0.01
ACGTcount: A:0.40, C:0.14, G:0.18, T:0.28
Consensus pattern (215 bp):
AATGATGCGATTTCCCGAGCATGGAATGTTCAGAAAATTGCTCGAAGGAATGGATCGTCTTGAAT
ACTTTAAGGAACAAAAGTTATAAAAAACTCGTAAAAGTTTGACAAGTTCGGAAGTTCGGCCAAGA
ACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAA
ATGACAAACTATTTAGACCA
Done.