Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001245.1 Kokia drynarioides strain JFW-HI SEQ_112615, 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, 626
Length: 1044
ACGTcount: A:0.39, C:0.14, G:0.19, T:0.27
Warning! 10 characters in sequence are not A, C, G, or T
Found at i:392 original size:215 final size:217
Alignment explanation
Indices: 1--406 Score: 475
Period size: 215 Copynumber: 1.9 Consensus size: 217
* *
1 TTTTCATTCAAAGAGCAAAAGTTGTTTACCAAATGACAAATAGTTTAGAAAAAAAATGATGCGAT
1 TTTTCATTCAAAGAGCAAAAGTAGTTTACAAAATGACAAATAGTTTAG-AAAAAAATGATGCGAT
* * *
66 TTCCCAAGCATGAAATGTTAAAAAAATTGCTCGAAGGAATGGATCGCCATGAATACTTTATGGAA
65 TTCCCAAGCATGAAATGTTAAAAAAATTGCTCGAAGGAATGGATCGCCATGAATACTCTAAGAAA
* ** *
131 CTGATGTTATGAAAGAACTCGTAAAAGTTTTCCAAGTTCAGAAGTTCGGCCAAGAACCAAGATAG
130 CTGAAGTTATGAAAGAACTCGTAAAAGTCGTCCAAGTTCAGAAGTTCAGCCAAGAACCAAGATAG
196 AAACAACTCTCACGTAAGAAAGT
195 AAACAACTCTCACGTAAGAAAGT
* * **
219 TTTTCATTGAAAGA-CGAAAAGTAGTTTAGAAAATGACAAAGTA-TTTAG-ACCAAATGATGCGA
1 TTTTCATTCAAAGAGC-AAAAGTAGTTTACAAAATGACAAA-TAGTTTAGAAAAAAATGATGCGA
* * * * * * * * *
281 TTTCCCGAGTATGTAATGTTCAAAAAATTGCTCTAA-GAATGGGTTGTCTTGAATACTCTAAGAA
64 TTTCCCAAGCATGAAATGTTAAAAAAATTGCTCGAAGGAATGGATCGCCATGAATACTCTAAGAA
** * *
345 A-TCGAAGTTATTG-AAGAACTCGTAAAAGCTCGT-CAAGTTTGGAAGTTCATCTAAGAACCAAG
129 ACT-GAAGTTA-TGAAAGAACTCGTAAAAG-TCGTCCAAGTTCAGAAGTTCAGCCAAGAACCAAG
407 NNNNNNNNNN
Statistics
Matches: 157, Mismatches: 26, Indels: 13
0.80 0.13 0.07
Matches are distributed among these distances:
214 1 0.01
215 67 0.43
216 47 0.30
217 1 0.01
218 39 0.25
219 2 0.01
ACGTcount: A:0.39, C:0.14, G:0.19, T:0.27
Consensus pattern (217 bp):
TTTTCATTCAAAGAGCAAAAGTAGTTTACAAAATGACAAATAGTTTAGAAAAAAATGATGCGATT
TCCCAAGCATGAAATGTTAAAAAAATTGCTCGAAGGAATGGATCGCCATGAATACTCTAAGAAAC
TGAAGTTATGAAAGAACTCGTAAAAGTCGTCCAAGTTCAGAAGTTCAGCCAAGAACCAAGATAGA
AACAACTCTCACGTAAGAAAGT
Found at i:898 original size:215 final size:213
Alignment explanation
Indices: 419--1044 Score: 650
Period size: 215 Copynumber: 2.9 Consensus size: 213
409 NNNNNNNNTA
* * * * *
419 GAAGAACTCGTCAAAGTTTGTCAAGTTTAGAAGTTCATCCAATATCTAAGAGAGAAACAATTCTC
1 GAAGAACTCGTAAAAG-TTGTCAAGTTTAGAAGTTCATCCAAGAACCAAGAGAGAAACAACTCTC
* ** *
484 ATGTAAATAAGTTTTTCATTCAAAGA-GCAAAAGTTGTTTACCAAATGACAAATAGTTTAGAAAA
65 ACGTAAATAAGTTTTTCATTCAAAGACG-AAAAGTTGTTTAGAAAATGACAAATA-TTTAG--AC
548 AAAATGATGCGATTTCCCAAGCATGAAATGTTAAAAAAATTGCTCGAAGGAATGGATCGCCATGA
126 AAAATGATGCGATTTCCCAAGCATGAAATGTTAAAAAAATTGCTCGAAGGAATGGATCGCCATGA
* * * *
613 ATACTTTATGGAACTGATGTTAT
191 ATACTCTAAGAAACTGAAGTTAT
* * ** *
636 GAAAGAACTCGTAAAAGTTTTCCAAGTTCAGAAGTTCGGCCAAGAACCAAGATAGAAACAACTCT
1 G-AAGAACTCGTAAAAGTTGT-CAAGTTTAGAAGTTCATCCAAGAACCAAGAGAGAAACAACTCT
* * *
701 CACGTAAGA-AAGTTTTTCATTGAAAGACGAAAAGTAGTTTAGAAAATGACAAAGTATTTAGACC
64 CACGTAA-ATAAGTTTTTCATTCAAAGACGAAAAGTTGTTTAGAAAATGACAAA-TATTTAGACA
* * * * * * * * *
765 AAATGATGCGATTTCCCGAGTATGTAATGTTCAAAAAATTGCTCTAA-GAATGGGTTGTCTTGAA
127 AAATGATGCGATTTCCCAAGCATGAAATGTTAAAAAAATTGCTCGAAGGAATGGATCGCCATGAA
829 TACTCTAAGAAA-TCGAAGTTATT
192 TACTCTAAGAAACT-GAAGTTA-T
* * * * *
852 GAAGAACTCGTAAAAGCTCGTCAAGTTTGGAAGTTCATCTAAGAACCAAGGGAAAAACAACTCTC
1 GAAGAACTCGTAAAAG-TTGTCAAGTTTAGAAGTTCATCCAAGAACCAAGAGAGAAACAACTCTC
* * * * * **
917 ACGGAAATAGGTTTTTAATTCAAAGACCAAAAGTTGTTTAGAATATGGTAAACTATTTAGACAAA
65 ACGTAAATAAGTTTTTCATTCAAAGACGAAAAGTTGTTTAGAAAATGACAAA-TATTTAGACAAA
* *** * * *
982 ATGATGTGATTTCCTGTGCATGGAATGCTT-GAAAAATTGCTCGAAGGAATGGATCGTCATGAA
129 ATGATGCGATTTCCCAAGCATGAAATG-TTAAAAAAATTGCTCGAAGGAATGGATCGCCATGAA
Statistics
Matches: 337, Mismatches: 61, Indels: 23
0.80 0.14 0.05
Matches are distributed among these distances:
214 2 0.01
215 166 0.49
216 63 0.19
217 4 0.01
218 98 0.29
219 4 0.01
ACGTcount: A:0.39, C:0.14, G:0.19, T:0.28
Consensus pattern (213 bp):
GAAGAACTCGTAAAAGTTGTCAAGTTTAGAAGTTCATCCAAGAACCAAGAGAGAAACAACTCTCA
CGTAAATAAGTTTTTCATTCAAAGACGAAAAGTTGTTTAGAAAATGACAAATATTTAGACAAAAT
GATGCGATTTCCCAAGCATGAAATGTTAAAAAAATTGCTCGAAGGAATGGATCGCCATGAATACT
CTAAGAAACTGAAGTTAT
Done.