Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014481.1 Kokia drynarioides strain JFW-HI SEQ_129520, 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, 662
Length: 1104
ACGTcount: A:0.41, C:0.14, G:0.17, T:0.27
Found at i:513 original size:216 final size:215
Alignment explanation
Indices: 117--1100 Score: 909
Period size: 216 Copynumber: 4.6 Consensus size: 215
107 TCGAATGATA
* * * ** *
117 AAAAGTTTGACAAGTTTGGAAGTTCATCCAAGAACCAAGAGAGAAACAATTGTCATGTAAAT-A-
1 AAAA-TTTGACAAGTTCGGAAGTTCAGCCAAGAACCAAGAGAGAAACAGTCCTCACGTAAATAAG
* * *
180 TTTTTAATTCAAAGACGAAAAGTTG-ATTACAAAATGAAAAACTATTTAGACCAAACAATGTGAT
65 TTTTTAATTCAAAGACCAAAAGTTGTA-TACAAAATGAAAAACTATTTAGACCAAATAATGCGAT
* * * * *
244 TTCCCAAGCGTAGAATGTTCGAGAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAA
129 TTCCCGAGCATGGAATGTTCGAAAAATTGGTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAA
* *
309 CTGAAGTTATAAAAGAACTCAT
194 CCGAAGTTATAAAAGAACTCGT
* * * * * *
331 AAAAGCTTGACAAGTTCGAAAGTTCAGCCAAGAACAAAGAGGGAAGCAGTTCTCACGTAAATAAG
1 AAAA-TTTGACAAGTTCGGAAGTTCAGCCAAGAACCAAGAGAGAAACAGTCCTCACGTAAATAAG
* * * *
396 TTTTTAATTCAAAGAGCAAAAGTTGTATACGAAATGACAAACTATTTAGACCAAATAATGTGATT
65 TTTTTAATTCAAAGACCAAAAGTTGTATACAAAATGAAAAACTATTTAGACCAAATAATGCGATT
** * * * * * * *
461 TTTCGGGCATTGAATGTTCGAAAAACTGGTAGAACG-ATAGGATCGGCTTGAATAATTTAAGGAA
130 TCCCGAGCATGGAATGTTCGAAAAATTGGTCGAAGGAAT-GGATCGTCTTGAATACTTTAAGGAA
525 CCGAAGTTATAAAAGAACTCGT
194 CCGAAGTTATAAAAGAACTCGT
* *
547 AAAATTTGACAAGTTCGGAAGTTCATCCAAAAACC-A-AGAG--A-A-TCCTCACGTAAATAAGT
1 AAAATTTGACAAGTTCGGAAGTTCAGCCAAGAACCAAGAGAGAAACAGTCCTCACGTAAATAAGT
* * * * *** *
606 TTTCAATTCAAACACCAAAAGTTGTTTACAAAATTAAAAAAC-ATTTAGAATGAATGATGCGATT
66 TTTTAATTCAAAGACCAAAAGTTGTATACAAAA-TGAAAAACTATTTAGACCAAATAATGCGATT
* * * * * * * * * *
670 TCCTGAGCATGGAATGCTCGAAAAATTAGTCGAAGGAATGGGTCATCTTTAATGCTCTCAGAAAC
130 TCCCGAGCATGGAATGTTCGAAAAATTGGTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAAC
*
735 CGAAGTTATAAAAGAACTGGT
195 CGAAGTTATAAAAGAACTCGT
* *
756 AAATATTTGACAAGTTCTGAAGTTC-GTCCAAGAACCAAGAGAGAAACAGTCCTCATGTAAATAA
1 AAA-ATTTGACAAGTTCGGAAGTTCAG-CCAAGAACCAAGAGAGAAACAGTCCTCACGTAAATAA
* * * *
820 GTTTATAATTCAAAGACCAAAAGGTT-TTTACAAAATGACAAACTATTTAGACCAAATGATGCGA
64 GTTTTTAATTCAAAGACCAAAA-GTTGTATACAAAATGAAAAACTATTTAGACCAAATAATGCGA
* ** * * * *
884 TTTCCCGAGCATGGAATGTTTGAAAAATTGCACAAAGGAATGGATCGTCTTTAATGCTCTCAA-G
128 TTTCCCGAGCATGGAATGTTCGAAAAATTGGTCGAAGGAATGGATCGTCTTGAATACT-TTAAGG
* * *
948 AACCAAAGTTATAATAAAAAAACTTGT
192 AACCGAAG-T-T-ATAAAAGAACTCGT
* * * * * ** * * * *
975 AAATTTTTGAAAAGTTTGAAAGTTAATACAAGAACCAAGAGAG-AACATATTCTCATGCAAATAA
1 AAA-ATTTGACAAGTTCGGAAGTTCAGCCAAGAACCAAGAGAGAAACA-GTCCTCACGTAAATAA
* * * * * * * * *
1039 ATTTTAAATTCAAACACCAAAAGTTGTTTACCATATGACAAACTATTTTGACCAAATGATGC
64 GTTTTTAATTCAAAGACCAAAAGTTGTATACAAAATGAAAAACTATTTAGACCAAATAATGC
1101 AATT
Statistics
Matches: 631, Mismatches: 116, Indels: 41
0.80 0.15 0.05
Matches are distributed among these distances:
209 127 0.20
210 37 0.06
211 1 0.00
212 4 0.01
213 3 0.00
214 54 0.09
215 36 0.06
216 245 0.39
217 6 0.01
218 8 0.01
219 110 0.17
ACGTcount: A:0.41, C:0.14, G:0.17, T:0.27
Consensus pattern (215 bp):
AAAATTTGACAAGTTCGGAAGTTCAGCCAAGAACCAAGAGAGAAACAGTCCTCACGTAAATAAGT
TTTTAATTCAAAGACCAAAAGTTGTATACAAAATGAAAAACTATTTAGACCAAATAATGCGATTT
CCCGAGCATGGAATGTTCGAAAAATTGGTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAACC
GAAGTTATAAAAGAACTCGT
Done.