Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013289.1 Kokia drynarioides strain JFW-HI SEQ_128311, 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: 9371
ACGTcount: A:0.24, C:0.22, G:0.19, T:0.35
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:42 original size:18 final size:17
Alignment explanation
Indices: 1--46 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 17
1 ATAAATTTAAATTTTTAA
1 ATAAATTT-AATTTTTAA
**
19 GCAAATTTAATTTTTAAA
1 ATAAATTTAATTTTT-AA
37 ATAAATTTAA
1 ATAAATTTAA
47 AGGGAGTATG
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
17 7 0.30
18 16 0.70
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (17 bp):
ATAAATTTAATTTTTAA
Found at i:719 original size:139 final size:140
Alignment explanation
Indices: 506--1665 Score: 1868
Period size: 139 Copynumber: 8.3 Consensus size: 140
496 CTTTGACCTG
** *
506 CTTCTCAGTGTCTCATCTGGAAGATTTGCTCGTTTCGAGCCTCGTTTGGGTCTTCTTCTCAGTGT
1 CTTCTCAGTACCTCATCTGGAAGATTCGCTCGTTTCGAGCCTCGTTTGGGTCTTCTTCTCAGTGT
* * * ** *
571 CTCACCAGGAAGATGATCCCATCACTGTTTCAATCCGCTCCTT-TGTATCTCATCAGGAAGGCAA
66 CTCATCAGGAAGATGATCCCATCATTGTTCCAATCCGCTTTTTCTGTATCTCATCAGGAAGGCGA
635 ATTTGGTTCA
131 ATTTGGTTCA
645 CTTCTCAGTACCTCATCTGGAAGATTCGCTCGTTTCGAGCCTCGTTTGGGTCTTCTTCTCAGTGT
1 CTTCTCAGTACCTCATCTGGAAGATTCGCTCGTTTCGAGCCTCGTTTGGGTCTTCTTCTCAGTGT
* *
710 CTCATCAGGAAGATGATCCCATCATTGTTCCAATCCGC-TTTTCTGCATCTCATCAGGAAGGCGT
66 CTCATCAGGAAGATGATCCCATCATTGTTCCAATCCGCTTTTTCTGTATCTCATCAGGAAGGCGA
774 ATTTGGTTCA
131 ATTTGGTTCA
* *
784 CTTCTCAGTACCCCATCTGGAAGATTCGCTCGTTTCGAGCCTCGTTTGGGTCTTCTTCTCAATGT
1 CTTCTCAGTACCTCATCTGGAAGATTCGCTCGTTTCGAGCCTCGTTTGGGTCTTCTTCTCAGTGT
* *
849 CTCATCAGGAAGATGATCCCATCATTGTTCCAATCCGC-TTTTCTGTATCTCATCCGGAAGGCGT
66 CTCATCAGGAAGATGATCCCATCATTGTTCCAATCCGCTTTTTCTGTATCTCATCAGGAAGGCGA
913 ATTTGGTTCA
131 ATTTGGTTCA
* *
923 CTTCTCAGTACCTCATTTGGAAGATTTGCTCGTTTCGAGCCTCGTTTGGGTCTTCTTCTCAGTGT
1 CTTCTCAGTACCTCATCTGGAAGATTCGCTCGTTTCGAGCCTCGTTTGGGTCTTCTTCTCAGTGT
*
988 CTCATCAGGAAGATGATCCCATCATTGTTTCAATCCGCTTTTT-TGTATCTCATCAGGAAGGCGA
66 CTCATCAGGAAGATGATCCCATCATTGTTCCAATCCGCTTTTTCTGTATCTCATCAGGAAGGCGA
1052 ATTTGGTTCA
131 ATTTGGTTCA
* *
1062 CTTCTCAGTACCTCATCTGGAAGATTCACTCTTTTCGAGCCTCGTTTGGGTCTTCTTCTCAGTGT
1 CTTCTCAGTACCTCATCTGGAAGATTCGCTCGTTTCGAGCCTCGTTTGGGTCTTCTTCTCAGTGT
* *
1127 CTCATCAGAAAGATGATCCCATCATTGTTCCAATCCG-TTTTTCTGTATCTCATCAGGAAGGCGT
66 CTCATCAGGAAGATGATCCCATCATTGTTCCAATCCGCTTTTTCTGTATCTCATCAGGAAGGCGA
1191 ATTTGGTTCA
131 ATTTGGTTCA
* *
1201 CTTCTCAGTACCTTATCTGGAAGATTCACTCGTTTCGAGCCTCGTTTGGGTCTTCTTCTCAGTGT
1 CTTCTCAGTACCTCATCTGGAAGATTCGCTCGTTTCGAGCCTCGTTTGGGTCTTCTTCTCAGTGT
* * * * *
1266 CTCATCAAGAAGATGATCCCATCATTGTTTCAATCCGC-TTCTCTATATCTCATCAGGAAGACGA
66 CTCATCAGGAAGATGATCCCATCATTGTTCCAATCCGCTTTTTCTGTATCTCATCAGGAAGGCGA
1330 ATTTGGTTCA
131 ATTTGGTTCA
* * *
1340 CTTCTTAGTACCTCATCTAGAAGATTCGCTCGTTTCGAGCCTCATTTGGGTCTTCTTCTCAGTGT
1 CTTCTCAGTACCTCATCTGGAAGATTCGCTCGTTTCGAGCCTCGTTTGGGTCTTCTTCTCAGTGT
* * *
1405 CTCATCAGGAAGATGATCCCATCATTGTTCCAATCCGCTTTTT-TATATCTCATCAGGAATGCGT
66 CTCATCAGGAAGATGATCCCATCATTGTTCCAATCCGCTTTTTCTGTATCTCATCAGGAAGGCGA
*
1469 ATTTGGTTTA
131 ATTTGGTTCA
* *
1479 CTTCTCAGTACCTCATCTGGAAGATTCGCTCGTTTCGAGCCTCGTTTGGATCTTCTTCTCCGTGT
1 CTTCTCAGTACCTCATCTGGAAGATTCGCTCGTTTCGAGCCTCGTTTGGGTCTTCTTCTCAGTGT
* * * *
1544 CTCATTAGGAAGATGATCCCATCATTGTTTCAATCCTC-TTTTCTGTATCTCATCAGGAAGACGA
66 CTCATCAGGAAGATGATCCCATCATTGTTCCAATCCGCTTTTTCTGTATCTCATCAGGAAGGCGA
1608 ATTTGGTTCA
131 ATTTGGTTCA
* *
1618 CTTCTTAGTACCTCATCTGGAAGATTCGCTCGTTTCGAGCCTCATTTG
1 CTTCTCAGTACCTCATCTGGAAGATTCGCTCGTTTCGAGCCTCGTTTG
1666 ATTTGGGCTT
Statistics
Matches: 950, Mismatches: 65, Indels: 12
0.93 0.06 0.01
Matches are distributed among these distances:
138 11 0.01
139 932 0.98
140 7 0.01
ACGTcount: A:0.19, C:0.25, G:0.19, T:0.37
Consensus pattern (140 bp):
CTTCTCAGTACCTCATCTGGAAGATTCGCTCGTTTCGAGCCTCGTTTGGGTCTTCTTCTCAGTGT
CTCATCAGGAAGATGATCCCATCATTGTTCCAATCCGCTTTTTCTGTATCTCATCAGGAAGGCGA
ATTTGGTTCA
Done.