Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013755.1 Kokia drynarioides strain JFW-HI SEQ_128783, 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: 3416
ACGTcount: A:0.23, C:0.20, G:0.20, T:0.34
Warning! 50 characters in sequence are not A, C, G, or T
Found at i:166 original size:17 final size:17
Alignment explanation
Indices: 144--200 Score: 87
Period size: 17 Copynumber: 3.4 Consensus size: 17
134 TGGACTTTTC
* *
144 TAAATTTAATTTTATAA
1 TAAATTTAAATTTAAAA
161 TAAATTTAAATTTAAAA
1 TAAATTTAAATTTAAAA
*
178 TAAACTTAAATTTAAAA
1 TAAATTTAAATTTAAAA
195 TAAATT
1 TAAATT
201 CAATTCCCAA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 36 1.00
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:1084 original size:198 final size:198
Alignment explanation
Indices: 832--1525 Score: 1016
Period size: 198 Copynumber: 3.5 Consensus size: 198
822 NNNNNNNNNN
832 CAGGGAGCTGTGGTTCGAAGATTTGCTCATGTCGAGCATGGGTTTGGTTTGGTCTTCTTCTCAGT
1 CAGGGAGCTGTGGTTCGAAGATTTGCTCATGTCGAGCATGGGTTTGGTTTGGTCTTCTTCTCAGT
* *
897 ATCTCATCAGGAAGATGACTGCGTTGTTTGTTTCAATCCGCTTCTCTGTATCTCATCAGGAAGAC
66 ATCTCATCAGGAAGATGACCGCGTTGTTCGTTTCAATCCGCTTCTCTGTATCTCATCAGGAAGAC
*
962 GAATTTGGTCTACTTCTCCGTATCTCATCAGGAAGCTAATTACTTCGACACGCTTCTTAGTATCT
131 GAATTTGGTCTACTTCTCCGTATCTCATCAGGAAGCTAATTACTTCGACACGCTTCTCAGTATCT
1027 CAT
196 CAT
* *
1030 CAGGGAGCTGTGGTTCGAATATTTGTTCATGTCGAGCATGGGTTTGGTTTGGTCTTCTTCTCAGT
1 CAGGGAGCTGTGGTTCGAAGATTTGCTCATGTCGAGCATGGGTTTGGTTTGGTCTTCTTCTCAGT
** * *
1095 ATCTCATCAACAAGATGACCGCGTTGGTCGTTTCAATCCACTTCTCTGTATCTCATCAGGAAGAC
66 ATCTCATCAGGAAGATGACCGCGTTGTTCGTTTCAATCCGCTTCTCTGTATCTCATCAGGAAGAC
*
1160 GAATTTGGTCTACTTCTCCGTATCTCATCAGGAAGCTAATTACTTTGACACGCTTCTCAGTATCT
131 GAATTTGGTCTACTTCTCCGTATCTCATCAGGAAGCTAATTACTTCGACACGCTTCTCAGTATCT
1225 CAT
196 CAT
* *
1228 CAGGGAGCCGTGGTTCGAAGATTTGCTCATGTCAAGCATGGGTTTGGTTTGGTCTTCTTCTCAGT
1 CAGGGAGCTGTGGTTCGAAGATTTGCTCATGTCGAGCATGGGTTTGGTTTGGTCTTCTTCTCAGT
*
1293 ATCTCATCAGGAAGATGACCGCGTTGTTCGTTTCAATCCGCTTCTCTGTATCTTATCAGGAAGAC
66 ATCTCATCAGGAAGATGACCGCGTTGTTCGTTTCAATCCGCTTCTCTGTATCTCATCAGGAAGAC
* * *
1358 GAATTTGGTCTACTTCTCCGTAACTCATCAGGAAGCTAACTGTTTATTGCTCCGATC-TGCTTCT
131 GAATTTGGTCTACTTCTCCGTATCTCATCAGGAAGCTAA----TTA---CTTCGA-CACGCTTCT
* * *
1422 CGGTGTGTCAT
188 CAGTATCTCAT
* * * ** * *
1433 CAGGAAGCTG-GGATTCAAAGACTTGCTCACATC-ATGCACGGGCTTGGTTTGGTCTTCTTCTCA
1 CAGGGAGCTGTGG-TTCGAAGATTTGCTCATGTCGA-GCATGGGTTTGGTTTGGTCTTCTTCTCA
* * *
1496 ATATCTCATCAGGAAGCTGACCACGTTGTT
64 GTATCTCATCAGGAAGATGACCGCGTTGTT
1526 TTGTGGGTAT
Statistics
Matches: 449, Mismatches: 37, Indels: 13
0.90 0.07 0.03
Matches are distributed among these distances:
198 347 0.77
202 3 0.01
204 3 0.01
205 95 0.21
206 1 0.00
ACGTcount: A:0.20, C:0.22, G:0.22, T:0.35
Consensus pattern (198 bp):
CAGGGAGCTGTGGTTCGAAGATTTGCTCATGTCGAGCATGGGTTTGGTTTGGTCTTCTTCTCAGT
ATCTCATCAGGAAGATGACCGCGTTGTTCGTTTCAATCCGCTTCTCTGTATCTCATCAGGAAGAC
GAATTTGGTCTACTTCTCCGTATCTCATCAGGAAGCTAATTACTTCGACACGCTTCTCAGTATCT
CAT
Done.