Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018400278.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_3487.0, 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, 991
Length: 1652
ACGTcount: A:0.27, C:0.08, G:0.09, T:0.25
Warning! 518 characters in sequence are not A, C, G, or T
Found at i:1135 original size:170 final size:170
Alignment explanation
Indices: 851--1162 Score: 423
Period size: 170 Copynumber: 1.8 Consensus size: 170
841 TGTTTTACCC
* *
851 ATGGATATCTTTTTCTTCACGTTTCTCGAGGTAAACACTCAATTATAATATGCTTTAATAAAAAT
1 ATGGATATCTTTTTCTTCACGTTTCTCGAGGCAAACACTCAATTAAAATATGCTTTAATAAAAAT
* * ** * **
916 ATAAAAAAATTTAATCTAAAATCAAATATGTTGTTATAAAATTATTTAATACGAGTAATAAGGCT
66 ATAAAAAAATTAAATCAAAAATCAAATATGAGGTAATAAAAACATTTAATACGAGTAATAAGGCT
981 TTCGAAAGCATGAGTAACTCTAAATGGACTTTTCTTGACA
131 TTCGAAAGCATGAGTAACTCTAAATGGACTTTTCTTGACA
* ** * * *
1021 ATGGATATCTTTTTCTTTACGTTTCTC-AGGGCAGTCATTCAATTAAAATCTGTTTTAATAAAAA
1 ATGGATATCTTTTTCTTCACGTTTCTCGA-GGCAAACACTCAATTAAAATATGCTTTAATAAAAA
* *
1085 -ATATAAAAAATTCAAAT-AAAAATCAATTATGAGGTAATAAAAACATTTAATGCGAGTAATAAG
65 TATA-AAAAAATT-AAATCAAAAATCAAATATGAGGTAATAAAAACATTTAATACGAGTAATAAG
1148 GCTTTCGAAAGCATG
128 GCTTTCGAAAGCATG
1163 GGNNNNNNNN
Statistics
Matches: 122, Mismatches: 17, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
169 4 0.03
170 115 0.94
171 3 0.02
ACGTcount: A:0.40, C:0.12, G:0.12, T:0.35
Consensus pattern (170 bp):
ATGGATATCTTTTTCTTCACGTTTCTCGAGGCAAACACTCAATTAAAATATGCTTTAATAAAAAT
ATAAAAAAATTAAATCAAAAATCAAATATGAGGTAATAAAAACATTTAATACGAGTAATAAGGCT
TTCGAAAGCATGAGTAACTCTAAATGGACTTTTCTTGACA
Done.