Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018401081.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_424.0, 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, 1000
Length: 2723
ACGTcount: A:0.24, C:0.08, G:0.08, T:0.21
Warning! 1065 characters in sequence are not A, C, G, or T
Found at i:2679 original size:171 final size:160
Alignment explanation
Indices: 2415--2723 Score: 352
Period size: 171 Copynumber: 1.9 Consensus size: 160
2405 AGTAATAAGG
* * *
2415 CTTTTAAAGGAATAGAAGACTATAAATGGGCTTTTCTTGCCAATGAATACTTTTTTCTTCACGTT
1 CTTTTAAAGGAATAGAAGACTATAAATAGGCTTTTCTTGCCAATGAATACATTTTTATTCACGTT
* * * * * *
2480 TCCTGAGGTAGAGATTCAGTTGTAGTCTGCTTTAACTAAAAATATTAAAAAATTCAACTTCATAT
66 TCCTGAGGTAGACAATCAGTTATAGTCTGCTTTAACAAAAAATA-TAAAAAATTCAACTTAAAAT
2545 CAATTATGAGATTATAAAACCATTTAAANNNNNNNNNNAGA
130 CAATTATGAGATTATAAAACCATTTAAA----------AGA
* ** * *
2586 CTTTTAAAGGAATGGGCGACTATAAATAGGCTTTTCTTGCTAATGAA-AGCATTTTTATTCATGT
1 CTTTTAAAGGAATAGAAGACTATAAATAGGCTTTTCTTGCCAATGAATA-CATTTTTATTCACGT
*
2650 TT-CTCGAGGTAGACAATCAGTTATAGTCTGTTTTAACAAAAAATATAAAAAATTCAACTTAAAA
65 TTCCT-GAGGTAGACAATCAGTTATAGTCTGCTTTAACAAAAAATATAAAAAATTCAACTTAAAA
2714 TCAATTATGA
129 TCAATTATGA
Statistics
Matches: 121, Mismatches: 15, Indels: 5
0.86 0.11 0.04
Matches are distributed among these distances:
170 30 0.25
171 91 0.75
ACGTcount: A:0.36, C:0.13, G:0.14, T:0.35
Consensus pattern (160 bp):
CTTTTAAAGGAATAGAAGACTATAAATAGGCTTTTCTTGCCAATGAATACATTTTTATTCACGTT
TCCTGAGGTAGACAATCAGTTATAGTCTGCTTTAACAAAAAATATAAAAAATTCAACTTAAAATC
AATTATGAGATTATAAAACCATTTAAAAGA
Done.