Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018402455.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_5532.0, 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, 601
Length: 1002
ACGTcount: A:0.35, C:0.11, G:0.13, T:0.33
Warning! 71 characters in sequence are not A, C, G, or T
Found at i:542 original size:170 final size:159
Alignment explanation
Indices: 339--663 Score: 352
Period size: 169 Copynumber: 2.0 Consensus size: 159
329 AGTAATAAGC
* * *
339 CTTTTGAAGGAATGGGTGCCTATAAAGGGACTTTTCTTGCCAATGAATGCTTTCTTCTTCACGTT
1 CTTTTGAAGGAATAGGTGACTATAAAGGGACTTTTCTTGCCAATGAATCCTTT-TT-TTCACGTT
* *
404 T-GAAGAGGTAAACATTCAATTATAATCTGTTTTAA-CAAAAAATG-TAAAAAATTCAACTTAAA
64 TCGAA-AGGTAAACATTCAATTATAATATGTTTTAATCAAAAAA-GAAAAAAAATTCAACTTAAA
*
466 GTCAATTATT-AGATTATAAAACCATTTAAAGNNNNNNNNNNGG
127 ATCAATT-TTGAGATTATAAAACCATTTAAAG----------GG
* * *
509 CTTTTGAAGGAATAGGTGACTATAAATGGACTTTTCTTGCCAATGAGTCCTTTTTTTTACGTTTC
1 CTTTTGAAGGAATAGGTGACTATAAAGGGACTTTTCTTGCCAATGAATCCTTTTTTTCACGTTTC
** * * * *
574 TCAAGGTAGACATTCAATTATAATATTTTTTAATCGAAAAAGAAAAAAAATTGAACTTAAAATCA
66 GAAAGGTAAACATTCAATTATAATATGTTTTAATCAAAAAAGAAAAAAAATTCAACTTAAAATCA
639 ATTTTGAGATTATAAAACCATTTAA
131 ATTTTGAGATTATAAAACCATTTAA
664 NNNNNNNNNN
Statistics
Matches: 136, Mismatches: 15, Indels: 9
0.85 0.09 0.06
Matches are distributed among these distances:
168 38 0.28
169 50 0.37
170 48 0.35
ACGTcount: A:0.36, C:0.12, G:0.14, T:0.35
Consensus pattern (159 bp):
CTTTTGAAGGAATAGGTGACTATAAAGGGACTTTTCTTGCCAATGAATCCTTTTTTTCACGTTTC
GAAAGGTAAACATTCAATTATAATATGTTTTAATCAAAAAAGAAAAAAAATTCAACTTAAAATCA
ATTTTGAGATTATAAAACCATTTAAAGGG
Done.