Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018402309.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_5391.0, 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, 847
Length: 1413
ACGTcount: A:0.29, C:0.10, G:0.11, T:0.28
Warning! 296 characters in sequence are not A, C, G, or T
Found at i:601 original size:171 final size:170
Alignment explanation
Indices: 4--973 Score: 993
Period size: 171 Copynumber: 5.7 Consensus size: 170
1 TTG
* * ** ** * * * * * *
4 CCAATGAATGCCTTTTTCTTCACATTTCTTGAGGTAGACATTTAATTATAATTTGTTTTGACCAA
1 CCAATGAATGGCTTTTTCTACATGTTTCTCAAGGCAGACATTCAATTATAGTCTATTTTAACCAA
* * *
69 AAATGTAAAAAAAATTGAACTTAAAATCAATTTTGAGATTATAAAACCATTTAAAGTGAGTAATA
66 AAATGT-AAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATA
* ** * * *
134 AGGCTTTTGAAGGAATCAGTCACTA-GAATAGACTTTTCTT
130 AGGCATTTGAAGGAATGGGTGACTATTAATGGACTTTTCTT
* * * * * **
174 CCTGATGAATGGCTTTTTCTACATGTTTCTTAAGACAGGCATTCAATTATTGTCTATTTTAATGA
1 CC-AATGAATGGCTTTTTCTACATGTTTCTCAAGGCAGACATTCAATTATAGTCTATTTTAACCA
* * * *
239 AAAATGTTAAAAAATTCAACTTAGAATCAATTATGAGATTATAAAATCATTTAATGCGAGTAATA
65 AAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATA
* * *
304 AGGC-TTTTAGAGGAATGGGTGGCTA-TAATGAACTTTTCTT
130 AGGCATTTGA-AGGAATGGGTGACTATTAATGGACTTTTCTT
* * * * * * * * *
344 GCCAATGAAT-ACATTTTTCTTCATGTTTTTCAAGGTAAAAATTAAATTATTGT-TCGTTTTAAC
1 -CCAATGAATGGC-TTTTTCTACATGTTTCTCAAGGCAGACATTCAATTATAGTCT-ATTTTAAC
* * * *
407 CAAAAATGTAAAACAATTCAACTTAAAATCAATTATGAGACTATAAAACCATTTACAGTGAGTAA
63 CAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAA
* *
472 TAAGGCATTTGAAAGAATAGGTGACTATTAATGGACTTTTCTT
128 TAAGGCATTTGAAGGAATGGGTGACTATTAATGGACTTTTCTT
* * * * * *
515 CTCAATGAATGGCTTTTTCTACATGTTCCTCGAGGCAGGCATTTAATTATACTCTATTTTAATCA
1 C-CAATGAATGGCTTTTTCTACATGTTTCTCAAGGCAGACATTCAATTATAGTCTATTTTAACCA
* * *
580 AAAATGTAAAAAAAATCAACTTAAAATCAATTATGAGATTATAAAACTATTTAAAACGAGTAATA
65 AAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATA
* * *
645 AGGCTTTTGATA-GAATGGGTGACTGTAAATGGACTTTTCTT
130 AGGCATTTGA-AGGAATGGGTGACTATTAATGGACTTTTCTT
* * * * ** *
686 GCCAATAAATGCCTTTTTTTTCATGTTTCTTGAGGTAGACATTCAATTATAGTCTATTTTAACCA
1 -CCAATGAATGGCTTTTTCTACATGTTTCTCAAGGCAGACATTCAATTATAGTCTATTTTAACCA
* * * * *
751 AAAAAGGAAAACAATTCAACTTAAAATCAATTATGGGATTATAAAACCATTCAAAGCGAGTAATA
65 AAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATA
* *
816 AGGCATTTGAAGGAATGGGTGA-TGATTAATGCACTTTTTTT
130 AGGCATTTGAAGGAATGGGTGACT-ATTAATGGACTTTTCTT
* ** * *
857 CTCAATGAATGGCTTTTTGTACATAATTCCCAAGGCA-AGCATTCAATTATAGTCTATTTTAATA
1 C-CAATGAATGGCTTTTTCTACATGTTTCTCAAGGCAGA-CATTCAATTATAGTCTATTTTAA-C
* * * * *
921 AAAAAATATAAAACAATTCAACATAAAATCAATTATGAGATTATAAAATCATT
63 CAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATT
974 NNNNNNNNNN
Statistics
Matches: 657, Mismatches: 126, Indels: 32
0.81 0.15 0.04
Matches are distributed among these distances:
169 6 0.01
170 202 0.31
171 399 0.61
172 50 0.08
ACGTcount: A:0.38, C:0.12, G:0.14, T:0.36
Consensus pattern (170 bp):
CCAATGAATGGCTTTTTCTACATGTTTCTCAAGGCAGACATTCAATTATAGTCTATTTTAACCAA
AAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAA
GGCATTTGAAGGAATGGGTGACTATTAATGGACTTTTCTT
Done.