Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018399894.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_3128.0, 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: 1962
ACGTcount: A:0.32, C:0.10, G:0.10, T:0.29
Warning! 378 characters in sequence are not A, C, G, or T
Found at i:445 original size:172 final size:171
Alignment explanation
Indices: 1--751 Score: 654
Period size: 170 Copynumber: 4.4 Consensus size: 171
* * * * * * ** *
1 ATGTAAAACAATTCAATTTAAACTTAATTATGAGATTAAAAAATTATTTAAAATAAGTAATAAGG
1 ATGTAAAAAAATTCAACTTAAAATCAATTATGACATTATAAAACCATTTAAAATGAGTAATAAGG
* * * *
66 CTTTTAAAAGAATAGGTGACTATAAATGGACTTTTCTTGCCAATGAATACCTTTTTCTTCACATT
66 CTTTTGAAAGAATAGGTGACTATAAATGAACTTTTCTTACCAATGAATACCTTTTTCTTCACGTT
* * *
131 TCTCGA-G-CAATCATTCAAATATAATCTGTTTTAACTAAAA
131 TCTCAAGGTAAAT-ATTCAATTATAATCTGTTTTAACTAAAA
* *
171 ATGTAAAAAAATTCAACTGAAACTCAATTATGACATTATAAAACCATTTAAAATGAGTAATAAGG
1 ATGTAAAAAAATTCAACTTAAAATCAATTATGACATTATAAAACCATTTAAAATGAGTAATAAGG
** *
236 CTTTTGAAAGAAT-GGCTGACTATAAATGAGTTTTTCTTACCAATGAATATCTTTTTCTTCACGT
66 CTTTTGAAAGAATAGG-TGACTATAAATGAACTTTTCTTACCAATGAATACCTTTTTCTTCACGT
* *
300 TTTTCAAGGTAAATATTCAATTATAATCTGTTTTAACCAAAA
130 TTCTCAAGGTAAATATTCAATTATAATCTGTTTTAACTAAAA
* ********** *
342 ATGTAAAAAAAAATCAACTTAAAATCAATTANNNNNNNNNNAAACCATTTAAAGTGAGTAATAAG
1 ATGT-AAAAAAATTCAACTTAAAATCAATTATGACATTATAAAACCATTTAAAATGAGTAATAAG
* * * ** *
407 GCTTTTGAAGGAATAGGTGGCTGTAAACAAACTTTTCTTACCAATGAAAACCCTTTTT-TTC-CT
65 GCTTTTGAAAGAATAGGTGACTATAAATGAACTTTTCTTACCAATGAATA-CCTTTTTCTTCAC-
* ** *
470 GTTTCTCAAGGTAGACGTTCAATTATAATCTGTTTTAACTAAGA
128 GTTTCTCAAGGTAAATATTCAATTATAATCTGTTTTAACTAAAA
** * * * * ***
514 ATGTAAAATTATTCAACTTAAAATCAATTTTCAGATTATAAAACTATTTAATGCGAGTAATAAGG
1 ATGTAAAAAAATTCAACTTAAAATCAATTATGACATTATAAAACCATTTAAAATGAGTAATAAGG
* * ** * *
579 CTTTT-AAAGGAATGGGTTACTATAAATTCACTTTTCTTGCCAATGAATACCTTTTTCTTCACAT
66 CTTTTGAAA-GAATAGGTGACTATAAATGAACTTTTCTTACCAATGAATACCTTTTTCTTCACGT
*********** * * * *
643 TTCNNNNNNNNNNCATTAAAGTAT-AGCTTGTTTTAA-AAAAA
130 TTCTCAAGGTAAATATTCAATTATAATC-TGTTTTAACTAAAA
* * * * **
684 ATGTAAAAAACTTTAACTTAAAATCAATTATGAAATTATAAAGCCATTTAAAGCGAGTAATAAGG
1 ATGTAAAAAAATTCAACTTAAAATCAATTATGACATTATAAAACCATTTAAAATGAGTAATAAGG
749 CTT
66 CTT
752 NNNNNNNNNN
Statistics
Matches: 466, Mismatches: 104, Indels: 22
0.79 0.18 0.04
Matches are distributed among these distances:
169 2 0.00
170 187 0.40
171 135 0.29
172 134 0.29
173 8 0.02
ACGTcount: A:0.39, C:0.13, G:0.11, T:0.35
Consensus pattern (171 bp):
ATGTAAAAAAATTCAACTTAAAATCAATTATGACATTATAAAACCATTTAAAATGAGTAATAAGG
CTTTTGAAAGAATAGGTGACTATAAATGAACTTTTCTTACCAATGAATACCTTTTTCTTCACGTT
TCTCAAGGTAAATATTCAATTATAATCTGTTTTAACTAAAA
Done.