Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018402013.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_5108.1, 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, 693
Length: 1155
ACGTcount: A:0.32, C:0.09, G:0.12, T:0.30
Warning! 189 characters in sequence are not A, C, G, or T
Found at i:840 original size:172 final size:170
Alignment explanation
Indices: 319--851 Score: 486
Period size: 172 Copynumber: 3.1 Consensus size: 170
309 NNNNNNNNNN
* *
319 AGATTATAAAACAATTTAAAGCGAGTAATAAGCCTTTTGAAGGAATGGGTAACTATAAATGGACT
1 AGATTATAAAACTATTTAAAGCGAGTAATAAGCCTTTTGAAGGAAT-GGTAACTCTAAATGGAC-
* * * * * *
384 CTTTTTCTT-AATGAATGGCTT-TTTTTGCATGTTTCTTGAGGTAAACATTCAATTACAGTCTGT
64 CTTTTTTTTCAATGAATGGCTTGTTTTT-CATGTTTCTCGAGATAGACATTTAATTATAGTCTGT
*
447 TGTAA-CAAAATATGTAAAAAAAATTCAACTTAAAATCAATCATG
128 TTTAATCAAAA-ATGT-AAAAAAATTCAACTTAAAATCAATCATG
* * * *
491 AGATTATAAAA-TCATTAAAAGCGGGTAATAAACCTTTTGAAAGAATGAGTAAC-CATAAAT-GA
1 AGATTATAAAACT-ATTTAAAGCGAGTAATAAGCCTTTTGAAGGAATG-GTAACTC-TAAATGGA
* * * * * * **
553 GCTTTTTTTCTCAACGAATGGATTGTTTTTTTATGTTTCTCGAGATAGATAATTACCTATAGTCT
63 CCTTTTTTT-TCAATGAATGGCTTG-TTTTTCATGTTTCTCGAGATAGACATTTAATTATAGTCT
* * * **********
618 GTTTGAATAAAAAATGTAAAAAAATTAAACTTAANNNNNNNNNNG
126 GTTTTAATCAAAAATGTAAAAAAATTCAACTTAAAATCAATCATG
* * * *
663 AGATTATAAAACTGTTTAAAGCGAGAAATAAGCTTTTTGAAGGAATAGGTGACTCTAAATGGACC
1 AGATTATAAAACTATTTAAAGCGAGTAATAAGCCTTTTGAAGGAAT-GGTAACTCTAAATGGACC
* * * *
728 TTTTTTTTCAATGAAT-GCTTGTTTCTTCACGTTTCTCAAGTTAGACATTTAATTATAGTATGTT
65 TTTTTTTTCAATGAATGGCTTGTTT-TTCATGTTTCTCGAGATAGACATTTAATTATAGTCTG-T
* * *
792 TTTAATCAAAAATGTAAAAAAATGCAACTTAAAATTAATTATG
128 TTTAATCAAAAATGTAAAAAAATTCAACTTAAAATCAATCATG
*
835 AGATTATAAAACCATTT
1 AGATTATAAAACTATTT
852 NNNNNNNNNN
Statistics
Matches: 277, Mismatches: 70, Indels: 28
0.74 0.19 0.07
Matches are distributed among these distances:
170 10 0.04
171 36 0.13
172 176 0.64
173 46 0.17
174 9 0.03
ACGTcount: A:0.38, C:0.11, G:0.14, T:0.35
Consensus pattern (170 bp):
AGATTATAAAACTATTTAAAGCGAGTAATAAGCCTTTTGAAGGAATGGTAACTCTAAATGGACCT
TTTTTTTCAATGAATGGCTTGTTTTTCATGTTTCTCGAGATAGACATTTAATTATAGTCTGTTTT
AATCAAAAATGTAAAAAAATTCAACTTAAAATCAATCATG
Done.