Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018402510.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_5584.0, 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, 642
Length: 1070
ACGTcount: A:0.36, C:0.13, G:0.14, T:0.32
Warning! 60 characters in sequence are not A, C, G, or T
Found at i:296 original size:170 final size:170
Alignment explanation
Indices: 1--1070 Score: 759
Period size: 171 Copynumber: 6.3 Consensus size: 170
* * **
1 AAGCGAGTAATAAGGCTTTCGAAGGCACGGGCGACTATAAATGGACTTTTCTTGATAATGGATAT
1 AAGCGAGTAATAAGGCTTTCGAAGGCATGGGTGACTATAAATGGACTTTTCTTGCCAATGGATAT
* * * * *
66 CTTTATCTTCACATTTCTTGAGGTAAACATACAATTATAATCTGTTTTCATAATAAATATAAAAA
66 CTTTTTCTTCACATTTCTCGAGGTAAACATTCAATTATAATCTGTTTTAATAAAAAATATAAAAA
* **********
131 AGTTCAACTTAAAACTAATTATGAGATTANNNNNNNNNNTA
131 AATTCAACTTAAAA-TAATTATGAGATTATAAAATCATTTA
** * * * * *
172 AAGCGACCAATAAGGCTTTCGAAGGCATGAGTTACAATAAATAGACTTTTCTTGCCAATCGATA-
1 AAGCGAGTAATAAGGCTTTCGAAGGCATGGGTGACTATAAATGGACTTTTCTTGCCAATGGATAT
* * * *
236 CTTTTTCTTCACGTTTATCGATGTAGACATTCAATTATAATCTGTTTTAATAAAAAATATAAAAA
66 CTTTTTCTTCACATTTCTCGAGGTAAACATTCAATTATAATCTGTTTTAATAAAAAATATAAAAA
* **********
301 AACTCAAACNNNNNNNNNNTATGAGATTATAAAATCATTTA
131 AATTC-AACTTAAAATAATTATGAGATTATAAAATCATTTA
* * *
342 AAGCGAGTAACAAGGCTTTCGAAGGCATGGGTAACTATAAATGGACTTTTCTTGCCAATGGATAC
1 AAGCGAGTAATAAGGCTTTCGAAGGCATGGGTGACTATAAATGGACTTTTCTTGCCAATGGATAT
* * * * ** *
407 CTTTTTCTTCACGTTTTTTTGAGGCAGCCATTCAATTATAAT-TTTTTTAATAAAAAATATAAAA
66 CTTTTTCTTCAC-ATTTCTCGAGGTAAACATTCAATTATAATCTGTTTTAATAAAAAATATAAAA
* * **********
471 AAATTAAAATTAAAATCAATTATGATG-TTNNNNNNNNNNTTA
130 AAATTCAACTTAAAAT-AATTATGA-GATTATAAAATCATTTA
* * * * * * *
513 AACCGAGTAATAAGGCTTTTGAAGGCAGGGGTGGCTATAAATTGACTTTTCTTGCTAATAGATAT
1 AAGCGAGTAATAAGGCTTTCGAAGGCATGGGTGACTATAAATGGACTTTTCTTGCCAATGGATAT
* * *
578 ATTTTTCTTCACATTTCTCGAGGTAAACATTCAATTATAATCTGTTTCACTAAAAAATATAAAAA
66 CTTTTTCTTCACATTTCTCGAGGTAAACATTCAATTATAATCTGTTTTAATAAAAAATATAAAAA
* ********* * *
643 AGTTCAACTTANNNNNNNNNNTGAGATTAAAAAACCATTTA
131 AATTCAACTTA-AAATAATTATGAGATTATAAAATCATTTA
* * * * *
684 AAGCGAGTGATAAGACTTTCGAAGGCATAGGTGACTATATATGGACTTTTCTTACCAATGGATAT
1 AAGCGAGTAATAAGGCTTTCGAAGGCATGGGTGACTATAAATGGACTTTTCTTGCCAATGGATAT
* ** * ********** *
749 CATTTTCTTCATGTTTCTCGAGGTAAACATTTAATTATAATCTNNNNNNNNNNAAATTATAAAAA
66 CTTTTTCTTCACATTTCTCGAGGTAAACATTCAATTATAATCTGTTTTAATAAAAAATATAAAAA
* *
814 AATTCAACTTCAAATCAATTATGAGGTTATGAAAAT-ATTTA
131 AATTCAACTTAAAAT-AATTATGAGATTAT-AAAATCATTTA
* * * * * * *
855 AGGCGAGTAATAAGGCTTCCAAAGGTATTGGCGACTATAAATGGACTTCTCTTGCCAATGGATAT
1 AAGCGAGTAATAAGGCTTTCGAAGGCATGGGTGACTATAAATGGACTTTTCTTGCCAATGGATAT
********** * * * * * * * *
920 NNNNNNNNNNATATTTTTTGAGGCAGACGTTCAATTATAATCTATTTTAATAAAAAATA-GAAAA
66 CTTTTTCTTCACATTTCTCGAGGTAAACATTCAATTATAATCTGTTTTAATAAAAAATATAAAAA
* * *
984 AGTTCAACTTAAAACCAATTGTGAGATTA-AAACA-CTATTTA
131 AATTCAACTTAAAA-TAATTATGAGATTATAAA-ATC-ATTTA
*
1025 AAGCGAGTCATAAGGCTTTCGAAGGCATGGGTGACTATAAATGGAC
1 AAGCGAGTAATAAGGCTTTCGAAGGCATGGGTGACTATAAATGGAC
Statistics
Matches: 669, Mismatches: 216, Indels: 29
0.73 0.24 0.03
Matches are distributed among these distances:
168 3 0.00
169 1 0.00
170 224 0.33
171 413 0.62
172 28 0.04
ACGTcount: A:0.36, C:0.13, G:0.14, T:0.32
Consensus pattern (170 bp):
AAGCGAGTAATAAGGCTTTCGAAGGCATGGGTGACTATAAATGGACTTTTCTTGCCAATGGATAT
CTTTTTCTTCACATTTCTCGAGGTAAACATTCAATTATAATCTGTTTTAATAAAAAATATAAAAA
AATTCAACTTAAAATAATTATGAGATTATAAAATCATTTA
Done.