Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018401762.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_4875.0, 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: 1917
ACGTcount: A:0.31, C:0.08, G:0.11, T:0.27
Warning! 441 characters in sequence are not A, C, G, or T
Found at i:388 original size:171 final size:171
Alignment explanation
Indices: 7--849 Score: 612
Period size: 171 Copynumber: 4.9 Consensus size: 171
1 TTACAG
* * * * * *
7 CGAGTAATGAGGCTTTTG-AGGAATGAGTGACTATAAA-AGGACTTTTCTTGCAA-ATGAATACC
1 CGAGTAATAAGGCTTCTGAAGGAATGAGTAACTATAAATA-GACTTTTCTTTCAACA--AATGCA
* * * * *
69 TTTTTCTTCATGTTTCT-TGAGATAGACATTCAATTACAGTTTGTTTTAACAAAAAAAATGTAAA
63 TTTTTCTTCAAGTTTCTCTAAGATAGACATTCAATTATAGTCTGTTTTAAC--CAAAAATGTAAA
* * * *
133 GAAATTCAACTTAAAATTAATTATGAGATTATGAAACAATTTAAAA
126 AAAAATCAACTTAAAATTAATTATGAGATTATAAAATAATTTAAAA
* *
179 CGAGTAATAAGGCTTCCGAAAGAATTG-GTAACTATAAATAGACTTTTCTTATCAACAAATGCAT
1 CGAGTAATAAGGCTTCTGAAGGAA-TGAGTAACTATAAATAGACTTTTCTT-TCAACAAATGCAT
* * *
243 TTTTCTTCAAGTTTCTC-AAGGTAGACATTCAATTATAGTCTATTTTAACCAAAAACGTAAAAAA
64 TTTTCTTCAAGTTTCTCTAAGATAGACATTCAATTATAGTCTGTTTTAACCAAAAATGTAAAAAA
* *
307 AATCAACTTAAAAATAATTATAAGATTATAAAATAATTTAAAA
129 AATCAACTTAAAATTAATTATGAGATTATAAAATAATTTAAAA
* * * * * ********* ** **
350 CGAGTACA-AAAGCTTTTGAAGGAATGGGTGACTATAAATGGNNNNNNNNNNTCAATGAATGGGT
1 CGAGTA-ATAAGGCTTCTGAAGGAATGAGTAACTATAAATAG-ACTTTTCTTTCAACAAATGCAT
* * *
414 TTTTCTAT-ACA-TTTC-CTAAGACA-AGCATTCAATTATAGTCTGTTTTATCTAAAAATGTGAA
64 TTTTCT-TCA-AGTTTCTCTAAGATAGA-CATTCAATTATAGTCTGTTTTAACCAAAAATGT-AA
* * * * **
475 AACAATTTAACTTAGAATTAATTATGAGACAATAAAATAATTTAAAA
125 AAAAAATCAACTTAAAATTAATTATGAGATTATAAAATAATTTAAAA
* * *
522 CGAGTAATAAGGCTTCT-AGAGGAATGAGTAACTATAAATGGACTTTTCTTGCCAACGAATGCAT
1 CGAGTAATAAGGCTTCTGA-AGGAATGAGTAACTATAAATAGACTTTTCTT-TCAACAAATGCAT
** * * *
586 TTTTCTTCGCGTTTCTCTAAG-TAGACATTGAATTATTGTCTGTTTTAACC-AAAATATAAAAAA
64 TTTTCTTCAAGTTTCTCTAAGATAGACATTCAATTATAGTCTGTTTTAACCAAAAATGTAAAAAA
*
649 AA-CAACTT-AAATTCAATTATGAGATTATAAAATAATTTAAAG
129 AATCAACTTAAAATT-AATTATGAGATTATAAAATAATTTAAAA
* ********** * * * **
691 CGCGTAATAAGGCTT-TNNNNNNNNNNGCTAACTTTAAATTGATTTTTCTTGTCAATGAATGGC-
1 CGAGTAATAAGGCTTCTGAAGGAATGAG-TAACTATAAATAGACTTTTCTT-TCAACAAAT-GCA
* * * * * * * *
754 TTTTTCTACACA-TTTCT-TGAGGTAGGCATTCAATTATTGT-TTTTTTAACAAAAAATGTTAAA
63 TTTTTCTTCA-AGTTTCTCTAAGATAGACATTCAATTATAGTCTGTTTTAACCAAAAATGTAAAA
*
816 AAATTCAACTTAAAATTAATTATGAGATTATAAA
127 AAAATCAACTTAAAATTAATTATGAGATTATAAA
850 NNNNNNNNNN
Statistics
Matches: 528, Mismatches: 113, Indels: 62
0.75 0.16 0.09
Matches are distributed among these distances:
168 17 0.03
169 112 0.21
170 35 0.07
171 147 0.28
172 133 0.25
173 77 0.15
174 6 0.01
175 1 0.00
ACGTcount: A:0.39, C:0.11, G:0.13, T:0.34
Consensus pattern (171 bp):
CGAGTAATAAGGCTTCTGAAGGAATGAGTAACTATAAATAGACTTTTCTTTCAACAAATGCATTT
TTCTTCAAGTTTCTCTAAGATAGACATTCAATTATAGTCTGTTTTAACCAAAAATGTAAAAAAAA
TCAACTTAAAATTAATTATGAGATTATAAAATAATTTAAAA
Done.