Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018401613.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_4732.0, 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: 4648
ACGTcount: A:0.20, C:0.06, G:0.07, T:0.18
Warning! 2263 characters in sequence are not A, C, G, or T
Found at i:3954 original size:171 final size:161
Alignment explanation
Indices: 3787--4245 Score: 375
Period size: 171 Copynumber: 2.7 Consensus size: 161
3777 AATGAATTCG
* * *
3787 TTTTTCTTCATGTTTCTCGAGGCAAGTATTCAATTATAGTCTGTTTTATCTAAAAATATAAAAAA
1 TTTTTCTTCACGTTTCTCGAGG-AAGAATTCAATTATAGTCTGTTTTAACTAAAAATATAAAAAA
* *
3852 ATTCAACTGAAAATCAATTATGAAATTATAAAACAATTTAAAGCGAGTAATAAGGCNNNNNNNNN
65 ATTCAACTTAAAATTAATTATGAAATTATAAAACAATTTAAAGCGAGTAATAAGGC---------
*
3917 NATGAGTGACTATAAATGGACTTTTCTTCTTAATGAATGGC
121 AATGAGTGACTATAAATGGACTTTTCTTCTTAATGAATGGC
* * **********
3958 TTTTTCTGCACGTTT-TCTGAGGTAGACATTCAATTATAGTCTGTNNNNNNNNNNAATATAAAAA
1 TTTTTCTTCACGTTTCTC-GAGGAAGA-ATTCAATTATAGTCTGTTTTAACTAAAAATATAAAAA
*
4022 AATTCAACTTAAAATTAATTATGTAATTATAAAACAATTTAAAGCGAGTAATAAGGNNNNNNNNN
64 AATTCAACTTAAAATTAATTATGAAATTATAAAACAATTTAAAGCGAGTAATAAGG---------
* * * * * *
4087 NAATGGGTGACTATAAATTGACTTTTTTTCTTAGTGAATGGT
120 CAATGAGTGACTATAAATGGACTTTTCTTCTTAATGAATGGC
* * * * *
4129 TTTTTCTAT-ACGTTTCTCAAGGTAAAAAATCAATTATAGTATGTTTTAACTAAAAATATAAATA
1 TTTTTCT-TCACGTTTCTCGAGG-AAGAATTCAATTATAGTCTGTTTTAACTAAAAATATAAAAA
* * * **
4193 AATTCAACTTAAAATTAATTTTGAGATTAT-AAACTATTTAAAGTAAGTAATAA
64 AATTCAACTTAAAATTAATTATGAAATTATAAAACAATTTAAAGCGAGTAATAA
4246 AGCTTTGGAA
Statistics
Matches: 227, Mismatches: 47, Indels: 29
0.75 0.16 0.10
Matches are distributed among these distances:
170 24 0.11
171 199 0.88
172 4 0.02
ACGTcount: A:0.37, C:0.09, G:0.12, T:0.35
Consensus pattern (161 bp):
TTTTTCTTCACGTTTCTCGAGGAAGAATTCAATTATAGTCTGTTTTAACTAAAAATATAAAAAAA
TTCAACTTAAAATTAATTATGAAATTATAAAACAATTTAAAGCGAGTAATAAGGCAATGAGTGAC
TATAAATGGACTTTTCTTCTTAATGAATGGC
Found at i:4380 original size:11 final size:11
Alignment explanation
Indices: 4366--4391 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
4356 GTAAACAAAT
4366 TCAACTTAAAA
1 TCAACTTAAAA
4377 TCAACTTAAAA
1 TCAACTTAAAA
4388 TCAA
1 TCAA
4392 TTATGAGACT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.54, C:0.19, G:0.00, T:0.27
Consensus pattern (11 bp):
TCAACTTAAAA
Done.