Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018399910.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_3143.0, 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: 2292
ACGTcount: A:0.22, C:0.07, G:0.08, T:0.20
Warning! 974 characters in sequence are not A, C, G, or T
Found at i:383 original size:171 final size:171
Alignment explanation
Indices: 4--1108 Score: 869
Period size: 171 Copynumber: 6.5 Consensus size: 171
1 AAG
* * * * * * * * * ** *
4 GCTTTTTCTTCATGTTTCTCGAGGCATAGACTCAATTATAATCTATTTT-ACCAAATACGTAAGA
1 GCTTTTTCTTCACGTTTCCCAAGGCACACATTCAATTATAATCTGTTTTAACTAAAAATATAAAA
* * * * *
68 AAATTTAA-TCTAAAATCAATTATGAGATTATAAAAT-CATTTTAAGTGAGTAGTAAGGTTTTTA
66 AAATTCAACT-TAAAATCAATTATGAGATTAT-AAATCCATTTAAAGTGAGTAATAAGGCTTTTG
* *
131 AAGGA-AT-GGTGACTATAAATGGACTTGTCTTC-CTAAT-AATA
129 AA-GACTTGGGTGACTATAAATGGACTTTTCTTCGC-AATGAATA
* * * ** * *
172 GCTTTTCCTTCACATTTTCCAAGGCACACAAACAATTATAATCCGTTTTAACCAAAAATATAAAA
1 GCTTTTTCTTCACGTTTCCCAAGGCACACATTCAATTATAATCTGTTTTAACTAAAAATATAAAA
* * **
237 AAATTCAACTTAAAATC-GTATATGAGGTTATAAATCCATTTAAAGCAAGTAATAAGGCTTTTGA
66 AAATTCAACTTAAAATCAAT-TATGAGATTATAAATCCATTTAAAGTGAGTAATAAGGCTTTTGA
301 AGACTTGGGTGACTATAAATGGACTTTTCTTCGCAATGAATA
130 AGACTTGGGTGACTATAAATGGACTTTTCTTCGCAATGAATA
* * * * *
343 GCTTTTTCTTCATGTTTCCCAAGGGAGACATTCAATTATAATCTGTTCTAACTGAAAATATAAGA
1 GCTTTTTCTTCACGTTTCCCAAGGCACACATTCAATTATAATCTGTTTTAACTAAAAATATAA-A
* * * * *
408 AAAATTCAACTTAAAATAAATTATCAGATTATAAAACTATTTAAAGTGAGTAATAAGGCTTTCGA
65 AAAATTCAACTTAAAATCAATTATGAGATTATAAATCCATTTAAAGTGAGTAATAAGGCTTTTGA
** * * * ** * *
473 AGGTTTGAGTGACTATAAAAGGACTTTTCATATCAATGGATG
130 AGACTTGGGTGACTATAAATGGACTTTTCTTCGCAATGAATA
* * * * * * * * * * * * *
515 GCTTTTGCTTCGCGTTTTCTAAGGTAGACATTTAATTATAATATATTTTAATTAGAAATGTACAA
1 GCTTTTTCTTCACGTTTCCCAAGGCACACATTCAATTATAATCTGTTTTAACTAAAAATATAAAA
* ** * *
580 AAATTTAACTTAAAATCAATTATGAGATTATAAAAGCATTTAAAGTGAGTGATAATGCTTTTGAA
66 AAATTCAACTTAAAATCAATTATGAGATTATAAATCCATTTAAAGTGAGTAATAAGGCTTTTGAA
* * ** * *
645 GGCCTGAACT-ACTATAAATAGG-GTTTTCTT-GTCATTGAA-A
131 GACTTG-GGTGACTATAAAT-GGACTTTTCTTCG-CAATGAATA
* * * * * * ** *
685 GGCTTTTTCTTCAAGTTTCTCGAGGCATACACTCAATTATAATCTGTTTTAACTAAATACGTAAG
1 -GCTTTTTCTTCACGTTTCCCAAGGCACACATTCAATTATAATCTGTTTTAACTAAAAATATAAA
* *
750 AAAATTCAA-TCTAAAATCAATTATGAGATTATAAAAT-CATTTTAAGTGAGTAGTAAGGCTTTT
65 AAAATTCAACT-TAAAATCAATTATGAGATTAT-AAATCCATTTAAAGTGAGTAATAAGGCTTTT
* * ** *
813 AAAGGA-AT-GGTGACTATAAATGGACTTTTCTTCTTAAT-AATG
128 GAA-GACTTGGGTGACTATAAATGGACTTTTCTTCGCAATGAATA
* * * * * *
855 GCTTTTCCTTCACATTTCCCAAGGCACACATACGATTATAATATGTTTTAACCAAAAATATAAAA
1 GCTTTTTCTTCACGTTTCCCAAGGCACACATTCAATTATAATCTGTTTTAACTAAAAATATAAAA
* * ***************
920 GAATTCAACTTAAAATC-ATATATGAGGTTATAAATCCATTTAAAGCNNNNNNNNNNNNNNTTGA
66 AAATTCAACTTAAAATCAAT-TATGAGATTATAAATCCATTTAAAGTGAGTAATAAGGCTTTTGA
* *
984 AGACTTGGGTGACTATAAATGGACTTTTCTTAGCAATGAATG
130 AGACTTGGGTGACTATAAATGGACTTTTCTTCGCAATGAATA
* * * * * *
1026 GCTTTTTCTTTATGTTTCCTAAGGTACAAATTCAATTATAATCTGTTCTAACTAAAAATATAAAA
1 GCTTTTTCTTCACGTTTCCCAAGGCACACATTCAATTATAATCTGTTTTAACTAAAAATAT-AAA
1091 AAAATTCAACTTAAAATC
65 AAAATTCAACTTAAAATC
1109 NNNNNNNNNN
Statistics
Matches: 733, Mismatches: 176, Indels: 52
0.76 0.18 0.05
Matches are distributed among these distances:
168 52 0.07
169 151 0.21
170 75 0.10
171 290 0.40
172 164 0.22
173 1 0.00
ACGTcount: A:0.37, C:0.13, G:0.13, T:0.35
Consensus pattern (171 bp):
GCTTTTTCTTCACGTTTCCCAAGGCACACATTCAATTATAATCTGTTTTAACTAAAAATATAAAA
AAATTCAACTTAAAATCAATTATGAGATTATAAATCCATTTAAAGTGAGTAATAAGGCTTTTGAA
GACTTGGGTGACTATAAATGGACTTTTCTTCGCAATGAATA
Done.