Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018402230.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_5315.0, 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: 2506
ACGTcount: A:0.29, C:0.10, G:0.10, T:0.27
Warning! 598 characters in sequence are not A, C, G, or T
Found at i:305 original size:171 final size:171
Alignment explanation
Indices: 1--397 Score: 420
Period size: 171 Copynumber: 2.3 Consensus size: 171
* * * * * *
1 TTCTTCACGTTTCTCGAGATAAACATTCAATTATAATCTATTTTAATAAAAAATGTAAAAAAATT
1 TTCTTCAAGTTTCCCAAGGTAAACATTCAATTATTATCTATTTTAATAAAAAATGTAAAAAAATA
** * * * *
66 TTACTTAAAGTCAATTACGAGATTATAAAAACGTTTAAAGCGAGTAATAAGGCATTCAAAAGCAT
66 CAACTTAAAATCAATTACGAGATTATAAAAACATTTAAAGCGAATAAAAAGGCATTCAAAAGCAT
* * *
131 GGGTGACTATAAGTAG-ACTTTTCTTGCCAATGGATATCTTT
131 GGGTGACTATAAAT-GTACTTTTCTTGCCAATGAATAGCTTT
*** ** *
172 TTCTTTGTGTTTCCCAAGGTAAACATTCAATTATTATCTATTTTAACCAAAAATGTATAAAAATA
1 TTCTTCAAGTTTCCCAAGGTAAACATTCAATTATTATCTATTTTAATAAAAAATGTAAAAAAATA
* * * * * * * ** *
237 CAAGTTAAAATCAGTTACGAGATTCTAAAAATATTTTAGGC-ACATAAAAAGGCTTTTGAAGGCA
66 CAACTTAAAATCAATTACGAGATTATAAAAACATTTAAAGCGA-ATAAAAAGGCATTCAAAAGCA
*
301 TGGGTGACTATAAATGTACTTTTCTTGCCAATGAATGGCTTT
130 TGGGTGACTATAAATGTACTTTTCTTGCCAATGAATAGCTTT
* * * * * *
343 TTCTTCAAGTTTTCCTAGGCAAACATTCAGTTATTATTTATTTTAATTAAAAATG
1 TTCTTCAAGTTTCCCAAGGTAAACATTCAATTATTATCTATTTTAATAAAAAATG
398 NNNNNNNNNN
Statistics
Matches: 183, Mismatches: 41, Indels: 4
0.80 0.18 0.02
Matches are distributed among these distances:
170 2 0.01
171 181 0.99
ACGTcount: A:0.37, C:0.13, G:0.13, T:0.37
Consensus pattern (171 bp):
TTCTTCAAGTTTCCCAAGGTAAACATTCAATTATTATCTATTTTAATAAAAAATGTAAAAAAATA
CAACTTAAAATCAATTACGAGATTATAAAAACATTTAAAGCGAATAAAAAGGCATTCAAAAGCAT
GGGTGACTATAAATGTACTTTTCTTGCCAATGAATAGCTTT
Found at i:1427 original size:168 final size:168
Alignment explanation
Indices: 1223--1581 Score: 451
Period size: 168 Copynumber: 2.1 Consensus size: 168
1213 TGTTCTACCC
* *
1223 AAAAATATAAAAAATTCAACTTAAAATCATTTATGAGATTATAAAATA-ATTTAGAGCGAGTAAT
1 AAAAATATAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAA-ACATTTAAAGCGAGTAAT
* * * **
1287 AAGGCTTTTGAAGGCATG-GGTGACTATAACT-AGACTTTTTTTGGTAATGAATATCTTTCTTCA
65 AAGGATTTTGAAGG--TGAGGTGACTATAAATCA-ACTTTTTGTGCCAATGAATAT-TTTCTTCA
* *
1350 -C-GTTTCCTA-AGGTAGGCATTCAATTATAATTTATTTTAATA
126 TCAGTTT-ATAGAGGTAGACATTCAATTATAATTTATTTTAATA
* *
1391 AAAAATATAAAAAATTCATCTTAAAGTCAATTATGAGATTATAAAAACATTTAAAGCGAGTAATA
1 AAAAATATAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAAACATTTAAAGCGAGTAATA
* * *
1456 AGGATTTTGAAGGTGCAGGTGTCTATAAATCAACTTTTTGTGCCAATGGATATTTTTTTCATCAT
66 AGGATTTTGAAGGTG-AGGTGACTATAAATCAACTTTTTGTGCCAATGAATATTTTCTTCATCA-
* *
1521 GTTTATAGAGGTAGATATTCAATTATAATTTGTTTTAATA
129 GTTTATAGAGGTAGACATTCAATTATAATTTATTTTAATA
1561 AAAAATATAAAAAAATTCAAC
1 AAAAATAT-AAAAAATTCAAC
1582 NNNNNNNNNN
Statistics
Matches: 165, Mismatches: 17, Indels: 15
0.84 0.09 0.08
Matches are distributed among these distances:
166 2 0.01
167 8 0.05
168 100 0.61
169 3 0.02
170 41 0.25
171 11 0.07
ACGTcount: A:0.40, C:0.09, G:0.14, T:0.37
Consensus pattern (168 bp):
AAAAATATAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAAACATTTAAAGCGAGTAATA
AGGATTTTGAAGGTGAGGTGACTATAAATCAACTTTTTGTGCCAATGAATATTTTCTTCATCAGT
TTATAGAGGTAGACATTCAATTATAATTTATTTTAATA
Done.