Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018399926.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_3157.0, 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, 604
Length: 1007
ACGTcount: A:0.38, C:0.14, G:0.14, T:0.35
Found at i:310 original size:171 final size:170
Alignment explanation
Indices: 16--1005 Score: 946
Period size: 171 Copynumber: 5.8 Consensus size: 170
6 TTTTGAAGAA
* * * * * *
16 ATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATGGC-TTTTCTTGATGTTTCCTGAGGCAG
1 ATGGGTGACTATAAATGGACTTTTCTTGTCAATCAATGACTTTTTCTTCACGTTTCCTAAGGCAG
* * ** * * *
80 ACATTCAATTATAATATGTTTTAATGAAAAATTTCAAAAAATTCAAGTTAAAATCAATTATGAGA
66 ACATTCAATTATAATCTATTTTAACCAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGA
* *
145 TTATAAAACCACTCAAAGCAAGTGATAAGGCTTTCAAAGGC
131 TTATAAAACCATTTAAAGCAAGT-ATAAGGCTTTCAAAGGC
* *
186 ATGGGTGACTATAAATGGACTTTTCTTGTCAATAAATGACTTTTTCTTCACGTTTTCC-AAGGTA
1 ATGGGTGACTATAAATGGACTTTTCTTGTCAATCAATGACTTTTTCTTCACG-TTTCCTAAGGCA
** * * * * * *
250 -ATTTTTTAATTATAATCTGTTTTAACCAGAAATGTAAAAAAACTCAACCTAAAATCAATTATGT
65 GA-CATTCAATTATAATCTATTTTAACCAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGA
* *
314 GATTATAAAACTACTTAAAGCGAA-TACTAAGGCTTTCAAAGGC
129 GATTATAAAACCATTTAAAGC-AAGTA-TAAGGCTTTCAAAGGC
* * * * * *
357 ATGGGTAACTATAAATGGACTATTT-TCGTCAATCAATGGC-TTTTCTTAACGTCT-CTCAAGAC
1 ATGGGTGACTATAAATGGACT-TTTCTTGTCAATCAATGACTTTTTCTTCACGTTTCCT-AAGGC
* * * * * * *
419 AGACATTCAACTATAATATATTTTAATCAAAAATATAAAAAAATTAAACTTAAAGTCGATTATGA
64 AGACATTCAATTATAATCTATTTTAACCAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGA
* * * **
484 GATTATAAAACCATTTAGAGCAAGTATTATGGATTTTGAAGGC
129 GATTATAAAACCATTTAAAGCAAGTA-TAAGGCTTTCAAAGGC
* ** * *
527 TTGAATGACTATAAATGGACTTTTCTTGTCAATAAAT-ACCTTTTTCTTCACCTTTCCTAAGGCA
1 ATGGGTGACTATAAATGGACTTTTCTTGTCAATCAATGA-CTTTTTCTTCACGTTTCCTAAGGCA
* * * * * *
591 GACATT-AAAT-TAATCTATTTTAGCTAAAAATGTAAATAAATTTAACCTAAAATCAATTAT-AT
65 GACATTCAATTATAATCTATTTTAACCAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGA-
* * *
653 GATTATAAAACCATTTAAAGCGAGTA-ACATAGCTTTTGAAA-GC
129 GATTATAAAACCATTTAAAGCAAGTATA-A-GGC-TTTCAAAGGC
* * * ** *
696 ATGGATGA-TAATAAATGGAGTTTTCTTGTCAATCAATGACTTTTTTTTCTTGTTTCCTAAGACA
1 ATGGGTGACT-ATAAATGGACTTTTCTTGTCAATCAATGACTTTTTCTTCACGTTTCCTAAGGCA
* ** *
760 GACATTCAATTATATTCTATTTTAATGAAAAATGTAAAAAAATTCAACTTAAAATCAATTACGAG
65 GACATTCAATTATAATCTATTTTAACCAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAG
* ** *
825 ATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTGGAAGGA
130 ATTATAAAACCATTTAAAGCAAGT-ATAAGGCTTTCAAAGGC
* * * * * * * * *
867 ATAGGTGGCTATAAATAGACTTTTTTTGCCAATCAATGGCTTTTTCTTCATGTTTCCCAAGGCCG
1 ATGGGTGACTATAAATGGACTTTTCTTGTCAATCAATGACTTTTTCTTCACGTTTCCTAAGGCAG
* * * * * * *
932 ACATGCAATTATAATTTGTTTCAGCAAAAAATGTAAAACAATTCAACTTAAAATCAATTATGAGA
66 ACATTCAATTATAATCTATTTTAACCAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGA
997 TTATAAAAC
131 TTATAAAAC
1006 TA
Statistics
Matches: 667, Mismatches: 126, Indels: 53
0.79 0.15 0.06
Matches are distributed among these distances:
167 1 0.00
168 3 0.00
169 131 0.20
170 178 0.27
171 337 0.51
172 16 0.02
173 1 0.00
ACGTcount: A:0.38, C:0.14, G:0.13, T:0.35
Consensus pattern (170 bp):
ATGGGTGACTATAAATGGACTTTTCTTGTCAATCAATGACTTTTTCTTCACGTTTCCTAAGGCAG
ACATTCAATTATAATCTATTTTAACCAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGA
TTATAAAACCATTTAAAGCAAGTATAAGGCTTTCAAAGGC
Done.