Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018398014.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_1321.0, 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: 1790
ACGTcount: A:0.30, C:0.09, G:0.08, T:0.26
Warning! 484 characters in sequence are not A, C, G, or T
Found at i:1044 original size:171 final size:171
Alignment explanation
Indices: 723--1124 Score: 476
Period size: 171 Copynumber: 2.4 Consensus size: 171
713 CCAAAAAATG
* * * *
723 TAAAACAA-TTCAGCTTAAAATCAATT-TTATCATTATAAAACCATTTAAAGCAAGTAATAATGC
1 TAAAA-AATTTCAGCTTAAAATCAATTATGA-GATTATAAAACTATTTAAAGCGAGTAATAATGC
** * * *
786 TTTCGAAAGCATGGGTGACTATAAATGGACTTTTCTTCCCAATGAATAGTTTTTTCTTCATGTTC
64 TTTCGAAAGCATGAATGACTATAAATGCACTTTTCTTCCCAATGAATAGCTTTATCTTCATGTTC
** * * *
851 CTTGAGGCAGACATTTAATTATAATATACTTTAA-ACAAAAACA
129 CTCAAGACAAACATTCAATTATAATATACTTTAATA-AAAAACA
* *
894 TAAAAAATTTCAGCTTAAAATCAATTATGAGATTATAAAACTATTTGAAGCGTGTAATAATGCTT
1 TAAAAAATTTCAGCTTAAAATCAATTATGAGATTATAAAACTATTTAAAGCGAGTAATAATGCTT
* * *
959 TCGAAAGCATGAATGACTATAAATGCATTTTTCTTGCTAATGAATAGCTTTATCTTAACAT-TT-
66 TCGAAAGCATGAATGACTATAAATGCACTTTTCTTCCCAATGAATAGCTTTATCTT--CATGTTC
* *
1022 CTCAAGACAAACATTCAATTATAATATATTTTAATAAAAAATA
129 CTCAAGACAAACATTCAATTATAATATACTTTAATAAAAAACA
* * * *
1065 TACAAAATTT-AACTTAAAATTAATTATGAGATTACAAAA-TCATTTAAAGCGAGTAATAAT
1 TAAAAAATTTCAGCTTAAAATCAATTATGAGATTATAAAACT-ATTTAAAGCGAGTAATAAT
1125 ACTTNNNNNN
Statistics
Matches: 198, Mismatches: 27, Indels: 13
0.83 0.11 0.05
Matches are distributed among these distances:
169 1 0.01
170 45 0.23
171 144 0.73
172 5 0.03
173 3 0.02
ACGTcount: A:0.42, C:0.13, G:0.10, T:0.35
Consensus pattern (171 bp):
TAAAAAATTTCAGCTTAAAATCAATTATGAGATTATAAAACTATTTAAAGCGAGTAATAATGCTT
TCGAAAGCATGAATGACTATAAATGCACTTTTCTTCCCAATGAATAGCTTTATCTTCATGTTCCT
CAAGACAAACATTCAATTATAATATACTTTAATAAAAAACA
Found at i:1684 original size:169 final size:171
Alignment explanation
Indices: 1474--1785 Score: 414
Period size: 169 Copynumber: 1.8 Consensus size: 171
1464 NNNNNNNNNN
* * * * * *
1474 CATTTAAAGTGAGCAATAATGCTTTCAAAAGCATAGGTGACTATAAATGCACTTTTCTTACTAAT
1 CATTTAAAGCGAGCAATAATACTTTCAAAAGCATAGGTGACTATAAATGAACTTTACCTACCAAT
* *
1539 GAATGG-GTTTTCTTTATGTTTCT-AAAGACAAACATTCAATTATAATATATTTTAATAAAAAAT
66 GAAAGGCGTTTTCTTTATATTTCTCAAA-ACAAACATTCAATTATAATATATTTTAATAAAAAAT
1602 AT-AAAAAATTCAATTTCAAATCAATTATGAGATTATAAAAC
130 ATAAAAAAATTCAATTTCAAATCAATTATGAGATTATAAAAC
* * * * * *
1643 CATTTAGAGCGAGTAATAATACTTTCGAAAGTATGGGTGACTATAAATGAACTTTACCTGCCAAT
1 CATTTAAAGCGAGCAATAATACTTTCAAAAGCATAGGTGACTATAAATGAACTTTACCTACCAAT
* * * * * *
1708 GAAAGGCTTTTTCTTTATATTTCTCAAAATAGATATTCAATTATAATATGTTTTAATCAAAAATA
66 GAAAGGCGTTTTCTTTATATTTCTCAAAACAAACATTCAATTATAATATATTTTAATAAAAAATA
1773 TAAAAAAATTCAA
131 TAAAAAAATTCAA
1786 CTTAA
Statistics
Matches: 120, Mismatches: 20, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
169 58 0.48
170 48 0.40
171 14 0.12
ACGTcount: A:0.42, C:0.12, G:0.11, T:0.36
Consensus pattern (171 bp):
CATTTAAAGCGAGCAATAATACTTTCAAAAGCATAGGTGACTATAAATGAACTTTACCTACCAAT
GAAAGGCGTTTTCTTTATATTTCTCAAAACAAACATTCAATTATAATATATTTTAATAAAAAATA
TAAAAAAATTCAATTTCAAATCAATTATGAGATTATAAAAC
Done.