Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018402754.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_5813.0, 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, 621
Length: 1036
ACGTcount: A:0.35, C:0.13, G:0.11, T:0.37
Warning! 50 characters in sequence are not A, C, G, or T
Found at i:695 original size:171 final size:171
Alignment explanation
Indices: 1--1036 Score: 531
Period size: 171 Copynumber: 6.1 Consensus size: 171
* * ** *
1 ATCTCATAATTGATTTTAAGTTGAATGTTTTTACATTTATGGTTAAAA-AGACTAGAA-TCGAAT
1 ATCTTATAATTGATTTTAAGTTGAATTTTTTTACATTTATAATTAAAACAGACTATAACT-GAAT
* * ** * * * * * *
64 GCTTACCTAGAGAAACGTGTAAAAAAA-TAATTTATTGAGGAAAAAAA-TCTATTTACAGTCACC
65 GCCTGCCTTCAGAAACATGAAAAAAAACTCATTCATTGA-GAAAAAAAGTCCATTTATAGTCACC
* * * **********
127 CATTTCTTCAAAAGCCTTATTACTCANNNNNNNNNNTTTTATA
129 CATTCCCTAAAAAGCCTTATTACTCACTTTAAATTATTTTATA
* * * * ** *
170 ATCTCATAATTAATTTTAAGTTAAATGTTTTCTTA-GTTT-TTGTTAAAACAGA-TGATAATTGA
1 ATCTTATAATTGATTTTAAGTTGAAT-TTTT-TTACATTTATAATTAAAACAGACT-ATAACTGA
* * * * * *
232 ATGCTTG-CTTGAAGAAACATGCACAAAAAGCT-ACTCATTGAG-ATAAAAGTCCATTTATAGTC
63 ATGCCTGCCTT-CAGAAACATG-AAAAAAAACTCATTCATTGAGAAAAAAAGTCCATTTATAGTC
*********** * ** *
294 ANNNNNNNNNNCAGAAGCCTTATTACTCGTTTTAAATTGTTTTATA
126 ACCCATTCCCTAAAAAGCCTTATTACTCACTTTAAATTATTTTATA
* * * * *
340 ATCTTATAATTTATTTTGAGTTGAATTGTTTTACATTTATAATTAAAACAGACTGTAATTGAATG
1 ATCTTATAATTGATTTTAAGTTGAATTTTTTTACATTTATAATTAAAACAGACTATAACTGAATG
* * * *
405 CCTGCCTTCAGAAACATGTAAAAAAATTCATTCATTGAGAAAAACAGTCCATTTATAGTCGCCCA
66 CCTGCCTTCAGAAACATGAAAAAAAACTCATTCATTGAGAAAAAAAGTCCATTTATAGTCACCCA
* ***
470 TTCCTTAAAAAGCCTTATTACTCACTTTAAATTATTTTNNN
131 TTCCCTAAAAAGCCTTATTACTCACTTTAAATTATTTTATA
******* * * **
511 NNNNNNNAATTGATTTTAAGATGAATTTTTTTACATTTCTTGTTAAAACAGACTATAACTGAATG
1 ATCTTATAATTGATTTTAAGTTGAATTTTTTTACATTTATAATTAAAACAGACTATAACTGAATG
* * * * * *
576 TCTGTCTTGAGAAACGTGCAAAAAAAACT-ATTCATTGGGAAAAAAAGTTCATTTATAGTCACCC
66 CCTGCCTTCAGAAACATG-AAAAAAAACTCATTCATTGAGAAAAAAAGTCCATTTATAGTCACCC
* * *
640 ATTCCCTCAAAAGCATTATTACTCACTTTAAATTATCTTATA
130 ATTCCCTAAAAAGCCTTATTACTCACTTTAAATTATTTTATA
********** * * *
682 ATCTTATAATTGATTTTAAGTTGAATTTTTTTNNNNNNNNNNGTTAAAATAGACAATAATTGAAT
1 ATCTTATAATTGATTTTAAGTTGAATTTTTTT-ACATTTATAATTAAAACAGACTATAACTGAAT
** * ** * *
747 GTTTGCCTTGAGAAACAAT-AAAAAAAAGGCATTCAGTTG-TAAGAAAAGTCCATTTATAGTCAC
65 GCCTGCCTTCAGAAAC-ATGAAAAAAAACTCATTCA-TTGAGAAAAAAAGTCCATTTATAGTCAC
** * ***********
810 CCATTCTTTTAAAAGCCNNNNNNNNNNTTTTAAATTATTTTATA
128 CCATTCCCTAAAAAGCCTTATTACTCACTTTAAATTATTTTATA
* * * * ** *
854 ATCCTAAAATTTATTTTAAGTTGAATTTTTTTGCATTTATGGTTAAAA-AGATTATAA-TCGAAT
1 ATCTTATAATTGATTTTAAGTTGAATTTTTTTACATTTATAATTAAAACAGACTATAACT-GAAT
* * * * * * * * *
917 TCTTGCCTTGAGAAACGTGTGAAAAAAA-TCATTCATTTAGGAAAATAGTCTATTTATAGTCA-C
65 GCCTGCCTTCAGAAACATG-AAAAAAAACTCATTCATTGAGAAAAAAAGTCCATTTATAGTCACC
* * * *
980 CATTTCCTTCAAAAGCCTTATTATTCACTTTAAATTGTTTTATA
129 CA-TTCCCTAAAAAGCCTTATTACTCACTTTAAATTATTTTATA
*
1024 ATCTCATAATTGA
1 ATCTTATAATTGA
Statistics
Matches: 645, Mismatches: 197, Indels: 49
0.72 0.22 0.05
Matches are distributed among these distances:
168 3 0.00
169 59 0.09
170 213 0.33
171 240 0.37
172 126 0.20
173 4 0.01
ACGTcount: A:0.35, C:0.13, G:0.11, T:0.37
Consensus pattern (171 bp):
ATCTTATAATTGATTTTAAGTTGAATTTTTTTACATTTATAATTAAAACAGACTATAACTGAATG
CCTGCCTTCAGAAACATGAAAAAAAACTCATTCATTGAGAAAAAAAGTCCATTTATAGTCACCCA
TTCCCTAAAAAGCCTTATTACTCACTTTAAATTATTTTATA
Done.