Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018400751.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_3930.0, 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, 763
Length: 1272
ACGTcount: A:0.25, C:0.11, G:0.08, T:0.24
Warning! 412 characters in sequence are not A, C, G, or T
Found at i:812 original size:172 final size:170
Alignment explanation
Indices: 526--932 Score: 505
Period size: 172 Copynumber: 2.4 Consensus size: 170
516 NNTTGAAAAG
526 AAAAGTCCATTTATAGTCACCCATT-CTTTCAAAAGCCTTATTACTCTGTTTAAATGGTTTTATA
1 AAAAGTCCATTTATAGTCACCCATTCCTTT-AAAAGCCTTATTACT-TGTTTAAATGGTTTTATA
* *
590 ATCTTATAATTGATTTTAAGTTAAATCTTTTTACATTTTTGGTTAAAACAGACTATAATTAAAT-
64 ATCTCATAATTGATTTTAAGTTAAATCTTTTTACATTTTTAGTTAAAACAGACTATAATTAAATG
* * **
654 ATCTGTCTTGAGAAACATGCAAAAAAAGCTTGTTCATTGAGAAC
129 CT-TGTCTCGAGAAACATGCAAAAAAAG-TCATTCATTGAGAAC
* * * *
698 AAAAGTCTATTTATACTCACCCATTCCTTTAAAAGCCTCATTACTTGTTTTAAAAGGTTTTATAA
1 AAAAGTCCATTTATAGTCACCCATTCCTTTAAAAGCCTTATTACTTG-TTTAAATGGTTTTATAA
*********
763 TCTCATAATTGATTTNNNNNNNNNNT-TTTTTACATTTTTAGTTAAAACAGACTATAATTAAATG
65 TCTCATAATTGATTT-TAAGTTAAATCTTTTTACATTTTTAGTTAAAACAGACTATAATTAAATG
*
827 CTTGTCTCGAGAAACATGCAAAAAAAGTCATTCATTGAGAAG
129 CTTGTCTCGAGAAACATGCAAAAAAAGTCATTCATTGAGAAC
* * * * *
869 AAAAGTCCAATTACAGTCACCCATTCCTTCAAAAGGCTTATTACTCGCTTTAAATGGTTTTATA
1 AAAAGTCCATTTATAGTCACCCATTCCTTTAAAAGCCTTATTACTTG-TTTAAATGGTTTTATA
933 NNNNNNNNNN
Statistics
Matches: 201, Mismatches: 30, Indels: 9
0.84 0.12 0.04
Matches are distributed among these distances:
171 68 0.34
172 127 0.63
173 6 0.03
ACGTcount: A:0.34, C:0.15, G:0.11, T:0.37
Consensus pattern (170 bp):
AAAAGTCCATTTATAGTCACCCATTCCTTTAAAAGCCTTATTACTTGTTTAAATGGTTTTATAAT
CTCATAATTGATTTTAAGTTAAATCTTTTTACATTTTTAGTTAAAACAGACTATAATTAAATGCT
TGTCTCGAGAAACATGCAAAAAAAGTCATTCATTGAGAAC
Done.