Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018400402.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_360.0, 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: 2860
ACGTcount: A:0.17, C:0.07, G:0.07, T:0.19
Warning! 1445 characters in sequence are not A, C, G, or T
Found at i:1756 original size:171 final size:160
Alignment explanation
Indices: 1607--1920 Score: 396
Period size: 170 Copynumber: 1.9 Consensus size: 160
1597 NNNNNNNNNN
* * * *
1607 TTTATAATCTCATT-ATTGATTTTAAGTTAATTTTTTTTACATTTTTGATTAAAACAGAATGTAA
1 TTTATAATCTC-TTAATTGATTGTAAGTTAATTTTTTCTAC-TTTTTCATTAAAACAGAATATAA
* *
1671 TTGAATCGCTACCTAGGGAAAGGTGAAGACAAAAGCATTCATTAGCAAGAAAAGGAAATTTATTG
64 TTGAATCGCTACCTAGGGAAAGGTGAAGACAAAAACATTCATTAGCAAGAAAAGGAAATTTATAG
1736 TCTCCCATTCCTTTAAAAGCCTTNNNNNNNNNNTTAAATAGT
129 TCTCCCATTCCTTTAAAAGCCTT----------TTAAATAGT
* *
1778 TTTATAATCTCTTAATTGATTGTAAGTTGATTTTTTCTACTTTTTCATTAAAACAGACTATAATT
1 TTTATAATCTCTTAATTGATTGTAAGTTAATTTTTTCTACTTTTTCATTAAAACAGAATATAATT
* * * **
1843 GAATGGCTACCTTGGGAAAGGTGCAGACAAAAACATTCATTAGCAAGAAAAGTCAATTTATAGTC
66 GAATCGCTACCTAGGGAAAGGTGAAGACAAAAACATTCATTAGCAAGAAAAGGAAATTTATAGTC
1908 TCCCATTCCTTTA
131 TCCCATTCCTTTA
1921 NNNNNNNNNN
Statistics
Matches: 129, Mismatches: 13, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
170 95 0.74
171 34 0.26
ACGTcount: A:0.34, C:0.13, G:0.13, T:0.37
Consensus pattern (160 bp):
TTTATAATCTCTTAATTGATTGTAAGTTAATTTTTTCTACTTTTTCATTAAAACAGAATATAATT
GAATCGCTACCTAGGGAAAGGTGAAGACAAAAACATTCATTAGCAAGAAAAGGAAATTTATAGTC
TCCCATTCCTTTAAAAGCCTTTTAAATAGT
Done.