Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397861.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_1165.0, 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: 8300
ACGTcount: A:0.19, C:0.07, G:0.07, T:0.19
Warning! 3938 characters in sequence are not A, C, G, or T
Found at i:667 original size:171 final size:169
Alignment explanation
Indices: 279--698 Score: 439
Period size: 171 Copynumber: 2.4 Consensus size: 169
269 NNNNNNNNNN
* * * *
279 GCCTTATTACTCGCTTTAAATGGTTTTATAATCTCATAATTGGTTTTAAGTTAAGTTTTTTTTAC
1 GCCTTATTACTCACTTTAAATGGTTTTAT-ATCTCAAAATTGATTTTAAGTTAAATTTTTTTTAC
*
344 ATTTTTGATTAAAACAGACTATAATGGAATGCCTACCTTGGGAAACGTGAAGACAAAAGTATTCA
65 ATTTTT-ATTAAAACAGACTATAATGGAATGCCTACCTTGGGAAACGTGAAGACAAAAGCATTCA
* * *
409 TTGGCAAGAGAAGTCCATTTATAGTCTCCATTCTTTCAAAA
129 TTCGCAAGAAAAGTCAATTTATAGTCTCCATTCTTTCAAAA
* *********
450 GCCTTATTACTCGCTTTAAATGGTTTTATANNNNNNNNNNTGATTTTAAGTTAAATTTTTTTTAC
1 GCCTTATTACTCACTTTAAATGGTTTTATA-TCTCAAAATTGATTTTAAGTTAAATTTTTTTTAC
* * * *
515 ATTTTTATTAAAACAGACTATATTTGAATGGCTACCTTGGGAAACGTGAAGACAAAAGCATTCTT
65 ATTTTTATTAAAACAGACTATAATGGAATGCCTACCTTGGGAAACGTGAAGACAAAAGCATTCAT
580 TCGCAAGAAAAGTCAATTTATAGTCTCGCATTCCTTT-AAAA
130 TCGCAAGAAAAGTCAATTTATAGTCTC-CATT-CTTTCAAAA
********** * * *
621 GNNNNNNNNNNCACTTTAAATGGTTTTATGATCTCAAAATTGATTTTAA-TTCGAATTCTTTGTA
1 GCCTTATTACTCACTTTAAATGGTTTTAT-ATCTCAAAATTGATTTTAAGTT-AAATTTTTTTTA
685 CATTTTTAGTTAAA
64 CATTTTTA-TTAAA
699 TTACATTATA
Statistics
Matches: 201, Mismatches: 42, Indels: 11
0.79 0.17 0.04
Matches are distributed among these distances:
170 81 0.40
171 110 0.55
172 10 0.05
ACGTcount: A:0.31, C:0.13, G:0.13, T:0.38
Consensus pattern (169 bp):
GCCTTATTACTCACTTTAAATGGTTTTATATCTCAAAATTGATTTTAAGTTAAATTTTTTTTACA
TTTTTATTAAAACAGACTATAATGGAATGCCTACCTTGGGAAACGTGAAGACAAAAGCATTCATT
CGCAAGAAAAGTCAATTTATAGTCTCCATTCTTTCAAAA
Found at i:1781 original size:171 final size:171
Alignment explanation
Indices: 1604--1951 Score: 405
Period size: 171 Copynumber: 2.0 Consensus size: 171
1594 NNNNNNNNNN
* ** * *
1604 ATCTCATAATTGATTTTAAGTTGAATTTTT-T-CGCATTTATGGTTAAAACAGAGTATAATTGAA
1 ATCTCATAATTGATTTTAAGTTAAATTTTTATAAAC-TTT-TGATTAAAACAGAATATAATTGAA
* * * ** * *** *
1667 TGTCTACCTTGAGAAACATGAAGAGAAAGGCATTCAATGGTAAGAAAAGTTTGTTTATAGTCTCC
64 TGCCTACCATGAGAAACATGAAGACAAAAACATTCAATGGCAAGAAAAGTCAATTTATAGTATCC
1732 CATT-CTTTCAAAAGCCTAATTACTCGCATTAAATGGTTTTATA
129 CATTCCTTT-AAAAGCCTAATTACTCGCATTAAATGGTTTTATA
* * *
1775 ATCTCATAATTGATTTTAGGTTAAATTTTTATAAACTTTTGATTAAAGCAGAATGTAATTGAATG
1 ATCTCATAATTGATTTTAAGTTAAATTTTTATAAACTTTTGATTAAAACAGAATATAATTGAATG
* * * * * *
1840 CCTAGCATGGGAAACGTGAAGACAAAAACATTCATTTGCAAGAAAAGTCAATTTATATTATCCCA
66 CCTACCATGAGAAACATGAAGACAAAAACATTCAATGGCAAGAAAAGTCAATTTATAGTATCCCA
* * *
1905 TTCCTTTAAAAGCCTTATTACTCTCTTTAAATGGTTTTATA
131 TTCCTTTAAAAGCCTAATTACTCGCATTAAATGGTTTTATA
1946 ATCTCA
1 ATCTCA
1952 AANNNNNNNN
Statistics
Matches: 147, Mismatches: 27, Indels: 6
0.82 0.15 0.03
Matches are distributed among these distances:
171 138 0.94
172 8 0.05
173 1 0.01
ACGTcount: A:0.35, C:0.14, G:0.14, T:0.37
Consensus pattern (171 bp):
ATCTCATAATTGATTTTAAGTTAAATTTTTATAAACTTTTGATTAAAACAGAATATAATTGAATG
CCTACCATGAGAAACATGAAGACAAAAACATTCAATGGCAAGAAAAGTCAATTTATAGTATCCCA
TTCCTTTAAAAGCCTAATTACTCGCATTAAATGGTTTTATA
Done.