Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018399507.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_2767.0, 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: 3304
ACGTcount: A:0.23, C:0.09, G:0.08, T:0.25
Warning! 1128 characters in sequence are not A, C, G, or T
Found at i:1176 original size:170 final size:169
Alignment explanation
Indices: 752--1571 Score: 581
Period size: 171 Copynumber: 4.8 Consensus size: 169
742 NNNNNNNNNA
* * * *
752 TTTTTATATATTTTTTATTAAAACAGATTATAATTGAAGGTCTGCCTCA-AGAAACATGAAGCAA
1 TTTTT-TATA-TTTTTATTAAAACAGATTATAATTGAATGTCTACCT-AGAGAAACGTGAAGAAA
* * * * *
816 AAGATA-CTCATTGGCAAGAAAAGTCCGTTTATAGTTACCCATCCCTTCAAAAGCCTTATTACTC
63 AAGATATC-CATTAGCAAGAAAAGTCCATTTATAGTCACTCATGCCTTCAAAAGCCTTATTACTC
* * *********** * *
880 GCTTTAAAT-GATTTTATAACCTCATAANNNNNNNNNNTTTTAAT
127 GCTTTAAATAG-TTTT-TAATCTCACAATTAGTTTTAAGTTAAAC
* * * * * * *
924 TTTTTTATATTTTTTATTAAAATATATTATAATTGAATGTCTGCATCGAAAAACGTGAACAAAAA
1 TTTTTTATA-TTTTTATTAAAACAGATTATAATTGAATGTCTACCTAGAGAAACGTGAAGAAAAA
* * * * *
989 GATATGCATTGGCAAGAAAAGTCCATTTATAGTAACTCATGCCCTCAAAAGTCTTATTACTCGCT
65 GATATCCATTAGCAAGAAAAGTCCATTTATAGTCACTCATGCCTTCAAAAGCCTTATTACTCGCT
**********
1054 TTAAATAGTTTTTAATCNNNNNNNNNNTTTTAAGTTAAAC
130 TTAAATAGTTTTTAATCTCACAATTAGTTTTAAGTTAAAC
* * *
1094 TTTTTTATATTTATTATTAAAACAGACTATAATTGTATGTTTACCTAGAGAAACGTGAAGAAAAA
1 TTTTTTATATTT-TTATTAAAACAGATTATAATTGAATGTCTACCTAGAGAAACGTGAAGAAAAA
********** * *
1159 GATATCCATTAGCAAGAAANNNNNNNNNNTAGTCACCCATGCCTTCGAAAGCCTTATTACTCGCT
65 GATATCCATTAGCAAGAAAAGTCCATTTATAGTCACTCATGCCTTCAAAAGCCTTATTACTCGCT
* * *
1224 TCAAATAGTTTTTTCATCTCACAATTAGTTTTAAGTCAAAC
130 TTAAATAG-TTTTTAATCTCACAATTAGTTTTAAGTTAAAC
* * * *
1265 TTTTTTATATTTGTTGTTAAAATAGATTATAATTGAATGTTTGCCTCAG-GAAACGTGAAGAAAA
1 TTTTTTATATTT-TTATTAAAACAGATTATAATTGAATGTCTACCT-AGAGAAACGTGAAGAAAA
* * * * * * * * ** *
1329 AAATGTCCACTGGCAAGAAAAGTTCATTGATACTCAC-CTATGCGTTTGAAAGCCTTATTACTCA
64 AGATATCCATTAGCAAGAAAAGTCCATTTATAGTCACTC-ATGCCTTCAAAAGCCTTATTACTCG
* ********* * *
1393 CTTTAAATGGTTTTNNNNNNNNNNAATTGGTTTTAAGTTAAAT
128 CTTTAAATAGTTTT-TAATCTCACAATTAGTTTTAAGTTAAAC
* * *
1436 TTTTTTATAATTTGTATTTAAACAGATTATAATTGAATGTCTACCTTA-AGAAATGTGAAGAAAA
1 TTTTTTAT-ATTTTTATTAAAACAGATTATAATTGAATGTCTACC-TAGAGAAACGTGAAGAAAA
* * * *
1500 AGATATCCATTAGCAAGAAAGGTCCATTTATAGTCACTTATGCCTTCAGAAGCCTTATTACTTGC
64 AGATATCCATTAGCAAGAAAAGTCCATTTATAGTCACTCATGCCTTCAAAAGCCTTATTACTCGC
1565 TTTAAAT
129 TTTAAAT
1572 GATTTTATAA
Statistics
Matches: 504, Mismatches: 132, Indels: 25
0.76 0.20 0.04
Matches are distributed among these distances:
169 3 0.01
170 123 0.24
171 365 0.72
172 13 0.03
ACGTcount: A:0.34, C:0.14, G:0.12, T:0.35
Consensus pattern (169 bp):
TTTTTTATATTTTTATTAAAACAGATTATAATTGAATGTCTACCTAGAGAAACGTGAAGAAAAAG
ATATCCATTAGCAAGAAAAGTCCATTTATAGTCACTCATGCCTTCAAAAGCCTTATTACTCGCTT
TAAATAGTTTTTAATCTCACAATTAGTTTTAAGTTAAAC
Done.