Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018400021.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_3244.0, 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: 2718
ACGTcount: A:0.18, C:0.07, G:0.07, T:0.20
Warning! 1295 characters in sequence are not A, C, G, or T
Found at i:664 original size:170 final size:170
Alignment explanation
Indices: 362--1176 Score: 909
Period size: 170 Copynumber: 4.8 Consensus size: 170
352 NNNNNNNNNN
* * * * * *
362 TAAGTTGAATTATTTTATATTTTTTGTTAAAACAGACTATAAGTGATTGTTTACTTCGAGAAACG
1 TAAGTTGAATT-TTTTATATTTTTTGTTAAAACAGACTATAATTGAATGTCTGCCTGGAGAAACG
* * * * * * *
427 TGTAAAAAAAACCATTCGTTGAGAAAAAAAGTTAATTTATAGTCACCCATTCTTTCAAAAAGCTT
65 TGTAAAAAAAGCCATTCATTGAGAAGAAAAGTTCATTTATAGTCACTCATTCCTTCAAAAGGCTT
* *
492 ATTACTTGCTTTAAACGGTTTTATAATCTCATAATTGATTT
130 ATTACTCGCTTTAAATGGTTTTATAATCTCATAATTGATTT
*
533 TAAGTTGAATTTTTTATATTTTTTGTTAAAACAGACTATAATTGAATGTCTGCCTGGAAAAACGT
1 TAAGTTGAATTTTTTATATTTTTTGTTAAAACAGACTATAATTGAATGTCTGCCTGGAGAAACGT
* * * *
598 TTAAAAAAAGCTATTCATTGGGAAGAAAAGTTCATTTATAGTCACTCATTCCTTTAAAAGGCTTA
66 GTAAAAAAAGCCATTCATTGAGAAGAAAAGTTCATTTATAGTCACTCATTCCTTCAAAAGGCTTA
663 TTACTCGCTTTAAATGGTTTTATAATCTCATAATTGATTT
131 TTACTCGCTTTAAATGGTTTTATAATCTCATAATTGATTT
** * *
703 TAAGTTGAATTTTTT-TGCA-TTTTTGATTAAAACATTCTATAATTGAATGTCTACCTCGAGAAA
1 TAAGTTGAATTTTTTAT--ATTTTTTG-TTAAAACAGACTATAATTGAATGTCTGCCTGGAGAAA
* * * * * * * *
766 CCTG-AAGAAGCAAG-CATTCTTTGACAAGAAAAGTTCATTCAGAGTCACCCATTCCTTCAAAAA
63 CGTGTAA-AA-AAAGCCATTCATTGAGAAGAAAAGTTCATTTATAGTCACTCATTCCTTCAAAAG
* * * *
829 GCTTATTCCTCGCTTTAAAT-ATTTTATAATCTCGTAATTGATTA
126 GCTTATTACTCGCTTTAAATGGTTTTATAATCTCATAATTGATTT
* * *
873 TAAGTTGAATTTTTTTATATTTTTTATT-AAACAGACTATAAGTGATTGTCTGCCTTGG-GAAAC
1 TAAGTTGAA-TTTTTTATATTTTTTGTTAAAACAGACTATAATTGAATGTCTGCC-TGGAGAAAC
* ** * * *
936 GTGCAAAAAAAATCATTTATTGAGAAGAAAAGTCCATTTATAGTCACTCATTCCTTCAAAAGTCT
64 GTGTAAAAAAAGCCATTCATTGAGAAGAAAAGTTCATTTATAGTCACTCATTCCTTCAAAAGGCT
*
1001 TATTAC-CTACTTTAAATGGTTTTATAATCTCATAATTGA-TT
129 TATTACTC-GCTTTAAATGGTTTTATAATCTCATAATTGATTT
* * * *
1042 TAATGTTGAATTTTTT-TACCTTTTTTTTTAAAATAGACTATAATTGAAAGCCTGCCTTAGGA-A
1 TAA-GTTGAATTTTTTATA--TTTTTTGTTAAAACAGACTATAATTGAATGTCTGCC-T-GGAGA
* * * *
1105 AA-GTGTAGAAAAAGCCATTGATTGAGAGGAAAAGTCCATTTATAGTCA-TCTATTCCTTCAAAA
61 AACGTGTAAAAAAAGCCATTCATTGAGAAGAAAAGTTCATTTATAGTCACTC-ATTCCTTCAAAA
*
1168 GGTTTATTA
125 GGCTTATTA
1177 NNNNNNNNNN
Statistics
Matches: 545, Mismatches: 79, Indels: 40
0.82 0.12 0.06
Matches are distributed among these distances:
168 5 0.01
169 97 0.18
170 234 0.43
171 200 0.37
172 9 0.02
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.39
Consensus pattern (170 bp):
TAAGTTGAATTTTTTATATTTTTTGTTAAAACAGACTATAATTGAATGTCTGCCTGGAGAAACGT
GTAAAAAAAGCCATTCATTGAGAAGAAAAGTTCATTTATAGTCACTCATTCCTTCAAAAGGCTTA
TTACTCGCTTTAAATGGTTTTATAATCTCATAATTGATTT
Done.