Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018400132.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_3348.0, 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: 2072
ACGTcount: A:0.35, C:0.11, G:0.12, T:0.32
Warning! 214 characters in sequence are not A, C, G, or T
Found at i:951 original size:172 final size:171
Alignment explanation
Indices: 733--1552 Score: 742
Period size: 172 Copynumber: 4.8 Consensus size: 171
723 NNNNNNNNNN
* * * * *
733 TGGGTAACTATAAATGGACTTTTCTTGTCAATGAATGCCTTTTTCTTCAAGTGTCTCGAGCTAGA
1 TGGGTGACTATAAATAGACTTTTCTTGCCAATGAATGCCTTTTTCTTCAAGTTTCTCGAGGTAGA
* * * *
798 CATTCAGTTATAATATGTTTTAACAAAAAATGTAAAAAAATTTGAACTTAAAATGAATTTTGAGA
66 CATTCAATTATAATCTGTTTTAACAAAAAATGTAAAAAAA-TTGAACTTAAAATCAATTATGAGA
* * * *
863 TTATAAAACTATTCAAAGTGAGTAATAAGGATTTTGAAGCAA
130 TTATAAAACTATTTAAAGCGAGTAATAAGGCTTTTGAAGGAA
* * * *
905 TGGGTGACTATATATAGACTTTTCTTACCAATGAATACCTTTTTCTTTACAG-TTCTC-ATGGTA
1 TGGGTGACTATAAATAGACTTTTCTTGCCAATGAATGCCTTTTTCTTCA-AGTTTCTCGA-GGTA
* * * * * * * *
968 CACATTCAATTATAATTTGTTCTAACTAAAAATGTAAAAAAATTCAACTTAAAATTAATTATAAC
64 GACATTCAATTATAATCTGTTTTAACAAAAAATGTAAAAAAATTGAACTTAAAATCAATTATGAG
***
1033 ATTAT-AAACTATTTAAAGCGAGTAATAAGGCTTTTGAAATTA
129 ATTATAAAACTATTTAAAGCGAGTAATAAGGCTTTTGAAGGAA
* * ** * * *
1075 TGAGG-GACTATAAATGGACTTTCCTT-CCAAATGAATGATTTTTTCTACATGTTTCTTGAGGTA
1 TG-GGTGACTATAAATAGACTTTTCTTGCC-AATGAATGCCTTTTTCTTCAAGTTTCTCGAGGTA
* * * * * * * * * *
1138 GGCATTCAGTTATAGTTTATTTTAATAGAAATTATAAAAACAAATTG-ACTTAAAATCAATTAAG
64 GACATTCAATTATAATCTGTTTTAACAAAAAATGT-AAAA-AAATTGAACTTAAAATCAATTATG
* *
1202 AGATTATAAAACCATTTAAAGCGTGTAATAAGGCTTTTGAAGGAA
127 AGATTATAAAACTATTTAAAGCGAGTAATAAGGCTTTTGAAGGAA
* * * * *
1247 TAGGTGGCTCTAAAT-GAACTTTTCTTGCCAATGAATGCCTTTTTATTCAAGTTTCTAGAGGTAG
1 TGGGTGACTATAAATAG-ACTTTTCTTGCCAATGAATGCCTTTTTCTTCAAGTTTCTCGAGGTAG
********** * * * *
1311 ACATTCAATTATAATCTGTTTNNNNNNNNNNTGTACAAAGAATTGAAATTTAAATCAAATT-CGA
65 ACATTCAATTATAATCTGTTTTAACAAAAAATGTA-AAAAAATTGAACTTAAAATC-AATTATGA
*
1375 GATTATAAAATCT-TTTAAA-CTGAGTAATAAGGCTTTTAAAGGAA
128 GATTATAAAA-CTATTTAAAGC-GAGTAATAAGGCTTTTGAAGGAA
* * * * * * *
1419 TGAGTGACTATAAATAGAGTTTTCTTGCGAATGAATGTCTTTTTCTTCACGTTTCTCAAGCTAGA
1 TGGGTGACTATAAATAGACTTTTCTTGCCAATGAATGCCTTTTTCTTCAAGTTTCTCGAGGTAGA
* * * * * *
1484 CATTCAATTAGAATCTGTTTTAACCAAAAATGTAAAAGAATTCAACTTAAAATCAATTATTAGTT
66 CATTCAATTATAATCTGTTTTAACAAAAAATGTAAAAAAATTGAACTTAAAATCAATTATGAGAT
1549 TATA
131 TATA
1553 NNNNNNNNNN
Statistics
Matches: 511, Mismatches: 118, Indels: 39
0.76 0.18 0.06
Matches are distributed among these distances:
169 3 0.01
170 102 0.20
171 85 0.17
172 311 0.61
173 10 0.02
ACGTcount: A:0.37, C:0.12, G:0.14, T:0.36
Consensus pattern (171 bp):
TGGGTGACTATAAATAGACTTTTCTTGCCAATGAATGCCTTTTTCTTCAAGTTTCTCGAGGTAGA
CATTCAATTATAATCTGTTTTAACAAAAAATGTAAAAAAATTGAACTTAAAATCAATTATGAGAT
TATAAAACTATTTAAAGCGAGTAATAAGGCTTTTGAAGGAA
Done.