Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018401263.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_4408.0, 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, 636
Length: 1061
ACGTcount: A:0.33, C:0.11, G:0.10, T:0.31
Warning! 150 characters in sequence are not A, C, G, or T
Found at i:765 original size:171 final size:170
Alignment explanation
Indices: 246--1051 Score: 622
Period size: 170 Copynumber: 4.7 Consensus size: 170
236 NNNNNNNNNN
** ** * * *
246 TTTTTCTTCACATTTCTTGAGGTAGACATTCAATTATAATCTGTTTTAATAAAATATACAAAAAA
1 TTTTTCTTCATGTTTCTCAAGGTACACATTCAATTATAATCTGTTTTAATAAAAAATA-TAAAAA
* *** * * * * *
311 ACTCAACTTAAAATTAATTA-GAAGGTTATAAAATCATTTAAAGCGAGTAATAAGGCTTCCGAAG
65 ATTCAACTTAAACCCAATTATG-AGATTATAAAACCATTTAAAGTGACTAATAAGGCTTCCAAAG
** * * * * *
375 TTATGAGTGACTATAAATGCACTTTTCTTGC-AAATGGATATC
129 ACATGGGTGACTATACATGGACTTTTCTT-CTCAATAGATATC
********** * * *
417 TTTTNNNNNNNNNNTCTCGAGGCAGACATTCAATTATAA-CATGTTTTAATAAAAAATTATAAAA
1 TTTTTCTTCATGTTTCTCAAGGTACACATTCAATTATAATC-TGTTTTAATAAAAAA-TAT-AAA
* ** * ** * * * * *
481 AAACTCAACTTAAAATCAATTATGAGGTTATAAAATTATTTAAATTAAGTAATTAGGCTTTCGAA
63 AAATTCAACTTAAACCCAATTATGAGATTATAAAACCATTTAAAGTGACTAATAAGGC-TTCCAA
* * * **********
546 TG-CATGGGTGACTATAAATAGAC-TTTNNNNNNNNNNGA-ATGGC
127 AGACATGGGTGACTATACATGGACTTTTCTTCTCAATAGATAT--C
* * * * * *
589 TTTTTCTTCATGTTTCTTAAAGTAGACATTCAATAACAATCTGTTTAAATAAAAAATATAAAAAA
1 TTTTTCTTCATGTTTCTCAAGGTACACATTCAATTATAATCTGTTTTAATAAAAAATAT-AAAAA
* ** * * * *
654 ACTCAACTTAAAATCAATTTTGAGATTATAAAATCA-TTAATAGCGAGTAATAAGGTCTT-CAAA
65 ATTCAACTTAAACCCAATTATGAGATTATAAAACCATTTAA-AGTGACTAATAAGG-CTTCCAAA
* *
717 GATATGGGTGACTATACATGGACTTTTGTTCTCAATAGATATC
128 GACATGGGTGACTATACATGGACTTTTCTTCTCAATAGATATC
* *
760 TTTTTCTTCACGTTTCTCAAGGTACACCTTCAATTATAATCTGTTTTAATAAAAAATATAAAAAA
1 TTTTTCTTCATGTTTCTCAAGGTACACATTCAATTATAATCTGTTTTAATAAAAAATATAAAAAA
* * *
825 TTCAACTTAAACCCAATTATGAGATTACT-AAACCATTTAAAGTGACTAATAAAGCTTCCGAAGG
66 TTCAACTTAAACCCAATTATGAGATTA-TAAAACCATTTAAAGTGACTAATAAGGCTTCCAAAGA
* *
889 CATGGGTGACTATACATGGACTTTTCTTGTCAATGGATATC
130 CATGGGTGACTATACATGGACTTTTCTTCTCAATAGATATC
* * * ** * *
930 TTTTTTTTCATATTTCTCGAGGTACACAGCCAATTATAATCTATTTTAATAAAAAATTTAAAAAA
1 TTTTTCTTCATGTTTCTCAAGGTACACATTCAATTATAATCTGTTTTAATAAAAAATATAAAAAA
*
995 TTCAACTTAAACCCAATTATGAGATTACAAAACCATTTAAAGTGACTAATAAGGCTT
66 TTCAACTTAAACCCAATTATGAGATTATAAAACCATTTAAAGTGACTAATAAGGCTT
1052 TCGAAGGCAT
Statistics
Matches: 509, Mismatches: 108, Indels: 37
0.78 0.17 0.06
Matches are distributed among these distances:
169 3 0.01
170 206 0.40
171 175 0.34
172 116 0.23
173 9 0.02
ACGTcount: A:0.38, C:0.13, G:0.12, T:0.34
Consensus pattern (170 bp):
TTTTTCTTCATGTTTCTCAAGGTACACATTCAATTATAATCTGTTTTAATAAAAAATATAAAAAA
TTCAACTTAAACCCAATTATGAGATTATAAAACCATTTAAAGTGACTAATAAGGCTTCCAAAGAC
ATGGGTGACTATACATGGACTTTTCTTCTCAATAGATATC
Done.