Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018398254.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_1557.0, 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: 5322
ACGTcount: A:0.21, C:0.07, G:0.06, T:0.19
Warning! 2449 characters in sequence are not A, C, G, or T
Found at i:1313 original size:170 final size:170
Alignment explanation
Indices: 805--1836 Score: 694
Period size: 170 Copynumber: 6.0 Consensus size: 170
795 NNNNNNATTC
* * *
805 AACTTAAAATCAATTATGAGATTACAAAATCATTTAAAGCGAGTAATAATACTTTCGAAAGTATG
1 AACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAATACTTTCGAAGGTATG
* * * ** *
870 GGTGACAATAAATGGACTTTACCTACCAATAAAAGGCTTTTTCTTCACAATTCTCAAGATAGACA
66 GGTGACTATAAATGGACTTTACCTGCCAATGAAAGGCTTTTTCTTCACGTTTCTTAAGATAGACA
* * * * *
935 TTTAATTATAATTTATTTTAATAAAAAATAGAAAAAAAATTC
131 TTCAATTATAATCTATTTTAATTAAAAAT--ATAAAAAATTT
********** * *
977 AACTTAAAATCAATTATGAGATTANNNNNNNNNNTAAAGCGTGTAATAATACTTTCGAAGGCATG
1 AACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAATACTTTCGAAGGTATG
* * * * * ** * * * *
1042 GGTGACTAAAAATGCACTTTTCTTGCTAATGACTGGCTTTATT-TTCATGTTT-TTCTAGACAAA
66 GGTGACTATAAATGGACTTTACCTGCCAATGAAAGGCTTT-TTCTTCACGTTTCTT-AAGATAGA
* **********
1105 CATTCAATTATAATATATTTTNNNNNNNNNNATAAAAAATTT
129 CATTCAATTATAATCTATTTTAATTAAAAATATAAAAAATTT
* * **
1147 AATTTAAAATCAGTTATCTGATTATAAAACCATTTAAAGCGAGTAATAATACTTTCGAAGGTATG
1 AACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAATACTTTCGAAGGTATG
* * * *
1212 GGTGGCTATAAATGGACTTTACCGGCTAATGAAAGGCTTTTTCTTGACGTTTCTTAAGATAGACA
66 GGTGACTATAAATGGACTTTACCTGCCAATGAAAGGCTTTTTCTTCACGTTTCTTAAGATAGACA
* * *
1277 TTCAATTATAATCTGTTTTAATTAAAAATTTAAAAAACTT
131 TTCAATTATAATCTATTTTAATTAAAAATATAAAAAATTT
* ********** * * * * *
1317 AACATAAAATCAATTATGANNNNNNNNNNCCACTTAAAGAGAGTAATATTACTTTCGAAGGCATA
1 AACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAATACTTTCGAAGGTATG
* * * * * * * * *
1382 GGTCACTATATATAGACTTTTCTTGCCAAT-AAATGGTTTTTTCTTCATGTTTCTTGAGA-CGA-
66 GGTGACTATAAATGGACTTTACCTGCCAATGAAA-GGCTTTTTCTTCACGTTTCTTAAGATAGAC
* * *
1444 ACTATCAATTATAATCTATTTTAACCTAAAACGTA-AAAAAATTC
130 A-T-TCAATTATAATCTATTTTAA-TTAAAA-ATATAAAAAATTT
********** * * * * *
1488 AACTTAAAATCNNNNNNNNNNTTATAAACCCATTTAAAACGAGTAACAATGCTGTCGAAGGTATG
1 AACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAATACTTTCGAAGGTATG
* * * ** * * *
1553 GGTGACTATAAATGTACTTTTCCTGCTAATGAATCGCTTTTTCTTCTCGTTT-TTCAAGACAAAC
66 GGTGACTATAAATGGACTTTACCTGCCAATGAAAGGCTTTTTCTTCACGTTTCTT-AAGATAGAC
*
1617 ATTCAATTATAATATATTTTAA-TAACAAATATAAAAAATTT
130 ATTCAATTATAATCTATTTTAATTAA-AAATATAAAAAATTT
********** *
1658 AACTTAAAATCAATTANNNNNNNNNNAAACCATTTAAAGCGAGTAATAATACTTTCGAACGTATG
1 AACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAATACTTTCGAAGGTATG
* * ** * *
1723 GGTAACTATACATGGACTTTACCTGCCAATGAAAGATTTTTTTTTTCACGTTTCTCAAGATAGAC
66 GGTGACTATAAATGGACTTTACCTGCCAATGAAAG-GCTTTTTCTTCACGTTTCTTAAGATAGAC
* * * * *
1788 ATTCAACTATAATCTGTTTTAATAAAAAATGTAAAAAAATTC
130 ATTCAATTATAATCTATTTTAATTAAAAATAT-AAAAAATTT
1830 AACTTAA
1 AACTTAA
1837 NNNNNNNNNN
Statistics
Matches: 636, Mismatches: 205, Indels: 38
0.72 0.23 0.04
Matches are distributed among these distances:
168 1 0.00
169 13 0.02
170 326 0.51
171 158 0.25
172 135 0.21
173 3 0.00
ACGTcount: A:0.37, C:0.13, G:0.11, T:0.34
Consensus pattern (170 bp):
AACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAATACTTTCGAAGGTATG
GGTGACTATAAATGGACTTTACCTGCCAATGAAAGGCTTTTTCTTCACGTTTCTTAAGATAGACA
TTCAATTATAATCTATTTTAATTAAAAATATAAAAAATTT
Done.