genome.fa.s1153.2.7.7.80.10.50.1000.txt.html

Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NW_018398406.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_1705.0, 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: 3133
ACGTcount: A:0.23, C:0.07, G:0.09, T:0.21

Warning! 1249 characters in sequence are not A, C, G, or T


Found at i:583 original size:170 final size:169

Alignment explanation


    Indices: 246--707  Score: 550
    Period size: 170  Copynumber: 2.7  Consensus size: 169

        236 NNNNNNNNNN

                                           *         *               *       
        246 TATAAATGGACTTTTCTT-CTCAATGAATGGTTTTTTCTGCACAT-TTTC-CAATGAAAACATTC
          1 TATAAATGGACTTTTCTTGC-CAATGAAT-GCTTTTTCT--TCATGTTTCTCAATG-TAACATTC

             *                                      *                        
        308 ATTTATAGTCTGTTTTAACCAAAAATGTGAAAAAAGTT-AGCTTAAAATCAA-T-T---ATTATA
         61 AATTATAGTCTGTTTTAACCAAAAATGTG-AAAAAGTTCAACTTAAAATCAATTATGAGATTATA

               *         *           *                   
        367 AAATAATTTAAAGTGAGTAATAAAGTTTTTAAAGGAATAAGAGAC
        125 AAACAATTTAAAGCGAGTAATAAAGCTTTTAAAGGAATAAGAGAC

                                                                      *      
        412 TATAAATGGACTTTTCTTGCCAATGAATGCTTGTTTCTTCATGTTTCTCAATGTAACTGTTCAAT
          1 TATAAATGGACTTTTCTTGCCAATGAATGCTT-TTTCTTCATGTTTCTCAATGTAAC-ATTCAAT

                                  *                *                         
        477 TATAGTCTG-TTTAACCAAAAAAGTGAAAAAGTTCAACTCAAAATCAATTATGAGATTATAAAAC
         64 TATAGTCTGTTTTAACCAAAAATGTGAAAAAGTTCAACTTAAAATCAATTATGAGATTATAAAAC

                               *      *        *     
        541 AATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATATGAGAC
        129 AATTTAAAGCGAGTAATAAAGCTTTTAAAGGAATAAGAGAC

                     *          *    *              *                      * 
        582 TATAAATGGTCTTTTCTTGCAAATGTATGCTTTTTCTTCACGTTTCTC-ATGGTAGACATTCAGT
          1 TATAAATGGACTTTTCTTGCCAATGAATGCTTTTTCTTCATGTTTCTCAAT-GTA-ACATTCAAT

                                     *     **        *                    
        646 TATAGTCTGTTTTAACCAAAAATGTAAAAAAAATCAACTTAGAATCAATTATGAGATTATAA
         64 TATAGTCTGTTTTAACCAAAAATGTGAAAAAGTTCAACTTAAAATCAATTATGAGATTATAA

        708 NNNNNNNNNN


Statistics
Matches: 256,  Mismatches: 26, Indels: 24
        0.84            0.08        0.08

Matches are distributed among these distances:
 164   11  0.04
 165   36  0.14
 166   51  0.20
 167    2  0.01
 168    2  0.01
 169   32  0.12
 170  122  0.48

ACGTcount: A:0.38, C:0.12, G:0.14, T:0.36


Consensus pattern (169 bp):   
TATAAATGGACTTTTCTTGCCAATGAATGCTTTTTCTTCATGTTTCTCAATGTAACATTCAATTA
TAGTCTGTTTTAACCAAAAATGTGAAAAAGTTCAACTTAAAATCAATTATGAGATTATAAAACAA
TTTAAAGCGAGTAATAAAGCTTTTAAAGGAATAAGAGAC
Done.