Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NW_018403156.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_823.0, 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: 19653
ACGTcount: A:0.17, C:0.06, G:0.06, T:0.16

Warning! 10673 characters in sequence are not A, C, G, or T


Found at i:4584 original size:170 final size:172

Alignment explanation


    Indices: 4270--4651  Score: 454
    Period size: 170  Copynumber: 2.2  Consensus size: 172

       4260 ACTTGAACCC

                      * *      *   *    *                                   *
       4270 AAAATCAATTTTAAGATTAGAAATCCATCTAAAGTGAGTAATAAGGCATTTGAAAGAATAGGAGG
          1 AAAATCAATTATGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCATTTGAAAGAATAGGAGA

            *                 *     *      *                    *    *      *
       4335 TTATAAATGCACTTTTTTTTGCCATTGAATGTTTTTTTCTTCACGTTTCATGGGGTAGACATTCC
         66 CTATAAATGCACTTTTTTCTGCCAATGAATGCTTTTTTCTTCACGTTTCATGAGGTAAACATTCA

                                        *               
       4400 GTTGTAATCTATTTTAA-CTAAAAATATTAAAAAATTACAA-TT
        131 GTTGTAATCTATTTTAATC-AAAAATATCAAAAAATT-CAACTT

                                               *               *        *  * 
       4442 AAAATCAATTATGAGATTATAAAACCATTTAAA-TTAGTAATAAGGC-TTTTAAAGGAATGGGTG
          1 AAAATCAATTATGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCATTTGAAA-GAATAGGAG

                                                                  *          
       4505 ACTATAAATAG-AC-TTTTTCTGCCAATGAATGCTTTTTTCTTCACGTTTC-TCTAGGTAAACAT
         65 ACTATAAAT-GCACTTTTTTCTGCCAATGAATGCTTTTTTCTTCACGTTTCAT-GAGGTAAACAT

                     *                *                  
       4567 TCAGTTGTAGTCTATTTTAATCAAAAGTATCAAAAAATTCAACTT
        128 TCAGTTGTAATCTATTTTAATCAAAAATATCAAAAAATTCAACTT

                 *                   *        *     
       4612 AAAATTAATTATGAGATTATAAAACGATTTAAAGCGAGTA
          1 AAAATCAATTATGAGATTATAAAACCATTTAAAGTGAGTA

       4652 NNNNNNNNNN


Statistics
Matches: 179,  Mismatches: 25, Indels: 13
        0.82            0.12        0.06

Matches are distributed among these distances:
 169    4  0.02
 170  113  0.63
 171   33  0.18
 172   29  0.16

ACGTcount: A:0.38, C:0.11, G:0.14, T:0.37


Consensus pattern (172 bp):   
AAAATCAATTATGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCATTTGAAAGAATAGGAGA
CTATAAATGCACTTTTTTCTGCCAATGAATGCTTTTTTCTTCACGTTTCATGAGGTAAACATTCA
GTTGTAATCTATTTTAATCAAAAATATCAAAAAATTCAACTT

Found at i:10938 original size:341 final size:340

Alignment explanation


    Indices: 10277--10938  Score: 709
    Period size: 341  Copynumber: 1.9  Consensus size: 340

      10267 NNNNNNNNNT

                                *                     * *      * *           
      10277 AAGGCTTTTAAAGAAATGGGTGACTATAAAAAGACTTGTCTTTCTAATGAATGTTTTTTTCTTCA
          1 AAGGCTTTTAAAGAAATGGGCGACTATAAAAAGACTTGTCTTGCCAATGAAGGCTTTTTTCTTCA

                   *                                *                        
      10342 CGTTTCTTAAGGTAGACCTTCAATTATAATCTGTTTTAACTAACAATGTAAAAAAATTAAACCTA
         66 CGTTTCTCAAGGTAGACCTTCAATTATAATCTGTTTTAACCAACAATGTAAAAAAATTAAACCTA

                *                          *                 *********     * 
      10407 AAATCAATTTTAAGATTAGAAATCCATTTAATGCGAGTAATAAGGCTTNNNNNNNNNNAGGAGGC
        131 AAATAAATTTTAAGATTAGAAATCCATTTAAAGCGAGTAATAAGGCTT-AGAAGGAATAGGAGAC

                            *                         *       *              
      10472 TATAAATGGGCTTTTCTTGCCAATGAATGCTTTTTTCTTCATGTTTCACAGGGTAAACATTCAGT
        195 TATAAATGGGCTTTTCCTGCCAATGAATGCTTTTTTCTTCATATTTCACAAGGTAAACATTCAGT

                               *   *                ********** * *           
      10537 TATAGTCTACTTTAACCAACAATGTAAAAAAACTCAACTTNNNNNNNNNNATGCGATTATAAAAC
        260 TATAGTCTACTTTAACCAAAAATATAAAAAAACTCAACTTAAAATCAATTACGAGATTATAAAAC

                            
      10602 CATTTAAAGCAAGTAA
        325 CATTTAAAGCAAGTAA

                         *                **     *                           
      10618 AAGGCTTTTAAAGGAATGGGCGACTATAAATGGACTTTTCTTGCCAATGAAGGCTTTTTTCTTCA
          1 AAGGCTTTTAAAGAAATGGGCGACTATAAAAAGACTTGTCTTGCCAATGAAGGCTTTTTTCTTCA

                     *          *                                   *  *     
      10683 CGTTTCTCATGGTAGACCTTTAATTATAATCTGTTTTAACCAACAATGTAAACAAACTTGAACCT
         66 CGTTTCTCAAGGTAGACCTTCAATTATAATCTGTTTTAACCAACAATGTAAA-AAAATTAAACCT

                           *                  *      ********                
      10748 AAAATAAATTTTAAGGTTAGAAATCCATTTAAAGTGAGTNNNNNNNNNNTT-GAAGGAATAGGAG
        130 AAAATAAATTTTAAGATTAGAAATCCATTTAAAGCGAGT--AATAAGGCTTAGAAGGAATAGGAG

                                 *                                    *      
      10812 ACTATAAATGGGCTTTTCCTGTCAATGAATGCTTTTTT-TTCATATTTCTA-AAGGTAGACATTC
        193 ACTATAAATGGGCTTTTCCTGCCAATGAATGCTTTTTTCTTCATATTTC-ACAAGGTAAACATTC

            *        * *                *      *                            
      10875 TGTTATAGTTTGCTTTAACCAAAAATATTAAAAAATTCAACTTAAAATCAATTACGAGATTATA
        257 AGTTATAGTCTACTTTAACCAAAAATATAAAAAAACTCAACTTAAAATCAATTACGAGATTATA

      10939 NNNNNNNNNN


Statistics
Matches: 257,  Mismatches: 60, Indels: 8
        0.79            0.18        0.02

Matches are distributed among these distances:
 341  169  0.66
 342   86  0.33
 344    2  0.01

ACGTcount: A:0.34, C:0.13, G:0.14, T:0.34


Consensus pattern (340 bp):   
AAGGCTTTTAAAGAAATGGGCGACTATAAAAAGACTTGTCTTGCCAATGAAGGCTTTTTTCTTCA
CGTTTCTCAAGGTAGACCTTCAATTATAATCTGTTTTAACCAACAATGTAAAAAAATTAAACCTA
AAATAAATTTTAAGATTAGAAATCCATTTAAAGCGAGTAATAAGGCTTAGAAGGAATAGGAGACT
ATAAATGGGCTTTTCCTGCCAATGAATGCTTTTTTCTTCATATTTCACAAGGTAAACATTCAGTT
ATAGTCTACTTTAACCAAAAATATAAAAAAACTCAACTTAAAATCAATTACGAGATTATAAAACC
ATTTAAAGCAAGTAA
Done.