Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NW_018400857.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_4026.0, 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: 2269
ACGTcount: A:0.26, C:0.10, G:0.11, T:0.24

Warning! 659 characters in sequence are not A, C, G, or T


Found at i:1920 original size:172 final size:171

Alignment explanation


    Indices: 1617--2269  Score: 460
    Period size: 171  Copynumber: 3.8  Consensus size: 171

       1607 AGTTACGAGA

                   **         **              **  *   *     *    *  *        
       1617 TTATAAAAGCATTTAAAGTAAGTAATAAGGCTTTTGGATGGCATGGGTGACTACAAGTAGGCTTT
          1 TTATAAATCCATTTAAAGCGAGTAATAAGGC-TTCCGAAGGCGTGGGTAACTATAAATAGGCTTT

                                              ***           *   *  * *       
       1682 TCTTGCCAATGAATGGCTCTTTCTTCATGTTTCTTGTGGTAA-ACATTCAATGATTATCTATTTT
         65 TCTTGCCAATGAATGGCTCTTTCTTCATGTTTCTCAAGG-AAGACATTTAATTATAAACTATTTT

                             *     *                    
       1746 AACCAAAAAT-TCAAAACAATGCTACTTAAAATCAATTATGAGG
        129 AACCAAAAATGT-AAAAAAATGCAACTTAAAATCAATTATGAGG

                                               *             *               
       1789 TTATACAA-CCATTTAAAGCGAGTAATGAA-GCTTTCGAAGGCGTGGGTGACTATAAA-ATGGAC
          1 TTATA-AATCCATTTAAAGCGAGTAAT-AAGGCTTCCGAAGGCGTGGGTAACTATAAATA-GG-C

                 *               *   *                             *      *  
       1851 TTTTCCTGCCAATGAATGGCTTTTTTTTCATGTTTCTCAAGGAAGACATTTAATTCTAAACTGTT
         62 TTTTCTTGCCAATGAATGGCTCTTTCTTCATGTTTCTCAAGGAAGACATTTAATTATAAACTATT

                                  *   *            ******
       1916 TTAACCAAAAATGTAAAAAAATTCAATTTAAAATCAATTNNNNNN
        127 TTAACCAAAAATGTAAAAAAATGCAACTTAAAATCAATTATGAGG

            ****                                     *       *               
       1961 NNNNAAATCCATTTAAAGCGAGTAATAAGGCTTCCGAAGGCTTGGGTAATTATAAATAGGCTTTT
          1 TTATAAATCCATTTAAAGCGAGTAATAAGGCTTCCGAAGGCGTGGGTAACTATAAATAGGCTTTT

                *                          *             *                   
       2026 CTTGTCAATGAATGGCTCTTTCTTCATGTTTTTCAA-GATAGACAGTTAATTATAAACTATTTTA
         66 CTTGCCAATGAATGGCTCTTTCTTCATGTTTCTCAAGGA-AGACATTTAATTATAAACTATTTTA

               *     **         *       **********   **
       2090 A-CTAAAATAAAAAAAGAATTCAACTTANNNNNNNNNNTGAAA
        130 ACCAAAAATGTAAAAA-AATGCAACTTAAAATCAATTATGAGG

                   *                     **  **      *     *                *
       2132 TTATAAAACCATTTAAAGCGAGTAATAAGATTTTTGAAGGCATGGGTGACTATAAAT-GGACTTG
          1 TTATAAATCCATTTAAAGCGAGTAATAAGGCTTCCGAAGGCGTGGGTAACTATAAATAGG-CTTT

                  *                 *           *   *   *            * *    *
       2196 TCTTGCAAATGAATGGCT-TATTCCTCATGTTTCTCGAGGTAGAGATTTAATTATAATCCATTTG
         65 TCTTGCCAATGAATGGCTCT-TTCTTCATGTTTCTCAAGGAAGACATTTAATTATAAACTATTTT

                      
       2260 AACCAAAAAT
        129 AACCAAAAAT


Statistics
Matches: 377,  Mismatches: 89, Indels: 30
        0.76            0.18        0.06

Matches are distributed among these distances:
 170   17  0.05
 171  197  0.52
 172  157  0.42
 173    6  0.02

ACGTcount: A:0.35, C:0.13, G:0.16, T:0.34


Consensus pattern (171 bp):   
TTATAAATCCATTTAAAGCGAGTAATAAGGCTTCCGAAGGCGTGGGTAACTATAAATAGGCTTTT
CTTGCCAATGAATGGCTCTTTCTTCATGTTTCTCAAGGAAGACATTTAATTATAAACTATTTTAA
CCAAAAATGTAAAAAAATGCAACTTAAAATCAATTATGAGG
Done.