Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NW_018400922.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_4084.0, 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: 2282
ACGTcount: A:0.29, C:0.11, G:0.10, T:0.25

Warning! 573 characters in sequence are not A, C, G, or T


Found at i:305 original size:171 final size:169

Alignment explanation


    Indices: 22--636  Score: 648
    Period size: 171  Copynumber: 3.6  Consensus size: 169

         12 ATTATGGCAC

                    * *                                                      
         22 ATTTTAACTAGAAATGTAAAAAAATCCAACTTAAAATCAATTATGTAG-ATATAAAACCATTTAA
          1 ATTTTAACAAAAAATGT-AAAAAATCCAACTTAAAATCAATTATG-AGAATATAAAACCATTTAA

              **     *          *             *      *                       
         86 AGTTAGTAACAAGGCTTTCAGAGGCTTGAGTGACAATAAATAGACTTTTCTCTTTCATGCATGGC
         64 AGCGAGTAATAAGGCTTTCAAAGGCTTGAGTGACTATAAATGGACTTTTCTCTTTCATG-ATGGC

                *     *           *                   
        151 TTTTGCTTCACGTTTCCCAAGGTAGTCATTCAATTATAATAT
        128 TTTTACTTCATGTTTCCCAAGGCAGTCATTCAATTATAATAT

                    *     **                             *          **       
        193 ATTTTAACCAAAAACATAAAAAAGTCCAACTTAAAATCAATTATGTGAATATAAAATTATTTAAA
          1 ATTTTAACAAAAAATGTAAAAAA-TCCAACTTAAAATCAATTATGAGAATATAAAACCATTTAAA

                                 *        *                      *           
        258 GCGAGTAATAAGGCTTTCAAAAGCTTGAGTAACTATAAATGGACTTTTCTC-TCCACTAGATGGC
         65 GCGAGTAATAAGGCTTTCAAAGGCTTGAGTGACTATAAATGGACTTTTCTCTTTCA-T-GATGGC

                 *  *         *     **    *            
        322 TTTTATTTTATGTTTCCCGAGGCAAACATTTAATTAT-ATCAT
        128 TTTTACTTCATGTTTCCCAAGGCAGTCATTCAATTATAAT-AT

                                     *  *              **      *    *        
        364 ATTTTAACAAAAAATGTAAAACAATTCAGCTTAAAATCAATTACAAGAATAGAAAATCATTTAAA
          1 ATTTTAACAAAAAATGTAAAA-AATCCAACTTAAAATCAATTATGAGAATATAAAACCATTTAAA

                              *        *         * *                         
        429 GCGAGTAATAAGGCTTTCGAAGGCTTGTGTGACTATGGAGTGG-CTTTTCTCTCTGTC--GAATG
         65 GCGAGTAATAAGGCTTTCAAAGGCTTGAGTGACTAT-AAATGGACTTTTCTCT-T-TCATG-ATG

                           *                      *  *  
        491 GCTTTTACTTCATGTCTCCCAAGGCAGTCATTCAATTACAACAT
        126 GCTTTTACTTCATGTTTCCCAAGGCAGTCATTCAATTATAATAT

             *      **                 *                  *          *       
        535 AGTTTAACTGAAAATGTAAGAAAATCCTACTTAAAATCAATTATGAAAATATAAAACTATTTAAA
          1 ATTTTAACAAAAAATGTAA-AAAATCCAACTTAAAATCAATTATGAGAATATAAAACCATTTAAA

                             *              *    
        600 GCGAGTAATAAGGCTTTTAAAGGCTTGAGTGAATATA
         65 GCGAGTAATAAGGCTTTCAAAGGCTTGAGTGACTATA

        637 NNNNNNNNNN


Statistics
Matches: 363,  Mismatches: 68, Indels: 27
        0.79            0.15        0.06

Matches are distributed among these distances:
 170   13  0.04
 171  338  0.93
 172   10  0.03
 173    1  0.00
 174    1  0.00

ACGTcount: A:0.39, C:0.14, G:0.14, T:0.33


Consensus pattern (169 bp):   
ATTTTAACAAAAAATGTAAAAAATCCAACTTAAAATCAATTATGAGAATATAAAACCATTTAAAG
CGAGTAATAAGGCTTTCAAAGGCTTGAGTGACTATAAATGGACTTTTCTCTTTCATGATGGCTTT
TACTTCATGTTTCCCAAGGCAGTCATTCAATTATAATAT

Found at i:1325 original size:171 final size:168

Alignment explanation


    Indices: 1105--1624  Score: 592
    Period size: 171  Copynumber: 3.0  Consensus size: 168

       1095 NNNNNNNNNN

                          *      *        *                        *         
       1105 GGCTTTTGCTTCATATTTCCCAAGGCAAACTTTCAATTATAGAATATTTTAATCAGAAATGTAAA
          1 GGCTTTTGCTTCATGTTT-CCTAGGCAAACATTCAATTATAGAATATTTTAA-CAAAAATGTAAA

                  *          *                   *        *                  
       1170 AAAATCTAACTTAAAATAAATTATGAGACTATAAAACTATTTAAAGTGAGTAATACGACTTTCAA
         64 AAAATCCAACTTAAAATCAATTATGAGA-TATAAAACCATTTAAAGCGAGTAATACGACTTTCAA

                     *          **            *      
       1235 AGGCTTGAGAGACTATAAATTAACTTTTCTCTCCCATGGAT
        128 AGGCTTGAGTGACTATAAATGGACTTTTCTCTCCAATGGAT

                         *          *                 *            *         
       1276 GGCTTTTGCTTCACGTTTCCTGAGACAAACATTCAATTATAGTATATTTTAACTATAAATGTAAA
          1 GGCTTTTGCTTCATGTTTCCT-AGGCAAACATTCAATTATAGAATATTTTAAC-AAAAATGTAAA

                       *               *                   *     *           
       1341 AAAATCCAACTAAAAATCAATTATGACAATATAAAACCATTTAAAGCAAGTAAAACGACTTTCAA
         64 AAAATCCAACTTAAAATCAATTATGA-GATATAAAACCATTTAAAGCGAGTAATACGACTTTCAA

                                       **********    
       1406 AGGCTTGAGTGACTATAAATGGACTTTNNNNNNNNNNGGAT
        128 AGGCTTGAGTGACTATAAATGGACTTTTCTCTCCAATGGAT

                                           *          *  *                   
       1447 GGCTTTTGCTTCATGTTTCCCTAGGCAAACAATCAATTATAGCATGTTTTAACCAAAAATGTAAA
          1 GGCTTTTGCTTCATGTTT-CCTAGGCAAACATTCAATTATAGAATATTTTAA-CAAAAATGTAAA

                                    *        *                     * **    * 
       1512 AAAATCCAACTTAAAATCAATTATAAGTATATATAACCATTTAAAGCGAGTAATAAGGGTTTCTA
         64 AAAATCCAACTTAAAATCAATTATGAG-ATATAAAACCATTTAAAGCGAGTAATACGACTTTCAA

                                                      
       1577 AGGCTTGAGTGACTATAAATGGA-TATTTCTCTCCAATGGAT
        128 AGGCTTGAGTGACTATAAATGGACT-TTTCTCTCCAATGGAT

                   
       1618 GGCTTTT
          1 GGCTTTT

       1625 NNNNNNNNNN


Statistics
Matches: 288,  Mismatches: 54, Indels: 14
        0.81            0.15        0.04

Matches are distributed among these distances:
 170    4  0.01
 171  279  0.97
 172    5  0.02

ACGTcount: A:0.38, C:0.15, G:0.13, T:0.32


Consensus pattern (168 bp):   
GGCTTTTGCTTCATGTTTCCTAGGCAAACATTCAATTATAGAATATTTTAACAAAAATGTAAAAA
AATCCAACTTAAAATCAATTATGAGATATAAAACCATTTAAAGCGAGTAATACGACTTTCAAAGG
CTTGAGTGACTATAAATGGACTTTTCTCTCCAATGGAT
Done.