Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NW_018400761.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_394.0, 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: 2889
ACGTcount: A:0.28, C:0.09, G:0.10, T:0.27

Warning! 757 characters in sequence are not A, C, G, or T


Found at i:312 original size:171 final size:171

Alignment explanation


    Indices: 135--453  Score: 399
    Period size: 171  Copynumber: 1.9  Consensus size: 171

        125 NNNNNNNNNN

                                                   **                        
        135 CTTAAAATCAATTATGAGATTATAAAACAATTAAAAGCGGGTAATAAGGCTTTTGAAGAAATGAG
          1 CTTAAAATCAATTATGAGATTATAAAACAATTAAAAGCGAATAATAAGGCTTTTGAAGAAATGAG

                                                       *  *                  
        200 TGACTATAAAT-GAATATTTCCTA-TCAATGAATGCATTTTTCCTCCCATTTCTCAAGGTAGACA
         66 TGACTATAAATGGAAT-TTTCCTACT-AATGAATGCATTTTTCATCACATTTCTCAAGGTAGACA

                                                       
        263 TTCAATTATTACCTGTTTTATTCAAAAATATAAAAAAATTTAA
        129 TTCAATTATTACCTGTTTTATTCAAAAATATAAAAAAATTTAA

                    *                  *    **           *         ** *    * 
        306 CTTAAAATTAATTATGAGATTATAAAATAATTTGAAGCGAATAATGAGGCTTTTGGTGGAATGGG
          1 CTTAAAATCAATTATGAGATTATAAAACAATTAAAAGCGAATAATAAGGCTTTTGAAGAAATGAG

                          *     *            *           *    * **     *     
        371 TGACTATAAATGGACTTTTCTTACTAATGAATGTATTTTTCATCATATTTTTTGAGGTATACATT
         66 TGACTATAAATGGAATTTTCCTACTAATGAATGCATTTTTCATCACATTTCTCAAGGTAGACATT

                    **        
        436 CAATTATTGTCTGTTTTA
        131 CAATTATTACCTGTTTTA

        454 ACCAAAAAAG


Statistics
Matches: 123,  Mismatches: 23, Indels: 4
        0.82            0.15        0.03

Matches are distributed among these distances:
 171  119  0.97
 172    4  0.03

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


Consensus pattern (171 bp):   
CTTAAAATCAATTATGAGATTATAAAACAATTAAAAGCGAATAATAAGGCTTTTGAAGAAATGAG
TGACTATAAATGGAATTTTCCTACTAATGAATGCATTTTTCATCACATTTCTCAAGGTAGACATT
CAATTATTACCTGTTTTATTCAAAAATATAAAAAAATTTAA

Found at i:1391 original size:171 final size:160

Alignment explanation


    Indices: 905--1688  Score: 452
    Period size: 171  Copynumber: 4.6  Consensus size: 160

        895 NNNNNNNNNN

                                                                   **    *   
        905 ATAAATGGACTTTTCTTACCAATGAATGCATTTTTCTTCACAT-TTCTTGAGGTAGGCATTCAAT
          1 ATAAATGGACTTTTCTTACCAATGAATGC-TTTTTCTT--CATGTTCTTGAGGTAAACATTTAAT

                                    *    *                *         **       
        969 TATAGTCTGTTTT-ATCTAAAAATATAAATAAATTCAACTTAAAATCANNNNNNNNNNTAT-AAA
         63 TATAGTC-GTTTTAATC-AAAAATGTAAAAAAATTCAACTTAAAATTA--------ATTATGAAA

             *                *                  *    * 
       1032 ACAATTTAAAGTGAGTAAAAAGGCTTTTGAAGGAATATGTGATT
        118 ATAATTTAAAGTGAGTAATAAGGCTTTTGAAGGAAT-GGTGACT

                   *                *               *        **   *  *    *  
       1076 ATAAATGTACTTTTCTT-CTCAATAAATGACTTTTT-TACACAT-TTCTCAAGGCAAGCATTCAA
          1 ATAAATGGACTTTTCTTAC-CAATGAATG-CTTTTTCT--TCATGTTCTTGAGGTAAACATTTAA

                   *         *          * *      *        *            *     
       1138 TTATAGACCGTTTTAATGAAAAATGTAATACAATTCATCTTAAAATCAATTATG-AAATTATNNN
         62 TTATAG-TCGTTTTAATCAAAAATGTAAAAAAATTCAACTTAAAATTAATTATGAAAATAAT---

                 **                        *            
       1202 NNNNNNNAAAGTGAGTAATAAGGCTTTTGAACGAATGTGTGACT
        123 -----TTAAAGTGAGTAATAAGGCTTTTGAAGGAATG-GTGACT

                                   *    * *                                  
       1246 ATAAATGGACTTTTCTTACCAATAAATATCATTTTCTTCATGTTTCTTGAGGTAAACATTTAATT
          1 ATAAATGGACTTTTCTTACCAATGAAT-GCTTTTTCTTCATG-TTCTTGAGGTAAACATTTAATT

                          *      *                                      ***  
       1311 ATAGTCCGTTTTAAGCAAAAACGTAAAAAAATTCAACTTAAAATTAATTATGANNNNNNNNNNTA
         64 ATAGT-CGTTTTAATCAAAAATGTAAAAAAATTCAACTTAAAATTAATTATGA-------AAATA

                    *         *                      
       1376 ATTTAAAGCGAGTAATAATGCTTTTGAAGGAATAGGTGACT
        121 ATTTAAAGTGAGTAATAAGGCTTTTGAAGGAAT-GGTGACT

             *    * **           *                  *    * *      *     *    
       1417 ACAAATAGTTTTTTCTTACCAGTGAATGCGTTTTTCTTCACGTTCCTAATGGTAGACATTCAATT
          1 ATAAATGGACTTTTCTTACCAATGAATGC-TTTTTCTTCATGTTCTTGA-GGTAAACATTTAATT

              *   *    *                    *                       ***      
       1482 ATTGT-TTTTTTATCAAAAATGTAAAAAAATTTAACTTAAAATTAATTANNNNNNNNNNAAATAA
         64 ATAGTCGTTTTAATCAAAAATGTAAAAAAATTCAACTTAAAATTAATTA-------TGAAAATAA

                                          *         
       1546 TTTAAAGTGAGTAATAAGGCTTTTGAAGGAGTGAGTGACT
        122 TTTAAAGTGAGTAATAAGGCTTTTGAAGGAATG-GTGACT

                      *         *               * *                 *        
       1586 ATAAATGGACGTTTCTT-CTTAATGAATGGCTTTTTATACATGGTTCTTGAGGTAAGCATTTAAT
          1 ATAAATGGACTTTTCTTAC-CAATGAAT-GCTTTTTCTTCAT-GTTCTTGAGGTAAACATTTAAT

                        *                          
       1650 TATAGTCAGTTTAAATCAAAAATGTAAAAAAATTCAACT
         63 TATAGTC-GTTTTAATCAAAAATGTAAAAAAATTCAACT

       1689 NNNNNNNNNN


Statistics
Matches: 469,  Mismatches: 98, Indels: 92
        0.71            0.15        0.14

Matches are distributed among these distances:
 162    8  0.02
 168    2  0.00
 169  121  0.26
 170  132  0.28
 171  201  0.43
 172    2  0.00
 179    3  0.01

ACGTcount: A:0.36, C:0.11, G:0.13, T:0.35


Consensus pattern (160 bp):   
ATAAATGGACTTTTCTTACCAATGAATGCTTTTTCTTCATGTTCTTGAGGTAAACATTTAATTAT
AGTCGTTTTAATCAAAAATGTAAAAAAATTCAACTTAAAATTAATTATGAAAATAATTTAAAGTG
AGTAATAAGGCTTTTGAAGGAATGGTGACT
Done.