Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NW_018402419.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_5499.0, 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, 825

Length: 1375
ACGTcount: A:0.37, C:0.14, G:0.16, T:0.33


Found at i:312 original size:171 final size:169

Alignment explanation


    Indices: 10--1375  Score: 1376
    Period size: 171  Copynumber: 8.0  Consensus size: 169

          1 TTCAACGTC

                     *                              *    *                *  
         10 AAATCAATTATGAGATTATAAAACCATTTAAAGAGAGTAAAAAGGATTTTGATA-GCTTGGGAGA
          1 AAATCAATTTTGAGATTATAAAACCATTTAAAGAGAGTAATAAGGCTTTTGA-AGGCTTGGGTGA

                  * ***         *                      *     *     *     *   
         74 CTATAATTTCACTTTT-TGTACCAATGAATGGCTTTTTCTTTACGTTTCTCAAGGCAAACACTCA
         65 CTATAAATGGGCTTTTCT-TGCCAATGAATGGCTTTTTC-TTATGTTTCCCAAGGAAAACATTCA

                  * * *        *                       
        138 ATTATACTATTTTTTAACCCAAAATGTATAAAAACTCAACTTA
        128 ATTATAATCTGTTTTAACCAAAAATGTA-AAAAACTCAACTTA

                     *     *  *                                            * 
        181 AAATCAATTATGAGAATACAAAACCATTTAAAGAGAGTAATAAGGCTTTTGAAGGCTTGGGTGTC
          1 AAATCAATTTTGAGATTATAAAACCATTTAAAGAGAGTAATAAGGCTTTTGAAGGCTTGGGTGAC

               *   *                               *                         
        246 TATGAATAGGCTTTTCTTGCCAATGAATGGCTTTTTCTTTTGGTTTCCCAAGGAAAACATTCAAT
         66 TATAAATGGGCTTTTCTTGCCAATGAATGGCTTTTTCTTAT-GTTTCCCAAGGAAAACATTCAAT

                     * *            *        *        
        311 TATAATCTGGTCTAGA-CAAAAATATAAAAAAATTCAACTTA
        130 TATAATCTGTTTTA-ACCAAAAATGT-AAAAAACTCAACTTA

                                           *   *                  *          
        352 AAATCAATTTTGA-AGTTATAAAACCATTTATAGATAGTAATAAGGCTTTTGAACGCTTGGGTGA
          1 AAATCAATTTTGAGA-TTATAAAACCATTTAAAGAGAGTAATAAGGCTTTTGAAGGCTTGGGTGA

                        *                    *        *    *   **            
        416 CTATAAATGGGCCTTTCTTGCCAATGAATGGCTATTTCTTTAGGTTTTCCATTGAAAACATTCAA
         65 CTATAAATGGGCTTTTCTTGCCAATGAATGGCTTTTTC-TTATGTTTCCCAAGGAAAACATTCAA

                          *         *                 
        481 TTATAATCTGTTTTCACCAAAAATATAAAAAACTACAACTTA
        129 TTATAATCTGTTTTAACCAAAAATGTAAAAAACT-CAACTTA

                          *   *                                           *  
        523 AAATCAATTTTGAGGTTAGAAAACCATTTAAAGAGAGTAATAAGGCTTTTGAAGGCTTGGGTAAC
          1 AAATCAATTTTGAGATTATAAAACCATTTAAAGAGAGTAATAAGGCTTTTGAAGGCTTGGGTGAC

                       *      *             *        *    *   *      *    ** 
        588 TATAAATGGGCCTTTCTTTCCAATGAATGGCTCTTTCTTCAGGTTTTCCATGGAAAAAATTCTGT
         66 TATAAATGGGCTTTTCTTGCCAATGAATGGCTTTTTCTT-ATGTTTCCCAAGGAAAACATTCAAT

                       *   *       *                 
        653 TATAATCTGTTGTAAACAAAAATATAAAAAACTTCAACTTA
        130 TATAATCTGTTTTAACCAAAAATGTAAAAAAC-TCAACTTA

                     **   *            *                   *           *  *  
        694 AAATCAATTCGGAGGTTATAAAACCATGTAAAGAGAGTAATAAGGCTATTGAAGGCTTGTGTAAC
          1 AAATCAATTTTGAGATTATAAAACCATTTAAAGAGAGTAATAAGGCTTTTGAAGGCTTGGGTGAC

                                          *   *         *   *       *        
        759 TATAAATGGGCTTTTCTTGCCAATGAATGGGTTTCTCTTCATGTCTCCAAAGGAAAGCATTCAAT
         66 TATAAATGGGCTTTTCTTGCCAATGAATGGCTTTTTCTT-ATGTTTCCCAAGGAAAACATTCAAT

            *       *       *               * *      
        824 GATAATCTCTTTTAACAAAAAATGTAAAAGAATTAAACTTA
        130 TATAATCTGTTTTAACCAAAAATGTAAAA-AACTCAACTTA

                       *  **   *    **    *    *                   *  *      
        865 AAATCAATTTTAAGGCTATTAAACTGTTTAGAGAGGGTAATAAGGCTTTTGAAGGATTAGGTGAC
          1 AAATCAATTTTGAGATTATAAAACCATTTAAAGAGAGTAATAAGGCTTTTGAAGGCTTGGGTGAC

            *                             *            **  ***   *          *
        930 AATAAATGGGCTTTTCTTGCCAATGAATGGGTTTTTCTTCATGCCTCTTGAGGCAAACATTCAAA
         66 TATAAATGGGCTTTTCTTGCCAATGAATGGCTTTTTCTT-ATGTTTCCCAAGGAAAACATTCAAT

              * *  *    * *    *            *        
        995 TACAGTCAGTTTGACCCAACAATGTAAGAAAATTCAACTTA
        130 TATAATCTGTTTTAACCAAAAATGTAA-AAAACTCAACTTA

                         *           *           *                           
       1036 AAAT-ATATTTTGCGATTATAAAACAATTTAAAGAGAATAATAAGGCTTTTGAAGGCTTGGGTGA
          1 AAATCA-ATTTTGAGATTATAAAACCATTTAAAGAGAGTAATAAGGCTTTTGAAGGCTTGGGTGA

                                             *               *               
       1100 CTATAAATGGGCTTTTCTTGCCAATGAATGGCTCTTTCTTCATGTTTCCTAAGGAAAACATTCAA
         65 CTATAAATGGGCTTTTCTTGCCAATGAATGGCTTTTTCTT-ATGTTTCCCAAGGAAAACATTCAA

                                  * *       *         
       1165 TTATAATCTGTTTTAACCAAAAGTATAAAAAAATGCAACTTA
        129 TTATAATCTGTTTTAACCAAAAATGTAAAAAACT-CAACTTA

             *            *                                        *  *      
       1207 AGATCAATTTTGAGGTTATAAAACCATTTAAAGAGAGTAATAAGGCTTTTGAAGGATTAGGTGAC
          1 AAATCAATTTTGAGATTATAAAACCATTTAAAGAGAGTAATAAGGCTTTTGAAGGCTTGGGTGAC

              *        *        *   *     **    *           *    *          *
       1272 TACAAATGGG-GTTTCTTGCAAATAAATGGGATTTTGTTCATGTTTCCAAAGGCAAACATTCAAA
         66 TATAAATGGGCTTTTCTTGCCAATGAATGGCTTTTTCTT-ATGTTTCCCAAGGAAAACATTCAAT

                 *  *    * *      *  *              
       1336 TATAACCTATTTTCAGCAAAAAGGTGAAAAACTTCAACTT
        130 TATAATCTGTTTTAACCAAAAATGTAAAAAAC-TCAACTT


Statistics
Matches: 998,  Mismatches: 179, Indels: 37
        0.82            0.15        0.03

Matches are distributed among these distances:
 170   93  0.09
 171  894  0.90
 172   11  0.01

ACGTcount: A:0.37, C:0.14, G:0.16, T:0.33


Consensus pattern (169 bp):   
AAATCAATTTTGAGATTATAAAACCATTTAAAGAGAGTAATAAGGCTTTTGAAGGCTTGGGTGAC
TATAAATGGGCTTTTCTTGCCAATGAATGGCTTTTTCTTATGTTTCCCAAGGAAAACATTCAATT
ATAATCTGTTTTAACCAAAAATGTAAAAAACTCAACTTA

Found at i:958 original size:21 final size:21

Alignment explanation


    Indices: 929--968  Score: 62
    Period size: 21  Copynumber: 1.9  Consensus size: 21

        919 GATTAGGTGA

                                 
        929 CAATAAATGGGCTTTTCTTGC
          1 CAATAAATGGGCTTTTCTTGC

                *      *       
        950 CAATGAATGGGTTTTTCTT
          1 CAATAAATGGGCTTTTCTT

        969 CATGCCTCTT


Statistics
Matches: 17,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  21   17  1.00

ACGTcount: A:0.23, C:0.15, G:0.20, T:0.42


Consensus pattern (21 bp):   
CAATAAATGGGCTTTTCTTGC

Done.