Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NW_018403261.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_935.0, 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: 1768
ACGTcount: A:0.25, C:0.08, G:0.09, T:0.24

Warning! 589 characters in sequence are not A, C, G, or T


Found at i:299 original size:172 final size:170

Alignment explanation


    Indices: 2--631  Score: 640
    Period size: 172  Copynumber: 3.7  Consensus size: 170

          1 A

                      *  *         **  *    *  *                     *       
          2 AAAAATTCAACTTAAAATCAATTACGACATTACAAAACTATTTAAAGTGAGTAATAATGCTTTTG
          1 AAAAATTCAAATTTAAATCAATTTTGAGATTATAAGAC-ATTTAAAGTGAGTAATAAGGCTTTTG

                *   **                                                       
         67 AAGGTATGCATGACTATAAATGGACTTTTCTTGCCAATGAATACTTTTTTCTTCATGTTTCTCAT
         65 AAGGAATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATACTTTTTTCTTCATGTTTCTCAT

                                *                  * 
        132 GGTAGACATTCAATTCTAGTTTATTTTAACCAAAAATGTGC
        130 GGTAGACATTCAATTCTAGTATATTTTAACCAAAAATGTAC

               *                                                 *           
        173 GAAGAATTCAAATTTAAATCAATTTTGAGATTATAATGACATTTAAAGTGAGTGATAAGGCTTTT
          1 -AAAAATTCAAATTTAAATCAATTTTGAGATTATAA-GACATTTAAAGTGAGTAATAAGGCTTTT

                          **        *      *       *    *    *     *       * 
        238 GAAGGAATGGGTGAAGATAAATGGGCTTTTCATGCCAATAAAT-GTTCTCTTCTTTATGTTTCCC
         64 GAAGGAATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATACTT-TTTTCTTCATGTTTCTC

             **      *      **  *   *                 * *
        302 AAAGTAGACGTTCAATGATAATATGTTTTAACCAGAAAA-GCAAA
        128 ATGGTAGACATTCAATTCTAGTATATTTTAACCA-AAAATG-TAC

                    *                           *         *    *             
        346 AAAAATT-GAATTTAAAATCAATTTTGAGATTATAAAACTATTTAATGTGATTAATAAGGCTTTT
          1 AAAAATTCAAATTT-AAATCAATTTTGAGATTATAAGAC-ATTTAAAGTGAGTAATAAGGCTTTT

                       **          *          **                             
        410 -AAGGCAATGGCCGACTATAAATAGACTTTTCTTATCAATGAATACTTTTTTCTTCATGTTTCTC
         64 GAAGG-AATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATACTTTTTTCTTCATGTTTCTC

                    *             *    *    *          
        474 ATGGTAGAGATTCAATTCTAGTCTATTCTAACAAAAAATGTAC
        128 ATGGTAGACATTCAATTCTAGTATATTTTAACCAAAAATGTAC

                          *                       *        ***               
        517 AAAACATTCAAATTGAAATCAATTTTGAGATTATAAAGCCATTTAAACAAAGTAATAAGG-TTCT
          1 AAAA-ATTCAAATTTAAATCAATTTTGAGATTAT-AAGACATTTAAAGTGAGTAATAAGGCTT-T

                      *                       *                
        581 TGAAGGAATGAGTGACTATAAATGGACTTTTCTTACCAATGAATACTTTTT
         63 TGAAGGAATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATACTTTTT

        632 NNNNNNNNNN


Statistics
Matches: 364,  Mismatches: 80, Indels: 28
        0.77            0.17        0.06

Matches are distributed among these distances:
 171   24  0.07
 172  321  0.88
 173   19  0.05

ACGTcount: A:0.37, C:0.12, G:0.14, T:0.36


Consensus pattern (170 bp):   
AAAAATTCAAATTTAAATCAATTTTGAGATTATAAGACATTTAAAGTGAGTAATAAGGCTTTTGA
AGGAATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATACTTTTTTCTTCATGTTTCTCATG
GTAGACATTCAATTCTAGTATATTTTAACCAAAAATGTAC

Found at i:1271 original size:172 final size:173

Alignment explanation


    Indices: 959--1365  Score: 464
    Period size: 172  Copynumber: 2.3  Consensus size: 173

        949 NNNNNNNNNC

                               *  *            **        *        *          
        959 AAAAGATATAAAAAAAATTTAACTTAAAATCAATTACG-GCATTACAAAACTATATAAAGTGAGT
          1 AAAAGA-A-AAAAAAAATTCAAATTAAAATCAATTTTGAG-ATTATAAAACTATTTAAAGTGAGT

                 *      *              *                 *            * *    
       1023 AATAATACTTTTTAAGATATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATGTTTTTTTCT
         63 AATAAGACTTTTGAAGATATGGGTGACGATAAATGGACTTTTCTTACCAATGAATGTTCTCTTCT

                        *             * *  * *            
       1088 TCATGTTTCTCATGGTAGACATTCAATTCCAGTCTGTTTTAACCA-
        128 TCATGTTTCTCAGGGTAGACATTCAACTACAATATGTTTTAACCAG

                   * *   *          *                                        
       1133 AAAATG-CACAAAGAATTCAAATTTAAATCAATTTTGAGATTATAAAGAC-ATTTAAAGTGAGTA
          1 AAAA-GAAAAAAAAAATTCAAATTAAAATCAATTTTGAGATTATAAA-ACTATTTAAAGTGAGTA

                 *                              *                            
       1196 ATAAGGCTTTTGAAGGA-ATGGGTGACGATAAATGGGCTTTTCTTACCAATGAATGTTCTCTTCT
         64 ATAAGACTTTTGAA-GATATGGGTGACGATAAATGGACTTTTCTTACCAATGAATGTTCTCTTCT

             *                  *        *                
       1260 TTATGTTTCTCAGGGTAGACGTTCAACTATAATATGTTTTAACCAG
        128 TCATGTTTCTCAGGGTAGACATTCAACTACAATATGTTTTAACCAG

                             *  *                      *                
       1306 AAAAGAAAAAAAAAATTGAACTTAAAATCAATTTTGAGATTATCAAACTATTTAAAGTGA
          1 AAAAGAAAAAAAAAATTCAAATTAAAATCAATTTTGAGATTATAAAACTATTTAAAGTGA

       1366 TNNNNNNNNN


Statistics
Matches: 193,  Mismatches: 33, Indels: 15
        0.80            0.14        0.06

Matches are distributed among these distances:
 172  135  0.70
 173   53  0.27
 174    4  0.02
 175    1  0.01

ACGTcount: A:0.39, C:0.12, G:0.14, T:0.35


Consensus pattern (173 bp):   
AAAAGAAAAAAAAAATTCAAATTAAAATCAATTTTGAGATTATAAAACTATTTAAAGTGAGTAAT
AAGACTTTTGAAGATATGGGTGACGATAAATGGACTTTTCTTACCAATGAATGTTCTCTTCTTCA
TGTTTCTCAGGGTAGACATTCAACTACAATATGTTTTAACCAG
Done.