Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NW_018400603.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_3795.0, 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: 3275
ACGTcount: A:0.26, C:0.09, G:0.09, T:0.27

Warning! 986 characters in sequence are not A, C, G, or T


Found at i:977 original size:171 final size:171

Alignment explanation


    Indices: 387--1177  Score: 664
    Period size: 171  Copynumber: 4.6  Consensus size: 171

        377 NNTTCTTTAC

                  *      *                         *      *                  
        387 GTTTCTCGAGGTAAACATTCAATTATAGTCTGTTTTAACTAAAAATTTAGAAA-AATTCAACTTA
          1 GTTTCTAGAGGTAGACATTCAATTATAGTCTGTTTTAACCAAAAATATA-AAACAATTCAACTTA

                                               * *                     *     
        451 AAATCAATTATGAGATTATAAAACAATTTAAAGTGGGCAATAAGGCTTTTGAAGAAATGGGTGAC
         65 AAATCAATTATGAGATTATAAAACAATTTAAAGTGAGTAATAAGGCTTTTGAAGAAATGAGTGAC

                  **********                          
        516 TATAAANNNNNNNNNNTTGCCAATGAATGTCTTTTTCTTCAT
        130 TATAAATGGACTTTTTTTGCCAATGAATGTCTTTTTCTTCAT

                       **   *            *  *                    *  *        
        558 GTTTCTTA-A-ACAGATATTCAATTATAGACTATTTTAACCAAAAATATAAAATAACTCAACTTA
          1 GTTTC-TAGAGGTAGACATTCAATTATAGTCTGTTTTAACCAAAAATATAAAACAATTCAACTTA

                *             **********    **                   *       *   
        621 AAATTAATTATGAGATTANNNNNNNNNNTAAACCGAGTAATAAGGCTTTTGAATAAATGAGAGAC
         65 AAATCAATTATGAGATTATAAAACAATTTAAAGTGAGTAATAAGGCTTTTGAAGAAATGAGTGAC

                      *                          *    *
        686 TATAAATGGAGTTTTTTTGCCAATGAATG-CTTGTTTTTTCAC
        130 TATAAATGGACTTTTTTTGCCAATGAATGTCTT-TTTCTTCAT

                  *          *    *               *       *          *    ***
        728 GTTTCTTGAGGTAGACACTCAAATATAGTCTGTTTTAATCAAAAATGTAAAACAATTGAACTNNN
          1 GTTTCTAGAGGTAGACATTCAATTATAGTCTGTTTTAACCAAAAATATAAAACAATTCAACTTAA

            *******                *        *           *         *          
        793 NNNNNNNTATGAGATTATAAAACCATTTAAAGCGAGTACA-AAGCCTTTTGAAGGAAT-AGGTGA
         66 AATCAATTATGAGATTATAAAACAATTTAAAGTGAGTA-ATAAGGCTTTTGAAGAAATGA-GTGA

                    *            *   *                 
        856 CTATAAATAGACTTTTTTTGCTAATCAATGTCTTTTTCTTCAT
        129 CTATAAATGGACTTTTTTTGCCAATGAATGTCTTTTTCTTCAT

                            *                        * *  *             *    
        899 GTTTCTAGAGGTAGACGTTCAATTATAGTCTGTTTTAACCATATATGTAAAACAATTCAATTTAA
          1 GTTTCTAGAGGTAGACATTCAATTATAGTCTGTTTTAACCAAAAATATAAAACAATTCAACTTAA

                          *                  *    *  *                       
        964 AATCAATTATGAGACTATAAAACAATTTAAAGTAAGTAGTAGGGCTTTTGAATG-AATGAGTGAC
         66 AATCAATTATGAGATTATAAAACAATTTAAAGTGAGTAATAAGGCTTTTGAA-GAAATGAGTGAC

                           *               *          
       1028 TATAAATGGACTTTTCTTGCCAATGAATGTCATTTTCTTCAT
        130 TATAAATGGACTTTTTTTGCCAATGAATGTCTTTTTCTTCAT

             *   *     *                * *            *         *     *   * 
       1070 ATTTTTTA-AGCTAGACATTCAATTATAATATGTTTTAACCAATAATATAAAAAAATTTGAACCT
          1 -GTTTCTAGAGGTAGACATTCAATTATAGTCTGTTTTAACCAAAAATATAAAACAA-TTCAACTT

                      *                                  
       1134 AAAATCAATTTTGAGATTATAAAATC-ATTTAAAGTGAGTAATAA
         64 AAAATCAATTATGAGATTATAAAA-CAATTTAAAGTGAGTAATAA

       1178 NNNNNNNNNN


Statistics
Matches: 472,  Mismatches: 134, Indels: 27
        0.75            0.21        0.04

Matches are distributed among these distances:
 169    7  0.01
 170  121  0.26
 171  289  0.61
 172   54  0.11
 173    1  0.00

ACGTcount: A:0.37, C:0.11, G:0.13, T:0.35


Consensus pattern (171 bp):   
GTTTCTAGAGGTAGACATTCAATTATAGTCTGTTTTAACCAAAAATATAAAACAATTCAACTTAA
AATCAATTATGAGATTATAAAACAATTTAAAGTGAGTAATAAGGCTTTTGAAGAAATGAGTGACT
ATAAATGGACTTTTTTTGCCAATGAATGTCTTTTTCTTCAT

Found at i:3055 original size:15 final size:15

Alignment explanation


    Indices: 3037--3067  Score: 53
    Period size: 15  Copynumber: 2.1  Consensus size: 15

       3027 CAATTTTTTT

                           
       3037 ATATTTTTAATTAAA
          1 ATATTTTTAATTAAA

                    *      
       3052 ATATTTTTTATTAAA
          1 ATATTTTTAATTAAA

             
       3067 A
          1 A

       3068 CGGACTATAA


Statistics
Matches: 15,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  15   15  1.00

ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55


Consensus pattern (15 bp):   
ATATTTTTAATTAAA
Done.