Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NW_018402280.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_5363.0, 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: 4997
ACGTcount: A:0.17, C:0.05, G:0.06, T:0.16

Warning! 2810 characters in sequence are not A, C, G, or T


Found at i:1618 original size:171 final size:171

Alignment explanation


    Indices: 1441--2179  Score: 554
    Period size: 171  Copynumber: 4.3  Consensus size: 171

       1431 GACAAGCATG

                                *                 *            *  *   *      
       1441 CAATTATAGTCTGTTTTAATAAAAAATATAAAAAAATTTAACTTAAAATTAATTTTGAAATTATA
          1 CAATTATAGTCTGTTTTAATCAAAAATATAAAAAAATTCAACTTAAAATTAGTTATGAGATTATA

               **                   *       *      *                       * 
       1506 AAATTATTTAAAGTGAGTAATAAGGCTTTCGATGGAATGTGTGACTATAAATGGACTTTTCTTGC
         66 AAACCATTTAAAGTGAGTAATAAGCCTTTCGAAGGAATGAGTGACTATAAATGGACTTTTCTTAC

                                                      
       1571 CAATGAA-CACCCTTTTCTTCATATTTCTTAAGGTAGACATT
        131 CAATGAATC-CCCTTTTCTTCATATTTCTTAAGGTAGACATT

                   *  *        *        *                *    *    *    *    
       1612 CAATTATTGTTTGTTTT-AGCTAAAAATGTAAAAAAATTCAACTTGAAATCAGTTTTGAGGTTAT
          1 CAATTATAGTCTGTTTTAATC-AAAAATATAAAAAAATTCAACTTAAAATTAGTTATGAGATTAT

                *                    **********                     *        
       1676 AAAATCATTTAAAGTGAGTAATAAGNNNNNNNNNNGAATGAGTGACTATAAATGGATTTTTCTTA
         65 AAAACCATTTAAAGTGAGTAATAAGCCTTTCGAAGGAATGAGTGACTATAAATGGACTTTTCTTA

            *                            *      *           
       1741 TCAATGAATCCCTTTTTCTTTTTCTTCATGTTTCTTGAGGTAGACA-T
        130 CCAATGAATCCC-----C-TTTTCTTCATATTTCTTAAGGTAGACATT

                         *          *    *    *       *          *           
       1788 CTAATTATAGTCTATTTTAATCAAGAATAGAAAAGAATTCAATTTAAAATTAGGTATGAGATTAT
          1 C-AATTATAGTCTGTTTTAATCAAAAATATAAAAAAATTCAACTTAAAATTAGTTATGAGATTAT

                                  **********                      *         *
       1853 AAAACCATTTAAAGTGAGTAATNNNNNNNNNNAAGGAATGAGTGACTATAAATGAACTTTTCTTG
         65 AAAACCATTTAAAGTGAGTAATAAGCCTTTCGAAGGAATGAGTGACTATAAATGGACTTTTCTTA

                *      **          *  *     *          
       1918 CCAACGAATCCTTTTTTCTTCATGTTCCTTAAAGTA-AGCATT
        130 CCAATGAATCCCCTTTTCTTCATATTTCTTAAGGTAGA-CATT

                      *        *                      **********             
       1960 CAATTATAGTTTGTTTTAACCAAAAATATAAAAAAATTCAACNNNNNNNNNNTTATGAGATTAT-
          1 CAATTATAGTCTGTTTTAATCAAAAATATAAAAAAATTCAACTTAAAATTAGTTATGAGATTATA

                                          **      * *                        
       2024 AAACCAATTT-AAGTGAGTAATAAGCCTTTTTAAGGAAAGGGTGACTATAAATGGACTTTTCTTA
         66 AAACC-ATTTAAAGTGAGTAATAAGCCTTTCGAAGGAATGAGTGACTATAAATGGACTTTTCTTA

            *    *   * **         *      *      *  *  
       2088 TCAATAAATGCTTTTTTCTTCACATTTCTCAAGGTACACGTT
        130 CCAATGAATCCCCTTTTCTTCATATTTCTTAAGGTAGACATT

                   *           *       *                      
       2130 CAATTATTGTCTGTTTTAACCAAAAATGTAAAAAAAATTCAACTTAAAAT
          1 CAATTATAGTCTGTTTTAATCAAAAATAT-AAAAAAATTCAACTTAAAAT

       2180 NNNNNNNNNN


Statistics
Matches: 442,  Mismatches: 111, Indels: 30
        0.76            0.19        0.05

Matches are distributed among these distances:
 170  103  0.23
 171  196  0.44
 172    3  0.01
 176    3  0.01
 177  135  0.31
 178    2  0.00

ACGTcount: A:0.36, C:0.11, G:0.12, T:0.36


Consensus pattern (171 bp):   
CAATTATAGTCTGTTTTAATCAAAAATATAAAAAAATTCAACTTAAAATTAGTTATGAGATTATA
AAACCATTTAAAGTGAGTAATAAGCCTTTCGAAGGAATGAGTGACTATAAATGGACTTTTCTTAC
CAATGAATCCCCTTTTCTTCATATTTCTTAAGGTAGACATT

Found at i:3724 original size:12 final size:12

Alignment explanation


    Indices: 3704--3733  Score: 51
    Period size: 12  Copynumber: 2.5  Consensus size: 12

       3694 TAAAACAATT

                        
       3704 TAAAGCGAGTAA
          1 TAAAGCGAGTAA

                *       
       3716 TAAATCGAGTAA
          1 TAAAGCGAGTAA

                  
       3728 TAAAGC
          1 TAAAGC

       3734 TTTTAAAGGT


Statistics
Matches: 16,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  12   16  1.00

ACGTcount: A:0.50, C:0.10, G:0.20, T:0.20


Consensus pattern (12 bp):   
TAAAGCGAGTAA
Done.