Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NW_018402571.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_5643.0, 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, 846

Length: 1410
ACGTcount: A:0.24, C:0.09, G:0.11, T:0.25

Warning! 429 characters in sequence are not A, C, G, or T


Found at i:442 original size:172 final size:170

Alignment explanation


    Indices: 1--807  Score: 761
    Period size: 172  Copynumber: 4.7  Consensus size: 170

                      *   *                 *     *    *                    *
          1 TAAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTCTCTTACCAATGAATGTCTTTTTCTTT
          1 TAAGGCTTTTAAAGAAATGGGTGACTATAAATAGACTTTTCTTGCCAATGAATGT-TTTTTCTTC

             *           *     *       *  * *  *              *  *           
         66 ACGTTTGC-CGAGCTAGACGTTCAATTATAGTCT-ATTTAA-CAAAAGATATAAAAAACATTCAA
         65 ATGTTT-CTCGAGGTAGACATTCAATTCTAATATGTTTTAACCAAAA-ATGTACAAAA-ATTCAA

            *  *           *        *  * *         * *    
        128 CTTAAAATC-ATTTACG-GCATTACAAGACCATTTAAAGCGGGTAA
        127 ATTTAAATCAATTT-TGAG-ATTATAAAAACATTTAAAGTGAGTAA

                  *   *   **                *          *    *                
        172 TAAGGCATTTGAAGGTATGGGTGACTATAAATGGACTTTTCTTCCCAAAGAATGCTTTTTTCTTC
          1 TAAGGCTTTTAAAGAAATGGGTGACTATAAATAGACTTTTCTTGCCAATGAATG-TTTTTTCTTC

                           *                                       *         
        237 ATGTTTCTCGAGGTATACATTCAATTCTAATATGTTTTAACCAAAAATGTACAATGAATTCAAAT
         65 ATGTTTCTCGAGGTAGACATTCAATTCTAATATGTTTTAACCAAAAATGTACAA-AAATTCAAAT

                  *         *                       * 
        302 TTAAATAAATTTTGAGGTTATAAAAACATTTAAAGTGAGTGA
        129 TTAAATCAATTTTGAGATTATAAAAACATTTAAAGTGAGTAA

                                                *                           *
        344 TAAGGCTTTTAAAGAAATGGGTGACTATAAATAGACCTTTCTTGCCAATGAATGTTCTTTTCTTT
          1 TAAGGCTTTTAAAGAAATGGGTGACTATAAATAGACTTTTCTTGCCAATGAATGTT-TTTTCTTC

                      *      **       *                          *       *  *
        409 ATGTTTCTCGGGGTAGATGTTCAATTATAATATGTTTTAACCAGAAAA-GTAAAAAAAATTGAAC
         65 ATGTTTCTCGAGGTAGACATTCAATTCTAATATGTTTTAACCA-AAAATGT-ACAAAAATTCAAA

              *                                     *   
        473 TTAAAATCAATTTTGAGATTAT-AAAACTATTTAAAGTGATTAA
        128 TTTAAATCAATTTTGAGATTATAAAAAC-ATTTAAAGTGAGTAA

                      *                                           *          
        516 TAAGGCTTTTGAAGAAATGGGTGACTATAAATAGACTTTTCTTGCCAATGAATACTTTTTTCTTC
          1 TAAGGCTTTTAAAGAAATGGGTGACTATAAATAGACTTTTCTTGCCAATGAAT-GTTTTTTCTTC

                     *                    * * *      *                       
        581 ATGTTTCT-TATGGTAGACATTCAATTCTAGTCTATTTTAAGCAAAAATGTACAAAACATTCAAA
         65 ATGTTTCTCGA-GGTAGACATTCAATTCTAATATGTTTTAACCAAAAATGTACAAAA-ATTCAAA

                          *           *        *       
        645 TTTAAATCAATTTTAAGATTATAAAACCATTTAAACTGAGTAA
        128 TTTAAATCAATTTTGAGATTATAAAAACATTTAAAGTGAGTAA

                   *      *   *             *                     *          
        688 TAAGGCTCTTAAAGGAATAGGTGACTATAAATGGACTTTTCTTGCCAATGAATACTTTTTTCTTC
          1 TAAGGCTTTTAAAGAAATGGGTGACTATAAATAGACTTTTCTTGCCAATGAAT-GTTTTTTCTTC

                   *        *    *     *   * *     *         *       
        753 A-GATTTGT-GAAGGTGGACAATCAATCCTAGTCTGTTTCAACCAAAAACGTACAAA
         65 ATG-TTTCTCG-AGGTAGACATTCAATTCTAATATGTTTTAACCAAAAATGTACAAA

        808 GANNNNNNNN


Statistics
Matches: 532,  Mismatches: 86, Indels: 35
        0.81            0.13        0.05

Matches are distributed among these distances:
 170    1  0.00
 171   98  0.18
 172  408  0.77
 173   25  0.05

ACGTcount: A:0.36, C:0.13, G:0.15, T:0.36


Consensus pattern (170 bp):   
TAAGGCTTTTAAAGAAATGGGTGACTATAAATAGACTTTTCTTGCCAATGAATGTTTTTTCTTCA
TGTTTCTCGAGGTAGACATTCAATTCTAATATGTTTTAACCAAAAATGTACAAAAATTCAAATTT
AAATCAATTTTGAGATTATAAAAACATTTAAAGTGAGTAA

Found at i:751 original size:344 final size:342

Alignment explanation


    Indices: 1--751  Score: 942
    Period size: 344  Copynumber: 2.2  Consensus size: 342

                      *                           *    *                     
          1 TAAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTCTCTTACCAATGAATGTCTTTTTCTTT
          1 TAAGGCTTTTAAAGGAATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATGT-TTTTTCTTT

                                         * *                                 
         66 ACGTTTGCCGAGCTAGACGTTCAATTATAGTCTATTTAACAAAAGATATAAAAAACATTCAACTT
         65 ACGTTTGCCGAGCTAGACGTTCAATTATAATATATTTAACAAAAGATATAAAAAACATTCAACTT

                                  *             *                  **        
        131 AAAATCATTTACGGCATTACAAGACCATTTAAAGCGGGTAATAAGGCATTTGAAGGTATGGGTGA
        130 AAAATCATTTACGGCATTACAAAACCATTTAAAGCGAGTAATAAGGCATTTGAAGAAATGGGTGA

                    *                    *                          *        
        196 CTATAAATGGACTTTTCTTCCCAAAGAATGCTTTTTTCTTCATGTTTCTCGAGGTATACATTCAA
        195 CTATAAATAGACTTTTCTTCCCAAAGAATACTTTTTTCTTCATGTTTCTCGAGGTAGACATTCAA

                     *                     *                      *  *       
        261 TTCTAATATGTTTTAACCAAAAATGTACAATGAATTCAAATTTAAATAAATTTTGAGGTTATAAA
        260 TTCTAATATATTTTAACCAAAAATGTACAATAAATTCAAATTTAAATAAATTTTAAGATTATAAA

                      *     * 
        326 AACATTTAAAGTGAGTGA
        325 AACATTTAAACTGAGTAA

                          *                 *   *                            
        344 TAAGGCTTTTAAAGAAATGGGTGACTATAAATAGACCTTTCTTGCCAATGAATGTTCTTTTCTTT
          1 TAAGGCTTTTAAAGGAATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATGTT-TTTTCTTT

             *         * *    *                *                            *
        409 ATGTTT-CTCGGGGTAGATGTTCAATTATAATATGTTTTAACCAGAAA-AGTA-AAAAAA-ATTG
         65 ACGTTTGC-CGAGCTAGACGTTCAATTATAATAT-ATTTAA-CA-AAAGA-TATAAAAAACATTC

                             *        *     *        *  *         *          
        470 AACTTAAAATCAATTT-TGAG-ATTATAAAACTATTTAAAGTGATTAATAAGGCTTTTGAAGAAA
        125 AACTTAAAATC-ATTTACG-GCATTACAAAACCATTTAAAGCGAGTAATAAGGCATTTGAAGAAA

                                      *    *                         *       
        533 TGGGTGACTATAAATAGACTTTTCTTGCCAATGAATACTTTTTTCTTCATGTTTCT-TATGGTAG
        188 TGGGTGACTATAAATAGACTTTTCTTCCCAAAGAATACTTTTTTCTTCATGTTTCTCGA-GGTAG

                         * *        *                               *        
        597 ACATTCAATTCTAGTCTATTTTAAGCAAAAATGTACAA-AACATTCAAATTTAAATCAATTTTAA
        252 ACATTCAATTCTAATATATTTTAACCAAAAATGTACAATAA-ATTCAAATTTAAATAAATTTTAA

                      *                
        661 GATTATAAAACCATTTAAACTGAGTAA
        316 GATTATAAAAACATTTAAACTGAGTAA

                   *          *                                   *         
        688 TAAGGCTCTTAAAGGAATAGGTGACTATAAATGGACTTTTCTTGCCAATGAATACTTTTTTCTT
          1 TAAGGCTTTTAAAGGAATGGGTGACTATAAATGGACTTTTCTTGCCAATGAAT-GTTTTTTCTT

        752 CAGATTTGTG


Statistics
Matches: 350,  Mismatches: 47, Indels: 21
        0.84            0.11        0.05

Matches are distributed among these distances:
 342    2  0.01
 343   84  0.24
 344  243  0.69
 345   16  0.05
 346    5  0.01

ACGTcount: A:0.36, C:0.13, G:0.15, T:0.36


Consensus pattern (342 bp):   
TAAGGCTTTTAAAGGAATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATGTTTTTTCTTTA
CGTTTGCCGAGCTAGACGTTCAATTATAATATATTTAACAAAAGATATAAAAAACATTCAACTTA
AAATCATTTACGGCATTACAAAACCATTTAAAGCGAGTAATAAGGCATTTGAAGAAATGGGTGAC
TATAAATAGACTTTTCTTCCCAAAGAATACTTTTTTCTTCATGTTTCTCGAGGTAGACATTCAAT
TCTAATATATTTTAACCAAAAATGTACAATAAATTCAAATTTAAATAAATTTTAAGATTATAAAA
ACATTTAAACTGAGTAA
Done.