Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NW_018402656.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_5724.0, 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: 2095
ACGTcount: A:0.27, C:0.10, G:0.09, T:0.29

Warning! 514 characters in sequence are not A, C, G, or T


Found at i:669 original size:170 final size:171

Alignment explanation


    Indices: 363--973  Score: 460
    Period size: 171  Copynumber: 3.6  Consensus size: 171

        353 GTCTATCTCG

                  * *    *     *        *         * *              *         
        363 AGAAACATGAAGACAAAAGTATTCATTGACAAAAAAAGCCCATTTATAGTCACCCATT-CTTTC-
          1 AGAAACGTAAAGAAAAAAGCATTCATTGGCAAAAAAAGTCTATTTATAGTCACCCCTTGC-TTCA

                  *        *   *        * *               **********   **    
        426 AAAGCCTTATTACTCGCTTTAAATGGTTTTCTAATCTCATAATTGANNNNNNNNNNAATTTTTTT
         65 AAAGCCATATTACTCACTTCAAATGGTTGTATAATCTCATAATTGATTTTAAGTTGAATAGTTTT

                        *                        *  *  
        491 ACATTTTTCATTGAAACAGACTATAATTGAATA-TATGCCTTA
        130 ACATTTTTCATTAAAACAGACTATAATTGAATATTA-ACCCTA

                    *        *  *        *        *                 *        
        533 AGAAACGTGAAG-AAAAGGCGTTCATTGGTAAGAAAAATTC-ATTTATAGTCACCCTTTGCTTCA
          1 AGAAACGTAAAGAAAAAAGCATTCATTGGCAA-AAAAAGTCTATTTATAGTCACCCCTTGCTTCA

                                                 *                           
        596 AAAGCCATATTACTCACTTCAAATGGTTGTATAATCTTATAATTGATTTTAAGTTGAATAGTTTT
         65 AAAGCCATATTACTCACTTCAAATGGTTGTATAATCTCATAATTGATTTTAAGTTGAATAGTTTT

             *       *       * *            *        *
        661 ATATTTTTCGTTAAAACGGGCTATAATTGAATGTTAACCCTG
        130 ACATTTTTCATTAAAACAGACTATAATTGAATATTAACCCTA

                 *                 *                       *                 
        703 AGAAATGTAAAGAAAAAAGCATTTATTGGCAAAAAAAGTCTATTTATTGTCACCCCTTGCTTCAA
          1 AGAAACGTAAAGAAAAAAGCATTCATTGGCAAAAAAAGTCTATTTATAGTCACCCCTTGCTTCAA

               *                                             ***********     
        768 AAGTCATATTACTCACTTCAAATGGTTGTATAATCTCATAATTGATTTTNNNNNNNNNNTTTTTA
         66 AAGCCATATTACTCACTTCAAATGGTTGTATAATCTCATAATTGATTTTAAGTTGAATAGTTTTA

            *                 *            *  *   * *
        833 TATTTTTCATTAAAACAGGCTATAATTGAATGTTGACCTTG
        131 CATTTTTCATTAAAACAGACTATAATTGAATATTAACCCTA

                 *  *              *   *    *   *            * * * *  *      
        874 AGAAATGTGAAGAAAAAAGCATTTATTAGCAAGAAATGTCTATTTATAGCCTCGCATTCCTTCAA
          1 AGAAACGTAAAGAAAAAAGCATTCATTGGCAAAAAAAGTCTATTTATAGTCACCCCTTGCTTCAA

               * *        *   *                 
        939 AAGTCTTATTACTCGCTTTAAATGGTT-TATAATCT
         66 AAGCCATATTACTCACTTCAAATGGTTGTATAATCT

        974 AATATTTGNN


Statistics
Matches: 359,  Mismatches: 76, Indels: 12
        0.80            0.17        0.03

Matches are distributed among these distances:
 169   32  0.09
 170  120  0.33
 171  207  0.58

ACGTcount: A:0.34, C:0.14, G:0.13, T:0.36


Consensus pattern (171 bp):   
AGAAACGTAAAGAAAAAAGCATTCATTGGCAAAAAAAGTCTATTTATAGTCACCCCTTGCTTCAA
AAGCCATATTACTCACTTCAAATGGTTGTATAATCTCATAATTGATTTTAAGTTGAATAGTTTTA
CATTTTTCATTAAAACAGACTATAATTGAATATTAACCCTA

Found at i:793 original size:171 final size:171

Alignment explanation


    Indices: 487--973  Score: 523
    Period size: 171  Copynumber: 2.9  Consensus size: 171

        477 NNNNNAATTT

                 *          *      *             *   *  * *     *  *        *
        487 TTTTACATTTTTCATTGAAACAGACTATAATTGAAT-ATATGCCTTAAGAAACGTGAAG-AAAAG
          1 TTTTATATTTTTCATTAAAACAGGCTATAATTGAATGTTA-ACCCTGAGAAATGTAAAGAAAAAA

              *  *     *        *                 *            *             
        550 GCGTTCATTGGTAAGAAAAATTC-ATTTATAGTCACCCTTTGCTTCAAAAGCCATATTACTCACT
         65 GCATTTATTGGCAA-AAAAAGTCTATTTATAGTCACCCATTGCTTCAAAAGTCATATTACTCACT

                               *                       
        614 TCAAATGGTTGTATAATCTTATAATTGATTTTAAGTTGAATAG
        129 TCAAATGGTTGTATAATCTCATAATTGATTTTAAGTTGAATAG

                         *       *                                           
        657 TTTTATATTTTTCGTTAAAACGGGCTATAATTGAATGTTAACCCTGAGAAATGTAAAGAAAAAAG
          1 TTTTATATTTTTCATTAAAACAGGCTATAATTGAATGTTAACCCTGAGAAATGTAAAGAAAAAAG

                                        *       *                            
        722 CATTTATTGGCAAAAAAAGTCTATTTATTGTCACCCCTTGCTTCAAAAGTCATATTACTCACTTC
         66 CATTTATTGGCAAAAAAAGTCTATTTATAGTCACCCATTGCTTCAAAAGTCATATTACTCACTTC

                                          ***********
        787 AAATGGTTGTATAATCTCATAATTGATTTTNNNNNNNNNNT
        131 AAATGGTTGTATAATCTCATAATTGATTTTAAGTTGAATAG

                                                   *   *          *          
        828 TTTTATATTTTTCATTAAAACAGGCTATAATTGAATGTTGACCTTGAGAAATGTGAAGAAAAAAG
          1 TTTTATATTTTTCATTAAAACAGGCTATAATTGAATGTTAACCCTGAGAAATGTAAAGAAAAAAG

                    *    *   *            * * *    *           *        *   *
        893 CATTTATTAGCAAGAAATGTCTATTTATAGCCTCGCATTCCTTCAAAAGTCTTATTACTCGCTTT
         66 CATTTATTGGCAAAAAAAGTCTATTTATAGTCACCCATTGCTTCAAAAGTCATATTACTCACTTC

                             
        958 AAATGGTT-TATAATCT
        131 AAATGGTTGTATAATCT

        974 AATATTTGNN


Statistics
Matches: 266,  Mismatches: 48, Indels: 6
        0.83            0.15        0.02

Matches are distributed among these distances:
 170   59  0.22
 171  207  0.78

ACGTcount: A:0.34, C:0.14, G:0.13, T:0.37


Consensus pattern (171 bp):   
TTTTATATTTTTCATTAAAACAGGCTATAATTGAATGTTAACCCTGAGAAATGTAAAGAAAAAAG
CATTTATTGGCAAAAAAAGTCTATTTATAGTCACCCATTGCTTCAAAAGTCATATTACTCACTTC
AAATGGTTGTATAATCTCATAATTGATTTTAAGTTGAATAG
Done.