Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NW_018398184.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_1488.0, 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: 3260
ACGTcount: A:0.24, C:0.11, G:0.09, T:0.26

Warning! 990 characters in sequence are not A, C, G, or T


Found at i:1524 original size:171 final size:172

Alignment explanation


    Indices: 1231--1795  Score: 612
    Period size: 171  Copynumber: 3.3  Consensus size: 172

       1221 NNCTCGCTTT

                          *               *  *  ** *                  *      
       1231 AAATGGTTTTATAATCTCATAATTGATTTTAAGCTGTGTTTTTTTATATTTTTGA-TTGAAACAG
          1 AAATGGTTTTATAACCTCATAATTGATTTTGAGTTGAATGTTTTTATATTTTT-ATTTAAAACAG

                     *          *        *       *                       *   
       1295 ATTATAATTAAATGTTTTCCTTGGGAAACATGAAGT-GAAACCCATTCATTGGCAAGAAAATCCC
         65 ATTATAATTGAATGTTTTCCATGGGAAACCTGAAGTAAAAACCCATTCATTGGCAAGAAAAGCCC

                 *       *                             
       1359 ATTTACAGTCACCGAAGCCTTCAAATGCCTTATTACTCTTTTA
        130 ATTTATAGTCACCCAAGCCTTCAAATGCCTTATTACTCTTTTA

                *              *                                           * 
       1402 AAATAGTTTTATAACCTCAAAATTGATTTTGAGTTGAATGTTTTTATATTTTTATTTAAAACATA
          1 AAATGGTTTTATAACCTCATAATTGATTTTGAGTTGAATGTTTTTATATTTTTATTTAAAACAGA

             *               *                                 *           * 
       1467 TCATAATTGAATGTTTTTCATGGGAAACCTGAA-TAAAAACCCATTCATTGACAAGAAAAGCCTA
         66 TTATAATTGAATGTTTTCCATGGGAAACCTGAAGTAAAAACCCATTCATTGGCAAGAAAAGCCCA

                 **          *      *                *
       1531 TTTATTTTCACCCAAGCTTTCAAAAGCCTTATTACTCTTTTT
        131 TTTATAGTCACCCAAGCCTTCAAATGCCTTATTACTCTTTTA

                             * *               *                             
       1573 AAATGGTTTTATAACCTTAGAATTGATTTT-AGGTCGAATGTTTTTATATTTTT-TTTAAAACAG
          1 AAATGGTTTTATAACCTCATAATTGATTTTGA-GTTGAATGTTTTTATATTTTTATTTAAAACAG

               **                  *           *     ***   *     *           
       1636 ATTGCAATTGAATGTTTTCCATGAGAAACCT-AAGGAAAAAGATATTGATTGGTAAGAAAAGCCC
         65 ATTATAATTGAATGTTTTCCATGGGAAACCTGAAGTAAAAACCCATTCATTGGCAAGAAAAGCCC

                                         *           *  
       1700 ATTTATAGTCACCCAAGCCTTCAAAAT-CTTTATTACTC-TCTA
        130 ATTTATAGTCACCCAAGCCTTC-AAATGCCTTATTACTCTTTTA

                                        *                     *      
       1742 CAAATGGTTTTATAATCC-CATAATTG-GTTTGAAGTTGAAT-TATTTTACATTTTT
          1 -AAATGGTTTTATAA-CCTCATAATTGATTTTG-AGTTGAATGT-TTTTATATTTTT

       1796 GATTAACNNN


Statistics
Matches: 328,  Mismatches: 56, Indels: 21
        0.81            0.14        0.05

Matches are distributed among these distances:
 169    8  0.02
 170  126  0.38
 171  194  0.59

ACGTcount: A:0.34, C:0.14, G:0.13, T:0.40


Consensus pattern (172 bp):   
AAATGGTTTTATAACCTCATAATTGATTTTGAGTTGAATGTTTTTATATTTTTATTTAAAACAGA
TTATAATTGAATGTTTTCCATGGGAAACCTGAAGTAAAAACCCATTCATTGGCAAGAAAAGCCCA
TTTATAGTCACCCAAGCCTTCAAATGCCTTATTACTCTTTTA

Found at i:2864 original size:171 final size:171

Alignment explanation


    Indices: 2579--3107  Score: 549
    Period size: 171  Copynumber: 3.1  Consensus size: 171

       2569 NNNNNNNNNT

                                              *                  *           
       2579 AAGCCTTCAAAAGCCTTATTACTCTCTGTAAATGGTTTTATAATCTCATAATTCATTTGAAGTTG
          1 AAGCCTTCAAAAGCCTTATTACTCTCTGTAAATGATTTTATAATCTCATAATTGATTTGAAGTTG

               *               *                                             
       2644 AATGATTTTACATGTTTGGTTAACAGAGATTATAATTAAATGTTTGCCTTGAGAAGCACAAAGAA
         66 AATTATTTTACATGTTTGGCTAACAGAGATTATAATTAAATGTTTGCCTTGAGAAGCACAAAGAA

                                                     
       2709 AAACCCATTCATTAGCAAGAAAAACCCATTTATAGTCACCC
        131 AAACCCATTCATTAGCAAGAAAAACCCATTTATAGTCACCC

                              *                           *          *       
       2750 AAGCCTTCAAAAGCCTTACTACTCTCTGTAAATGATTTTATAATCTTATAATTGATTAGAAGTTG
          1 AAGCCTTCAAAAGCCTTATTACTCTCTGTAAATGATTTTATAATCTCATAATTGATTTGAAGTTG

                                **********       *                  **       
       2815 AATTATTTTACATGTTTGGCNNNNNNNNNNTATAATTGAATGTTTGCCTTGAGAAGTGCAAAGAA
         66 AATTATTTTACATGTTTGGCTAACAGAGATTATAATTAAATGTTTGCCTTGAGAAGCACAAAGAA

                *    *   *         *          *******
       2880 AAACTCATTTATTGGCAAGAAAAGCCCATTTATANNNNNNN
        131 AAACCCATTCATTAGCAAGAAAAACCCATTTATAGTCACCC

            ***                               *        *                     
       2921 NNNCCTTCAAAAGCCTTATTACTCTCTGT-AATCAATTTTATAGTCTCATAATTGATTTGAAGTT
          1 AAGCCTTCAAAAGCCTTATTACTCTCTGTAAAT-GATTTTATAATCTCATAATTGATTTGAAGTT

                       *       ***     *           * *     *      *     ** * 
       2985 GAATTATTTTATAT-TTGTTATTAACACAGATTATAATTTATTGTTTACCTTGATAAGCATGAGG
         65 GAATTATTTTACATGTT-TGGCTAACAGAGATTATAATTAAATGTTTGCCTTGAGAAGCACAAAG

                *        *           *   *            *
       3049 AAAATCCCATTCACTAGCAAGAAAAGCCCCTTTATAGTCACCT
        129 AAAAACCCATTCATTAGCAAGAAAAACCCATTTATAGTCACCC

                            
       3092 AAGCCTTCAAAAGCCT
          1 AAGCCTTCAAAAGCCT

       3108 AANNNNNNNN


Statistics
Matches: 278,  Mismatches: 78, Indels: 4
        0.77            0.22        0.01

Matches are distributed among these distances:
 170    5  0.02
 171  273  0.98

ACGTcount: A:0.33, C:0.16, G:0.13, T:0.34


Consensus pattern (171 bp):   
AAGCCTTCAAAAGCCTTATTACTCTCTGTAAATGATTTTATAATCTCATAATTGATTTGAAGTTG
AATTATTTTACATGTTTGGCTAACAGAGATTATAATTAAATGTTTGCCTTGAGAAGCACAAAGAA
AAACCCATTCATTAGCAAGAAAAACCCATTTATAGTCACCC
Done.