Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NW_018399731.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_2975.0, 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, 974

Length: 1624
ACGTcount: A:0.34, C:0.11, G:0.11, T:0.34

Warning! 158 characters in sequence are not A, C, G, or T


Found at i:501 original size:172 final size:162

Alignment explanation


    Indices: 323--805  Score: 368
    Period size: 172  Copynumber: 2.9  Consensus size: 162

        313 NNNNNNNNNN

                    *       *           *     *  *       *             *     
        323 ATTACTCGGTTTAAATGGTTTTATAATCTCATAATTGTTTTTAAGTTCAA-TTTTTTTTGCATTT
          1 ATTACTCGCTTTAAATAGTTTTATAATCACATAACTGATTTTAAGCTCAATTTTTTTTTACATTT

                     * *   *             *                                   
        387 TT-GCTTAATATAGATTATAATTGAAAGTTTACATT-AAGAAACATGAAGAAAAAGGCATTCATT
         66 TTCG-TTAAAACAGACTATAATTGAAAGTCTAC-TTCAAGAAACATGAAGAAAAA-GCATTCATT

                                                         
        450 GGCAAGAAAAGTCCATNNNNNNNNNNTCATTCTTTCAAAAGCCTT
        128 GGCAAGAAAAGTCCAT----------TCATTCTTTCAAAAGCCTT

                                                                             
        495 ATTACTCGCTTTAAATAGTTTTATAATCACATAACTGATTTTAAGCTCAATTTTTTTTTACATTT
          1 ATTACTCGCTTTAAATAGTTTTATAATCACATAACTGATTTTAAGCTCAATTTTTTTTTACATTT

                                     *         *     **   *                  
        560 TTCGTTAAAACAGACTATAATTGAATGTCTACTTCGAGAAAGGTGATGAAAAAGCATTCATTGGC
         66 TTCGTTAAAACAGACTATAATTGAAAGTCTACTTCAAGAAACATGAAGAAAAAGCATTCATTGGC

                                *                   * 
        625 AAGAAAAGTCCATGTATAGCCTCTCATTTCTTAAAAAGCCCT
        131 AAGAAAAGTCCA--T-T--CAT-TC-TTTC---AAAAGCCTT

                   *      * *           **    *            *     *      *    
        667 ATTACTCACTTTAAGTGGTTTTATAATCTGATAATTGATTTTAAG-TTAA-TTGTTTTTATATTT
          1 ATTACTCGCTTTAAATAGTTTTATAATCACATAACTGATTTTAAGCTCAATTTTTTTTTACATTT

              *                       *      *         *            *    *   
        730 TTGGTTAAAACA-ATCTATAATTGAATGTCTACCT-AGAGAAATATGAAGAACAAAACATTTATT
         66 TTCGTTAAAACAGA-CTATAATTGAAAGTCTACTTCA-AGAAACATGAAGAA-AAAGCATTCATT

             **          
        793 GATAAGAAAAGTC
        128 GGCAAGAAAAGTC

        806 TGTTTATAGT


Statistics
Matches: 258,  Mismatches: 38, Indels: 31
        0.79            0.12        0.09

Matches are distributed among these distances:
 165    1  0.00
 167    2  0.01
 168    2  0.01
 169    5  0.02
 170   53  0.21
 171   24  0.09
 172  117  0.45
 173   52  0.20
 174    2  0.01

ACGTcount: A:0.35, C:0.12, G:0.13, T:0.38


Consensus pattern (162 bp):   
ATTACTCGCTTTAAATAGTTTTATAATCACATAACTGATTTTAAGCTCAATTTTTTTTTACATTT
TTCGTTAAAACAGACTATAATTGAAAGTCTACTTCAAGAAACATGAAGAAAAAGCATTCATTGGC
AAGAAAAGTCCATTCATTCTTTCAAAAGCCTT

Found at i:1392 original size:172 final size:171

Alignment explanation


    Indices: 1095--1624  Score: 543
    Period size: 172  Copynumber: 3.1  Consensus size: 171

       1085 NNNNNNNCTA

                   *                  *           *      *            *   *  
       1095 TTTTAACTAAAAATGTAAAAAAAATTGAACTTTAAAATTAATTATAAGATTATAAAACCATTGAA
          1 TTTTAACAAAAAATGT-AAAAAAATTTAAC-TTAAAATCAATTATGAGATTATAAAACTATTTAA

              * *   *              *      *         *           **           
       1160 AGTGGGTAGTAAGGCTTTTGAAGGAATGAGTGACTATAAACGGACTTTTCTTATCAATGAATGCT
         64 AGCGAGTAATAAGGCTTTTGAAGAAATGAGAGACTATAAATGGACTTTTCTTGCCAATGAATGCT

                                 *  *                    * 
       1225 TTTTTCTTCAAGTTTCTCT-AGGTCGACATTCAATTATATAGAT-TG
        129 TTTTTCTTCAAGTTTCT-TGAAGTAGACATTCAA-T-TATAG-TCCG

                   *      *               *                                  
       1270 TTTTAACCAAAAATATAAAAAAATTTAACTCAAAATCAATTATGAGATTATAAAACTATTTAAAG
          1 TTTTAACAAAAAATGTAAAAAAATTTAACTTAAAATCAATTATGAGATTATAAAACTATTTAAAG

                             *            *     *                       **   
       1335 CGAGTAAT-AGGCTTTTTAAGAAATGAGAGGCTATAGATGGACTTTTCTTGCCAATGAATTTTTT
         66 CGAGTAATAAGGCTTTTGAAGAAATGAGAGACTATAAATGGACTTTTCTTGCCAATGAATGCTTT

                *   *               *                
       1399 TTTCATCATGTTTCTTGAAGTAGATATTCAATTATAGTCCG
        131 TTTCTTCAAGTTTCTTGAAGTAGACATTCAATTATAGTCCG

                   *             *                  *                        
       1440 TTTTAATGAAAAAATGTAAAACAA-TTAAGCTTAAAATCAGTTATGTA-ATTATAAAACTATTTA
          1 TTTTAA-CAAAAAATGTAAAAAAATTTAA-CTTAAAATCAATTATG-AGATTATAAAACTATTTA

                                             *          *                    
       1503 AAGCGAGTAATAAGGCTTTTGAA-AGAATGAGACACTATAAATGAACTTTTCTTGCCAATGAATG
         63 AAGCGAGTAATAAGGCTTTTGAAGA-AATGAGAGACTATAAATGGACTTTTCTTGCCAATGAATG

             *          *              *  *          *  **
       1567 CCTTTTTCTTCACGTTTCTT-AAGGTAAACTTTCAATTATAATCTA
        127 CTTTTTTCTTCAAGTTTCTTGAA-GTAGACATTCAATTATAGTCCG

                   *     
       1612 TTTTAACTAAAAA
          1 TTTTAACAAAAAA


Statistics
Matches: 296,  Mismatches: 51, Indels: 20
        0.81            0.14        0.05

Matches are distributed among these distances:
 169    1  0.00
 170   16  0.05
 171   64  0.22
 172  153  0.52
 173   36  0.12
 174   12  0.04
 175   14  0.05

ACGTcount: A:0.39, C:0.11, G:0.13, T:0.37


Consensus pattern (171 bp):   
TTTTAACAAAAAATGTAAAAAAATTTAACTTAAAATCAATTATGAGATTATAAAACTATTTAAAG
CGAGTAATAAGGCTTTTGAAGAAATGAGAGACTATAAATGGACTTTTCTTGCCAATGAATGCTTT
TTTCTTCAAGTTTCTTGAAGTAGACATTCAATTATAGTCCG
Done.