Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NW_018398276.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_1580.0, 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: 3980
ACGTcount: A:0.24, C:0.06, G:0.08, T:0.23

Warning! 1544 characters in sequence are not A, C, G, or T


Found at i:2763 original size:171 final size:170

Alignment explanation


    Indices: 2477--2802  Score: 402
    Period size: 171  Copynumber: 1.9  Consensus size: 170

       2467 ACAAATTGAG

                    *                   *        *           *               
       2477 CTTAAAATCAATTATGAGATTATAAAATTATTTAGAATGAGCAAAAAGGCTATTGAAGGAATGGA
          1 CTTAAAATAAATTATGAGATTATAAAATGATTTAGAACGAGCAAAAAGGATATTGAAGGAATGGA

              *      *             *           *                    *      * 
       2542 AGGCTATAATTGAACTTTTCTTATCAATAAATACTTTTTTCTTCATGTTTCTCGAGGCAGACATT
         66 AGACTATAAATGAACTTTTCTTACCAATAAATACTGTTTTCTTCATGTTTCTCGAGACAGACAAT

            *           *                            
       2607 TAATTATAGTCTGTTTTAATAGAAAATATTAAAAAATTTAA
        131 CAATTATAGTCTATTTTAATA-AAAATATTAAAAAATTTAA

                                                      * **      *            
       2648 CTTAAAATAAATTATGAGATTATAAAATGATTTA-AAGCGAGTATTAAGGATTTTGAAGGAATGG
          1 CTTAAAATAAATTATGAGATTATAAAATGATTTAGAA-CGAGCAAAAAGGATATTGAAGGAATGG

            **           *         *     *   *          *             *      
       2712 CTGACTATAAATGGACTTTTCTTGCCAATGAATGCTGTTTTCTTTATGTTTCTCGAGATAGACAA
         65 AAGACTATAAATGAACTTTTCTTACCAATAAATACTGTTTTCTTCATGTTTCTCGAGACAGACAA

                    *                 
       2777 TCAATTATTGTCTATTTTAATAAAAA
        130 TCAATTATAGTCTATTTTAATAAAAA

       2803 NNNNNNNNNN


Statistics
Matches: 129,  Mismatches: 25, Indels: 3
        0.82            0.16        0.02

Matches are distributed among these distances:
 170    6  0.05
 171  123  0.95

ACGTcount: A:0.38, C:0.10, G:0.15, T:0.38


Consensus pattern (170 bp):   
CTTAAAATAAATTATGAGATTATAAAATGATTTAGAACGAGCAAAAAGGATATTGAAGGAATGGA
AGACTATAAATGAACTTTTCTTACCAATAAATACTGTTTTCTTCATGTTTCTCGAGACAGACAAT
CAATTATAGTCTATTTTAATAAAAATATTAAAAAATTTAA

Found at i:3124 original size:171 final size:171

Alignment explanation


    Indices: 2839--3165  Score: 398
    Period size: 171  Copynumber: 1.9  Consensus size: 171

       2829 NNNTATTAGA

                         *   * *               *                             
       2839 TTATAAAACCATTTAAAGCTAGTAATAAGGCTTTTGAAGGACTAGGACACTATAAATGGACTTTT
          1 TTATAAAACCATTCAAACCGAGTAATAAGGCTTTTAAAGGACTAGGACACTATAAATGGACTTTT

               *                 *                                           
       2904 CTTGCCAATGAATGCTTGTTTGGTCATATTTCCTAATATAGACATTCAATTATTA-CCTGTTTTA
         66 CTTACCAATGAATGCTTGTTTAGTCATATTTCCTAATATAGACATTCAATTA-TAGCCTGTTTTA

                                                        
       2968 AT-AGAAAATATAAAATAA-TTCAACTTAAAATCAATTTTGGGC
        130 ATGA-AAAATATAAAA-AACTTCAACTTAAAATCAATTTTGGGC

                                                            * *              
       3010 TTATAAAACCATTCAAACCGAGTAATAAGGCTTTTAAAGGACT-GAGAGATTATAAATGGAAC-T
          1 TTATAAAACCATTCAAACCGAGTAATAAGGCTTTTAAAGGACTAG-GACACTATAAATGG-ACTT

                    *  *             *    *      *        *            *     
       3073 TTCTTACCCATTAATGCCTT-TTTATTCA-CTTTCCTTATAGTAGATATTCAATTATAGTCTGTT
         64 TTCTTACCAATGAATG-CTTGTTTAGTCATATTTCCTAATA-TAGACATTCAATTATAGCCTGTT

                        *                 
       3136 TTAATGAAAAATGTAAAAAACTTCAACTTA
        127 TTAATGAAAAATATAAAAAACTTCAACTTA

       3166 NNNNNNNNNN


Statistics
Matches: 133,  Mismatches: 16, Indels: 14
        0.82            0.10        0.09

Matches are distributed among these distances:
 170   14  0.11
 171  113  0.85
 172    6  0.05

ACGTcount: A:0.37, C:0.14, G:0.13, T:0.36


Consensus pattern (171 bp):   
TTATAAAACCATTCAAACCGAGTAATAAGGCTTTTAAAGGACTAGGACACTATAAATGGACTTTT
CTTACCAATGAATGCTTGTTTAGTCATATTTCCTAATATAGACATTCAATTATAGCCTGTTTTAA
TGAAAAATATAAAAAACTTCAACTTAAAATCAATTTTGGGC
Done.