Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NW_018400189.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_3403.0, 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, 735

Length: 1226
ACGTcount: A:0.37, C:0.11, G:0.13, T:0.35

Warning! 43 characters in sequence are not A, C, G, or T


Found at i:291 original size:171 final size:169

Alignment explanation


    Indices: 18--614  Score: 669
    Period size: 171  Copynumber: 3.5  Consensus size: 169

          8 TTCCTAAGGC

                           *   *   *  *                  *  *                
         18 AGACATTCAATTATATTCTTTTTTAATTATAAATATAAAAAAATTTAAGTTAAAATCAATTATGA
          1 AGACATTCAATTATAATCTGTTTAAACTA-AAATATAAAAAAATTCAACTTAAAATCAATTAT-A

            *    *              *                        *                   
         83 CATTACAAAACCATTTAAAGTAAGTAATAAAGCTTTTGAAGGAATTGGTGACTATAAATGGACTT
         64 GATTATAAAACCATTTAAAGCAAGTAATAAAGCTTTTGAAGGAATGGGTGACTATAAATGGACTT

                                        *            
        148 TTCTTGTCAATGAATGCCCTTTTCTTTACGTTTCTTGAAGT
        129 TTCTTGTCAATGAATGCCCTTTTCTTTATGTTTCTTGAAGT

                             *                                      *        
        189 AGACATTCAATTATAATATGTTTAAACTGAAAATATAAAAAAATTCAACTTAAAATTAATTATAA
          1 AGACATTCAATTATAATCTGTTTAAACT-AAAATATAAAAAAATTCAACTTAAAATCAATTAT-A

                *              * *        *            *                     
        254 GATTGTAAAACCATTTAAAACGAGTAATAAGGCTTTTGAAGGAGTGGGTGACTATAAATGGACTT
         64 GATTATAAAACCATTTAAAGCAAGTAATAAAGCTTTTGAAGGAATGGGTGACTATAAATGGACTT

              *     *        **       *           *  
        319 TTTTTGTCGATGAATGCTTTTTTCTTCATGTTTCTTGAGGT
        129 TTCTTGTCAATGAATGCCCTTTTCTTTATGTTTCTTGAAGT

             *                                *     *       *              * 
        360 AAACATTCAATTATAATCTGTTTAAACTAGAAATGTAAAACAATTCAATTTAAAATCAATTATGG
          1 AGACATTCAATTATAATCTGTTTAAACTA-AAATATAAAAAAATTCAACTTAAAATCAATTATAG

                     *             *               *                      *  
        425 CATTATAAAGCCATTTAAAGCAAATAATAAAGCTTTTGATGGAATGGGTGACTATAAATGGAGTT
         65 -ATTATAAAACCATTTAAAGCAAGTAATAAAGCTTTTGAAGGAATGGGTGACTATAAATGGACTT

                                             *    *     
        490 TTCTTG-CGAATGAATG-CCTCTTTCTTTATGTCTC-TCAAGGT
        129 TTCTTGTC-AATGAATGCCCT-TTTCTTTATGTTTCTTGAA-GT

                         * *    *     * *     *                     *     *  
        531 AGACATTCAATTACATTCTATTTTAACCAAAAATGTAAAAAAATTCAACTTAAAATTAATTGTTA
          1 AGACATTCAATTATAATCT-GTTTAAACTAAAATATAAAAAAATTCAACTTAAAATCAATT-ATA

             *  *              
        596 GTTTTTAAAACCATTTAAA
         64 GATTATAAAACCATTTAAA

        615 NNNNNNNNNN


Statistics
Matches: 355,  Mismatches: 63, Indels: 16
        0.82            0.15        0.04

Matches are distributed among these distances:
 170    6  0.02
 171  339  0.95
 172   10  0.03

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


Consensus pattern (169 bp):   
AGACATTCAATTATAATCTGTTTAAACTAAAATATAAAAAAATTCAACTTAAAATCAATTATAGA
TTATAAAACCATTTAAAGCAAGTAATAAAGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTT
CTTGTCAATGAATGCCCTTTTCTTTATGTTTCTTGAAGT

Found at i:1019 original size:173 final size:172

Alignment explanation


    Indices: 658--1177  Score: 668
    Period size: 173  Copynumber: 3.0  Consensus size: 172

        648 NNNNNNNNNN

                *             *                                              
        658 TAAGTCTTTTGAAGGAATAGGTGACTATAAATAGAGTTTTCTTATCAATGAATATCTTTTTCTTC
          1 TAAGGCTTTTGAAGGAATGGGTGACTATAAATAGAGTTTTCTTATCAATGAATATCTTTTTCTTC

             *      *          *     *      *        *         *             
        723 ATGTTTCTCGAGGTAGACAATCAATCATAATCGATTTTAACCAAAAATGTGCAAAG-AATTCAAC
         66 ACGTTTCTTGAGGTAGACATTCAATTATAATCTATTTTAACAAAAAATGT-AAAAGAAATTCAAC

                        *                 *       *     
        787 TTAAAATCAATTTTGAGATTATAAAACCATATAAAGA-GAGTAA
        130 TTAAAATCAATTATGAGATTATAAAACCATTTAAA-ACAAGTAA

                                               *       *     *    *         *
        830 TAAGGCTTTTGAAGGAATGGGTGACTATAAATAGACTTTTCTTGTCAATAAATACCTTTTTCTTT
          1 TAAGGCTTTTGAAGGAATGGGTGACTATAAATAGAGTTTTCTTATCAATGAATATCTTTTTCTTC

                                           *         *                       
        895 ACGTTTCTTGAGGTAGACATTCAATTATAATATATTTTAACTAAAAATGTAAAAAGAAATTCAAC
         66 ACGTTTCTTGAGGTAGACATTCAATTATAATCTATTTTAACAAAAAATGT-AAAAGAAATTCAAC

                                *                      
        960 TTAAAATCAATTATGAGATTGTAAAACCATTTAAAACAAGTAA
        130 TTAAAATCAATTATGAGATTATAAAACCATTTAAAACAAGTAA

                               **           *                    *        *  
       1003 TAAGGCTTTTGAAGGAATGACTGACTATAAATGGAGTTTTCTTATCAATGAATGTCTTTTTCCTC
          1 TAAGGCTTTTGAAGGAATGGGTGACTATAAATAGAGTTTTCTTATCAATGAATATCTTTTTCTTC

                     *  *                *   *    *               *          
       1068 ACGTTTCTTAAGTTAGACATTCAATTATATTCTGTTTTGACAAAAAATGTAAAACAAA-TCAACT
         66 ACGTTTCTTGAGGTAGACATTCAATTATAATCTATTTTAACAAAAAATGTAAAAGAAATTCAACT

                         *  *  *      *       *       
       1132 TAAAATCAATTATTAGTTTCTAAAACTATTTAAAGCAAGTAA
        131 TAAAATCAATTATGAGATTATAAAACCATTTAAAACAAGTAA

                
       1174 TAAG
          1 TAAG

       1178 ACATTCGAAT


Statistics
Matches: 303,  Mismatches: 43, Indels: 5
        0.86            0.12        0.01

Matches are distributed among these distances:
 171   47  0.16
 172  113  0.37
 173  143  0.47

ACGTcount: A:0.39, C:0.12, G:0.13, T:0.36


Consensus pattern (172 bp):   
TAAGGCTTTTGAAGGAATGGGTGACTATAAATAGAGTTTTCTTATCAATGAATATCTTTTTCTTC
ACGTTTCTTGAGGTAGACATTCAATTATAATCTATTTTAACAAAAAATGTAAAAGAAATTCAACT
TAAAATCAATTATGAGATTATAAAACCATTTAAAACAAGTAA
Done.