Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NW_018398593.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_1884.0, 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: 3640
ACGTcount: A:0.22, C:0.07, G:0.07, T:0.22

Warning! 1514 characters in sequence are not A, C, G, or T


Found at i:837 original size:170 final size:158

Alignment explanation


    Indices: 650--981  Score: 353
    Period size: 168  Copynumber: 2.0  Consensus size: 158

        640 TTTCTTTACA

                  *                                              *           
        650 TTTCTCGAGGAAGACATTCAATTATAAAATGTTTTAATAAAAATATAAAAAAATTCAAATTAAAA
          1 TTTCTCAAGGAAGACATTCAATTATAAAATGTTTTAATAAAAA-ATAAAAAAAAT-AAATTAAAA

                                *         *               *                * 
        715 GCAATTATGAGGTTATAAAATCATTCAAAGTGAGAAATAAGGCTTTTGAAAGCATGGGTGACTCT
         64 GCAATTATGAGGTTATAAAAACATTCAAAGCGAGAAATAAGGCTTTCGAAAGCATGGGTGACTAT

                         *  *                        
        780 AAATGGACTTT-TTTTGCCAATGGATATCTNNNNNNNNNNG
        129 AAATGGA-TTTATCTTACCAATGGATATCT----------G

                      *       *        **                                  * 
        820 TTTCTCAAGGCAGACATTTAATTATAATCTGTTTTAATAAAAAATAAAAAAAATAAATTAAAATC
          1 TTTCTCAAGGAAGACATTCAATTATAAAATGTTTTAATAAAAAATAAAAAAAATAAATTAAAAGC

                                   * **     *               * *              
        885 AATTATGAGGTTATAAAAACATTTACTGCGAGTAATAAGGCTTTCGAAGGTATGGGTGACTATAA
         66 AATTATGAGGTTATAAAAACATTCAAAGCGAGAAATAAGGCTTTCGAAAGCATGGGTGACTATAA

                                       *
        950 ATGGATTTATCTTACCAATGGAT-TCTT
        131 ATGGATTTATCTTACCAATGGATATCTG

                 
        977 TTTCT
          1 TTTCT

        982 TCACATTTCT


Statistics
Matches: 141,  Mismatches: 20, Indels: 15
        0.80            0.11        0.09

Matches are distributed among these distances:
 157    5  0.04
 167    6  0.04
 168   82  0.58
 169   10  0.07
 170   38  0.27

ACGTcount: A:0.39, C:0.10, G:0.15, T:0.33


Consensus pattern (158 bp):   
TTTCTCAAGGAAGACATTCAATTATAAAATGTTTTAATAAAAAATAAAAAAAATAAATTAAAAGC
AATTATGAGGTTATAAAAACATTCAAAGCGAGAAATAAGGCTTTCGAAAGCATGGGTGACTATAA
ATGGATTTATCTTACCAATGGATATCTG

Found at i:953 original size:168 final size:170

Alignment explanation


    Indices: 537--1149  Score: 554
    Period size: 170  Copynumber: 3.6  Consensus size: 170

        527 NNNNNNNNNN

                                         *                       *         * 
        537 AATTAAAATCAATTATGAGGTTATAAAATTATTTAATGCGAGTAATAAGGCTTCCGAAGGCATAG
          1 AATTAAAATCAATTATGAGGTTATAAAATCATTTAATGCGAGTAATAAGGCTTTCGAAGGCATGG

              *    *          *    *                               *         
        602 GTTACTAGAAATGGACCTGTTTTAACC-ATGGATATCTTTTTCTTTACATTTCTCGAGGAAGACA
         66 GTGACTATAAATGGA-CTTTTTTTACCAATGGATATCTTTTTCTTTACATTTCTCAAGGAAGACA

                                                 *   
        666 TTCAATTATAAAATGTTTTAATAAAAATATAAAAAAATTCA
        130 TTCAATTATAAAATGTTTTAATAAAAATATAAAAAAAATCA

                    *                        *  * *   *           *   *      
        707 AATTAAAAGCAATTATGAGGTTATAAAATCATTCAAAGTGAGAAATAAGGCTTTTGAAAGCATGG
          1 AATTAAAATCAATTATGAGGTTATAAAATCATTTAATGCGAGTAATAAGGCTTTCGAAGGCATGG

                  *                *             ***********          *      
        772 GTGACTCTAAATGGACTTTTTTTGCCAATGGATATCTNNNNNNNNNNGTTTCTCAAGGCAGACAT
         66 GTGACTATAAATGGACTTTTTTTACCAATGGATATCTTTTTCTTTACATTTCTCAAGGAAGACAT

             *        **                            
        837 TTAATTATAATCTGTTTTAATAAAAA-ATAAAAAAAAT-A
        131 TCAATTATAAAATGTTTTAATAAAAATATAAAAAAAATCA

                                        *      *                        *    
        875 AATTAAAATCAATTATGAGGTTATAAAAACATTTACTGCGAGTAATAAGGCTTTCGAAGGTATGG
          1 AATTAAAATCAATTATGAGGTTATAAAATCATTTAATGCGAGTAATAAGGCTTTCGAAGGCATGG

                                 *                       *         *         
        940 GTGACTATAAATGGA-TTTATCTTACCAATGGAT-TCTTTTTCTTCACATTTCTCGA-GATAGAC
         66 GTGACTATAAATGGACTTT-TTTTACCAATGGATATCTTTTTCTTTACATTTCTCAAGGA-AGAC

               *   *    *  *     *              *******
       1002 ATTTAATCATAATATATTTTATTAAAAAATATAAAANNNNNNN
        129 ATTCAATTATAAAATGTTTTAAT-AAAAATATAAAAAAAATCA

            ***                          ** *   * *         **    *        * 
       1045 NNNTAAAATCAATTATGAGGTTATAAAATTGTGTAAAGTGAGTAATAAATCTTTGGAAGGCATAG
          1 AATTAAAATCAATTATGAGGTTATAAAATCATTTAATGCGAGTAATAAGGCTTTCGAAGGCATGG

                                *  *      *         
       1110 GTGACTATAAATGGACTTTTCTTGCCAATGAATATCTTTT
         66 GTGACTATAAATGGACTTTTTTTACCAATGGATATCTTTT

       1150 NNNNNNNNNN


Statistics
Matches: 349,  Mismatches: 86, Indels: 15
        0.78            0.19        0.03

Matches are distributed among these distances:
 166    1  0.00
 167   36  0.10
 168   87  0.25
 169   24  0.07
 170  192  0.55
 171    9  0.03

ACGTcount: A:0.38, C:0.10, G:0.15, T:0.34


Consensus pattern (170 bp):   
AATTAAAATCAATTATGAGGTTATAAAATCATTTAATGCGAGTAATAAGGCTTTCGAAGGCATGG
GTGACTATAAATGGACTTTTTTTACCAATGGATATCTTTTTCTTTACATTTCTCAAGGAAGACAT
TCAATTATAAAATGTTTTAATAAAAATATAAAAAAAATCA
Done.