Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NW_018399989.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_3215.0, 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, 972

Length: 1620
ACGTcount: A:0.33, C:0.10, G:0.13, T:0.31

Warning! 194 characters in sequence are not A, C, G, or T


Found at i:371 original size:171 final size:169

Alignment explanation


    Indices: 66--1046  Score: 990
    Period size: 171  Copynumber: 5.8  Consensus size: 169

         56 TTAGGAAAAC

                 *          *  *                           *   *             
         66 ATTCATTTATAGTCTGCTTGAACCAAAAA-AGTGAAAAAATTCAACTCAAAGTCAATTATGAGAT
          1 ATTCAATTATAGTCTGTTTTAACCAAAAATA-T-AAAAAATTCAACTTAAAATCAATTATGAGAT

                   **    *                            ** *                *  
        130 TATAAAATAATTTGAAGCGAGTAATAAGGCTTTTGAAGGAATAAGAGACTATAAATGGACTTGTC
         64 TATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTC

                    *                                 
        195 TTGCCAATAAATGCTTGTTTCTTCATGTTTCTCGAGGTAAAT
        129 TTGCCAATGAATGCTT-TTTCTTCATGTTTCTCGAGGTAAAT

               *      *                                                *     
        237 ATTTAATTATTGTCTGTTTTAACCAAAAATATAAAACAATTCAACTTAAAATCAATTATTAGATT
          1 ATTCAATTATAGTCTGTTTTAACCAAAAATATAAAA-AATTCAACTTAAAATCAATTATGAGATT

                        *        *                  *               *        
        302 ATAAAACCATTTGAAGCGAGTGATAAGGCTTTTGAAGGAACGGGTGACTATAAATGCACTTTTCT
         65 ATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCT

                                                   *
        367 TGCCAATGAATGCTTTTT-TT-ATGTTTCTCGAGGTAAAG
        130 TGCCAATGAATGCTTTTTCTTCATGTTTCTCGAGGTAAAT

                       *          **       *     *         *        *        
        405 ATTCAATTATATTCTGTTTTAATGAAAAATCTTAAAATATTCAACTTTAAA-CAAACTATGAGAT
          1 ATTCAATTATAGTCTGTTTTAACCAAAAAT-ATAAAAAATTCAACTTAAAATC-AATTATGAGAT

                    *         *    *     *             *   *                 
        469 TATAAAACTATTTAAAGCCAGTACTAAGGTTTTTGAAGGAATGAGTGGCTATAAATGGACCTTTT
         64 TATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGGA-CTTTT

            *                         *    *  *  *     
        534 TTTGCCAATGAATGCCTTTTTCTTCACGTTTTTCAAGATAAAT
        128 CTTGCCAATGAATG-CTTTTTCTTCATGTTTCTCGAGGTAAAT

               *           *       *                                 *       
        577 ATTGAATTATAGTCTATTTTAACTAAAAATATAAAAAATTCAACTTAAAAGT-AATTGTGAGATT
          1 ATTCAATTATAGTCTGTTTTAACCAAAAATATAAAAAATTCAACTTAAAA-TCAATTATGAGATT

                 * *   *    *     *                        * *      *        
        641 ATAAAGCAATTGAAAGAGAGTAGTAAGGCTTTTGAAGGAATGGGTGATTGTAAATGAACTTTTCT
         65 ATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCT

             *                  **  *       *   * * *
        706 TTCCAATGAATGCATTTTTCAACACGTTTCTCAAGGCAGAC
        130 TGCCAATGAATGC-TTTTTCTTCATGTTTCTCGAGGTAAAT

                           *      **      *    *         *                   
        747 ATTCAATTATAGTCTATTTTAATGAAAAATGTAGAGAAATTCAACCTAAAATCAATTATGAGATT
          1 ATTCAATTATAGTCTGTTTTAACCAAAAATATA-AAAAATTCAACTTAAAATCAATTATGAGATT

               *  *                                  *                *      
        812 ATAGAATCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATAGGTGACTATAAATGGATTTTTCT
         65 ATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCT

                          *        *                   
        877 T-CTCAATGAATAGTTTTTTC-TGATGTTTCTCGA-GTCAAA-
        130 TGC-CAATGAAT-GCTTTTTCTTCATGTTTCTCGAGGT-AAAT

                         *         *      *       *  * *                     
        916 ATTCAATTATAGTTTGTTTTAACTAAAAATGTGAAAAATTTTAGCTTAAAATCAATTATGAGATT
          1 ATTCAATTATAGTCTGTTTTAACCAAAAATAT-AAAAAATTCAACTTAAAATCAATTATGAGATT

                   *         *  *                *   ** *      *   *         
        981 ATAAAACAATTTAAAGCAAGAAATAAGGCTTTTGAAGCAATAAGAGACTATTAATAGACTTTTCT
         65 ATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCT

             
       1046 T
        130 T

       1047 TTCAATTAAC


Statistics
Matches: 671,  Mismatches: 122, Indels: 36
        0.81            0.15        0.04

Matches are distributed among these distances:
 167    1  0.00
 168  112  0.17
 169  136  0.20
 170   93  0.14
 171  289  0.43
 172   40  0.06

ACGTcount: A:0.38, C:0.11, G:0.15, T:0.36


Consensus pattern (169 bp):   
ATTCAATTATAGTCTGTTTTAACCAAAAATATAAAAAATTCAACTTAAAATCAATTATGAGATTA
TAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTT
GCCAATGAATGCTTTTTCTTCATGTTTCTCGAGGTAAAT

Found at i:642 original size:339 final size:336

Alignment explanation


    Indices: 102--1017  Score: 1021
    Period size: 339  Copynumber: 2.7  Consensus size: 336

         92 AAAAGTGAAA

                           *    *                     *                      
        102 AAATTCAA-CTCAAAGTCAATTATGAGATTATAAAATAATTTGAAGCGAGTAATAAGGCTTTTGA
          1 AAATTCAACCT-AAAATCAACTATGAGATTATAAAATAATTTAAAGCGAGTAATAAGGCTTTTGA

                     *                * *        *                           
        166 AGGAATAAGAGACTATAAATGGACTTGTCTTGCCAATAAATGCTTGTTTCTTCATGTTTCTCGAG
         65 AGGAAT-AGTGACTATAAATGGACTTTTTTTGCCAATGAATGCTT-TTTCTTCATGTTTCTCGA-

                     *      *            *                                   
        231 GTAAATATTTAATTATTGTCTGTTTTAACCAAAAATATAAAACAATTCAACTTAAAATCAATTAT
        127 GTAAATATTCAATTATAGTCTGTTTTAACTAAAAATATAAAA-AATTCAACTTAAAATCAATTAT

            *                                                             *  
        296 TAGATTATAAAACCATTTGAAGCGAGTGATAAGGCTTTTGAAGGAACGGGTGACTATAAATGCAC
        191 GAGATTATAAAACCATTTGAAGCGAGT-ATAAGGCTTTTGAAGGAACGGGTGACTATAAATGAAC

                                      ** *       *   *   *           *   *   
        361 TTTTCTTGCCAATGAATGC-TTTTT-TTATGTTTCTCGAGGTAAAGATTCAATTATATTCTGTTT
        255 TTTTCTTGCCAATGAATGCATTTTTAACACGTTTCTCAAGGCAAACATTCAATTATAGTCTATTT

                        *     
        424 TAATGAAAAATCTTA-A-
        320 TAATGAAAAAT-GTAGAG

                      * *                                    *    *     *    
        440 AATATTCAACTTTAAA-CAAACTATGAGATTATAAAACT-ATTTAAAGCCAGTACTAAGGTTTTT
          1 AA-ATTCAACCTAAAATC-AACTATGAGATTATAAAA-TAATTTAAAGCGAGTAATAAGGCTTTT

                         *                                           *    *  
        503 GAAGGAATGAGTGGCTATAAATGGACCTTTTTTTGCCAATGAATGCCTTTTTCTTCACGTTTTTC
         63 GAAGGAAT-AGTGACTATAAATGGA-CTTTTTTTGCCAATGAATG-CTTTTTCTTCATGTTTCTC

            *           *           *                                        
        568 AAGATAAATATTGAATTATAGTCTATTTTAACTAAAAATATAAAAAATTCAACTTAAAAGT-AAT
        125 GAG-TAAATATTCAATTATAGTCTGTTTTAACTAAAAATATAAAAAATTCAACTTAAAA-TCAAT

             *             *  *       *                       *      * *     
        632 TGTGAGATTAT-AAAGCAATTGAAAGAGAGTAGTAAGGCTTTTGAAGGAATGGGTGATTGTAAAT
        188 TATGAGATTATAAAACCATTTG-AAGCGAGTA-TAAGGCTTTTGAAGGAACGGGTGACTATAAAT

                       *                                    *                
        696 GAACTTTTCTTTCCAATGAATGCATTTTTCAACACGTTTCTCAAGGCAGACATTCAATTATAGTC
        251 GAACTTTTCTTGCCAATGAATGCATTTTT-AACACGTTTCTCAAGGCAAACATTCAATTATAGTC

                                  
        761 TATTTTAATGAAAAATGTAGAG
        315 TATTTTAATGAAAAATGTAGAG

                               *            *   *                            
        783 AAATTCAACCTAAAATCAATTATGAGATTATAGAATCATTTAAAGCGAGTAATAAGGCTTTTGAA
          1 AAATTCAACCTAAAATCAACTATGAGATTATAAAATAATTTAAAGCGAGTAATAAGGCTTTTGAA

                                                        *        *           
        848 GGAATAGGTGACTATAAATGGA-TTTTTCTT-CTCAATGAATAGTTTTTTC-TGATGTTTCTCGA
         66 GGAATA-GTGACTATAAATGGACTTTTT-TTGC-CAATGAAT-GCTTTTTCTTCATGTTTCTCGA

                                *                *       *  * *              
        910 GTCAAA-ATTCAATTATAGTTTGTTTTAACTAAAAATGTGAAAAATTTTAGCTTAAAATCAATTA
        127 GT-AAATATTCAATTATAGTCTGTTTTAACTAAAAATAT-AAAAAATTCAACTTAAAATCAATTA

                          *    *    *   *               
        974 TGAGATTATAAAACAATTTAAAGCAAGAAATAAGGCTTTTGAAG
        190 TGAGATTATAAAACCATTTGAAGCGAG-TATAAGGCTTTTGAAG

       1018 CAATAAGAGA


Statistics
Matches: 483,  Mismatches: 69, Indels: 50
        0.80            0.11        0.08

Matches are distributed among these distances:
 338   12  0.02
 339  182  0.38
 340  142  0.29
 341   30  0.06
 342  114  0.24
 343    3  0.01

ACGTcount: A:0.38, C:0.11, G:0.15, T:0.36


Consensus pattern (336 bp):   
AAATTCAACCTAAAATCAACTATGAGATTATAAAATAATTTAAAGCGAGTAATAAGGCTTTTGAA
GGAATAGTGACTATAAATGGACTTTTTTTGCCAATGAATGCTTTTTCTTCATGTTTCTCGAGTAA
ATATTCAATTATAGTCTGTTTTAACTAAAAATATAAAAAATTCAACTTAAAATCAATTATGAGAT
TATAAAACCATTTGAAGCGAGTATAAGGCTTTTGAAGGAACGGGTGACTATAAATGAACTTTTCT
TGCCAATGAATGCATTTTTAACACGTTTCTCAAGGCAAACATTCAATTATAGTCTATTTTAATGA
AAAATGTAGAG
Done.