Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NW_018397821.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_1122.0, 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: 3863
ACGTcount: A:0.29, C:0.10, G:0.10, T:0.26

Warning! 947 characters in sequence are not A, C, G, or T


Found at i:303 original size:171 final size:171

Alignment explanation


    Indices: 75--388  Score: 429
    Period size: 171  Copynumber: 1.8  Consensus size: 171

         65 CCCCAAGGTA

                                *                      *   *           *     
         75 AACATTCAATTATAACCTTTTTAAACCAAAACGTAAAAAAATTTAACTTAAAATCAATTTTGAGA
          1 AACATTCAATTATAACCTTTCTAAACCAAAACGTAAAAAAATTCAACCTAAAATCAATTATGAGA

                   * *                    *                    *             
        140 TTATAAAGCCATTTAAAGTGAGTAATAAGGCTTTTG-AAGAAATGGGTGACTATAAATAAACTTT
         66 TTATAAAACAATTTAAAGTGAGTAATAAGGATTTTGAAAG-AATGGGTGACCATAAATAAACTTT

                                                       
        204 TCTT-ACCAATGAATACCCTTTCCTTGACAATTTTATGAGGCG
        130 TCTTGA-CAATGAATACCCTTTCCTTGACAATTTTATGAGGCG

                           *                 *   *              *            
        246 AACATTCAATTATAATCTATTCT-AACCAAAAAGGT-CAAAAATTCAACCTAGAATCAATTATGA
          1 AACATTCAATTATAACCT-TTCTAAACC-AAAACGTAAAAAAATTCAACCTAAAATCAATTATGA

             *                                                          * *  
        309 GGTTATAAAACAATTTAAAGTGAGTAATAAGGATTTTGAAAGAATGGGTGACCATAAATAGAGTT
         64 GATTATAAAACAATTTAAAGTGAGTAATAAGGATTTTGAAAGAATGGGTGACCATAAATAAACTT

                           
        374 TTCTTGACAATGAAT
        129 TTCTTGACAATGAAT

        389 GCCTTTTCAA


Statistics
Matches: 124,  Mismatches: 15, Indels: 8
        0.84            0.10        0.05

Matches are distributed among these distances:
 171  111  0.90
 172   13  0.10

ACGTcount: A:0.42, C:0.13, G:0.13, T:0.32


Consensus pattern (171 bp):   
AACATTCAATTATAACCTTTCTAAACCAAAACGTAAAAAAATTCAACCTAAAATCAATTATGAGA
TTATAAAACAATTTAAAGTGAGTAATAAGGATTTTGAAAGAATGGGTGACCATAAATAAACTTTT
CTTGACAATGAATACCCTTTCCTTGACAATTTTATGAGGCG

Found at i:2305 original size:171 final size:168

Alignment explanation


    Indices: 1535--2319  Score: 463
    Period size: 171  Copynumber: 4.6  Consensus size: 168

       1525 NNNNNNNNNN

                                                              *   *   *      
       1535 AGTAATAAGGCTTTTGAAGAAATGGGTGACTATAAATGGACTTTTCTTGCAAATAAATACCATTT
          1 AGTAATAAGGCTTTTGAA-AAATGGGTGACTATAAATGGAC-TTTCTTGCCAATGAATGCC-TTT

             * *         *                      *  *                     *   
       1600 TTTTCAT-GTTTCCTAAGGTAGACATTCAATTATAAGCTATACAAACCAAAAACATCAAAATATA
         63 TCTAC-TCGTTTCTTAAGGTAGACATTCAATTATAATCTGTACAAACCAAAAACATCAAAAAATA

               *                     *                 
       1664 CAATCTAAAATCAATTATGAGGTTAGAAAACCATTTAAAA-TG
        127 CAACCTAAAATCAATTATGAGGTTATAAAACCA-TTAAAAGTG

            *             *                          *           *           
       1706 GGTAATAAGGCTTTCGAAACAATGGGTGACTATAAATGGAGTTTTCTTGCCAAAGAATGCCTTTC
          1 AGTAATAAGGCTTTTGAAA-AATGGGTGACTATAAATGGA-CTTTCTTGCCAATGAATGCCTTT-

              *            *  **   *              *   ***         ***     *  
       1771 TCAACAT-GTTTCTTGAGAAAGAGATTC-ATATATAATTTGTTTTAACCAAAAGTGTTCAAAGAA
         63 TCTAC-TCGTTTCTTAAGGTAGACATTCAAT-TATAATCTGTACAAACCAAAA-ACATCAAAAAA

             *   ** *    *   **********      *   *      
       1834 TTCAAATTTAAATTAATNNNNNNNNNNTAAAACTATTTAAAGTG
        125 TACAACCTAAAATCAATTATGAGGTTATAAAACCATTAAAAGTG

                  *        *                      *      *          **    *  
       1878 AGTAATGAGGC-TTTCAAAGGAATGGGTGACTATAAATAGACTTTTTGTGCCAATGGTTGTCATT
          1 AGTAATAAGGCTTTTGAAA--AATGGGTGACTATAAATGGACTTTCT-TGCCAATGAATG-CCTT

                * *           **                  *   ***         *  *       
       1942 TTCTTCACGTTTCTCT-ATCTAGACATTCAATTATAATATGTTTTAACCAAAAATATAAAAAAAT
         62 TTCTACTCGTTTCT-TAAGGTAGACATTCAATTATAATCTGTACAAACCAAAAACATCAAAAAAT

            *  * *           *    **      *             
       2006 TCAGCTTAAAAT-AATTTTGAGACTATAAAGCCAATT-AAAGTG
        126 ACAACCTAAAATCAATTATGAGGTTATAAAACC-ATTAAAAGTG

                                  **********                *     *   *  *   
       2048 AGTAATAAGGCTTTTGAAGAAANNNNNNNNNNTAAATGGACTTTTCTTACCAATAAATACTTTTT
          1 AGTAATAAGGCTTTTGAA-AAATGGGTGACTATAAATGGAC-TTTCTTGCCAATGAATGC-CTTT

                *   *    **                                             **   
       2113 TCT-TTACATTTCCCAAGGTAGACATTCAATTATAATCTGTACAAACCAAAAACATCAAATTATA
         63 TCTACT-CGTTTCTTAAGGTAGACATTCAATTATAATCTGTACAAACCAAAAACATCAAAAAATA

                                                      
       2177 CAACCTAAAATCAATTATGAGGTTATAAAACCATTAAAAGTG
        127 CAACCTAAAATCAATTATGAGGTTATAAAACCATTAAAAGTG

                                                            *                
       2219 AGTAATAAGGCTTTTGAAATAATGGGTGACTATAAATGGAGCTTTCTTACCAATGAATGCCTTTC
          1 AGTAATAAGGCTTTTGAAA-AATGGGTGACTATAAATGGA-CTTTCTTGCCAATGAATGCCTTT-

                          *       *             
       2284 TCTACTCGTTTCTTGAGGTAGAGATTCAATTATAAT
         63 TCTACTCGTTTCTTAAGGTAGACATTCAATTATAAT

       2320 TTTGTTTTAC


Statistics
Matches: 444,  Mismatches: 145, Indels: 50
        0.69            0.23        0.08

Matches are distributed among these distances:
 169    1  0.00
 170  112  0.25
 171  221  0.50
 172  103  0.23
 173    7  0.02

ACGTcount: A:0.38, C:0.13, G:0.14, T:0.33


Consensus pattern (168 bp):   
AGTAATAAGGCTTTTGAAAAATGGGTGACTATAAATGGACTTTCTTGCCAATGAATGCCTTTTCT
ACTCGTTTCTTAAGGTAGACATTCAATTATAATCTGTACAAACCAAAAACATCAAAAAATACAAC
CTAAAATCAATTATGAGGTTATAAAACCATTAAAAGTG

Done.