Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NW_018403278.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_953.0, 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: 11292
ACGTcount: A:0.19, C:0.06, G:0.07, T:0.17

Warning! 5796 characters in sequence are not A, C, G, or T


Found at i:2409 original size:342 final size:333

Alignment explanation


    Indices: 1774--2479  Score: 719
    Period size: 342  Copynumber: 2.1  Consensus size: 333

       1764 NNNNNNNNNN

                     *           *                                 *         
       1774 AATTATGAGTTTATAAAACCATTTAAAGTGAGTTATTAAGCTTTTGAAGGAATAGGTGACAATAA
          1 AATTATGAGATTATAAAACCACTTAAAGTGAGTTATTAAGCTTTTGAAGGAATAGATGACAATAA

              *   *                             *        *                   
       1839 ACTGACTTTTCTTGCCAATATATATCTTTTTCTTCATGTTTCACAGGGTAGAAATTCAATTATAA
         66 ACGGACATTTCTTGCCAATATATATCTTTTTCTTCACGTTTCACAAGGTAGAAATTCAATTATAA

               **                                *       *   * *             
       1904 TCTGTTTTAAACAAAAGTATAAAAAAATCGAACTGAATATCAATTTTGAGATTATAAAACCATTT
        131 TCTACTTTAAACAAAAGTATAAAAAAATCGAACTGAAAATCAATTATGACAATATAAAACCATTT

                    *                     * *                       *        
       1969 AAAGCGAGTAATAAGGNNNNNNNNNNAATGGGTGACTATAAATAGACTTTTCTTGCTAATGAATG
        196 AAAGCGAGCAATAAGG----------AATGAGAGACTATAAATAGACTTTTCTTGCCAATGAATG

                           *                       *        *              * 
       2034 GCTTTTTTTAATGTTTCATGAGATAGACATTCAATTATAGTTTGTTTTCACAAAAAAATG-AATA
        251 GCTTTTTTTAATGTTGCATGAGATAGACATTCAATTATACTTTGTTTTAAC-AAAAAATGTAAAA

                              *
       2098 A-AAATTCAACTTAAAATC
        315 ACAAATTCAACTTAAAATA

                    *         *               *   *                     *    
       2116 AATTATGAAATTATAAAATCACTTAAAGTGAGTTGTTAGGCTTTTGAAGGAATAGATGACTATAA
          1 AATTATGAGATTATAAAACCACTTAAAGTGAGTTATTAAGCTTTTGAAGGAATAGATGACAATAA

                         ***      *             *      **                    
       2181 ACGGACATTTCTTTTGAATCA-CTATCTTTTTCTTCGCGTTTCTTAAGGTA-AACATTCAATTAT
         66 ACGGACATTTCTTGCCAAT-ATATATCTTTTTCTTCACGTTTCACAAGGTAGAA-ATTCAATTAT

                               *                  *                          
       2244 AATCTACTTTACCAA-AAATGTA-AAAAAAATC-AACTTAAAATCAATTATGACAATATAAAACC
        129 AATCTACTTTA--AACAAAAGTATAAAAAAATCGAACTGAAAATCAATTATGACAATATAAAACC

                         *                                                   
       2306 ATTTAAAGCGAGCGATAAGGNNNNNNNNNNAATGAGAGACTATAAATAGACTTTTCTTGCCAATG
        192 ATTTAAAGCGAGCAATAAGG----------AATGAGAGACTATAAATAGACTTTTCTTGCCAATG

                           *             *   *                        *      
       2371 AAT-GCTTTTTTCTTCATG-TGCAATGAGGTAGGCATTCAATTATACTTTGTTTTAACCAAAAAT
        247 AATGGC-TTTTT-TTAATGTTGC-ATGAGATAGACATTCAATTATACTTTGTTTTAACAAAAAAT

                         *           
       2434 GTAAAAACAAATTTAACTTAAAATA
        309 GTAAAAACAAATTCAACTTAAAATA

                                 
       2459 AATTATGAGATTATAAAACCA
          1 AATTATGAGATTATAAAACCA

       2480 TTNNNNNNNN


Statistics
Matches: 311,  Mismatches: 44, Indels: 17
        0.84            0.12        0.05

Matches are distributed among these distances:
 340    2  0.01
 341  105  0.34
 342  161  0.52
 343   41  0.13
 344    2  0.01

ACGTcount: A:0.39, C:0.12, G:0.13, T:0.34


Consensus pattern (333 bp):   
AATTATGAGATTATAAAACCACTTAAAGTGAGTTATTAAGCTTTTGAAGGAATAGATGACAATAA
ACGGACATTTCTTGCCAATATATATCTTTTTCTTCACGTTTCACAAGGTAGAAATTCAATTATAA
TCTACTTTAAACAAAAGTATAAAAAAATCGAACTGAAAATCAATTATGACAATATAAAACCATTT
AAAGCGAGCAATAAGGAATGAGAGACTATAAATAGACTTTTCTTGCCAATGAATGGCTTTTTTTA
ATGTTGCATGAGATAGACATTCAATTATACTTTGTTTTAACAAAAAATGTAAAAACAAATTCAAC
TTAAAATA
Done.