Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NW_018400161.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_3377.0, 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: 2982
ACGTcount: A:0.22, C:0.07, G:0.09, T:0.23

Warning! 1142 characters in sequence are not A, C, G, or T


Found at i:2037 original size:172 final size:161

Alignment explanation


    Indices: 1831--2161  Score: 295
    Period size: 171  Copynumber: 2.0  Consensus size: 161

       1821 ATTGGTGGCT

                        *                      *         * *             *   
       1831 ATAAATGGACTTTTCTGGCCAATCAATACTTTTTTGTTCATGTTTTTGAAGGTA-GACATTTAAT
          1 ATAAATGGACTTCTCTGGCCAATCAATACTTTTTTATTCATGTTTCTCAAGGTAGGA-ATTCAAT

             **                      **   *          *         *        **   
       1895 CCTAGTGTGTTTTAACCAAAAATGCGCAAAGAATTCAAATTTAAATTAATTTTGAGATTATGAAA
         65 CAAAGTGTG-TTTAACCAAAAATGCAAAAACAATTCAAATTAAAATTAATTATGAGATTACAAAA

                      *                      
       1960 CCATTTAAAATGAGTAATAAGGCTTTTGAAGAA
        129 CCATTTAAAACGAGTAATAAGGCTTTTGAAGAA

                                      *      *   *          *                
       1993 ATNNNNNNNNNNAAATGGACTTCTCTTGCCAATGAATGCTTTTTTATTTATGTTTCTCAAGGTAG
          1 AT----------AAATGGACTTCTCTGGCCAATCAATACTTTTTTATTCATGTTTCTCAAGGTAG

                     *     *        *       *          *  *               *  
       2058 GAATTCAATTAAAGTTTGTTTAACTAAAAATGTAAAAACAATTTAACTTAAAATTAATTATGGGA
         56 GAATTCAATCAAAGTGTGTTTAACCAAAAATGCAAAAACAATTCAAATTAAAATTAATTATGAGA

              *              *                     
       2123 TTGCAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAG
        121 TTACAAAACCATTTAAAACGAGTAATAAGGCTTTTGAAG

       2162 GTATAGGTGA


Statistics
Matches: 130,  Mismatches: 28, Indels: 13
        0.76            0.16        0.08

Matches are distributed among these distances:
 162    2  0.02
 171   71  0.55
 172   55  0.42
 173    2  0.02

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


Consensus pattern (161 bp):   
ATAAATGGACTTCTCTGGCCAATCAATACTTTTTTATTCATGTTTCTCAAGGTAGGAATTCAATC
AAAGTGTGTTTAACCAAAAATGCAAAAACAATTCAAATTAAAATTAATTATGAGATTACAAAACC
ATTTAAAACGAGTAATAAGGCTTTTGAAGAA

Found at i:2260 original size:171 final size:160

Alignment explanation


    Indices: 2017--2347  Score: 306
    Period size: 171  Copynumber: 2.0  Consensus size: 160

       2007 ATGGACTTCT

                         *          *               *               * *      
       2017 CTTGCCAATGAATGCTTTTTTATTTATGTTTCTCAAGGTAGGAATTCAATTAAAGTTTGTTTAAC
          1 CTTGCCAATGAATACTTTTTTATTCATGTTTCTCAAGGTAAGAATTCAATTAAAGTCTATTTAAC

            *                      *       *       *    *          *         
       2082 TAAAAATGTA-AAAACAATTTAACTTAAAATTAATTATGGGATTGCAAAACCATTTAAAGCGAGT
         66 CAAAAATGTACAAAACAA-TTAAATTAAAATCAATTATGAGATTACAAAACCATTGAAAGCGAGT

                   *    *   **   *         
       2146 AATAAGGCTTTTGAAGGTATAGGTGACTATA
        130 AATAAGGATTTTAAAGAAATAAGTGACTATA

                                           *             *                ** 
       2177 NNNNNNNNNNCTTGCCAATGAATACTTTTTTCTTCATGTTTCTCATGGTATAG-ATTCAATTTCA
          1 ----------CTTGCCAATGAATACTTTTTTATTCATGTTTCTCAAGGTA-AGAATTCAATTAAA

                                                 *         *        * *      
       2241 GTCTATTGTAACCAAAAATGTACAAAACAATTAAATTTAAATCAATTTTGAGATTATACAACCAT
         55 GTCTATT-TAACCAAAAATGTACAAAACAATTAAATTAAAATCAATTATGAGATTACAAAACCAT

                  *                                   
       2306 TGAAAGTGAGTAATAAGGATTTTAAAGAAATAAGTGACTATA
        119 TGAAAGCGAGTAATAAGGATTTTAAAGAAATAAGTGACTATA

       2348 AATGGACTTC


Statistics
Matches: 133,  Mismatches: 25, Indels: 5
        0.82            0.15        0.03

Matches are distributed among these distances:
 170   50  0.38
 171   76  0.57
 172    7  0.05

ACGTcount: A:0.37, C:0.11, G:0.14, T:0.35


Consensus pattern (160 bp):   
CTTGCCAATGAATACTTTTTTATTCATGTTTCTCAAGGTAAGAATTCAATTAAAGTCTATTTAAC
CAAAAATGTACAAAACAATTAAATTAAAATCAATTATGAGATTACAAAACCATTGAAAGCGAGTA
ATAAGGATTTTAAAGAAATAAGTGACTATA
Done.