Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NW_018400399.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_3598.0, 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, 837

Length: 1395
ACGTcount: A:0.24, C:0.09, G:0.07, T:0.25

Warning! 482 characters in sequence are not A, C, G, or T


Found at i:974 original size:171 final size:167

Alignment explanation


    Indices: 613--1395  Score: 704
    Period size: 171  Copynumber: 4.6  Consensus size: 167

        603 NNNNNNNNNN

                      *          *                          *    *  *        
        613 TGAATGTTTACCTTGAGAAACATGAAGAAACAAGCATTCATTGATAA-GAAAAGCGTATTTAGAG
          1 TGAATGTTTATCTTGAGAAACGTGAAGAAA-AAGCATTCATTGA-AACAAAAATC-CATTTAGAG

                          *                *                                 
        677 TCACCTATTCC-TTCAAAAGCTTATTACTCGTTTTAAATAGTTTTATAATCTCATAATTGATTTT
         63 TCACC-ATTCCTTTAAAAAGCTTATTACTCGCTTTAAATAGTTTTATAATCTCATAATTGATTTT

                           *    *            *    *   
        741 AAGTTGAATTTTTTTGCATTGTTGATTAAAACATACTATAAT
        127 AAGTTGAATTTTTTTACATTTTTG-TTAAAACAGACTAAAAT

                *     *                                    *                 
        783 TGAACGTTTACCTTGAGAAACGTGAAGAAACAAGCATTCATTGACAAGAAAAATCCATTTAGAGT
          1 TGAATGTTTATCTTGAGAAACGTGAAGAAA-AAGCATTCATTGA-AACAAAAATCCATTTAGAGT

                                                *  *      *         *        
        848 CATCCATTCCTTTAAAAAGCTTATTACTCGCTTTAATTATTTTTATTATCTCATAACTGATTTTA
         64 CA-CCATTCCTTTAAAAAGCTTATTACTCGCTTTAAATAGTTTTATAATCTCATAATTGATTTTA

             *                                       
        913 AATTGAATTTTTTTACATTTTTAGTTAAAACAGACTAAAAT
        128 AGTTGAATTTTTTTACATTTTT-GTTAAAACAGACTAAAAT

               *         *       *  *                      *             * * 
        954 TGATTGTTTATCTCGAGAAACATGCA-AAAAAGCCAGTT-ATTGAAAAAAAAATCCATTTATAAT
          1 TGAATGTTTATCTTGAGAAACGTGAAGAAAAAG-CA-TTCATTGAAACAAAAATCCATTTAGAGT

                              *         *      *   *         *  *            
       1017 CACTCATT-CTTTCAAAAGGCTTATTACCCGCTTTTAATGGTTTTATAACCTAATAATTGATTTT
         64 CAC-CATTCCTTT-AAAAAGCTTATTACTCGCTTTAAATAGTTTTATAATCTCATAATTGATTTT

                                            *      *   
       1081 AAGTTGAATTTTTTTGA-ATTCTTT-TTAAAATAGACTATAAT
        127 AAGTTGAATTTTTTT-ACATT-TTTGTTAAAACAGACTAAAAT

                 ***                *            *               *           
       1122 TGAATACCTATCTTGAGAAACGTGTAGAAAAAGCTTACTCATTGGAAACAAAAGTCCATTTAGAG
          1 TGAATGTTTATCTTGAGAAACGTGAAGAAAAAGC--ATTCATT-GAAACAAAAATCCATTTAGAG

                          *                **        *                       
       1187 TCACCCATT-CTTTCAAAAGCTTTATTACTCTATTTAAATAATTTTATAATCTCATAATTGATTT
         63 TCA-CCATTCCTTTAAAAAGC-TTATTACTCGCTTTAAATAGTTTTATAATCTCATAATTGATTT

              *      *               *        *         
       1251 TAGGTTGAACTTTTTTACATTTTTCTTTAAAACAAAC-AATAAT
        126 TAAGTTGAATTTTTTTACATTTTT-GTTAAAACAGACTAA-AAT

             *       *    **     *   *  *          *      *      *  *     *  
       1294 TCAATGTCTAAT-TCAAGAAATGTGCAGTAAAAGCCATTGATTGAGGACAAAAGTCTATTTATAG
          1 TGAATGT-TTATCTTGAGAAACGTGAAGAAAAAG-CATTCATTGA-AACAAAAATCCATTTAGAG

                         *    *                   
       1358 TCACCCATTCCTTCAAAAGGCTTATTACTCGCTTTAAA
         63 TCA-CCATTCCTTTAAAAAGCTTATTACTCGCTTTAAA


Statistics
Matches: 502,  Mismatches: 86, Indels: 49
        0.79            0.14        0.08

Matches are distributed among these distances:
 168   40  0.08
 169   91  0.18
 170   89  0.18
 171  237  0.47
 172   42  0.08
 173    3  0.01

ACGTcount: A:0.36, C:0.14, G:0.11, T:0.38


Consensus pattern (167 bp):   
TGAATGTTTATCTTGAGAAACGTGAAGAAAAAGCATTCATTGAAACAAAAATCCATTTAGAGTCA
CCATTCCTTTAAAAAGCTTATTACTCGCTTTAAATAGTTTTATAATCTCATAATTGATTTTAAGT
TGAATTTTTTTACATTTTTGTTAAAACAGACTAAAAT
Done.