Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NW_018400563.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_3756.0, 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, 665

Length: 1109
ACGTcount: A:0.35, C:0.14, G:0.12, T:0.36

Warning! 50 characters in sequence are not A, C, G, or T


Found at i:313 original size:171 final size:169

Alignment explanation


    Indices: 1--714  Score: 548
    Period size: 172  Copynumber: 4.2  Consensus size: 169

                     *              *                *  *          *         
          1 TGAATGCTTGCCTCAAGAAACATGTAGAAAAA-GCTATTCATTAAGAAGAAAAGTTCATTTATAG
          1 TGAATGCTTACCTCAAGAAACATGAAGAAAAAGGC-ATTCACTAGGAAGAAAAGTCCATTTATAG

                               *             *                **********     
         65 TCACACATTCTTATAAAAGTCTTATTACTCGCTTTAAATGGTTTTATAATNNNNNNNNNNA-TTT
         65 TCAC-CATTCTT-TAAAAGCCTTATTACTCGCTCTAAATGGTTTTATAATCTCATAATTAATTTT

                             *                         
        129 TAGATTGAATTTTTTTATATTTTTGTTTAAAACAGACTATAAT
        128 TAG-TTGAATTTTTTTACATTTTTGTTTAAAACAGACTATAAT

                         *         *                                         
        172 TGAATGCTTACCTTAAGAAACATAAAGAAAAAGGCATTCACTAGGAAGAAAAGTCCATTTATAGT
          1 TGAATGCTTACCTCAAGAAACATGAAGAAAAAGGCATTCACTAGGAAGAAAAGTCCATTTATAGT

                        *                      *                             
        237 CACCGAGTTCTTCAAAAGCCTTATTACTCGCTCTACATGGTTTTATAATCTCATAATTAATTTTT
         66 CACC-A-TTCTTTAAAAGCCTTATTACTCGCTCTAAATGGTTTTATAATCTCATAATTAATTTTT

                *                                      
        302 AGTTTAATTTTTTTTACATTTTT-TATTAAAACAGACTATAAT
        129 AGTTGAA-TTTTTTTACATTTTTGT-TTAAAACAGACTATAAT

                *         **     **                      *           *       
        344 TGAACG-TCTACCTTGAGAAATGTGAAGAAAAAGGCATTCACTAGTAA-ACAAAGTCTATTTATA
          1 TGAATGCT-TACCTCAAGAAACATGAAGAAAAAGGCATTCACTAGGAAGA-AAAGTCCATTTATA

                                            **********                  *    
        407 GTCACCCATTCTTTTAAAAGCCTTATTACTCGNNNNNNNNNNTTTTATAATCTCATAATTGATTT
         64 GTCA-CCATTC-TTTAAAAGCCTTATTACTCGCTCTAAATGGTTTTATAATCTCATAATTAATTT

             *              *      * *        *        
        472 TAAGTTGAATTTTTTTGCA-TTTCGGTTAAAACAAACTATAAT
        127 TTAGTTGAATTTTTTTACATTTTTGTTTAAAACAGACTATAAT

                     *    *         *        *        *                   *  
        514 TGAATGCTTGCCTCGAGAAACATGTAG-AAAAGCCATTCA-TTGAGAAGAAAAGTCCATTTAGAG
          1 TGAATGCTTACCTCAAGAAACATGAAGAAAAAGGCATTCACTAG-GAAGAAAAGTCCATTTATAG

                  ********                   *     *          *   *    *     
        577 TCACNNNNNNNNNNAAAAGCCTTATTACTCGCTTTAAATTGTTTTATAATTTCAGAATTGATTTT
         65 TCAC--CATTCTTTAAAAGCCTTATTACTCGCTCTAAATGGTTTTATAATCTCATAATTAATTTT

            *      *                *     *       *   
        642 AAGTTGATTTTTTTTACA-TTTTGGTTAAACCAGACTACAAT
        128 TAGTTGAATTTTTTTACATTTTTGTTTAAAACAGACTATAAT

            **         *          *          
        683 CAAATG-TCTATCTCAAGAAACGTGAAGAAAAA
          1 TGAATGCT-TACCTCAAGAAACATGAAGAAAAA

        715 AGCACTCATT


Statistics
Matches: 433,  Mismatches: 92, Indels: 37
        0.77            0.16        0.07

Matches are distributed among these distances:
 168    4  0.01
 169  121  0.28
 170   44  0.10
 171  113  0.26
 172  149  0.34
 173    2  0.00

ACGTcount: A:0.35, C:0.13, G:0.12, T:0.36


Consensus pattern (169 bp):   
TGAATGCTTACCTCAAGAAACATGAAGAAAAAGGCATTCACTAGGAAGAAAAGTCCATTTATAGT
CACCATTCTTTAAAAGCCTTATTACTCGCTCTAAATGGTTTTATAATCTCATAATTAATTTTTAG
TTGAATTTTTTTACATTTTTGTTTAAAACAGACTATAAT

Done.