Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NW_018401949.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_5048.0, 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: 1801
ACGTcount: A:0.31, C:0.13, G:0.11, T:0.30

Warning! 262 characters in sequence are not A, C, G, or T


Found at i:1357 original size:172 final size:172

Alignment explanation


    Indices: 955--1689  Score: 656
    Period size: 172  Copynumber: 4.3  Consensus size: 172

        945 NNNNNNNTTA

                                                         *          *       *
        955 CCCATTCCTTCAAAAGCCTTATTAATCACTTTAAATGGTTTTATAGTCTCAAAATTAATTTAAAC
          1 CCCATTCCTTCAAAAGCCTTATTAATCACTTTAAATGGTTTTATAATCTCAAAATTGATTTAAAT

                                             *   *           *  * *          
       1020 TTGAATTCTTTGTGCATTTTTGGTTAAAACACACTAGGATTGAATGTCTTCCTTCAGAAACATGA
         66 TTGAATTCTTTGTGCATTTTTGGTTAAAACACATTAGAATTGAATGTCTACCATGAGAAACATGA

                       *       *  *                  *
       1085 AGAAAAAAGCACTCATTGGTAAAAAAAGTCCATTTATAGTCA
        131 AGAAAAAAGCATTCATTGGCAAGAAAAGTCCATTTATAGTCG

             **   **     *          * * *   *               *                
       1127 CTTATTAATTCAAGAGCCTTATTACTTAGTTTCAATGGTTTTATAATCCCAAAATTGATTTAAAT
          1 CCCATTCCTTCAAAAGCCTTATTAATCACTTTAAATGGTTTTATAATCTCAAAATTGATTTAAAT

                          *            *  * *             *     *            
       1192 TTGAATGT-TTTGTACATTTTTGGTTAGAATAGATTAGAATTGAATCTCTACAATGAGAAACATG
         66 TTGAAT-TCTTTGTGCATTTTTGGTTAAAACACATTAGAATTGAATGTCTACCATGAGAAACATG

            *         *   *                *   *       
       1256 TAGAAAAAAGTATTAATTGGCAAGAAAAGTCTATTCATAGTCG
        130 AAGAAAAAAGCATTCATTGGCAAGAAAAGTCCATTTATAGTCG

                                                 *          *   *            
       1299 CCCATTGCC-TCAAAAGCCTTATTAATCACTTTAAATAGTTTTATAATTTCACAATTGATTTTAA
          1 CCCATT-CCTTCAAAAGCCTTATTAATCACTTTAAATGGTTTTATAATCTCAAAATTGA-TTTAA

            **********                        *    *               *   *     
       1363 NNNNNNNNNNTTT-TGC-TTTTCTGGTTAAAACATATTATAATTGAATGTCTACCCTGACAAACA
         64 ATTTGAATTCTTTGTGCATTTT-TGGTTAAAACACATTAGAATTGAATGTCTACCATGAGAAACA

             *       *                      *              
       1426 TAAAGAATAGAA-CATTCATTGGCAAGAAAAGCCCATTTATAGTCAG
        128 TGAAGAA-AAAAGCATTCATTGGCAAGAAAAGTCCATTTATAGTC-G

                                    *           *                            
       1472 -CCATTCCTTCAAAAGCCTTATTACTCACTTTAAA-CGTCTTTATAATCTCAAAATTGATTTAAA
          1 CCCATTCCTTCAAAAGCCTTATTAATCACTTTAAATGGT-TTTATAATCTCAAAATTGATTTAAA

                                    ***********             *                
       1535 TTTGAATTCTTTGTGCATTTTTGGNNNNNNNNNNCTAGAATTGAATGTTTACCATGAGAAACATG
         65 TTTGAATTCTTTGTGCATTTTTGGTTAAAACACATTAGAATTGAATGTCTACCATGAGAAACATG

                *             *                       *
       1600 AAGACAAAAGCATTCATTAGCAAGAAAAGTCCATTTATAGTCA
        130 AAGAAAAAAGCATTCATTGGCAAGAAAAGTCCATTTATAGTCG

             *   *    *      *      *  *        *     *    
       1643 CACATACCTTTAAAAGCATTATTACTCGCTTTAAATAGTTTTGTAAT
          1 CCCATTCCTTCAAAAGCCTTATTAATCACTTTAAATGGTTTTATAAT

       1690 GCCNNNNNNN


Statistics
Matches: 435,  Mismatches: 114, Indels: 28
        0.75            0.20        0.05

Matches are distributed among these distances:
 171   19  0.04
 172  397  0.91
 173   19  0.04

ACGTcount: A:0.35, C:0.15, G:0.12, T:0.35


Consensus pattern (172 bp):   
CCCATTCCTTCAAAAGCCTTATTAATCACTTTAAATGGTTTTATAATCTCAAAATTGATTTAAAT
TTGAATTCTTTGTGCATTTTTGGTTAAAACACATTAGAATTGAATGTCTACCATGAGAAACATGA
AGAAAAAAGCATTCATTGGCAAGAAAAGTCCATTTATAGTCG
Done.