Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NW_018398728.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_2011.0, 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: 3521
ACGTcount: A:0.21, C:0.08, G:0.06, T:0.21

Warning! 1533 characters in sequence are not A, C, G, or T


Found at i:3109 original size:171 final size:168

Alignment explanation


    Indices: 2715--3209  Score: 481
    Period size: 171  Copynumber: 2.9  Consensus size: 168

       2705 NNNNNNNNNN

                        * *                      *          *                
       2715 TTTT-ATTAAAAAAGACTATAATTGAATGTCTACCTCAAGAAACGTGAGGAAACAAGAATTCATT
          1 TTTTGATTAAAACATACTATAATTG-ATGTCTACCTCGAGAAACGTGAAGAAACAA-AATTCATT

             *           *                  *   *    * *        *            
       2779 GGCAAGAAAAGTCTATTTAGAGTCACCCATTCCTCTAAAAATCGTATTACTCACTTTAAA-ATGT
         64 GACAAGAAAAGTCCATTTAGAGTCACCCATTCTTC-GAAAAGCTTATTACTCGCTTTAAATA-GT

                      *      *   *   *  *          *  
       2843 TTTATAATCTCATAATTAATTGTAAGTTGAATTTTTTTATAT
        127 TTTATAATCTTATAATTGATTTTAAATTCAATTTTTTTACAT

                                     *********      *  *                 *   
       2885 TTTTGATTAAAACATACTATAATTNNNNNNNNNNCTCGAGGAATGTGAAGAAACAAATATTTATT
          1 TTTTGATTAAAACATACTATAATT-GATGTCTACCTCGAGAAACGTGAAGAAACAAA-ATTCATT

              *       *         *           *                                
       2950 GATAAGAAAACTCCATTTAGTGTCACCCATTATTTCGAAAAGCTTATTACTCGCTTTAAATAGTT
         64 GACAAGAAAAGTCCATTTAGAGTCACCCATT-CTTCGAAAAGCTTATTACTCGCTTTAAATAGTT

                 *        *                          
       3015 TTATATTCTTATAACTGATTTTAAATTCAATTTTTTTACAT
        128 TTATAATCTTATAATTGATTTTAAATTCAATTTTTTTACAT

                                                        * *          *       
       3056 TTTTGATTAAAACATACTATAATTGATCGTCTACCTCGAGAAACATAAAGAAACAAGCATTCATT
          1 TTTTGATTAAAACATACTATAATTGAT-GTCTACCTCGAGAAACGTGAAGAAACAA-AATTCATT

              *  *                     *            * *                  *   
       3121 GAGAACAAAAGTCCATTTAGAGTCACCTATTCCTTCGAAAGGGTTATTACTCGCTTTAAATTGTT
         64 GACAAGAAAAGTCCATTTAGAGTCACCCATT-CTTCGAAAAGCTTATTACTCGCTTTAAATAGTT

                   *                
       3186 TTATAATATTATAATTGATTTTAA
        128 TTATAATCTTATAATTGATTTTAA

       3210 GTTGAATTNN


Statistics
Matches: 255,  Mismatches: 63, Indels: 13
        0.77            0.19        0.04

Matches are distributed among these distances:
 170    5  0.02
 171  247  0.97
 172    3  0.01

ACGTcount: A:0.36, C:0.14, G:0.11, T:0.37


Consensus pattern (168 bp):   
TTTTGATTAAAACATACTATAATTGATGTCTACCTCGAGAAACGTGAAGAAACAAAATTCATTGA
CAAGAAAAGTCCATTTAGAGTCACCCATTCTTCGAAAAGCTTATTACTCGCTTTAAATAGTTTTA
TAATCTTATAATTGATTTTAAATTCAATTTTTTTACAT
Done.