Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NW_018401100.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_4258.0, 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: 4248
ACGTcount: A:0.21, C:0.09, G:0.08, T:0.24

Warning! 1596 characters in sequence are not A, C, G, or T


Found at i:767 original size:172 final size:171

Alignment explanation


    Indices: 589--954  Score: 416
    Period size: 172  Copynumber: 2.1  Consensus size: 171

        579 NNNNNNNNNN

                                                     *                       
        589 TAATCTCATAATTGATTTTAAGTTCAATTTTTTTTGT-ATTTTTACTCAAAACAGATTATAATTG
          1 TAATCTCATAATTGATTTTAAGTTCAATTTTTTTT-TAATTATTACTCAAAACAGATTATAATTG

             *                 **                *    *                      
        653 AGTGTCTACATCT-AGAAATGTAAAGAAAAAGAAATTTATTGGGAAGAAAACTCCATTTATAGTC
         65 AATGTCTA-ATCTGAGAAACATAAAGAAAAAGAAATTCATT-AGAAGAAAACTCCATTTATAGTC

                      *                   *              *
        717 -TCC-TATTCTTTCAAAAGCCATATTACTCGCTTTAAATGGTTTTC
        128 ATCCAT-TTCGTT-AAAAGCCATATTACTCACTTTAAATGGTTTTA

                    *           *                       ** *    *  *         
        761 TAATCTCAAAATTGATTTTAGGTTCAATTTTTTTTTACATTATTGGTTAAAATAGCTTATAATTG
          1 TAATCTCATAATTGATTTTAAGTTCAATTTTTTTTTA-ATTATTACTCAAAACAGATTATAATTG

                    * *          *   *     **                *               
        826 AATGTCTATTTTGAGAAACATGAAGCAAAAGGCATTCATTAGAAGAAAAGTCCATTTATAGTCAT
         65 AATGTCTAATCTGAGAAACATAAAGAAAAAGAAATTCATTAGAAGAAAACTCCATTTATAGTCAT

                             *             *          
        891 CCATTTCGTTAAAAGCCTTATTACTCACTTTGAATGGTTTTA
        130 CCATTTCGTTAAAAGCCATATTACTCACTTTAAATGGTTTTA

                *                 
        933 TAATATCATAATTGATTTTAAG
          1 TAATCTCATAATTGATTTTAAG

        955 NNNNNNNNNN


Statistics
Matches: 161,  Mismatches: 28, Indels: 10
        0.81            0.14        0.05

Matches are distributed among these distances:
 171    1  0.01
 172  103  0.64
 173   56  0.35
 174    1  0.01

ACGTcount: A:0.35, C:0.12, G:0.12, T:0.40


Consensus pattern (171 bp):   
TAATCTCATAATTGATTTTAAGTTCAATTTTTTTTTAATTATTACTCAAAACAGATTATAATTGA
ATGTCTAATCTGAGAAACATAAAGAAAAAGAAATTCATTAGAAGAAAACTCCATTTATAGTCATC
CATTTCGTTAAAAGCCATATTACTCACTTTAAATGGTTTTA

Found at i:3182 original size:172 final size:172

Alignment explanation


    Indices: 2806--3191  Score: 479
    Period size: 172  Copynumber: 2.2  Consensus size: 172

       2796 NNNNNNNNNN

                                                         *  *                
       2806 AAAGTCCATTTATAGTCACCCATTCTTTCAAAAGCCTTATTACTCGCTTTGAATGATTTTATAAT
          1 AAAGTCCATTTATAGTCACCCATTCTTTCAAAAGCCTTATTACTCACTGTGAATGATTTTATAAT

                               *        *                           *        
       2871 CTAATAATTAAGTTTAAGTGCAATTTTTTTTACATTTTTGGTTACAACAGACTATATTTGAATGT
         66 CTAATAATTAAGTTTAAGTCCAATTTTTATTACATTTTTGGTTACAACAGACTATAATTGAATGT

            *   *  *              *    *              
       2936 TTACTTTGAGAAACATGAAGAACAAAGCATTCATTAGCAAGA
        131 CTACCTTAAGAAACATGAAGAAAAAAGAATTCATTAGCAAGA

                      **********     *                                       
       2978 AAAGTCCATTNNNNNNNNNNCATTCCTTCAAAAGCCTTATTACTCACTGTGAAT-AGTTTTATAA
          1 AAAGTCCATTTATAGTCACCCATTCTTTCAAAAGCCTTATTACTCACTGTGAATGA-TTTTATAA

               *        *                    *                    *          
       3042 TCTGATAATTAATTTTAAGTCCAATTTTTATTATATTTTTGGTTACAACAGACTGTAATTGAATG
         65 TCTAATAATTAAGTTTAAGTCCAATTTTTATTACATTTTTGGTTACAACAGACTATAATTGAATG

                           *  *                 *      
       3107 TCTACCTTAAGAAACGTGGAGAAAAAAGAATTCATTGGCAAGA
        130 TCTACCTTAAGAAACATGAAGAAAAAAGAATTCATTAGCAAGA

                                               *       
       3150 AAAG-CCTATTTATAGTCACCCATTCTTTCAAAAGTCTTATTA
          1 AAAGTCC-ATTTATAGTCACCCATTCTTTCAAAAGCCTTATTA

       3192 TTCGCTTTAA


Statistics
Matches: 172,  Mismatches: 40, Indels: 4
        0.80            0.19        0.02

Matches are distributed among these distances:
 171    3  0.02
 172  169  0.98

ACGTcount: A:0.34, C:0.15, G:0.12, T:0.37


Consensus pattern (172 bp):   
AAAGTCCATTTATAGTCACCCATTCTTTCAAAAGCCTTATTACTCACTGTGAATGATTTTATAAT
CTAATAATTAAGTTTAAGTCCAATTTTTATTACATTTTTGGTTACAACAGACTATAATTGAATGT
CTACCTTAAGAAACATGAAGAAAAAAGAATTCATTAGCAAGA
Done.