Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NW_018400023.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_3246.0, 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: 3916
ACGTcount: A:0.24, C:0.09, G:0.08, T:0.25

Warning! 1327 characters in sequence are not A, C, G, or T


Found at i:2283 original size:171 final size:160

Alignment explanation


    Indices: 2106--2432  Score: 332
    Period size: 171  Copynumber: 2.0  Consensus size: 160

       2096 NNNNTACTTG

                                                        *    **      *       
       2106 CTTTAAATGGTTTTATAATCTTATAACTGATTTTAAGTTGAATTCTTTTGTATTCTTGGTTAAAA
          1 CTTTAAATGGTTTTATAATCTTATAACTGATTTTAAGTTGAATTATTTTACATTCTTAGTTAAAA

                *   *   *           *   *      * *        *         *        
       2171 CAGATTGTCATTGAATGTCTACCTTGAGCAA-AGTGATAAAAAAGGTATTCATTGGCAAGAAAAG
         66 CAGACTGTAATTAAATGTCTACCTAGAGAAACAGTAAGAAAAAA-GCATTCATTGGAAAGAAAAG

              *            *                          
       2235 TCTATTTATAGTCACTTATTCCTTCAANNNNNNNNNNNCTCA
        130 TCCATTTATAGTCACATATTCCTTCAA-----------CTCA

                                  *   *                           *          
       2277 CTTTAAATGGTTTTATAATCTTCTAATTGATTTTAAGTTGAATTATTTTACATTTTTAGTTAAAA
          1 CTTTAAATGGTTTTATAATCTTATAACTGATTTTAAGTTGAATTATTTTACATTCTTAGTTAAAA

              *                              *       *                  *    
       2342 CATACTGTAATTAAATGTCTACCTAGAGAAACATTAAGAAACAAGCATTCATTGGAAAGACAAGT
         66 CAGACTGTAATTAAATGTCTACCTAGAGAAACAGTAAGAAAAAAGCATTCATTGGAAAGAAAAGT

                        *             
       2407 CCATTTATAGTCTCATATTCCTTCAA
        131 CCATTTATAGTCACATATTCCTTCAA

       2433 AAGCCTTATT


Statistics
Matches: 132,  Mismatches: 23, Indels: 2
        0.84            0.15        0.01

Matches are distributed among these distances:
 171  124  0.94
 172    8  0.06

ACGTcount: A:0.33, C:0.13, G:0.12, T:0.38


Consensus pattern (160 bp):   
CTTTAAATGGTTTTATAATCTTATAACTGATTTTAAGTTGAATTATTTTACATTCTTAGTTAAAA
CAGACTGTAATTAAATGTCTACCTAGAGAAACAGTAAGAAAAAAGCATTCATTGGAAAGAAAAGT
CCATTTATAGTCACATATTCCTTCAACTCA

Found at i:3031 original size:170 final size:171

Alignment explanation


    Indices: 2665--3035  Score: 435
    Period size: 170  Copynumber: 2.2  Consensus size: 171

       2655 NNNNNNNNNN

                                              **      *    *                 
       2665 TTCATTGGCAAGAAAAGTCCATTTATAGTCACCCTTTCCTTCCAAAGCCATATTATTCACTGTAA
          1 TTCATTGGCAAGAAAAGTCCATTTATAGTCACCCAATCCTTCAAAAGACATATTATTCACTGTAA

                          *                              *            *      
       2730 ATAGTTTTATAATCTCATAATTGATTTTAAGTTGAATTCTTTTACCTTTTTGGTTAAAGCAGACT
         66 ATAGTTTTATAATCACATAATTGATTTTAAGTTGAATTCTTTTACATTTTTGGTTAAAACAGACT

                 **********             *            
       2795 AGAATNNNNNNNNNNCCTCAAGAAACATGAAGAAAAAGACA
        131 AGAATTGATTGTTTACCTCAAGAAACATAAAGAAAAAGACA

                *  *           *                              *           *  
       2836 TTCACTGACAA-AAAAGGTTCATTTATAGTCA-CCAATCCTTCAAAAGACTTATTATTCACTTTA
          1 TTCATTGGCAAGAAAA-GTCCATTTATAGTCACCCAATCCTTCAAAAGACATATTATTCACTGTA

               *                                          *                  
       2899 AATGGTTTTATAATCACATAATTGATTTTAAGTTGAATGT-TTTTAGATTTTTGGTTAAAACAGA
         65 AATAGTTTTATAATCACATAATTGATTTTAAGTTGAAT-TCTTTTACATTTTTGGTTAAAACAGA

               *                **                      
       2963 CTATAATTGATTGTTTACCTTGAGAAACATAAAGAGAAAAG-CA
        129 CTAGAATTGATTGTTTACCTCAAGAAACATAAAGA-AAAAGACA

                                          
       3006 TTCATTGGCAAGAAAAGTCCATTTATAGTC
          1 TTCATTGGCAAGAAAAGTCCATTTATAGTC

       3036 TCCTANNNNN


Statistics
Matches: 165,  Mismatches: 31, Indels: 9
        0.80            0.15        0.04

Matches are distributed among these distances:
 170  132  0.80
 171   33  0.20

ACGTcount: A:0.35, C:0.15, G:0.13, T:0.35


Consensus pattern (171 bp):   
TTCATTGGCAAGAAAAGTCCATTTATAGTCACCCAATCCTTCAAAAGACATATTATTCACTGTAA
ATAGTTTTATAATCACATAATTGATTTTAAGTTGAATTCTTTTACATTTTTGGTTAAAACAGACT
AGAATTGATTGTTTACCTCAAGAAACATAAAGAAAAAGACA
Done.