Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NW_018402473.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_5549.0, 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: 4503
ACGTcount: A:0.20, C:0.06, G:0.08, T:0.18

Warning! 2159 characters in sequence are not A, C, G, or T


Found at i:3778 original size:171 final size:171

Alignment explanation


    Indices: 3454--3878  Score: 552
    Period size: 171  Copynumber: 2.5  Consensus size: 171

       3444 NNNNNNNNTC

                             *          *      *                *            
       3454 AAAAATGTAAAAAAATTTAACTTAAAATTAATTATTAGATTATAAAACTATTCAAAGCGAGTAAT
          1 AAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACTATTTAAAGCGAGTAAT

               *              *      *                            *        * 
       3519 AAGTCTTTTGAAGGAATGGGTGACTGTAAATGGACTTTTCCTCTCAATCAATGGCCTTTTCAGTA
         66 AAGACTTTTGAAGGAATGAGTGACTATAAATGGACTTTTCCTCTCAATCAATGGACTTTTCAGCA

                       *                              
       3584 CGTTTCTCGAGTTAGACATTCAATTATT-GTCTGTTTTAA-A
        131 CGTTTCTCGAGGTAGACATTCAATT-TTAGTCTGTTTTAACA

                   *                                *       *                
       3624 GAAAAATATAAAAAAATTCAACTTAAAATCAATTATGAGAATATAAAAATATTTAAAGCG-GATA
          1 -AAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACTATTTAAAGCGAG-TA

                                                      *       *      *    ** 
       3688 ATAAGACTTTTGAAGGAATGAGTGACTATAAATGGACTTTTCTTCTCAATGAATGGATTTTTTTG
         64 ATAAGACTTTTGAAGGAATGAGTGACTATAAATGGACTTTTCCTCTCAATCAATGGACTTTTCAG

                               *                        
       3753 CACGTTT-TCAGAGGTAGATATTCAATTTTAGTCTGTTTTAACA
        129 CACGTTTCTC-GAGGTAGACATTCAATTTTAGTCTGTTTTAACA

                         **         *           *                   *        
       3796 AAAAATGTAAAAAGTTTCAACTTATAATCAATTATGCGATTATAAAACTATTTAAAACGAGTAAT
          1 AAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACTATTTAAAGCGAGTAAT

               *       *      
       3861 AAGCCTTTTGAGGGAATG
         66 AAGACTTTTGAAGGAATG

       3879 GNNNNNNNNN


Statistics
Matches: 220,  Mismatches: 29, Indels: 10
        0.85            0.11        0.04

Matches are distributed among these distances:
 170    5  0.02
 171  213  0.97
 172    2  0.01

ACGTcount: A:0.40, C:0.11, G:0.15, T:0.35


Consensus pattern (171 bp):   
AAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACTATTTAAAGCGAGTAAT
AAGACTTTTGAAGGAATGAGTGACTATAAATGGACTTTTCCTCTCAATCAATGGACTTTTCAGCA
CGTTTCTCGAGGTAGACATTCAATTTTAGTCTGTTTTAACA

Found at i:4340 original size:171 final size:171

Alignment explanation


    Indices: 3986--4503  Score: 659
    Period size: 171  Copynumber: 3.0  Consensus size: 171

       3976 NNNNNNNNNN

                                    *         *          *        *   *      
       3986 AAATCAATTATGAGATTATAAAACCATTTAAAGCAAGTAATAAGCTTTTTGAAGAAATAGGTGAC
          1 AAATCAATTATGAGATTATAAAACTATTTAAAGCGAGTAATAAGCCTTTTGAAGGAATGGGTGAC

                               *           *         *             *         
       4051 TATAAATGGACATTTT-TTATCAATGAAT-GTTTGTTTCCTTCACGTTTCTCGAGGTAGACATTC
         66 TATAAATGGAC-TTTTCTTCTCAATGAATGGCTT-TTT-CTGCACGTTTCTCGAGATAGACATTC

                 *   *        *         *               
       4114 AATTAAAGTATGTTTTAATAAAAAATGTCAAAAAATTCAACTTA
        128 AATTATAGTCTGTTTTAACAAAAAATGTAAAAAAATTCAACTTA

                                             *              *                
       4158 AAATCAATTATGAGATTATAAAACTATTTAAAGTGAGTAATAAGCCTTCTGAAGGAATGGGTGAC
          1 AAATCAATTATGAGATTATAAAACTATTTAAAGCGAGTAATAAGCCTTTTGAAGGAATGGGTGAC

                  *                 *                           *            
       4223 TATAAACGGACTTTTCTTCTCAATCAATGGCTTTTTCTGCACGTTTCTCGAGTTAGACATTCAAT
         66 TATAAATGGACTTTTCTTCTCAATGAATGGCTTTTTCTGCACGTTTCTCGAGATAGACATTCAAT

               **   *               *                 
       4288 TATTTTCTATTTTAA-AGAAAAATATAAAAAAATTCAACTTA
        131 TATAGTCTGTTTTAACA-AAAAATGTAAAAAAATTCAACTTA

                                               *        *       *      *     
       4329 AAATCAATTATGAGATTATAAAACTATTTAAAGCGGGTAATAAGACTTTTGACGGAATGAGTGAC
          1 AAATCAATTATGAGATTATAAAACTATTTAAAGCGAGTAATAAGCCTTTTGAAGGAATGGGTGAC

                      *                *        *                      *     
       4394 TATAAATGGAGTTTTCTTCTCAATGAACGGCTTTTTTTGCACGTTT-T-GAAAGATAGATATTCA
         66 TATAAATGGACTTTTCTTCTCAATGAATGGCTTTTTCTGCACGTTTCTCG--AGATAGACATTCA

                                            **         
       4457 ATTATAGTCTGTTTTAACAAAAAATGTAAAAAGTTTCAACTTA
        129 ATTATAGTCTGTTTTAACAAAAAATGTAAAAAAATTCAACTTA

                
       4500 AAAT
          1 AAAT


Statistics
Matches: 301,  Mismatches: 39, Indels: 13
        0.85            0.11        0.04

Matches are distributed among these distances:
 169    1  0.00
 170    2  0.01
 171  213  0.71
 172   82  0.27
 173    3  0.01

ACGTcount: A:0.39, C:0.12, G:0.14, T:0.36


Consensus pattern (171 bp):   
AAATCAATTATGAGATTATAAAACTATTTAAAGCGAGTAATAAGCCTTTTGAAGGAATGGGTGAC
TATAAATGGACTTTTCTTCTCAATGAATGGCTTTTTCTGCACGTTTCTCGAGATAGACATTCAAT
TATAGTCTGTTTTAACAAAAAATGTAAAAAAATTCAACTTA
Done.