genome.fa.s1568.2.7.7.80.10.50.1000.txt.html

Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NW_018398821.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_2105.0, 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: 4467
ACGTcount: A:0.24, C:0.08, G:0.10, T:0.23

Warning! 1568 characters in sequence are not A, C, G, or T


Found at i:3436 original size:171 final size:169

Alignment explanation


    Indices: 3220--3775  Score: 498
    Period size: 171  Copynumber: 3.3  Consensus size: 169

       3210 NNNNNNNNNN

                                                  *            *             
       3220 TGGGTGACTATAAATGGACTTTTATTGTCAATGAATGCCTTTTTCTTTACGGTTCTTAAGGTAAG
          1 TGGGTGACTATAAATGGACTTTTATTGTCAATGAATGCATTTTTCTTTACGATTCTTAAGGTAAG

                                                   *                         
       3285 CATTCAATTATAGTCGGTTTAATAAAAAATGTAGAAAAATTTTCACTTTAAATTAATTACGGCAT
         66 CATTCAATTATAGTCGGTTTAAT-AAAAATGTA-AAAAAATTTCACTTTAAATTAATTACGGCAT

                              *   *                  
       3350 TACAAAACCATTTAAAGTAAGTTATAATGCTTTTGAAGGTA
        129 TACAAAACCATTTAAAGTGAGTAATAATGCTTTTGAAGGTA

                                  **   *    *              * *      *        
       3391 TGGGTGACTATAAATGGACTTTCCTTGACAATAAATGCATTTTTCTTCATGATTCTCAAGGT-AG
          1 TGGGTGACTATAAATGGACTTTTATTGTCAATGAATGCATTTTTCTTTACGATTCTTAAGGTAAG

                      *     **********             *         *            ** 
       3455 ACATTCAATTCTAGNNNNNNNNNNCCAAAAATGTACAATGAAA--TCAAATTTAAATTAATTTTG
         66 -CATTCAATTATAG--TCGGTTTAATAAAAATGTA-AA-AAAATTTC-ACTTTAAATTAATTACG

                   *     *                        * *   ** 
       3518 AG-ATTAGAAAACAATTTAAAGTGAGTAAT-ATGGCTTCTAAAGAAA
        125 -GCATTACAAAACCATTTAAAGTGAGTAATAAT-GCTTTTGAAGGTA

                           *                                    *            
       3563 TGGGTGACTATAAATAGACTTTTATTGTCAATGAATG-ACTTTTTCTTTACGTTTC-TAGAGGTA
          1 TGGGTGACTATAAATGGACTTTTATTGTCAATGAATGCA-TTTTTCTTTACGATTCTTA-AGGTA

             *               *                *          *    *    *         
       3626 AACATTCAATTATAGTCTGTTTAACTAAAAATGAAAAAAAAATTTAACTTAAAATCAATTACGGC
         64 AGCATTCAATTATAGTCGGTTTAA-TAAAAATG-TAAAAAAATTTCACTTTAAATTAATTACGGC

                  *  *         *          *            
       3691 ATTACACAATCATTTAAAGCGAGTAATAATACTTTTGAAGGTA
        127 ATTACAAAACCATTTAAAGTGAGTAATAATGCTTTTGAAGGTA

                         *         *   *               
       3734 TGGGTGACTATAAGTGGACTTTTCTTGCCAATGAATGC-TTTT
          1 TGGGTGACTATAAATGGACTTTTATTGTCAATGAATGCATTTT

       3776 NNNNNNNNNN


Statistics
Matches: 291,  Mismatches: 77, Indels: 35
        0.72            0.19        0.09

Matches are distributed among these distances:
 170   10  0.03
 171  155  0.53
 172  122  0.42
 173    4  0.01

ACGTcount: A:0.36, C:0.12, G:0.15, T:0.35


Consensus pattern (169 bp):   
TGGGTGACTATAAATGGACTTTTATTGTCAATGAATGCATTTTTCTTTACGATTCTTAAGGTAAG
CATTCAATTATAGTCGGTTTAATAAAAATGTAAAAAAATTTCACTTTAAATTAATTACGGCATTA
CAAAACCATTTAAAGTGAGTAATAATGCTTTTGAAGGTA
Done.