Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NW_018400251.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_3460.0, 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: 3627
ACGTcount: A:0.28, C:0.09, G:0.09, T:0.26

Warning! 1018 characters in sequence are not A, C, G, or T


Found at i:923 original size:141 final size:141

Alignment explanation


    Indices: 655--928  Score: 313
    Period size: 141  Copynumber: 1.9  Consensus size: 141

        645 CATAATTGAT

                                 *                              *  * **      
        655 TTTAAGTTAAATTGTTTTATATTTTTGACTAAAACAGACAATAATTGAATGTTTGTCTTGAGAAA
          1 TTTAAGTTAAATTGTTTTATACTTTTGACTAAAACAGACAATAATTGAATGTCTGACAAGAGAAA

                *                   *                  *                     
        720 CATGTAGAAAAAACCATTCATTGAGAAGAAAAGCTCATTTATAGTCACCAATTCCTTTAAAAGCC
         66 CATGAAGAAAAAACCATTCATTGACAAGAAAAGCTCATTTATACTCACCAATTCCTTTAAAAGCC

                       
        785 TTACTACCCGC
        131 TTACTACCCGC

                       *                **                                   
        796 TTTAAGTTGAACTT-TTTTATACTTTTGGTTAAAACAGACAATAATTGAATGTCT-ACAAAGAGA
          1 TTTAAGTT-AAATTGTTTTATACTTTTGACTAAAACAGACAATAATTGAATGTCTGAC-AAGAGA

                        *  *    *   **     *                 *  *            
        859 AACATGAAGAAACAAGCATTTATTTCCAAGACAAG-TCCATTTATACTCTCCTATT-CTTTCAAA
         64 AACATGAAGAAAAAACCATTCATTGACAAGAAAAGCT-CATTTATACTCACCAATTCCTTT-AAA

                   
        922 AGCCTTA
        127 AGCCTTA

        929 TTACTCGATT


Statistics
Matches: 110,  Mismatches: 19, Indels: 8
        0.80            0.14        0.06

Matches are distributed among these distances:
 140    6  0.05
 141  100  0.91
 142    4  0.04

ACGTcount: A:0.38, C:0.16, G:0.12, T:0.34


Consensus pattern (141 bp):   
TTTAAGTTAAATTGTTTTATACTTTTGACTAAAACAGACAATAATTGAATGTCTGACAAGAGAAA
CATGAAGAAAAAACCATTCATTGACAAGAAAAGCTCATTTATACTCACCAATTCCTTTAAAAGCC
TTACTACCCGC

Found at i:3593 original size:171 final size:169

Alignment explanation


    Indices: 3182--3626  Score: 464
    Period size: 171  Copynumber: 2.6  Consensus size: 169

       3172 NNNNNNNNNN

                                      *                *                     
       3182 ATGTAAAAAAATTCAACTTAAAATCAGTTATGAGATTATAAAATCATTTAAAGCAAGTAATGAGG
          1 ATGTAAAAAAATTC-ACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCAAGTAATGAGG

                            *                                         ** *   
       3247 CTTTTGAAGGAATACGAGACTATAAATGCACTTTTTTTACCAATGAATACTTTTTTCTTTAGAAT
         65 CTTTTGAAGGAATACGTGACTATAAATG-ACTTTTTTTACCAATGAATACTTTTTTCTGCACAAT

                           *       *         * *     
       3312 TCTTGAGGTAAACATTCAATTATTGTCTGTTTTGATGAAAA
        129 TCTTGAGGTAAACATCCAATTATAGTCTGTTTTAAAGAAAA

              *        *   *                         **********   *          
       3353 ATCTAAAAAAACTCAATTGAAAATCAATTATGAGATTATAANNNNNNNNNNAGCGAGTAATGAGG
          1 ATGTAAAAAAATTCACTT-AAAATCAATTATGAGATTATAAAACCATTTAAAGCAAGTAATGAGG

                     *   **                                                  
       3418 CTTTTGAAGAAATTTGTGACTATAAATGAACTTTTTTT-CTCAATGAATGAC-TTTTTCTGCACA
         65 CTTTTGAAGGAATACGTGACTATAAATG-ACTTTTTTTAC-CAATGAAT-ACTTTTTTCTGCACA

            *            *              *              
       3481 TTTCTTGAGGTAAGCATCCAATTATAGTTTGTTTTAAAGAAAA
        127 ATTCTTGAGGTAAACATCCAATTATAGTCTGTTTTAAAGAAAA

                    *               *                        *   *           
       3524 ATGTAAAAGAATTCAGCTTAAAATTAATTATGAGATTATAAAACCATTTCAAGTAAGTAAT-ATG
          1 ATGTAAAAAAATTCA-CTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCAAGTAATGA-G

                          **                       
       3588 GCTTTTGAAGGAATGGGTGACTATAAATTGACTTTTTTT
         64 GCTTTTGAAGGAATACGTGACTATAAA-TGACTTTTTTT

       3627 G


Statistics
Matches: 218,  Mismatches: 50, Indels: 12
        0.78            0.18        0.04

Matches are distributed among these distances:
 170    5  0.02
 171  207  0.95
 172    6  0.03

ACGTcount: A:0.38, C:0.10, G:0.15, T:0.36


Consensus pattern (169 bp):   
ATGTAAAAAAATTCACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCAAGTAATGAGGC
TTTTGAAGGAATACGTGACTATAAATGACTTTTTTTACCAATGAATACTTTTTTCTGCACAATTC
TTGAGGTAAACATCCAATTATAGTCTGTTTTAAAGAAAA
Done.