Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NW_018400234.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_3443.0, 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: 2153
ACGTcount: A:0.29, C:0.09, G:0.11, T:0.28

Warning! 504 characters in sequence are not A, C, G, or T


Found at i:293 original size:172 final size:171

Alignment explanation


    Indices: 1--374  Score: 439
    Period size: 172  Copynumber: 2.2  Consensus size: 171

                                           *                      *          
          1 TATAGTCTGTTTTAATCAAAAATGTAAAAAAGTTCAACTTAAAATCAATTATTATATTATAAAAC
          1 TATAGTCTGTTTTAATCAAAAATGTAAAAAATTTCAACTTAAAATCAATTATTAGATTATAAAAC

                 *                    *          *          *              * 
         66 CATTTGAAGTGATGAATAAGGCTTTTGAAGAAATGGGTGACTGTAAATGGACTTTTCTTGT-CGA
         66 CATTTAAAGTGATGAATAAGGCTTTTAAAGAAATGGGAGACTGTAAATAGACTTTTCTT-TCCAA

                 *             ***         *            
        130 TGAATGCTCTTTTCTTCATGTTTCTCG-AGATAAA-ATTTCAAT
        130 TGAATACTCTTTTCTTCATACATCT-GAAGACAAACA-TTCAAT

                                                  *                          
        172 TATAGTCTGTTTTAATCAAAAATGTAAAACAATTTCAATTTAAAATCAATTATTAGATTATAAAA
          1 TATAGTCTGTTTTAATCAAAAATGTAAAA-AATTTCAACTTAAAATCAATTATTAGATTATAAAA

                     **********            *        *                        
        237 CCATTTAAANNNNNNNNNNAGGCTTTTAAAGGAATGGGAGGCTGTAAATAGACTTTTCTTTCCAA
         65 CCATTTAAAGTGATGAATAAGGCTTTTAAAGAAATGGGAGACTGTAAATAGACTTTTCTTTCCAA

                    *                    *            
        302 TGAATACTTTTTTCTTCATACATCTGAAGGCAAACATTCAAT
        130 TGAATACTCTTTTCTTCATACATCTGAAGACAAACATTCAAT

                            *              
        344 TATAGTCTGTTTTAATGAAAAATGTAAAAAA
          1 TATAGTCTGTTTTAATCAAAAATGTAAAAAA

        375 ATTNNNNNNN


Statistics
Matches: 171,  Mismatches: 28, Indels: 8
        0.83            0.14        0.04

Matches are distributed among these distances:
 171   33  0.19
 172  137  0.80
 173    1  0.01

ACGTcount: A:0.37, C:0.11, G:0.13, T:0.36


Consensus pattern (171 bp):   
TATAGTCTGTTTTAATCAAAAATGTAAAAAATTTCAACTTAAAATCAATTATTAGATTATAAAAC
CATTTAAAGTGATGAATAAGGCTTTTAAAGAAATGGGAGACTGTAAATAGACTTTTCTTTCCAAT
GAATACTCTTTTCTTCATACATCTGAAGACAAACATTCAAT

Found at i:1005 original size:171 final size:171

Alignment explanation


    Indices: 636--1078  Score: 405
    Period size: 171  Copynumber: 2.6  Consensus size: 171

        626 NNNNNNNNNN

                                                                 *           
        636 CTATAAATAGACTTTTCTTGCCAATGAATGCTTTTTTCTTCACATTTCTTGAGGCAAACATTCAA
          1 CTATAAATAGACTTTTCTTGCCAATGAATGCTTTTTTCTTCACATTTCTTGAGACAAACATTCAA

                                                                             
        701 TTATAGCCTGTTTTAATAAAAAATAGAAAAAAATTCAATATAAAATCAATTATAAGATTAGAAAA
         66 TTATAGCCTGTTTTAATAAAAAATAGAAAAAAATTCAATATAAAATCAATTATAAGATTAGAAAA

                  *                   *              
        766 CCATTTGAAGCGAGTAATAAGGCTTTTGAACAAACGAGTGA
        131 CCATTTAAAGCGAGTAATAAGGCTTTGGAACAAACGAGTGA

                    *            *           *          *          *** *     
        807 CTATAAATGGACTTATT-TTGTCAATGAATGCTCTTTTCTTCACGTTTCTTGAGATGGATATTCA
          1 CTATAAATAGACTT-TTCTTGCCAATGAATGCTTTTTTCTTCACATTTCTTGAGACAAACATTCA

                   *          *               *          ********** *      * 
        871 ATTATAGTCTGTTTTAATCAAAAAT-GTAAAAAATTTCAACT-TANNNNNNNNNNTTAGATTATA
         65 ATTATAGCCTGTTTTAATAAAAAATAG-AAAAAAATTCAA-TATAAAATCAATTATAAGATTAGA

                         *                   **  *       
        934 AAACCATTTAAAGTGAGTAATAAGGCTTTGGAAGGAATG-G-GAA
        128 AAACCATTTAAAGCGAGTAATAAGGCTTTGGAACAAACGAGTG-A

               *                           *           *  **        *        
        977 GCTGTAAATAGACTTTTCTTGCCAATGAATGTTTTTTTCTT--TATGCCTCTGAAGGCAAACATT
          1 -CTATAAATAGACTTTTCTTGCCAATGAATGCTTTTTTCTTCACATTTCT-TG-AGACAAACATT

                     *       *  *       *          
       1040 CAATTATAGTCTGTTTTCATGAAAAATATAAAAAGAATT
         63 CAATTATAGCCTGTTTTAATAAAAAATAGAAAAA-AATT

       1079 GAANNNNNNN


Statistics
Matches: 214,  Mismatches: 48, Indels: 19
        0.76            0.17        0.07

Matches are distributed among these distances:
 169    4  0.02
 170    7  0.03
 171  197  0.92
 172    6  0.03

ACGTcount: A:0.36, C:0.12, G:0.14, T:0.35


Consensus pattern (171 bp):   
CTATAAATAGACTTTTCTTGCCAATGAATGCTTTTTTCTTCACATTTCTTGAGACAAACATTCAA
TTATAGCCTGTTTTAATAAAAAATAGAAAAAAATTCAATATAAAATCAATTATAAGATTAGAAAA
CCATTTAAAGCGAGTAATAAGGCTTTGGAACAAACGAGTGA
Done.