Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NW_018402241.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_5326.0, 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: 2024
ACGTcount: A:0.31, C:0.09, G:0.11, T:0.28

Warning! 415 characters in sequence are not A, C, G, or T


Found at i:539 original size:172 final size:166

Alignment explanation


    Indices: 281--709  Score: 436
    Period size: 166  Copynumber: 2.5  Consensus size: 166

        271 AAACATTCAT

                      *                  *        *                          
        281 CTTAAAATCAGTTATGAGATTATAAAACCTTTTAAAGCAAGTAATAAGGCTTTTG-AGAGAATGA
          1 CTTAAAATCAATTATGAGATTATAAAACCATTTAAA-CGAGTAATAAGGCTTTTGAAG-GAATGA

            ***    *     *          *         ***   *            **          
        345 CTCACTACAAATGGACTTTTCTTGTCAATGAATATAATTTTC-TTTAGGTTTCTTGAGCTAGACA
         64 AAAACTATAAATGAACTTTTCTTGCCAATGAAT-GCCTTTACGTTTA----TCAAG-GC-AGACA

                    **  *       *                      *  
        409 TTCAATTATTATTTGTTTTAGCC-ATAAATGTAAAAAAAAA-TGAA
        122 TTCAATTACAATCTGTTTTAACCAAT-AATGTAAAAAAAAAGTAAA

                         *                                                *  
        453 CTTAAAATCAATTTTGAGATTATAAAACCATTTACAACGAGTAATAAGGCTTTTGAAGGAATTAA
          1 CTTAAAATCAATTATGAGATTATAAAACCATTTA-AACGAGTAATAAGGCTTTTGAAGGAATGAA

             *  *                 *                                          
        518 AGACCATAAATGAACTTTTCTTACCAATGAATGCCTTTACGTTTATCAAGGCAGACATTCAATTA
         65 AAACTATAAATGAACTTTTCTTGCCAATGAATGCCTTTACGTTTATCAAGGCAGACATTCAATTA

                                 *               
        583 CAATCTGTTTTAACCAATAATTTAAAAAAAAAGTAAA
        130 CAATCTGTTTTAACCAATAATGTAAAAAAAAAGTAAA

                 *  *        *              *                          *     
        620 CTTAAGATGAATTATGACATTATAAAACCATTAAAACGAGTAATAAGGCTTTTGAAGGAGTGAAA
          1 CTTAAAATCAATTATGAGATTATAAAACCATTTAAACGAGTAATAAGGCTTTTGAAGGAATGAAA

                                      
        685 AACTATAAAT-AGACTTTTCTTGCCA
         66 AACTATAAATGA-ACTTTTCTTGCCA

        710 NNNNNNNNNN


Statistics
Matches: 216,  Mismatches: 35, Indels: 18
        0.80            0.13        0.07

Matches are distributed among these distances:
 165    1  0.00
 166   86  0.40
 167   36  0.17
 168    3  0.01
 171    4  0.02
 172   82  0.38
 173    4  0.02

ACGTcount: A:0.41, C:0.13, G:0.13, T:0.33


Consensus pattern (166 bp):   
CTTAAAATCAATTATGAGATTATAAAACCATTTAAACGAGTAATAAGGCTTTTGAAGGAATGAAA
AACTATAAATGAACTTTTCTTGCCAATGAATGCCTTTACGTTTATCAAGGCAGACATTCAATTAC
AATCTGTTTTAACCAATAATGTAAAAAAAAAGTAAA

Found at i:1033 original size:172 final size:170

Alignment explanation


    Indices: 855--1170  Score: 384
    Period size: 172  Copynumber: 1.8  Consensus size: 170

        845 AGAATGGGTT

                             *    *   *             *    *   ***           * 
        855 ACTATAAATGGACTTTTGTTACCAATGAATACCATTTTCTTCATGTTTCTTGAGGTAAACATTCA
          1 ACTATAAATGGACTTTTCTTACAAATAAATACCATTTTCTACATGATTCCCAAGGTAAACATTAA

            *              *      *                *   *           *         
        920 GGTATAATCT-TTTTCA-GCCATAAATGTAAAACAAATTTAACTTAAAATCAATTTTGAGATTAT
         66 AGTATAATCTGTTTTAATG--AAAAATGT-AAA-AAATTCAACCTAAAATCAATTATGAGATTAT

                 *                                      
        983 AAAACTATTTAAAGTGAGCACCAAGGTCTTTACAGGAATATGAG
        127 AAAACCATTTAAAGTGAGCACCAAGGTCTTTACAGGAATATGAG

                                           **                        **      
       1027 ACTATAAATGGACTTTTCTTACAAATAAATAGGATTTTCTACATGATTCCCAAGGTAGGCATTAA
          1 ACTATAAATGGACTTTTCTTACAAATAAATACCATTTTCTACATGATTCCCAAGGTAAACATTAA

             *                          *                                    
       1092 ATTATAATCTGTTTTAATGAAAAATGTAGAAAATTCAACCTAAAATCAATTATGAGATTATAAAA
         66 AGTATAATCTGTTTTAATGAAAAATGTAAAAAATTCAACCTAAAATCAATTATGAGATTATAAAA

                          
       1157 CCATTTAAAGTGAG
        131 CCATTTAAAGTGAG

       1171 TTATTCGGCT


Statistics
Matches: 120,  Mismatches: 22, Indels: 6
        0.81            0.15        0.04

Matches are distributed among these distances:
 170   45  0.38
 171    2  0.02
 172   67  0.56
 173    5  0.04
 174    1  0.01

ACGTcount: A:0.40, C:0.13, G:0.13, T:0.34


Consensus pattern (170 bp):   
ACTATAAATGGACTTTTCTTACAAATAAATACCATTTTCTACATGATTCCCAAGGTAAACATTAA
AGTATAATCTGTTTTAATGAAAAATGTAAAAAATTCAACCTAAAATCAATTATGAGATTATAAAA
CCATTTAAAGTGAGCACCAAGGTCTTTACAGGAATATGAG
Done.