Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NW_018401561.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_4684.0, 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: 3079
ACGTcount: A:0.23, C:0.09, G:0.07, T:0.24

Warning! 1143 characters in sequence are not A, C, G, or T


Found at i:925 original size:171 final size:171

Alignment explanation


    Indices: 684--993  Score: 383
    Period size: 171  Copynumber: 1.8  Consensus size: 171

        674 TGGATTAAAA

                                            ***             *    * *    * ** 
        684 TGGTTTTATAATCTCCAAATTGATTTTAAGTTTTTTTTTTTTAGTTTTTTGGTTATAACATATTA
          1 TGGTTTTATAATCTCCAAATTGATTTTAAGTTGAATTTTTTTAGTTTTCTGGTCAAAACAGAAAA

                                                 *       *   *               
        749 TAATTGAATGTCTAAATT-AAAAAACATGAAGAAAAAGACATTCATTGGTAAGAAAAGTCTATTT
         66 TAATTGAATGTCT-AATTCAAAAAACATGAAGAAAAACACATTCAATGGCAAGAAAAGTCTATTT

              *                                       
        813 ATTGTCACCCTTTCTTTCAAAAGAGTTATTACTCACATTAAT
        130 ATCGTCACCCTTTCTTTCAAAAGAGTTATTACTCACATTAAT

                                        *                                    
        855 TGGTTTTATAATCT-CATAATTGATTTTGAGTTGAATTTTTTTA-TATTTCTGGTCAAAACAGAA
          1 TGGTTTTATAATCTCCA-AATTGATTTTAAGTTGAATTTTTTTAGT-TTTCTGGTCAAAACAGAA

                            *     *   **            **            *          
        918 AATAATTGAATGTCTACTTCAAGAAATGTGAAGAAAAACATGTTCAATGGCAAGCAAAGTCTATT
         64 AATAATTGAATGTCTAATTCAAAAAACATGAAGAAAAACACATTCAATGGCAAGAAAAGTCTATT

                       
        983 TATCGTCACCC
        129 TATCGTCACCC

        994 ATTCCTTTAA


Statistics
Matches: 115,  Mismatches: 21, Indels: 6
        0.81            0.15        0.04

Matches are distributed among these distances:
 170    6  0.05
 171  109  0.95

ACGTcount: A:0.35, C:0.12, G:0.13, T:0.40


Consensus pattern (171 bp):   
TGGTTTTATAATCTCCAAATTGATTTTAAGTTGAATTTTTTTAGTTTTCTGGTCAAAACAGAAAA
TAATTGAATGTCTAATTCAAAAAACATGAAGAAAAACACATTCAATGGCAAGAAAAGTCTATTTA
TCGTCACCCTTTCTTTCAAAAGAGTTATTACTCACATTAAT

Found at i:1752 original size:167 final size:159

Alignment explanation


    Indices: 1579--1893  Score: 305
    Period size: 172  Copynumber: 1.9  Consensus size: 159

       1569 NNNNNNNNNN

                                       *        *                *           
       1579 ATAATTGATTTTAAATTAAATTTTTTTGCATTTTTGGCTAAAACAGACT-ATAGTTG-TCTACCT
          1 ATAATTGATTTTAAATTAAATTTTTTTACATTTTTGACTAAAACAGA-TAATAATTGATCTACCT

                                                  *                        * 
       1642 CAAGAAACA-TGAAG-AAAAAGGCATTCATTGGCAAGACAAGTCCATTTATAGTCACCCATTCTT
         65 CAAGAAA-AGTGAAGAAAAAAGGCATTCATTGGCAAGAAAAGTCCATTTATAGTCACCCATTCCT

                  *                                  
       1705 TCAAAATCCTTATTACNNNNNNNNNNTAGTTTTATAATTCC
        129 TCAAAAGCCTTATTAC----------TAGTTTTATAATTCC

                          *  *          *      * *     *                     
       1746 ATAATTGATTTTAAGTTGAATTTTTTTATATTTTTTATTAAAATAGATAATAATTGACTATCTAC
          1 ATAATTGATTTTAAATTAAATTTTTTTACATTTTTGACTAAAACAGATAATAATTG---ATCTAC

              *                   *           *          *                   
       1811 CTTAAGAAAAGTGAAGAAAAAATGCATTCATTGGTAAGAAAAGTCTATTTATAGTCACCCATTCC
         63 CTCAAGAAAAGTGAAGAAAAAAGGCATTCATTGGCAAGAAAAGTCCATTTATAGTCACCCATTCC

               *    *         
       1876 TTCGAAAGGCTTATTACT
        128 TTCAAAAGCCTTATTACT

       1894 CACTATAAAT


Statistics
Matches: 123,  Mismatches: 18, Indels: 19
        0.77            0.11        0.12

Matches are distributed among these distances:
 162    1  0.01
 166    1  0.01
 167   45  0.37
 170    1  0.01
 171   18  0.15
 172   57  0.46

ACGTcount: A:0.35, C:0.13, G:0.11, T:0.37


Consensus pattern (159 bp):   
ATAATTGATTTTAAATTAAATTTTTTTACATTTTTGACTAAAACAGATAATAATTGATCTACCTC
AAGAAAAGTGAAGAAAAAAGGCATTCATTGGCAAGAAAAGTCCATTTATAGTCACCCATTCCTTC
AAAAGCCTTATTACTAGTTTTATAATTCC
Done.