Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NW_018401672.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_4788.0, 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: 1721
ACGTcount: A:0.23, C:0.16, G:0.18, T:0.22

Warning! 351 characters in sequence are not A, C, G, or T


Found at i:1575 original size:22 final size:22

Alignment explanation


    Indices: 1544--1625  Score: 78
    Period size: 22  Copynumber: 3.7  Consensus size: 22

       1534 CGCCACTAGG

                 *                
       1544 GCATGTCATGTCACCGCATTGA
          1 GCATGGCATGTCACCGCATTGA

                               *   
       1566 GCATGGCATGTCA-CGCCACTGA
          1 GCATGGCATGTCACCG-CATTGA

                 *         *    *  
       1588 GCATGTCATGTCACCCCACTAGA
          1 GCATGGCATGTCACCGCA-TTGA

                            
       1611 GCATGG-ATTGTCACC
          1 GCATGGCA-TGTCACC

       1626 CGTATGGGGC


Statistics
Matches: 49,  Mismatches: 7, Indels: 7
        0.78            0.11        0.11

Matches are distributed among these distances:
  21    2  0.04
  22   32  0.65
  23   15  0.31

ACGTcount: A:0.23, C:0.30, G:0.23, T:0.23


Consensus pattern (22 bp):   
GCATGGCATGTCACCGCATTGA

Found at i:1613 original size:45 final size:45

Alignment explanation


    Indices: 1524--1624  Score: 134
    Period size: 45  Copynumber: 2.2  Consensus size: 45

       1514 TGCAACTGCG

                *              *               *   *     
       1524 TGGCGTGTCACGCCACTAGGGCATGTCATGTCACCGCATTGAGCA
          1 TGGCATGTCACGCCACTAGAGCATGTCATGTCACCCCATAGAGCA

                                                          
       1569 TGGCATGTCACGCCACT-GAGCATGTCATGTCACCCCACTAGAGCA
          1 TGGCATGTCACGCCACTAGAGCATGTCATGTCACCCCA-TAGAGCA

                        
       1614 TGG-ATTGTCAC
          1 TGGCA-TGTCAC

       1625 CCGTATGGGG


Statistics
Matches: 50,  Mismatches: 4, Indels: 4
        0.86            0.07        0.07

Matches are distributed among these distances:
  44   19  0.38
  45   31  0.62

ACGTcount: A:0.22, C:0.30, G:0.26, T:0.23


Consensus pattern (45 bp):   
TGGCATGTCACGCCACTAGAGCATGTCATGTCACCCCATAGAGCA

Found at i:1637 original size:23 final size:23

Alignment explanation


    Indices: 1611--1716  Score: 106
    Period size: 23  Copynumber: 4.6  Consensus size: 23

       1601 CCCCACTAGA

                                   
       1611 GCATGGATTGTCACCCGTATGGG
          1 GCATGGATTGTCACCCGTATGGG

                  *      *          
       1634 GCATGGCTTGTCATCCG-ATTGGG
          1 GCATGGATTGTCACCCGTA-TGGG

                   *      *  *     
       1657 GCATGGAGTGTCACTCGAATGGG
          1 GCATGGATTGTCACCCGTATGGG

                *             *  * 
       1680 GCATAGATTGTCACCCGTCTGAG
          1 GCATGGATTGTCACCCGTATGGG

                * *       
       1703 GCATTGCTTGTCAC
          1 GCATGGATTGTCAC

       1717 TCGTC


Statistics
Matches: 67,  Mismatches: 14, Indels: 4
        0.79            0.16        0.05

Matches are distributed among these distances:
  22    1  0.01
  23   65  0.97
  24    1  0.01

ACGTcount: A:0.18, C:0.23, G:0.32, T:0.27


Consensus pattern (23 bp):   
GCATGGATTGTCACCCGTATGGG

Done.