Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NW_018398828.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_2111.0, 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: 10283
ACGTcount: A:0.16, C:0.06, G:0.06, T:0.17

Warning! 5642 characters in sequence are not A, C, G, or T


Found at i:2985 original size:28 final size:28

Alignment explanation


    Indices: 2936--3008  Score: 103
    Period size: 28  Copynumber: 2.6  Consensus size: 28

       2926 NGAGAGTTTT

                             *          
       2936 AACATGTTTGTCTTAATTTAGACAAG-A
          1 AACATGTTTGTCTTAATCTAGACAAGAA

                                         
       2963 AACATGTTTGATCTTAATCTAGACAAGAA
          1 AACATGTTTG-TCTTAATCTAGACAAGAA

              *        *     
       2992 AATATGTTTGTTTTAAT
          1 AACATGTTTGTCTTAAT

       3009 TTAAAATAAG


Statistics
Matches: 41,  Mismatches: 3, Indels: 3
        0.87            0.06        0.06

Matches are distributed among these distances:
  27   10  0.24
  28   21  0.51
  29   10  0.24

ACGTcount: A:0.37, C:0.10, G:0.14, T:0.40


Consensus pattern (28 bp):   
AACATGTTTGTCTTAATCTAGACAAGAA

Found at i:8835 original size:28 final size:28

Alignment explanation


    Indices: 8785--8858  Score: 105
    Period size: 28  Copynumber: 2.6  Consensus size: 28

       8775 NNNNNGTTTT

                              *         
       8785 AACATGTTTGTCTTAATTTAGACAAG-A
          1 AACATGTTTGTCTTAATTCAGACAAGAA

                                         
       8812 AACATGTTTGATCTTAATTCAGACAAGAA
          1 AACATGTTTG-TCTTAATTCAGACAAGAA

              *        *      
       8841 AATATGTTTGTTTTAATT
          1 AACATGTTTGTCTTAATT

       8859 TAAAACAAGC


Statistics
Matches: 42,  Mismatches: 3, Indels: 3
        0.88            0.06        0.06

Matches are distributed among these distances:
  27   10  0.24
  28   22  0.52
  29   10  0.24

ACGTcount: A:0.36, C:0.09, G:0.14, T:0.41


Consensus pattern (28 bp):   
AACATGTTTGTCTTAATTCAGACAAGAA

Found at i:8866 original size:29 final size:28

Alignment explanation


    Indices: 8788--8919  Score: 122
    Period size: 30  Copynumber: 4.5  Consensus size: 28

       8778 NNGTTTTAAC

                                       *
       8788 ATGTTTGTCTTAATTTAGACAAG-AAAC
          1 ATGTTTGTCTTAATTTAGACAAGAAAAT

                            *            
       8815 ATGTTTGATCTTAATTCAGACAAGAAAAT
          1 ATGTTTG-TCTTAATTTAGACAAGAAAAT

                    *         *           
       8844 ATGTTTGTTTTAATTTAAAACAAGCAAAAT
          1 ATGTTTGTCTTAATTT-AGACAAG-AAAAT

               *           *   *           
       8874 ATTTTTTGTCTTAATCTAGGCAAGATAAAAT
          1 A-TGTTTGTCTTAATTTAGACAAG--AAAAT

              *   *        
       8905 ATTTTTCTCTTAATT
          1 ATGTTTGTCTTAATT

       8920 AAGGGTAAGA


Statistics
Matches: 86,  Mismatches: 13, Indels: 9
        0.80            0.12        0.08

Matches are distributed among these distances:
  27    7  0.08
  28   22  0.26
  29   16  0.19
  30   23  0.27
  31   18  0.21

ACGTcount: A:0.37, C:0.10, G:0.11, T:0.42


Consensus pattern (28 bp):   
ATGTTTGTCTTAATTTAGACAAGAAAAT

Found at i:10057 original size:32 final size:32

Alignment explanation


    Indices: 10015--10084  Score: 88
    Period size: 32  Copynumber: 2.2  Consensus size: 32

      10005 TTTCTTATGA

                 *               *           
      10015 CTATTTTTTTTTGT-GAAAATTGAGTTTTTCTT
          1 CTATTATTTTTTGTAGAAAA-AGAGTTTTTCTT

                        *                   
      10047 CTATTATTTTTTTTAGAAAAAGAGTTTTTCTT
          1 CTATTATTTTTTGTAGAAAAAGAGTTTTTCTT

            *     
      10079 ATATTA
          1 CTATTA

      10085 AAATTATATT


Statistics
Matches: 33,  Mismatches: 4, Indels: 2
        0.85            0.10        0.05

Matches are distributed among these distances:
  32   28  0.85
  33    5  0.15

ACGTcount: A:0.26, C:0.06, G:0.10, T:0.59


Consensus pattern (32 bp):   
CTATTATTTTTTGTAGAAAAAGAGTTTTTCTT
Done.