Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NW_018400382.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_3582.0, 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, 679

Length: 1133
ACGTcount: A:0.35, C:0.11, G:0.16, T:0.33

Warning! 50 characters in sequence are not A, C, G, or T


Found at i:314 original size:168 final size:162

Alignment explanation


    Indices: 140--467  Score: 346
    Period size: 171  Copynumber: 2.0  Consensus size: 162

        130 NNNNNTGAGA

                                               *               *           * 
        140 TTATAAAACCATTT-AA-AGAGT-ATAAGGC-TCTTGAAGGCTTGCGTGACTATAAATGGGCTTT
          1 TTATAAAACCATTTAAAGAGAGTAATAAGGCAT-TGGAAGGCTTGCGTGACAATAAATGGGCTAT

                 *   *                           *                     *     
        201 TCTTGTCAATGAATAG-CTTTTTCTTCAGGTTTTCAATGG-AAGACATTCAATTATAATCTATTT
         65 TCTTGCCAAGGAAT-GTCTTTTTCTTCAGGTTTTCAAAGGCAA-ACATTCAATTATAATATATTT

                               *    *                    
        264 TAAACAAAAATATAA-AAACATTCGACTTAAANNNNNNNNNNAGG
        128 TAAACAAAAATATAACAAAAATTCAACTTAAA----------AGG

                                                        *                    
        308 TTATAAAACCATTTAAAGAGAGTAATAAGGCATTGGAAGGCTTGGGTGACAATAAATGGGCTATT
          1 TTATAAAACCATTTAAAGAGAGTAATAAGGCATTGGAAGGCTTGCGTGACAATAAATGGGCTATT

                           *          **                                   * 
        373 CTTGCCAAGGAATGTGTTTTTCTTCATTTTTTCAAAGGCAAACATTCAATTATAATATATTTTGA
         66 CTTGCCAAGGAATGTCTTTTTCTTCAGGTTTTCAAAGGCAAACATTCAATTATAATATATTTTAA

            * *                           
        438 CCGAAAATATAACAAAAATTCAACTTAAAA
        131 ACAAAAATATAACAAAAATTCAACTTAAAA

        468 TCAATTATGC


Statistics
Matches: 137,  Mismatches: 16, Indels: 20
        0.79            0.09        0.12

Matches are distributed among these distances:
 162    1  0.01
 168   14  0.10
 169    2  0.01
 170    6  0.04
 171   97  0.71
 172   17  0.12

ACGTcount: A:0.37, C:0.12, G:0.15, T:0.33


Consensus pattern (162 bp):   
TTATAAAACCATTTAAAGAGAGTAATAAGGCATTGGAAGGCTTGCGTGACAATAAATGGGCTATT
CTTGCCAAGGAATGTCTTTTTCTTCAGGTTTTCAAAGGCAAACATTCAATTATAATATATTTTAA
ACAAAAATATAACAAAAATTCAACTTAAAAGG

Found at i:549 original size:172 final size:161

Alignment explanation


    Indices: 321--643  Score: 387
    Period size: 172  Copynumber: 1.9  Consensus size: 161

        311 TAAAACCATT

                                            *                                
        321 TAAAGAGAGTAATAAGGCATTGGAAGGCTTGGGTGACAATAAATGGGCTATTCTTGCCAAG-GAA
          1 TAAAGAGAGTAATAAGGCATTGGAAGGCTTGGCTGACAATAAATGGGCTATTCTTGCC-AGTGAA

              *            *   *      *                       *    *         
        385 TGTGTTTTTCTTCATTTTTTCAAAGGCAAACATTCAATTATAATATATTTTGACCGAAAATATAA
         65 TGGGTTTTTCTTCATGTTTCCAAAGGAAAACATTCAATTATAATATATTTCGACCAAAAATA-AA

            *                                
        450 CAAAAATTCAACTTAAAATCAATTATGCGATTA
        129 AAAAAATTCAACTTAAAATCAATTATGCGATTA

                                        *  *               *      *    *     
        483 TNNNNNNNNNNAAAGAGAGTAATAAGGCTTTTGAAGGCTTGGCTGACTATAAATTGGCTTTTCTT
          1 T----------AAAGAGAGTAATAAGGCATTGGAAGGCTTGGCTGACAATAAATGGGCTATTCTT

                              *           *                        *         
        548 GCCAGTGAATGGGTTTTTGTTCATGTTTCCCAAGGAAAACATTCAATTATAATATGTTTCGACCA
         56 GCCAGTGAATGGGTTTTTCTTCATGTTTCCAAAGGAAAACATTCAATTATAATATATTTCGACCA

                                           
        613 AAAATAAAAAAAAATTCAACTTAAAATCAAT
        121 AAAATAAAAAAAAATTCAACTTAAAATCAAT

        644 NNNNNNNNNN


Statistics
Matches: 134,  Mismatches: 16, Indels: 13
        0.82            0.10        0.08

Matches are distributed among these distances:
 162    1  0.01
 171   26  0.19
 172  107  0.80

ACGTcount: A:0.37, C:0.12, G:0.16, T:0.32


Consensus pattern (161 bp):   
TAAAGAGAGTAATAAGGCATTGGAAGGCTTGGCTGACAATAAATGGGCTATTCTTGCCAGTGAAT
GGGTTTTTCTTCATGTTTCCAAAGGAAAACATTCAATTATAATATATTTCGACCAAAAATAAAAA
AAAATTCAACTTAAAATCAATTATGCGATTA

Found at i:896 original size:49 final size:49

Alignment explanation


    Indices: 822--928  Score: 160
    Period size: 49  Copynumber: 2.2  Consensus size: 49

        812 CCAATTATGA

                             * **     **                     
        822 GACTATAAAACCATTTATAGTGAGTAGTAAGGCTTTTGAAGGCTTGGGT
          1 GACTATAAAACCATTTAAAAAGAGTAAAAAGGCTTTTGAAGGCTTGGGT

                                                             
        871 GACTATAAAACCATTTAAAAAGAGTAAAAAGGCTTTTGAAGGCTTGGGT
          1 GACTATAAAACCATTTAAAAAGAGTAAAAAGGCTTTTGAAGGCTTGGGT

            *        
        920 AACTATAAA
          1 GACTATAAA

        929 TAGGGTTTTT


Statistics
Matches: 52,  Mismatches: 6, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  49   52  1.00

ACGTcount: A:0.38, C:0.10, G:0.22, T:0.29


Consensus pattern (49 bp):   
GACTATAAAACCATTTAAAAAGAGTAAAAAGGCTTTTGAAGGCTTGGGT
Done.