Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NW_018400114.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_3331.0, 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: 4314
ACGTcount: A:0.20, C:0.07, G:0.07, T:0.21

Warning! 1964 characters in sequence are not A, C, G, or T


Found at i:725 original size:171 final size:169

Alignment explanation


    Indices: 441--1102  Score: 620
    Period size: 171  Copynumber: 3.9  Consensus size: 169

        431 NNNNATTTAT

                              **       *             *            *    *    *
        441 AGCGAGTAATAAGGCTTTTGAAGGCATTGGTGACTATAAATAGAC-TTTCTTGCTAATGGATATC
          1 AGCGAGTAATAAGGCTTTCAAAGGCATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATATT

                                              *                     *        
        505 TTTTTCTTCACGTTTCTC-AAGACAGACATTCAACTATAATCTATTTTAATATAAATTATAAAAA
         66 TTTTTCTTCACGTTTCTCAAAG-CAGACATTCAATTATAATCTATTTTAATA-AAAATATAAAAA

                *                              *      
        569 CATTTAAATTAAAATCAATTATGAGGTTATAAAATTAATTAA
        129 -ATTCAAATTAAAATCAATTATGAGGTTATAAAATCAATTAA

                      *                    *                                 
        611 AGCGAGTAATGAGGCTTTCAAAGGCATGGGTTACTATAAATGGACTTTTCTTGCCAATGAATATT
          1 AGCGAGTAATAAGGCTTTCAAAGGCATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATATT

                     *                                                       
        676 TTTTTCTTCCCGTTTCTCAAAGCAGACATTCAATTATAATC-ACTTTTAATAACAAATATAAAAA
         66 TTTTTCTTCACGTTTCTCAAAGCAGACATTCAATTATAATCTA-TTTTAATAA-AAATAT-AAAA

                *                          ********** 
        740 AATTTAAATTAAAATCAATTATGAGGTTATANNNNNNNNNNA
        128 AATTCAAATTAAAATCAATTATGAGGTTATAAAATCAATTAA

                *                          *        **          **    *      
        782 AGCGTGTAATAAGGCTTTCAAAGGCATGGGTTACTATAAACCGACTTTTCTTATCAA-AAGATAT
          1 AGCGAGTAATAAGGCTTTCAAAGGCATGGGTGACTATAAATGGACTTTTCTTGCCAATGA-ATAT

            *   *                *                      **********           
        846 GTTTATCTTCACGTTTCTCAAGGCAGACATTCAATTATAATCTGNNNNNNNNNNAAATATAAAAA
         65 TTTTTTCTTCACGTTTCTCAAAGCAGACATTCAATTATAATCT-ATTTTAATAAAAATATAAAAA

                                  *      *       *    
        911 ATCTCAAATTAAAATCAATTATAAGGTTAGAAAATCATTTAA
        129 AT-TCAAATTAAAATCAATTATGAGGTTATAAAATCAATTAA

                      *   *             *               *               *    
        953 AGCGAGTAAAAAAGCCTTT-AAAGGCATAGGTGACTATAAATGGGCTTTTCTTGCCAATGGATAT
          1 AGCGAGT-AATAAGGCTTTCAAAGGCATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATAT

                      *          * * * *                 *                   
       1017 CTTTTTT-TTTACGTTTC-CTGAGGTAAACATTCAATTATAATCTGTTTTAATAAAAATAT-AAA
         65 -TTTTTTCTTCACGTTTCTC-AAAGCAGACATTCAATTATAATCTATTTTAATAAAAATATAAAA

                    *               
       1079 AATTCAAACTAAAATCAATTATGA
        128 AATTCAAATTAAAATCAATTATGA

       1103 NNNNNNNNNN


Statistics
Matches: 393,  Mismatches: 86, Indels: 28
        0.78            0.17        0.06

Matches are distributed among these distances:
 168   19  0.05
 169    6  0.02
 170   56  0.14
 171  291  0.74
 172   21  0.05

ACGTcount: A:0.37, C:0.13, G:0.13, T:0.34


Consensus pattern (169 bp):   
AGCGAGTAATAAGGCTTTCAAAGGCATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATATT
TTTTTCTTCACGTTTCTCAAAGCAGACATTCAATTATAATCTATTTTAATAAAAATATAAAAAAT
TCAAATTAAAATCAATTATGAGGTTATAAAATCAATTAA

Found at i:2895 original size:171 final size:161

Alignment explanation


    Indices: 2765--3191  Score: 371
    Period size: 171  Copynumber: 2.5  Consensus size: 161

       2755 NNNNNNNNNN

                                         *         *       *    *           *
       2765 TTATAATTGAATGTCTGCCTTGAGAAACATGAAGAAAAACATA-TCTTTTGATAAGAAAAGTCCG
          1 TTATAATTGAATGTCTGCCTTGAGAAACAGGAAGAAAAAAATATTC-ATTGACAAGAAAAGTCCA

                                *        *                                   
       2829 TTTATAGTAACCCATGCCTTTGAAAGCCTTATTANNNNNNNNNNATATTTTTATAACCTCATAAT
         65 TTTATAGTAACCCATGCCTTCGAAAGCCTCATTA----------ATATTTTTATAACCTCATAAT

                        *                             
       2894 TGATTTTAATTTTAAGTTTTTTATATTTGTTATTAAAAGTGA
        120 TGATTTTAATTTGAAGTTTTTTATATTTGTTATTAAAAGTGA

                              *                               *              
       2936 TTATAATTGAATGTCTGCTTTGAGAAACAGGAAGAAAAAAATATTCATTGGCAAGAAAAGTCCAT
          1 TTATAATTGAATGTCTGCCTTGAGAAACAGGAAGAAAAAAATATTCATTGACAAGAAAAGTCCAT

                     **                                           *   *      
       3001 TTATAGTAATGCATGCCTTCGAAAGCCTCATTACTCGCTTTAATTATTTTTATAGCCTTATAATT
         66 TTATAGTAACCCATGCCTTCGAAAGCCTC---A------TTAA-TATTTTTATAACCTCATAATT

                       *  *              *             
       3066 GATTTTAATTTAAATTTTTTTATATATT-CTATTAAAA-TAGA
        121 GATTTTAATTTGAAGTTTTTTATAT-TTGTTATTAAAAGT-GA

                 *           *                            *                  
       3107 TTATAGTTGAATGTCTGTCTTGAGAAA-AGTGAA-AAAAAAGATATCCATT-AGCAAGAAAAGTC
          1 TTATAATTGAATGTCTGCCTTGAGAAACAG-GAAGAAAAAA-ATATTCATTGA-CAAGAAAAGTC

            *         *   *        
       3169 TATTTATAGTCACCAATGCCTTC
         63 CATTTATAGTAACCCATGCCTTC

       3192 ANNNNNNNNN


Statistics
Matches: 214,  Mismatches: 26, Indels: 32
        0.79            0.10        0.12

Matches are distributed among these distances:
 170   10  0.05
 171  196  0.92
 172    4  0.02
 174    1  0.00
 180    3  0.01

ACGTcount: A:0.36, C:0.12, G:0.13, T:0.37


Consensus pattern (161 bp):   
TTATAATTGAATGTCTGCCTTGAGAAACAGGAAGAAAAAAATATTCATTGACAAGAAAAGTCCAT
TTATAGTAACCCATGCCTTCGAAAGCCTCATTAATATTTTTATAACCTCATAATTGATTTTAATT
TGAAGTTTTTTATATTTGTTATTAAAAGTGA
Done.