Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NW_018400341.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_3543.0, 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, 943

Length: 1573
ACGTcount: A:0.27, C:0.10, G:0.10, T:0.26

Warning! 430 characters in sequence are not A, C, G, or T


Found at i:436 original size:172 final size:171

Alignment explanation


    Indices: 142--480  Score: 446
    Period size: 172  Copynumber: 2.0  Consensus size: 171

        132 TTTGAACTTA

                                            *   *        * *                 
        142 AAATCAATTTTGAGAATATAAAACCATTTAAAGTGATTAATAAAATTTTTGAAGCAATGGGTGAC
          1 AAATCAATTTTGAGAATATAAAACCATTTAAACTGAGTAATAAAACTCTTGAAGCAATGGGTGAC

                              *         *       *                            
        207 TATAAATAGACTTTTCTTGTCAATGAATTCCTTTTTCTTTATGTTTCTCATGGAAGACATTCAAT
         66 TATAAATAGACTTTTCTTATCAATGAATGCCTTTTTATTTATGTTTCTCATGGAAGACATTCAAT

             *                             *          
        272 TCTAGTCTATTTGAACCAAAAATGTACAAAACATTCAAATTT
        131 TATAGTCTATTTGAACCAAAAATGTA-AAAAAATTCAAATTT

                           * *                        ***         *          
        314 AAATCAATTTTGAGATTCTAAAACCATTTAAACTGAGTAATACGGCTCTTGAAGGAATGGGTGAC
          1 AAATCAATTTTGAGAATATAAAACCATTTAAACTGAGTAATAAAACTCTTGAAGCAATGGGTGAC

             *     *                                       * *               
        379 TGTAAATGGACTTTTCTTATCAATGAATGCCTTTTTATTTATGTTTATTGA-GGAAGACATTCAA
         66 TATAAATAGACTTTTCTTATCAATGAATGCCTTTTTATTTATGTTT-CTCATGGAAGACATTCAA

                     *   *       **               
        443 TTATAGTCTGTTTTAACCAAATGTGTAAAAAAATTCAA
        130 TTATAGTCTATTTGAACCAAAAATGTAAAAAAATTCAA

        481 CTTAAANNNN


Statistics
Matches: 143,  Mismatches: 23, Indels: 3
        0.85            0.14        0.02

Matches are distributed among these distances:
 171   10  0.07
 172  131  0.92
 173    2  0.01

ACGTcount: A:0.37, C:0.12, G:0.14, T:0.37


Consensus pattern (171 bp):   
AAATCAATTTTGAGAATATAAAACCATTTAAACTGAGTAATAAAACTCTTGAAGCAATGGGTGAC
TATAAATAGACTTTTCTTATCAATGAATGCCTTTTTATTTATGTTTCTCATGGAAGACATTCAAT
TATAGTCTATTTGAACCAAAAATGTAAAAAAATTCAAATTT

Found at i:1429 original size:171 final size:171

Alignment explanation


    Indices: 1137--1573  Score: 499
    Period size: 171  Copynumber: 2.6  Consensus size: 171

       1127 NNNNNNCAAT

                      *             *                         **             
       1137 TTTGAGATTATAAAACCATTTAAAACGAGTAATAAGGCTTTTGAAGGTATTAGTGACTATAAATA
          1 TTTGAGATTACAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGTATGGGTGACTATAAATA

              *                 *            *     *       *          **     
       1202 GATTTTTCTTGCCAATGAATACTTTTTTCTACATGTTTCTAAAGGTATACATTCAATCCTAGTCT
         66 GACTTTTCTTGCCAATGAATGCTTTTTTCTACACGTTTCCAAAGGTAGACATTCAATCAGAGTCT

                         * *  *                       *
       1267 GTTTTAACCAAAACTGTGCAAA-AAATTCAAATT-AAATCAAC
        131 G-TTTAACCAAAAATAT-AAAACAAATTCAAATTAAAATCAAA

                                     * *   *          *                      
       1308 TTTGAGATTACAAAACCATTTAAAGTGCGTATTAAGGCTTTTAAAGG-AGTGGGTGACTATAAAT
          1 TTTGAGATTACAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGTA-TGGGTGACTATAAAT

                  *         *      *       **                           *    
       1372 AGACTTCTCTTGCCAACGAATGCCTTTTTCTTTACGTTTCGCAAA-GTAGGA-ATTCAATTAGAG
         65 AGACTTTTCTTGCCAATGAATGCTTTTTTCTACACGTTTC-CAAAGGTA-GACATTCAATCAGAG

             *                              *           
       1435 TTTGTTTAACCAAAAATATAAAACAAATTCAACTTAAAATCAAA
        128 TCTGTTTAACCAAAAATATAAAACAAATTCAAATTAAAATCAAA

             *         *         *                   *                       
       1479 TATG-GCATTAGAAAACCATTCAAAGCGAGTAATAAGGCTTCTGAAGGTATGGGTGACTATAAAT
          1 TTTGAG-ATTACAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGTATGGGTGACTATAAAT

                                           
       1543 AGACTTTTCTTGCCAATGAATGCTTTTTTCT
         65 AGACTTTTCTTGCCAATGAATGCTTTTTTCT


Statistics
Matches: 221,  Mismatches: 38, Indels: 14
        0.81            0.14        0.05

Matches are distributed among these distances:
 169    3  0.01
 170   25  0.11
 171  188  0.85
 172    5  0.02

ACGTcount: A:0.36, C:0.14, G:0.15, T:0.34


Consensus pattern (171 bp):   
TTTGAGATTACAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGTATGGGTGACTATAAATA
GACTTTTCTTGCCAATGAATGCTTTTTTCTACACGTTTCCAAAGGTAGACATTCAATCAGAGTCT
GTTTAACCAAAAATATAAAACAAATTCAAATTAAAATCAAA
Done.