Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NW_018400246.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_3454.0, 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, 735

Length: 1225
ACGTcount: A:0.30, C:0.11, G:0.11, T:0.30

Warning! 220 characters in sequence are not A, C, G, or T


Found at i:290 original size:172 final size:172

Alignment explanation


    Indices: 1--414  Score: 425
    Period size: 172  Copynumber: 2.4  Consensus size: 172

                                           *     *              *          * 
          1 TGACTATAAATGGACTTTTCTTCCCAATGAATACTTTTTTCTTCATGTTTCTTAAGGTAGACATT
          1 TGACTATAAATGGACTTTTCTTCCCAATGAACACTTTCTTCTTCATGTTTCTCAAGGTAGACAAT

             *   *    *         *     *   *              *               *   
         66 CCATTCTAACCTATTTTAACCAAAAATGTACAAAAAATTCAAATTTAAATCAATATTGAGATTAT
         66 CAATTATAACATATTTTAACAAAAAAAGTAAAAAAAATTCAAATTAAAATCAATATTGAGAATAT

                                                      
        131 AAAAATATTTAAAGTGAGTAATAAGGCTTTTAATGGAATGGG
        131 AAAAATATTTAAAGTGAGTAATAAGGCTTTTAATGGAATGGG

                                  *         *          *         **          
        173 TGACTATAAATGGACTTTTCTTGCCAATGAACCCTTTCTTCTTTATGTTTCTCGGGGTAGACAAT
          1 TGACTATAAATGGACTTTTCTTCCCAATGAACACTTTCTTCTTCATGTTTCTCAAGGTAGACAAT

                     *  *                          *  *           *          
        238 CAATTATAATATGTTTTAACAAAAAAAGTAAAAAAAATTGAACTTAAAATCAATTTTGAGAATAT
         66 CAATTATAACATATTTTAACAAAAAAAGTAAAAAAAATTCAAATTAAAATCAATATTGAGAATAT

                *      *** * ****    *          *      
        303 AAAACTATTTATCCTAAACCCTAAGCCTTTTGAA-GCAATGGG
        131 AAAAATATTTAAAGTGAGTAATAAGGCTTTT-AATGGAATGGG

             *         *        * *     *  *     *              * *        * 
        345 TTACTATAAATAGACTTTTCCTGCCAATAAATACTTTTTTCTTCATGTTTCTTATGGTAGACATT
          1 TGACTATAAATGGACTTTTCTTCCCAATGAACACTTTCTTCTTCATGTTTCTCAAGGTAGACAAT

                 
        410 CAATT
         66 CAATT

        415 CTAGTCTATT


Statistics
Matches: 196,  Mismatches: 45, Indels: 2
        0.81            0.19        0.01

Matches are distributed among these distances:
 172  194  0.99
 173    2  0.01

ACGTcount: A:0.36, C:0.14, G:0.12, T:0.37


Consensus pattern (172 bp):   
TGACTATAAATGGACTTTTCTTCCCAATGAACACTTTCTTCTTCATGTTTCTCAAGGTAGACAAT
CAATTATAACATATTTTAACAAAAAAAGTAAAAAAAATTCAAATTAAAATCAATATTGAGAATAT
AAAAATATTTAAAGTGAGTAATAAGGCTTTTAATGGAATGGG

Found at i:1147 original size:172 final size:170

Alignment explanation


    Indices: 656--1225  Score: 547
    Period size: 172  Copynumber: 3.3  Consensus size: 170

        646 NNCTAGCCTG

                         *   *                            *  *      *        
        656 TTTTAACCAAAAATGTACAAAGAATTCAAATTTAAATCAATTTTGATATCATAAAATCATTTAAA
          1 TTTTAACCAAAAAAGTAAAAAGAATTCAAATTTAAATCAATTTTGAGATTATAAAAACATTTAAA

                                     * *                              *     *
        721 GTGAGC-AATAAGGCTTTTAAAGGACTAGGTGACTATAAATGGACTTTTCTTGCCAATTAATGTT
         66 GTGA-CTAATAAGGCTTTTAAAGGAATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATG-C

                  *    *                *        *     
        785 TTTTTTTTTTACGTTTCT-AGAGGTAGACATTCAATTATAGTT
        129 TTTTTTCTTTATGTTTCTCA-AGGTAGAAATTCAATTCTAGTT

                            *      *    *  *  *         **    *   *    *  *  
        827 TGTTTAA-CAAAAAATATAAAAACAATTTAACTTCAAATCAATTACG-GCGTTACAAAACCACTT
          1 T-TTTAACCAAAAAA-GTAAAAAGAATTCAAATTTAAATCAATTTTGAG-ATTATAAAAACATTT

                *  *                  *    *                      *          
        890 AAAGCGAGTAATAAGGCTTTTAAAGGTATGGATGACTATAAATGGACTTTTCTTACCAATGAATG
         63 AAAGTGACTAATAAGGCTTTTAAAGGAATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATG

                   *  *                     *           
        955 CTTTTTTGTTCATGTTTCTCAAGGTAGAAATTGAATTCTAGTCT
        128 CTTTTTTCTTTATGTTTCTCAAGGTAGAAATTCAATTCTAGT-T

                              *                                        *     
        999 CTTTTAACCAAAAAAGTACAAAGAATTCAAATTTAAATCAATTTTGAGATTATAAAAACTTTTAA
          1 -TTTTAACCAAAAAAGTAAAAAGAATTCAAATTTAAATCAATTTTGAGATTATAAAAACATTTAA

                       *       *  *                                          
       1064 AGTGACTAATAGGGCTTTTGAACGAATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATGCT
         65 AGTGACTAATAAGGCTTTTAAAGGAATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATGCT

            * * *              *      *                *
       1129 CTCTCCTTTATGTTTCTCAGGGTAGAGATTCAATTACAATA-TA
        130 TTTTTCTTTATGTTTCTCAAGGTAGAAATTCAATT-C--TAGTT

                   * *     *     *    *  *  *               *     
       1172 TTTTAACTAGAAAAGCAAAAAAAATTGAACTTAAAATCAATTTTGAGAATATAA
          1 TTTTAACCAAAAAAGTAAAAAGAATTCAAATTTAAATCAATTTTGAGATTATAA


Statistics
Matches: 318,  Mismatches: 69, Indels: 23
        0.78            0.17        0.06

Matches are distributed among these distances:
 171   40  0.13
 172  265  0.83
 173   10  0.03
 174    1  0.00
 175    2  0.01

ACGTcount: A:0.38, C:0.12, G:0.14, T:0.35


Consensus pattern (170 bp):   
TTTTAACCAAAAAAGTAAAAAGAATTCAAATTTAAATCAATTTTGAGATTATAAAAACATTTAAA
GTGACTAATAAGGCTTTTAAAGGAATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATGCTT
TTTTCTTTATGTTTCTCAAGGTAGAAATTCAATTCTAGTT
Done.