Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NW_018402003.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_5099.0, 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: 2358
ACGTcount: A:0.29, C:0.09, G:0.11, T:0.29

Warning! 512 characters in sequence are not A, C, G, or T


Found at i:571 original size:171 final size:170

Alignment explanation


    Indices: 1--645  Score: 564
    Period size: 172  Copynumber: 3.8  Consensus size: 170

                   *         *                   * *  *             *  *     
          1 TATAAAAATATTTAAAGTGAGTAATAAGGCTTTTGAAGGAATAGGTGACTATAAATAGAGTTTTC
          1 TATAAAACTATTTAAAGCGAGTAATAAGGCTTTTGAAAGTATGGGTGACTATAAATGGACTTTTC

              *         *       *   * *                                      
         66 TTACCAATGAATGCCTTTTTGTTTTCGTTTCTTGAGGTAGACATTCAATTATAGTC-GATTTTAA
         66 TTGCCAATGAATACCTTTTTCTTTACATTTCTTGAGGTAGACATTCAATTATAGTCTG-TTTTAA

                     **                   **          
        130 CTAAAAATGTGAAAAAATTCAACCTAAAATTGATTATGGTAT
        130 CTAAAAATGAAAAAAAATTCAA-CTAAAATCAATTATGGTAT

                   *                                        *          * *   
        172 TATAAAATTATTTAAAGCGAGTAATAAGGCTTTTTG-AAGATATGGGTAACTATAAATGAAATTT
          1 TATAAAACTATTTAAAGCGAGTAATAAGGC-TTTTGAAAG-TATGGGTGACTATAAATGGACTTT

                      *   * *     *  * **                           * *      
        236 TCTTGCCAATAAATGCATTTTTATTCATTTTTCTTGAGGTTA-ACATTCAATTATAATATGTTTT
         64 TCTTGCCAATGAATACCTTTTTCTTTACATTTCTTGAGG-TAGACATTCAATTATAGTCTGTTTT

               *       * *            * *         *       
        300 AACAAAAAATTTACAAAAAATTCAATTTTAAATCAATTTTGAG-AT
        128 AACTAAAAA-TGAAAAAAAATTCAA-CTAAAATCAATTATG-GTAT

                    *       **     *             * *     *  *           *    
        345 TATAAAACCATTTAAATTGAGTATTAAGGCTTTTGAACGAATGGGCGAGTATAAATGGACCTTTC
          1 TATAAAACTATTTAAAGCGAGTAATAAGGCTTTTGAAAGTATGGGTGACTATAAATGGACTTTTC

                *                                        *   *    *        * 
        410 TTGCTAATGAATACCTTTTTCTTTACATTTCTTGAGGTAGACATTTAATAATAGCCTGTTTT-TC
         66 TTGCCAATGAATACCTTTTTCTTTACATTTCTTGAGGTAGACATTCAATTATAGTCTGTTTTAAC

                                                     *
        474 TCAAAAATGAAAAAAAATTCAACTAAAAATCAATTATGGTAA
        131 T-AAAAATGAAAAAAAATTCAACT-AAAATCAATTATGGTAT

                       *      *      **      *                              *
        516 TATAAAACTATGTAAAGCAAGTAATGGGGCTTTCGAAAGTATGGGTGACTATAAATGGACTTTTT
          1 TATAAAACTATTTAAAGCGAGTAATAAGGCTTTTGAAAGTATGGGTGACTATAAATGGACTTTTC

               *                    * **     **    *    *      *             
        581 TTGTCAATGAATA-CTTTTCTCTTCATGTTTCTCAAGGTGGACAATCAATTCTAGTCTGTTTTAA
         66 TTGCCAATGAATACCTTTT-TCTTTACATTTCTTGAGGTAGACATTCAATTATAGTCTGTTTTAA

             
        645 C
        130 C

        646 CNNNNNNNNN


Statistics
Matches: 369,  Mismatches: 92, Indels: 25
        0.76            0.19        0.05

Matches are distributed among these distances:
 170    7  0.02
 171  151  0.41
 172  156  0.42
 173   54  0.15
 174    1  0.00

ACGTcount: A:0.36, C:0.11, G:0.15, T:0.38


Consensus pattern (170 bp):   
TATAAAACTATTTAAAGCGAGTAATAAGGCTTTTGAAAGTATGGGTGACTATAAATGGACTTTTC
TTGCCAATGAATACCTTTTTCTTTACATTTCTTGAGGTAGACATTCAATTATAGTCTGTTTTAAC
TAAAAATGAAAAAAAATTCAACTAAAATCAATTATGGTAT

Found at i:1397 original size:172 final size:173

Alignment explanation


    Indices: 1006--1397  Score: 380
    Period size: 172  Copynumber: 2.3  Consensus size: 173

        996 TGTTTAAATG

                  *           *                   **                  **     
       1006 AAAAATGTACAAAGAATTAAAATTTAAATCAATTTTGATTTTATAAAACCATTTAAAGTGAGTAA
          1 AAAAATATACAAAGAATTCAAATTTAAATCAATTTTGAGATTATAAAACCATTTAAAGCAAGTAA

                                                       * *   *           *   
       1071 CAAGGCTTTTGAAGGAATGGGTGACAATAAATGGACTTTTCTTGCTAATGAATACTCTTTTTCTT
         66 CAAGGCTTTTGAAGGAATGGGTGACAATAAATGGACTTTTCTTACCAATAAATACTCTTTTCCTT

            *        ** *       *       *          *   
       1136 TACATTTCTTTAGGTAGACATTCAATTATAGTCTAATTTTCTC
        131 CACATTTCTCAACGTAGACAATCAATTAGAGTCTAATTTACTC

                  *      *  *    * **        **      *                       
       1179 AAAAATGTA-AAAAAAATCAACTAAAAATCAATAATG-GCAATATAAAACCATTTAAAGCAAGTA
          1 AAAAATATACAAAGAATTCAAATTTAAATCAATTTTGAG-ATTATAAAACCATTTAAAGCAAGTA

             **   *         *       * *                                      
       1242 ATGAGGGTTTTGAAGGTATGGGTGGCTATAAATGGACTTTTCTTACCAATAAATACT-TTTTCCT
         65 ACAAGGCTTTTGAAGGAATGGGTGACAATAAATGGACTTTTCTTACCAATAAATACTCTTTTCCT

               **           *           *       *         
       1306 TCATGTTTCTCAACGTGGACAATCAATTCGAGTCT-GTCTTAAC-C
        130 TCACATTTCTCAACGTAGACAATCAATTAGAGTCTAAT-TT-ACTC

                *                                           
       1350 AAAACTATACAAAGAATTCAAATTTAAATCAATTTTGAGATTATAAAA
          1 AAAAATATACAAAGAATTCAAATTTAAATCAATTTTGAGATTATAAAA

       1398 NNNNNNNNNN


Statistics
Matches: 169,  Mismatches: 45, Indels: 11
        0.75            0.20        0.05

Matches are distributed among these distances:
 170    1  0.01
 171   41  0.24
 172  117  0.69
 173   10  0.06

ACGTcount: A:0.40, C:0.13, G:0.13, T:0.34


Consensus pattern (173 bp):   
AAAAATATACAAAGAATTCAAATTTAAATCAATTTTGAGATTATAAAACCATTTAAAGCAAGTAA
CAAGGCTTTTGAAGGAATGGGTGACAATAAATGGACTTTTCTTACCAATAAATACTCTTTTCCTT
CACATTTCTCAACGTAGACAATCAATTAGAGTCTAATTTACTC
Done.