Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NW_018399244.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_2513.0, 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: 2768
ACGTcount: A:0.33, C:0.10, G:0.12, T:0.32

Warning! 376 characters in sequence are not A, C, G, or T


Found at i:528 original size:172 final size:171

Alignment explanation


    Indices: 343--665  Score: 389
    Period size: 172  Copynumber: 1.9  Consensus size: 171

        333 TGGATAACTA

                 *            *                   *        *  *  **        * 
        343 TAAATGGACTTTTCTTACTAATGAATGTCTATTT-CTTTATATTTCTTGATATCGACATTCAATT
          1 TAAATCGACTTTTCTTACCAATGAATG-CTATTTGCTTCATATTTCTCGAGATAAACATTCAACT

                          *        *          *          *                 **
        407 ATAATCTATTTTAAGCAAAAATATAAAAAAAATTGAACATAAAATTAATTTTGAGATAATAAAGT
         65 ATAATCTATTTTAAACAAAAATACAAAAAAAATTAAACAT-AAATCAATTTTGAGATAATAAAAC

                                                        
        472 CATTTAAAG-TGAGTAATAAGGCTCTTAAAGGAATGGGAGATTC
        129 CATTTAAAGAT-AGTAATAAGGCTCTTAAAGGAATGGGAGATTC

                            *            *          *         *              
        515 TAAATCGACTTTTCTTGCCAATGAATGCTTTTTGCTTCATGTTTCTCGAGGTAAACATTCAACTA
          1 TAAATCGACTTTTCTTACCAATGAATGCTATTTGCTTCATATTTCTCGAGATAAACATTCAACTA

              *   *       *  *   *       *                                   
        580 TAGTCTGTTTTAAATAAGAATGCAAAAAACATTAAACATAAATCAATTTTGAGATAATAAAACCA
         66 TAATCTATTTTAAACAAAAATACAAAAAAAATTAAACATAAATCAATTTTGAGATAATAAAACCA

                                 
        645 TTTAAAGATAGTAATAAGGCT
        131 TTTAAAGATAGTAATAAGGCT

        666 TTTGGAGGAA


Statistics
Matches: 125,  Mismatches: 24, Indels: 5
        0.81            0.16        0.03

Matches are distributed among these distances:
 171   47  0.38
 172   78  0.62

ACGTcount: A:0.40, C:0.11, G:0.13, T:0.36


Consensus pattern (171 bp):   
TAAATCGACTTTTCTTACCAATGAATGCTATTTGCTTCATATTTCTCGAGATAAACATTCAACTA
TAATCTATTTTAAACAAAAATACAAAAAAAATTAAACATAAATCAATTTTGAGATAATAAAACCA
TTTAAAGATAGTAATAAGGCTCTTAAAGGAATGGGAGATTC

Found at i:1093 original size:170 final size:169

Alignment explanation


    Indices: 738--1120  Score: 380
    Period size: 170  Copynumber: 2.2  Consensus size: 169

        728 TTCTCAAGGT

                     *                                   * *       *         
        738 AGACATTTAGTTATAGTTTGTTTTAACAAAAAATGTAAAAAAAATCATCTTAAAATCAATTATGA
          1 AGACATTTAATTATAGTTTGTTTTAACAAAAAATGT-AAAAAAATAAACTTAAAAGCAATTATGA

                                  *                                          
        803 GATTATAAAACCATTAAACATGTGTAACAAGATTTTTGAAGGAATGAAAGACTATAAATGGACTT
         65 GATTATAAAACCATTAAACA-GAGTAACAAGATTTTTGAAGGAATGAAAGACTATAAATGGACTT

                       *          *   *              
        868 TTATTCTCAATTAATGCCTTTTTCTATATGTTTCTATAGGC
        129 TTATTCTCAATGAATGCCTTTTCCTACATGTTTCTATAGGC

              *    *                   *              *                      
        909 AGGCATTCAATTATAGTTTGTTTTAACGAAAAATGTAAAAAATTAAACTTAAAAGCAATTATGAG
          1 AGACATTTAATTATAGTTTGTTTTAACAAAAAATGTAAAAAAATAAACTTAAAAGCAATTATGAG

                                     **********             **               
        974 ATTATAAAACCATTTAAAGC-GAGTNNNNNNNNNNTTGAAGGAAT-AGGTGACTATAAATGGACT
         66 ATTATAAAACCA-TTAAA-CAGAGTAACAAGATTTTTGAAGGAATGA-AAGACTATAAATGGACT

               *  *                                  ** 
       1037 TTTCTTGTCAATGAATGCCCTTTTCCT-CATGTTTCT-TGATTC
        128 TTTATTCTCAATGAATG-CCTTTTCCTACATGTTTCTAT-AGGC

                           * * *                       
       1079 AGACATTTAATTATAATATCTTTTAACCAAAAAA-GTAAAAAA
          1 AGACATTTAATTATAGTTTGTTTTAA-CAAAAAATGTAAAAAA

       1121 NNNNNNNNNN


Statistics
Matches: 172,  Mismatches: 34, Indels: 13
        0.79            0.16        0.06

Matches are distributed among these distances:
 169    2  0.01
 170  118  0.69
 171   51  0.30
 172    1  0.01

ACGTcount: A:0.39, C:0.11, G:0.13, T:0.35


Consensus pattern (169 bp):   
AGACATTTAATTATAGTTTGTTTTAACAAAAAATGTAAAAAAATAAACTTAAAAGCAATTATGAG
ATTATAAAACCATTAAACAGAGTAACAAGATTTTTGAAGGAATGAAAGACTATAAATGGACTTTT
ATTCTCAATGAATGCCTTTTCCTACATGTTTCTATAGGC
Done.