Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NW_018398902.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_2183.0, 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: 3542
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.27

Warning! 291 characters in sequence are not A, C, G, or T


Found at i:1004 original size:228 final size:228

Alignment explanation


    Indices: 399--1015  Score: 714
    Period size: 228  Copynumber: 2.7  Consensus size: 228

        389 ACTATTACCT

                *        *     *  *                 *                 *      
        399 TGGAAGTTGAGAGTTCTGATACCATTGACAATGTAAAAGCTAAGATCCAGGACAAGGAAGGTATC
          1 TGGAGGTTGAGAGCTCTGACACAATTGACAATGTAAAAGCAAAGATCCAGGACAAGGAGGGTATC

                    *         *                *                             
        464 CCTCCAGATCAACAGAGGCTGATATTTGCTGGCAAACAGTTGGAGGATGGGAGGACACTTGCAGA
         66 CCTCCAGACCAACAGAGGTTGATATTTGCTGGCAAGCAGTTGGAGGATGGGAGGACACTTGCAGA

            *              *           *  *           *   * *              * 
        529 TTACAATATCCAAAAAGAGTCAACCCTCCACTTGGTGCTGCGTCTGCGTGGAGGAATGCAGATTT
        131 CTACAATATCCAAAAGGAGTCAACCCTGCATTTGGTGCTGCGCCTGAGAGGAGGAATGCAGATAT

                *              *        *  **
        594 TTGTGAAGACCTTGACTGGTAAAACCATTACTT
        196 TTGTCAAGACCTTGACTGGGAAAACCATCACCC

                   *                       *  *     *        *  *            
        627 TGGAGGTGGAGAGCTCTGACACAATTGACAACGTCAAAGCCAAGATCCAAGATAAGGAGGGTATC
          1 TGGAGGTTGAGAGCTCTGACACAATTGACAATGTAAAAGCAAAGATCCAGGACAAGGAGGGTATC

              *  *        *        *        *            *                   
        692 CCACCTGACCAACAAAGGTTGATTTTTGCTGGGAAGCAGCTT-GAAGATGGGAGGACACTTGCAG
         66 CCTCCAGACCAACAGAGGTTGATATTTGCTGGCAAGCAG-TTGGAGGATGGGAGGACACTTGCAG

                *  *                             **       *        *         
        756 ACTATAACATCCAAAAGGAGTCAACCCTGCATTTGGTTTTGCGCCTTAGAGGAGGGATGCAGATA
        130 ACTACAATATCCAAAAGGAGTCAACCCTGCATTTGGTGCTGCGCCTGAGAGGAGGAATGCAGATA

                                              
        821 TTTGTCAAGACCTTGACTGGGAAAACCATCACCC
        195 TTTGTCAAGACCTTGACTGGGAAAACCATCACCC

                            *     *           *           *              *  *
        855 TGGAGGTTGAGAGCTCAGACACGATTGACAATGTGAAAGCAAAGATTCAGGACAAGGAGGGGATT
          1 TGGAGGTTGAGAGCTCTGACACAATTGACAATGTAAAAGCAAAGATCCAGGACAAGGAGGGTATC

                       *           *                          ** *  *  *  *  
        920 CCTCCAGACCAGCAGAGGTTGATCTTTGCTGGCAAGCAGTTGGAGGATGGTCGCACTCTGGCTGA
         66 CCTCCAGACCAACAGAGGTTGATATTTGCTGGCAAGCAGTTGGAGGATGGGAGGACACTTGCAGA

                        *        *         
        985 CTACAATATCCAGAAGGAGTCCACCCTGCAT
        131 CTACAATATCCAAAAGGAGTCAACCCTGCAT

       1016 CTTGTCCTTC


Statistics
Matches: 320,  Mismatches: 67, Indels: 4
        0.82            0.17        0.01

Matches are distributed among these distances:
 227    2  0.01
 228  316  0.99
 229    2  0.01

ACGTcount: A:0.30, C:0.20, G:0.27, T:0.22


Consensus pattern (228 bp):   
TGGAGGTTGAGAGCTCTGACACAATTGACAATGTAAAAGCAAAGATCCAGGACAAGGAGGGTATC
CCTCCAGACCAACAGAGGTTGATATTTGCTGGCAAGCAGTTGGAGGATGGGAGGACACTTGCAGA
CTACAATATCCAAAAGGAGTCAACCCTGCATTTGGTGCTGCGCCTGAGAGGAGGAATGCAGATAT
TTGTCAAGACCTTGACTGGGAAAACCATCACCC

Found at i:3070 original size:19 final size:19

Alignment explanation


    Indices: 3034--3072  Score: 51
    Period size: 19  Copynumber: 2.1  Consensus size: 19

       3024 ATATAGTAAA

                       *       
       3034 ATTTCATAAATTTACAAAG
          1 ATTTCATAAATGTACAAAG

                *        *     
       3053 ATTTTATAAATGTGCAAAG
          1 ATTTCATAAATGTACAAAG

             
       3072 A
          1 A

       3073 CTATATCAAA


Statistics
Matches: 17,  Mismatches: 3, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  19   17  1.00

ACGTcount: A:0.46, C:0.08, G:0.10, T:0.36


Consensus pattern (19 bp):   
ATTTCATAAATGTACAAAG
Done.