Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NW_018401919.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_5020.0, 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, 646

Length: 1077
ACGTcount: A:0.36, C:0.11, G:0.15, T:0.34

Warning! 50 characters in sequence are not A, C, G, or T


Found at i:526 original size:170 final size:161

Alignment explanation


    Indices: 222--561  Score: 344
    Period size: 170  Copynumber: 2.1  Consensus size: 161

        212 AAAAATCTAA

                                 *          *                 *      *       
        222 AAAAAT-TAACTTAAAATCAATTTTGAGATTGTAAAACCATTTAAAGCGAGGAATAAGGCTTTTG
          1 AAAAATGTAACTTAAAATCAAATTTGAGATTGCAAAACCATTTAAAGCGAAGAATAAAGCTTTTG

                   **   *     *                   *   *                      
        286 AAGGAATGGGTGGCTATACATGAACTTTTCTTGTCAATGAATGCCTTTTTCTTTACGTGTCACAA
         66 AAGGAATAAGTGACTATAAATGAACTTTTCTTGTCAATAAATACCTTTTTCTTTACGTGTCACAA

                           *    *          
        351 GGTAGACATTCAATTGTAATCTATTTTAACC
        131 GGTAGACATTCAATTATAATATATTTTAACC

                                                            *     *  *   *   
        382 AAAAATGTANNNNNNNNNNACTTAAAATCAAATTTGAGATTGCAAAACTATTTATAGTGAATAAT
          1 AAAAATGTA----------ACTTAAAATCAAATTTGAGATTGCAAAACCATTTAAAGCGAAGAAT

                                            *                     *          
        447 AAAGCTTTTGAAGGAATAAGTGACTATAAATGGA-TTTTCTT-TCCAATAAATATCTTTTTCTTT
         56 AAAGCTTTTGAAGGAATAAGTGACTATAAATGAACTTTTCTTGT-CAATAAATACCTTTTTCTTT

                *  ***                       *        
        510 ACGTTTCTTGAGGTAGACATTCAATTATAATATTTTTTAACC
        120 ACGTGTCACAAGGTAGACATTCAATTATAATATATTTTAACC

              *       
        552 AATAATGTAA
          1 AAAAATGTAA

        562 AAAAATTAAA


Statistics
Matches: 144,  Mismatches: 24, Indels: 24
        0.75            0.12        0.12

Matches are distributed among these distances:
 160    7  0.05
 161    2  0.01
 169    1  0.01
 170   67  0.47
 171   67  0.47

ACGTcount: A:0.36, C:0.11, G:0.14, T:0.36


Consensus pattern (161 bp):   
AAAAATGTAACTTAAAATCAAATTTGAGATTGCAAAACCATTTAAAGCGAAGAATAAAGCTTTTG
AAGGAATAAGTGACTATAAATGAACTTTTCTTGTCAATAAATACCTTTTTCTTTACGTGTCACAA
GGTAGACATTCAATTATAATATATTTTAACC

Found at i:971 original size:22 final size:23

Alignment explanation


    Indices: 935--981  Score: 60
    Period size: 22  Copynumber: 2.0  Consensus size: 23

        925 AATTTTGAGA

                                   
        935 TAATAAAGCCATTGAA-AATGGG
          1 TAATAAAGCCATTGAAGAATGGG

                     **             
        957 TAATAAAGCTTTTGAAGGAATGGG
          1 TAATAAAGCCATTGAA-GAATGGG

             
        981 T
          1 T

        982 GACCATAAAT


Statistics
Matches: 21,  Mismatches: 2, Indels: 2
        0.84            0.08        0.08

Matches are distributed among these distances:
  22   14  0.67
  24    7  0.33

ACGTcount: A:0.40, C:0.06, G:0.26, T:0.28


Consensus pattern (23 bp):   
TAATAAAGCCATTGAAGAATGGG
Done.