Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NW_018399944.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_3173.0, 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: 2252
ACGTcount: A:0.28, C:0.10, G:0.08, T:0.29

Warning! 570 characters in sequence are not A, C, G, or T


Found at i:386 original size:170 final size:160

Alignment explanation


    Indices: 193--508  Score: 298
    Period size: 170  Copynumber: 1.9  Consensus size: 160

        183 NNNNNNNNNC

                           *          **      *            *                *
        193 ATAATTCATTTTAAGTTGAATTTTTTGTATTTTTTATTAAAACAGACTATAATCT-AATGCCTAG
          1 ATAATTCATTTTAAGCTGAATTTTTTACATTTTTGATTAAAACAGACAATAAT-TGAATGCCTAC

              **      * **                                                  *
        257 CTTGAGAAACGTGCAAAAAAAG-CTATTAATTGAG-AAGAAAAGTCCATTTATAACCACCC-ATT
         65 CTCAAGAAACATAAAAAAAAAGACT-TTAATTG-GTAAGAAAAGTCCATTTATAACCACCCAATC

                                                        
        319 CTTTCAAAAGCCTTATTACTCGTTTNNNNNNNNNNTATAATCTT
        128 CTTT-AAAAGCCTTATTACTCGTTT----------TATAATCTT

                  *                            *                   *   **    
        363 ATAATTGATTTTAAGCTGAATTTTTTACATTTTTGGTTAAAACAGACAATAATTGCATGTTTACC
          1 ATAATTCATTTTAAGCTGAATTTTTTACATTTTTGATTAAAACAGACAATAATTGAATGCCTACC

                                      *                        **            
        428 TCAAGAAACATAAAAAAAAAGACTTTCATTGGTAAGAAAAGTCCATTTATAGTCACCCAATCCTT
         66 TCAAGAAACATAAAAAAAAAGACTTTAATTGGTAAGAAAAGTCCATTTATAACCACCCAATCCTT

                            
        493 TAAAAGCCTTATTACT
        131 TAAAAGCCTTATTACT

        509 NNNNNNNNNN


Statistics
Matches: 122,  Mismatches: 20, Indels: 8
        0.81            0.13        0.05

Matches are distributed among these distances:
 169    2  0.02
 170  112  0.92
 171    8  0.07

ACGTcount: A:0.36, C:0.15, G:0.10, T:0.35


Consensus pattern (160 bp):   
ATAATTCATTTTAAGCTGAATTTTTTACATTTTTGATTAAAACAGACAATAATTGAATGCCTACC
TCAAGAAACATAAAAAAAAAGACTTTAATTGGTAAGAAAAGTCCATTTATAACCACCCAATCCTT
TAAAAGCCTTATTACTCGTTTTATAATCTT

Found at i:789 original size:40 final size:38

Alignment explanation


    Indices: 718--804  Score: 122
    Period size: 40  Copynumber: 2.3  Consensus size: 38

        708 TGATTTTAAT

                     *            *               
        718 TTGAA-TTTGTTTTAATTTTTGTTAAAACAGACTATAA
          1 TTGAATTTTTTTTTAATTTTTGCTAAAACAGACTATAA

                *                                   
        755 TTGATTTTTTTTTTACATTTTTGACTAAAACAGACTATAA
          1 TTGAATTTTTTTTTA-ATTTTTG-CTAAAACAGACTATAA

                      
        795 TTGAATTTTT
          1 TTGAATTTTT

        805 ACTTGGAGAA


Statistics
Matches: 43,  Mismatches: 4, Indels: 3
        0.86            0.08        0.06

Matches are distributed among these distances:
  37    4  0.09
  38    8  0.19
  39    7  0.16
  40   24  0.56

ACGTcount: A:0.32, C:0.07, G:0.09, T:0.52


Consensus pattern (38 bp):   
TTGAATTTTTTTTTAATTTTTGCTAAAACAGACTATAA
Done.