Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NW_018398125.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_1428.0, 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: 3334
ACGTcount: A:0.33, C:0.17, G:0.09, T:0.38

Warning! 100 characters in sequence are not A, C, G, or T


Found at i:271 original size:41 final size:41

Alignment explanation


    Indices: 226--317  Score: 116
    Period size: 41  Copynumber: 2.2  Consensus size: 41

        216 ATTAAAATTG

                         *                             
        226 TTAATATTTTAATCATAATAAAT-TTAAATTATAAAT-AAATA
          1 TTAATATTTTAA-AAT-ATAAATATTAAATTATAAATAAAATA

                             *              *         
        267 TTAATATTTTAAAATATTAATGATTAAATTATGAATAAAATA
          1 TTAATATTTTAAAATATAAAT-ATTAAATTATAAATAAAATA

                     
        309 TTAATATTT
          1 TTAATATTT

        318 AAATGATCAA


Statistics
Matches: 45,  Mismatches: 3, Indels: 5
        0.85            0.06        0.09

Matches are distributed among these distances:
  39    5  0.11
  40    2  0.04
  41   24  0.53
  42   14  0.31

ACGTcount: A:0.51, C:0.01, G:0.02, T:0.46


Consensus pattern (41 bp):   
TTAATATTTTAAAATATAAATATTAAATTATAAATAAAATA

Found at i:293 original size:15 final size:15

Alignment explanation


    Indices: 262--334  Score: 50
    Period size: 16  Copynumber: 5.1  Consensus size: 15

        252 AATTATAAAT

                             
        262 AAATATTAAT-ATTTTA
          1 AAATATTAATGA--TTA

                           
        278 AAATATTAATGATT-
          1 AAATATTAATGATTA

                        *  
        292 -AA-ATT-ATGAATA
          1 AAATATTAATGATTA

                          *
        304 AAATATTAAT-ATTT
          1 AAATATTAATGATTA

                   *        
        318 AAATGATCAATGATTA
          1 AAAT-ATTAATGATTA

             
        334 A
          1 A

        335 CGTTTTAAAT


Statistics
Matches: 45,  Mismatches: 5, Indels: 14
        0.70            0.08        0.22

Matches are distributed among these distances:
  11    5  0.11
  12    3  0.07
  13    4  0.09
  14    9  0.20
  15    9  0.20
  16   14  0.31
  17    1  0.02

ACGTcount: A:0.52, C:0.01, G:0.05, T:0.41


Consensus pattern (15 bp):   
AAATATTAATGATTA

Found at i:319 original size:41 final size:41

Alignment explanation


    Indices: 249--334  Score: 122
    Period size: 41  Copynumber: 2.1  Consensus size: 41

        239 CATAATAAAT

                                                *     
        249 TTAAATTATAAATAAATATTAATATTTTAAAAT-ATTAATGA
          1 TTAAATTATAAATAAATATTAATATTTT-AAATGATCAATGA

                     *                                
        290 TTAAATTATGAATAAAATATTAATA-TTTAAATGATCAATGA
          1 TTAAATTATAAAT-AAATATTAATATTTTAAATGATCAATGA

                
        331 TTAA
          1 TTAA

        335 CGTTTTAAAT


Statistics
Matches: 41,  Mismatches: 2, Indels: 4
        0.87            0.04        0.09

Matches are distributed among these distances:
  40    4  0.10
  41   26  0.63
  42   11  0.27

ACGTcount: A:0.52, C:0.01, G:0.05, T:0.42


Consensus pattern (41 bp):   
TTAAATTATAAATAAATATTAATATTTTAAATGATCAATGA
Done.