Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NW_018400873.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_4040.0, 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, 640

Length: 1068
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.39


Found at i:103 original size:15 final size:16

Alignment explanation


    Indices: 83--116  Score: 52
    Period size: 16  Copynumber: 2.2  Consensus size: 16

         73 GTTTTAATAA

                            
         83 TAAATTATT-AAATTT
          1 TAAATTATTAAAATTT

                  *         
         98 TAAATTTTTAAAATTT
          1 TAAATTATTAAAATTT

               
        114 TAA
          1 TAA

        117 TGAAAATAAA


Statistics
Matches: 17,  Mismatches: 1, Indels: 1
        0.89            0.05        0.05

Matches are distributed among these distances:
  15    8  0.47
  16    9  0.53

ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53


Consensus pattern (16 bp):   
TAAATTATTAAAATTT

Found at i:357 original size:22 final size:20

Alignment explanation


    Indices: 316--368  Score: 72
    Period size: 22  Copynumber: 2.6  Consensus size: 20

        306 TTAAGCATAA

                                
        316 TAATA-TTAAATTAAAATAT
          1 TAATATTTAAATTAAAATAT

                              *   
        335 TAATATTTAAATTATTAATTAT
          1 TAATATTTAAATTA--AAATAT

                        
        357 TAATATTTAAAT
          1 TAATATTTAAAT

        369 AGTAAAATAA


Statistics
Matches: 30,  Mismatches: 1, Indels: 3
        0.88            0.03        0.09

Matches are distributed among these distances:
  19    5  0.17
  20    8  0.27
  22   17  0.57

ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49


Consensus pattern (20 bp):   
TAATATTTAAATTAAAATAT

Found at i:359 original size:15 final size:14

Alignment explanation


    Indices: 317--377  Score: 54
    Period size: 15  Copynumber: 4.3  Consensus size: 14

        307 TAAGCATAAT

                          
        317 AATATTAA-ATTAA
          1 AATATTAATATTAA

                           
        330 AATATTAATATTTAA
          1 AATATTAATA-TTAA

             *             
        345 ATTATTAATTATTAA
          1 AATATTAA-TATTAA

            *          *   
        360 TAT-TTAAATAGTAA
          1 AATATT-AATATTAA

                
        374 AATA
          1 AATA

        378 AAAATAAATA


Statistics
Matches: 38,  Mismatches: 5, Indels: 8
        0.75            0.10        0.16

Matches are distributed among these distances:
  13    8  0.21
  14   10  0.26
  15   18  0.47
  16    2  0.05

ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44


Consensus pattern (14 bp):   
AATATTAATATTAA
Done.