Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NW_018399632.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_2881.0, 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, 853

Length: 1422
ACGTcount: A:0.41, C:0.10, G:0.09, T:0.40


Found at i:171 original size:16 final size:17

Alignment explanation


    Indices: 139--172  Score: 52
    Period size: 17  Copynumber: 2.1  Consensus size: 17

        129 AAATTAAAAT

                        *    
        139 AAAATATTAATATTTTA
          1 AAAATATTAATAGTTTA

                             
        156 AAAATATTAAT-GTTTA
          1 AAAATATTAATAGTTTA

             
        172 A
          1 A

        173 CTTATTTAAC


Statistics
Matches: 16,  Mismatches: 1, Indels: 1
        0.89            0.06        0.06

Matches are distributed among these distances:
  16    5  0.31
  17   11  0.69

ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44


Consensus pattern (17 bp):   
AAAATATTAATAGTTTA

Found at i:494 original size:17 final size:16

Alignment explanation


    Indices: 448--520  Score: 51
    Period size: 15  Copynumber: 4.4  Consensus size: 16

        438 GTTATGAAAA

                            
        448 ATTAATATTTTAAATT
          1 ATTAATATTTTAAATT

              *  *             
        464 -TGAAAATTAATTAAAATT
          1 ATTAATATT--TT-AAATT

                           * 
        482 ATTAATATTTTAAACAT
          1 ATTAATATTTTAAA-TT

             *              
        499 AATAATA-TTTAAATT
          1 ATTAATATTTTAAATT

              *    
        514 ATAAATA
          1 ATTAATA

        521 CAATATTAGT


Statistics
Matches: 43,  Mismatches: 9, Indels: 11
        0.68            0.14        0.17

Matches are distributed among these distances:
  15   12  0.28
  16    9  0.21
  17   11  0.26
  18    5  0.12
  19    6  0.14

ACGTcount: A:0.52, C:0.01, G:0.01, T:0.45


Consensus pattern (16 bp):   
ATTAATATTTTAAATT

Found at i:586 original size:16 final size:16

Alignment explanation


    Indices: 561--594  Score: 50
    Period size: 16  Copynumber: 2.1  Consensus size: 16

        551 AATTTTAAAT

                            
        561 AAAATATTAATATGTA
          1 AAAATATTAATATGTA

                 *       *  
        577 AAAATGTTAATATTTA
          1 AAAATATTAATATGTA

              
        593 AA
          1 AA

        595 TTATTTATTA


Statistics
Matches: 16,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  16   16  1.00

ACGTcount: A:0.56, C:0.00, G:0.06, T:0.38


Consensus pattern (16 bp):   
AAAATATTAATATGTA

Found at i:1225 original size:15 final size:16

Alignment explanation


    Indices: 1216--1259  Score: 54
    Period size: 15  Copynumber: 2.8  Consensus size: 16

       1206 TGTGATTAGC

                             
       1216 AGGTATGTGAATTGCCA
          1 AGGTATGTG-ATTGCCA

                            
       1233 AGGTATGTGATTG-CA
          1 AGGTATGTGATTGCCA

              **        
       1248 AGCAATGTGATT
          1 AGGTATGTGATT

       1260 ACAGGAAAAT


Statistics
Matches: 25,  Mismatches: 2, Indels: 2
        0.86            0.07        0.07

Matches are distributed among these distances:
  15   12  0.48
  16    4  0.16
  17    9  0.36

ACGTcount: A:0.30, C:0.09, G:0.30, T:0.32


Consensus pattern (16 bp):   
AGGTATGTGATTGCCA
Done.