Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NW_018402884.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_5934.0, 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: 4534
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.40


Found at i:1284 original size:22 final size:22

Alignment explanation


    Indices: 1259--1305  Score: 67
    Period size: 22  Copynumber: 2.1  Consensus size: 22

       1249 TTTTGGCGAA

                  *           *   
       1259 TTTAAACATTTTTAAATATATT
          1 TTTAAAAATTTTTAAATAAATT

                         *        
       1281 TTTAAAAATTTTTTAATAAATT
          1 TTTAAAAATTTTTAAATAAATT

               
       1303 TTT
          1 TTT

       1306 TTAATGGCTT


Statistics
Matches: 22,  Mismatches: 3, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  22   22  1.00

ACGTcount: A:0.40, C:0.02, G:0.00, T:0.57


Consensus pattern (22 bp):   
TTTAAAAATTTTTAAATAAATT

Found at i:1293 original size:11 final size:11

Alignment explanation


    Indices: 1267--1306  Score: 53
    Period size: 12  Copynumber: 3.5  Consensus size: 11

       1257 AATTTAAACA

                    *  
       1267 TTTTTAAATAT
          1 TTTTTAAAAAT

                        
       1278 ATTTTTAAAAAT
          1 -TTTTTAAAAAT

                        
       1290 TTTTTAATAAAT
          1 TTTTTAA-AAAT

                 
       1302 TTTTT
          1 TTTTT

       1307 TAATGGCTTT


Statistics
Matches: 26,  Mismatches: 1, Indels: 2
        0.90            0.03        0.07

Matches are distributed among these distances:
  11    7  0.27
  12   19  0.73

ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62


Consensus pattern (11 bp):   
TTTTTAAAAAT

Found at i:1310 original size:13 final size:12

Alignment explanation


    Indices: 1266--1306  Score: 50
    Period size: 11  Copynumber: 3.6  Consensus size: 12

       1256 GAATTTAAAC

                  *    *
       1266 ATTTTTAAATAT
          1 ATTTTTTAATAA

                        
       1278 A-TTTTTAA-AA
          1 ATTTTTTAATAA

                        
       1288 ATTTTTTAATAA
          1 ATTTTTTAATAA

                   
       1300 ATTTTTT
          1 ATTTTTT

       1307 TAATGGCTTT


Statistics
Matches: 25,  Mismatches: 2, Indels: 4
        0.81            0.06        0.13

Matches are distributed among these distances:
  10    2  0.08
  11   13  0.52
  12   10  0.40

ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61


Consensus pattern (12 bp):   
ATTTTTTAATAA

Found at i:4350 original size:14 final size:14

Alignment explanation


    Indices: 4331--4361  Score: 62
    Period size: 14  Copynumber: 2.2  Consensus size: 14

       4321 TTTGCTTCGG

                          
       4331 TAGGAGTAAGATCT
          1 TAGGAGTAAGATCT

                          
       4345 TAGGAGTAAGATCT
          1 TAGGAGTAAGATCT

               
       4359 TAG
          1 TAG

       4362 TAAATTGATG


Statistics
Matches: 17,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  14   17  1.00

ACGTcount: A:0.35, C:0.06, G:0.29, T:0.29


Consensus pattern (14 bp):   
TAGGAGTAAGATCT
Done.