Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NW_018399316.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_2584.0, 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: 5600
ACGTcount: A:0.34, C:0.14, G:0.14, T:0.34

Warning! 200 characters in sequence are not A, C, G, or T


Found at i:2558 original size:28 final size:29

Alignment explanation


    Indices: 2494--2560  Score: 93
    Period size: 28  Copynumber: 2.3  Consensus size: 29

       2484 TTAATATAAA

                                   *     
       2494 AAAATTTATTTAAATATAAATTATAAAAT
          1 AAAATTTATTTAAATATAAATTAAAAAAT

                                          
       2523 AAGAATTTATTTAAATAT-AA-TAAAAAAT
          1 AA-AATTTATTTAAATATAAATTAAAAAAT

                      
       2551 ATAAATTTAT
          1 A-AAATTTAT

       2561 GTTTTCAAAA


Statistics
Matches: 35,  Mismatches: 1, Indels: 5
        0.85            0.02        0.12

Matches are distributed among these distances:
  28   15  0.43
  29    5  0.14
  30   15  0.43

ACGTcount: A:0.58, C:0.00, G:0.01, T:0.40


Consensus pattern (29 bp):   
AAAATTTATTTAAATATAAATTAAAAAAT

Found at i:3527 original size:2 final size:2

Alignment explanation


    Indices: 3520--3547  Score: 56
    Period size: 2  Copynumber: 14.0  Consensus size: 2

       3510 CTATCTGTGG

                                                     
       3520 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT

       3548 TTTTTTTTTT


Statistics
Matches: 26,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   26  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
AT

Found at i:3662 original size:20 final size:21

Alignment explanation


    Indices: 3625--3669  Score: 56
    Period size: 21  Copynumber: 2.2  Consensus size: 21

       3615 TCAAAATTTT

                      **         
       3625 TAAAATTTTTTCTATTTTATA
          1 TAAAATTTTTAATATTTTATA

                              *  
       3646 TAAAATTTTTAAT-TTTTTTA
          1 TAAAATTTTTAATATTTTATA

                
       3666 TAAA
          1 TAAA

       3670 TTATTTTATT


Statistics
Matches: 21,  Mismatches: 3, Indels: 1
        0.84            0.12        0.04

Matches are distributed among these distances:
  20   10  0.48
  21   11  0.52

ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60


Consensus pattern (21 bp):   
TAAAATTTTTAATATTTTATA

Found at i:3670 original size:19 final size:20

Alignment explanation


    Indices: 3621--3671  Score: 52
    Period size: 19  Copynumber: 2.6  Consensus size: 20

       3611 CCCATCAAAA

                           **   
       3621 TTTTTA-AAATTTTTTCTAT
          1 TTTTTATAAATTTTTAATAT

               *                 
       3640 TTTATATAAAATTTTTAAT-T
          1 TTTTTAT-AAATTTTTAATAT

                        
       3660 TTTTTATAAATT
          1 TTTTTATAAATT

       3672 ATTTTATTGA


Statistics
Matches: 26,  Mismatches: 4, Indels: 4
        0.76            0.12        0.12

Matches are distributed among these distances:
  19   10  0.38
  20    7  0.27
  21    9  0.35

ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65


Consensus pattern (20 bp):   
TTTTTATAAATTTTTAATAT

Found at i:5412 original size:21 final size:21

Alignment explanation


    Indices: 5379--5421  Score: 54
    Period size: 23  Copynumber: 2.0  Consensus size: 21

       5369 ATTTTCATTC

                                 
       5379 ATTTAAAAAATTA-A-ATATA
          1 ATTTAAAAAATTAGACATATA

                                   
       5398 ATTTATAAAATATTAGACATATA
          1 ATTTA-AAAA-ATTAGACATATA

             
       5421 A
          1 A

       5422 AAATATACAT


Statistics
Matches: 20,  Mismatches: 0, Indels: 4
        0.83            0.00        0.17

Matches are distributed among these distances:
  19    5  0.25
  20    4  0.20
  21    4  0.20
  22    1  0.05
  23    6  0.30

ACGTcount: A:0.58, C:0.02, G:0.02, T:0.37


Consensus pattern (21 bp):   
ATTTAAAAAATTAGACATATA
Done.