Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_207 ID=scaffold_207-JGI_221_v2.0

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: 9357
ACGTcount: A:0.33, C:0.20, G:0.16, T:0.31


Found at i:425 original size:2 final size:2

Alignment explanation


    Indices: 418--468  Score: 102
    Period size: 2  Copynumber: 25.5  Consensus size: 2

        408 TAAATAATAC

                                                                          
        418 AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT

                         
        460 AT AT AT AT A
          1 AT AT AT AT A

        469 GAAGTTAATA


Statistics
Matches: 49,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   49  1.00

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


Consensus pattern (2 bp):   
AT

Found at i:3865 original size:25 final size:25

Alignment explanation


    Indices: 3823--3885  Score: 74
    Period size: 25  Copynumber: 2.5  Consensus size: 25

       3813 TTAAGTGTTT

                          *      *    
       3823 TCAGTATAGT-CTATCTATAGTAGTC
          1 TCAGTATA-TACTACCTATAGCAGTC

                                    *
       3848 TCAGTATATACTACCTATAGCAGTT
          1 TCAGTATATACTACCTATAGCAGTC

                *        
       3873 TCAGGATATACTA
          1 TCAGTATATACTA

       3886 TCAAAGATAA


Statistics
Matches: 33,  Mismatches: 4, Indels: 2
        0.85            0.10        0.05

Matches are distributed among these distances:
  24    1  0.03
  25   32  0.97

ACGTcount: A:0.32, C:0.17, G:0.14, T:0.37


Consensus pattern (25 bp):   
TCAGTATATACTACCTATAGCAGTC

Found at i:8684 original size:16 final size:16

Alignment explanation


    Indices: 8663--8694  Score: 64
    Period size: 16  Copynumber: 2.0  Consensus size: 16

       8653 ATTTGTTACT

                            
       8663 TAGATTTTTTTTTGTC
          1 TAGATTTTTTTTTGTC

                            
       8679 TAGATTTTTTTTTGTC
          1 TAGATTTTTTTTTGTC

       8695 CAATTTGATA


Statistics
Matches: 16,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  16   16  1.00

ACGTcount: A:0.12, C:0.06, G:0.12, T:0.69


Consensus pattern (16 bp):   
TAGATTTTTTTTTGTC

Found at i:8700 original size:15 final size:16

Alignment explanation


    Indices: 8664--8700  Score: 58
    Period size: 16  Copynumber: 2.4  Consensus size: 16

       8654 TTTGTTACTT

                           *
       8664 AGATTTTTTTTTGTCT
          1 AGATTTTTTTTTGTCC

                            
       8680 AGATTTTTTTTTGTCC
          1 AGATTTTTTTTTGTCC

                  
       8696 A-ATTT
          1 AGATTT

       8701 GATACTTGGA


Statistics
Matches: 20,  Mismatches: 1, Indels: 1
        0.91            0.05        0.05

Matches are distributed among these distances:
  15    4  0.20
  16   16  0.80

ACGTcount: A:0.16, C:0.08, G:0.11, T:0.65


Consensus pattern (16 bp):   
AGATTTTTTTTTGTCC
Done.