Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_1081 ID=scaffold_1081-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, 642

Length: 1070
ACGTcount: A:0.23, C:0.02, G:0.24, T:0.52


Found at i:749 original size:27 final size:28

Alignment explanation


    Indices: 706--770  Score: 73
    Period size: 27  Copynumber: 2.4  Consensus size: 28

        696 TATGTGTATA

                                 *      
        706 GTTTATTATTTGTGATTT-GGGTTTAAG
          1 GTTTATTATTTGTGATTTAGGATTTAAG

                   *                   * 
        733 GTTTATTTTTTAG-GATTTAGGATTTATG
          1 GTTTATTATTT-GTGATTTAGGATTTAAG

                       
        761 GTTTA-TATTT
          1 GTTTATTATTT

        771 CGGGTTTATT


Statistics
Matches: 32,  Mismatches: 4, Indels: 4
        0.80            0.10        0.10

Matches are distributed among these distances:
  27   19  0.59
  28   13  0.41

ACGTcount: A:0.20, C:0.00, G:0.22, T:0.58


Consensus pattern (28 bp):   
GTTTATTATTTGTGATTTAGGATTTAAG

Found at i:778 original size:20 final size:20

Alignment explanation


    Indices: 747--813  Score: 73
    Period size: 20  Copynumber: 3.3  Consensus size: 20

        737 ATTTTTTAGG

                   *     *      
        747 ATTTAGGATTTATGGTTTAT
          1 ATTTAGGGTTTATAGTTTAT

                *        *      
        767 ATTTCGGGTTTATTGTTTA-
          1 ATTTAGGGTTTATAGTTTAT

                                 
        786 AGTTTAGGGTTTATAGTTTAT
          1 A-TTTAGGGTTTATAGTTTAT

                   
        807 CATTTAG
          1 -ATTTAG

        814 TGTCTAGTTT


Statistics
Matches: 39,  Mismatches: 5, Indels: 5
        0.80            0.10        0.10

Matches are distributed among these distances:
  19    1  0.03
  20   32  0.82
  21    5  0.13
  22    1  0.03

ACGTcount: A:0.22, C:0.03, G:0.21, T:0.54


Consensus pattern (20 bp):   
ATTTAGGGTTTATAGTTTAT

Found at i:1044 original size:28 final size:26

Alignment explanation


    Indices: 987--1047  Score: 86
    Period size: 28  Copynumber: 2.2  Consensus size: 26

        977 ATGATTTGTG

                              *        
        987 TTTAGGGTTTAAGTTTATGTTTAGGGT
          1 TTTA-GGTTTAAGTTTATATTTAGGGT

                                        
       1014 TTTAGGTTTAAGATTTATAATTTAGGGT
          1 TTTAGGTTTAAG-TTTAT-ATTTAGGGT

                  
       1042 TTTAGG
          1 TTTAGG

       1048 GTTTTAGGAT


Statistics
Matches: 31,  Mismatches: 1, Indels: 3
        0.89            0.03        0.09

Matches are distributed among these distances:
  26    8  0.26
  27    9  0.29
  28   14  0.45

ACGTcount: A:0.23, C:0.00, G:0.26, T:0.51


Consensus pattern (26 bp):   
TTTAGGTTTAAGTTTATATTTAGGGT

Found at i:1047 original size:8 final size:8

Alignment explanation


    Indices: 1034--1066  Score: 50
    Period size: 8  Copynumber: 4.2  Consensus size: 8

       1024 AGATTTATAA

                    
       1034 TTTAGGGT
          1 TTTAGGGT

                    
       1042 TTTAGGGT
          1 TTTAGGGT

                   *
       1050 TTTA-GGA
          1 TTTAGGGT

                    
       1057 TTTAGGGT
          1 TTTAGGGT

              
       1065 TT
          1 TT

       1067 AAGG


Statistics
Matches: 22,  Mismatches: 2, Indels: 2
        0.85            0.08        0.08

Matches are distributed among these distances:
   7    6  0.27
   8   16  0.73

ACGTcount: A:0.15, C:0.00, G:0.33, T:0.52


Consensus pattern (8 bp):   
TTTAGGGT
Done.