Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_439 ID=scaffold_439-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: 7188
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.30

Warning! 195 characters in sequence are not A, C, G, or T


Found at i:3100 original size:13 final size:13

Alignment explanation


    Indices: 3082--3107  Score: 52
    Period size: 13  Copynumber: 2.0  Consensus size: 13

       3072 AAAGAGATTT

                         
       3082 GTTTTCTAGTAAA
          1 GTTTTCTAGTAAA

                         
       3095 GTTTTCTAGTAAA
          1 GTTTTCTAGTAAA

       3108 AATTGAACAT


Statistics
Matches: 13,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   13  1.00

ACGTcount: A:0.31, C:0.08, G:0.15, T:0.46


Consensus pattern (13 bp):   
GTTTTCTAGTAAA

Found at i:3176 original size:19 final size:20

Alignment explanation


    Indices: 3136--3179  Score: 56
    Period size: 19  Copynumber: 2.3  Consensus size: 20

       3126 GTCTCTTTTC

                      *       * 
       3136 GCATT-CATTTCATGCATTT
          1 GCATTACATTACATGCATAT

                                
       3155 GCATTACATTACAT-CATAT
          1 GCATTACATTACATGCATAT

                  
       3174 GCATTA
          1 GCATTA

       3180 AAGATTATTA


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

Matches are distributed among these distances:
  19   15  0.68
  20    7  0.32

ACGTcount: A:0.30, C:0.20, G:0.09, T:0.41


Consensus pattern (20 bp):   
GCATTACATTACATGCATAT

Found at i:5055 original size:19 final size:19

Alignment explanation


    Indices: 5031--5070  Score: 55
    Period size: 19  Copynumber: 2.1  Consensus size: 19

       5021 GCAAATGTTC

                       *        
       5031 TTTCATT-CTTTACGATTTT
          1 TTTCATTCCTTCA-GATTTT

                               
       5050 TTTCATTCCTTCAGATTTT
          1 TTTCATTCCTTCAGATTTT

              
       5069 TT
          1 TT

       5071 CTGCCAAACC


Statistics
Matches: 19,  Mismatches: 1, Indels: 2
        0.86            0.05        0.09

Matches are distributed among these distances:
  19   15  0.79
  20    4  0.21

ACGTcount: A:0.15, C:0.17, G:0.05, T:0.62


Consensus pattern (19 bp):   
TTTCATTCCTTCAGATTTT

Found at i:6022 original size:21 final size:21

Alignment explanation


    Indices: 5998--6041  Score: 63
    Period size: 21  Copynumber: 2.1  Consensus size: 21

       5988 AAAAGTGATG

                             *    
       5998 TGAAAAAT-AAAAAGATGAAAA
          1 TGAAAAATGAAAAAG-TAAAAA

                                 
       6019 TGAAAAATGAAAAAGTAAAAA
          1 TGAAAAATGAAAAAGTAAAAA

              
       6040 TG
          1 TG

       6042 TAGAGGCTAA


Statistics
Matches: 21,  Mismatches: 1, Indels: 2
        0.88            0.04        0.08

Matches are distributed among these distances:
  21   15  0.71
  22    6  0.29

ACGTcount: A:0.68, C:0.00, G:0.16, T:0.16


Consensus pattern (21 bp):   
TGAAAAATGAAAAAGTAAAAA
Done.