Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01007174.1 Corchorus olitorius cultivar O-4 contig07199, 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, 714

Length: 1190
ACGTcount: A:0.28, C:0.20, G:0.17, T:0.35


Found at i:76 original size:36 final size:36

Alignment explanation


    Indices: 1--249  Score: 401
    Period size: 36  Copynumber: 6.8  Consensus size: 36

                                                 
          1 GACCTGTTTCCAGTCAACTTTGATAAACTGAAAAGAT
          1 GACCTGTTTCCAGTCAACTTTGATAAA-TGAAAAGAT

                                                
         38 GACCTGTTTCCAGTCAACTTTGATAAATGAAAAGAT
          1 GACCTGTTTCCAGTCAACTTTGATAAATGAAAAGAT

               *    *                            
         74 GACTTGTTCCCAGTCAACTTTGATAAACTGAAAAGAT
          1 GACCTGTTTCCAGTCAACTTTGATAAA-TGAAAAGAT

                                                
        111 GACCTGTTTCCAGTCAACTTTGATAAATGAAAAGAT
          1 GACCTGTTTCCAGTCAACTTTGATAAATGAAAAGAT

               *   *                            
        147 GACGTGTCTCCAGTCAACTTTGATAAATGAAAAGAT
          1 GACCTGTTTCCAGTCAACTTTGATAAATGAAAAGAT

                                                    
        183 GACCTGTTTCCAGTCAA-TTATGATAAATGCTGAAAAGAT
          1 GACCTGTTTCCAGTCAACTT-TGATAAA---TGAAAAGAT

                                        
        222 GACCTGTTTCCAGTCAACTTTGATAAAT
          1 GACCTGTTTCCAGTCAACTTTGATAAAT

        250 TAACCTGTTT


Statistics
Matches: 198,  Mismatches: 8, Indels: 13
        0.90            0.04        0.06

Matches are distributed among these distances:
  35    2  0.01
  36  100  0.51
  37   61  0.31
  39   33  0.17
  40    2  0.01

ACGTcount: A:0.35, C:0.18, G:0.17, T:0.31


Consensus pattern (36 bp):   
GACCTGTTTCCAGTCAACTTTGATAAATGAAAAGAT

Found at i:129 original size:73 final size:73

Alignment explanation


    Indices: 1--248  Score: 394
    Period size: 73  Copynumber: 3.4  Consensus size: 73

                    *                                                        
          1 GACCTGTTTCCAGTCAACTTTGATAAACTGAAAAGATGACCTGTTTCCAGTCAACTTTGATAAAT
          1 GACCTGTTCCCAGTCAACTTTGATAAACTGAAAAGATGACCTGTTTCCAGTCAACTTTGATAAAT

                    
         66 GAAAAGAT
         66 GAAAAGAT

               *                                                             
         74 GACTTGTTCCCAGTCAACTTTGATAAACTGAAAAGATGACCTGTTTCCAGTCAACTTTGATAAAT
          1 GACCTGTTCCCAGTCAACTTTGATAAACTGAAAAGATGACCTGTTTCCAGTCAACTTTGATAAAT

                    
        139 GAAAAGAT
         66 GAAAAGAT

               *                                                             
        147 GACGTG-TCTCCAGTCAACTTTGATAAA-TGAAAAGATGACCTGTTTCCAGTCAA-TTATGATAA
          1 GACCTGTTC-CCAGTCAACTTTGATAAACTGAAAAGATGACCTGTTTCCAGTCAACTT-TGATAA

                         
        209 ATGCTGAAAAGAT
         64 A---TGAAAAGAT

                    *                  
        222 GACCTGTTTCCAGTCAACTTTGATAAA
          1 GACCTGTTCCCAGTCAACTTTGATAAA

        249 TTAACCTGTT


Statistics
Matches: 164,  Mismatches: 5, Indels: 10
        0.92            0.03        0.06

Matches are distributed among these distances:
  71    2  0.01
  72   35  0.21
  73   94  0.57
  75   32  0.20
  76    1  0.01

ACGTcount: A:0.35, C:0.18, G:0.17, T:0.30


Consensus pattern (73 bp):   
GACCTGTTCCCAGTCAACTTTGATAAACTGAAAAGATGACCTGTTTCCAGTCAACTTTGATAAAT
GAAAAGAT
Done.