Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01014409.1 Corchorus olitorius cultivar O-4 contig14442, 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: 13170
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34


Found at i:9021 original size:38 final size:38

Alignment explanation


    Indices: 8971--9047  Score: 154
    Period size: 38  Copynumber: 2.0  Consensus size: 38

       8961 TAACATGGTA

                                                  
       8971 AAAATAGGTCATTCCTTTCTACATACAAATATACAATT
          1 AAAATAGGTCATTCCTTTCTACATACAAATATACAATT

                                                  
       9009 AAAATAGGTCATTCCTTTCTACATACAAATATACAATT
          1 AAAATAGGTCATTCCTTTCTACATACAAATATACAATT

             
       9047 A
          1 A

       9048 TATATCAACT


Statistics
Matches: 39,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  38   39  1.00

ACGTcount: A:0.43, C:0.18, G:0.05, T:0.34


Consensus pattern (38 bp):   
AAAATAGGTCATTCCTTTCTACATACAAATATACAATT

Found at i:10808 original size:71 final size:70

Alignment explanation


    Indices: 10692--10838  Score: 240
    Period size: 71  Copynumber: 2.1  Consensus size: 70

      10682 CTTATATGCT

                              **            *       *                        
      10692 CAAATATCTAATGAGAATTTAATACAAACTAAGAAATTGCTTTAAATAAAACTAATTACAAACTA
          1 CAAATATCTAATGAGAATCCAATACAAACTAAAAAATTGCCTTAAAT-AAACTAATTACAAACTA

                  
      10757 AACAAA
         65 AACAAA

                                                              *              
      10763 CAAATATCTAATGAGAATCCAATACAAACTAAAAAATTGCCTTAAATAAATTAATTACAAACTAA
          1 CAAATATCTAATGAGAATCCAATACAAACTAAAAAATTGCCTTAAATAAACTAATTACAAACTAA

                 
      10828 ACAAA
         66 ACAAA

                  
      10833 CAAATA
          1 CAAATA

      10839 AACAATTACT


Statistics
Matches: 71,  Mismatches: 5, Indels: 1
        0.92            0.06        0.01

Matches are distributed among these distances:
  70   28  0.39
  71   43  0.61

ACGTcount: A:0.56, C:0.14, G:0.05, T:0.25


Consensus pattern (70 bp):   
CAAATATCTAATGAGAATCCAATACAAACTAAAAAATTGCCTTAAATAAACTAATTACAAACTAA
ACAAA

Found at i:11174 original size:12 final size:13

Alignment explanation


    Indices: 11148--11180  Score: 50
    Period size: 12  Copynumber: 2.6  Consensus size: 13

      11138 TAAACTAATT

                         
      11148 ACAAACTAAACAA
          1 ACAAACTAAACAA

                      *  
      11161 ACAAA-TAAATAA
          1 ACAAACTAAACAA

                    
      11173 ACAAACTA
          1 ACAAACTA

      11181 TTAAACCTAC


Statistics
Matches: 18,  Mismatches: 1, Indels: 2
        0.86            0.05        0.10

Matches are distributed among these distances:
  12   11  0.61
  13    7  0.39

ACGTcount: A:0.70, C:0.18, G:0.00, T:0.12


Consensus pattern (13 bp):   
ACAAACTAAACAA

Found at i:11956 original size:74 final size:74

Alignment explanation


    Indices: 11849--11987  Score: 260
    Period size: 74  Copynumber: 1.9  Consensus size: 74

      11839 TCTTGAGTTT

                                                                             
      11849 TACTTTCACGAAATGTGAGTTTATTTGTAATTTATTTATTTATGTATTTAGTATTTTGGTAGTTA
          1 TACTTTCACGAAATGTGAGTTTATTTGTAATTTATTTATTTATGTATTTAGTATTTTGGTAGTTA

                     
      11914 CATGGGTTC
         66 CATGGGTTC

                      *                              *                       
      11923 TACTTTCACGGAATGTGAGTTTATTTGTAATTTATTTATTTCTGTATTTAGTATTTTGGTAGTTA
          1 TACTTTCACGAAATGTGAGTTTATTTGTAATTTATTTATTTATGTATTTAGTATTTTGGTAGTTA

      11988 TAGATGAAAT


Statistics
Matches: 63,  Mismatches: 2, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  74   63  1.00

ACGTcount: A:0.24, C:0.06, G:0.17, T:0.53


Consensus pattern (74 bp):   
TACTTTCACGAAATGTGAGTTTATTTGTAATTTATTTATTTATGTATTTAGTATTTTGGTAGTTA
CATGGGTTC
Done.