Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01011481.1 Corchorus olitorius cultivar O-4 contig11514, 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: 8599
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.28


Found at i:8096 original size:11 final size:11

Alignment explanation


    Indices: 8080--8148  Score: 66
    Period size: 14  Copynumber: 5.6  Consensus size: 11

       8070 AGAAAAGTGA

                       
       8080 CAAAACCAACC
          1 CAAAACCAACC

                          
       8091 CAAAACCACCAACC
          1 C-AAA--ACCAACC

                       
       8105 CAAAACCAACC
          1 CAAAACCAACC

                        * 
       8116 CAAAACCACCAAAC
          1 C-AAA--ACCAACC

                        
       8130 CAAAACCAACCC
          1 CAAAACCAA-CC

                   
       8142 CAAAACC
          1 CAAAACC

       8149 GAGCCTAAAA


Statistics
Matches: 49,  Mismatches: 2, Indels: 13
        0.77            0.03        0.20

Matches are distributed among these distances:
  11   14  0.29
  12   14  0.29
  13    6  0.12
  14   15  0.31

ACGTcount: A:0.54, C:0.46, G:0.00, T:0.00


Consensus pattern (11 bp):   
CAAAACCAACC

Found at i:8103 original size:14 final size:14

Alignment explanation


    Indices: 8084--8137  Score: 78
    Period size: 14  Copynumber: 4.1  Consensus size: 14

       8074 AAGTGACAAA

                          
       8084 ACCAACCCAAAACC
          1 ACCAACCCAAAACC

                          
       8098 ACCAACCC-AAA--
          1 ACCAACCCAAAACC

                          
       8109 ACCAACCCAAAACC
          1 ACCAACCCAAAACC

                 *        
       8123 ACCAAACCAAAACC
          1 ACCAACCCAAAACC

             
       8137 A
          1 A

       8138 ACCCCAAAAC


Statistics
Matches: 36,  Mismatches: 1, Indels: 6
        0.84            0.02        0.14

Matches are distributed among these distances:
  11    8  0.22
  12    3  0.08
  13    3  0.08
  14   22  0.61

ACGTcount: A:0.54, C:0.46, G:0.00, T:0.00


Consensus pattern (14 bp):   
ACCAACCCAAAACC

Found at i:8114 original size:25 final size:25

Alignment explanation


    Indices: 8080--8148  Score: 120
    Period size: 25  Copynumber: 2.7  Consensus size: 25

       8070 AGAAAAGTGA

                                   * 
       8080 CAAAACCAACCCAAAACCACCAACC
          1 CAAAACCAACCCAAAACCACCAAAC

                                     
       8105 CAAAACCAACCCAAAACCACCAAAC
          1 CAAAACCAACCCAAAACCACCAAAC

                               
       8130 CAAAACCAACCCCAAAACC
          1 CAAAACCAA-CCCAAAACC

       8149 GAGCCTAAAA


Statistics
Matches: 42,  Mismatches: 1, Indels: 1
        0.95            0.02        0.02

Matches are distributed among these distances:
  25   33  0.79
  26    9  0.21

ACGTcount: A:0.54, C:0.46, G:0.00, T:0.00


Consensus pattern (25 bp):   
CAAAACCAACCCAAAACCACCAAAC
Done.