Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01023389.1 Corchorus olitorius cultivar O-4 contig23422, 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: 10881
ACGTcount: A:0.36, C:0.17, G:0.16, T:0.31


Found at i:130 original size:69 final size:70

Alignment explanation


    Indices: 57--202  Score: 195
    Period size: 70  Copynumber: 2.1  Consensus size: 70

         47 TAATTTACAG

                 *  *      *                       *       *             *   
         57 TTTTATTCTACTAAACACTCTATTTTTATTTAA-TAAATCTAATATCTTTATAACTATTCTGTTT
          1 TTTTACTCAACTAAAAACTCTATTTTTATTTAACTAAATATAATATCCTTATAACTATTCTATTT

               * 
        121 TACTA
         66 TACCA

                                                 *               *     *     
        126 TTTTACTCAACTAAAAACTCTATTTTTATTTAACTAAGTATAATATCCTTATACCTATTTTATTT
          1 TTTTACTCAACTAAAAACTCTATTTTTATTTAACTAAATATAATATCCTTATAACTATTCTATTT

                 
        191 TACCA
         66 TACCA

                   
        196 TTTTACT
          1 TTTTACT

        203 ATTTTAATTT


Statistics
Matches: 66,  Mismatches: 10, Indels: 1
        0.86            0.13        0.01

Matches are distributed among these distances:
  69   30  0.45
  70   36  0.55

ACGTcount: A:0.32, C:0.16, G:0.01, T:0.51


Consensus pattern (70 bp):   
TTTTACTCAACTAAAAACTCTATTTTTATTTAACTAAATATAATATCCTTATAACTATTCTATTT
TACCA

Found at i:199 original size:70 final size:69

Alignment explanation


    Indices: 42--202  Score: 198
    Period size: 69  Copynumber: 2.3  Consensus size: 69

         32 TAATATTAAT

                   *             *  *      *                      *       *  
         42 TATTTTAATTTA-CAGTTTTATTCTACTAAACACTCTATTTTTATTTAATAAATCTAATATCTTT
          1 TATTTTATTTTACCA-TTTTACTCAACTAAAAACTCTATTTTTATTTAATAAATATAATATCCTT

                 
        106 ATAAC
         65 ATAAC

                * *      *                                      *            
        111 TATTCTGTTTTACTATTTTACTCAACTAAAAACTCTATTTTTATTTAACTAAGTATAATATCCTT
          1 TATTTTATTTTACCATTTTACTCAACTAAAAACTCTATTTTTATTTAA-TAAATATAATATCCTT

               * 
        176 ATACC
         65 ATAAC

                                  
        181 TATTTTATTTTACCATTTTACT
          1 TATTTTATTTTACCATTTTACT

        203 ATTTTAATTT


Statistics
Matches: 76,  Mismatches: 14, Indels: 3
        0.82            0.15        0.03

Matches are distributed among these distances:
  69   39  0.51
  70   37  0.49

ACGTcount: A:0.32, C:0.15, G:0.02, T:0.51


Consensus pattern (69 bp):   
TATTTTATTTTACCATTTTACTCAACTAAAAACTCTATTTTTATTTAATAAATATAATATCCTTA
TAAC

Found at i:8547 original size:6 final size:6

Alignment explanation


    Indices: 8536--8590  Score: 55
    Period size: 6  Copynumber: 9.8  Consensus size: 6

       8526 TAAAACCCAA

                                                           *      *
       8536 GAGAGG GAGA-G GAGAGG GAGAGG G-G-GG G-GAGG GAGAGA GAGAGA
          1 GAGAGG GAGAGG GAGAGG GAGAGG GAGAGG GAGAGG GAGAGG GAGAGG

                 *      
       8580 GAGAGA GAGAG
          1 GAGAGG GAGAG

       8591 ATGAAAAGAA


Statistics
Matches: 45,  Mismatches: 1, Indels: 6
        0.87            0.02        0.12

Matches are distributed among these distances:
   4    4  0.09
   5    9  0.20
   6   32  0.71

ACGTcount: A:0.36, C:0.00, G:0.64, T:0.00


Consensus pattern (6 bp):   
GAGAGG
Done.