Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01000359.1 Corchorus olitorius cultivar O-4 contig00359, 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, 646

Length: 1077
ACGTcount: A:0.39, C:0.14, G:0.14, T:0.33


Found at i:186 original size:107 final size:106

Alignment explanation


    Indices: 2--219  Score: 357
    Period size: 107  Copynumber: 2.0  Consensus size: 106

          1 G

                                       **                       *            
          2 AATTAGTTATATATTTTATTTCTAAAATTCTATAACAATATTATTAATTATGGAATTTACCCTTA
          1 AATTAGTTATATATTTTATTTCTAAAACCCTATAACAATATTATTAATTATGAAATTTACCCTTA

                                                     
         67 AAATAAAAATAAAATTTTAA-TTTGGGGCTAAACTTAGTGA
         66 AAATAAAAATAAAATTTTAATTTTGGGGCTAAACTTAGTGA

                    * *                                        *             
        107 AATTAGTTTTGTATTTTATTTCTAAAACCCTATAACAATAAATTATTAATTTTGAAATTTACCCT
          1 AATTAGTTATATATTTTATTTCTAAAACCCTATAACAAT--ATTATTAATTATGAAATTTACCCT

                                                       
        172 TAAAATAAAAATAAAATTTTAATTTTGGGGCTAAACTTAGTGA
         64 TAAAATAAAAATAAAATTTTAATTTTGGGGCTAAACTTAGTGA

                 
        215 AATTA
          1 AATTA

        220 AGGTTAAACT


Statistics
Matches: 104,  Mismatches: 6, Indels: 3
        0.92            0.05        0.03

Matches are distributed among these distances:
 105   35  0.34
 107   44  0.42
 108   25  0.24

ACGTcount: A:0.42, C:0.08, G:0.08, T:0.42


Consensus pattern (106 bp):   
AATTAGTTATATATTTTATTTCTAAAACCCTATAACAATATTATTAATTATGAAATTTACCCTTA
AAATAAAAATAAAATTTTAATTTTGGGGCTAAACTTAGTGA

Found at i:397 original size:19 final size:19

Alignment explanation


    Indices: 358--398  Score: 55
    Period size: 19  Copynumber: 2.2  Consensus size: 19

        348 AAACAAATTA

                         **    
        358 AAAACTACCCATTTTAAAT
          1 AAAACTACCCATTAGAAAT

                            *  
        377 AAAACTACCCATTAGAGAT
          1 AAAACTACCCATTAGAAAT

               
        396 AAA
          1 AAA

        399 TATAATATTT


Statistics
Matches: 19,  Mismatches: 3, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  19   19  1.00

ACGTcount: A:0.51, C:0.20, G:0.05, T:0.24


Consensus pattern (19 bp):   
AAAACTACCCATTAGAAAT
Done.