Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01008440.1 Corchorus olitorius cultivar O-4 contig08467, 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, 660

Length: 1100
ACGTcount: A:0.31, C:0.20, G:0.23, T:0.25


Found at i:247 original size:40 final size:40

Alignment explanation


    Indices: 202--681  Score: 660
    Period size: 40  Copynumber: 12.1  Consensus size: 40

        192 AAGGAATAGG

                      *   *  *             ** *     
        202 AACAACACCTCCCGATGAGGAAGGGCAAACTAAGAATTTA
          1 AACAACACCTTCCGGTGGGGAAGGGCAAACTGGGTATTTA

            *       *    *  *     *                 
        242 GACAACACTTTCCAGTAGGGAAAGGCAAACT-GGTATTTA
          1 AACAACACCTTCCGGTGGGGAAGGGCAAACTGGGTATTTA

                       *                            
        281 AACAACACCTTTCGGTGGGGAAGGGCAAACTGGGTATTTA
          1 AACAACACCTTCCGGTGGGGAAGGGCAAACTGGGTATTTA

                        *                           
        321 AACAACACCTTCTGGTGGGGAAGGGCAAACTGGGTATTTA
          1 AACAACACCTTCCGGTGGGGAAGGGCAAACTGGGTATTTA

                                       *            
        361 AACAACACCTTCCGGTGGGGAAGGGCAGACTGGGTATTTA
          1 AACAACACCTTCCGGTGGGGAAGGGCAAACTGGGTATTTA

                     *   *               *    *     
        401 AACAACACCCTCCAGT-GGGAA-GGCAAATTGGGAATTTA
          1 AACAACACCTTCCGGTGGGGAAGGGCAAACTGGGTATTTA

                     *                   *    *    *
        439 AACAACACCCTCCGGTGGGGAAGGGCAAATTGGGAATTTG
          1 AACAACACCTTCCGGTGGGGAAGGGCAAACTGGGTATTTA

                            *                       
        479 AACAACACCTTCCGGTAGGGAAGGGCAAACTGGGTATTTA
          1 AACAACACCTTCCGGTGGGGAAGGGCAAACTGGGTATTTA

                            *                 *     
        519 AACAACACCTTCCGGTAGGGAAGGGCAAACTGGGAATTTA
          1 AACAACACCTTCCGGTGGGGAAGGGCAAACTGGGTATTTA

            *                               *       
        559 TACAACACCTTCCGGTGGGGAAGGGCAAACTGTGTATTTA
          1 AACAACACCTTCCGGTGGGGAAGGGCAAACTGGGTATTTA

                                       *            
        599 AACAACACCTTCCGGTGGGGAAGGGCAGACTGGGTATTTA
          1 AACAACACCTTCCGGTGGGGAAGGGCAAACTGGGTATTTA

              *                          *    *     
        639 AATAACACCTTCCGGTGGGGAAGGGCAAATTGGGAATTTA
          1 AACAACACCTTCCGGTGGGGAAGGGCAAACTGGGTATTTA

               
        679 AAC
          1 AAC

        682 TAGACAAGAC


Statistics
Matches: 392,  Mismatches: 45, Indels: 6
        0.88            0.10        0.01

Matches are distributed among these distances:
  38   29  0.07
  39   41  0.10
  40  322  0.82

ACGTcount: A:0.33, C:0.19, G:0.28, T:0.20


Consensus pattern (40 bp):   
AACAACACCTTCCGGTGGGGAAGGGCAAACTGGGTATTTA

Found at i:619 original size:238 final size:239

Alignment explanation


    Indices: 202--681  Score: 752
    Period size: 238  Copynumber: 2.0  Consensus size: 239

        192 AAGGAATAGG

                                                            *                
        202 AACAACACCTCCCGATGAGGAAGGGCAAACTAAGAATTTAGACAACACTTTCCAGTAGGGAAAGG
          1 AACAACACCTCCCGATGAGGAAGGGCAAACTAAGAATTTAGACAACACCTTCCAGTAGGGAAAGG

                                     *    *                 *                
        267 CAAACTGGTATTTAAACAACACCTTTCGGTGGGGAAGGGCAAACTGGGTATTTAAACAACACCTT
         66 CAAACTGGTATTTAAACAACACCTTCCGGTAGGGAAGGGCAAACTGGGAATTTAAACAACACCTT

             *                                                               
        332 CTGGTGGGGAAGGGCAAACTGGGTATTTAAACAACACCTTCCGGTGGGGAAGGGCAGACTGGGTA
        131 CCGGTGGGGAAGGGCAAACTGGGTATTTAAACAACACCTTCCGGTGGGGAAGGGCAGACTGGGTA

                                                        
        397 TTTAAACAACACCCTCCAGT-GGGAA-GGCAAATTGGGAATTTA
        196 TTTAAACAACACCCTCCAGTGGGGAAGGGCAAATTGGGAATTTA

                           *  *           * **                     *        *
        439 AACAACACC-CTCCGGTGGGGAAGGGCAAATTGGGAATTT-GAACAACACCTTCCGGTAGGGAAG
          1 AACAACACCTC-CCGATGAGGAAGGGCAAACTAAGAATTTAG-ACAACACCTTCCAGTAGGGAAA

                                                                     *       
        502 GGCAAACTGGGTATTTAAACAACACCTTCCGGTAGGGAAGGGCAAACTGGGAATTTATACAACAC
         64 GGCAAACT-GGTATTTAAACAACACCTTCCGGTAGGGAAGGGCAAACTGGGAATTTAAACAACAC

                                    *                                        
        567 CTTCCGGTGGGGAAGGGCAAACTGTGTATTTAAACAACACCTTCCGGTGGGGAAGGGCAGACTGG
        128 CTTCCGGTGGGGAAGGGCAAACTGGGTATTTAAACAACACCTTCCGGTGGGGAAGGGCAGACTGG

                     *      *   *                          
        632 GTATTTAAATAACACCTTCCGGTGGGGAAGGGCAAATTGGGAATTTA
        193 GTATTTAAACAACACCCTCCAGTGGGGAAGGGCAAATTGGGAATTTA

               
        679 AAC
          1 AAC

        682 TAGACAAGAC


Statistics
Matches: 221,  Mismatches: 17, Indels: 7
        0.90            0.07        0.03

Matches are distributed among these distances:
 236    2  0.01
 237   59  0.27
 238  135  0.61
 239    5  0.02
 240   20  0.09

ACGTcount: A:0.33, C:0.19, G:0.28, T:0.20


Consensus pattern (239 bp):   
AACAACACCTCCCGATGAGGAAGGGCAAACTAAGAATTTAGACAACACCTTCCAGTAGGGAAAGG
CAAACTGGTATTTAAACAACACCTTCCGGTAGGGAAGGGCAAACTGGGAATTTAAACAACACCTT
CCGGTGGGGAAGGGCAAACTGGGTATTTAAACAACACCTTCCGGTGGGGAAGGGCAGACTGGGTA
TTTAAACAACACCCTCCAGTGGGGAAGGGCAAATTGGGAATTTA
Done.