Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01008799.1 Corchorus olitorius cultivar O-4 contig08826, 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: 2619
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.35


Found at i:699 original size:330 final size:328

Alignment explanation


    Indices: 7--1001  Score: 1273
    Period size: 330  Copynumber: 3.0  Consensus size: 328

          1 AAAATA

                                                          *               *  
          7 AGCCGAAATCGTGTACTAACAATCACGGTATTTGGCTAAAAACGCATTTTGGGGCCCCGACTTAG
          1 AGCCGAAATCGTGTACTAACAATCACGGTATTTGGCTAAAAACGC-GTTTGGGGCCCCGACTCAG

                *  *           *                                 **          
         72 TTTCGCAAGATTTTTAGCGCCAAGACTCATTGAAATATCTCTATTCAGCTAAGAAAATCTCAGCC
         65 TTTCCCATGATTTTTAGCGACAAGACTCATTGAAATATCTCTATTCAGCTAA-CCAATCTCAGCC

               *      *                                                      
        137 ACAATGGATTGAAGGATTTGTTTTTACGAGCATTAGAAACCAATTTC-ACCTT-AATTAGAAATT
        129 ACATTGGATTTAAGGATTTGTTTTTACGAGCATTAGAAACCAATTTCGA--TTGAA-TAGAAATT

                                                 *       * *                 
        200 AATTCAGAAAAAATA-GGAAAATGATATTAGAAGCGTCAAAAGCCTTTAAATATTTTTGGTGTTG
        191 AATTCAGAAAAAATAGGGAAAATGATATTAGAAGCGTGAAAAGCCGTCAAATATTTTTGGTGTTG

                                                                    *    *   
        264 AATTATATATTTTTATGAGTATTTTGGCCAAAAATTAAGGAAAAATATTTGGGGTCCATTTCTGC
        256 AATTATATATTTTTATGAGTATTTTGGCCAAAAATTAAGGAAAAATATTTGGGGTCAATTTTTGC

                   *
        329 AAAAATTA
        321 AAAAATTT

               *                     *           *     *                   * 
        337 AGCTGAAATCGTGTACTAACAATCATGGTATTTGGCTGAAAACACGTTCTGGGGCCCCGACTCGG
          1 AGCCGAAATCGTGTACTAACAATCACGGTATTTGGCTAAAAACGCGTT-TGGGGCCCCGACTCAG

                           *                           *                     
        402 TTTCCCATGATTTTTTGCGACAAGACTCATTGAAATATCTCTACTCAGCTAACCGAATCTCAGCC
         65 TTTCCCATGATTTTTAGCGACAAGACTCATTGAAATATCTCTATTCAGCTAACC-AATCTCAGCC

                                          *  *                       *     * 
        467 ACATTGGATTTAAGGATTTGTTTTTACGAGTATCAGAAACCAATTTCGATTGAAGTACAAATTTA
        129 ACATTGGATTTAAGGATTTGTTTTTACGAGCATTAGAAACCAATTTCGATTGAA-TAGAAATTAA

                                *       *   *             *          **      
        532 TTCAGAAAAAATAGGGAAAACGATATTAAAAGTGTGAAAAGCCGTCCAATATTTTTGCAGTTGAA
        193 TTCAGAAAAAATAGGGAAAATGATATTAGAAGCGTGAAAAGCCGTCAAATATTTTTGGTGTTGAA

                        *  *                  *  *           *               
        597 TTATATATTTTTTTGGGTATTTTGGCCAAAAATTGAGAAATAAATATTTCGGGTCAATTTTTGCA
        258 TTATATATTTTTATGAGTATTTTGGCCAAAAATTAAGGAA-AAATATTTGGGGTCAATTTTTGCA

               *   
        662 AAATTTT
        322 AAAATTT

                        *                                                    
        669 AGCCGAAATCGTTTACT-AC-ATCACGGTATTTGGCTAAAAACGCGTTTCGGGGCCCCGACTCAG
          1 AGCCGAAATCGTGTACTAACAATCACGGTATTTGGCTAAAAACGCGTTT-GGGGCCCCGACTCAG

               **          *                      *                          
        732 TTTTTCATGATTTTTGGC-ACCAAGACTCATTGAAATAACT-TAATTCAGCTAACCAA----A--
         65 TTTCCCATGATTTTTAGCGA-CAAGACTCATTGAAATATCTCT-ATTCAGCTAACCAATCTCAGC

             *                                        *                      
        789 -TC-TTGGATTTAAGGATTTGTTTTTACGAGCATTAGAAACCGATTTCGATTGAATCAGAAATTA
        128 CACATTGGATTTAAGGATTTGTTTTTACGAGCATTAGAAACCAATTTCGATTGAAT-AGAAATTA

                            **                              *       *        
        852 ATTCAGAAAAAATAGCAAAAAATGATATTAGAAGCGTGAAAAGCCGTCTAATATTTATGGTGTTG
        192 ATTCAGAAAAAATAG-GGAAAATGATATTAGAAGCGTGAAAAGCCGTCAAATATTTTTGGTGTTG

                     *                 **                                    
        917 AATTATATACTTTTATGAGTATTTTGGTAAAAAATTAAGGAAAAATATTTGGGGTCAATTTTTGC
        256 AATTATATATTTTTATGAGTATTTTGGCCAAAAATTAAGGAAAAATATTTGGGGTCAATTTTTGC

                    
        982 AAAAATTT
        321 AAAAATTT

              **        
        990 AGTTGAAATCGT
          1 AGCCGAAATCGT

       1002 TTAGGGGTCA


Statistics
Matches: 578,  Mismatches: 76, Indels: 31
        0.84            0.11        0.05

Matches are distributed among these distances:
 320    1  0.00
 321  108  0.19
 322   76  0.13
 325    1  0.00
 329    9  0.02
 330  261  0.45
 331   81  0.14
 332   41  0.07

ACGTcount: A:0.35, C:0.15, G:0.18, T:0.33


Consensus pattern (328 bp):   
AGCCGAAATCGTGTACTAACAATCACGGTATTTGGCTAAAAACGCGTTTGGGGCCCCGACTCAGT
TTCCCATGATTTTTAGCGACAAGACTCATTGAAATATCTCTATTCAGCTAACCAATCTCAGCCAC
ATTGGATTTAAGGATTTGTTTTTACGAGCATTAGAAACCAATTTCGATTGAATAGAAATTAATTC
AGAAAAAATAGGGAAAATGATATTAGAAGCGTGAAAAGCCGTCAAATATTTTTGGTGTTGAATTA
TATATTTTTATGAGTATTTTGGCCAAAAATTAAGGAAAAATATTTGGGGTCAATTTTTGCAAAAA
TTT

Done.