Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01010914.1 Corchorus olitorius cultivar O-4 contig10946, 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, 813

Length: 1355
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.31


Found at i:628 original size:333 final size:332

Alignment explanation


    Indices: 5--707  Score: 1138
    Period size: 333  Copynumber: 2.1  Consensus size: 332

          1 ATTC

                        *                                *                   
          5 ATCTAATAAAAACTTAGCCACATTGCATTTAAGGATTTATTTTTAGGAGCATTTGAATCTTGTTT
          1 ATCTAATAAAAAATTAGCCACATTGCATTTAAGGATTTATTTTTACGAGCATTTGAATCTTGTTT

                                 *                                           
         70 CGATTTAATTAGAATTAATTCTGAAAAAATATGAAAAACGATATTAAAAGCGTGAAAAGCCCTCC
         66 CGATTTAATTAGAATTAATTCAGAAAAAATATGAAAAACGATATTAAAAGCGTGAAAAGCCCTCC

                     *       *       *   *                     *          *  
        135 AATATTTTTGGCGTTAAGTTATATATATTTTATGAGTATTATATCCAAAAATTGAGGAAAAATTT
        131 AATATTTTTAGCGTTAAATTATATAAATTATATGAGTATTATATCCAAAAACTGAGGAAAAAATT

                                      *                          *           
        200 TTCGCGGTCATTTTTTGCAAAATTTTTGCCAAAATCGTGTACTAACCATCAAGGTTTTTGGCTAA
        196 TTCGCGGTCATTTTTTGCAAAATTTTAGCCAAAATCGTGTACTAACCATCAAGATTTTTGGCTAA

                     *     *    *                                            
        265 AAATGCGTTTCGGGGTCCCGGCTCAGTTTTGCATGAATTTTGGCGTCAAGACTCCTTGAAATATC
        261 AAATGCGTTCCGGGGACCCGACTCAGTTTTGCATGAATTTTGGCGTCAAGACTCCTTGAAATATC

              *   *
        330 TATATTG
        326 TAAATTA

                *       *                          *                         
        337 ATCTGATAAAAAGTTAGCCACATTGCATTTAAGGATTTGCTTTTT-CGAGCATTTGAATCTTGTT
          1 ATCTAATAAAAAATTAGCCACATTGCATTTAAGGATTT-ATTTTTACGAGCATTTGAATCTTGTT

                                                    *                    *   
        401 TCGATTTAATTAGAAATTAATTCAGAAAAAATATGAAAAATGATATTAAAAGCGTGAAAAGTCCT
         65 TCGATTTAATTAG-AATTAATTCAGAAAAAATATGAAAAACGATATTAAAAGCGTGAAAAGCCCT

                                                      *                      
        466 CCAATATTTTTAGCGTTAAATTATATAAATTATATGAGTATTTTATCCAAAAACTGAGGAAAAAA
        129 CCAATATTTTTAGCGTTAAATTATATAAATTATATGAGTATTATATCCAAAAACTGAGGAAAAAA

                                                             *   *           
        531 TTTTCGCGGTCATTTTTTGCAAAATTTTAGCCAAAATCGTGTACTAACCTTCACGATTTTTGGCT
        194 TTTTCGCGGTCATTTTTTGCAAAATTTTAGCCAAAATCGTGTACTAACCATCAAGATTTTTGGCT

                                     *            *                          
        596 AAAAATGCGTTCCGGGGACCCGACTTAGTTTTGCATGATTTTTGGCGTCAAGACTCCTTGAAATA
        259 AAAAATGCGTTCCGGGGACCCGACTCAGTTTTGCATGAATTTTGGCGTCAAGACTCCTTGAAATA

                     
        661 TCTAAATTA
        324 TCTAAATTA

                                         *        
        670 ATCTAATAAAAAATTAGCCACATTGCATTAAAGGATTT
          1 ATCTAATAAAAAATTAGCCACATTGCATTTAAGGATTT

        708 TTGAAGTCCG


Statistics
Matches: 341,  Mismatches: 28, Indels: 3
        0.92            0.08        0.01

Matches are distributed among these distances:
 332   67  0.20
 333  274  0.80

ACGTcount: A:0.34, C:0.14, G:0.16, T:0.36


Consensus pattern (332 bp):   
ATCTAATAAAAAATTAGCCACATTGCATTTAAGGATTTATTTTTACGAGCATTTGAATCTTGTTT
CGATTTAATTAGAATTAATTCAGAAAAAATATGAAAAACGATATTAAAAGCGTGAAAAGCCCTCC
AATATTTTTAGCGTTAAATTATATAAATTATATGAGTATTATATCCAAAAACTGAGGAAAAAATT
TTCGCGGTCATTTTTTGCAAAATTTTAGCCAAAATCGTGTACTAACCATCAAGATTTTTGGCTAA
AAATGCGTTCCGGGGACCCGACTCAGTTTTGCATGAATTTTGGCGTCAAGACTCCTTGAAATATC
TAAATTA
Done.