Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01002467.1 Corchorus olitorius cultivar O-4 contig02467, 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:0.36, C:0.15, G:0.15, T:0.34


Found at i:633 original size:332 final size:329

Alignment explanation


    Indices: 1--889  Score: 1196
    Period size: 332  Copynumber: 2.7  Consensus size: 329

                                    *                     *    **        *   
          1 TTTTTCCTCAATTTTTGGCCACAACTCTCATAAAATATATATAATTTAAAGGCAAAAAGATCGAA
          1 TTTTTCCTCAATTTTTGGCCACAATTCTCATAAAA-ATATATAATTCAAAGAAAAAAAGATTGAA

                      *                                           *      *   
         66 GGGTTTTTCACGCTTCTAATATCGTTTTTCCAATTTTTTCTGAATTAATTTCAAATAATATCGAA
         65 GGGTTTTTCAAGCTTCTAATATCGTTTTTCCAATTTTTTCTGAATTAATTTCAATTAA-ATAGAA

                          *              *           *      *       * *    * 
        131 ACATGATTC-GATGGTCGTAAAAACAAATCCTTAAATCCAATGTGGCTCAGATTTGTTTAGATAA
        129 ACATGATTCAGATGCTCGTAAAAACAAATTCTTAAATCCAAAGTGGCTGAGATTTGGTCAGATGA

                        *            *          *                  *    *    
        195 ATATAAATATTTTAA-GAAGTCTTCTTGCCAAAAATTATGCAAAAATGAGTCGGGGCCCCGAAAC
        194 ATATAAATATTTCAAGGAA-TCTTCGTG-CAAAAATCATGCAAAAATGAGTCGGGACCCCAAAAC

                     *                                    *         *        
        259 GCGTTTTTATCTTAAAACTGTGATAGAAAGTACACGATTTCGGCTACAATTTTGC-GAAATTGAT
        257 GCGTTTTTAACTTAAAACTGTGATAGAAAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGAT

                     
        323 C-CGAAAGA
        322 CACGAAA-A

                             *                   *           *               
        331 TTTTTCCTCAATTTTTTTGCCACAATTCTCATAAAAAAATATAATTCAATGAAAAAAAGATTGAA
          1 TTTTTCCTCAA-TTTTTGGCCACAATTCTCATAAAAATATATAATTCAAAGAAAAAAAGATTGAA

                                                         *                   
        396 GGGTTTTTCAAGCTTCTAATATCGTTTTTCCAATTTTTTTCTGAAGTAATTTCGAATTAAATAGA
         65 GGGTTTTTCAAGCTTCTAATATCGTTTTTCCAA-TTTTTTCTGAATTAATTTC-AATTAAATAGA

                                                       *                     
        461 AACATGATTCAGATGCTCGTAAAAACAAATTCTTAAATCCAAACTGGCTGAGATTTGGTCAGATG
        128 AACATGATTCAGATGCTCGTAAAAACAAATTCTTAAATCCAAAGTGGCTGAGATTTGGTCAGATG

                  *   *                                  *            *      
        526 AATATAGATAGTTCAAGGAATCTTCGTGCTAAAAATCATGCAAAACTGAGTCGGGACCTCAAAAC
        193 AATATAAATATTTCAAGGAATCTTCGTGC-AAAAATCATGCAAAAATGAGTCGGGACCCCAAAAC

                         *           *  *   *                                
        591 GCGTTTTTAACTTCAAA-TCGTGATGGATAGTGCACGATTTCGGCTAAAATTTTGCAAAAATTGA
        257 GCGTTTTTAACTTAAAACT-GTGATAGAAAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGA

               *     
        655 TCAGGAAAA
        321 TCACGAAAA

                    *                         *                        *     
        664 TTTTTCCTTAATTTTTGGCCACAATTCTCATAGACAATATATAATTCAAAGAAAAAAAGCTTGAA
          1 TTTTTCCTCAATTTTTGGCCACAATTCTCATA-AAAATATATAATTCAAAGAAAAAAAGATTGAA

                      *    *                                    *            
        729 GGGTTTTTCAGGCTTTTAATATCGTTTTTCC-ATTTTTTCTGAATTAATTTTTAATTAAATAGAA
         65 GGGTTTTTCAAGCTTCTAATATCGTTTTTCCAATTTTTTCTGAATTAA-TTTCAATTAAATAGAA

                   *  *                 *                                    
        793 ACATGATACAAATGCTCGTAAAAACAAAATCTTAAATCCAAAGTGGCTGAGATTTGGTCAGATGA
        129 ACATGATTCAGATGCTCGTAAAAACAAATTCTTAAATCCAAAGTGGCTGAGATTTGGTCAGATGA

                              *  *          
        858 ATATAAATATTTCAAGGATTCCTCGTGCAAAA
        194 ATATAAATATTTCAAGGAATCTTCGTGCAAAA

        890 CTAAGTCGGT


Statistics
Matches: 493,  Mismatches: 55, Indels: 22
        0.86            0.10        0.04

Matches are distributed among these distances:
 330   70  0.14
 331  167  0.34
 332  172  0.35
 333   80  0.16
 334    4  0.01

ACGTcount: A:0.36, C:0.15, G:0.15, T:0.34


Consensus pattern (329 bp):   
TTTTTCCTCAATTTTTGGCCACAATTCTCATAAAAATATATAATTCAAAGAAAAAAAGATTGAAG
GGTTTTTCAAGCTTCTAATATCGTTTTTCCAATTTTTTCTGAATTAATTTCAATTAAATAGAAAC
ATGATTCAGATGCTCGTAAAAACAAATTCTTAAATCCAAAGTGGCTGAGATTTGGTCAGATGAAT
ATAAATATTTCAAGGAATCTTCGTGCAAAAATCATGCAAAAATGAGTCGGGACCCCAAAACGCGT
TTTTAACTTAAAACTGTGATAGAAAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGATCACG
AAAA

Done.