Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01007008.1 Corchorus olitorius cultivar O-4 contig07033, 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, 604

Length: 1007
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33


Found at i:893 original size:324 final size:324

Alignment explanation


    Indices: 3--981  Score: 1188
    Period size: 335  Copynumber: 3.0  Consensus size: 324

          1 GT

                                                                *            
          3 CGGGGCTCGGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATCTCGGCTAAAAAC
          1 CGGGGCTCGGGAACGCGTTTTTAGCCAAAAACCGTGATGG-T-GTACACGATTTCGGCTAAAAAC

                                            *                                
         68 TGATCGAAAAAGTTTTTTTTCTCAATTTTTTTACCACAATACTCAGAAAAAATATATAATTCAAC
         64 TGATCGAAAAAGTTTTTTTTCTCAA-TTTTTTGCCACAATACTCAGAAAAAATATATAATTCAAC

                            *   *                                            
        133 GCCAAAAAAAATTGACCGG-TTTTTCACGC-GCTTCTAATATCGTTTTTCC-TTTTTTCCGAATT
        128 GCC-AAAAAAATTGACTGGCATTTTCACGCTGCTTCTAATATCGTTTTTCCATTTTTTCCGAATT

                                                                     *     * 
        195 AATTTTTAATTAAATTGAAACAAGATTCAGATGCTCGTAAAAACAAATACTTAAATCTAATGTCG
        192 AATTTTTAATTAAATTGAAACAAGATTCAGATGCTCGTAAAAACAAATACTTAAATCCAATGTGG

                         *                                     *         * * 
        260 CTGGGAGCCTGAGATTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTTTGCCAAAAATTAAG
        257 CT--GA--C--A-TTTGGTTAGATGAATATAGATATTTCAAGGAGTC-TTTGGCCAAAAATCATG

            *          
        325 AAAAACTGAGG
        314 CAAAACTGAGG

                        *                       *                          * 
        336 CGGGGTCCTC-GAAACGCGTTTTTAGCCAAAAAACCATGATGGTTAGTACACGATTTTCGGCTTA
          1 CGGGG--CTCGGGAACGCGTTTTTAGCC-AAAAACCGTGATGG-T-GTACACGA-TTTCGGCTAA

              *    * *   ***          *                                      
        400 AAGCTGACCCAAATTTTTTTTTTTCTGAATTTTTTGCCACAATACTCAGAAAAAATATATAATTC
         60 AAACTGATCGAAAAAGTTTTTTTTCTCAATTTTTTGCCACAATACTCAGAAAAAATATATAATTC

             * *       **                  *              *                  
        465 ACCACCAAAAAGTTTGA-TGGTCA-TTTCACTCTG--T-TAATATCATTTTTCCAATTTTTTTCC
        125 AACGCCAAAAAAATTGACTGG-CATTTTCACGCTGCTTCTAATATCGTTTTTCC-A-TTTTTTCC

                *     *         *                *         *     *    *      
        525 GAATCAATTTCTAATTAAATCGAAACAAGATTCAGATACTCGTAAAACCAAATCCTTATATCCAA
        187 GAATTAATTTTTAATTAAATTGAAACAAGATTCAGATGCTCGTAAAAACAAATACTTAAATCCAA

                              *                               *              
        590 TGTGGCTGACATTTGGTTTGATGAATATAGATATTTCAAGGAGTCTTTGCACCAAAAATCATGCA
        252 TGTGGCTGACATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTG-GCCAAAAATCATGCA

               *    *
        655 AAATTGAGT
        316 AAACTGAGG

             *            *                                                  
        664 CTGGGCTCGGGAACACGTTTTTAGCCAAAAACCGTGAT-G-GTACACGATTTCGGCTAAAAACTG
          1 CGGGGCTCGGGAACGCGTTTTTAGCCAAAAACCGTGATGGTGTACACGATTTCGGCTAAAAACTG

                *                                **                          
        727 ATCGGAAAAGTTTTTTTTCTCAATTTTTTGCCACAATTTTCAGAAAAAAATATATAATTCAACGC
         66 ATCGAAAAAGTTTTTTTTCTCAATTTTTTGCCACAATACTCAG-AAAAAATATATAATTCAACGC

                                                                             
        792 CAAAAAAATTGACTGGCATTTTCACGCTGCTTCTAATATCGTTTTTCCATTTTTTCCGAATTAAT
        130 CAAAAAAATTGACTGGCATTTTCACGCTGCTTCTAATATCGTTTTTCCATTTTTTCCGAATTAAT

                                    *                             *  **  *   
        857 TTTTAATTAAATTGAAACAAGATTTAGATGCTCGTAAAAACAAATACTTAAATCGAACATGCCTG
        195 TTTTAATTAAATTGAAACAAGATTCAGATGCTCGTAAAAACAAATACTTAAATCCAATGTGGCTG

             *    *   *                         *      *                
        922 AGATTTTGTTCGATGAATATAGATATTTCAAGGAGTATTTAGGTCAAAAATCATGCAAAA
        260 ACATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTT-GGCCAAAAATCATGCAAAA

        982 ACAGAAAATA


Statistics
Matches: 550,  Mismatches: 77, Indels: 47
        0.82            0.11        0.07

Matches are distributed among these distances:
 321   48  0.09
 322   39  0.07
 323   12  0.02
 324  121  0.22
 325    4  0.01
 326   28  0.05
 327   18  0.03
 328   54  0.10
 329    1  0.00
 331    1  0.00
 332   14  0.03
 333   10  0.02
 334   32  0.06
 335  138  0.25
 336   30  0.05

ACGTcount: A:0.34, C:0.17, G:0.15, T:0.33


Consensus pattern (324 bp):   
CGGGGCTCGGGAACGCGTTTTTAGCCAAAAACCGTGATGGTGTACACGATTTCGGCTAAAAACTG
ATCGAAAAAGTTTTTTTTCTCAATTTTTTGCCACAATACTCAGAAAAAATATATAATTCAACGCC
AAAAAAATTGACTGGCATTTTCACGCTGCTTCTAATATCGTTTTTCCATTTTTTCCGAATTAATT
TTTAATTAAATTGAAACAAGATTCAGATGCTCGTAAAAACAAATACTTAAATCCAATGTGGCTGA
CATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTGGCCAAAAATCATGCAAAACTGAGG
Done.