Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01019421.1 Corchorus olitorius cultivar O-4 contig19454, 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: 2920
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.33


Found at i:2481 original size:316 final size:313

Alignment explanation


    Indices: 1732--2666  Score: 1058
    Period size: 316  Copynumber: 2.9  Consensus size: 313

       1722 TTTTAGTCAT

                         *          *   *                        *      *    
       1732 AATACTCATAAAAAATATATAATTCAACGCCAAAAAGATTGAACGG-CTTTTCGCGCTTTGAATA
          1 AATACTCATAAAATATATATAATTTAACACCAAAAAGATTG-A-GGACTTTTCACGCTTTTAATA

                                              *                  *           
       1796 TCGTTTTTCATATTTGTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTTAGATGCTCGTA
         64 TCGTTTTTCATA-TT-TTTCTGAATTAATTTCTAGTTAAATCGAAACAAGATTCAGATGCTCGTA

                     *       *    *     *      *  *                          
       1861 AAAACAAATCCTTAAATGCAATATGGCTAAGATTTTATTAGATGAATATAGATATTTCAAGGAGT
        127 AAAACAAATTCTTAAATCCAATGTGGCTGAGATTTGATAAGATGAATATAGATATTTCAAGGAGT

            *     *            *      *    *        *                        
       1926 GTCGGCGCTAAAAATCATGTAAAACTGAGCTGGGGCCCCGAAACGCGTTTTTAGCCAAAAATCCG
        192 CTCGGCAC-AAAAATCATGCAAAACTTAG-TCGGGCCCCGGAACGCGTTTTTAGCCAAAAA-CC-

                 *              *        *               **   *             
       1991 TGATGGTTAGTACACGATTTTGGCTAAAACTTTGCAGAAAATTTTTTCCCCTATTTCTTGATAA
        253 -GATGATTAGTACACGATTTCGGCTAAAATTTTGCA-AAAA-TTTGACCCATATTTCTTGATAA

                          *                    *        *                    
       2055 AATACTCATAAAATTTATATAATTTAACACCAAAAGGATTGGAGAACTTTTCACGCTTTTAATAT
          1 AATACTCATAAAATATATATAATTTAACACCAAAAAGATT-GAGGACTTTTCACGCTTTTAATAT

             *                                                               
       2120 CATTTTTCATATTTTTCTGAATTAATTTCT-GATTAAATCGAAACAAGATTCAGATGCTCGTAAA
         65 CGTTTTTCATATTTTTCTGAATTAATTTCTAG-TTAAATCGAAACAAGATTCAGATGCTCGTAAA

               *           *                                *                
       2184 AACTAATTCTTAAATTCAATGTGGCTGAGATTTGATAAGATGAATATAAATATTTCAAGGAGTCT
        129 AACAAATTCTTAAATCCAATGTGGCTGAGATTTGATAAGATGAATATAGATATTTCAAGGAGTCT

              *                            *        *            *          *
       2249 CGACACAAAGAATCATGCAAAACTTAGTCGGTCCCCGGAATGCGTTTTTAGCCGAAAACCG-TGC
        194 CGGCACAAA-AATCATGCAAAACTTAGTCGGGCCCCGGAACGCGTTTTTAGCCAAAAACCGATGA

                                                                      * 
       2313 TTAGTACACGATTTCGGCTAAAATTTTGCAAAAA-TTGACCCGAAATATTT-TCTG-TCA
        258 TTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTTGACCC---ATATTTCT-TGATAA

               **               *                *                           
       2370 AATTTTGCATAAAATATATACAATTTAACACCAAAAATATTAGAGGACTTTTCACGCTTTTAATA
          1 AATACT-CATAAAATATATATAATTTAACACCAAAAAGATT-GAGGACTTTTCACGCTTTTAATA

                                                    *                        
       2435 TCGTTTTTCATATTTTTCTGAATTAGA-TTCTAGTTAAATTGAAACAAGATTCAGATGCTCGTAA
         64 TCGTTTTTCATATTTTTCTGAATTA-ATTTCTAGTTAAATCGAAACAAGATTCAGATGCTCGTAA

                        *          *     *   *               *     *    *    
       2499 AAACAAATTCTTCAATCCAATGTAGCTGACATTAGATTAA-ATGAATATGGATATCTCAAAGAGT
        128 AAACAAATTCTTAAATCCAATGTGGCTGAGATTTGA-TAAGATGAATATAGATATTTCAAGGAGT

              *    *               *                              *         *
       2563 CTTGGCGCCAAAAATCATGCAAATCTTAGTCGGGGCCCCGGAACGCGTTTTTAGGCAAAAACAGT
        192 CTCGGC-ACAAAAATCATGCAAAACTTAGTC-GGGCCCCGGAACGCGTTTTTAGCCAAAAAC--C

                    *  *             *             
       2628 GATGATTATTATACGATTTCGGCTAGAATTTTGCAAAAA
        253 GATGATTAGTACACGATTTCGGCTAAAATTTTGCAAAAA

       2667 CTTACTCGAA


Statistics
Matches: 526,  Mismatches: 69, Indels: 37
        0.83            0.11        0.06

Matches are distributed among these distances:
 313    5  0.01
 315   11  0.02
 316  219  0.42
 317   36  0.07
 319    3  0.01
 320   62  0.12
 321  123  0.23
 322    3  0.01
 323   63  0.12
 324    1  0.00

ACGTcount: A:0.36, C:0.16, G:0.15, T:0.33


Consensus pattern (313 bp):   
AATACTCATAAAATATATATAATTTAACACCAAAAAGATTGAGGACTTTTCACGCTTTTAATATC
GTTTTTCATATTTTTCTGAATTAATTTCTAGTTAAATCGAAACAAGATTCAGATGCTCGTAAAAA
CAAATTCTTAAATCCAATGTGGCTGAGATTTGATAAGATGAATATAGATATTTCAAGGAGTCTCG
GCACAAAAATCATGCAAAACTTAGTCGGGCCCCGGAACGCGTTTTTAGCCAAAAACCGATGATTA
GTACACGATTTCGGCTAAAATTTTGCAAAAATTTGACCCATATTTCTTGATAA
Done.