Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01010353.1 Corchorus olitorius cultivar O-4 contig10385, 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, 976

Length: 1627
ACGTcount: A:0.32, C:0.14, G:0.17, T:0.37


Found at i:1178 original size:335 final size:336

Alignment explanation


    Indices: 586--1221  Score: 807
    Period size: 335  Copynumber: 1.9  Consensus size: 336

        576 TTCGGGTCAG

                    *                                             *       *  
        586 ATTTTAGCGGAAATCGTGTACTAACCATCATGGTTTTCGGCTAAAAAACGCGTTTCGTGGCCCCG
          1 ATTTTAGCCGAAATCGTGTACTAACCATCATGGTTTTCGGCTAAAAAACGCGTTCCGTGGCCACG

                 *    *                    *                          * *    
        651 GCTCAGTTTTGCATGATTTTGGGCAGAAAGACTCCTTCAAATATCTATATTCATGTAAGCGAATC
         66 GCTCAATTTTACATGATTTTGGGCAGAAAGAATCCTTCAAATATCTATATTCATGTAACCAAATC

             *             *                * *                 *     *      
        716 TTAGCAAAAATGGATTTAAGGATTTGTTTTTATGGGCATCTAAATCTTGTTTTGATTTTATTAGA
        131 TCAGCAAAAATGGATATAAGGATTTGTTTTTACGAGCATCTAAATCTTGTTTCGATTTAATTAGA

                             *          *         **         *     *       * 
        781 AATAAATTCAGAAAAAAGGGAAAAATGATATTAGAAGCGTGAAAAACCCTTCAATTTTTTTGGTG
        196 AATAAATTCAGAAAAAAAGGAAAAATGACATTAGAAGCCCGAAAAACCCGTCAATCTTTTTGGCG

                              *                                              
        846 TTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGTGGAAACACTTTTCGGGTCAGTTT
        261 TTGAATTATATATTTTTTATGAGTATTGTGGCAAAAAATTGTGGAAACACTTTTCGGGTCAGTTT

                       
        911 TTTTTTGCAAA
        326 TTTTTTGCAAA

                                    *             *          *            *  
        922 ATTTTAGCCGAAATCGTGTACTAATCATCACT-GTTTTTGGCT-AAAAATGCGTTCCG-GAGTCA
          1 ATTTTAGCCGAAATCGTGTACTAACCATCA-TGGTTTTCGGCTAAAAAACGCGTTCCGTG-GCCA

                                  *    *            *            *           
        984 CGGCTCAATTTTACATGATTTTTGGCATAAAGAATCCTT-GAATATCTATATTGATCG-AACCAA
         64 CGGCTCAATTTTACATGATTTTGGGCAGAAAGAATCCTTCAAATATCTATATTCAT-GTAACCAA

                    * * *                           *   *   *                
       1047 ATCTCAGCCACATTGGATATAAGGATTTGTTTTTACGAGCTTCTGAATTTTGTTTCGATTTAATT
        128 ATCTCAGCAAAAATGGATATAAGGATTTGTTTTTACGAGCATCTAAATCTTGTTTCGATTTAATT

            *     *     *          *     *                    *              
       1112 TGAAATTAATT-TGTAAAAAAAATGAAAACTGACATTAGAAGCCCGAAAAGCCCGTCAATCTTTT
        193 AGAAATAAATTCAG--AAAAAAAGGAAAAATGACATTAGAAGCCCGAAAAACCCGTCAATCTTTT

                                                          
       1176 TGGCGTTGAATTATATATTTTTTATGAGTATTGTGGCAAAAAATTG
        256 TGGCGTTGAATTATATATTTTTTATGAGTATTGTGGCAAAAAATTG

       1222 AGAAAAAAAA


Statistics
Matches: 253,  Mismatches: 42, Indels: 11
        0.83            0.14        0.04

Matches are distributed among these distances:
 333    1  0.00
 334   81  0.32
 335  133  0.53
 336   37  0.15
 337    1  0.00

ACGTcount: A:0.31, C:0.14, G:0.18, T:0.36


Consensus pattern (336 bp):   
ATTTTAGCCGAAATCGTGTACTAACCATCATGGTTTTCGGCTAAAAAACGCGTTCCGTGGCCACG
GCTCAATTTTACATGATTTTGGGCAGAAAGAATCCTTCAAATATCTATATTCATGTAACCAAATC
TCAGCAAAAATGGATATAAGGATTTGTTTTTACGAGCATCTAAATCTTGTTTCGATTTAATTAGA
AATAAATTCAGAAAAAAAGGAAAAATGACATTAGAAGCCCGAAAAACCCGTCAATCTTTTTGGCG
TTGAATTATATATTTTTTATGAGTATTGTGGCAAAAAATTGTGGAAACACTTTTCGGGTCAGTTT
TTTTTTGCAAA
Done.