Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01001647.1 Corchorus capsularis cultivar CVL-1 contig01647, 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: 2528
ACGTcount: A:0.32, C:0.15, G:0.17, T:0.36


Found at i:549 original size:280 final size:280

Alignment explanation


    Indices: 12--561  Score: 632
    Period size: 280  Copynumber: 2.0  Consensus size: 280

          2 AAGCATAAGA

                *                       *                      *             
         12 TTTTGGCTAAAAACGCGTTCCGGAGCCCTGGCTCAATTTTGCATGATTTTTGGCGCAAAGACTCC
          1 TTTTAGCTAAAAACGCGTTCCGGAGCCCCGGCTCAATTTTGCATGATTTTTAGCGCAAAGACTCC

                          *                       *   *                   *  
         77 TTGAAATATCAAATTTTCATTGAACCAAAACTCAACCATATTGGATATAAGGATTTTTTTTTTCG
         66 TTGAAATATCAAATATTCATTGAACCAAAACTCAACCACATTAGATATAAGGATTTTTTTTTACG

                   *   *                      *                 *            
        142 AGCATCTTAATCTTGTTTCGATTTAATTAGGAATTAATTCGGAAAAAAAATGGAAAAACGATTTT
        131 AGCATCTAAATATTGTTTCGATTTAATTAGGAATAAATTCGGAAAAAAAATGCAAAAACGATTTT

                   *                                               *         
        207 AGAAGCGTGAAAAGCCCGTCAATCTTTTTGGCGTTGAATTATATATTTTTTCTGAGTATTGTGGC
        196 AGAAGCGGGAAAAGCCCGTCAATCTTTTTGGCGTTGAATTATATATTTTTTCTGACTATTGTGGC

                                 
        272 AAAAAATAATTTCGGGTCAGT
        261 AAAAAA-AATTTCGGGTCAGT

                                *   *           *                     **     
        293 TTTTAGCTAAAAAACGCGTTTCGGGGCCCCGGCTCAGTTTTGCATGATTTTTAGCAG-GGAGACT
          1 TTTTAGCT-AAAAACGCGTTCCGGAGCCCCGGCTCAATTTTGCATGATTTTTAGC-GCAAAGACT

                         *                  *   ***          *               
        357 CCTTGAAATATC-TATATTCATCT-AACCAAATCTCGGTCACATTAGATTTAAGGA-TTTTTTTT
         64 CCTTGAAATATCAAATATTCAT-TGAACCAAAACTCAACCACATTAGATATAAGGATTTTTTTTT

                  *              *                                        *  
        419 ACGAGCTTCTAAATATTGTTTTGATTTAATT-GGAAATAAATT-GGAAAAAAAATGCAATAATC-
        128 ACGAGCATCTAAATATTGTTTCGATTTAATTAGG-AATAAATTCGGAAAAAAAATGCAA-AAACG

                       *           **    * *     *          * *              
        481 ATATTTA-AAGTGAGGAAAA-CCTTTCATTTTTTTTTTGCGTTGAATTGTCTATTTTTTCTGACT
        191 AT-TTTAGAAGCG-GGAAAAGCCCGTCA-ATCTTTTTGGCGTTGAATTATATATTTTTTCTGACT

                   *          
        544 ATTGTGGTAAAAAAAATT
        253 ATTGTGGCAAAAAAAATT

        562 GAGGAAAAAT


Statistics
Matches: 225,  Mismatches: 36, Indels: 18
        0.81            0.13        0.06

Matches are distributed among these distances:
 279   31  0.14
 280   96  0.43
 281   38  0.17
 282   59  0.26
 283    1  0.00

ACGTcount: A:0.31, C:0.14, G:0.17, T:0.37


Consensus pattern (280 bp):   
TTTTAGCTAAAAACGCGTTCCGGAGCCCCGGCTCAATTTTGCATGATTTTTAGCGCAAAGACTCC
TTGAAATATCAAATATTCATTGAACCAAAACTCAACCACATTAGATATAAGGATTTTTTTTTACG
AGCATCTAAATATTGTTTCGATTTAATTAGGAATAAATTCGGAAAAAAAATGCAAAAACGATTTT
AGAAGCGGGAAAAGCCCGTCAATCTTTTTGGCGTTGAATTATATATTTTTTCTGACTATTGTGGC
AAAAAAAATTTCGGGTCAGT

Done.