Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01005750.1 Corchorus capsularis cultivar CVL-1 contig05768, 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, 880

Length: 1467
ACGTcount: A:0.37, C:0.14, G:0.16, T:0.33


Found at i:642 original size:324 final size:313

Alignment explanation


    Indices: 1--689  Score: 896
    Period size: 324  Copynumber: 2.2  Consensus size: 313

                          *   *        *                                     
          1 ATTTTGAGGAGTCTTGGCACAAAAAATTATGCAAAACTGAGTCGGGGCCCCGGAACGCGTTTTTA
          1 ATTTTGAGGAGTCTAGGCGCAAAAAATCATGCAAAACTGAGTCGGGGCCCCGGAACGCGTTTTTA

             *          *  *  *                   *          *               
         66 GCCAAAAACCGTGATGTACACGATTTCGGCTAAAAAAATTTGACCCGAATGTTTTTTACTCAATT
         66 GACAAAAACCGTAATATAAACGATTTCGGCTAAAAAAAATTGACCCGAAAGTTTTTTACTCAATT

                 *      *                    *     *       *        *        
        131 GTTTGGCACAATGATAATAAAAAATATATAACTTAAAATGAAAAAGATTGAAGGGCGTTTAACGC
        131 GTTTGCCACAATAATAATAAAAAATATATAACTGAAAATCAAAAAGAATGAAGGGCCTTTAACGC

               *     *                                                       
        196 TGCTAATATCGTTTTTTTTTTGAAGAAATTTCTAATTAAATCGGAAAAAGATTCTGATGCTCGTA
        196 TGCAAATATAGTTTTTTTTTTGAAGAAATTTCTAATTAAATCGGAAAAAGATTCTGATGCTCGTA

                 *   *          * * *    *             *      *  
        261 AAAATGAATTCTTAAATCCACTTTTTGTATGATTTCGATAGATTAATATATAT
        261 AAAATAAATCCTTAAATCCAATATGTGTAAGATTTCGATAGATCAATATAGAT

                                                                   *         
        314 ATTTTGAGGAGTCTAGGCGCAAAAAATCATGCAAAACTGAGTCGGGGCCCCGGAATGCGTTTTTA
          1 ATTTTGAGGAGTCTAGGCGCAAAAAATCATGCAAAACTGAGTCGGGGCCCCGGAACGCGTTTTTA

              *                                                              
        379 GATAAAAACCGTAATAACATAAACGATTTCGGCTAAAATTTTGAAAAATTGACCCGAAAG-TTTT
         66 GACAAAAACCGTAAT---ATAAACGATTTCGGCT-AAA-----AAAAATTGACCCGAAAGTTTTT

                      *         *                                            
        443 TACTCAATTTTTTTGCCACACTAATAATAAAAAAATATATAACTGAAGAA-CAAAAAGAATGAAG
        122 TACTCAA-TTGTTTGCCACAATAATAAT-AAAAAATATATAACTGAA-AATCAAAAAGAATGAAG

                   *     *                       **       **                 
        507 GGCCTTTTACGCTTCAAATATAGTTTTTTTTTTTGAATTAATTTCTGTTTAAATCGGAAAAAGAT
        184 GGCCTTTAACGCTGCAAATATAG-TTTTTTTTTTGAAGAAATTTCTAATTAAATCGGAAAAAGAT

                           *                                  *              
        572 TCTGATGCTCGTAAATATAAATCCTTAAATCCAATATGTGTAAGATTTCGTTAGATCAATATAGA
        248 TCTGATGCTCGTAAAAATAAATCCTTAAATCCAATATGTGTAAGATTTCGATAGATCAATATAGA

             
        637 T
        313 T

                 *                               *              
        638 ATTTTAAGGAGTCTAGGCGCAAAAAATCATGCAAAACGGAGTCGGGGCCCCG
          1 ATTTTGAGGAGTCTAGGCGCAAAAAATCATGCAAAACTGAGTCGGGGCCCCG

        690 TAAACGATTT


Statistics
Matches: 324,  Mismatches: 39, Indels: 15
        0.86            0.10        0.04

Matches are distributed among these distances:
 313   73  0.23
 316   14  0.04
 317    3  0.01
 321   11  0.03
 322   31  0.10
 323   47  0.15
 324  145  0.45

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


Consensus pattern (313 bp):   
ATTTTGAGGAGTCTAGGCGCAAAAAATCATGCAAAACTGAGTCGGGGCCCCGGAACGCGTTTTTA
GACAAAAACCGTAATATAAACGATTTCGGCTAAAAAAAATTGACCCGAAAGTTTTTTACTCAATT
GTTTGCCACAATAATAATAAAAAATATATAACTGAAAATCAAAAAGAATGAAGGGCCTTTAACGC
TGCAAATATAGTTTTTTTTTTGAAGAAATTTCTAATTAAATCGGAAAAAGATTCTGATGCTCGTA
AAAATAAATCCTTAAATCCAATATGTGTAAGATTTCGATAGATCAATATAGAT
Done.