Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01004843.1 Corchorus capsularis cultivar CVL-1 contig04861, 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: 3323
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.31


Found at i:1186 original size:49 final size:49

Alignment explanation


    Indices: 1061--1534  Score: 555
    Period size: 49  Copynumber: 9.8  Consensus size: 49

       1051 AGTTTTCACT

                *                                *           
       1061 TGCTATTTCCCAAAATGCCCTTCCCGGACGGAAGGCATTTATTTTTACC
          1 TGCTTTTTCCCAAAATGCCCTTCCCGGACGGAAGGCACTTATTTTTACC

                           *                       *         
       1110 TG-TTTTTCCCAAAACGCCCTTCCCGGACGGAAGGCACTGATTTTTACC
          1 TGCTTTTTCCCAAAATGCCCTTCCCGGACGGAAGGCACTTATTTTTACC

                *                                *          *
       1158 TGCTATTTCCCAAAATGCCCTTCCCGGACGGAAGGCATTTATTTTTACT
          1 TGCTTTTTCCCAAAATGCCCTTCCCGGACGGAAGGCACTTATTTTTACC

                           **                      *         
       1207 TG-TTTTTCCCAAAACACCCTTCCCGGACGGAAGGCACTGATTTTTACC
          1 TGCTTTTTCCCAAAATGCCCTTCCCGGACGGAAGGCACTTATTTTTACC

              *       *    *            *        * *  *     *
       1255 TGTTTTTTCCTAAAACGCCCTTCCCGGAAGGAAGGCAATAATCTTTACT
          1 TGCTTTTTCCCAAAATGCCCTTCCCGGACGGAAGGCACTTATTTTTACC

                                                            *
       1304 TG-TTTTTCCCAAAATGCCCTTCCCGGACGGAAGGCACTTA-TTTTACT
          1 TGCTTTTTCCCAAAATGCCCTTCCCGGACGGAAGGCACTTATTTTTACC

                       *                       * *            
       1351 TGCTATTTTCCAAAAATGCCCTTCCCGGACGGAAGACGCTTATTTTTACC
          1 TGCT-TTTTCCCAAAATGCCCTTCCCGGACGGAAGGCACTTATTTTTACC

             *            *                        *        *
       1401 TACTTTTTCCCAAAGTGCCCTTCCCGGACGGAAGGCACTCATTTTTACT
          1 TGCTTTTTCCCAAAATGCCCTTCCCGGACGGAAGGCACTTATTTTTACC

                      *    *            *       **   *       
       1450 TGCTTTTTCCTAAAACGCCCTTCCCGGATGGAAGG-TGTTAGTTTTA-C
          1 TGCTTTTTCCCAAAATGCCCTTCCCGGACGGAAGGCACTTATTTTTACC

                      **           *     * *      
       1497 TCGCTTTTTCTTAAAATGCCCTTTCCGGATGAAAGGCA
          1 T-GCTTTTTCCCAAAATGCCCTTCCCGGACGGAAGGCA

       1535 AGTTCACTTT


Statistics
Matches: 364,  Mismatches: 54, Indels: 14
        0.84            0.12        0.03

Matches are distributed among these distances:
  47    9  0.02
  48  157  0.43
  49  189  0.52
  50    9  0.02

ACGTcount: A:0.22, C:0.28, G:0.17, T:0.33


Consensus pattern (49 bp):   
TGCTTTTTCCCAAAATGCCCTTCCCGGACGGAAGGCACTTATTTTTACC

Found at i:1227 original size:97 final size:97

Alignment explanation


    Indices: 1061--1484  Score: 580
    Period size: 97  Copynumber: 4.4  Consensus size: 97

       1051 AGTTTTCACT

                                                            *                
       1061 TGCTATTTCCCAAAATGCCCTTCCCGGACGGAAGGCATTTATTTTTACCTGTTTTTCCCAAAACG
          1 TGCTATTTCCCAAAATGCCCTTCCCGGACGGAAGGCATTTATTTTTACTTGTTTTTCCCAAAACG

                                            
       1126 CCCTTCCCGGACGGAAGGCACTGATTTTTACC
         66 CCCTTCCCGGACGGAAGGCACTGATTTTTACC

                                                                            *
       1158 TGCTATTTCCCAAAATGCCCTTCCCGGACGGAAGGCATTTATTTTTACTTGTTTTTCCCAAAACA
          1 TGCTATTTCCCAAAATGCCCTTCCCGGACGGAAGGCATTTATTTTTACTTGTTTTTCCCAAAACG

                                            
       1223 CCCTTCCCGGACGGAAGGCACTGATTTTTACC
         66 CCCTTCCCGGACGGAAGGCACTGATTTTTACC

              * *     *    *            *        * *  *                    * 
       1255 TGTTTTTTCCTAAAACGCCCTTCCCGGAAGGAAGGCAATAATCTTTACTTGTTTTTCCCAAAATG
          1 TGCTATTTCCCAAAATGCCCTTCCCGGACGGAAGGCATTTATTTTTACTTGTTTTTCCCAAAACG

                                  *        *
       1320 CCCTTCCCGGACGGAAGGCACTTA-TTTTACT
         66 CCCTTCCCGGACGGAAGGCACTGATTTTTACC

                       *                       * **            **           *
       1351 TGCTATTTTCCAAAAATGCCCTTCCCGGACGGAAGACGCTTATTTTTACCTACTTTTTCCCAAAG
          1 TGCTA-TTTCCCAAAATGCCCTTCCCGGACGGAAGGCATTTATTTTTA-CTTGTTTTTCCCAAAA

            *                       *        *
       1416 TGCCCTTCCCGGACGGAAGGCACTCATTTTTACT
         64 CGCCCTTCCCGGACGGAAGGCACTGATTTTTACC

                *     *    *            *      
       1450 TGCTTTTTCCTAAAACGCCCTTCCCGGATGGAAGG
          1 TGCTATTTCCCAAAATGCCCTTCCCGGACGGAAGG

       1485 TGTTAGTTTT


Statistics
Matches: 291,  Mismatches: 33, Indels: 5
        0.88            0.10        0.02

Matches are distributed among these distances:
  96    9  0.03
  97  207  0.71
  98   64  0.22
  99   11  0.04

ACGTcount: A:0.22, C:0.29, G:0.17, T:0.32


Consensus pattern (97 bp):   
TGCTATTTCCCAAAATGCCCTTCCCGGACGGAAGGCATTTATTTTTACTTGTTTTTCCCAAAACG
CCCTTCCCGGACGGAAGGCACTGATTTTTACC
Done.