Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01014161.1 Corchorus capsularis cultivar CVL-1 contig14182, 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: 2129
ACGTcount: A:0.26, C:0.21, G:0.22, T:0.30


Found at i:75 original size:49 final size:49

Alignment explanation


    Indices: 5--190  Score: 225
    Period size: 49  Copynumber: 3.8  Consensus size: 49

          1 AATC

                                                      *      
          5 TTTACTTG-TTTTTCCCAAAATGCCCTTCCCGGACGGAAGGCACTTA-T
          1 TTTACTTGCTTTTTCCCAAAATGCCCTTCCCGGACGGAAGGCGCTTATT

                             *               *    *  *        
         52 TTTACTTGCTATTTTCCAAAAATGCCCTTCCCGAACGGGAGACGCTTATT
          1 TTTACTTGCT-TTTTCCCAAAATGCCCTTCCCGGACGGAAGGCGCTTATT

                 * *            *                         *   
        102 TTTACCTACTTTTTCCCAAAGTGCCCTTCCCGGAC-GAAGGGCGCTAATT
          1 TTTACTTGCTTTTTCCCAAAATGCCCTTCCCGGACGGAA-GGCGCTTATT

                            *    *            *     
        151 TTTACTTGCTTTTTCCTAAAACGCCCTTCCCGGATGGAAG
          1 TTTACTTGCTTTTTCCCAAAATGCCCTTCCCGGACGGAAG

        191 ACGTTGGTTT


Statistics
Matches: 115,  Mismatches: 19, Indels: 8
        0.81            0.13        0.06

Matches are distributed among these distances:
  47    8  0.07
  48    3  0.03
  49   92  0.80
  50   12  0.10

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


Consensus pattern (49 bp):   
TTTACTTGCTTTTTCCCAAAATGCCCTTCCCGGACGGAAGGCGCTTATT

Found at i:193 original size:98 final size:98

Alignment explanation


    Indices: 13--193  Score: 258
    Period size: 98  Copynumber: 1.8  Consensus size: 98

          3 TCTTTACTTG

                                                *                        *   
         13 TTTTTCCCAAAATGCCCTTCCCGGACGGAAGGCACTTATTTTACTTGCTATTTTCCAAAAATGCC
          1 TTTTTCCCAAAATGCCCTTCCCGGACGGAAGGCACTAATTTTACTTGCTATTTTCCAAAAACGCC

                        *                    
         78 CTTCCCGAACGGGAGACGCTTATTTTTACCTAC
         66 CTTCCCGAACGGAAGACGCTTATTTTTACCTAC

                       *                      *                       *      
        111 TTTTTCCCAAAGTGCCCTTCCCGGAC-GAAGGGCGCTAATTTTTACTTGCT-TTTTCCTAAAACG
          1 TTTTTCCCAAAATGCCCTTCCCGGACGGAA-GGCACTAA-TTTTACTTGCTATTTTCCAAAAACG

                     * *        
        174 CCCTTCCCGGATGGAAGACG
         64 CCCTTCCCGAACGGAAGACG

        194 TTGGTTTTAC


Statistics
Matches: 73,  Mismatches: 8, Indels: 4
        0.86            0.09        0.05

Matches are distributed among these distances:
  97    3  0.04
  98   59  0.81
  99   11  0.15

ACGTcount: A:0.22, C:0.29, G:0.18, T:0.31


Consensus pattern (98 bp):   
TTTTTCCCAAAATGCCCTTCCCGGACGGAAGGCACTAATTTTACTTGCTATTTTCCAAAAACGCC
CTTCCCGAACGGAAGACGCTTATTTTTACCTAC
Done.