Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01023057.1 Corchorus olitorius cultivar O-4 contig23090, 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: 17545
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32


Found at i:11352 original size:147 final size:147

Alignment explanation


    Indices: 11078--11363  Score: 455
    Period size: 147  Copynumber: 1.9  Consensus size: 147

      11068 ATAGATGACA

                          *                 *                *   *        *  
      11078 CAACATTAAGTATGTTTGGTGGGCTTTTGTGGGCCTTGAATCATCCCCATTTTGACTCGTAATAG
          1 CAACATTAAGTATGCTTGGTGGGCTTTTGTGGACCTTGAATCATCCCCACTTTAACTCGTAACAG

                                      *                              *       
      11143 GCTCAAATTGAACCATTTACAAAAATGTTTAAAATCTAATTAGCGTTTTAACCTTAAGAATTGTA
         66 GCTCAAATTGAACCATTTACAAAAATATTTAAAATCTAATTAGCGTTTTAACCTTAAAAATTGTA

                             
      11208 CTTATGAATGTACGGGT
        131 CTTATGAATGTACGGGT

                *                            *    *                * *       
      11225 CAACCTTAAGTATGCTTGGTGGGCTTTTGTGGATCTTGGATCATCCCCACTTTAAGTTGTAACAG
          1 CAACATTAAGTATGCTTGGTGGGCTTTTGTGGACCTTGAATCATCCCCACTTTAACTCGTAACAG

                                               *                             
      11290 GCTCAAATTGAACCATTTACAAAAATATTTAAAATTTAATTAGCGTTTTAACCTTAAAAATTGTA
         66 GCTCAAATTGAACCATTTACAAAAATATTTAAAATCTAATTAGCGTTTTAACCTTAAAAATTGTA

                     
      11355 CTTATGAAT
        131 CTTATGAAT

      11364 ATATAGTCTT


Statistics
Matches: 126,  Mismatches: 13, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
 147  126  1.00

ACGTcount: A:0.31, C:0.16, G:0.17, T:0.36


Consensus pattern (147 bp):   
CAACATTAAGTATGCTTGGTGGGCTTTTGTGGACCTTGAATCATCCCCACTTTAACTCGTAACAG
GCTCAAATTGAACCATTTACAAAAATATTTAAAATCTAATTAGCGTTTTAACCTTAAAAATTGTA
CTTATGAATGTACGGGT

Found at i:15269 original size:59 final size:59

Alignment explanation


    Indices: 15197--15314  Score: 227
    Period size: 59  Copynumber: 2.0  Consensus size: 59

      15187 GTGTGATCAG

                                                                       
      15197 TTGATAAAGCATTTGGACTCTGAAAAAGTGAGGAAATTAAAAAATAATCATGAGTTCAA
          1 TTGATAAAGCATTTGGACTCTGAAAAAGTGAGGAAATTAAAAAATAATCATGAGTTCAA

                                                     *                 
      15256 TTGATAAAGCATTTGGACTCTGAAAAAGTGAGGAAATTAAAGAATAATCATGAGTTCAA
          1 TTGATAAAGCATTTGGACTCTGAAAAAGTGAGGAAATTAAAAAATAATCATGAGTTCAA

      15315 AAAATGTTAA


Statistics
Matches: 58,  Mismatches: 1, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
  59   58  1.00

ACGTcount: A:0.45, C:0.08, G:0.19, T:0.27


Consensus pattern (59 bp):   
TTGATAAAGCATTTGGACTCTGAAAAAGTGAGGAAATTAAAAAATAATCATGAGTTCAA
Done.