Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01007269.1 Corchorus olitorius cultivar O-4 contig07294, 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: 2428
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.34


Found at i:1804 original size:21 final size:22

Alignment explanation


    Indices: 1739--1841  Score: 111
    Period size: 22  Copynumber: 4.8  Consensus size: 22

       1729 AGTAGTTTAT

                          *    *  
       1739 TTTAGTTGCTGGAATTTG-CAA
          1 TTTAGTTGCTGGAAATTGTAAA

                *   *  *          
       1760 TTTACTTGTTGCAAATTGTAAA
          1 TTTAGTTGCTGGAAATTGTAAA

                          *    *  
       1782 TTTAGTTGCTGGAATTTG-CAA
          1 TTTAGTTGCTGGAAATTGTAAA

                *      *          
       1803 TTTACTTGCTGCAAATTGTAAA
          1 TTTAGTTGCTGGAAATTGTAAA

                             
       1825 TTTAGTTGCTGGAAATT
          1 TTTAGTTGCTGGAAATT

       1842 CAAATTTGCT


Statistics
Matches: 64,  Mismatches: 16, Indels: 3
        0.77            0.19        0.04

Matches are distributed among these distances:
  21   31  0.48
  22   33  0.52

ACGTcount: A:0.27, C:0.10, G:0.19, T:0.44


Consensus pattern (22 bp):   
TTTAGTTGCTGGAAATTGTAAA

Found at i:1848 original size:21 final size:22

Alignment explanation


    Indices: 1739--1848  Score: 118
    Period size: 21  Copynumber: 5.1  Consensus size: 22

       1729 AGTAGTTTAT

                          *       
       1739 TTTAGTTGCTGGAATTTGC-AA
          1 TTTAGTTGCTGGAAATTGCAAA

                *   *  *      *   
       1760 TTTACTTGTTGCAAATTGTAAA
          1 TTTAGTTGCTGGAAATTGCAAA

                          *       
       1782 TTTAGTTGCTGGAATTTGC-AA
          1 TTTAGTTGCTGGAAATTGCAAA

                *      *      *   
       1803 TTTACTTGCTGCAAATTGTAAA
          1 TTTAGTTGCTGGAAATTGCAAA

                                  
       1825 TTTAGTTGCTGGAAATT-CAAA
          1 TTTAGTTGCTGGAAATTGCAAA

               
       1846 TTT
          1 TTT

       1849 GCTTTATTGA


Statistics
Matches: 70,  Mismatches: 17, Indels: 4
        0.77            0.19        0.04

Matches are distributed among these distances:
  21   37  0.53
  22   33  0.47

ACGTcount: A:0.28, C:0.10, G:0.18, T:0.44


Consensus pattern (22 bp):   
TTTAGTTGCTGGAAATTGCAAA

Found at i:1848 original size:43 final size:43

Alignment explanation


    Indices: 1739--1838  Score: 191
    Period size: 43  Copynumber: 2.3  Consensus size: 43

       1729 AGTAGTTTAT

                                         *             
       1739 TTTAGTTGCTGGAATTTGCAATTTACTTGTTGCAAATTGTAAA
          1 TTTAGTTGCTGGAATTTGCAATTTACTTGCTGCAAATTGTAAA

                                                       
       1782 TTTAGTTGCTGGAATTTGCAATTTACTTGCTGCAAATTGTAAA
          1 TTTAGTTGCTGGAATTTGCAATTTACTTGCTGCAAATTGTAAA

                          
       1825 TTTAGTTGCTGGAA
          1 TTTAGTTGCTGGAA

       1839 ATTCAAATTT


Statistics
Matches: 56,  Mismatches: 1, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
  43   56  1.00

ACGTcount: A:0.27, C:0.10, G:0.20, T:0.43


Consensus pattern (43 bp):   
TTTAGTTGCTGGAATTTGCAATTTACTTGCTGCAAATTGTAAA
Done.