Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01018056.1 Corchorus olitorius cultivar O-4 contig18089, 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: 7086
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.31


Found at i:889 original size:76 final size:76

Alignment explanation


    Indices: 752--903  Score: 184
    Period size: 76  Copynumber: 2.0  Consensus size: 76

        742 ACAAAGACCC

                                                               *             
        752 CGACTCCACCTGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCTTGAGAACCCAGAT
          1 CGACTCCACCTGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCCTGAGAACCCAGAT

                       
        817 GGACAGTGTCA
         66 GGACAGTGTCA

                    *     *              *                            **     
        828 CGACTCCAGCTGGGTGCCCACATGGTTTGTC-TGAAG-ACCCATGT-GTTTCGCCTGATCACCCA
          1 CGACTCCACCTGGGCGCCCACATGG-TTGCCTTG-AGCACCCATGTGGTTT-GCCTGAGAACCCA

                 * *      
        890 GATGGGCTGTGTCA
         63 GATGGACAGTGTCA

        904 TAGCTCATCA


Statistics
Matches: 65,  Mismatches: 8, Indels: 6
        0.82            0.10        0.08

Matches are distributed among these distances:
  75    4  0.06
  76   55  0.85
  77    6  0.09

ACGTcount: A:0.18, C:0.30, G:0.28, T:0.24


Consensus pattern (76 bp):   
CGACTCCACCTGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCCTGAGAACCCAGAT
GGACAGTGTCA

Found at i:4300 original size:21 final size:21

Alignment explanation


    Indices: 4261--4305  Score: 56
    Period size: 21  Copynumber: 2.1  Consensus size: 21

       4251 GTAAGTGGTG

                               * 
       4261 AAGTAGTGAAATTGATGAATA
          1 AAGTAGTGAAATTGATGAACA

                       *          
       4282 AAGTGAGTGAATTTG-TGAACA
          1 AAGT-AGTGAAATTGATGAACA

               
       4303 AAG
          1 AAG

       4306 GTAATAGAAG


Statistics
Matches: 21,  Mismatches: 2, Indels: 2
        0.84            0.08        0.08

Matches are distributed among these distances:
  21   12  0.57
  22    9  0.43

ACGTcount: A:0.44, C:0.02, G:0.27, T:0.27


Consensus pattern (21 bp):   
AAGTAGTGAAATTGATGAACA

Found at i:6867 original size:21 final size:21

Alignment explanation


    Indices: 6834--6882  Score: 55
    Period size: 21  Copynumber: 2.3  Consensus size: 21

       6824 AAGAATTGTA

                          *      
       6834 GCTT-CTTGGAAATGACTCTT
          1 GCTTCCTTGGAAATCACTCTT

                    *      *     
       6854 GCTTCCTTTGAAATCCCTCTT
          1 GCTTCCTTGGAAATCACTCTT

                    
       6875 GCATTCCT
          1 GC-TTCCT

       6883 AAAGCATTGA


Statistics
Matches: 24,  Mismatches: 3, Indels: 2
        0.83            0.10        0.07

Matches are distributed among these distances:
  20    4  0.17
  21   15  0.62
  22    5  0.21

ACGTcount: A:0.16, C:0.29, G:0.14, T:0.41


Consensus pattern (21 bp):   
GCTTCCTTGGAAATCACTCTT
Done.