Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01018063.1 Corchorus olitorius cultivar O-4 contig18096, 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: 13218
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34


Found at i:2531 original size:12 final size:12

Alignment explanation


    Indices: 2511--2543  Score: 50
    Period size: 11  Copynumber: 2.8  Consensus size: 12

       2501 TGGTGGGGGC

                     *  
       2511 AAGAAAAAATGA
          1 AAGAAAAAAAGA

                        
       2523 AA-AAAAAAAGA
          1 AAGAAAAAAAGA

                      
       2534 AAGAAAAAAA
          1 AAGAAAAAAA

       2544 AACATGGGTA


Statistics
Matches: 19,  Mismatches: 1, Indels: 2
        0.86            0.05        0.09

Matches are distributed among these distances:
  11   10  0.53
  12    9  0.47

ACGTcount: A:0.85, C:0.00, G:0.12, T:0.03


Consensus pattern (12 bp):   
AAGAAAAAAAGA

Found at i:11243 original size:57 final size:57

Alignment explanation


    Indices: 11152--11267  Score: 214
    Period size: 57  Copynumber: 2.0  Consensus size: 57

      11142 TATCCGTTTC

                                         *            *              
      11152 CTTTCACACAATAAATGTTATAATAAATCTTATCCCCCCTATTTCTACTTAATTATT
          1 CTTTCACACAATAAATGTTATAATAAATCATATCCCCCCTATCTCTACTTAATTATT

                                                                     
      11209 CTTTCACACAATAAATGTTATAATAAATCATATCCCCCCTATCTCTACTTAATTATT
          1 CTTTCACACAATAAATGTTATAATAAATCATATCCCCCCTATCTCTACTTAATTATT

              
      11266 CT
          1 CT

      11268 ACAAAATAAA


Statistics
Matches: 57,  Mismatches: 2, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  57   57  1.00

ACGTcount: A:0.34, C:0.24, G:0.02, T:0.41


Consensus pattern (57 bp):   
CTTTCACACAATAAATGTTATAATAAATCATATCCCCCCTATCTCTACTTAATTATT

Found at i:11392 original size:42 final size:42

Alignment explanation


    Indices: 11333--11413  Score: 144
    Period size: 42  Copynumber: 1.9  Consensus size: 42

      11323 TAAGGATCAG

                   *                                  
      11333 GATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTTCTAT
          1 GATTTGAATTGAGTATTTCTTAATTTACAAAGAATTTTCTAT

                                         *         
      11375 GATTTGAATTGAGTATTTCTTAATTTACAGAGAATTTTC
          1 GATTTGAATTGAGTATTTCTTAATTTACAAAGAATTTTC

      11414 AAGACTTAGC


Statistics
Matches: 37,  Mismatches: 2, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  42   37  1.00

ACGTcount: A:0.31, C:0.07, G:0.15, T:0.47


Consensus pattern (42 bp):   
GATTTGAATTGAGTATTTCTTAATTTACAAAGAATTTTCTAT
Done.