Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01014670.1 Corchorus olitorius cultivar O-4 contig14703, 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: 18087
ACGTcount: A:0.37, C:0.17, G:0.19, T:0.27


Found at i:13888 original size:19 final size:19

Alignment explanation


    Indices: 13864--13903  Score: 71
    Period size: 19  Copynumber: 2.1  Consensus size: 19

      13854 CTTTAAATAA

                               
      13864 AAAAAAGAAAGAAATAAAG
          1 AAAAAAGAAAGAAATAAAG

                  *            
      13883 AAAAAATAAAGAAATAAAG
          1 AAAAAAGAAAGAAATAAAG

              
      13902 AA
          1 AA

      13904 TTGGACTTGG


Statistics
Matches: 20,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  19   20  1.00

ACGTcount: A:0.80, C:0.00, G:0.12, T:0.07


Consensus pattern (19 bp):   
AAAAAAGAAAGAAATAAAG

Found at i:13891 original size:11 final size:11

Alignment explanation


    Indices: 13862--13896  Score: 54
    Period size: 11  Copynumber: 3.2  Consensus size: 11

      13852 ACCTTTAAAT

                       
      13862 AAAAA-AAAGA
          1 AAAAATAAAGA

                        
      13872 AAGAAATAAAGA
          1 AA-AAATAAAGA

                       
      13884 AAAAATAAAGA
          1 AAAAATAAAGA

              
      13895 AA
          1 AA

      13897 TAAAGAATTG


Statistics
Matches: 23,  Mismatches: 0, Indels: 3
        0.88            0.00        0.12

Matches are distributed among these distances:
  10    2  0.09
  11   14  0.61
  12    7  0.30

ACGTcount: A:0.83, C:0.00, G:0.11, T:0.06


Consensus pattern (11 bp):   
AAAAATAAAGA

Found at i:14890 original size:19 final size:20

Alignment explanation


    Indices: 14849--14890  Score: 52
    Period size: 20  Copynumber: 2.1  Consensus size: 20

      14839 TGATTAAATG

                       *        
      14849 AACTCTAGAAAGTGTATTCA
          1 AACTCTAGAAACTGTATTCA

                                 
      14869 AACTCT-GAAACTCGTATT-A
          1 AACTCTAGAAACT-GTATTCA

               
      14888 AAC
          1 AAC

      14891 CCTATAAGAC


Statistics
Matches: 20,  Mismatches: 1, Indels: 3
        0.83            0.04        0.12

Matches are distributed among these distances:
  19    9  0.45
  20   11  0.55

ACGTcount: A:0.40, C:0.19, G:0.12, T:0.29


Consensus pattern (20 bp):   
AACTCTAGAAACTGTATTCA

Found at i:15245 original size:13 final size:12

Alignment explanation


    Indices: 15227--15271  Score: 54
    Period size: 14  Copynumber: 3.5  Consensus size: 12

      15217 ATTTTATTAC

                         
      15227 TGTTTTATTAAAT
          1 TGTTTTA-TAAAT

                        
      15240 TGTTTTATAAAT
          1 TGTTTTATAAAT

            *             
      15252 GGTTTTAAATAAAT
          1 TGTTTT--ATAAAT

                  
      15266 TGTTTT
          1 TGTTTT

      15272 GGGTGCATGA


Statistics
Matches: 28,  Mismatches: 2, Indels: 3
        0.85            0.06        0.09

Matches are distributed among these distances:
  12   10  0.36
  13    7  0.25
  14   11  0.39

ACGTcount: A:0.31, C:0.00, G:0.11, T:0.58


Consensus pattern (12 bp):   
TGTTTTATAAAT

Found at i:17889 original size:34 final size:34

Alignment explanation


    Indices: 17851--17934  Score: 123
    Period size: 34  Copynumber: 2.5  Consensus size: 34

      17841 AAAAATTGAA

                             **               
      17851 TGGGAACTTTCCCAATTTGAAAACTTAAAACCGG
          1 TGGGAACTTTCCCAATTACAAAACTTAAAACCGG

                         *                 *  
      17885 TGGGAACTTTCCCGATTACAAAACTTAAAACTGG
          1 TGGGAACTTTCCCAATTACAAAACTTAAAACCGG

                      *     
      17919 TGGGAACTTTTCCAAT
          1 TGGGAACTTTCCCAAT

      17935 AAAAAAAAAC


Statistics
Matches: 44,  Mismatches: 6, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  34   44  1.00

ACGTcount: A:0.33, C:0.20, G:0.18, T:0.29


Consensus pattern (34 bp):   
TGGGAACTTTCCCAATTACAAAACTTAAAACCGG
Done.