Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01012090.1 Corchorus olitorius cultivar O-4 contig12123, 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: 3365
ACGTcount: A:0.40, C:0.16, G:0.16, T:0.29


Found at i:2870 original size:17 final size:16

Alignment explanation


    Indices: 2844--2887  Score: 52
    Period size: 17  Copynumber: 2.7  Consensus size: 16

       2834 AGAAATAGGG

                 *          
       2844 AGGAAAGGAAATAACA
          1 AGGAAGGGAAATAACA

                          ** 
       2860 AGGGAAGGGAAATAGGA
          1 A-GGAAGGGAAATAACA

                       
       2877 AGGAAGGGAAA
          1 AGGAAGGGAAA

       2888 GGAAGTCATA


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

Matches are distributed among these distances:
  16   11  0.46
  17   13  0.54

ACGTcount: A:0.55, C:0.02, G:0.39, T:0.05


Consensus pattern (16 bp):   
AGGAAGGGAAATAACA

Found at i:2881 original size:16 final size:16

Alignment explanation


    Indices: 2835--2887  Score: 61
    Period size: 16  Copynumber: 3.2  Consensus size: 16

       2825 TGAGAGGAAA

                    *     * 
       2835 GAAATAGGGAGGAAAG
          1 GAAATAGGAAGGAAGG

                  **         
       2851 GAAATAACAAGGGAAGG
          1 GAAATAGGAA-GGAAGG

                            
       2868 GAAATAGGAAGGAAGG
          1 GAAATAGGAAGGAAGG

                
       2884 GAAA
          1 GAAA

       2888 GGAAGTCATA


Statistics
Matches: 30,  Mismatches: 6, Indels: 2
        0.79            0.16        0.05

Matches are distributed among these distances:
  16   17  0.57
  17   13  0.43

ACGTcount: A:0.53, C:0.02, G:0.40, T:0.06


Consensus pattern (16 bp):   
GAAATAGGAAGGAAGG

Found at i:2925 original size:60 final size:60

Alignment explanation


    Indices: 2859--2978  Score: 240
    Period size: 60  Copynumber: 2.0  Consensus size: 60

       2849 AGGAAATAAC

                                                                        
       2859 AAGGGAAGGGAAATAGGAAGGAAGGGAAAGGAAGTCATATTTCCTCCATCATGTTTGGTA
          1 AAGGGAAGGGAAATAGGAAGGAAGGGAAAGGAAGTCATATTTCCTCCATCATGTTTGGTA

                                                                        
       2919 AAGGGAAGGGAAATAGGAAGGAAGGGAAAGGAAGTCATATTTCCTCCATCATGTTTGGTA
          1 AAGGGAAGGGAAATAGGAAGGAAGGGAAAGGAAGTCATATTTCCTCCATCATGTTTGGTA

       2979 TGAAGGAAAG


Statistics
Matches: 60,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  60   60  1.00

ACGTcount: A:0.37, C:0.10, G:0.32, T:0.22


Consensus pattern (60 bp):   
AAGGGAAGGGAAATAGGAAGGAAGGGAAAGGAAGTCATATTTCCTCCATCATGTTTGGTA

Done.