Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01010368.1 Corchorus olitorius cultivar O-4 contig10400, 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: 7246
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34


Found at i:1041 original size:20 final size:20

Alignment explanation


    Indices: 1003--1041  Score: 51
    Period size: 20  Copynumber: 1.9  Consensus size: 20

        993 CATATAAAAT

                    * *   *     
       1003 AATAATAATTTATTTTTAAA
          1 AATAATAACTAATTATTAAA

                               
       1023 AATAATAACTAATTATTAA
          1 AATAATAACTAATTATTAA

       1042 TTTTTTAAAA


Statistics
Matches: 16,  Mismatches: 3, Indels: 0
        0.84            0.16        0.00

Matches are distributed among these distances:
  20   16  1.00

ACGTcount: A:0.54, C:0.03, G:0.00, T:0.44


Consensus pattern (20 bp):   
AATAATAACTAATTATTAAA

Found at i:1044 original size:27 final size:24

Alignment explanation


    Indices: 998--1052  Score: 67
    Period size: 23  Copynumber: 2.2  Consensus size: 24

        988 ATAATCATAT

                                    
        998 AAAATAATAATAATTTA-TTTTTA
          1 AAAATAATAATAATTTATTTTTTA

                                        
       1021 AAAATAATAACTAATTATTAATTTTTTA
          1 AAAATAATAA-TAA-T-TT-ATTTTTTA

                
       1049 AAAA
          1 AAAA

       1053 AAAGTAAAAA


Statistics
Matches: 27,  Mismatches: 0, Indels: 5
        0.84            0.00        0.16

Matches are distributed among these distances:
  23   10  0.37
  24    3  0.11
  25    1  0.04
  26    2  0.07
  27    1  0.04
  28   10  0.37

ACGTcount: A:0.55, C:0.02, G:0.00, T:0.44


Consensus pattern (24 bp):   
AAAATAATAATAATTTATTTTTTA

Found at i:5888 original size:22 final size:20

Alignment explanation


    Indices: 5863--5919  Score: 53
    Period size: 22  Copynumber: 2.6  Consensus size: 20

       5853 CATATTTAGG

                                  
       5863 TTATCAAAGTTTCAAATGG-AA
          1 TTATCAAA-TTTCAAA-GGTAA

                           *      
       5884 TTTATCACAATTTCATAGGTAA
          1 -TTATCA-AATTTCAAAGGTAA

                          
       5906 TTATCAAAATTTCA
          1 TTATC-AAATTTCA

       5920 TAACGTGGTT


Statistics
Matches: 31,  Mismatches: 1, Indels: 7
        0.79            0.03        0.18

Matches are distributed among these distances:
  21   14  0.45
  22   15  0.48
  23    2  0.06

ACGTcount: A:0.40, C:0.12, G:0.09, T:0.39


Consensus pattern (20 bp):   
TTATCAAATTTCAAAGGTAA

Found at i:5936 original size:22 final size:22

Alignment explanation


    Indices: 5885--5962  Score: 77
    Period size: 22  Copynumber: 3.6  Consensus size: 22

       5875 CAAATGGAAT

                  *          *   *
       5885 TTATCACAATTTCAT-AGGTAA
          1 TTATCAAAATTTCATAACGTAG

                                * 
       5906 TTATCAAAATTTCATAACGTGG
          1 TTATCAAAATTTCATAACGTAG

                *       *   **    
       5928 TTATTAAAATTTAATAGGGTAG
          1 TTATCAAAATTTCATAACGTAG

                         
       5950 TTATCAAAATTTC
          1 TTATCAAAATTTC

       5963 TTAAAAATAT


Statistics
Matches: 45,  Mismatches: 11, Indels: 1
        0.79            0.19        0.02

Matches are distributed among these distances:
  21   14  0.31
  22   31  0.69

ACGTcount: A:0.38, C:0.10, G:0.12, T:0.40


Consensus pattern (22 bp):   
TTATCAAAATTTCATAACGTAG

Found at i:6247 original size:16 final size:16

Alignment explanation


    Indices: 6226--6258  Score: 57
    Period size: 16  Copynumber: 2.1  Consensus size: 16

       6216 TTAAATTTAA

                     *      
       6226 TTTAAATTTTAACAAG
          1 TTTAAATTTCAACAAG

                            
       6242 TTTAAATTTCAACAAG
          1 TTTAAATTTCAACAAG

             
       6258 T
          1 T

       6259 ATATATGATT


Statistics
Matches: 16,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  16   16  1.00

ACGTcount: A:0.42, C:0.09, G:0.06, T:0.42


Consensus pattern (16 bp):   
TTTAAATTTCAACAAG
Done.