Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01023017.1 Corchorus olitorius cultivar O-4 contig23050, 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: 8788
ACGTcount: A:0.32, C:0.20, G:0.14, T:0.34


Found at i:2433 original size:30 final size:30

Alignment explanation


    Indices: 2397--2456  Score: 120
    Period size: 30  Copynumber: 2.0  Consensus size: 30

       2387 TTTTTGATCG

                                          
       2397 ATTTTCTTCTTTTAATTTAGAATTGAAGAT
          1 ATTTTCTTCTTTTAATTTAGAATTGAAGAT

                                          
       2427 ATTTTCTTCTTTTAATTTAGAATTGAAGAT
          1 ATTTTCTTCTTTTAATTTAGAATTGAAGAT

       2457 CTTATATGGA


Statistics
Matches: 30,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  30   30  1.00

ACGTcount: A:0.30, C:0.07, G:0.10, T:0.53


Consensus pattern (30 bp):   
ATTTTCTTCTTTTAATTTAGAATTGAAGAT

Found at i:2771 original size:48 final size:48

Alignment explanation


    Indices: 2714--2808  Score: 138
    Period size: 48  Copynumber: 2.0  Consensus size: 48

       2704 AAAAAAATAC

                                  **   *                     
       2714 ATACCACTAATAATAATAATTATTA-TTATAATAAGTTTAATAATTATA
          1 ATACCACTAATAATAATAA-TACCACTAATAATAAGTTTAATAATTATA

                          *                                
       2762 ATACCACTAATAATTATAATACCACTAATAATAAGTTTAATAATTAT
          1 ATACCACTAATAATAATAATACCACTAATAATAAGTTTAATAATTAT

       2809 TATAATAATA


Statistics
Matches: 42,  Mismatches: 4, Indels: 2
        0.88            0.08        0.04

Matches are distributed among these distances:
  47    3  0.07
  48   39  0.93

ACGTcount: A:0.49, C:0.09, G:0.02, T:0.39


Consensus pattern (48 bp):   
ATACCACTAATAATAATAATACCACTAATAATAAGTTTAATAATTATA

Found at i:2772 original size:18 final size:18

Alignment explanation


    Indices: 2751--2793  Score: 86
    Period size: 18  Copynumber: 2.4  Consensus size: 18

       2741 ATAATAAGTT

                              
       2751 TAATAATTATAATACCAC
          1 TAATAATTATAATACCAC

                              
       2769 TAATAATTATAATACCAC
          1 TAATAATTATAATACCAC

                   
       2787 TAATAAT
          1 TAATAAT

       2794 AAGTTTAATA


Statistics
Matches: 25,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  18   25  1.00

ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35


Consensus pattern (18 bp):   
TAATAATTATAATACCAC

Found at i:2820 original size:18 final size:18

Alignment explanation


    Indices: 2721--2822  Score: 50
    Period size: 18  Copynumber: 5.7  Consensus size: 18

       2711 TACATACCAC

                              
       2721 TAATAATAATAATTATTA
          1 TAATAATAATAATTATTA

             *              *    
       2739 TTATAATAAGTTTAATAATTA
          1 TAATAATAA---TAATTATTA

                 ** *    *    
       2760 TAATACCACTAATAATTA
          1 TAATAATAATAATTATTA

                 ** *         
       2778 TAATACCACTAA-TA--A
          1 TAATAATAATAATTATTA

                  *            
       2793 TAAGT-TTAATAATTATTA
          1 TAA-TAATAATAATTATTA

                        
       2811 TAATAATAATAA
          1 TAATAATAATAA

       2823 GTCTAAATTA


Statistics
Matches: 65,  Mismatches: 11, Indels: 16
        0.71            0.12        0.17

Matches are distributed among these distances:
  15    8  0.12
  16    3  0.05
  17    2  0.03
  18   39  0.60
  21   13  0.20

ACGTcount: A:0.52, C:0.06, G:0.02, T:0.40


Consensus pattern (18 bp):   
TAATAATAATAATTATTA
Done.