Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01012713.1 Corchorus olitorius cultivar O-4 contig12746, 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: 13503
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.33


Found at i:7 original size:2 final size:2

Alignment explanation


    Indices: 1--34  Score: 68
    Period size: 2  Copynumber: 17.0  Consensus size: 2

                                                              
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

         35 CATAACAAAC


Statistics
Matches: 32,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   32  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
TA

Found at i:7727 original size:9 final size:9

Alignment explanation


    Indices: 7715--7783  Score: 138
    Period size: 9  Copynumber: 7.7  Consensus size: 9

       7705 GCGGTGCAGT

                     
       7715 CGGTTTAGG
          1 CGGTTTAGG

                     
       7724 CGGTTTAGG
          1 CGGTTTAGG

                     
       7733 CGGTTTAGG
          1 CGGTTTAGG

                     
       7742 CGGTTTAGG
          1 CGGTTTAGG

                     
       7751 CGGTTTAGG
          1 CGGTTTAGG

                     
       7760 CGGTTTAGG
          1 CGGTTTAGG

                     
       7769 CGGTTTAGG
          1 CGGTTTAGG

                  
       7778 CGGTTT
          1 CGGTTT

       7784 TCAATACTTA


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

Matches are distributed among these distances:
   9   60  1.00

ACGTcount: A:0.10, C:0.12, G:0.43, T:0.35


Consensus pattern (9 bp):   
CGGTTTAGG

Found at i:9099 original size:9 final size:10

Alignment explanation


    Indices: 9087--9128  Score: 61
    Period size: 9  Copynumber: 4.4  Consensus size: 10

       9077 TCATATTCAT

                      
       9087 TCATCAAT-A
          1 TCATCAATCA

                      
       9096 TCATCAATCA
          1 TCATCAATCA

            *         
       9106 CCATCAAT-A
          1 TCATCAATCA

                      
       9115 TCATCAATCA
          1 TCATCAATCA

                
       9125 TCAT
          1 TCAT

       9129 ATTTACTTAG


Statistics
Matches: 29,  Mismatches: 2, Indels: 3
        0.85            0.06        0.09

Matches are distributed among these distances:
   9   16  0.55
  10   13  0.45

ACGTcount: A:0.40, C:0.29, G:0.00, T:0.31


Consensus pattern (10 bp):   
TCATCAATCA

Found at i:9099 original size:19 final size:19

Alignment explanation


    Indices: 9088--9124  Score: 74
    Period size: 19  Copynumber: 1.9  Consensus size: 19

       9078 CATATTCATT

                               
       9088 CATCAATATCATCAATCAC
          1 CATCAATATCATCAATCAC

                              
       9107 CATCAATATCATCAATCA
          1 CATCAATATCATCAATCA

       9125 TCATATTTAC


Statistics
Matches: 18,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  19   18  1.00

ACGTcount: A:0.43, C:0.30, G:0.00, T:0.27


Consensus pattern (19 bp):   
CATCAATATCATCAATCAC

Found at i:9872 original size:17 final size:17

Alignment explanation


    Indices: 9837--9895  Score: 57
    Period size: 17  Copynumber: 3.5  Consensus size: 17

       9827 GGGGGGGGGT

                        * *   
       9837 TTAATACTTTCTGATTTA
          1 TTAATA-TTTCTAAATTA

                             
       9855 TTAATATTTCTAAATTA
          1 TTAATATTTCTAAATTA

                   * *       
       9872 TTAATA-ATATAAATTA
          1 TTAATATTTCTAAATTA

             *      
       9888 TAAATATT
          1 TTAATATT

       9896 ATATATATAT


Statistics
Matches: 34,  Mismatches: 6, Indels: 3
        0.79            0.14        0.07

Matches are distributed among these distances:
  16   13  0.38
  17   15  0.44
  18    6  0.18

ACGTcount: A:0.42, C:0.05, G:0.02, T:0.51


Consensus pattern (17 bp):   
TTAATATTTCTAAATTA

Found at i:9886 original size:16 final size:16

Alignment explanation


    Indices: 9865--9898  Score: 50
    Period size: 16  Copynumber: 2.1  Consensus size: 16

       9855 TTAATATTTC

                    *       
       9865 TAAATTATTAATAATA
          1 TAAATTATAAATAATA

                         *  
       9881 TAAATTATAAATATTA
          1 TAAATTATAAATAATA

              
       9897 TA
          1 TA

       9899 TATATATATC


Statistics
Matches: 16,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  16   16  1.00

ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44


Consensus pattern (16 bp):   
TAAATTATAAATAATA
Done.