Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01024538.1 Corchorus olitorius cultivar O-4 contig24571, 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: 10692
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32


Found at i:2672 original size:40 final size:40

Alignment explanation


    Indices: 2578--3036  Score: 699
    Period size: 40  Copynumber: 11.6  Consensus size: 40

       2568 CGACCGATCA

                                                    
       2578 GGGAAGGGCAAACTGGGAATTTAAACAACACCTTCCGGT-
          1 GGGAAGGGCAAACTGGGAATTTAAACAACACCTTCCGGTG

                             **    *                
       2617 GGGAAGGGCAAACTGGGTGTTTAGACAACACCTTCCGGTG
          1 GGGAAGGGCAAACTGGGAATTTAAACAACACCTTCCGGTG

                                        *           
       2657 GGGAAGGGCAAACTGGGAATTTAAACAAAACCTTCCGGTG
          1 GGGAAGGGCAAACTGGGAATTTAAACAACACCTTCCGGTG

                    *            *        *     **  
       2697 GGGAAGGGAAAACTGGGAATTCAAACAACAACTTCCAATG
          1 GGGAAGGGCAAACTGGGAATTTAAACAACACCTTCCGGTG

                                                 *  
       2737 GGGAAGGGCAAACTGGGAATTTAAACAACACCTTCCGATG
          1 GGGAAGGGCAAACTGGGAATTTAAACAACACCTTCCGGTG

                             *     *                
       2777 GGGAAGGGCAAACTGGGTATTTAGACAACACCTTCCGGTG
          1 GGGAAGGGCAAACTGGGAATTTAAACAACACCTTCCGGTG

                   *                             *  
       2817 GGGAAGGACAAACTGGGAATTTAAACAACACCTTCCGATG
          1 GGGAAGGGCAAACTGGGAATTTAAACAACACCTTCCGGTG

            *             *                     *   
       2857 AGGAAGGGCAAACTAGGAATTTAAACAACACCTTCCAGTG
          1 GGGAAGGGCAAACTGGGAATTTAAACAACACCTTCCGGTG

                                   *      *         
       2897 GGGAAGGGCAAACTGGGAATTTACACAACAGCTTCCGGTG
          1 GGGAAGGGCAAACTGGGAATTTAAACAACACCTTCCGGTG

                                   *           *    
       2937 GGGAAGGGCAAACTGGG--TTTACACAACACCTTCTGGTG
          1 GGGAAGGGCAAACTGGGAATTTAAACAACACCTTCCGGTG

                                                    
       2975 GGGAAGGGCAAACTGGGAATTTAAACAACACCTTCCGGTG
          1 GGGAAGGGCAAACTGGGAATTTAAACAACACCTTCCGGTG

                             *    
       3015 GGGAAGGGCAAACTGGGTATTT
          1 GGGAAGGGCAAACTGGGAATTT

       3037 GGGCTAGACA


Statistics
Matches: 378,  Mismatches: 39, Indels: 5
        0.90            0.09        0.01

Matches are distributed among these distances:
  38   36  0.10
  39   36  0.10
  40  306  0.81

ACGTcount: A:0.33, C:0.19, G:0.30, T:0.18


Consensus pattern (40 bp):   
GGGAAGGGCAAACTGGGAATTTAAACAACACCTTCCGGTG

Found at i:8032 original size:29 final size:30

Alignment explanation


    Indices: 7993--8050  Score: 91
    Period size: 30  Copynumber: 2.0  Consensus size: 30

       7983 TTTGATCAAT

                              *           
       7993 TTTATTAA-TTTCCAAAATCTTCTTTTGGG
          1 TTTATTAATTTTCCAAAACCTTCTTTTGGG

                  *                      
       8022 TTTATTTATTTTCCAAAACCTTCTTTTGG
          1 TTTATTAATTTTCCAAAACCTTCTTTTGG

       8051 AATTATCCAA


Statistics
Matches: 26,  Mismatches: 2, Indels: 1
        0.90            0.07        0.03

Matches are distributed among these distances:
  29    7  0.27
  30   19  0.73

ACGTcount: A:0.22, C:0.16, G:0.09, T:0.53


Consensus pattern (30 bp):   
TTTATTAATTTTCCAAAACCTTCTTTTGGG

Found at i:8895 original size:41 final size:41

Alignment explanation


    Indices: 8811--8905  Score: 100
    Period size: 41  Copynumber: 2.3  Consensus size: 41

       8801 CTAAAACCAT

                                    *         **     
       8811 GGACCAAATTGAATCAAATAATAACTAAAATCCTGTATCAG
          1 GGACCAAATTGAATCAAATAATAAATAAAATCCTAAATCAG

                *      *        *          *      *  
       8852 GGACTAAATTGCATCAAATAGTAAATAAAATTCTAAATTAG
          1 GGACCAAATTGAATCAAATAATAAATAAAATCCTAAATCAG

               *    *    
       8893 GGAACAAAGTGAA
          1 GGACCAAATTGAA

       8906 CATGAAAACA


Statistics
Matches: 42,  Mismatches: 12, Indels: 0
        0.78            0.22        0.00

Matches are distributed among these distances:
  41   42  1.00

ACGTcount: A:0.48, C:0.13, G:0.15, T:0.24


Consensus pattern (41 bp):   
GGACCAAATTGAATCAAATAATAAATAAAATCCTAAATCAG

Found at i:9918 original size:16 final size:16

Alignment explanation


    Indices: 9897--9928  Score: 55
    Period size: 16  Copynumber: 2.0  Consensus size: 16

       9887 TGTGTGTATA

                            
       9897 GAGTCTGTGGAGATGG
          1 GAGTCTGTGGAGATGG

                  *         
       9913 GAGTCTTTGGAGATGG
          1 GAGTCTGTGGAGATGG

       9929 AGGGTGTGAG


Statistics
Matches: 15,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  16   15  1.00

ACGTcount: A:0.19, C:0.06, G:0.47, T:0.28


Consensus pattern (16 bp):   
GAGTCTGTGGAGATGG
Done.