Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01020165.1 Corchorus olitorius cultivar O-4 contig20198, 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: 25154
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.31


Found at i:2027 original size:21 final size:21

Alignment explanation


    Indices: 2002--2051  Score: 91
    Period size: 21  Copynumber: 2.4  Consensus size: 21

       1992 GAGACAAGAG

                                 
       2002 GAGAGTGCTCGTCATGAAGCA
          1 GAGAGTGCTCGTCATGAAGCA

                                 
       2023 GAGAGTGCTCGTCATGAAGCA
          1 GAGAGTGCTCGTCATGAAGCA

               *    
       2044 GAGCGTGC
          1 GAGAGTGC

       2052 ACGAATGCAA


Statistics
Matches: 28,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  21   28  1.00

ACGTcount: A:0.26, C:0.20, G:0.36, T:0.18


Consensus pattern (21 bp):   
GAGAGTGCTCGTCATGAAGCA

Found at i:2894 original size:32 final size:32

Alignment explanation


    Indices: 2728--2916  Score: 157
    Period size: 33  Copynumber: 5.8  Consensus size: 32

       2718 CTACAACATG

                       * *                 * *
       2728 GTGGCGTTTGTGTTACAAAAGA-GCCACAATATG
          1 GTGGCGTTT-TCTGACAAAA-ACGCCACAATTTT

                       * *             *  *  
       2761 GTGGCGTTTGTGTTACAAAAACGCCACTATATT
          1 GTGGCGTTT-TCTGACAAAAACGCCACAATTTT

                      *            *          
       2794 GTGGCGTCTAAT-TGACAAAAACACCACAATTTT
          1 GTGGCGT-T-TTCTGACAAAAACGCCACAATTTT

                       *               *  *  
       2827 GTGGCGTTTGTGTGACAAAAACGCCACCATCTT
          1 GTGGCGTTT-TCTGACAAAAACGCCACAATTTT

                      *    *      *         
       2860 GTGGCGTTTTTTGACCAAAACGTCACAATTTT
          1 GTGGCGTTTTCTGACAAAAACGCCACAATTTT

                                     
       2892 GTGGCGCTTTTCTGACAAAAACGCC
          1 GTGGCG-TTTTCTGACAAAAACGCC

       2917 GTAGAATTAA


Statistics
Matches: 131,  Mismatches: 19, Indels: 12
        0.81            0.12        0.07

Matches are distributed among these distances:
  32   27  0.21
  33  102  0.78
  34    2  0.02

ACGTcount: A:0.28, C:0.21, G:0.22, T:0.30


Consensus pattern (32 bp):   
GTGGCGTTTTCTGACAAAAACGCCACAATTTT

Found at i:2908 original size:65 final size:66

Alignment explanation


    Indices: 2751--2916  Score: 201
    Period size: 66  Copynumber: 2.5  Consensus size: 66

       2741 TACAAAAGAG

                   * *           * *             *                           
       2751 CCACAATATGGTGGCGTTTGTGTTACAAAAACGCCACTATATTGTGGCGTCTAATTGACAAAAAC
          1 CCACAATTTTGTGGCGTTTGTCTGACAAAAACGCCACCATATTGTGGCGTCTAATTGACAAAAAC

             
       2816 A
         66 A

                                 *                  *           **     *     
       2817 CCACAATTTTGTGGCGTTTGTGTGACAAAAACGCCACCATCTTGTGGCGT-TTTTTGACCAAAAC
          1 CCACAATTTTGTGGCGTTTGTCTGACAAAAACGCCACCATATTGTGGCGTCTAATTGACAAAAAC

            *
       2881 G
         66 A

            *                                   
       2882 TCACAATTTTGTGGCGCTTT-TCTGACAAAAACGCC
          1 CCACAATTTTGTGGCG-TTTGTCTGACAAAAACGCC

       2917 GTAGAATTAA


Statistics
Matches: 88,  Mismatches: 11, Indels: 3
        0.86            0.11        0.03

Matches are distributed among these distances:
  65   40  0.45
  66   48  0.55

ACGTcount: A:0.28, C:0.22, G:0.20, T:0.30


Consensus pattern (66 bp):   
CCACAATTTTGTGGCGTTTGTCTGACAAAAACGCCACCATATTGTGGCGTCTAATTGACAAAAAC
A

Found at i:19595 original size:27 final size:27

Alignment explanation


    Indices: 19561--19618  Score: 107
    Period size: 27  Copynumber: 2.1  Consensus size: 27

      19551 ACTCTGCTGT

                                      *
      19561 TTTGGGTTTTATATGTTGGTTTCATGG
          1 TTTGGGTTTTATATGTTGGTTTCATGA

                                       
      19588 TTTGGGTTTTATATGTTGGTTTCATGA
          1 TTTGGGTTTTATATGTTGGTTTCATGA

                
      19615 TTTG
          1 TTTG

      19619 TATTGGAAGG


Statistics
Matches: 30,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  27   30  1.00

ACGTcount: A:0.12, C:0.03, G:0.28, T:0.57


Consensus pattern (27 bp):   
TTTGGGTTTTATATGTTGGTTTCATGA

Found at i:19751 original size:13 final size:13

Alignment explanation


    Indices: 19733--19787  Score: 101
    Period size: 13  Copynumber: 4.2  Consensus size: 13

      19723 GCGACTGTGG

                         
      19733 CTCTGTGCTCTGC
          1 CTCTGTGCTCTGC

                   *     
      19746 CTCTGTGTTCTGC
          1 CTCTGTGCTCTGC

                         
      19759 CTCTGTGCTCTGC
          1 CTCTGTGCTCTGC

                         
      19772 CTCTGTGCTCTGC
          1 CTCTGTGCTCTGC

               
      19785 CTC
          1 CTC

      19788 CGTCTCTTTA


Statistics
Matches: 40,  Mismatches: 2, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  13   40  1.00

ACGTcount: A:0.00, C:0.38, G:0.22, T:0.40


Consensus pattern (13 bp):   
CTCTGTGCTCTGC

Found at i:24150 original size:27 final size:27

Alignment explanation


    Indices: 24108--24168  Score: 68
    Period size: 27  Copynumber: 2.3  Consensus size: 27

      24098 TCTTCATTAT

                       *    *          
      24108 AGGGGTAAAATCGTAATTTTATCAATC
          1 AGGGGTAAAATAGTAAATTTATCAATC

                    *           *  *   
      24135 AGGGGTAACATAGTAAATTTGTCCATC
          1 AGGGGTAAAATAGTAAATTTATCAATC

             *     
      24162 ACGGGTA
          1 AGGGGTA

      24169 TTTTTGGTAA


Statistics
Matches: 28,  Mismatches: 6, Indels: 0
        0.82            0.18        0.00

Matches are distributed among these distances:
  27   28  1.00

ACGTcount: A:0.34, C:0.13, G:0.23, T:0.30


Consensus pattern (27 bp):   
AGGGGTAAAATAGTAAATTTATCAATC
Done.