Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01018107.1 Corchorus olitorius cultivar O-4 contig18140, 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: 10021
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.33


Found at i:3918 original size:17 final size:17

Alignment explanation


    Indices: 3896--3949  Score: 72
    Period size: 17  Copynumber: 3.2  Consensus size: 17

       3886 CACCCCCCCG

                  *          
       3896 GATCACTAGTGATCTAA
          1 GATCACCAGTGATCTAA

                         *   
       3913 GATCACCAGTGATGTAA
          1 GATCACCAGTGATCTAA

                   *      *  
       3930 GATCACCGGTGATCAAA
          1 GATCACCAGTGATCTAA

               
       3947 GAT
          1 GAT

       3950 TACATAGGTT


Statistics
Matches: 32,  Mismatches: 5, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  17   32  1.00

ACGTcount: A:0.35, C:0.19, G:0.22, T:0.24


Consensus pattern (17 bp):   
GATCACCAGTGATCTAA

Found at i:9573 original size:28 final size:27

Alignment explanation


    Indices: 9522--9704  Score: 197
    Period size: 28  Copynumber: 6.6  Consensus size: 27

       9512 CTTTACTTCT

                *          *            
       9522 CATTGTGGTCATTTTTCATGTCTAGGGG
          1 CATTTTGGTCATTTTCCAT-TCTAGGGG

            *                           
       9550 GATTTTGGTCATTTTCCATATCTAGGGG
          1 CATTTTGGTCATTTTCCAT-TCTAGGGG

                           *            
       9578 CATTTTGGTCATTTTTCATGTCTAGGGG
          1 CATTTTGGTCATTTTCCAT-TCTAGGGG

                             * *  *     
       9606 CATTTTGGTCATTTTTCAAATCCAGGGG
          1 CATTTTGGTCA-TTTTCCATTCTAGGGG

                          *       *    *
       9634 CATTTTGGTCATTTGCACATTCAAGGGT
          1 CATTTTGGTCATTTTC-CATTCTAGGGG

                          *             
       9662 CATTTTGGTCATTTGCACATTC-AGGGG
          1 CATTTTGGTCATTTTC-CATTCTAGGGG

                            
       9689 TCATTTTGGTCATTTT
          1 -CATTTTGGTCATTTT

       9705 AAGTTCACTT


Statistics
Matches: 134,  Mismatches: 18, Indels: 6
        0.85            0.11        0.04

Matches are distributed among these distances:
  27    8  0.06
  28  121  0.90
  29    5  0.04

ACGTcount: A:0.17, C:0.16, G:0.23, T:0.43


Consensus pattern (27 bp):   
CATTTTGGTCATTTTCCATTCTAGGGG

Found at i:9587 original size:56 final size:55

Alignment explanation


    Indices: 9522--9704  Score: 226
    Period size: 56  Copynumber: 3.3  Consensus size: 55

       9512 CTTTACTTCT

                *                       *                           
       9522 CATTGTGGTCATTTTTCATGTCTAGGGGGATTTTGGTCATTTTCCATATCTAGGGG
          1 CATTTTGGTCATTTTTCATGTCTAGGGGCATTTTGGTCATTTTCCATATC-AGGGG

                                                       *  *         
       9578 CATTTTGGTCATTTTTCATGTCTAGGGGCATTTTGGTCATTTTTCAAATCCAGGGG
          1 CATTTTGGTCATTTTTCATGTCTAGGGGCATTTTGGTCATTTTCCATAT-CAGGGG

                           **      *    *              *             
       9634 CATTTTGGTCATTTGCACAT-TCAAGGGTCATTTTGGTCATTTGCACAT-TCAGGGG
          1 CATTTTGGTCATTT-TTCATGTCTAGGGGCATTTTGGTCATTTTC-CATATCAGGGG

                            
       9689 TCATTTTGGTCATTTT
          1 -CATTTTGGTCATTTT

       9705 AAGTTCACTT


Statistics
Matches: 111,  Mismatches: 12, Indels: 9
        0.84            0.09        0.07

Matches are distributed among these distances:
  55    6  0.05
  56   99  0.89
  57    6  0.05

ACGTcount: A:0.17, C:0.16, G:0.23, T:0.43


Consensus pattern (55 bp):   
CATTTTGGTCATTTTTCATGTCTAGGGGCATTTTGGTCATTTTCCATATCAGGGG

Found at i:9668 original size:84 final size:84

Alignment explanation


    Indices: 9521--9704  Score: 230
    Period size: 84  Copynumber: 2.2  Consensus size: 84

       9511 ACTTTACTTC

                 *             **  *     *             *       *             
       9521 TCATTGTGGTCATTTTTCATGTCTAGGGGGATTTTGGTCATTTTCCATATCTAGGGGCATTTTGG
          1 TCATTTTGGTCATTTTTCAAATCCAGGGGCATTTTGGTCATTTGCCATATCAAGGGGCATTTTGG

                   **            
       9586 TCATTT-TTCATGTCTAGGGG
         66 TCATTTGCACAT-TC-AGGGG

                                                                     *       
       9606 -CATTTTGGTCATTTTTCAAATCCAGGGGCATTTTGGTCATTTGCACAT-TCAAGGGTCATTTTG
          1 TCATTTTGGTCATTTTTCAAATCCAGGGGCATTTTGGTCATTTGC-CATATCAAGGGGCATTTTG

                                
       9669 GTCATTTGCACATTCAGGGG
         65 GTCATTTGCACATTCAGGGG

                            
       9689 TCATTTTGGTCATTTT
          1 TCATTTTGGTCATTTT

       9705 AAGTTCACTT


Statistics
Matches: 86,  Mismatches: 10, Indels: 7
        0.83            0.10        0.07

Matches are distributed among these distances:
  83    5  0.06
  84   75  0.87
  85    6  0.07

ACGTcount: A:0.17, C:0.16, G:0.23, T:0.43


Consensus pattern (84 bp):   
TCATTTTGGTCATTTTTCAAATCCAGGGGCATTTTGGTCATTTGCCATATCAAGGGGCATTTTGG
TCATTTGCACATTCAGGGG
Done.