Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01012546.1 Corchorus capsularis cultivar CVL-1 contig12567, 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: 20757
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32


Found at i:2736 original size:29 final size:30

Alignment explanation


    Indices: 2684--2758  Score: 98
    Period size: 29  Copynumber: 2.5  Consensus size: 30

       2674 CATTAGGTTG

                                          
       2684 AGGGGGCAAAACGTCCCAAAATTGAAGTTC
          1 AGGGGGCAAAACGTCCCAAAATTGAAGTTC

                       *       *          
       2714 AGGGGGCAAAATGT-CCAAGATTGAAGTTC
          1 AGGGGGCAAAACGTCCCAAAATTGAAGTTC

              *  **         
       2743 AGAGGATAAAACGTCC
          1 AGGGGGCAAAACGTCC

       2759 AAACGATACA


Statistics
Matches: 38,  Mismatches: 6, Indels: 2
        0.83            0.13        0.04

Matches are distributed among these distances:
  29   24  0.63
  30   14  0.37

ACGTcount: A:0.37, C:0.17, G:0.28, T:0.17


Consensus pattern (30 bp):   
AGGGGGCAAAACGTCCCAAAATTGAAGTTC

Found at i:3447 original size:31 final size:31

Alignment explanation


    Indices: 3357--3458  Score: 114
    Period size: 31  Copynumber: 3.3  Consensus size: 31

       3347 TCCTTTTGTG

                *      *      *  *      ** 
       3357 CACGCGGCATGCCACGTGCCATTTTTTGAAA
          1 CACGTGGCATGACACGTGTCACTTTTTGGTA

                       *                   
       3388 CACGTGGCATGCCACGTGTCACTTTTTGGTA
          1 CACGTGGCATGACACGTGTCACTTTTTGGTA

                    *     *                
       3419 CACGTGGCGTGACATGTGTCACTTTTTGGTA
          1 CACGTGGCATGACACGTGTCACTTTTTGGTA

              *      
       3450 CATGTGGCA
          1 CACGTGGCA

       3459 CGACTTTTTG


Statistics
Matches: 61,  Mismatches: 10, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  31   61  1.00

ACGTcount: A:0.19, C:0.25, G:0.26, T:0.30


Consensus pattern (31 bp):   
CACGTGGCATGACACGTGTCACTTTTTGGTA

Found at i:9164 original size:3 final size:3

Alignment explanation


    Indices: 9158--9182  Score: 50
    Period size: 3  Copynumber: 8.3  Consensus size: 3

       9148 TACCCAAAAA

                                             
       9158 AAG AAG AAG AAG AAG AAG AAG AAG A
          1 AAG AAG AAG AAG AAG AAG AAG AAG A

       9183 TTTGAGTTAT


Statistics
Matches: 22,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   22  1.00

ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00


Consensus pattern (3 bp):   
AAG

Found at i:12331 original size:79 final size:79

Alignment explanation


    Indices: 12242--12400  Score: 291
    Period size: 79  Copynumber: 2.0  Consensus size: 79

      12232 GCAGAAAATC

                                                             *               
      12242 ATGATCATACAATTTATTCTGAATTCCTGATACTAAAAACACAGATTTAGTAACGAATATATGAA
          1 ATGATCATACAATTTATTCTGAATTCCTGATACTAAAAACACAGATTTAATAACGAATATATGAA

                          
      12307 TATCAACAAAAGTT
         66 TATCAACAAAAGTT

                                     *          *                            
      12321 ATGATCATACAATTTATTCTGAATTTCTGATACTAATAACACAGATTTAATAACGAATATATGAA
          1 ATGATCATACAATTTATTCTGAATTCCTGATACTAAAAACACAGATTTAATAACGAATATATGAA

                          
      12386 TATCAACAAAAGTT
         66 TATCAACAAAAGTT

             
      12400 A
          1 A

      12401 ACTCTATTTT


Statistics
Matches: 77,  Mismatches: 3, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  79   77  1.00

ACGTcount: A:0.45, C:0.13, G:0.09, T:0.33


Consensus pattern (79 bp):   
ATGATCATACAATTTATTCTGAATTCCTGATACTAAAAACACAGATTTAATAACGAATATATGAA
TATCAACAAAAGTT

Found at i:19269 original size:240 final size:240

Alignment explanation


    Indices: 18836--19318  Score: 822
    Period size: 240  Copynumber: 2.0  Consensus size: 240

      18826 TCCACAGCTC

                                  *                   * *                    
      18836 CTATAAGACTAACACGCTCAGCGGCTCAGAAAGGGGCTATAATCTCAAATGATGGCATCCAGGTG
          1 CTATAAGACTAACACGCTCAGCAGCTCAGAAAGGGGCTATAAACCCAAATGATGGCATCCAGGTG

                   *                                                         
      18901 GAGATCCGCGATGATGATATGAAGAGAAAGATTCCAGGCAAGAAAAACAGGTCGAGTCAGCCAGC
         66 GAGATCCACGATGATGATATGAAGAGAAAGATTCCAGGCAAGAAAAACAGGTCGAGTCAGCCAGC

                                            *                                
      18966 AGTTTGCCAAGGAAATGAAAATTTGGCCAATGCAGAGGAGAATGACTTGACACATGCGACAGATT
        131 AGTTTGCCAAGGAAATGAAAATTTGGCCAATGAAGAGGAGAATGACTTGACACATGCGACAGATT

                                                    *    
      19031 CAGATTCATCCAATGGGAAGATTGCAGCTGCTGAGAGCAATGTGG
        196 CAGATTCATCCAATGGGAAGATTGCAGCTGCTGAGAGCAAGGTGG

                    *    *             *                                     
      19076 CTATAAGATTAACTCGCTCAGCAGCTCGGAAAGGGGCTATAAACCCAAATGATGGCATCCAGGTG
          1 CTATAAGACTAACACGCTCAGCAGCTCAGAAAGGGGCTATAAACCCAAATGATGGCATCCAGGTG

                                        *         *                          
      19141 GAGATCCACGATGATGATATGAAGAGAAGGATTCCAGGGAAGAAAAACAGGTCGAGTCAGCCAGC
         66 GAGATCCACGATGATGATATGAAGAGAAAGATTCCAGGCAAGAAAAACAGGTCGAGTCAGCCAGC

                  *                   *                        *    *        
      19206 AGTTTGTCAAGGAAATGAAAATTTGGGCAATGAAGAGGAGAATGACTTGACTCATGTGACAGATT
        131 AGTTTGCCAAGGAAATGAAAATTTGGCCAATGAAGAGGAGAATGACTTGACACATGCGACAGATT

                      *                                  
      19271 CAGATTCATCTAATGGGAAGATTGCAGCTGCTGAGAGCAAGGTGG
        196 CAGATTCATCCAATGGGAAGATTGCAGCTGCTGAGAGCAAGGTGG

               
      19316 CTA
          1 CTA

      19319 CAACGAAATC


Statistics
Matches: 227,  Mismatches: 16, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
 240  227  1.00

ACGTcount: A:0.35, C:0.18, G:0.28, T:0.20


Consensus pattern (240 bp):   
CTATAAGACTAACACGCTCAGCAGCTCAGAAAGGGGCTATAAACCCAAATGATGGCATCCAGGTG
GAGATCCACGATGATGATATGAAGAGAAAGATTCCAGGCAAGAAAAACAGGTCGAGTCAGCCAGC
AGTTTGCCAAGGAAATGAAAATTTGGCCAATGAAGAGGAGAATGACTTGACACATGCGACAGATT
CAGATTCATCCAATGGGAAGATTGCAGCTGCTGAGAGCAAGGTGG
Done.