Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01023430.1 Corchorus olitorius cultivar O-4 contig23463, 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: 8840
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.28


Found at i:3647 original size:43 final size:42

Alignment explanation


    Indices: 3459--3787  Score: 375
    Period size: 41  Copynumber: 7.8  Consensus size: 42

       3449 CAATAACCAA

                                     *  *             * 
       3459 AAAGTCCCCAAACACATATATAACAAAGGGGCAATTCTAT-TCC
          1 AAAGTCCCCAAACACATATATAACACAGAGGC-A-TCTATATAC

                    *                         *        
       3502 AAAAGTCCTCAAACACATATATAACACAGAGGCACCTATAT-C
          1 -AAAGTCCCCAAACACATATATAACACAGAGGCATCTATATAC

            *                           *   **  *      
       3544 CAAGTCCCCAAACAC--ATATAACACAGGGGCGCCTTTATTAC
          1 AAAGTCCCCAAACACATATATAACACAGAGGCATCTATA-TAC

                   *                                  
       3585 AAAGTCCTCAAACACATATATAACACAGAGGCATCTATAT-C
          1 AAAGTCCCCAAACACATATATAACACAGAGGCATCTATATAC

                                        *               
       3626 AAAGTCCCCAAACACATATATAACACAGGGGCAACTCTAT-TAC
          1 AAAGTCCCCAAACACATATATAACACAGAGGC-A-TCTATATAC

                   *                          *       
       3669 AAAGTCCTCAAACACATATATAACACAGAGGCATTTATAT-C
          1 AAAGTCCCCAAACACATATATAACACAGAGGCATCTATATAC

                                        *       *      
       3710 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTAC
          1 AAAGTCCCCAAACACATATATAACACAGAGGCATCTATA-TAC

                    *       *                  
       3753 AAAAGTCCTCAAACACTTATATAACACAGAGGCAT
          1 -AAAGTCCCCAAACACATATATAACACAGAGGCAT

       3788 TTCTCCTTAT


Statistics
Matches: 246,  Mismatches: 27, Indels: 24
        0.83            0.09        0.08

Matches are distributed among these distances:
  39   19  0.08
  40    1  0.00
  41   98  0.40
  42   11  0.04
  43   57  0.23
  44   60  0.24

ACGTcount: A:0.42, C:0.26, G:0.11, T:0.21


Consensus pattern (42 bp):   
AAAGTCCCCAAACACATATATAACACAGAGGCATCTATATAC

Found at i:3673 original size:84 final size:85

Alignment explanation


    Indices: 3459--3787  Score: 531
    Period size: 84  Copynumber: 3.9  Consensus size: 85

       3449 CAATAACCAA

                                     *        *      *                       
       3459 AAAGTCCCCAAACACATATATAACAAAGGGGCAATTCTATTCCAAAAGTCCTCAAACACATATAT
          1 AAAGTCCCCAAACACATATATAACACAGGGGCAACTCTATTACAAAAGTCCTCAAACACATATAT

                        *       
       3524 AACACAGAGGCACCTATATC
         66 AACACAGAGGCATCTATATC

            *                               **  *                            
       3544 CAAGTCCCCAAACAC--ATATAACACAGGGGCGCCTTTATTAC-AAAGTCCTCAAACACATATAT
          1 AAAGTCCCCAAACACATATATAACACAGGGGCAACTCTATTACAAAAGTCCTCAAACACATATAT

                                
       3606 AACACAGAGGCATCTATATC
         66 AACACAGAGGCATCTATATC

                                                                             
       3626 AAAGTCCCCAAACACATATATAACACAGGGGCAACTCTATTAC-AAAGTCCTCAAACACATATAT
          1 AAAGTCCCCAAACACATATATAACACAGGGGCAACTCTATTACAAAAGTCCTCAAACACATATAT

                         *      
       3690 AACACAGAGGCATTTATATC
         66 AACACAGAGGCATCTATATC

                                             *                         *     
       3710 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTACAAAAGTCCTCAAACACTTATAT
          1 AAAGTCCCCAAACACATATATAACACAGGGGCAACTCTATTACAAAAGTCCTCAAACACATATAT

                         
       3775 AACACAGAGGCAT
         66 AACACAGAGGCAT

       3788 TTCTCCTTAT


Statistics
Matches: 226,  Mismatches: 15, Indels: 6
        0.91            0.06        0.02

Matches are distributed among these distances:
  82   54  0.24
  83   20  0.09
  84  105  0.46
  85   47  0.21

ACGTcount: A:0.42, C:0.26, G:0.11, T:0.21


Consensus pattern (85 bp):   
AAAGTCCCCAAACACATATATAACACAGGGGCAACTCTATTACAAAAGTCCTCAAACACATATAT
AACACAGAGGCATCTATATC

Found at i:5394 original size:13 final size:13

Alignment explanation


    Indices: 5360--5396  Score: 56
    Period size: 13  Copynumber: 2.8  Consensus size: 13

       5350 TATCTTACTG

                    *    
       5360 TTTTGGTTAATTA
          1 TTTTGGTTTATTA

              *          
       5373 TTGTGGTTTATTA
          1 TTTTGGTTTATTA

                       
       5386 TTTTGGTTTAT
          1 TTTTGGTTTAT

       5397 AACTCTGATT


Statistics
Matches: 21,  Mismatches: 3, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  13   21  1.00

ACGTcount: A:0.16, C:0.00, G:0.19, T:0.65


Consensus pattern (13 bp):   
TTTTGGTTTATTA
Done.