Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01003114.1 Corchorus capsularis cultivar CVL-1 contig03122, 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, 889

Length: 1483
ACGTcount: A:0.31, C:0.18, G:0.13, T:0.38


Found at i:33 original size:22 final size:22

Alignment explanation


    Indices: 5--263  Score: 173
    Period size: 22  Copynumber: 12.0  Consensus size: 22

          1 ATTG

                   *              
          5 CCTTTTTGCTTTTTACTGATTA
          1 CCTTTTTACTTTTTACTGATTA

                       *  *       
         27 CCTTTTTACTTCTTGCTGATTA
          1 CCTTTTTACTTTTTACTGATTA

                       *         * 
         49 GCC-TTTTACTCTTTACTGATCA
          1 -CCTTTTTACTTTTTACTGATTA

                       *         *
         71 CCTTTTTAC-TCTTACTGATTT
          1 CCTTTTTACTTTTTACTGATTA

                       *     *    
         92 CC-TTTTACTTCTTACTTATTA
          1 CCTTTTTACTTTTTACTGATTA

                        *          
        113 CCTTTTTTAC-TCTTACTGATTA
          1 CC-TTTTTACTTTTTACTGATTA

                                *  
        135 --TTATTTACTTTTTACTGACTA
          1 CCTT-TTTACTTTTTACTGATTA

                        *   *      
        156 -CTATTTTAC-TCTTATTGATTA
          1 CCT-TTTTACTTTTTACTGATTA

                *        *        
        177 CCTTCTTACTTTTCACTGATTA
          1 CCTTTTTACTTTTTACTGATTA

                       *      *     
        199 -CTATTTTACTCTTTACTAATTTA
          1 CCT-TTTTACTTTTTACTGA-TTA

                      **     *     
        222 CCATTTTT-CCCTTT-CAGA-TA
          1 CC-TTTTTACTTTTTACTGATTA

                    *             
        242 CCTTTTTTTCTTTTTACTGATT
          1 CC-TTTTTACTTTTTACTGATT

        264 GCATGCTATT


Statistics
Matches: 185,  Mismatches: 34, Indels: 35
        0.73            0.13        0.14

Matches are distributed among these distances:
  19    2  0.01
  20   20  0.11
  21   54  0.29
  22   85  0.46
  23   18  0.10
  24    5  0.03
  25    1  0.01

ACGTcount: A:0.18, C:0.22, G:0.05, T:0.55


Consensus pattern (22 bp):   
CCTTTTTACTTTTTACTGATTA

Found at i:120 original size:43 final size:43

Alignment explanation


    Indices: 8--220  Score: 181
    Period size: 43  Copynumber: 5.0  Consensus size: 43

          1 ATTGCCT

                *   *                         *       *  
          8 TTTTGCTTTTTACTGATTACC-TTTTTACTTCTTGCTGATTAGCC
          1 TTTTACTTCTTACTGATTACCTTTTTTAC-TCTTACTGATT-TCC

                              *                         
         52 TTTTAC-TCTTTACTGATCACC-TTTTTACTCTTACTGATTTCC
          1 TTTTACTTC-TTACTGATTACCTTTTTTACTCTTACTGATTTCC

                          *                             
         94 TTTTACTTCTTACTTATTACCTTTTTTACTCTTACTGATTAT--
          1 TTTTACTTCTTACTGATTACCTTTTTTACTCTTACTGATT-TCC

                     *       *     *           *     *  
        136 TATTTACTTTTTACTGACTA-CTATTTTACTCTTATTGATTACC
          1 T-TTTACTTCTTACTGATTACCTTTTTTACTCTTACTGATTTCC

                                    *              *    
        179 TTCTTACTT-TTCACTGATTA-CTATTTTACTCTTTACTAATTT
          1 TT-TTACTTCTT-ACTGATTACCTTTTTTACTC-TTACTGATTT

        221 ACCATTTTTC


Statistics
Matches: 142,  Mismatches: 17, Indels: 20
        0.79            0.09        0.11

Matches are distributed among these distances:
  42   40  0.28
  43   71  0.50
  44   31  0.22

ACGTcount: A:0.19, C:0.21, G:0.05, T:0.55


Consensus pattern (43 bp):   
TTTTACTTCTTACTGATTACCTTTTTTACTCTTACTGATTTCC

Found at i:150 original size:64 final size:63

Alignment explanation


    Indices: 13--215  Score: 182
    Period size: 64  Copynumber: 3.1  Consensus size: 63

          3 TGCCTTTTTG

                                        *  *                         *       
         13 CTTTTTACTGATTACCTTTTTACTTCTTGCTGATTAGCC-TTTTACTCTTTACTGATCACCTT-T
          1 CTTTTTACTGATTACC-TTTTACTTCTTACTTATTA-CCTTTTTACTC-TTACTGATTA--TTAT

               
         76 TTA
         61 TTA

               *         *                                                  
         79 C-TCTTACTGATTTCCTTTTACTTCTTACTTATTACCTTTTTTACTCTTACTGATTATTATTTA
          1 CTTTTTACTGATTACCTTTTACTTCTTACTTATTACC-TTTTTACTCTTACTGATTATTATTTA

                       *    *                        *     *           *     
        142 CTTTTTACTGACTACTATTTTAC-TCTTA-TTGATTACCTTCTTACTTTTCACTGATTACTATTT
          1 CTTTTTACTGATTAC-CTTTTACTTCTTACTT-ATTACCTTTTTACTCTT-ACTGATTATTA-TT

              
        205 TA
         62 TA

              *      
        207 CTCTTTACT
          1 CTTTTTACT

        216 AATTTACCAT


Statistics
Matches: 116,  Mismatches: 13, Indels: 17
        0.79            0.09        0.12

Matches are distributed among these distances:
  62    2  0.02
  63   18  0.16
  64   57  0.49
  65   38  0.33
  66    1  0.01

ACGTcount: A:0.19, C:0.22, G:0.05, T:0.55


Consensus pattern (63 bp):   
CTTTTTACTGATTACCTTTTACTTCTTACTTATTACCTTTTTACTCTTACTGATTATTATTTA

Found at i:545 original size:55 final size:55

Alignment explanation


    Indices: 458--579  Score: 199
    Period size: 55  Copynumber: 2.2  Consensus size: 55

        448 CTTAGTTATC

                            *          *                           
        458 GATTTACTGATTACTATTACCTTGACTTTGATTAATCTCTTTTGACTTAATTACT
          1 GATTTACTGATTACTACTACCTTGACTCTGATTAATCTCTTTTGACTTAATTACT

                                *                      *         * 
        513 GATTTACTGATTACTACTACTTTGACTCTGATTAATCTCTTTTTACTTAATTATT
          1 GATTTACTGATTACTACTACCTTGACTCTGATTAATCTCTTTTGACTTAATTACT

                        
        568 GATTTACTGATT
          1 GATTTACTGATT

        580 GGCTTGAGCA


Statistics
Matches: 62,  Mismatches: 5, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  55   62  1.00

ACGTcount: A:0.25, C:0.16, G:0.09, T:0.50


Consensus pattern (55 bp):   
GATTTACTGATTACTACTACCTTGACTCTGATTAATCTCTTTTGACTTAATTACT
Done.