Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_451 ID=scaffold_451-JGI_221_v2.0

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: 6856
ACGTcount: A:0.33, C:0.22, G:0.14, T:0.31


Found at i:303 original size:28 final size:28

Alignment explanation


    Indices: 232--327  Score: 124
    Period size: 28  Copynumber: 3.4  Consensus size: 28

        222 TTAATAAGTC

                            * *          
        232 CGCACACTTAGTGC-TCAATAATCAAACT
          1 CGCACACTTAGTGCTTTACTAAT-AAACT

                                        
        260 CGCACACTTAGTGCTTTACTAATAAACT
          1 CGCACACTTAGTGCTTTACTAATAAACT

                                       * 
        288 CGCACACTTAGTGCTTTAC-AATTAAATT
          1 CGCACACTTAGTGCTTTACTAA-TAAACT

               *        
        316 CGCGCACTTAGT
          1 CGCACACTTAGT

        328 ATCGAAAGTC


Statistics
Matches: 62,  Mismatches: 4, Indels: 4
        0.89            0.06        0.06

Matches are distributed among these distances:
  27    2  0.03
  28   54  0.87
  29    6  0.10

ACGTcount: A:0.31, C:0.26, G:0.12, T:0.30


Consensus pattern (28 bp):   
CGCACACTTAGTGCTTTACTAATAAACT

Found at i:6623 original size:23 final size:23

Alignment explanation


    Indices: 6559--6856  Score: 269
    Period size: 23  Copynumber: 12.8  Consensus size: 23

       6549 CATATATATA

                                   
       6559 TATATACAAAATTGGACAGCATT
          1 TATATACAAAATTGGACAGCATT

                *         *        *
       6582 TATACACCAAAATTTGACAGCATG
          1 TATATA-CAAAATTGGACAGCATT

                                   
       6606 TATATACAAAATTGGACAGCATT
          1 TATATACAAAATTGGACAGCATT

                             *      *
       6629 TAT-TCACCAAAATTGGGCAGCATA
          1 TATAT-A-CAAAATTGGACAGCATT

              *    *  *          * 
       6653 TAAATACCAATTTGGACAGCACT
          1 TATATACAAAATTGGACAGCATT

                *        *   *    *
       6676 TATACACAAAATTTGACGGCATG
          1 TATATACAAAATTGGACAGCATT

                      *            
       6699 TATATACAAAGTTGGACAGCATT
          1 TATATACAAAATTGGACAGCATT

                             *      *
       6722 TAT-TCACCAAAATTGGGCAGCATA
          1 TATAT-A-CAAAATTGGACAGCATT

                   *  *       *  * 
       6746 TATATACCAATTTGGACAACACT
          1 TATATACAAAATTGGACAGCATT

                *        *        *
       6769 TATACACAAAATTTGACAGCATG
          1 TATATACAAAATTGGACAGCATT

                              *    
       6792 TATATACAAAATTGGACAACATT
          1 TATATACAAAATTGGACAGCATT

                                    *
       6815 TAT-TCACCAAAATTGGACAGCATA
          1 TATAT-A-CAAAATTGGACAGCATT

                   *  *       
       6839 TATATACCAATTTGGACA
          1 TATATACAAAATTGGACA


Statistics
Matches: 214,  Mismatches: 51, Indels: 20
        0.75            0.18        0.07

Matches are distributed among these distances:
  22    3  0.01
  23  133  0.62
  24   75  0.35
  25    3  0.01

ACGTcount: A:0.41, C:0.18, G:0.13, T:0.28


Consensus pattern (23 bp):   
TATATACAAAATTGGACAGCATT

Found at i:6628 original size:47 final size:47

Alignment explanation


    Indices: 6556--6856  Score: 372
    Period size: 47  Copynumber: 6.4  Consensus size: 47

       6546 CAGCATATAT

                                                    *      
       6556 ATATATATACAAAATTGGACAGCATTTATACACCAAAATTTGACAGC
          1 ATATATATACAAAATTGGACAGCATTTATACACCAAAATTGGACAGC

              *                          *            *    
       6603 ATGTATATACAAAATTGGACAGCATTTATTCACCAAAATTGGGCAGC
          1 ATATATATACAAAATTGGACAGCATTTATACACCAAAATTGGACAGC

                 *    *  *          *               *   *  
       6650 ATATAAATACCAATTTGGACAGCACTTATACA-CAAAATTTGACGGC
          1 ATATATATACAAAATTGGACAGCATTTATACACCAAAATTGGACAGC

              *          *               *            *    
       6696 ATGTATATACAAAGTTGGACAGCATTTATTCACCAAAATTGGGCAGC
          1 ATATATATACAAAATTGGACAGCATTTATACACCAAAATTGGACAGC

                      *  *       *  *               *      
       6743 ATATATATACCAATTTGGACAACACTTATACA-CAAAATTTGACAGC
          1 ATATATATACAAAATTGGACAGCATTTATACACCAAAATTGGACAGC

              *                  *       *                 
       6789 ATGTATATACAAAATTGGACAACATTTATTCACCAAAATTGGACAGC
          1 ATATATATACAAAATTGGACAGCATTTATACACCAAAATTGGACAGC

                      *  *       
       6836 ATATATATACCAATTTGGACA
          1 ATATATATACAAAATTGGACA


Statistics
Matches: 213,  Mismatches: 39, Indels: 4
        0.83            0.15        0.02

Matches are distributed among these distances:
  46   76  0.36
  47  137  0.64

ACGTcount: A:0.41, C:0.18, G:0.13, T:0.28


Consensus pattern (47 bp):   
ATATATATACAAAATTGGACAGCATTTATACACCAAAATTGGACAGC

Found at i:6705 original size:93 final size:93

Alignment explanation


    Indices: 6556--6856  Score: 512
    Period size: 93  Copynumber: 3.2  Consensus size: 93

       6546 CAGCATATAT

                      *  *          *                                        
       6556 ATATATATACAAAATTGGACAGCATTTATACACCAAAATTTGACAGCATGTATATACAAAATTGG
          1 ATATATATACCAATTTGGACAGCACTTATACA-CAAAATTTGACAGCATGTATATACAAAATTGG

                                         
       6621 ACAGCATTTATTCACCAAAATTGGGCAGC
         65 ACAGCATTTATTCACCAAAATTGGGCAGC

                 *                                     *               *     
       6650 ATATAAATACCAATTTGGACAGCACTTATACACAAAATTTGACGGCATGTATATACAAAGTTGGA
          1 ATATATATACCAATTTGGACAGCACTTATACACAAAATTTGACAGCATGTATATACAAAATTGGA

                                        
       6715 CAGCATTTATTCACCAAAATTGGGCAGC
         66 CAGCATTTATTCACCAAAATTGGGCAGC

                                 *                                           
       6743 ATATATATACCAATTTGGACAACACTTATACACAAAATTTGACAGCATGTATATACAAAATTGGA
          1 ATATATATACCAATTTGGACAGCACTTATACACAAAATTTGACAGCATGTATATACAAAATTGGA

              *                    *    
       6808 CAACATTTATTCACCAAAATTGGACAGC
         66 CAGCATTTATTCACCAAAATTGGGCAGC

                                 
       6836 ATATATATACCAATTTGGACA
          1 ATATATATACCAATTTGGACA


Statistics
Matches: 195,  Mismatches: 12, Indels: 1
        0.94            0.06        0.00

Matches are distributed among these distances:
  93  167  0.86
  94   28  0.14

ACGTcount: A:0.41, C:0.18, G:0.13, T:0.28


Consensus pattern (93 bp):   
ATATATATACCAATTTGGACAGCACTTATACACAAAATTTGACAGCATGTATATACAAAATTGGA
CAGCATTTATTCACCAAAATTGGGCAGC
Done.