Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_305 ID=scaffold_305-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: 8372
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.32


Found at i:198 original size:3 final size:3

Alignment explanation


    Indices: 190--243  Score: 108
    Period size: 3  Copynumber: 18.0  Consensus size: 3

        180 TACTATGGTT

                                                                           
        190 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
          1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA

                   
        238 ATA ATA
          1 ATA ATA

        244 TGGTAATGAT


Statistics
Matches: 51,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   51  1.00

ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33


Consensus pattern (3 bp):   
ATA

Found at i:851 original size:22 final size:22

Alignment explanation


    Indices: 820--870  Score: 84
    Period size: 22  Copynumber: 2.3  Consensus size: 22

        810 AATCACGCCT

                 *                
        820 ACCGCTGGTCATCGGCGTCGGC
          1 ACCGCCGGTCATCGGCGTCGGC

                                  
        842 ACCGCCGGTCATCGGCGTCGGC
          1 ACCGCCGGTCATCGGCGTCGGC

            *      
        864 GCCGCCG
          1 ACCGCCG

        871 TATACGACGG


Statistics
Matches: 27,  Mismatches: 2, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  22   27  1.00

ACGTcount: A:0.08, C:0.41, G:0.37, T:0.14


Consensus pattern (22 bp):   
ACCGCCGGTCATCGGCGTCGGC

Found at i:2467 original size:45 final size:45

Alignment explanation


    Indices: 1669--2465  Score: 1045
    Period size: 45  Copynumber: 17.7  Consensus size: 45

       1659 TCTTCAATCC

                    *   *          *                    *
       1669 ACTTCGCTGCCAGTACAGGAAGATAAGATCTGCTATCTTTGATCG
          1 ACTTCGCTACCAATACAGGAAGACAAGATCTGCTATCTTTGATCT

                *   *     *                       * *   *
       1714 ACTTTGCTGCCAATTCAGGAAGACAAGATCTGCTATCTCTAATCA
          1 ACTTCGCTACCAATACAGGAAGACAAGATCTGCTATCTTTGATCT

                *   *   *                   *      *     
       1759 ACTTTGCTGCCAGTACAGGAAGACAAGATCTGTTATCTTCGATCT
          1 ACTTCGCTACCAATACAGGAAGACAAGATCTGCTATCTTTGATCT

                           *                    *        
       1804 ACTTCGCTACCAATATAGGAAGACAAGATCTGCTATGTTTGATCT
          1 ACTTCGCTACCAATACAGGAAGACAAGATCTGCTATCTTTGATCT

                    *        *              *      *     
       1849 ACTTCGCTGCCAATACAAGAAGACAAGATCTGTTATCTTCGATCT
          1 ACTTCGCTACCAATACAGGAAGACAAGATCTGCTATCTTTGATCT

             *             *                    *        
       1894 ATTTCGCTACCAATATAGGAAGACAAGATCTGCTATGTTTGATCT
          1 ACTTCGCTACCAATACAGGAAGACAAGATCTGCTATCTTTGATCT

                    *                       *      *     
       1939 ACTTCGCTGCCAATACAGGAAGACAAGATCTGTTATCTTCGATCT
          1 ACTTCGCTACCAATACAGGAAGACAAGATCTGCTATCTTTGATCT

                           *                             
       1984 ACTTCGCTACCAATATAGGAAGACAAGATCTGCTATCTTTGATCT
          1 ACTTCGCTACCAATACAGGAAGACAAGATCTGCTATCTTTGATCT

                    *       *      *        *      *   * 
       2029 ACTTCGCTGCCAATACCGGAAGAAAAGATCTGTTATCTTCGATTT
          1 ACTTCGCTACCAATACAGGAAGACAAGATCTGCTATCTTTGATCT

                           *                    *        
       2074 ACTTCGCTACCAATATAGGAAGACAAGATCTGCTATTTTTGATCT
          1 ACTTCGCTACCAATACAGGAAGACAAGATCTGCTATCTTTGATCT

                    *   *                   *      *     
       2119 ACTTCGCTGCCAGTACAGGAAGACAAGATCTGTTATCTTCGATCT
          1 ACTTCGCTACCAATACAGGAAGACAAGATCTGCTATCTTTGATCT

                           *               *             
       2164 ACTTCGCTACCAATATAGGAAGACAAGATCTCCTATCTTTGATCT
          1 ACTTCGCTACCAATACAGGAAGACAAGATCTGCTATCTTTGATCT

                 *         *               *             
       2209 ACTTCACTACCAATATAGGAAGACAAGATCTCCTATCTTTGATCT
          1 ACTTCGCTACCAATACAGGAAGACAAGATCTGCTATCTTTGATCT

                 *                    *     *    * *     
       2254 ACTTCACTACCAATACAGGAAGACAAAATCTGTTATCCTCGATCT
          1 ACTTCGCTACCAATACAGGAAGACAAGATCTGCTATCTTTGATCT

                           *    *               *        
       2299 ACTTCGCTACCAATATAGGATGACAAGATCTGCTATTTTTGATCT
          1 ACTTCGCTACCAATACAGGAAGACAAGATCTGCTATCTTTGATCT

                 *  *   *                   *      *     
       2344 ACTTCACTGCCAGTACAGGAAGACAAGATCTGTTATCTTCGATCT
          1 ACTTCGCTACCAATACAGGAAGACAAGATCTGCTATCTTTGATCT

                     *     *                *            
       2389 ACTTCGCTATCAATATAGGAAGACAAGATCTGTTATCTTTGATCT
          1 ACTTCGCTACCAATACAGGAAGACAAGATCTGCTATCTTTGATCT

                                            
       2434 ACTTCGCTACCAATACAGGAAGACAAGATCTG
          1 ACTTCGCTACCAATACAGGAAGACAAGATCTG

       2466 TTGTTTTCAA


Statistics
Matches: 650,  Mismatches: 102, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  45  650  1.00

ACGTcount: A:0.30, C:0.23, G:0.17, T:0.30


Consensus pattern (45 bp):   
ACTTCGCTACCAATACAGGAAGACAAGATCTGCTATCTTTGATCT

Found at i:6614 original size:14 final size:14

Alignment explanation


    Indices: 6595--6621  Score: 54
    Period size: 14  Copynumber: 1.9  Consensus size: 14

       6585 TGGTTCAATT

                          
       6595 CTTTACTAGAAAAA
          1 CTTTACTAGAAAAA

                         
       6609 CTTTACTAGAAAA
          1 CTTTACTAGAAAA

       6622 CAAATCTCTT


Statistics
Matches: 13,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  14   13  1.00

ACGTcount: A:0.48, C:0.15, G:0.07, T:0.30


Consensus pattern (14 bp):   
CTTTACTAGAAAAA
Done.