Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_15174

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: 2583
ACGTcount: A:0.31, C:0.19, G:0.26, T:0.24


Found at i:2509 original size:30 final size:29

Alignment explanation


    Indices: 2473--2557  Score: 116
    Period size: 30  Copynumber: 2.8  Consensus size: 29

       2463 CCAGCAGAAA

                                          
       2473 GACACAAATGACAAGGAAACAAACGGCAAG
          1 GACACAAATGACAAGG-AACAAACGGCAAG

                       *        *         
       2503 GACACAAATGAGAAGGAACTGAACGGCAAG
          1 GACACAAATGACAAGGAAC-AAACGGCAAG

                  *                  
       2533 GACACAGATGACAAGGGAACAAACG
          1 GACACAAATGACAA-GGAACAAACG

       2558 ACATTGAAGG


Statistics
Matches: 48,  Mismatches: 5, Indels: 4
        0.84            0.09        0.07

Matches are distributed among these distances:
  29    3  0.06
  30   40  0.83
  31    5  0.10

ACGTcount: A:0.49, C:0.19, G:0.27, T:0.05


Consensus pattern (29 bp):   
GACACAAATGACAAGGAACAAACGGCAAG

Found at i:2547 original size:15 final size:15

Alignment explanation


    Indices: 2473--2548  Score: 64
    Period size: 15  Copynumber: 5.1  Consensus size: 15

       2463 CCAGCAGAAA

                           
       2473 GACACAAATGACAAG
          1 GACACAAATGACAAG

              *     * *    
       2488 GAAACAAACGGCAAG
          1 GACACAAATGACAAG

                       *   
       2503 GACACAAATGAGAAG
          1 GACACAAATGACAAG

                  *  * *    
       2518 GA-ACTGAACGGCAAG
          1 GACAC-AAATGACAAG

                  *        
       2533 GACACAGATGACAAG
          1 GACACAAATGACAAG

             
       2548 G
          1 G

       2549 GAACAAACGA


Statistics
Matches: 44,  Mismatches: 15, Indels: 4
        0.70            0.24        0.06

Matches are distributed among these distances:
  14    2  0.05
  15   40  0.91
  16    2  0.05

ACGTcount: A:0.49, C:0.18, G:0.28, T:0.05


Consensus pattern (15 bp):   
GACACAAATGACAAG

Found at i:2560 original size:15 final size:14

Alignment explanation


    Indices: 2476--2560  Score: 53
    Period size: 15  Copynumber: 5.7  Consensus size: 14

       2466 GCAGAAAGAC

                 *         
       2476 ACAAATGACAAGGAA
          1 ACAAACGACAAGG-A

                   *      
       2491 ACAAACGGCAAGGA
          1 ACAAACGACAAGGA

                  *  *     
       2505 CACAAATGAGAAGGA
          1 -ACAAACGACAAGGA

               *    *      
       2520 ACTGAACGGCAAGGA
          1 AC-AAACGACAAGGA

                * *         
       2535 CACAGATGACAAGGGA
          1 -ACAAACGACAA-GGA

                      
       2551 ACAAACGACA
          1 ACAAACGACA

       2561 TTGAAGGGCA


Statistics
Matches: 51,  Mismatches: 15, Indels: 8
        0.69            0.20        0.11

Matches are distributed among these distances:
  14    3  0.06
  15   43  0.84
  16    5  0.10

ACGTcount: A:0.51, C:0.19, G:0.26, T:0.05


Consensus pattern (14 bp):   
ACAAACGACAAGGA
Done.