Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_05905

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, 388

Length: 648
ACGTcount: A:0.35, C:0.17, G:0.28, T:0.20


Found at i:535 original size:297 final size:297

Alignment explanation


    Indices: 1--554  Score: 869
    Period size: 297  Copynumber: 1.9  Consensus size: 297

                                        * *                 *                
          1 ATGGCGAAGAAGCATTTGAAAGTGAGGATCGAAGCCAAACGACTGAAAGCCGAGATGGGAAAGGT
          1 ATGGCGAAGAAGCATTTGAAAGTGAGGACCAAAGCCAAACGACTGAAAACCGAGATGGGAAAGGT

             *           *                                        *          
         66 ACGGGAAGACCAATTATGCTTAAGAGAGGAGCAGACAAAACTAATAACAAGGTTTGGAGAGATTG
         66 AAGGGAAGACCAACTATGCTTAAGAGAGGAGCAGACAAAACTAATAACAAGGTTCGGAGAGATTG

                                * *         *                             *  
        131 AGAGGCAATGCAATGAACTGCAGCAAGAAGCTGAAATGATAGCCAAGCAATCAGCCATGACTGGA
        131 AGAGGCAATGCAATGAACTGAAACAAGAAGCTCAAATGATAGCCAAGCAATCAGCCATGACTCGA

                       *  *                             *                    
        196 ATCAAGCTGAGTCTGATGTTGGGAATTCTGAAAGCTCGTGAGGGTGGAGATTTGGTTCAAGCCGC
        196 ATCAAGCTGAGACTCATGTTGGGAATTCTGAAAGCTCGTGAGGGAGGAGATTTGGTTCAAGCCGC

                                                 
        261 TGATCTCACTCGCTTCCTTGGGACTGATAACCCAGAC
        261 TGATCTCACTCGCTTCCTTGGGACTGATAACCCAGAC

                                    *                                        
        298 ATGGCGAAGAAGCATTTGAAAGTGCGGACCAAAGCCAAACGACTGAAAACCGAGATGGGAAAGGT
          1 ATGGCGAAGAAGCATTTGAAAGTGAGGACCAAAGCCAAACGACTGAAAACCGAGATGGGAAAGGT

                     *             *          *     *  * *                   
        363 AAGGGAAGATCAACTATGCTTAATAGAGGAGCAGTCAAAATTAGTGACAAGGTTCGGAGAGATTG
         66 AAGGGAAGACCAACTATGCTTAAGAGAGGAGCAGACAAAACTAATAACAAGGTTCGGAGAGATTG

                            *                       *                        
        428 AGAGGCAATGCAATGAGCTGAAACAAGAAGCTCAAATGATGGCCAAGCAATCAGCCATGACTCGA
        131 AGAGGCAATGCAATGAACTGAAACAAGAAGCTCAAATGATAGCCAAGCAATCAGCCATGACTCGA

            *                                                               
        493 CTCAAGCTG-GAACTCATGTTGGGAA-TCTTGAAAGCTCGTGAGGGAGGAGATTTGGTTCAAGC
        196 ATCAAGCTGAG-ACTCATGTTGGGAATTC-TGAAAGCTCGTGAGGGAGGAGATTTGGTTCAAGC

        555 TGCTAACCTG


Statistics
Matches: 232,  Mismatches: 23, Indels: 4
        0.90            0.09        0.02

Matches are distributed among these distances:
 296    3  0.01
 297  229  0.99

ACGTcount: A:0.35, C:0.17, G:0.29, T:0.19


Consensus pattern (297 bp):   
ATGGCGAAGAAGCATTTGAAAGTGAGGACCAAAGCCAAACGACTGAAAACCGAGATGGGAAAGGT
AAGGGAAGACCAACTATGCTTAAGAGAGGAGCAGACAAAACTAATAACAAGGTTCGGAGAGATTG
AGAGGCAATGCAATGAACTGAAACAAGAAGCTCAAATGATAGCCAAGCAATCAGCCATGACTCGA
ATCAAGCTGAGACTCATGTTGGGAATTCTGAAAGCTCGTGAGGGAGGAGATTTGGTTCAAGCCGC
TGATCTCACTCGCTTCCTTGGGACTGATAACCCAGAC
Done.