Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_21381

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, 223

Length: 372
ACGTcount: A:0.23, C:0.26, G:0.21, T:0.31


Found at i:299 original size:143 final size:143

Alignment explanation


    Indices: 41--302  Score: 402
    Period size: 143  Copynumber: 1.8  Consensus size: 143

         31 ATCAGCAAGA

                                                                             
         41 GTTCGGCCATCTTCAAGCTGCTTTCCAGCAAAAATCAACCTCTGCTGGTCCGGTGGGATCCCTTC
          1 GTTCGGCCATCTTCAAGCTGCTTTCCAGCAAAAATCAACCTCTGCTGGTCCGGTGGGATCCCTTC

                                                                             
        106 CTTATCCTGAATCTTGGCCTTAACATTATCAATCGTATCAGAACTCTCCACCTCCAACGTAATAG
         66 CTTATCCTGAATCTTGGCCTTAACATTATCAATCGTATCAGAACTCTCCACCTCCAACGTAATAG

                         
        171 TTTTTCCAGTGAG
        131 TTTTTCCAGTGAG

                                       *     *            *     *            
        184 GTTCGGCCATCTTCAAGCTG-TTTACCGGCAAAGAT-AAGCCTCTGTTGGTCTGGTGGGATCCCT
          1 GTTCGGCCATCTTCAAGCTGCTTT-CCAGCAAAAATCAA-CCTCTGCTGGTCCGGTGGGATCCCT

                 *  *  *           *           *           *        
        247 TCCTTGTCTTGGATCTTGGCCTTGACATTATCAATTGTATCAGAACTTTCCACCTC
         64 TCCTTATCCTGAATCTTGGCCTTAACATTATCAATCGTATCAGAACTCTCCACCTC

        303 GAGGGTGATG


Statistics
Matches: 107,  Mismatches: 10, Indels: 4
        0.88            0.08        0.03

Matches are distributed among these distances:
 142    5  0.05
 143  102  0.95

ACGTcount: A:0.21, C:0.28, G:0.19, T:0.32


Consensus pattern (143 bp):   
GTTCGGCCATCTTCAAGCTGCTTTCCAGCAAAAATCAACCTCTGCTGGTCCGGTGGGATCCCTTC
CTTATCCTGAATCTTGGCCTTAACATTATCAATCGTATCAGAACTCTCCACCTCCAACGTAATAG
TTTTTCCAGTGAG

Done.