Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_21383

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, 219

Length: 366
ACGTcount: A:0.22, C:0.26, G:0.20, T:0.31


Found at i:287 original size:137 final size:137

Alignment explanation


    Indices: 41--296  Score: 381
    Period size: 137  Copynumber: 1.9  Consensus size: 137

         31 GTCCGCAAGA

                                                                             
         41 GTTCGGCCATCTTCAAGCTGCTTTCCAGCAAAAATCAACCTCTGCTGGTCCAGTGGGATCCCTTC
          1 GTTCGGCCATCTTCAAGCTGCTTTCCAGCAAAAATCAACCTCTGCTGGTCCAGTGGGATCCCTTC

                                                                             
        106 CTTATCCTGAATCTTGGCCTTAACATTATCAATCGTATCAGAACTCTCCACCTCCAACGTAATAG
         66 CTTATCCTGAATCTTGGCCTTAACATTATCAATCGTATCAGAACTCTCCACCTCCAACGTAATAG

                   
        171 TTTTTCC
        131 TTTTTCC

                                       *     *            *     **           
        178 GTTCGGCCATCTTCAAGCTG-TTTACCGGCAAAGAT-AAGCCTCTGTTGGTCTGGTGGGATCCCT
          1 GTTCGGCCATCTTCAAGCTGCTTT-CCAGCAAAAATCAA-CCTCTGCTGGTCCAGTGGGATCCCT

                 *  *  *           *           *           *        
        241 TCCTTGTCTTGGATCTTGGCCTTGACATTATCAATTGTATCAGAACTTTCCACCTC
         64 TCCTTATCCTGAATCTTGGCCTTAACATTATCAATCGTATCAGAACTCTCCACCTC

        297 GAGGGTGATG


Statistics
Matches: 106,  Mismatches: 11, Indels: 4
        0.88            0.09        0.03

Matches are distributed among these distances:
 136    5  0.05
 137  101  0.95

ACGTcount: A:0.21, C:0.29, G:0.18, T:0.33


Consensus pattern (137 bp):   
GTTCGGCCATCTTCAAGCTGCTTTCCAGCAAAAATCAACCTCTGCTGGTCCAGTGGGATCCCTTC
CTTATCCTGAATCTTGGCCTTAACATTATCAATCGTATCAGAACTCTCCACCTCCAACGTAATAG
TTTTTCC
Done.