Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_33520

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: 1872
ACGTcount: A:0.30, C:0.15, G:0.22, T:0.33


Found at i:1063 original size:105 final size:105

Alignment explanation


    Indices: 866--1067  Score: 262
    Period size: 105  Copynumber: 1.9  Consensus size: 105

        856 TCACTTGATA

                           *              *     *                            
        866 TTGTCACGTATACTATATTGATTGATGCACTTTGCACAGAAGGAATGATTTCTAAAGCTGTAGAG
          1 TTGTCACGTATACTACATTGATTGATGCACATTGCAAAGAAGGAATGATTTCTAAAGCTGTAGAG

                       *        *                   
        931 ATCGTTGACACGATAAGAAAGCAAGGCATTGAACCCAATG
         66 ATCGTTGACACAATAAGAAAACAAGGCATTGAACCCAATG

                            *   *                      *   *                 
        971 TTGTCACGTATACTACGTTGGTTGATGCACATTGCAAAGAAGGGATGGTTTCTAAAGCTG-AGGA
          1 TTGTCACGTATACTACATTGATTGATGCACATTGCAAAGAAGGAATGATTTCTAAAGCTGTA-GA

            *  *           * *     *         
       1035 TATTGTTGACACAATGATAAAACGAGGCATTGA
         65 GATCGTTGACACAATAAGAAAACAAGGCATTGA

       1068 GCCTGATGTT


Statistics
Matches: 82,  Mismatches: 14, Indels: 2
        0.84            0.14        0.02

Matches are distributed among these distances:
 104    1  0.01
 105   81  0.99

ACGTcount: A:0.33, C:0.15, G:0.24, T:0.28


Consensus pattern (105 bp):   
TTGTCACGTATACTACATTGATTGATGCACATTGCAAAGAAGGAATGATTTCTAAAGCTGTAGAG
ATCGTTGACACAATAAGAAAACAAGGCATTGAACCCAATG

Done.