Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_20266

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: 3729
ACGTcount: A:0.30, C:0.17, G:0.22, T:0.31


Found at i:3117 original size:210 final size:207

Alignment explanation


    Indices: 2625--3118  Score: 634
    Period size: 210  Copynumber: 2.4  Consensus size: 207

       2615 ATTGCAGAGC

                                                  *         *           * ** 
       2625 ATTAAGCAAGATTGGAGACGGATTATCTACCTCCACTTGTCTCAAAGAATTAGATCTA-TATCAT
          1 ATTAAGCAAGATTGGAGACGGATTATCTACCTCCACTTATCTCAAA-ATTTAGATCTATTTTTGT

                  *              * *                                    *    
       2689 CTTAATATAAGTTTGCTTCCAGATTTGAAAGGATTTTCCTCTCTTCAAAATCTATCAATTGAAAG
         65 CTTAATTTAAGTTTGCTTCCAAAATTGAAAGGATTTTCCTCTCTTCAAAATCTATCAATTCAAAG

            *   **                     *     **   *                    *     
       2754 GTGCGCTGAGTTGGAAGTTATTCCGATTACCGGGGGATTTTCATCTCTTGAAAAGCTTAGCATTC
        130 CTGCAATGAGTTGGAAGTTATTCCGATAACCGGAAGATGTTCATCTCTTGAAAAGCTTAACATTC

              ***        
       2819 TCTTTTGCAAAAA
        195 TCAGCTGCAAAAA

                                                  *                          
       2832 ATTAAGCAAGATTGGAGACGGATTATCTACCTCCACTTCTCTCAAAATATTAGATCTAAATTTTT
          1 ATTAAGCAAGATTGGAGACGGATTATCTACCTCCACTTATCTCAAAAT-TTAGATCT--ATTTTT

              *              *           *                                   
       2897 GTTTTAATTTAAGTTTGTTTCCAAAATTGGAAGGATTTTCCTCTCTTCAAAATCTATCAATTCAA
         63 GTCTTAATTTAAGTTTGCTTCCAAAATTGAAAGGATTTTCCTCTCTTCAAAATCTATCAATTCAA

                                 *   *                                       
       2962 AGCTGCAATGAGTTGGAAGTTCTTCTGATAACCGGAAGATGTTCATCTCTTGAAAAAG-TTAACA
        128 AGCTGCAATGAGTTGGAAGTTATTCCGATAACCGGAAGATGTTCATCTCTTG-AAAAGCTTAACA

                             
       3026 TT-TCCAGCTGCAAAAA
        192 TTCT-CAGCTGCAAAAA

                                                                *            
       3042 ATTAAGCAAGATTGGAGACGGATTATCTACCTCCACTTATCTCAAATATTTACATCTATTTGGTT
          1 ATTAAGCAAGATTGGAGACGGATTATCTACCTCCACTTATCTCAAA-ATTTAGATCTATTT--TT

               *        
       3107 GTCCTAATTTAA
         63 GTCTTAATTTAA

       3119 AGCCCATGCC


Statistics
Matches: 249,  Mismatches: 29, Indels: 15
        0.85            0.10        0.05

Matches are distributed among these distances:
 206    1  0.00
 207   53  0.21
 208    4  0.02
 209    2  0.01
 210  182  0.73
 211    7  0.03

ACGTcount: A:0.31, C:0.18, G:0.16, T:0.35


Consensus pattern (207 bp):   
ATTAAGCAAGATTGGAGACGGATTATCTACCTCCACTTATCTCAAAATTTAGATCTATTTTTGTC
TTAATTTAAGTTTGCTTCCAAAATTGAAAGGATTTTCCTCTCTTCAAAATCTATCAATTCAAAGC
TGCAATGAGTTGGAAGTTATTCCGATAACCGGAAGATGTTCATCTCTTGAAAAGCTTAACATTCT
CAGCTGCAAAAA
Done.