Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_18197

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: 2214
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.32


Found at i:1023 original size:144 final size:144

Alignment explanation


    Indices: 418--991  Score: 979
    Period size: 144  Copynumber: 4.0  Consensus size: 144

        408 AAACAACTGG

                          *                       *      *         *       **
        418 CTTGTTGGTCCAATCCCATCTTCTGTCAGCAACTTAACCAATCTTGCCTCGTTGTACCTTCAAAG
          1 CTTGTTGGTCCAATACCATCTTCTGTCAGCAACTTAACTAATCTTACCTCGTTGTTCCTTCAACT

                *     *                                                      
        483 CAACAAACTTGATGGATCCATTCCACAAGATATTGGGAGACTAACGAATTTGGTTGAATTGGATC
         66 CAACCAACTTAATGGATCCATTCCACAAGATATTGGGAGACTAACGAATTTGGTTGAATTGGATC

                          
        548 TATCCTCCAATAAT
        131 TATCCTCCAATAAT

                                                                             
        562 CTTGTTGGTCCAATACCATCTTCTGTCAGCAACTTAACTAATCTTACCTCGTTGTTCCTTCAACT
          1 CTTGTTGGTCCAATACCATCTTCTGTCAGCAACTTAACTAATCTTACCTCGTTGTTCCTTCAACT

                *        *                          *                        
        627 CAACGAACTTAATCGATCCATTCCACAAGATATTGGGAGAATAACGAATTTGGTTGAATTGGATC
         66 CAACCAACTTAATGGATCCATTCCACAAGATATTGGGAGACTAACGAATTTGGTTGAATTGGATC

                          
        692 TATCCTCCAATAAT
        131 TATCCTCCAATAAT

                                                                  *          
        706 CTTGTTGGTCCAATACCATCTTCTGTCAGCAACTTAACTAATCTTACCTCGTTGATCCTTCAACT
          1 CTTGTTGGTCCAATACCATCTTCTGTCAGCAACTTAACTAATCTTACCTCGTTGTTCCTTCAACT

                   *                 *                                       
        771 CAACCAAATTAATGGATCCATTCCAGAAGATATTGGGAGACTAACGAATTTGGTTGAATTGGATC
         66 CAACCAACTTAATGGATCCATTCCACAAGATATTGGGAGACTAACGAATTTGGTTGAATTGGATC

                        * 
        836 TATCCTCCAATAGT
        131 TATCCTCCAATAAT

                                                                             
        850 CTTGTTGGTCCAATACCATCTTCTGTCAGCAACTTAACTAATCTTACCTCGTTGTTCCTTCAACT
          1 CTTGTTGGTCCAATACCATCTTCTGTCAGCAACTTAACTAATCTTACCTCGTTGTTCCTTCAACT

                                     *              *                        
        915 CAACCAACTTAATGGATCCATTCCAGAAGATATTGGGAGATTAACGAATTTGGTT-AATTTGGAT
         66 CAACCAACTTAATGGATCCATTCCACAAGATATTGGGAGACTAACGAATTTGGTTGAA-TTGGAT

                         
        979 CTATCCTCCAATA
        130 CTATCCTCCAATA

        992 GGCTTTCAGG


Statistics
Matches: 409,  Mismatches: 20, Indels: 2
        0.95            0.05        0.00

Matches are distributed among these distances:
 143    2  0.00
 144  407  1.00

ACGTcount: A:0.29, C:0.24, G:0.15, T:0.33


Consensus pattern (144 bp):   
CTTGTTGGTCCAATACCATCTTCTGTCAGCAACTTAACTAATCTTACCTCGTTGTTCCTTCAACT
CAACCAACTTAATGGATCCATTCCACAAGATATTGGGAGACTAACGAATTTGGTTGAATTGGATC
TATCCTCCAATAAT
Done.