Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_04734

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, 336

Length: 561
ACGTcount: A:0.28, C:0.22, G:0.24, T:0.26


Found at i:86 original size:16 final size:16

Alignment explanation


    Indices: 67--98  Score: 64
    Period size: 16  Copynumber: 2.0  Consensus size: 16

         57 CTTCGTCTCC

                            
         67 GTGGTGGTATGCAAAT
          1 GTGGTGGTATGCAAAT

                            
         83 GTGGTGGTATGCAAAT
          1 GTGGTGGTATGCAAAT

         99 ATTTGTTAAG


Statistics
Matches: 16,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  16   16  1.00

ACGTcount: A:0.25, C:0.06, G:0.38, T:0.31


Consensus pattern (16 bp):   
GTGGTGGTATGCAAAT

Found at i:499 original size:228 final size:227

Alignment explanation


    Indices: 83--561  Score: 599
    Period size: 228  Copynumber: 2.1  Consensus size: 227

         73 GTATGCAAAT

                            *     *                       *  *     *        *
         83 GTGGTGGTATGCAAATATTTGTTAAGACTCTTACCGGAAAGACCATTACTTTGGAGGTTGAGAGT
          1 GTGGTGGTATGCAAATTTTTGTGAAGACTCTTACCGGAAAGACCATCACCTTGGAAGTTGAGAGC

                 *                    *  *              *                    
        148 TCAGATACCATTGACAATGTCAAGGCTAAGATCCAGGACAAAGAGGGTATTCCCCCAGACCAACA
         66 TCAGACACCATTGACAATGTCAAGGCCAAAATCCAGGACAAAGAAGGTATTCCCCCAGACCAACA

                                                 *    *     *  *             
        213 GAGGTTGATCTTTGCCGGTAAGCAACTTGAAGATGGCCGCACTCTCGCTGATTACAACATCCAAA
        131 GAGGTTGATCTTTGCCGGTAAGCAACTTGAAGATGGCAGCACACTCGCAGACTACAACAT-CAAA

                                            *
        278 AGGAATCCACCCTCCACTTGGTGCTTCGTCTTT
        195 AGGAATCCACCCTCCACTTGGTGCTTCGTCTTC

            *            *                              *                    
        311 TTGGTGGTATGCAGATTTTTGTGAAGACTCTTACCAGGAAA-ACGATCACCTTGGAAGTTGAGAG
          1 GTGGTGGTATGCAAATTTTTGTGAAGACTCTTACC-GGAAAGACCATCACCTTGGAAGTTGAGAG

               *     *                             *  *                      
        375 CTCTGACACTATTGACAATGTCAAGGCCAAAATCCAGGATAAGGAAGGTA-TCCCTCCAGACCAA
         65 CTCAGACACCATTGACAATGTCAAGGCCAAAATCCAGGACAAAGAAGGTATTCCC-CCAGACCAA

                                        *               *     *              
        439 CAGAGGTTGAT-TTT-CACGGGTAAGCAGCTTG-AGAATGGCAGGACACTTGCAGACTACAACAT
        129 CAGAGGTTGATCTTTGC-C-GGTAAGCAACTTGAAG-ATGGCAGCACACTCGCAGACTACAACAT

            *          *        *     *          
        501 TAAAAGGAATCGACCCTCCATTTGGTTCTTCGTCTTC
        191 CAAAAGGAATCCACCCTCCACTTGGTGCTTCGTCTTC

                   *                
        538 GTGGTGGGATGCAAATTTTTGTGA
          1 GTGGTGGTATGCAAATTTTTGTGA


Statistics
Matches: 214,  Mismatches: 32, Indels: 11
        0.83            0.12        0.04

Matches are distributed among these distances:
 226    1  0.00
 227   63  0.29
 228  145  0.68
 229    5  0.02

ACGTcount: A:0.29, C:0.21, G:0.24, T:0.26


Consensus pattern (227 bp):   
GTGGTGGTATGCAAATTTTTGTGAAGACTCTTACCGGAAAGACCATCACCTTGGAAGTTGAGAGC
TCAGACACCATTGACAATGTCAAGGCCAAAATCCAGGACAAAGAAGGTATTCCCCCAGACCAACA
GAGGTTGATCTTTGCCGGTAAGCAACTTGAAGATGGCAGCACACTCGCAGACTACAACATCAAAA
GGAATCCACCCTCCACTTGGTGCTTCGTCTTC
Done.