Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_11004

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, 851

Length: 1419
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.31


Found at i:612 original size:153 final size:153

Alignment explanation


    Indices: 326--615  Score: 366
    Period size: 153  Copynumber: 1.9  Consensus size: 153

        316 CACGGTCTTT

                          *   *                          * *             *   
        326 GTGAAGGAGATATTCCTAGTGATATTTCTGGTCTATCCTCTTTGAGACGTCTTAATCTTAGCGGT
          1 GTGAAGGAGATATTACTAATGATATTTCTGGTCTATCCTCTTTGAAAAGTCTTAATCTTAGAGGT

                            **     *              *     *   *    *    *   *  
        391 AACAATTTCATCAACATGCCTGCCCCTCTTACTCGACTTTACAAGCTTGAATTTCTTATATTGGC
         66 AACAATTTCATCAACACACCTGCACCTCTTACTCGACTATACAACCTTCAATTCCTTAGATTAGC

                                   
        456 AAATTGCGGCTTATGCCATTTTG
        131 AAATTGCGGCTTATGCCATTTTG

                                         *                       *           
        479 GTGAAGGAGATATTACTAATGATATTTCTTGTCTATCCTCTTTGAAAAGTCTTGATCTTAGAGAG
          1 GTGAAGGAGATATTACTAATGATATTTCTGGTCTATCCTCTTTGAAAAGTCTTAATCTTAGAG-G

                      *   *          *               *                *     *
        544 -AACAATTTCGTCAGCACACCTGCATCTCTTACTCGACTATCCAACCTTCAATTCCTTGGATTAT
         65 TAACAATTTCATCAACACACCTGCACCTCTTACTCGACTATACAACCTTCAATTCCTTAGATTAG

                    
        608 CAAATTGC
        130 CAAATTGC

        616 AGGGAGCTTA


Statistics
Matches: 114,  Mismatches: 22, Indels: 2
        0.83            0.16        0.01

Matches are distributed among these distances:
 153  113  0.99
 154    1  0.01

ACGTcount: A:0.26, C:0.22, G:0.16, T:0.36


Consensus pattern (153 bp):   
GTGAAGGAGATATTACTAATGATATTTCTGGTCTATCCTCTTTGAAAAGTCTTAATCTTAGAGGT
AACAATTTCATCAACACACCTGCACCTCTTACTCGACTATACAACCTTCAATTCCTTAGATTAGC
AAATTGCGGCTTATGCCATTTTG
Done.