Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_30325

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: 1806
ACGTcount: A:0.30, C:0.19, G:0.26, T:0.24


Found at i:1099 original size:147 final size:144

Alignment explanation


    Indices: 671--1111  Score: 481
    Period size: 147  Copynumber: 3.0  Consensus size: 144

        661 AGTTTTGAAC

                      *                               *      *     * *       
        671 CCAAGTCGACTATAGTTCAGTCTGGCATTTCATCGAACAATTTAGATGCGGAAAACGTAATTAAG
          1 CCAAGTCGACAATAGTTCAGTCTGGCATTTCATCGAAC-ATTGAGATGCTGAAAATGCAATTAAG

                              *                   *                          
        736 GAAGATAACTTGACATCTCAACTTAAGGAGGAGGTTACTGAAATGGATGATTC-TGAGGTTGTGG
         65 GAAGATAAC-TGACATCTGAACTTAAGGAGGAGGTTACCGAAATGGATGATTCTTGA--TTGTGG

               *               
        800 AAGTTAAA-TATAATGTAG
        127 AAGATAAAGT-TAATGTAG

             *     *    *           *                            **          
        818 CGAAGTCTACAACAGTTCAGTCTGACATTTCATCGAACATTGGAGATGCTGAAGGTGCAATTAAG
          1 CCAAGTCGACAATAGTTCAGTCTGGCATTTCATCGAACATT-GAGATGCTGAAAATGCAATTAAG

                       *                                           * * *  * *
        883 GAAGATAACCTAACATCTGAACTTAAGGAGGAGGTTACCGAAATGGATGATTCTGGGGTCGTAGC
         65 GAAGATAA-CTGACATCTGAACTTAAGGAGGAGGTTACCGAAATGGATGATTCT-TGATTGTGGA

                       *     
        948 AGATAAAGTTACTGTAG
        128 AGATAAAGTTAATGTAG

                  *  **    *     *                                       *   
        965 CCAAGTGGAGGATAGCTCAGTGTGGCATTTCATCGAACATTAGAGATGCTGAAAATGCAATCAAG
          1 CCAAGTCGACAATAGTTCAGTCTGGCATTTCATCGAACATT-GAGATGCTGAAAATGCAATTAAG

                    *     *                    *       *  *                  
       1030 GAAGATAGGCTGACGTCTGAACTTAAGGAGGAGGTCACCGAAAGGGTTGATTCCTTGATTGTGGA
         65 GAAGATA-ACTGACATCTGAACTTAAGGAGGAGGTTACCGAAATGGATGATT-CTTGATTGTGGA

                             
       1095 AGATAAAGTTAATGTAG
        128 AGATAAAGTTAATGTAG

       1112 AAAAGAATGA


Statistics
Matches: 241,  Mismatches: 46, Indels: 14
        0.80            0.15        0.05

Matches are distributed among these distances:
 146    3  0.01
 147  233  0.97
 148    4  0.02
 149    1  0.00

ACGTcount: A:0.34, C:0.14, G:0.26, T:0.26


Consensus pattern (144 bp):   
CCAAGTCGACAATAGTTCAGTCTGGCATTTCATCGAACATTGAGATGCTGAAAATGCAATTAAGG
AAGATAACTGACATCTGAACTTAAGGAGGAGGTTACCGAAATGGATGATTCTTGATTGTGGAAGA
TAAAGTTAATGTAG
Done.