Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_18428

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, 285

Length: 476
ACGTcount: A:0.35, C:0.18, G:0.19, T:0.28


Found at i:357 original size:99 final size:99

Alignment explanation


    Indices: 121--378  Score: 272
    Period size: 99  Copynumber: 2.6  Consensus size: 99

        111 GGAAGAAATG

                        *     *     *                 *  *  * *              
        121 CTCCCAAAAGATAGAGTTCATACAACTCAATC-AGTTTACTCAGAGCGCAAGGTTAACTCAATTA
          1 CTCCCAAAAGATGGAGTTTATACAGCTCAATCGA-TTTACTCGGAACGTAGGGTTAACTCAATTA

                         *            *        
        185 AAGCAAATCAATTTAATAGTCATATTGGAAGTAGC
         65 AAGCAAATCAATTCAATAGTCATATTAGAAGTAGC

                             *   *            *                  *     * *   
        220 CTCCCAAAAGATGGAGTATATCCAGCTCAA-CTGGTTTACTCGGAACGTAGGGCTAACTTAGTTA
          1 CTCCCAAAAGATGGAGTTTATACAGCTCAATC-GATTTACTCGGAACGTAGGGTTAACTCAATTA

                *                                
        284 AAGCTAAT-AATCTCAAT-GATCATATTAGAAGTAGC
         65 AAGCAAATCAAT-TCAATAG-TCATATTAGAAGTAGC

                                       *            *   **              
        319 CTCCCAAAAGATGGAGTTTATACAGCTAAATCGATTTACTTGGATTGTAGGGTTAACTCA
          1 CTCCCAAAAGATGGAGTTTATACAGCTCAATCGATTTACTCGGAACGTAGGGTTAACTCA

        379 CTTCATGAAA


Statistics
Matches: 129,  Mismatches: 25, Indels: 10
        0.79            0.15        0.06

Matches are distributed among these distances:
  98    5  0.04
  99  123  0.95
 100    1  0.01

ACGTcount: A:0.36, C:0.19, G:0.18, T:0.28


Consensus pattern (99 bp):   
CTCCCAAAAGATGGAGTTTATACAGCTCAATCGATTTACTCGGAACGTAGGGTTAACTCAATTAA
AGCAAATCAATTCAATAGTCATATTAGAAGTAGC

Found at i:398 original size:99 final size:99

Alignment explanation


    Indices: 204--421  Score: 233
    Period size: 99  Copynumber: 2.2  Consensus size: 99

        194 AATTTAATAG

                                                 *     *     *               
        204 TCATATTGGAAGTAGCCTCCCAAAAGATGGAGTATATCCAGCTCAACTGGTTTACTCGGAACGTA
          1 TCATATTGGAAGTAGCCTCCCAAAAGATGGAGTATATACAGCTAAACTGATTTACTCGGAACGTA

                     * *       *  *  *     *  
        269 GGGCTAACTTAGTTAAAGCTAATAATCTCAATGA
         66 GGGCTAACTCACTTAAAGCAAAAAAACTCAACGA

                   *                         *                       *   **  
        303 TCATATTAGAAGTAGCCTCCCAAAAGATGGAGTTTATACAGCTAAA-TCGATTTACTTGGATTGT
          1 TCATATTGGAAGTAGCCTCCCAAAAGATGGAGTATATACAGCTAAACT-GATTTACTCGGAACGT

                *          * *                 *
        367 AGGGTTAACTCACTTCATG-AAAAAACACTCAACGG
         65 AGGGCTAACTCACTTAAAGCAAAAAA-ACTCAACGA

                *               
        402 TCATGTTGGAAGTAGCCTCC
          1 TCATATTGGAAGTAGCCTCC

        422 AAGATGAGCT


Statistics
Matches: 97,  Mismatches: 20, Indels: 4
        0.80            0.17        0.03

Matches are distributed among these distances:
  98    5  0.05
  99   92  0.95

ACGTcount: A:0.33, C:0.19, G:0.20, T:0.28


Consensus pattern (99 bp):   
TCATATTGGAAGTAGCCTCCCAAAAGATGGAGTATATACAGCTAAACTGATTTACTCGGAACGTA
GGGCTAACTCACTTAAAGCAAAAAAACTCAACGA
Done.