Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_13296

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, 770

Length: 1284
ACGTcount: A:0.31, C:0.15, G:0.23, T:0.31


Found at i:296 original size:105 final size:104

Alignment explanation


    Indices: 167--719  Score: 491
    Period size: 105  Copynumber: 5.3  Consensus size: 104

        157 ATGATAAAAA

                  *            *                    *     *                  
        167 AAGGCAGTAAGCCTAATGTCGTCACATATAGTATATTGATCGATGCGCTTTGCAAGCAGGGAATG
          1 AAGGCATTAAGCCTAATGTTGTCACATATAGTATATTGATAGATGCTCTTTGCAAG-AGGGAATG

            * *  *                      *     *     
        232 ATATCCAAAGCCGAAGATATTGTTGGCATAATGACAAAGC
         65 GTTTCTAAAGCCGAAGATATTGTTGGCACAATGAGAAAGC

                                           *        *           *     *      
        272 AAGGCATTAAGCCTAATGTTGTCACATATAGCATATTGATCGATGCTCTTTGTAAGAAAGGAATG
          1 AAGGCATTAAGCCTAATGTTGTCACATATAGTATATTGATAGATGCTCTTTGCAAG-AGGGAATG

            *              *    *  *     *    *     
        337 ATTTCTAAAGCCGAAAATATCGTCGGCACTATGACAAAGC
         65 GTTTCTAAAGCCGAAGATATTGTTGGCACAATGAGAAAGC

                        * *                      *      *                 *  
        377 AAGGCATTAAGCTTGATGTTGTCACATATAGTATATTCATAGATACTCTTTGCAAGATGGGGGA-
          1 AAGGCATTAAGCCTAATGTTGTCACATATAGTATATTGATAGATGCTCTTTGCAAGA--GGGAAT

                             * *      * * *          
        441 GGTTTCTAAAGCCGAAGTTGTTGTTGACGCGATGAGAAAGC
         64 GGTTTCTAAAGCCGAAGATATTGTTGGCACAATGAGAAAGC

                    *       *         *       *          * *           *  *  
        482 AAGGCATCGAA-CCTACTGTTGTCACGTATAGTACATTGATAGATTCGCTTTGCAAGAATGGTAT
          1 AAGGCAT-TAAGCCTAATGTTGTCACATATAGTATATTGATAGATGCTCTTTGCAAG-AGGGAAT

                   *    *   **            *          
        546 GGTTTCTGAAGCTGAATTTATTGTTGGCACGATGAGAAAGC
         64 GGTTTCTAAAGCCGAAGATATTGTTGGCACAATGAGAAAGC

                **               *    *    *         *   *             ** *  
        587 AAGGTGTTGAA-CCTAATGTTATCACGTATAATATATTGATGGATTCTCTTTGCAAGATTAGTAT
          1 AAGGCATT-AAGCCTAATGTTGTCACATATAGTATATTGATAGATGCTCTTTGCAAGA-GGGAAT

                   *    *         *      *           
        651 GGTTTCTGAAGCTGAAGATATTTTTGGCAGAATGAGAAAGC
         64 GGTTTCTAAAGCCGAAGATATTGTTGGCACAATGAGAAAGC

                    *     *             
        692 AAGGCATTGAGCCTGATGTTGTCACATA
          1 AAGGCATTAAGCCTAATGTTGTCACATA

        720 CAACACTCTG


Statistics
Matches: 369,  Mismatches: 71, Indels: 16
        0.81            0.16        0.04

Matches are distributed among these distances:
 104    6  0.02
 105  357  0.97
 106    6  0.02

ACGTcount: A:0.32, C:0.15, G:0.24, T:0.30


Consensus pattern (104 bp):   
AAGGCATTAAGCCTAATGTTGTCACATATAGTATATTGATAGATGCTCTTTGCAAGAGGGAATGG
TTTCTAAAGCCGAAGATATTGTTGGCACAATGAGAAAGC

Found at i:454 original size:210 final size:210

Alignment explanation


    Indices: 167--719  Score: 547
    Period size: 210  Copynumber: 2.6  Consensus size: 210

        157 ATGATAAAAA

                  *            *                    *   * *                  
        167 AAGGCAGTAAGCCTAATGTCGTCACATATAGTATATTGATCGATGCGCTTTGCAAGCA-GGGAAT
          1 AAGGCATTAAGCCTAATGTTGTCACATATAGTATATTGATAGATACTCTTTGCAAG-ATGGGAAT

             * *  *                      *     *                             
        231 GATATCCAAAGCCGAAGATATTGTTGGCATAATGACAAAGCAAGGCATTAAGCCTAATGTTGTCA
         65 GGTTTCTAAAGCCGAAGATATTGTTGGCACAATGAGAAAGCAAGGCATTAAGCCTAATGTTGTCA

                     *      *     *     *                                    
        296 CATATAGCATATTGATCGATGCTCTTTGTAAGAAAGGAATGATTTCTAAAGCCGAAAATATCGTC
        130 CATATAGCACATTGATAGATGCGCTTTGCAAGAAAGGAATGATTTCTAAAGCCGAAAATATCGTC

                 *          
        361 GGCACTATGACAAAGC
        195 GGCACGATGACAAAGC

                        * *                      *                        *  
        377 AAGGCATTAAGCTTGATGTTGTCACATATAGTATATTCATAGATACTCTTTGCAAGATGGGGGA-
          1 AAGGCATTAAGCCTAATGTTGTCACATATAGTATATTGATAGATACTCTTTGCAAGAT-GGGAAT

                             * *      * * *                  *       *       
        441 GGTTTCTAAAGCCGAAGTTGTTGTTGACGCGATGAGAAAGCAAGGCATCGAA-CCTACTGTTGTC
         65 GGTTTCTAAAGCCGAAGATATTGTTGGCACAATGAGAAAGCAAGGCAT-TAAGCCTAATGTTGTC

              *     *            *             *  *   *     *    *   **   *  
        505 ACGTATAGTACATTGATAGATTCGCTTTGCAAGAATGGTATGGTTTCTGAAGCTGAATTTATTGT
        129 ACATATAGCACATTGATAGATGCGCTTTGCAAGAAAGGAATGATTTCTAAAGCCGAAAATATCGT

            *          *     
        570 TGGCACGATGAGAAAGC
        194 CGGCACGATGACAAAGC

                **               *    *    *         *   *             ** *  
        587 AAGGTGTTGAA-CCTAATGTTATCACGTATAATATATTGATGGATTCTCTTTGCAAGATTAGTAT
          1 AAGGCATT-AAGCCTAATGTTGTCACATATAGTATATTGATAGATACTCTTTGCAAGATGGGAAT

                   *    *         *      *                   *     *         
        651 GGTTTCTGAAGCTGAAGATATTTTTGGCAGAATGAGAAAGCAAGGCATTGAGCCTGATGTTGTCA
         65 GGTTTCTAAAGCCGAAGATATTGTTGGCACAATGAGAAAGCAAGGCATTAAGCCTAATGTTGTCA

                
        716 CATA
        130 CATA

        720 CAACACTCTG


Statistics
Matches: 271,  Mismatches: 66, Indels: 12
        0.78            0.19        0.03

Matches are distributed among these distances:
 209    4  0.01
 210  259  0.96
 211    8  0.03

ACGTcount: A:0.32, C:0.15, G:0.24, T:0.30


Consensus pattern (210 bp):   
AAGGCATTAAGCCTAATGTTGTCACATATAGTATATTGATAGATACTCTTTGCAAGATGGGAATG
GTTTCTAAAGCCGAAGATATTGTTGGCACAATGAGAAAGCAAGGCATTAAGCCTAATGTTGTCAC
ATATAGCACATTGATAGATGCGCTTTGCAAGAAAGGAATGATTTCTAAAGCCGAAAATATCGTCG
GCACGATGACAAAGC

Done.