Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_25643

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: 2190
ACGTcount: A:0.29, C:0.24, G:0.21, T:0.26


Found at i:998 original size:75 final size:74

Alignment explanation


    Indices: 896--1859  Score: 770
    Period size: 75  Copynumber: 13.0  Consensus size: 74

        886 AACCAAACAC

                                  *         *          *    *   **  * *     *
        896 CTAAATTTCCCGAACCTGAACCCCAAGCTATATCTTGTGAACCCACTGCAATTGACGTTTTTGGT
          1 CTAAATTTCCCGAACCTGAACCTCAAGC-ATACCTTGTGAACCTACTGGAATCAACATGTTTGGG

                      
        961 AAACAGGCTT
         65 AAACAGGCTT

                         * *               *         *  **                  *
        971 CTAAATTTCCCGAGCATGAACCTCAAGCGATGCCTTGTGAATCTGGTGGAATCAACATGTTTGGT
          1 CTAAATTTCCCGAACCTGAACCTCAAGC-ATACCTTGTGAACCTACTGGAATCAACATGTTTGGG

              *        
       1036 AAGC-GGCCTT
         65 AAACAGG-CTT

                      *         *     *       **                             
       1046 CTAAATTTCCTGAACCTGAAACTCAACCAATGA-AGTGTGAACCTACTGGAATCAACATGTTTGG
          1 CTAAATTTCCCGAACCTGAACCTCAAGC-AT-ACCTTGTGAACCTACTGGAATCAACATGTTTGG

                 *     
       1110 GAAACGGGCTT
         64 GAAACAGGCTT

                      *                    *          * *   *    *           
       1121 CTAAATTTCCTGAACCTGAACCTCAAGGCATGCCTTGTGAACGTGCTGAAATCCACATGTTTGGG
          1 CTAAATTTCCCGAACCTGAACCTCAA-GCATACCTTGTGAACCTACTGGAATCAACATGTTTGGG

              *       
       1186 AAGCAGGCTT
         65 AAACAGGCTT

                    * *             *                  * *       *  *       *
       1196 CTAAATTTGCTGAACCTGAACCTCGAGCCATACCTTGTGAACCCATTGGAATCGACGTGTTTGGA
          1 CTAAATTTCCCGAACCTGAACCTCAAG-CATACCTTGTGAACCTACTGGAATCAACATGTTTGGG

                      
       1261 AAACAGGCTT
         65 AAACAGGCTT

                                           *             *                   
       1271 CTAAATTTCCCGAACCTGAACCTCTAAGCATGCAC-TGTGAACCTGCTGGAATCAACATGTTT-G
          1 CTAAATTTCCCGAACCTGAACCTC-AAGCATAC-CTTGTGAACCTACTGGAATCAACATGTTTGG

                        
       1334 GAAAGCAGGCTT
         64 GAAA-CAGGCTT

                                *      * * *            *                    
       1346 CTAAATTTCCCGAACCTGAAACTCAACCCGTGCAC-TGTGAACCAACTGGAATCAACATGTTT-G
          1 CTAAATTTCCCGAACCTGAACCTCAA-GCATAC-CTTGTGAACCTACTGGAATCAACATGTTTGG

                        
       1409 GAAAGCAGGCTT
         64 GAAA-CAGGCTT

                      *         *      *   *            *              *     
       1421 CTAAATTTCCTGAACCTGAAACTCAACCCATGCAC-TGTGAACCAACTGGAATCAACATTTTTGG
          1 CTAAATTTCCCGAACCTGAACCTCAA-GCATAC-CTTGTGAACCTACTGGAATCAACATGTTTGG

                      *
       1485 GAAACAGGCTA
         64 GAAACAGGCTT

                      *     *              *       *   *  *               *  
       1496 CTAAATTTCCTGAACCCGAACCTCAAGCCATGCCTTGTGGACCAACAGGAATCAACATG-TTCGG
          1 CTAAATTTCCCGAACCTGAACCTCAAG-CATACCTTGTGAACCTACTGGAATCAACATGTTTGGG

                   * * 
       1560 AAAGCAGCCAT
         65 AAA-CAGGCTT

                 *             *           *                               * 
       1571 CTAAAATT------CCTGACCCTCAAGCCATGCCTTGTGAATCC-ACTGGAATCAACAAT-TTCG
          1 CTAAATTTCCCGAACCTGAACCTCAAG-CATACCTTGTGAA-CCTACTGGAATCAAC-ATGTTTG

                *       
       1628 GGAAGCAGGCTT
         63 GGAAACAGGCTT

                                 *     *   **    *        **                 
       1640 CTAAATTTCCCGAACCTGAACTTCGAACCATGTCTTGCGAACCTACCAGAATCAACAT-TTTCGG
          1 CTAAATTTCCCGAACCTGAACCTC-AAGCATACCTTGTGAACCTACTGGAATCAACATGTTT-GG

                  *    
       1704 GAAACAAGCTT
         64 GAAACAGGCTT

                                       *               *      * *            
       1715 CTAAATTT------CCTGAACCTCAAACCATACCTTGTGAACCCACTGGACTTAACATGTTTGGG
          1 CTAAATTTCCCGAACCTGAACCTC-AAGCATACCTTGTGAACCTACTGGAATCAACATGTTTGGG

                 *    
       1774 AAACAAGCTT
         65 AAACAGGCTT

                *    **                                *       *             
       1784 CTAAGTTTCTTGAACCTGAACAC-CAAGCCATACCTTGTGAACTTACTGGACTCAACATGTTTGG
          1 CTAAATTTCCCGAACCTGAAC-CTCAAG-CATACCTTGTGAACCTACTGGAATCAACATGTTTGG

            *          
       1848 TAAACAGGCTT
         64 GAAACAGGCTT

             
       1859 C
          1 C

       1860 ATCTAGGCAA


Statistics
Matches: 734,  Mismatches: 120, Indels: 70
        0.79            0.13        0.08

Matches are distributed among these distances:
  69  101  0.14
  70   12  0.02
  74   25  0.03
  75  582  0.79
  76   14  0.02

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


Consensus pattern (74 bp):   
CTAAATTTCCCGAACCTGAACCTCAAGCATACCTTGTGAACCTACTGGAATCAACATGTTTGGGA
AACAGGCTT

Found at i:1288 original size:225 final size:223

Alignment explanation


    Indices: 896--1859  Score: 874
    Period size: 225  Copynumber: 4.3  Consensus size: 223

        886 AACCAAACAC

                      *           *     *  **          *    *   **  * *     *
        896 CTAAATTTCCCGAACCTGAACCCCAAGCTATATCTTGTGAACCCACTGCAATTGACGTTTTTGGT
          1 CTAAATTTCCTGAACCTGAACCTCAAGCCATGCCTTGTGAA-CTACTGGAATCAACATGTTTGGG

              *                    * *            *            *  **         
        961 AAACAGGCTTCTAAATTTCCCGAGCATGAACCTCAAGCGATGCCTTGTGAATCTGGTGGAATCAA
         65 AAGCAGGCTTCTAAATTTCCCGAACCTGAACCTCAAGCCATGCCTTGTGAACCTACTGGAATCAA

                     *  *                                        *           
       1026 CATGTTTGGTAAGC-GGCCTTCTAAATTTCCTGAACCTGAAACTCAACCAATGAAGTGTGAACCT
        130 CATGTTTGGGAAACAGG-CTTCTAAATTTCCTGAACCTGAAACTCAACC-ATGCA-TGTGAACCT

                                      *     
       1090 ACTGGAATCAACATGTTTGGGAAA-CGGGCTT
        192 ACTGGAATCAACATGTTTGGGAAAGCAGGCTT

                                       *                *   *    *           
       1121 CTAAATTTCCTGAACCTGAACCTCAAGGCATGCCTTGTGAACGTGCTGAAATCCACATGTTTGGG
          1 CTAAATTTCCTGAACCTGAACCTCAAGCCATGCCTTGTGAAC-TACTGGAATCAACATGTTTGGG

                              * *             *      *           * *       * 
       1186 AAGCAGGCTTCTAAATTTGCTGAACCTGAACCTCGAGCCATACCTTGTGAACCCATTGGAATCGA
         65 AAGCAGGCTTCTAAATTTCCCGAACCTGAACCTCAAGCCATGCCTTGTGAACCTACTGGAATCAA

             *       *                    *         *      *                *
       1251 CGTGTTTGGAAAACAGGCTTCTAAATTTCCCGAACCTGAACCTCTAAGCATGCACTGTGAACCTG
        130 CATGTTTGGGAAACAGGCTTCTAAATTTCCTGAACCTGAAACTC-AACCATGCA-TGTGAACCTA

                                           
       1316 CTGGAATCAACATGTTT-GGAAAGCAGGCTT
        193 CTGGAATCAACATGTTTGGGAAAGCAGGCTT

                      *         *     *  *              *                    
       1346 CTAAATTTCCCGAACCTGAAACTCAACCCGTGCAC-TGTGAACCAACTGGAATCAACATGTTTGG
          1 CTAAATTTCCTGAACCTGAACCTCAAGCCATGC-CTTGTGAA-CTACTGGAATCAACATGTTTGG

            *                    *         *     *                 *         
       1410 AAAGCAGGCTTCTAAATTTCCTGAACCTGAAACTCAACCCATGCAC-TGTGAACCAACTGGAATC
         64 GAAGCAGGCTTCTAAATTTCCCGAACCTGAACCTCAAGCCATGC-CTTGTGAACCTACTGGAATC

                 *               *                *   *             *    *   
       1474 AACATTTTTGGGAAACAGGCTACTAAATTTCCTGAACCCGAACCTCAAGCCATGCCTTGTGGACC
        128 AACATGTTTGGGAAACAGGCTTCTAAATTTCCTGAACCTGAAACTCAA-CCATG-CATGTGAACC

            *  *               *         * * 
       1539 AACAGGAATCAACATG-TTCGGAAAGCAGCCAT
        191 TACTGGAATCAACATGTTTGGGAAAGCAGGCTT

                 *                                     *                  *  
       1571 CTAAAATTCCTG-A-C----CCTCAAGCCATGCCTTGTGAATCCACTGGAATCAACAAT-TTCGG
          1 CTAAATTTCCTGAACCTGAACCTCAAGCCATGCCTTGTGAA-CTACTGGAATCAAC-ATGTTTGG

                                            *           *    *        **     
       1629 GAAGCAGGCTTCTAAATTTCCCGAACCTGAACTTCGAA-CCATGTCTTGCGAACCTACCAGAATC
         64 GAAGCAGGCTTCTAAATTTCCCGAACCTGAACCTC-AAGCCATGCCTTGTGAACCTACTGGAATC

                              *                     *                        
       1693 AACAT-TTTCGGGAAACAAGCTTCTAAATTTCCTGAACCTCAAAC-CATACC-T---TGTGAACC
        128 AACATGTTT-GGGAAACAGGCTTCTAAATTTCCTGAACCTGAAACTCA-ACCATGCATGTGAACC

            *      * *                  *    
       1752 CACTGGACTTAACATGTTTGGGAAA-CAAGCTT
        191 TACTGGAATCAACATGTTTGGGAAAGCAGGCTT

                *    *                      *                  *             
       1784 CTAAGTTTCTTGAACCTGAACAC-CAAGCCATACCTTGTGAACTTACTGGACTCAACATGTTTGG
          1 CTAAATTTCCTGAACCTGAAC-CTCAAGCCATGCCTTGTGAAC-TACTGGAATCAACATGTTTGG

            *  *        
       1848 TAAACAGGCTTC
         64 GAAGCAGGCTTC

       1860 ATCTAGGCAA


Statistics
Matches: 604,  Mismatches: 109, Indels: 58
        0.78            0.14        0.08

Matches are distributed among these distances:
 213   32  0.05
 214    8  0.01
 215    1  0.00
 217    1  0.00
 218   12  0.02
 219  162  0.27
 220    5  0.01
 223    1  0.00
 224   11  0.02
 225  362  0.60
 226    9  0.01

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


Consensus pattern (223 bp):   
CTAAATTTCCTGAACCTGAACCTCAAGCCATGCCTTGTGAACTACTGGAATCAACATGTTTGGGA
AGCAGGCTTCTAAATTTCCCGAACCTGAACCTCAAGCCATGCCTTGTGAACCTACTGGAATCAAC
ATGTTTGGGAAACAGGCTTCTAAATTTCCTGAACCTGAAACTCAACCATGCATGTGAACCTACTG
GAATCAACATGTTTGGGAAAGCAGGCTT

Done.