Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_25645

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: 5328
ACGTcount: A:0.30, C:0.17, G:0.23, T:0.29


Found at i:4064 original size:420 final size:417

Alignment explanation


    Indices: 3360--4632  Score: 1595
    Period size: 420  Copynumber: 3.0  Consensus size: 417

       3350 GGTATCTTAC

                 *   *              *          *                ** *     *  *
       3360 TGTTGCAATCCAAAGACATTGCCGCGGTTGGCTTGCAAGGAAGGATCTTTTGAAGCAAAGGAATG
          1 TGTTGTAATACAAAGACATTGCCGTGGTTGGCTTGTAAGGAAGGATCTTTTGTTGAAAAGGGATT

                                           **                *               
       3425 CTGTAATAAAGATCCAAAGAGCAATACGGTGTGTAATATGTCAGAAGGCGTTTCATCTT-CAGAA
         66 CTGTAATAAAGATCCAAAGAGCAATACGGTGCCTAATATGTCAGAAGGCATTTCAT-TTACAGAA

             *    *        *          *                       ** *           
       3489 ATTGGCTGCTATTGAGATTCAAAGGGCTATCAGAGGGCAAATTTCTCGAAAAAAGCTTTTAGGAG
        130 ACTGGCAGCTATTGATATTCAAAGGGTTATCAG-GGGCAAA-TTCTCGAAGTAGGCTTTTAGGAG

                       **   *         **       **      *        *            
       3554 CATCTTCCTTTTGTGCGGCTAGTGCTTCCAGTTACGGTTGTAATATGTCAAAGGGCTTCTTCCAG
        193 CATCTTCCTTTCATGCAGCTAGTGCTGGCAGTTACAATTGTAACATGTCAAAAGGCTTCTTCCAG

                                             *                       *       
       3619 AGTTTTGAACTAAAATTAGTGATTACTTCAGTTTTGAAACTGCAAAGGTGGTGGAGAAGTGTTCT
        258 AGTTTTGAACTAAAATTAGTGATTACTTCAGTTCTGAAACTGCAAAGGTGGTGGAGAGGTGTTCT

                                                          *                  
       3684 GTTACTTAAATTAAGAACGAAATCAGCAATCATTATTCAGAGTCATTCACGGGGATGGATTGCTA
        323 GTTACTTAAATTAAGAAC-AAATCAGCAATCATTATTCAGAGTCATGCACGGGGATGGATTGCTA

                           * *             
       3749 AGCAAAAAGCATATATAGAGAGGCATTGTAT
        387 AGCAAAAAGCATATAGAAAGAGGCATTGTAT

                *                                                            
       3780 TGTTTTAATACAAAGACATTGCCGTGGTTGGCTTGTAAGGAAGGAT-TTTTCGTTGAAAAGGGAT
          1 TGTTGTAATACAAAGACATTGCCGTGGTTGGCTTGTAAGGAAGGATCTTTT-GTTGAAAAGGGAT

                                   *                             *        *  
       3844 TCTGTAATAAAGATCCAAAGAGCGATACGGTGCCTAATATGTCAGAAGGCATTCCATTTACATAA
         65 TCTGTAATAAAGATCCAAAGAGCAATACGGTGCCTAATATGTCAGAAGGCATTTCATTTACAGAA

                                                    *                        
       3909 ACTGGCAGCTATTGATATTCAAAGGGTTATCAGGGGTCAACTGTCTCGAAGTAGGCTTTTAGGAG
        130 ACTGGCAGCTATTGATATTCAAAGGGTTATCAGGGG-CAAAT-TCTCGAAGTAGGCTTTTAGGAG

                           *     *                     *                     
       3974 CATCTTCCTTTCATGTAGCTACTGCTGGCAGTTACAATTGTAAGATGTCAAAAGGCTTCTTCCAG
        193 CATCTTCCTTTCATGCAGCTAGTGCTGGCAGTTACAATTGTAACATGTCAAAAGGCTTCTTCCAG

                                                                           * 
       4039 AGTTTTGAACTAAAATTAGTGATTACTTCAGTTCTGAAACTGCAAAGGTGGTGGAGAGGTGTTAT
        258 AGTTTTGAACTAAAATTAGTGATTACTTCAGTTCTGAAACTGCAAAGGTGGTGGAGAGGTGTTCT

                                          *                                  
       4104 GTTACTTAAATTAAGAACAAAATCAGCAATAATTATTCAGAGTCATGCACGGGGATGGATTGCTA
        323 GTTACTTAAATTAAGAAC-AAATCAGCAATCATTATTCAGAGTCATGCACGGGGATGGATTGCTA

                 *     * **   *   *         
       4169 AGCGAGAAA-CTTGCAGACAGAAGCATTGTAT
        387 AGC-AAAAAGCATATAGAAAGAGGCATTGTAT

                              **                          *         *        
       4200 TGTTGTAATACAAAGACAGAGCCGTGGTTGGCTTGTAAGGAAGGATGTTTTGTTGAGAAGGGATT
          1 TGTTGTAATACAAAGACATTGCCGTGGTTGGCTTGTAAGGAAGGATCTTTTGTTGAAAAGGGATT

                                      *  *                   *               
       4265 CTGTAATAAAGATCCAAAGAGCAATAAGGAGCCTAATATGTCAGAAGGCCTTTCATTTACAGAAA
         66 CTGTAATAAAGATCCAAAGAGCAATACGGTGCCTAATATGTCAGAAGGCATTTCATTTACAGAAA

                       *        *  *                                      *  
       4330 CTGGCAGCTATAGATATTCAGAGTGTTATCAGGGGCCAAATTGCTCGAAGTAGGCTTTTAGGGGC
        131 CTGGCAGCTATTGATATTCAAAGGGTTATCAGGGG-CAAATT-CTCGAAGTAGGCTTTTAGGAGC

             *           *      *   *    *  * *             *  **           *
       4395 AACTT-CTGTTCAGGCAGCTGGTGGTGG-TGCCTGCAATTGTAACATGGCAGGAGGCTTCTTCCG
        194 ATCTTCCT-TTCATGCAGCTAGTGCTGGCAG-TTACAATTGTAACATGTCAAAAGGCTTCTTCCA

                      *   *           *                                      
       4458 GAGTTTTGAATTAACATTAGTGATTATTTCAGTTCTGAAACTGCAAAGGTGGTGGAGAGGTGTTC
        257 GAGTTTTGAACTAAAATTAGTGATTACTTCAGTTCTGAAACTGCAAAGGTGGTGGAGAGGTGTTC

                        *    *    *    **        *    *   *        *         
       4523 TGTTACTTAAATCAAGAGCAAGGTCAGTTATCATTATCCAGACTCACGCACGGGGCTGGATTGCT
        322 TGTTACTTAAATTAAGAACAA-ATCAGCAATCATTATTCAGAGTCATGCACGGGGATGGATTGCT

             *        **                     
       4588 AGGCAAAAAGTGTATAGAAAGAGG-ACTTGTAT
        386 AAGCAAAAAGCATATAGAAAGAGGCA-TTGTAT

                         
       4620 TGTTGTAATACAA
          1 TGTTGTAATACAA

       4633 TCATATTGGA


Statistics
Matches: 741,  Mismatches: 100, Indels: 24
        0.86            0.12        0.03

Matches are distributed among these distances:
 419   21  0.03
 420  712  0.96
 421    8  0.01

ACGTcount: A:0.31, C:0.15, G:0.25, T:0.29


Consensus pattern (417 bp):   
TGTTGTAATACAAAGACATTGCCGTGGTTGGCTTGTAAGGAAGGATCTTTTGTTGAAAAGGGATT
CTGTAATAAAGATCCAAAGAGCAATACGGTGCCTAATATGTCAGAAGGCATTTCATTTACAGAAA
CTGGCAGCTATTGATATTCAAAGGGTTATCAGGGGCAAATTCTCGAAGTAGGCTTTTAGGAGCAT
CTTCCTTTCATGCAGCTAGTGCTGGCAGTTACAATTGTAACATGTCAAAAGGCTTCTTCCAGAGT
TTTGAACTAAAATTAGTGATTACTTCAGTTCTGAAACTGCAAAGGTGGTGGAGAGGTGTTCTGTT
ACTTAAATTAAGAACAAATCAGCAATCATTATTCAGAGTCATGCACGGGGATGGATTGCTAAGCA
AAAAGCATATAGAAAGAGGCATTGTAT
Done.