Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_17362

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: 2580
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.26


Found at i:2161 original size:207 final size:205

Alignment explanation


    Indices: 1513--2313  Score: 1062
    Period size: 204  Copynumber: 3.9  Consensus size: 205

       1503 AAATTCAGAC

                                   *                             *           
       1513 ATTGTAAATCAAGGCACTGCTCCCAGAAGAATACGCTTG-ATGAAACTTTCTAGTGGGCCAATGA
          1 ATTGTAAATCAAGGCACTGCTCCAAGAAGAATACGCTTGCATGAAACTTTCTACTGGGCCAATGA

                     *                  *  *    **            *              
       1577 AAGGTTCTGTAGGCTGTGTCGATGGTGGAAAAATGATGAG-CACTGGCCTTGTTGAAGAAGAAGA
         66 AAGGTTCTGCAGGCTGTGTCGATGGTGGGAACATGACAAGTC-CTGGCCTCGTT---GAAGAAGA

                                                        *                    
       1641 AGTTCAGTCTGCTCTAACTGAGGTCACAGAAGCTGAAGCTGCAGAACAGACTTCTAGCTCTGATG
        127 AGTTCAGTCTGCTCTAACTGAGGTCACAGAAGCTGAAGCTGCAGGACAGACTTCTAGCTCTGATG

                          
       1706 AGTCAGAGAAGAAT
        192 AGTCAGAGAAGAAT

                         *      *             *        *         *      *    
       1720 ATTGTAAATCAAGTCACTGCACCAAGAAGAATACACTTGCAAACGAAACTTTCCACTGGGGCAAT
          1 ATTGTAAATCAAGGCACTGCTCCAAGAAGAATACGCTTGC--ATGAAACTTTCTACTGGGCCAAT

                                  *                *                         
       1785 GAAAGGTTCTGCAGGCTGTGTCAATGGTGGGAACATGACTAGTCCTGGCCTCGTT---GAAGAAG
         64 GAAAGGTTCTGCAGGCTGTGTCGATGGTGGGAACATGACAAGTCCTGGCCTCGTTGAAGAAGAAG

                *        *                          *  * *            *      
       1847 TTCAATCTGCTCTTACTGAGGTCACAGAAGCTGAAGCTGCTGGGCTGACTTCTAGCTCAGATGAG
        129 TTCAGTCTGCTCTAACTGAGGTCACAGAAGCTGAAGCTGCAGGACAGACTTCTAGCTCTGATGAG

             *          
       1912 TTAGAGAAGAAT
        194 TCAGAGAAGAAT

                                                *       *  *           *     
       1924 ATTGTAAATCAAGGCACTGCTCCAAGAAGAATACGCCTGCAAATTAATCTTTCTACTGGACCAAT
          1 ATTGTAAATCAAGGCACTGCTCCAAGAAGAATACGCTTGC--ATGAAACTTTCTACTGGGCCAAT

                                            *                                
       1989 GAAAGGTTCTGCAGGCTGTGTCGATGGTGGGAGCATGACAAGTCCTGGCCTCGTTGAAGAAGAAG
         64 GAAAGGTTCTGCAGGCTGTGTCGATGGTGGGAACATGACAAGTCCTGGCCTCGTTGAAGAAGAAG

                            *                                                
       2054 TTCAGTCTGCTCTAACCGAGGTCACAGAAGCTGAAGCTGCAGGACAGACTTCTAGCTCTGATGAG
        129 TTCAGTCTGCTCTAACTGAGGTCACAGAAGCTGAAGCTGCAGGACAGACTTCTAGCTCTGATGAG

                   *    
       2119 TCAGAGATGAAT
        194 TCAGAGAAGAAT

                    *    *  *      *                   *                     
       2131 ATTGTAAACCAAGCCATTGCTCCTAGAAGAATACG-TT---TGCAACTTTCTACTGGGCCAATGA
          1 ATTGTAAATCAAGGCACTGCTCCAAGAAGAATACGCTTGCATGAAACTTTCTACTGGGCCAATGA

             *               *                                 * *           
       2192 ATGGTTCTGCAGGCTGTATCGATGGTGGGAACATGACAAGTCCTGGCCTCGGTAAAGAAGAAGTT
         66 AAGGTTCTGCAGGCTGTGTCGATGGTGGGAACATGACAAGTCCTGGCCTCGTTGAAGAAGAAGTT

                    *          *        *       *         *          
       2257 CAGTCTGCGCTAACTGAGGCCACAGAAGATGAAGCTACAGGACAGATTTCTAGCTCT
        131 CAGTCTGCTCTAACTGAGGTCACAGAAGCTGAAGCTGCAGGACAGACTTCTAGCTCT

       2314 TGCAAGACTT


Statistics
Matches: 522,  Mismatches: 65, Indels: 20
        0.86            0.11        0.03

Matches are distributed among these distances:
 201  131  0.25
 204  183  0.35
 206    1  0.00
 207  141  0.27
 210   65  0.12
 211    1  0.00

ACGTcount: A:0.30, C:0.20, G:0.26, T:0.24


Consensus pattern (205 bp):   
ATTGTAAATCAAGGCACTGCTCCAAGAAGAATACGCTTGCATGAAACTTTCTACTGGGCCAATGA
AAGGTTCTGCAGGCTGTGTCGATGGTGGGAACATGACAAGTCCTGGCCTCGTTGAAGAAGAAGTT
CAGTCTGCTCTAACTGAGGTCACAGAAGCTGAAGCTGCAGGACAGACTTCTAGCTCTGATGAGTC
AGAGAAGAAT
Done.