Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_25689

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, 779

Length: 1299
ACGTcount: A:0.30, C:0.23, G:0.22, T:0.24


Found at i:580 original size:228 final size:228

Alignment explanation


    Indices: 154--1259  Score: 1107
    Period size: 228  Copynumber: 4.9  Consensus size: 228

        144 CTCTGACAAG

                          *  *  *        *     *      * *     *  *           
        154 ATGCAAATCTTTGTTAAAACCCTCACTGGCAAGACCATCACCCTCGAGGTGGAGAGTTCAGACAC
          1 ATGCAAATCTTTGTCAAGACTCTCACTGGAAAGACAATCACCTTGGAGGTTGAAAGTTCAGACAC

                        *     *           *                 *  *     *       
        219 CATTGATAATGTGAAGGCTAAGATCCAAGATAAGGAAGGGATCCCACCGGATCAGCAGAGGCTTA
         66 CATTGATAATGTAAAGGCAAAGATCCAAGACAAGGAAGGGATCCCACCAGACCAGCAAAGGCTTA

                                   *     *  *            *     *  *         *
        284 TCTTTGCTGGCAAA-CAACTTGAGGATGGCCGCACGC-TAGCCGACTACAACATTCAGAAA-GAA
        131 TCTTTGCTGG-AAAGCAACTTGAAGATGGTCGGAC-CTTAGCCGATTACAATATCCA-AAAGGAG

                    *                       *   
        346 TCCACCCTTCACTTGGTTCTTCGACTTCGTGGCGGC
        193 TCCACCCTCCACTTGGTTCTTCGACTTCGTGGTGGC

                                                  *                 *  *     
        382 ATGCAAATCTTTGTCAAGACTCTCACTGGAAAGACAATTACCTTGGAGGTTGAAAGCTCTGACAC
          1 ATGCAAATCTTTGTCAAGACTCTCACTGGAAAGACAATCACCTTGGAGGTTGAAAGTTCAGACAC

            *  *                                               *     *       
        447 AATAGATAATGTAAAGGCAAAGATCCAAGACAAGGAAGGGATCCCACCAGATCAGCAGAGGCTTA
         66 CATTGATAATGTAAAGGCAAAGATCCAAGACAAGGAAGGGATCCCACCAGACCAGCAAAGGCTTA

                            *              *        *                 *      
        512 TCTTTGCTGGAAAGCAGCTTGAAGATGGTCGCACCTTAGCTGATTACAATATCCAAAAAGAGTCC
        131 TCTTTGCTGGAAAGCAACTTGAAGATGGTCGGACCTTAGCCGATTACAATATCCAAAAGGAGTCC

                     * *  *     *     *      
        577 ACCCTCCACCTAGTACTTCGTCTTCGAGGTGGC
        196 ACCCTCCACTTGGTTCTTCGACTTCGTGGTGGC

                             *                    *           *  *     *  *  
        610 ATGCAAATCTTTGTCAAAACTCTCACTGGAAAGACAATTACCTTGGAGGTGGAGAGTTCGGATAC
          1 ATGCAAATCTTTGTCAAGACTCTCACTGGAAAGACAATCACCTTGGAGGTTGAAAGTTCAGACAC

                               *     *  *     *     *              *      *  
        675 CATTGATAATGTGAAA-GCCAAGATTCAGGACAAAGAAGGAATCCCACCAGACCAACAAA-GATT
         66 CATTGATAATGT-AAAGGCAAAGATCCAAGACAAGGAAGGGATCCCACCAGACCAGCAAAGGCTT

               *           *              **                 *        *      
        738 GATTTTTGCTGGAAAACAACTTGAAGATGGAAGGACTCTT-GCCGATTATAATATCCAGAAGGAG
        130 -ATCTTTGCTGGAAAGCAACTTGAAGATGGTCGGAC-CTTAGCCGATTACAATATCCAAAAGGAG

              *  *     *        *  *           *
        802 TCTACTCTCCATTTGGTTCTCCGCCTTCGTGGTGGT
        193 TCCACCCTCCACTTGGTTCTTCGACTTCGTGGTGGC

                 *        *        *  *        *     *                 *  *  
        838 ATGCAGATCTTTGTAAAGACTCTTACCGGAAAGACCATCACTTTGGAGGTTGAAAGTTCCGATAC
          1 ATGCAAATCTTTGTCAAGACTCTCACTGGAAAGACAATCACCTTGGAGGTTGAAAGTTCAGACAC

                  *     *                                 *                 *
        903 CATTGACAATGTGAAGGCAAAGATCCAAGACAAGG-AGGGTATCCCCCCAGACCAGCAAAGGCTC
         66 CATTGATAATGTAAAGGCAAAGATCCAAGACAAGGAAGGG-ATCCCACCAGACCAGCAAAGGCTT

                       *     *  *         *    *  *     *                    
        967 ATCTTTGCTGGCAAGCAGCTCGAAGATGGTAGGACATTGGCCGACTACAATATCCAAAAGGAGTC
        130 ATCTTTGCTGGAAAGCAACTTGAAGATGGTCGGACCTTAGCCGATTACAATATCCAAAAGGAGTC

            *     *            *  *  *        *
       1032 TACCCTTCACTTGGTGT-TGCGGCTGCGTGGTGGG
        195 CACCCTCCACTTGGT-TCTTCGACTTCGTGGTGGC

                 *        *        *           *         *                   
       1066 ATGCAGATCTTTGTTAAGACTCTTACTGGAAAGACTATCA-CTCTAGAGGTTGAAAGTTCAGACA
          1 ATGCAAATCTTTGTCAAGACTCTCACTGGAAAGACAATCACCT-TGGAGGTTGAAAGTTCAGACA

                   *     *           *                                      *
       1130 CCATTGACAATGTTAAGGCAAAGATTCAAGACAAGGAAGGGATCCCACCAGACCAGCAAAGGCTC
         65 CCATTGATAATGTAAAGGCAAAGATCCAAGACAAGGAAGGGATCCCACCAGACCAGCAAAGGCTT

              *        *                        *  *  *     *                
       1195 ATATTTGCTGGCAAGCAACTTGAAGATGG-CAGGACATTGGCTGATTATAATATCCAAAAGGAGT
        130 ATCTTTGCTGGAAAGCAACTTGAAGATGGTC-GGACCTTAGCCGATTACAATATCCAAAAGGAGT

             
       1259 C
        194 C

       1260 TACTCTGCAT


Statistics
Matches: 738,  Mismatches: 126, Indels: 28
        0.83            0.14        0.03

Matches are distributed among these distances:
 227   18  0.02
 228  707  0.96
 229   13  0.02

ACGTcount: A:0.31, C:0.22, G:0.23, T:0.23


Consensus pattern (228 bp):   
ATGCAAATCTTTGTCAAGACTCTCACTGGAAAGACAATCACCTTGGAGGTTGAAAGTTCAGACAC
CATTGATAATGTAAAGGCAAAGATCCAAGACAAGGAAGGGATCCCACCAGACCAGCAAAGGCTTA
TCTTTGCTGGAAAGCAACTTGAAGATGGTCGGACCTTAGCCGATTACAATATCCAAAAGGAGTCC
ACCCTCCACTTGGTTCTTCGACTTCGTGGTGGC

Found at i:1018 original size:456 final size:455

Alignment explanation


    Indices: 154--1293  Score: 1282
    Period size: 456  Copynumber: 2.5  Consensus size: 455

        144 CTCTGACAAG

                                *        *     *      * *                    
        154 ATGCAAATCTTTGTTAAAACCCTCACTGGCAAGACCATCACCCTCGAGGTGGAGAGTTCAGACAC
          1 ATGCAAATCTTTGTTAAAACTCTCACTGGAAAGACAATCACCTTAGAGGTGGAGAGTTCAGACAC

                              *     *     *                 *  *       * *   
        219 CATTGATAATGTGAAGGCTAAGATCCAAGATAAGGAAGGGATCCCACCGGATCAGCAGAGGCTTA
         66 CATTGATAATGTGAAGGCAAAGATTCAAGACAAGGAAGGGATCCCACCAGACCAGCA-AAGATTA

             *                    *      * *  *        *  *  *  *     *  *  *
        284 TCTTTGCTGGCAAACAACTTGAGGATGGCCGCACGCTAGCCGACTACAACATTCAGAAAGAATCC
        130 TATTTGCTGGCAAACAACTTGAAGATGGCAGGACTCTAGCCGATTATAATATCCAGAAGGAGTCT

              *  *  *           *        *  *              *           *     
        349 ACCCTTCACTTGGTTCTTCGACTTCGTGGCGGCATGCAAATCTTTGTCAAGACTCTCACTGGAAA
        195 ACTCTCCATTTGGTTCTTCGCCTTCGTGGTGGTATGCAAATCTTTGTAAAGACTCTCACCGGAAA

                  *                    *           *                         
        414 GACAATTACCTTGGAGGTTGAAAGCTCTGACACAATAGATAATGTAAAGGCAAAGATCCAAGACA
        260 GACAATCACCTTGGAGGTTGAAAGCTCCGACACAATAGACAATGTAAAGGCAAAGATCCAAGACA

                               *     *     *                    *         *  
        479 AGGAAGGGATCCCACCAGATCAGCAGAGGCTTATCTTTGCTGGAAAGCAGCTTGAAGATGGTCGC
        325 AGGAAGGGATCCCACCAGACCAGCAAAGGCTCATCTTTGCTGGAAAGCAGCTCGAAGATGGTAGC

              *     *  *                                          *  *       
        544 ACCTTAGCTGATTACAATATCCAAAAAGAGTCCACCCTCCACCTAGTACTT-CGTCTTCGAGGTG
        390 ACATTAGCCGACTACAATATCCAAAAAGAGTCCACCCTCCACCTAGT-CTTGCGGCTGCGAGGTG

              
        608 GC
        454 GC

                          *                       *     *              *  *  
        610 ATGCAAATCTTTGTCAAAACTCTCACTGGAAAGACAATTACCTTGGAGGTGGAGAGTTCGGATAC
          1 ATGCAAATCTTTGTTAAAACTCTCACTGGAAAGACAATCACCTTAGAGGTGGAGAGTTCAGACAC

                           *  *        *     *     *              *          
        675 CATTGATAATGTGAAAGCCAAGATTCAGGACAAAGAAGGAATCCCACCAGACCAACAAAGATTGA
         66 CATTGATAATGTGAAGGCAAAGATTCAAGACAAGGAAGGGATCCCACCAGACCAGCAAAGATT-A

             *        *                 *        *                           
        740 TTTTTGCTGGAAAACAACTTGAAGATGGAAGGACTCTTGCCGATTATAATATCCAGAAGGAGTCT
        130 TATTTGCTGGCAAACAACTTGAAGATGGCAGGACTCTAGCCGATTATAATATCCAGAAGGAGTCT

                             *                    *                 *        
        805 ACTCTCCATTTGGTTCTCCGCCTTCGTGGTGGTATGCAGATCTTTGTAAAGACTCTTACCGGAAA
        195 ACTCTCCATTTGGTTCTTCGCCTTCGTGGTGGTATGCAAATCTTTGTAAAGACTCTCACCGGAAA

               *     *              *     *  *  *        *                   
        870 GACCATCACTTTGGAGGTTGAAAGTTCCGATACCATTGACAATGTGAAGGCAAAGATCCAAGACA
        260 GACAATCACCTTGGAGGTTGAAAGCTCCGACACAATAGACAATGTAAAGGCAAAGATCCAAGACA

                          *                             *                    
        935 AGG-AGGGTATCCCCCCAGACCAGCAAAGGCTCATCTTTGCTGGCAAGCAGCTCGAAGATGGTAG
        325 AGGAAGGG-ATCCCACCAGACCAGCAAAGGCTCATCTTTGCTGGAAAGCAGCTCGAAGATGGTAG

            *     *                    *     *     *   * *  *           *    
        999 GACATTGGCCGACTACAATATCCAAAAGGAGTCTACCCTTCACTTGGTGTTGCGGCTGCGTGGTG
        389 CACATTAGCCGACTACAATATCCAAAAAGAGTCCACCCTCCACCTAGTCTTGCGGCTGCGAGGTG

             *
       1064 GG
        454 GC

                 *           *     *           *               *  *          
       1066 ATGCAGATCTTTGTTAAGACTCTTACTGGAAAGACTATCA-CTCTAGAGGTTGAAAGTTCAGACA
          1 ATGCAAATCTTTGTTAAAACTCTCACTGGAAAGACAATCACCT-TAGAGGTGGAGAGTTCAGACA

                   *     *                                                * *
       1130 CCATTGACAATGTTAAGGCAAAGATTCAAGACAAGGAAGGGATCCCACCAGACCAGCAAAGGCTC
         65 CCATTGATAATGTGAAGGCAAAGATTCAAGACAAGGAAGGGATCCCACCAGACCAGCAAA-GATT

                          *                        *  *              *       
       1195 ATATTTGCTGGCAAGCAACTTGAAGATGGCAGGACAT-TGGCTGATTATAATATCCAAAAGGAGT
        129 ATATTTGCTGGCAAACAACTTGAAGATGGCAGGAC-TCTAGCCGATTATAATATCCAGAAGGAGT

                   *         *           *      
       1259 CTACTCTGCATCTT-GTCCTTCGCCTTCGCGGTGGT
        193 CTACTCTCCAT-TTGGTTCTTCGCCTTCGTGGTGGT

       1294 TTCTAA


Statistics
Matches: 566,  Mismatches: 111, Indels: 14
        0.82            0.16        0.02

Matches are distributed among these distances:
 455   12  0.02
 456  549  0.97
 457    5  0.01

ACGTcount: A:0.31, C:0.22, G:0.23, T:0.24


Consensus pattern (455 bp):   
ATGCAAATCTTTGTTAAAACTCTCACTGGAAAGACAATCACCTTAGAGGTGGAGAGTTCAGACAC
CATTGATAATGTGAAGGCAAAGATTCAAGACAAGGAAGGGATCCCACCAGACCAGCAAAGATTAT
ATTTGCTGGCAAACAACTTGAAGATGGCAGGACTCTAGCCGATTATAATATCCAGAAGGAGTCTA
CTCTCCATTTGGTTCTTCGCCTTCGTGGTGGTATGCAAATCTTTGTAAAGACTCTCACCGGAAAG
ACAATCACCTTGGAGGTTGAAAGCTCCGACACAATAGACAATGTAAAGGCAAAGATCCAAGACAA
GGAAGGGATCCCACCAGACCAGCAAAGGCTCATCTTTGCTGGAAAGCAGCTCGAAGATGGTAGCA
CATTAGCCGACTACAATATCCAAAAAGAGTCCACCCTCCACCTAGTCTTGCGGCTGCGAGGTGGC

Done.