Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga01g01219.F1

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, 741

Length: 1236
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.27


Found at i:878 original size:456 final size:457

Alignment explanation


    Indices: 100--1036  Score: 1148
    Period size: 456  Copynumber: 2.1  Consensus size: 457

         90 CCACCCTTCA

                        *        *  *              *           *           * 
        100 CTTGGTTCTTCGACTTCGTGGCGGCATGCAAATCTTTGTCAAGACTCTCACTGGAAAGACAATTA
          1 CTTGGTTCTTCGCCTTCGTGGTGGTATGCAAATCTTTGTAAAGACTCTCACCGGAAAGACAATCA

                               *           *                                 
        165 CCTTGGAGGTTGAAAGCTCTGACACAATAGATAATGTAAAGGCAAAGATCCAAGACAAGGAAGGG
         66 CCTTGGAGGTTGAAAGCTCCGACACAATAGACAATGTAAAGGCAAAGATCCAAGACAAGGAAGGG

                       *     *     *                    *         *    *     
        230 ATCCCACCAGATCAGCAGAGGCTTATCTTTGCTGGAAAGCAGCTTGAAGATGGTCGCACCTTAGC
        131 ATCCCACCAGACCAGCAAAGGCTCATCTTTGCTGGAAAGCAGCTCGAAGATGGTAGCACATTAGC

            *  *                                         *  *                
        295 TGATTACAATATCCAAAAAGAGTCCACCCTCCACCTAGTACTTCGTCTTCGAGGTGGCATGCAAA
        196 CGACTACAATATCCAAAAAGAGTCCACCCTCCACCTAGTACTTCGGCTGCGAGGTGGCATGCAAA

                                           *     *        *     *  *        *
        360 TCTTTGTCAAAACTCTCACTGGAAAGACAATTACCTTGGAGGTGGAGAGTTCGGATACCATTGAT
        261 TCTTTGTCAAAACTCTCACTGGAAAGACAATCACCTTAGAGGTGGAAAGTTCAGACACCATTGAC

                       *        *                                 * *  *     
        425 AATGTGAAAGCCAAGATTCAGGACAAAGAAGGAATCCCACCAGACCAACAAAGATTGATTTTTGC
        326 AATGTGAAAGCAAAGATTCAAGACAAAGAAGGAATCCCACCAGACCAACAAAGACTCATATTTGC

                                           *                 *               
        490 TGGAAAACAACTTGAAGATGGAAGGAC-TCTTGCCGATTATAATATCCAGAAGGAGTCTACTCTC
        391 TGGAAAACAACTTGAAGATGGAAGGACAT-TGGCCGATTATAATATCCAAAAGGAGTCTACTCTC

               
        554 CAT
        455 CAT

                     *                    *                 *           *    
        557 -TTGGTTCTCCGCCTTCGTGGTGGTATGCAGATCTTTGTAAAGACTCTTACCGGAAAGACCATCA
          1 CTTGGTTCTTCGCCTTCGTGGTGGTATGCAAATCTTTGTAAAGACTCTCACCGGAAAGACAATCA

             *              *     *  *  *        *                           
        621 CTTTGGAGGTTGAAAGTTCCGATACCATTGACAATGTGAAGGCAAAGATCCAAGACAAGG-AGGG
         66 CCTTGGAGGTTGAAAGCTCCGACACAATAGACAATGTAAAGGCAAAGATCCAAGACAAGGAAGGG

                  *                             *                    *     * 
        685 TATCCCCCCAGACCAGCAAAGGCTCATCTTTGCTGGCAAGCAGCTCGAAGATGGTAGGACATTGG
        131 -ATCCCACCAGACCAGCAAAGGCTCATCTTTGCTGGAAAGCAGCTCGAAGATGGTAGCACATTAG

                               *     *     *   * *   *           *     *     
        750 CCGACTACAATATCCAAAAGGAGTCTACCCTTCACTTGGT-GTTGCGGCTGCGTGGTGGGATGCA
        195 CCGACTACAATATCCAAAAAGAGTCCACCCTCCACCTAGTACTT-CGGCTGCGAGGTGGCATGCA

            *        *  *     *           *               *                  
        814 GATCTTTGTTAAGACTCTTACTGGAAAGACTATCA-CTCTAGAGGTTGAAAGTTCAGACACCATT
        259 AATCTTTGTCAAAACTCTCACTGGAAAGACAATCACCT-TAGAGGTGGAAAGTTCAGACACCATT

                    *  *                 *     *              *     *        
        878 GACAATGTTAAGGCAAAGATTCAAGACAAGGAAGGGATCCCACCAGACCAGCAAAGGCTCATATT
        323 GACAATGTGAAAGCAAAGATTCAAGACAAAGAAGGAATCCCACCAGACCAACAAAGACTCATATT

                  *  *              *           *                            
        943 TGCTGGCAAGCAACTTGAAGATGGCAGGACATTGGCTGATTATAATATCCAAAAGGAGTCTACTC
        388 TGCTGGAAAACAACTTGAAGATGGAAGGACATTGGCCGATTATAATATCCAAAAGGAGTCTACTC

             *   
       1008 TGCAT
        453 TCCAT

                  *           *      
       1013 CTT-GTCCTTCGCCTTCGCGGTGGT
          1 CTTGGTTCTTCGCCTTCGTGGTGGT

       1037 TTCTAAGTAA


Statistics
Matches: 402,  Mismatches: 73, Indels: 11
        0.83            0.15        0.02

Matches are distributed among these distances:
 455    8  0.02
 456  391  0.97
 457    3  0.01

ACGTcount: A:0.30, C:0.22, G:0.24, T:0.24


Consensus pattern (457 bp):   
CTTGGTTCTTCGCCTTCGTGGTGGTATGCAAATCTTTGTAAAGACTCTCACCGGAAAGACAATCA
CCTTGGAGGTTGAAAGCTCCGACACAATAGACAATGTAAAGGCAAAGATCCAAGACAAGGAAGGG
ATCCCACCAGACCAGCAAAGGCTCATCTTTGCTGGAAAGCAGCTCGAAGATGGTAGCACATTAGC
CGACTACAATATCCAAAAAGAGTCCACCCTCCACCTAGTACTTCGGCTGCGAGGTGGCATGCAAA
TCTTTGTCAAAACTCTCACTGGAAAGACAATCACCTTAGAGGTGGAAAGTTCAGACACCATTGAC
AATGTGAAAGCAAAGATTCAAGACAAAGAAGGAATCCCACCAGACCAACAAAGACTCATATTTGC
TGGAAAACAACTTGAAGATGGAAGGACATTGGCCGATTATAATATCCAAAAGGAGTCTACTCTCC
AT

Found at i:1003 original size:228 final size:227

Alignment explanation


    Indices: 1--1005  Score: 1007
    Period size: 228  Copynumber: 4.4  Consensus size: 227

                     *  *     *     *                        *      * *  ** *
          1 GATCCCACCGGATCAGCAGAGGCTTATCTTTGCTGGCAAA-CAACTTGAGGATGGCCGCACGCTA
          1 GATCCCACCAGACCAGCAAAGGCTCATCTTTGCTGG-AAAGCAACTTGAAGATGGCAGGACATTG

                 *     *  *         *  *     *                       *       
         65 GCCGACTACAACATTCAGAAA-GAATCCACCCTTCACTTGGTTCTTCGACTTCGTGGCGGCATGC
         65 GCCGATTACAATATCCA-AAAGGAGTCTACCCTCCACTTGGTTC-TCGACTTCGTGGTGGCATGC

                                              *                 *  *     *  *
        129 AAATCTTTGTCAAGACTCTCACTGGAAAGACAATTACCTTGGAGGTTGAAAGCTCTGACACAATA
        128 AAATCTTTGTCAAGACTCTCACTGGAAAGACAATCACCTTGGAGGTTGAAAGTTCAGACACCATT

              *     *                          
        194 GATAATGTAAAGGCAAAGATCCAAGACAAGGAAGG
        193 GACAATGTGAAGGCAAAGATCCAAGACAAGGAAGG

                        *     *     *                 *               *  *  *
        229 GATCCCACCAGATCAGCAGAGGCTTATCTTTGCTGGAAAGCAGCTTGAAGATGGTC-GCACCTTA
          1 GATCCCACCAGACCAGCAAAGGCTCATCTTTGCTGGAAAGCAACTTGAAGATGG-CAGGACATTG

              *                 *     *         * *  *     *     *           
        293 GCTGATTACAATATCCAAAAAGAGTCCACCCTCCACCTAGTACTTCGTCTTCGAGGTGGCATGCA
         65 GCCGATTACAATATCCAAAAGGAGTCTACCCTCCACTTGGTTC-TCGACTTCGTGGTGGCATGCA

                        *                    *           *  *     *  *       
        358 AATCTTTGTCAAAACTCTCACTGGAAAGACAATTACCTTGGAGGTGGAGAGTTCGGATACCATTG
        129 AATCTTTGTCAAGACTCTCACTGGAAAGACAATCACCTTGGAGGTTGAAAGTTCAGACACCATTG

             *        *  *     *  *     *     
        423 ATAATGTGAAAGCCAAGATTCAGGACAAAGAAGG
        194 ACAATGTGAAGGCAAAGATCCAAGACAAGGAAGG

            *              *     ** *  *           *              *         *
        457 AATCCCACCAGACCAACAAAGATTGATTTTTGCTGGAAAACAACTTGAAGATGGAAGGAC-TCTT
          1 GATCCCACCAGACCAGCAAAGGCTCATCTTTGCTGGAAAGCAACTTGAAGATGGCAGGACAT-TG

                    *        *           *     *           *           *     
        521 GCCGATTATAATATCCAGAAGGAGTCTACTCTCCATTTGGTTCTCCGCCTTCGTGGTGGTATGCA
         65 GCCGATTACAATATCCAAAAGGAGTCTACCCTCCACTTGGTTCT-CGACTTCGTGGTGGCATGCA

            *        *        *  *        *     *                 *  *       
        586 GATCTTTGTAAAGACTCTTACCGGAAAGACCATCACTTTGGAGGTTGAAAGTTCCGATACCATTG
        129 AATCTTTGTCAAGACTCTCACTGGAAAGACAATCACCTTGGAGGTTGAAAGTTCAGACACCATTG

                                              
        651 ACAATGTGAAGGCAAAGATCCAAGACAAGG-AGG
        194 ACAATGTGAAGGCAAAGATCCAAGACAAGGAAGG

                   *                             *     *  *        *         
        684 GTATCCCCCCAGACCAGCAAAGGCTCATCTTTGCTGGCAAGCAGCTCGAAGATGGTAGGACATTG
          1 G-ATCCCACCAGACCAGCAAAGGCTCATCTTTGCTGGAAAGCAACTTGAAGATGGCAGGACATTG

                 *                          *               *  *        *    
        749 GCCGACTACAATATCCAAAAGGAGTCTACCCTTCACTTGGTGT-TGCGGCTGCGTGGTGGGATGC
         65 GCCGATTACAATATCCAAAAGGAGTCTACCCTCCACTTGGT-TCT-CGACTTCGTGGTGGCATGC

             *        *        *           *         *                       
        813 AGATCTTTGTTAAGACTCTTACTGGAAAGACTATCA-CTCTAGAGGTTGAAAGTTCAGACACCAT
        128 AAATCTTTGTCAAGACTCTCACTGGAAAGACAATCACCT-TGGAGGTTGAAAGTTCAGACACCAT

                     *           *              
        877 TGACAATGTTAAGGCAAAGATTCAAGACAAGGAAGG
        192 TGACAATGTGAAGGCAAAGATCCAAGACAAGGAAGG

                                       *        *                            
        913 GATCCCACCAGACCAGCAAAGGCTCATATTTGCTGGCAAGCAACTTGAAGATGGCAGGACATTGG
          1 GATCCCACCAGACCAGCAAAGGCTCATCTTTGCTGGAAAGCAACTTGAAGATGGCAGGACATTGG

             *     *                    
        978 CTGATTATAATATCCAAAAGGAGTCTAC
         66 CCGATTACAATATCCAAAAGGAGTCTAC

       1006 TCTGCATCTT


Statistics
Matches: 652,  Mismatches: 114, Indels: 22
        0.83            0.14        0.03

Matches are distributed among these distances:
 227   12  0.02
 228  633  0.97
 229    7  0.01

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


Consensus pattern (227 bp):   
GATCCCACCAGACCAGCAAAGGCTCATCTTTGCTGGAAAGCAACTTGAAGATGGCAGGACATTGG
CCGATTACAATATCCAAAAGGAGTCTACCCTCCACTTGGTTCTCGACTTCGTGGTGGCATGCAAA
TCTTTGTCAAGACTCTCACTGGAAAGACAATCACCTTGGAGGTTGAAAGTTCAGACACCATTGAC
AATGTGAAGGCAAAGATCCAAGACAAGGAAGG
Done.