Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_903 ID=scaffold_903-JGI_221_v2.0

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: 2783
ACGTcount: A:0.25, C:0.17, G:0.20, T:0.31

Warning! 215 characters in sequence are not A, C, G, or T


Found at i:1818 original size:302 final size:301

Alignment explanation


    Indices: 1272--2782  Score: 2041
    Period size: 302  Copynumber: 5.0  Consensus size: 301

       1262 NNNNNNNNNN

                     *                    *      *    *               *      
       1272 TTTGAAACGATATTTGGTCGAATTTGCATTAAAATTCAAGGCGCAAGTGCGATAAGGGTCAGCCT
          1 TTTGAAACGTTATTTGGTCGAATTTGCATTCAAATTCGAGGCACAAGTGCGATAAGGGGCAGCCT

                              *  *                           *              *
       1337 TTATATAAATAGATTGCGTAAAAGTTGACGGGTGCGATCATACCAGCACAAATGCACCGGATCTG
         66 TTATATAAATAGATTGCGCAAGAGTTGACGGGTGCGATCATACCAGCACTAATGCACCGGATC-C

              *           *  *                 *        *             * **   
       1402 ATTAGAACTCCGCAATTTAGCGTGCTTGGGCGAGATTAGTACTACGATGGGTGACCTCTTTTGAA
        130 ATCAGAACTCCGCAGTTAAGCGTGCTTGGGCGAGAGTAGTACTAGGATGGGTGACCTCCTGGGAA

                  *                         *                                
       1467 GTCCTCATGTTGCACCCCTCCCATTTTATTTCTTATAAAGTTTTTTTAGTTGCATTTTCTCCACG
        195 GTCCTCGTGTTGCACCCCTCCCATTTTATTTCATATAAAGTTTTTTTAGTTGCATTTTCTCCACG

                                   *                   
       1532 TGGTGTAACT-ATTTCGTTATTTACGTTTTGCGAAATAAATAA
        260 TGGTGTAACTCA-TTCGTTATTTGCGTTTTGCGAAATAAATAA

                       *      *                        *                *    
       1574 TTTGAAACGTTGTTTGGTAGAATTTGCATTCAAATTCGAGGCAAAAGTGCGATAAGGGGCGGCCT
          1 TTTGAAACGTTATTTGGTCGAATTTGCATTCAAATTCGAGGCACAAGTGCGATAAGGGGCAGCCT

              *              *                         *  *      *           
       1639 TTGTATAAATAGATTGCACAAGAGTTGACGGGTGCGATCATACTAGTACTAATACACCGGATTCC
         66 TTATATAAATAGATTGCGCAAGAGTTGACGGGTGCGATCATACCAGCACTAATGCACCGGA-TCC

                                              *         *               *    
       1704 ATCAGAACTCCGCAGTTAAGCGTGCTTGGGCGAGTGTAGTACTACGATGGGTGACCTCCTAGGAA
        130 ATCAGAACTCCGCAGTTAAGCGTGCTTGGGCGAGAGTAGTACTAGGATGGGTGACCTCCTGGGAA

                *           *                                     *          
       1769 GTCCACGTGTTGCACCGCTCCCATTTTATTTCATATAAAGTTTTTTTAGTTGCAATTTCTCCACG
        195 GTCCTCGTGTTGCACCCCTCCCATTTTATTTCATATAAAGTTTTTTTAGTTGCATTTTCTCCACG

                      *    *                      *   
       1834 TGGTGTAACTAATTCCTTATTTGCGTTTTGCGAAATAACTAA
        260 TGGTGTAACTCATTCGTTATTTGCGTTTTGCGAAATAAATAA

                   *       *         **                    *                 
       1876 TTTGAAAAGTTATTTTGTCGAATTTAAATTCAAATTCGAGGCACAAGGGCGATAAGGGGCAGCCT
          1 TTTGAAACGTTATTTGGTCGAATTTGCATTCAAATTCGAGGCACAAGTGCGATAAGGGGCAGCCT

                             *    *            *                             
       1941 TTATATAAATAGATTGCACAAGGGTTGACGGGTGCAATCATACCAGCACTAATGCACCGGATCCT
         66 TTATATAAATAGATTGCGCAAGAGTTGACGGGTGCGATCATACCAGCACTAATGCACCGGATCC-

               *      *  *     *  *        *        *                  *   * 
       2006 AT-TGAAACTTCGTAGTTAGGCATGCTTGGGAGAGAGTAGAACTAGGATGGGTGACCTCTTGGCA
        130 ATCAG-AACTCCGCAGTTAAGCGTGCTTGGGCGAGAGTAGTACTAGGATGGGTGACCTCCTGGGA

                                  *                *                         
       2070 AGTCCTCGTGTTGCACCCCTCCTATTTTATTTCATATAATGTTTTTTTTTAGTTGCATTTTCTCC
        194 AGTCCTCGTGTTGCACCCCTCCCATTTTATTTCATATAAAG--TTTTTTTAGTTGCATTTTCTCC

              *               *                          
       2135 ACATGGTGTAACTCATTCCTTATTTGCGTTTTGCGAAATAAATAA
        257 ACGTGGTGTAACTCATTCGTTATTTGCGTTTTGCGAAATAAATAA

                   *                                  *    *                 
       2180 TTTGAAAAGTTATTTGGTCGAATTTGCATTCAAATTCGAGGCGCAAGGGCGATAAGGGGCAGCCT
          1 TTTGAAACGTTATTTGGTCGAATTTGCATTCAAATTCGAGGCACAAGTGCGATAAGGGGCAGCCT

                                       *              *     *         *      
       2245 TTATATAAATAGATTGCGCAAGAGTTGGCGGGTGCGATCATAACAGCATTAATGCACCAGATCTC
         66 TTATATAAATAGATTGCGCAAGAGTTGACGGGTGCGATCATACCAGCACTAATGCACCGGATC-C

               *         *         * *                                       
       2310 ATCTGAACTCCGCTGTTAAGCGTCCATGGGCGAGAGTAGTACTAGGATGGGTGACCTCCTGGGAA
        130 ATCAGAACTCCGCAGTTAAGCGTGCTTGGGCGAGAGTAGTACTAGGATGGGTGACCTCCTGGGAA

                                   *                                    *   *
       2375 GTCCTCGTGTTGCACCCCTCCCAATTTATTTCATAT-AA-TTTTTTTAGTTGCATTTTCTTCACA
        195 GTCCTCGTGTTGCACCCCTCCCATTTTATTTCATATAAAGTTTTTTTAGTTGCATTTTCTCCACG

            **                           *            
       2438 ACGTGTAACTCATTCGTTATTTGCGTTTTCCGAAATAAATAA
        260 TGGTGTAACTCATTCGTTATTTGCGTTTTGCGAAATAAATAA

                  *  *        *                                     **       
       2480 TTTGAATCGATATTTGGTTGAATTTGCATT-AAATTCGAGGCACAAGTGCGATAAGAAGCAGCCT
          1 TTTGAAACGTTATTTGGTCGAATTTGCATTCAAATTCGAGGCACAAGTGCGATAAGGGGCAGCCT

                  *                                        *          *      
       2544 TTATATGAATAGATTGCGCAAGAGTTGATC-GGTGCGATCATACCAGAACTAATGCACTGGATCC
         66 TTATATAAATAGATTGCGCAAGAGTTGA-CGGGTGCGATCATACCAGCACTAATGCACCGGAT-C

                        *                         *                    *     
       2608 CATCAGAACTCCTCAGTTAAGCGTGCTTGGGCGAGAGTTGTACTAGGATGGGTGACCTCTTGGGA
        129 CATCAGAACTCCGCAGTTAAGCGTGCTTGGGCGAGAGTAGTACTAGGATGGGTGACCTCCTGGGA

                             *  *                            *               
       2673 AGTCCTCGTGTTGCACCTCTTCCATTTTATTTCATAT-AA-TTTTTTTAATTGCATTTTCTTCC-
        194 AGTCCTCGTGTTGCACCCCTCCCATTTTATTTCATATAAAGTTTTTTTAGTTGCATTTTC-TCCA

                                      *                 
       2735 CGTGGTGTAACTCATTCGTTATTTGCATTTTGCGAAATAAATAA
        258 CGTGGTGTAACTCATTCGTTATTTGCGTTTTGCGAAATAAATAA

                
       2779 TTTG
          1 TTTG

       2783 C


Statistics
Matches: 1067,  Mismatches: 131, Indels: 25
        0.87            0.11        0.02

Matches are distributed among these distances:
 299  238  0.22
 300   92  0.09
 301    4  0.00
 302  461  0.43
 303    4  0.00
 304  265  0.25
 305    3  0.00

ACGTcount: A:0.27, C:0.18, G:0.22, T:0.33


Consensus pattern (301 bp):   
TTTGAAACGTTATTTGGTCGAATTTGCATTCAAATTCGAGGCACAAGTGCGATAAGGGGCAGCCT
TTATATAAATAGATTGCGCAAGAGTTGACGGGTGCGATCATACCAGCACTAATGCACCGGATCCA
TCAGAACTCCGCAGTTAAGCGTGCTTGGGCGAGAGTAGTACTAGGATGGGTGACCTCCTGGGAAG
TCCTCGTGTTGCACCCCTCCCATTTTATTTCATATAAAGTTTTTTTAGTTGCATTTTCTCCACGT
GGTGTAACTCATTCGTTATTTGCGTTTTGCGAAATAAATAA

Done.