Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_104 ID=scaffold_104-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: 13547
ACGTcount: A:0.28, C:0.22, G:0.17, T:0.33


Found at i:1413 original size:44 final size:44

Alignment explanation


    Indices: 1234--1679  Score: 188
    Period size: 44  Copynumber: 10.2  Consensus size: 44

       1224 CTCCTGGGGA

                                     **         *       
       1234 AGATAAGATTCGCCGTCTTCAATCTGCTCCACTACTACTTAGGG
          1 AGATAAGATTCGCCGTCTTCAATCTATTCCACTACTGCTTAGGG

                         ***                    *      *    
       1278 AGATAAGA-TCTGTAATCTTCAA-C-ATGTCCCACTGCTGAC-CAGGG
          1 AGATAAGATTC-GCCGTCTTCAATCTAT-T-CCACTACTG-CTTAGGG

                    * *  * *   *                   *     
       1322 AGATAAGACTAG-TGGCTTAAATCTATTTCC-CTACT-CCTAGGG
          1 AGATAAGATTCGCCGTCTTCAATCTA-TTCCACTACTGCTTAGGG

                                 *     *       *         
       1364 AAGATAAGATTCGCCGTCTTCGATCTACTCCACTATTGCTTAGGG
          1 -AGATAAGATTCGCCGTCTTCAATCTATTCCACTACTGCTTAGGG

                         **    *   *          *     *    
       1409 AGATAAGA-TCTGTAGTCTCCAACCTATTCCACTGCTGCTCAGGG
          1 AGATAAGATTC-GCCGTCTTCAATCTATTCCACTACTGCTTAGGG

             *   *        * **  *                   *     
       1453 AAATAGGACTT-G-TGGGTTAAATCTATTTCC-CTACT-CCTAGGG
          1 AGATAAGA-TTCGCCGTCTTCAATCTA-TTCCACTACTGCTTAGGG

                        *        *    **       *         
       1495 AAGATAAGATTCACCGTCTTCGATCTGCTCCACTATTGCTTAGGG
          1 -AGATAAGATTCGCCGTCTTCAATCTATTCCACTACTGCTTAGGG

                         **    *   *                *    
       1540 AGATAAGA-TCGGTAGTCTCCAACCTATTCCACTACTGCTCAGGG
          1 AGATAAGATTC-GCCGTCTTCAATCTATTCCACTACTGCTTAGGG

             *            * *   *      *            * *   
       1584 AAATAAGACTT-G-TGGCTTAAATCTGTTTCC-CTACT-CCTGGGG
          1 AGATAAGA-TTCGCCGTCTTCAATCT-ATTCCACTACTGCTTAGGG

                                 *    **       *         
       1626 AAGATAAGATTCGCCGTCTTCGATCTGCTCCACTATTGCTTAGGG
          1 -AGATAAGATTCGCCGTCTTCAATCTATTCCACTACTGCTTAGGG

                     
       1671 AGATAAGAT
          1 AGATAAGAT

       1680 CTATAATCTT


Statistics
Matches: 285,  Mismatches: 86, Indels: 62
        0.66            0.20        0.14

Matches are distributed among these distances:
  41    1  0.00
  42   17  0.06
  43   73  0.26
  44  170  0.60
  45   21  0.07
  46    3  0.01

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


Consensus pattern (44 bp):   
AGATAAGATTCGCCGTCTTCAATCTATTCCACTACTGCTTAGGG

Found at i:1441 original size:131 final size:131

Alignment explanation


    Indices: 1194--1859  Score: 987
    Period size: 131  Copynumber: 5.1  Consensus size: 131

       1184 GTCAGGAAAG

                   *  *          **                                     *    
       1194 TAAGACTCGTCGCTTAAATCTGCTTCCCTACTCCTGGGGAAGATAAGATTCGCCGTCTTCAATCT
          1 TAAGACTAGTGGCTTAAATCTATTTCCCTACTCCTGGGGAAGATAAGATTCGCCGTCTTCGATCT

                     * *                              * * *                  
       1259 GCTCCACTACTACTTAGGGAGATAAGATCTGTAATCTTCAACATGTCCCACTGCTGACCAGGGAG
         66 GCTCCACTATTGCTTAGGGAGATAAGATCTGTAATCTTCAACCTATTCCACTGCTGACCAGGGAG

             
       1324 A
        131 A

                                               *                             
       1325 TAAGACTAGTGGCTTAAATCTATTTCCCTACTCCTAGGGAAGATAAGATTCGCCGTCTTCGATCT
          1 TAAGACTAGTGGCTTAAATCTATTTCCCTACTCCTGGGGAAGATAAGATTCGCCGTCTTCGATCT

            *                                *   *                           
       1390 ACTCCACTATTGCTTAGGGAGATAAGATCTGTAGTCTCCAACCTATTCCACTGCTG-CTCAGGGA
         66 GCTCCACTATTGCTTAGGGAGATAAGATCTGTAATCTTCAACCTATTCCACTGCTGAC-CAGGGA

            * 
       1454 AA
        130 GA

              *    *    *                      *               *             
       1456 TAGGACTTGTGGGTTAAATCTATTTCCCTACTCCTAGGGAAGATAAGATTCACCGTCTTCGATCT
          1 TAAGACTAGTGGCTTAAATCTATTTCCCTACTCCTGGGGAAGATAAGATTCGCCGTCTTCGATCT

                                         *   *   *              *            
       1521 GCTCCACTATTGCTTAGGGAGATAAGATCGGTAGTCTCCAACCTATTCCACTACTG-CTCAGGGA
         66 GCTCCACTATTGCTTAGGGAGATAAGATCTGTAATCTTCAACCTATTCCACTGCTGAC-CAGGGA

            * 
       1585 AA
        130 GA

                   *             *                                           
       1587 TAAGACTTGTGGCTTAAATCTGTTTCCCTACTCCTGGGGAAGATAAGATTCGCCGTCTTCGATCT
          1 TAAGACTAGTGGCTTAAATCTATTTCCCTACTCCTGGGGAAGATAAGATTCGCCGTCTTCGATCT

                                          *                                  
       1652 GCTCCACTATTGCTTAGGGAGATAAGATCTATAATCTTCAACCTA-TCCTACTGCTGACCAGGGA
         66 GCTCCACTATTGCTTAGGGAGATAAGATCTGTAATCTTCAACCTATTCC-ACTGCTGACCAGGGA

              
       1716 GA
        130 GA

              *                                                   *          
       1718 TAGGACTAGTGGCTTAAATCTATTTCCCTACTCCTGGGGAAGATAAGATTCGCCATCTTCGATCT
          1 TAAGACTAGTGGCTTAAATCTATTTCCCTACTCCTGGGGAAGATAAGATTCGCCGTCTTCGATCT

                                 *                        *                  
       1783 GCTCCACTATTGCTTAGGGAGCTAAGATCTGTAATCTTCAACCTATCCCACTGCTGACCAGGGAG
         66 GCTCCACTATTGCTTAGGGAGATAAGATCTGTAATCTTCAACCTATTCCACTGCTGACCAGGGAG

             
       1848 A
        131 A

              *        
       1849 TAGGACTAGTG
          1 TAAGACTAGTG

       1860 TCTTTGATCA


Statistics
Matches: 491,  Mismatches: 40, Indels: 8
        0.91            0.07        0.01

Matches are distributed among these distances:
 130    4  0.01
 131  484  0.99
 132    3  0.01

ACGTcount: A:0.26, C:0.24, G:0.20, T:0.29


Consensus pattern (131 bp):   
TAAGACTAGTGGCTTAAATCTATTTCCCTACTCCTGGGGAAGATAAGATTCGCCGTCTTCGATCT
GCTCCACTATTGCTTAGGGAGATAAGATCTGTAATCTTCAACCTATTCCACTGCTGACCAGGGAG
A

Done.