Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_87 ID=scaffold_87-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: 15041
ACGTcount: A:0.29, C:0.21, G:0.17, T:0.32


Found at i:2222 original size:129 final size:129

Alignment explanation


    Indices: 2063--2722  Score: 1108
    Period size: 129  Copynumber: 5.1  Consensus size: 129

       2053 ACTACTGCTT

                        *      *                                             
       2063 AGGGAGATAAGATCTGATATGATCCACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTA
          1 AGGGAGATAAGACCTGATACGATCCACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTA

                        *           *                                       
       2128 ATCCGCTCCACTATAATCTCAGGGTGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTC
         66 ATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTC

             *        *             *                                        
       2192 AAGGAGATAATACCTGATACGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTA
          1 AGGGAGATAAGACCTGATACGATCCACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTA

                                                            *               
       2257 ATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTACTCCGCTGTAATCTC
         66 ATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTC

                         *          *        *                               
       2321 AGGGAGATAAGACTTGATACGATCTACTCTACTATAACTTCAGAGAGATAAGATCCTTTATTTTA
          1 AGGGAGATAAGACCTGATACGATCCACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTA

                *       *                                                   
       2386 ATCCACTCCACTATAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTC
         66 ATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTC

                                               *                             
       2450 AGGGAGATAAGACCTGATACGATCCACTCTACTGTCACTTCAGAGAGATAAGATCCTTTATTTTA
          1 AGGGAGATAAGACCTGATACGATCCACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTA

                                         *                          *       
       2515 ATCCGCTCCACTGTAATCTCA-GG-GATAAGATTACTAGCTTCAATCTGCTCCGCTATAATCTC
         66 ATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTC

              *                                                              
       2577 AGAGAGATAAGACCTGATACGATCCACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTA
          1 AGGGAGATAAGACCTGATACGATCCACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTA

                *     *           *                                        *
       2642 ATCCACTCCATTGTAATCTCAGAGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTT
         66 ATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTC

                        *    
       2706 AGGGAGATAAGATCTGA
          1 AGGGAGATAAGACCTGA

       2723 GATTCTTTGA


Statistics
Matches: 496,  Mismatches: 33, Indels: 4
        0.93            0.06        0.01

Matches are distributed among these distances:
 127  119  0.24
 128    3  0.01
 129  374  0.75

ACGTcount: A:0.30, C:0.22, G:0.17, T:0.31


Consensus pattern (129 bp):   
AGGGAGATAAGACCTGATACGATCCACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTA
ATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTC

Found at i:2272 original size:44 final size:44

Alignment explanation


    Indices: 2084--2670  Score: 294
    Period size: 44  Copynumber: 13.7  Consensus size: 44

       2074 ATCTGATATG

                    *                                  * 
       2084 ATCCACTCTACTGTAA-CTTCAGAGAGATAAGATCCTTTATTTTA
          1 ATCCACTCCACTGTAATC-TCAGAGAGATAAGATCCTTTATTTCA

                *       *         * *    *       *   *    
       2128 ATCCGCTCCACTATAATCTCAGGGTGATAGGAT--TACTAGCTTCA
          1 ATCCACTCCACTGTAATCTCAGAGAGATAAGATCCT-TTA-TTTCA

               **    *                     *      *   * *
       2172 ATCTGCTCCGCTGTAATCTCA-AGGAGATAATA-CC-TGA-TACG
          1 ATCCACTCCACTGTAATCTCAGA-GAGATAAGATCCTTTATTTCA

               *    *                                  * 
       2213 ATCTACTCTACTGTAA-CTTCAGAGAGATAAGATCCTTTATTTTA
          1 ATCCACTCCACTGTAATC-TCAGAGAGATAAGATCCTTTATTTCA

                *                 *      *       *   *    
       2257 ATCCGCTCCACTGTAATCTCAGGGAGATAGGAT--TACTAGCTTCA
          1 ATCCACTCCACTGTAATCTCAGAGAGATAAGATCCT-TTA-TTTCA

               *     *            *              *   * *
       2301 ATCTACTCCGCTGTAATCTCAGGGAGATAAGA--CTTGA-TACG
          1 ATCCACTCCACTGTAATCTCAGAGAGATAAGATCCTTTATTTCA

               *    *   *                              * 
       2342 ATCTACTCTACTATAA-CTTCAGAGAGATAAGATCCTTTATTTTA
          1 ATCCACTCCACTGTAATC-TCAGAGAGATAAGATCCTTTATTTCA

                        *         *      *       *   *    
       2386 ATCCACTCCACTATAATCTCAGGGAGATAGGAT--TACTAGCTTCA
          1 ATCCACTCCACTGTAATCTCAGAGAGATAAGATCCT-TTA-TTTCA

               **    *            *              *   * *
       2430 ATCTGCTCCGCTGTAATCTCAGGGAGATAAGA-CC-TGA-TACG
          1 ATCCACTCCACTGTAATCTCAGAGAGATAAGATCCTTTATTTCA

                    *     *                            * 
       2471 ATCCACTCTACTGTCA-CTTCAGAGAGATAAGATCCTTTATTTTA
          1 ATCCACTCCACTGTAATC-TCAGAGAGATAAGATCCTTTATTTCA

                *                                *   *    
       2515 ATCCGCTCCACTGTAATCTCAG-G-GATAAGAT--TACTAGCTTCA
          1 ATCCACTCCACTGTAATCTCAGAGAGATAAGATCCT-TTA-TTTCA

               **    *  *                        *   * *
       2557 ATCTGCTCCGCTATAATCTCAGAGAGATAAGA-CC-TGA-TACG
          1 ATCCACTCCACTGTAATCTCAGAGAGATAAGATCCTTTATTTCA

                    *                                  * 
       2598 ATCCACTCTACTGTAA-CTTCAGAGAGATAAGATCCTTTATTTTA
          1 ATCCACTCCACTGTAATC-TCAGAGAGATAAGATCCTTTATTTCA

                      *                  
       2642 ATCCACTCCATTGTAATCTCAGAGAGATA
          1 ATCCACTCCACTGTAATCTCAGAGAGATA

       2671 GGATTACTAG


Statistics
Matches: 401,  Mismatches: 102, Indels: 80
        0.69            0.17        0.14

Matches are distributed among these distances:
  40    5  0.01
  41  109  0.27
  42   40  0.10
  43   22  0.05
  44  220  0.55
  45    5  0.01

ACGTcount: A:0.30, C:0.23, G:0.16, T:0.31


Consensus pattern (44 bp):   
ATCCACTCCACTGTAATCTCAGAGAGATAAGATCCTTTATTTCA

Done.