Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_1053 ID=scaffold_1053-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, 744

Length: 1241
ACGTcount: A:0.32, C:0.18, G:0.24, T:0.26


Found at i:245 original size:132 final size:132

Alignment explanation


    Indices: 8--1241  Score: 1943
    Period size: 132  Copynumber: 9.3  Consensus size: 132

          1 CAGAAGG

                                                               * *           
          8 TGAAGATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATAGTAAATCTTATCT
          1 TGAAGATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCAAATCTTATCT

                          *           *    *                        *        
         73 TTCCAAGATAGTGGAAAGCAGATTTAGGCCAAAAAGCCTTGTCTCTCTGAGCAGCATCGGAGATG
         66 TTCCAAGATAGTGGGAAGCAGATTTAAGCCACAAAGCCTTGTCTCTCTGAGCAGCAGCGGAGATG

              
        138 GT
        131 GT

                                                                           * 
        140 TGAAGATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCAAATCTTATAT
          1 TGAAGATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCAAATCTTATCT

                                *      *                       *           * 
        205 TTCCAAGATAGTGGGAAGCAAATTTAACCCACAAAGCCTTGTCTCTCTGAGTAGCAGCGGAGAAG
         66 TTCCAAGATAGTGGGAAGCAGATTTAAGCCACAAAGCCTTGTCTCTCTGAGCAGCAGCGGAGATG

              
        270 GT
        131 GT

                                   *  *  *                    * *           *
        272 TGAAGATTGTAGATCTTATCTCCATATGCCGTAGTGGAGCAGATCAAAGACGACAAATCTTATCA
          1 TGAAGATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCAAATCTTATCT

                                                               *       *   * 
        337 TTCCAAGATAGTGGGAAGCAGATTTAAGCCACAAAGCCTTGTCTCTCTGAGTAGCAGCGCAGAAG
         66 TTCCAAGATAGTGGGAAGCAGATTTAAGCCACAAAGCCTTGTCTCTCTGAGCAGCAGCGGAGATG

              
        402 GT
        131 GT

                                                                 *           
        404 TGAAGATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGTAAATCTTATCT
          1 TGAAGATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCAAATCTTATCT

                          *                 *                          *     
        469 TTCCAAGATAGTGGAAAGCAGATTTAAGCCAAAAAAGCCTTGTCTCTCTGAGCAGCAGCAGAGAT
         66 TTCCAAGATAGTGGGAAGCAGATTTAAGCC-ACAAAGCCTTGTCTCTCTGAGCAGCAGCGGAGAT

               
        534 GGT
        130 GGT

                                                  *              *           
        537 TGAAGATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAACAGATCAAAGATGGTAAATCTTATCT
          1 TGAAGATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCAAATCTTATCT

                          *                *     *                           
        602 TTCCAAGATAGTGGAAAGCAGATTTAAGCCAAAAAGCTTTGTCTCTCTGAGCAGCAGCGGAGATG
         66 TTCCAAGATAGTGGGAAGCAGATTTAAGCCACAAAGCCTTGTCTCTCTGAGCAGCAGCGGAGATG

              
        667 GT
        131 GT

                                                                             
        669 TGAAGATTGTAGATCTTATCTCCCTAAGGCAGTAGTGGAGCAGATCAAAGATGGCAAATTCTTAT
          1 TGAAGATTGTAGATCTTATCTCCCTAA-GCAGTAGTGGAGCAGATCAAAGATGGCAAA-TCTTAT

                                              *            *        *        
        734 CTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTGAGCAGTAGCGGAG-
         64 CTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACAAAGCCTTGTCTCTCTGAGCAGCAGCGGAGA

                 
        798 TAGGT
        129 T-GGT

                                                                             
        803 TGAAGATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCAAATCTTATCT
          1 TGAAGATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCAAATCTTATCT

                                *                           *  *     *     * 
        868 TTCCAAGATAGTGGGAAGCAAATTTAAGCCACAAAGCCTTGTCTCTCTAAGTAGCAGTGGAGAAG
         66 TTCCAAGATAGTGGGAAGCAGATTTAAGCCACAAAGCCTTGTCTCTCTGAGCAGCAGCGGAGATG

              
        933 GT
        131 GT

                       *       *               *                             
        935 TGAAGATTGTATATCTTATATCCCTAAGCAGTAGTAGAGCAGATCAAAGATGGCAAATCTTATCT
          1 TGAAGATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCAAATCTTATCT

                                                            *  *     *     * 
       1000 TTCCAAGATAGTGGGAAGCAGATTTAAGCCACAAAGCCTTGTCTCTCTAAGTAGCAGTGGAGAAG
         66 TTCCAAGATAGTGGGAAGCAGATTTAAGCCACAAAGCCTTGTCTCTCTGAGCAGCAGCGGAGATG

              
       1065 GT
        131 GT

                       *       *               *                             
       1067 TGAA-ATTGTATATCTTATATCCCTAAGCAGTAGTAGAGCAGATCAAAGATGGCAAATCTTATCT
          1 TGAAGATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCAAATCTTATCT

                                            *            *        * *        
       1131 TTCCAAGATAGTGGGAAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTGAGCAGTAACGGAG-TA
         66 TTCCAAGATAGTGGGAAGCAGATTTAAGCCACAAAGCCTTGTCTCTCTGAGCAGCAGCGGAGAT-

               
       1195 GGT
        130 GGT

                                                        
       1198 TGAAGATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGAT
          1 TGAAGATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGAT


Statistics
Matches: 1027,  Mismatches: 68, Indels: 14
        0.93            0.06        0.01

Matches are distributed among these distances:
 131  122  0.12
 132  626  0.61
 133  185  0.18
 134   94  0.09

ACGTcount: A:0.32, C:0.18, G:0.24, T:0.27


Consensus pattern (132 bp):   
TGAAGATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCAAATCTTATCT
TTCCAAGATAGTGGGAAGCAGATTTAAGCCACAAAGCCTTGTCTCTCTGAGCAGCAGCGGAGATG
GT

Found at i:464 original size:44 final size:44

Alignment explanation


    Indices: 406--1241  Score: 199
    Period size: 44  Copynumber: 19.0  Consensus size: 44

        396 CAGAAGGTTG

                 *   *                                * 
        406 AAGATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCA
          1 AAGATGGTAAATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTA

                                *                         *
        450 AAGATGGTAAATCTTATCTTTCC-AAG-A-TAGTGGAAAGCAGATTT
          1 AAGATGGTAAATCTTATC-TCCCTAAGCAGTAGTGG--AGCAGATTA

               *****    *   *    *  *     *  **       *  *
        494 AAGCCAAAAAAGCCTTGTCTCTCTGAGCAGCAGCAGAG-ATGGTTG
          1 AAGATGGTAAA-TCTTATCTCCCTAAGCAGTAGTGGAGCA-GATTA

                 *   *                          *     * 
        539 AAGATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAACAGATCA
          1 AAGATGGTAAATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTA

                                *                         *
        583 AAGATGGTAAATCTTATCTTTCC-AAG-A-TAGTGGAAAGCAGATTT
          1 AAGATGGTAAATCTTATC-TCCCTAAGCAGTAGTGG--AGCAGATTA

                ****   *    *    *  *     *  *        *  *
        627 AAG-CCAAAAAGCTTTGTCTCTCTGAGCAGCAGCGGAG-ATGGTTG
          1 AAGATGGTAAATC-TTATCTCCCTAAGCAGTAGTGGAGCA-GATTA

                 *   *                                 * 
        671 AAGATTGTAGATCTTATCTCCCTAAGGCAGTAGTGGAGCAGATCA
          1 AAGATGGTAAATCTTATCTCCCTAA-GCAGTAGTGGAGCAGATTA

                   *             *                         *
        716 AAGATGGCAAATTCTTATCTTTCC-AAG-A-TAGTGGGAAGCAGATTT
          1 AAGATGGTAAA-TCTTATC-TCCCTAAGCAGTAGT-GG-AGCAGATTA

               *****  **   *       *        *    *  *  *
        761 AAGCCACCAAGCCTTGTCTCCCTGAGCAGTAGCGGAGTAGGTTG
          1 AAGATGGTAAATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTA

                 *   *                                * 
        805 AAGATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCA
          1 AAGATGGTAAATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTA

                   *            *                     *   *
        849 AAGATGGCAAATCTTATCTTTCC-AAG-A-TAGTGGGAAGCAAATTT
          1 AAGATGGTAAATCTTATC-TCCCTAAGCAGTAGT-GG-AGCAGATTA

                ****    *   *    *     *  *       *  *  *
        893 AAG-CCACAAAGCCTTGTCTCTCTAAGTAGCAGTGGAGAAGGTTG
          1 AAGATGGTAAA-TCTTATCTCCCTAAGCAGTAGTGGAGCAGATTA

                 *   *       *               *        * 
        937 AAGATTGTATATCTTATATCCCTAAGCAGTAGTAGAGCAGATCA
          1 AAGATGGTAAATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTA

                   *            *                         *
        981 AAGATGGCAAATCTTATCTTTCC-AAG-A-TAGTGGGAAGCAGATTT
          1 AAGATGGTAAATCTTATC-TCCCTAAGCAGTAGT-GG-AGCAGATTA

                ****    *   *    *     *  *       *  *  *
       1025 AAG-CCACAAAGCCTTGTCTCTCTAAGTAGCAGTGGAGAAGGTTG
          1 AAGATGGTAAA-TCTTATCTCCCTAAGCAGTAGTGGAGCAGATTA

                 *   *       *               *        * 
       1069 AA-ATTGTATATCTTATATCCCTAAGCAGTAGTAGAGCAGATCA
          1 AAGATGGTAAATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTA

                   *            *                         *
       1112 AAGATGGCAAATCTTATCTTTCC-AAG-A-TAGTGGGAAGCAGATTT
          1 AAGATGGTAAATCTTATC-TCCCTAAGCAGTAGT-GG-AGCAGATTA

               *****  **   *       *       **    *  *  *
       1156 AAGCCACCAAGCCTTGTCTCCCTGAGCAGTAACGGAGTAGGTTG
          1 AAGATGGTAAATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTA

                 *   *                                
       1200 AAGATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGAT
          1 AAGATGGTAAATCTTATCTCCCTAAGCAGTAGTGGAGCAGAT


Statistics
Matches: 532,  Mismatches: 210, Indels: 100
        0.63            0.25        0.12

Matches are distributed among these distances:
  42   24  0.05
  43   62  0.12
  44  329  0.62
  45   85  0.16
  46   26  0.05
  47    6  0.01

ACGTcount: A:0.32, C:0.18, G:0.23, T:0.27


Consensus pattern (44 bp):   
AAGATGGTAAATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTA
Done.