Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_1003 ID=scaffold_1003-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, 935

Length: 1559
ACGTcount: A:0.26, C:0.24, G:0.18, T:0.31


Found at i:238 original size:132 final size:132

Alignment explanation


    Indices: 1--1559  Score: 2269
    Period size: 132  Copynumber: 11.8  Consensus size: 132

                   *                 *                                       
          1 CCATCTTTGATCTGCTCCACTACTGATTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACT
          1 CCATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACT

               *                                      *                      
         66 ACTACTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCTACTGTATTGGGAAGATAAGATT
         66 ACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATT

              
        131 CA
        131 CA

                                     *                                       
        133 CCATCTTCGATCTGCTCCACTACTGATTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACT
          1 CCATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACT

              *                                           *                  
        198 ACGGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTATATTGGGAAGATAAGATT
         66 ACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATT

              
        263 CA
        131 CA

                *                              *                             
        265 CCATGTTCGATCTGCTCCACTACTGCTTAGGGTGATAGAATCTGCAATCTTCAACCTACTCCACT
          1 CCATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACT

                  *          *                     *                         
        330 ACTGCTGAGGGTGATAGTACTAATGGCTTAAATCTGCTTTTCCACTGTATTGGGAAGATAAGATT
         66 ACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATT

              
        395 CA
        131 CA

                                      *   *             *            *    ** 
        397 CCATCTTCGATCTGCAT-CACTACTGGTTATGGTGACAGAATCTACAATCTTCAACCGACTCTGC
          1 CCATCTTCGATCTGC-TCCACTACTGCTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCAC

                                              *                   *      *   
        461 TACTGCTTAGGGTGATAGGACTAATGGCTTAAATTTGCTTCTCCACTGTATTGGAAAGATAGGAT
         65 TACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGAT

               
        526 TCA
        130 TCA

                 *                       *              *      *    *        
        529 CCATCGTCGATCTGCTCCACTACTGCTTAAGGTGACAGAATCTGGAATCTTTAACCAACTCCACT
          1 CCATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACT

                   *   *   *              *  *        *                 *    
        594 ACTGCTTTGGGAGATTGGACTAATGGCTTACATTTGCTTCTCTACTGTATTGGGAAGATATGATT
         66 ACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATT

              
        659 CA
        131 CA

                *  *    *   *                                         **   * 
        661 CCATTTTTGATCCGCTGCACTACTGCTTAGGGTGACAGAATCTGCAATCTTCAACCTAGACCAGT
          1 CCATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACT

                   **              *                      *                  
        726 ACTGCTTTTGGTGATAGGACTAACGGCTTAAATCTGCTTCTCCACTATATTGGGAAGATAAGATT
         66 ACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATT

              
        791 CA
        131 CA

                   *               *                        *                
        793 CCATCTTGGATCTGCTCCACTACAGCTTAGGGTGACAGAATCTGCAATATTCAACCTACTCCACT
          1 CCATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACT

                                                                             
        858 ACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATT
         66 ACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATT

              
        923 CA
        131 CA

            *   *                                *       *                   
        925 TCATATTCGATCTGCTCCACTACT-CTTTAGGGTGACTGAATCTGTAATCTTCAACCTACTCCAC
          1 CCATCTTCGATCTGCTCCACTACTGC-TTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCAC

             *      *  **      *    *                  *                     
        989 TGCTGCTTTGGAAGATAGGTCTAACGGCTTAAATCTGCTTCTCTACTGTATTGGGAAGATAAGAT
         65 TACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGAT

               
       1054 TCA
        130 TCA

                         *     *                 *     *       *             
       1057 CCATCTTCGATCTACTCCATTACTGCTTAGGGTGACAAAATCTTCAATCTTTAACCTACTCCACT
          1 CCATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACT

                     * *   * *            *               * *   *       *    
       1122 ACTGCTTAGAGAGATTGAACTAATGGCTTACATCTGCTTCTCCACTATCTTGAGAAGATATGATT
         66 ACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATT

              
       1187 CA
        131 CA

                       *    *   *                                    *       
       1189 CCATCTTCGATTTGCTGCACAACTGCTTAGGGTGACAGAATCTGCAATCTTCAACCTCCTCCACT
          1 CCATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACT

                             *       *                                     * 
       1254 ACTGCTTAGGGTGATAGCACTAATGACTTAAATCTGCTTCTCCACTGTATTGGGAAGATAA-AAT
         66 ACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATT

              
       1318 CA
        131 CA

            *   *   *                                   *                    
       1320 TCATATTCAATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGTAATCTTCAACCTACTCCACT
          1 CCATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACT

                                       *       *       *  *                  
       1385 ACTGCTTAGGGTGATAGGACTAATGGCCTAAATCTACTTCTCCGCTATATTGGGAAGATAAGATT
         66 ACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATT

              
       1450 CA
        131 CA

                                *                                          * 
       1452 CCATCTTCGATCTGCTCCACAACTGCTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCAGT
          1 CCATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACT

                           *                           
       1517 ACTGCTTAGGGTGATTGGACTAATGGCTTAAATCTGCTTCTCC
         66 ACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCC


Statistics
Matches: 1264,  Mismatches: 158, Indels: 10
        0.88            0.11        0.01

Matches are distributed among these distances:
 131  118  0.09
 132  1144  0.91
 133    2  0.00

ACGTcount: A:0.26, C:0.24, G:0.18, T:0.31


Consensus pattern (132 bp):   
CCATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACT
ACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATT
CA

Found at i:342 original size:44 final size:44

Alignment explanation


    Indices: 15--346  Score: 175
    Period size: 44  Copynumber: 7.5  Consensus size: 44

          5 CTTTGATCTG

                       *         *                      
         15 CTCCACTACTGATTAGGGTGACAGAATCTGCAATCTTCAACCTA
          1 CTCCACTACTGCTTAGGGTGATAGAATCTGCAATCTTCAACCTA

                      *             *              *  *  *
         59 CTCCACTACTACTTAGGGTGATAGGA-CT--AATGGCTTAAATCTG
          1 CTCCACTACTGCTTAGGGTGATAGAATCTGCAAT--CTTCAACCTA

              * *          *    *       *   * *      * *  *
        102 CTTCTCTACTG-TATTGGGAAGATAAGATTC-ACCATCTTCGATCTG
          1 CTCCACTACTGCT-TAGGG-TGAT-AGAATCTGCAATCTTCAACCTA

                       *         *                      
        147 CTCCACTACTGATTAGGGTGACAGAATCTGCAATCTTCAACCTA
          1 CTCCACTACTGCTTAGGGTGATAGAATCTGCAATCTTCAACCTA

                     *              *              *        *
        191 CTCCACTACGGCTTAGGGTGATAGGA-CT--AATGGCTTAAATCTGCTT
          1 CTCCACTACTGCTTAGGGTGATAGAATCTGCAAT--CTTCAA-C--CTA

                       *       *       *   * *  *   * *  *
        237 CTCCACTA-T-ATT-GGGAAGATAAGATTC-ACCATGTTCGATCTG
          1 CTCCACTACTGCTTAGGG-TGAT-AGAATCTGCAATCTTCAACCTA

                                                        
        279 CTCCACTACTGCTTAGGGTGATAGAATCTGCAATCTTCAACCTA
          1 CTCCACTACTGCTTAGGGTGATAGAATCTGCAATCTTCAACCTA

                         *          
        323 CTCCACTACTGCTGAGGGTGATAG
          1 CTCCACTACTGCTTAGGGTGATAG

        347 TACTAATGGC


Statistics
Matches: 209,  Mismatches: 55, Indels: 48
        0.67            0.18        0.15

Matches are distributed among these distances:
  41    6  0.03
  42   11  0.05
  43   42  0.20
  44  102  0.49
  45   31  0.15
  46   13  0.06
  47    4  0.02

ACGTcount: A:0.27, C:0.24, G:0.19, T:0.30


Consensus pattern (44 bp):   
CTCCACTACTGCTTAGGGTGATAGAATCTGCAATCTTCAACCTA

Found at i:1259 original size:44 final size:43

Alignment explanation


    Indices: 1201--1530  Score: 147
    Period size: 44  Copynumber: 7.5  Consensus size: 43

       1191 ATCTTCGATT

                *   *                                   
       1201 TGCTGCACAACTGCTTAGGGTGACAGAATCTGCAATCTTCAACC
          1 TGCTCCACTACTGCTTAGGGTGACAGAATCT-CAATCTTCAACC

             *                     *  *             *  * 
       1245 TCCTCCACTACTGCTTAGGGTGATAGCA-CT-AATGACTTAAATC
          1 TGCTCCACTACTGCTTAGGGTGACAGAATCTCAAT--CTTCAACC

                * * *        *    *  * *          *     * 
       1288 TGCTTCTCCACTG-TATTGGGAAGATAAAATCATC-ATATTCAATC
          1 TGCTCCACTACTGCT-TAGGG-TGACAGAATC-TCAATCTTCAACC

                                            *           
       1332 TGCTCCACTACTGCTTAGGGTGACAGAATCTGTAATCTTCAACC
          1 TGCTCCACTACTGCTTAGGGTGACAGAATCT-CAATCTTCAACC

             *                     *  *           * *       
       1376 TACTCCACTACTGCTTAGGGTGATAGGA-CT-AATGGCCTAAATCTAC
          1 TGCTCCACTACTGCTTAGGGTGACAGAATCTCAAT--CTTCAA-C--C

             *    *      *       *   *   *  * *      * * 
       1422 TTCTCCGCTA-T-ATT-GGGAAGATAAGATTCACCATCTTCGATC
          1 TGCTCCACTACTGCTTAGGG-TGA-CAGAATCTCAATCTTCAACC

                    *                                   
       1464 TGCTCCACAACTGCTTAGGGTGACAGAATCTGCAATCTTCAACC
          1 TGCTCCACTACTGCTTAGGGTGACAGAATCT-CAATCTTCAACC

             *     *               
       1508 TACTCCAGTACTGCTTAGGGTGA
          1 TGCTCCACTACTGCTTAGGGTGA

       1531 TTGGACTAAT


Statistics
Matches: 204,  Mismatches: 59, Indels: 46
        0.66            0.19        0.15

Matches are distributed among these distances:
  41    6  0.03
  42   10  0.05
  43   43  0.21
  44  119  0.58
  45   11  0.05
  46   13  0.06
  47    2  0.01

ACGTcount: A:0.27, C:0.25, G:0.18, T:0.29


Consensus pattern (43 bp):   
TGCTCCACTACTGCTTAGGGTGACAGAATCTCAATCTTCAACC
Done.