Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_315 ID=scaffold_315-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: 8289
ACGTcount: A:0.25, C:0.22, G:0.24, T:0.28


Found at i:5160 original size:340 final size:337

Alignment explanation


    Indices: 4428--5337  Score: 1030
    Period size: 340  Copynumber: 2.7  Consensus size: 337

       4418 CAAACGCACA

                                                          *                  
       4428 GTTCCAATTCTCGGCGAGACTTCC-GAAGCCGAGAAACAGTCAAAATCTGGTCAAAAACGAGCTT
          1 GTTCC-ATTCTCGGCGAGACTTCCTG-AGCCGAGAAACAGTCAAAAACTGGTCAAAAACGAGCTT

                     *          *      **        *            *        *     
       4492 TTCTGACCACTTTTTGACTCGTTCTCTAAAGCGTTTTAAGCGGATAGCTCTAAGCGAGGTACTCG
         64 TTCTGACCAATTTTTGACTCTTTCTCTGGAGCG-TTTCAGCGGATAGCTCAAAGCGAGGGACTCG

                                         *         *              ** *  *    
       4557 CGGAGCTTTTCCGACTGGAAAATCGCACTGAGCGGGTCAATTCCAAGCGAG-CTTCCCTGGTTTC
        128 CGGAGCTTTTCCGACTGGAAAATCGCACTCAGCGGGTCATTTCCAAGCG-GCCTAACTTGCTTTC

               * *   *            **      * *       *    *                   
       4621 GGCCCAATCCGCGAACA-TTCGCCTTTGACCCGAAAAATTTAGTCGATGTAATCCATATGTCGAT
        192 GGCTCGATCGGCGAA-ATTTCGATTTTGACGCTAAAAATTCAGTCAATGTAATCCA-ATGTCGAT

               * * **           *      **   *    *            *  *           
       4685 TTTTCTCTTTTTTGGACTGAGAAAAAATTTCAGGATTTCAGTCGCATCCTTCGTATTTGGAGGCG
        255 TTTACGCGATTTTGGACTGAAAAAAAAAATCAAGATTGCAGTCGCATCCTACGAATTTGGAGGCG

                         *    
       4750 TAGAATCGATTCCGCACG
        320 TAGAATCGATTCCACACG

              *    *             *          *      *  * *                    
       4768 GTCCCGACTCAT-GGCGAGACATCCTGAGCCGGGATAA-GGTTATAAACTGGTCAAAAACGAG-T
          1 GTTCC-ATTC-TCGGCGAGACTTCCTGAGCCGAGA-AACAGTCAAAAACTGGTCAAAAACGAGCT

                   *                                        *               *
       4830 TTGTCTGCCCAATTTTTGACTCTTTCTCTGGAGCGTTTCAGCGGATAGTTCAAAGCGAGGGACTT
         63 TT-TCTGACCAATTTTTGACTCTTTCTCTGGAGCGTTTCAGCGGATAGCTCAAAGCGAGGGACTC

             *                                                      *        
       4895 GTGGAGCTTTTCCGACTGGAAAATCGCACTCAGCGGGTCATTTCCAAGCGGCCTAAGTTGCTTTC
        127 GCGGAGCTTTTCCGACTGGAAAATCGCACTCAGCGGGTCATTTCCAAGCGGCCTAACTTGCTTTC

                       *                    *       *  *            *        
       4960 GGCTCGATCGGTGAAATTTCGATTTTGACGCTTAAAATTCGGTTAATGTAA-CGC-CTGTCGATT
        192 GGCTCGATCGGCGAAATTTCGATTTTGACGCTAAAAATTCAGTCAATGTAATC-CAATGTCGATT

                                                                             
       5023 TTACGCGATTTTGGACTGATAAAAAAAAAATCAAGATTGCAGTCGCAT-CTAACGAATTTTGGAG
        256 TTACGCGATTTTGGACTG--AAAAAAAAAATCAAGATTGCAGTCGCATCCT-ACGAA-TTTGGAG

                                 
       5087 GCGTAGAATCGATTCCACACG
        317 GCGTAGAATCGATTCCACACG

                                        *                          *      *  
       5108 GTTCCATTTCTCGGCGAGACTTCCTGAGTCGAGAAACAGTCAAAAACTGGTCAAACACGAGCATT
          1 GTTCCA-TTCTCGGCGAGACTTCCTGAGCCGAGAAACAGTCAAAAACTGGTCAAAAACGAGCTTT

              *                                                   *          
       5173 TCAGACCAATTTTTGACTCTTTCTCTGGAGCGTGTTCAGCGGATAGCTCGAAA-TGAGGGACTCG
         65 TCTGACCAATTTTTGACTCTTTCTCTGGAGCGT-TTCAGCGGATAGCTC-AAAGCGAGGGACTCG

                      *              *      *                  *             
       5237 CGGAGCTTTTTCGACTGGAAAATCGTACTCAGTGGGTCATTTCCAAGCGGCATAACTTGCTTTCG
        128 CGGAGCTTTTCCGACTGGAAAATCGCACTCAGCGGGTCATTTCCAAGCGGCCTAACTTGCTTTCG

                          *                     
       5302 GCTCGATCGGCGAACTTTCGATTTTGACGCTAAAAA
        193 GCTCGATCGGCGAAATTTCGATTTTGACGCTAAAAA

       5338 CCTGCGGAAT


Statistics
Matches: 476,  Mismatches: 77, Indels: 33
        0.81            0.13        0.06

Matches are distributed among these distances:
 337   22  0.05
 338    5  0.01
 339  150  0.32
 340  175  0.37
 341  121  0.25
 342    3  0.01

ACGTcount: A:0.25, C:0.23, G:0.23, T:0.28


Consensus pattern (337 bp):   
GTTCCATTCTCGGCGAGACTTCCTGAGCCGAGAAACAGTCAAAAACTGGTCAAAAACGAGCTTTT
CTGACCAATTTTTGACTCTTTCTCTGGAGCGTTTCAGCGGATAGCTCAAAGCGAGGGACTCGCGG
AGCTTTTCCGACTGGAAAATCGCACTCAGCGGGTCATTTCCAAGCGGCCTAACTTGCTTTCGGCT
CGATCGGCGAAATTTCGATTTTGACGCTAAAAATTCAGTCAATGTAATCCAATGTCGATTTTACG
CGATTTTGGACTGAAAAAAAAAATCAAGATTGCAGTCGCATCCTACGAATTTGGAGGCGTAGAAT
CGATTCCACACG

Found at i:7049 original size:36 final size:36

Alignment explanation


    Indices: 7000--8289  Score: 1904
    Period size: 36  Copynumber: 35.6  Consensus size: 36

       6990 CTCCTCAGCA

                    *                           
       7000 CCTTAGGGCTCAGGGGGCTGACCCCCGCGTTCGGCT
          1 CCTTAGGGTTCAGGGGGCTGACCCCCGCGTTCGGCT

                *            *                  
       7036 CCTTGGGGTTCAGGGGGATGACCCCCGCGTTCGGCT
          1 CCTTAGGGTTCAGGGGGCTGACCCCCGCGTTCGGCT

                *            *         *        
       7072 CCTTGGGGTTCAGGGGGATGACCCCCGTGTTCGGCT
          1 CCTTAGGGTTCAGGGGGCTGACCCCCGCGTTCGGCT

                *                             * 
       7108 CCTTGGGGTTCAGGGGGCTGACCCCCGCGTTCGGAT
          1 CCTTAGGGTTCAGGGGGCTGACCCCCGCGTTCGGCT

                *            *                  
       7144 CCTTGGGGTTCAGGGGGATGACCCCCGCG-TCGGCT
          1 CCTTAGGGTTCAGGGGGCTGACCCCCGCGTTCGGCT

                *            *         *    *   
       7179 CCTTGGGGTTCAGGGGGATGA-CCCCGTGTTCAGCT
          1 CCTTAGGGTTCAGGGGGCTGACCCCCGCGTTCGGCT

            *   *                             * 
       7214 TCTTGGGGTTCAGGGGGCTGACCCCCGCGTTCGGAT
          1 CCTTAGGGTTCAGGGGGCTGACCCCCGCGTTCGGCT

                 *                               
       7250 CCTTACGGTTCAGGGGGCTGACCCCCCGCGTTCGGCT
          1 CCTTAGGGTTCAGGGGGCTGA-CCCCCGCGTTCGGCT

               *                               *      
       7287 CCTAAGGGTTCAGGGGGCTGAGGCTGACCCCCGCGGTCGGCT
          1 CCTTAGGGTTCA---GG--G-GGCTGACCCCCGCGTTCGGCT

                                          *      
       7329 CCTTAGGGTTCAGGGGGCTGACCCCCCGCGGTCGGCT
          1 CCTTAGGGTTCAGGGGGCTGA-CCCCCGCGTTCGGCT

                                          *      
       7366 CCTTAGGGTTCAGGGGGCTGACCCCCCGCGGTCGGCT
          1 CCTTAGGGTTCAGGGGGCTGA-CCCCCGCGTTCGGCT

                 *                              
       7403 CCTTACGGTTCAGGGGGCTGACCCCCGCGTTCGGCT
          1 CCTTAGGGTTCAGGGGGCTGACCCCCGCGTTCGGCT

                                                 
       7439 CCTTAGGGTTCAGGGGGCTGACCCCCCGCGTTCGGCT
          1 CCTTAGGGTTCAGGGGGCTGA-CCCCCGCGTTCGGCT

                *                       *        
       7476 -CTAAAGGGTTCAGGGGGCTGACCCCCGTGTTCGGCT
          1 CCT-TAGGGTTCAGGGGGCTGACCCCCGCGTTCGGCT

            *   *                           *     
       7512 TCTTGGGGTTCAGGGGGCTGACCCCCCGCGCTCCGGCT
          1 CCTTAGGGTTCAGGGGGCTGA-CCCCCGCG-TTCGGCT

                *            * *                
       7550 CCTTGGGGTTCAGGGGGATCACCCCCGCGTTCGGCT
          1 CCTTAGGGTTCAGGGGGCTGACCCCCGCGTTCGGCT

                             *              *   
       7586 CCTTAGGGTTCAGGGGGATGACCCCCGCGTTCCGCT
          1 CCTTAGGGTTCAGGGGGCTGACCCCCGCGTTCGGCT

                               *         *      
       7622 CCTTAGGGTTCAGGGGGCTCACCCCCGCGGTCGGCT
          1 CCTTAGGGTTCAGGGGGCTGACCCCCGCGTTCGGCT

                    *                    *      
       7658 CCTTAGGGATCAGGGGGCTGACCCCCGCGGTCGGCT
          1 CCTTAGGGTTCAGGGGGCTGACCCCCGCGTTCGGCT

                               *                
       7694 CCTTAGGGTTCAGGGGGCTTACCCCCGCGTTCGGCT
          1 CCTTAGGGTTCAGGGGGCTGACCCCCGCGTTCGGCT

               *                          *     
       7730 CCTCAGGGTTCAGGGGGCTGACCCCCGCGTCCGGCT
          1 CCTTAGGGTTCAGGGGGCTGACCCCCGCGTTCGGCT

               *            *            *      
       7766 CCTCAGGGTTCAGGGGCCTGACCCCCGCGGTCGGCT
          1 CCTTAGGGTTCAGGGGGCTGACCCCCGCGTTCGGCT

                 *                              
       7802 CCTTACGGTTCAGGGGGCTGACCCCCGCGTTCGGCT
          1 CCTTAGGGTTCAGGGGGCTGACCCCCGCGTTCGGCT

                                                
       7838 CCTTAGGGTTCAGGGGGCTGACCCCCGCGTTCGGCT
          1 CCTTAGGGTTCAGGGGGCTGACCCCCGCGTTCGGCT

              **                       *        
       7874 CCAAAGGGTTCAGGGGGCTGACCCCCGTGTTCGGCT
          1 CCTTAGGGTTCAGGGGGCTGACCCCCGCGTTCGGCT

            *   *                               
       7910 TCTTGGGGTTCAGGGGGCTGACCCCCGCGTTCGGCT
          1 CCTTAGGGTTCAGGGGGCTGACCCCCGCGTTCGGCT

                *            *                  
       7946 CCTTGGGGTTCAGGGGGATGACCCCCGCGTTCGGCT
          1 CCTTAGGGTTCAGGGGGCTGACCCCCGCGTTCGGCT

                             *            *     
       7982 CCTTAGGGTTCAGGGGGATGACCCCCGCGTCCGGCT
          1 CCTTAGGGTTCAGGGGGCTGACCCCCGCGTTCGGCT

                                                
       8018 CCTTAGGGTTCAGGGGGCTGACCCCCGCGTTCGGCT
          1 CCTTAGGGTTCAGGGGGCTGACCCCCGCGTTCGGCT

                                                
       8054 CCTTAGGGTTCAGGGGGCTGACCCCCGCGTTCGGCT
          1 CCTTAGGGTTCAGGGGGCTGACCCCCGCGTTCGGCT

                                                
       8090 CCTTAGGGTTCAGGGGGCTGACCCCCGCGTTCGGCT
          1 CCTTAGGGTTCAGGGGGCTGACCCCCGCGTTCGGCT

                                                
       8126 CCTTAGGGTTCAGGGGGCTGACCCCCGCGTTCGGCT
          1 CCTTAGGGTTCAGGGGGCTGACCCCCGCGTTCGGCT

                                  *       *     
       8162 CCTTAGGGTTCAGGGGGCTGA-ACCCGCGTCCGGCT
          1 CCTTAGGGTTCAGGGGGCTGACCCCCGCGTTCGGCT

                                         *      
       8197 CCTTAGGGTTCAGGGGGCTGACCCCCGCGGTCGGCT
          1 CCTTAGGGTTCAGGGGGCTGACCCCCGCGTTCGGCT

                                         *      
       8233 CCTTAGGGTTCAGGGGGCTGACCCCCGCGGTCGGCT
          1 CCTTAGGGTTCAGGGGGCTGACCCCCGCGTTCGGCT

                  *   *          
       8269 CCTTAGTGTTAAGGGGGCTGA
          1 CCTTAGGGTTCAGGGGGCTGA


Statistics
Matches: 1157,  Mismatches: 81, Indels: 32
        0.91            0.06        0.03

Matches are distributed among these distances:
  34    6  0.01
  35   83  0.07
  36  862  0.75
  37  146  0.13
  38   24  0.02
  39    2  0.00
  40    2  0.00
  42   26  0.02
  43    6  0.01

ACGTcount: A:0.09, C:0.33, G:0.37, T:0.21


Consensus pattern (36 bp):   
CCTTAGGGTTCAGGGGGCTGACCCCCGCGTTCGGCT

Done.