Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_985 ID=scaffold_985-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: 3017
ACGTcount: A:0.15, C:0.13, G:0.11, T:0.18

Warning! 1309 characters in sequence are not A, C, G, or T


Found at i:239 original size:132 final size:132

Alignment explanation


    Indices: 1--739  Score: 1047
    Period size: 132  Copynumber: 5.6  Consensus size: 132

                                      *              *                       
          1 CTTAGGGTGACAGAATCTGCAATCTTTAACCTACTCCACTATTGCTTAGGGTGATAGGACTAATG
          1 CTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTGCTTAGGGTGATAGGACTAATG

            *                                         *                   * *
         66 ACTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCATCATATTCGATCTGCTCCACAAT
         66 GCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCATATTCGATCTGCTCCACTAC

              
        131 TG
        131 TG

            *                  *               *           *   *      *    * 
        133 TTTAGGGTGACAGAATCTGTAATCTTCAACCTACTACACTACTGCTTTGGGAGATAGGTCTAACG
          1 CTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTGCTTAGGGTGATAGGACTAATG

                             *                            *        *         
        198 GCTTAAATCTGCTTCTCTACTGTATTGGGAAGATAAGATTCACCATCTTCGATCTACTCCACTAC
         66 GCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCATATTCGATCTGCTCCACTAC

              
        263 TG
        131 TG

                              *   *                              *    *      
        265 CTTAGGGTGACAGAATCTACAAACTTCAACCTACTCCACTACTGCTTAGGGTGGTAGGCCTAATG
          1 CTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTGCTTAGGGTGATAGGACTAATG

                               * *       *  *         *       *              
        330 GCTTAAATCTGCTTCTCCATTATATTGGGGAGGTAAGATTCATCATATTCAATCTGCTCCACTAC
         66 GCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCATATTCGATCTGCTCCACTAC

              
        395 TG
        131 TG

            *                                                *               
        397 TTTAGGGTGACAG-ATCTGCAATCTTCAACCTACTCCACTACTGCTTAGTGTGATAGGACTAATG
          1 CTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTGCTTAGGGTGATAGGACTAATG

            *         *                      *  *         *        *         
        461 ACTTAAATCTACTTCTCCACTGTATTGGGAAGAAAACATTCACCATCTTCGATCTCCAT-CACTA
         66 GCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCATATTCGATCTGC-TCCACTA

                
        525 CTAG
        130 CT-G

                                           *                  * *      *     
        529 -TTAGGGTGACAGAATCTGCAATCTTCAACCGACTCCACTACTGCTTAGGATAATAGGAGTAATG
          1 CTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTGCTTAGGGTGATAGGACTAATG

                       *             *                                       
        593 GCTTAAATCTGGTTCTCCACTGTATAGGGAAGATAAGATTCACCA-ACTTCGATCTGCTCCACTA
         66 GCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCATA-TTCGATCTGCTCCACTA

               
        657 CTG
        130 CTG

                                                                             
        660 CTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCC-CGTACTGCTTAGGGTGATAGGACTAAT
          1 CTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCAC-TACTGCTTAGGGTGATAGGACTAAT

                            
        724 GGCTTAAATCTGCTTC
         65 GGCTTAAATCTGCTTC

        740 NNNNNNNNNN


Statistics
Matches: 529,  Mismatches: 71, Indels: 14
        0.86            0.12        0.02

Matches are distributed among these distances:
 131  113  0.21
 132  416  0.79

ACGTcount: A:0.27, C:0.23, G:0.18, T:0.31


Consensus pattern (132 bp):   
CTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTGCTTAGGGTGATAGGACTAATG
GCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCATATTCGATCTGCTCCACTAC
TG

Found at i:557 original size:263 final size:264

Alignment explanation


    Indices: 1--739  Score: 1092
    Period size: 263  Copynumber: 2.8  Consensus size: 264

                                      *              *                       
          1 CTTAGGGTGACAGAATCTGCAATCTTTAACCTACTCCACTATTGCTTAGGGTGATAGGACTAATG
          1 CTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTGCTTAGGGTGATAGGACTAATG

            *                                                             * *
         66 ACTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCATCATATTCGATCTGCTCCACAAT
         66 GCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCATCATATTCGATCTGCTCCACTAC

                                 *               *           *   *      *    
        131 TGTTTAGGGTGACAGAATCTGTAATCTTCAACCTACTACACTACTGCTTTGGGAGATAGGTCTAA
        131 TGTTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTGCTTAGGGTGATAGGACTAA

            *                  *               *  *                          
        196 CGGCTTAAATCTGCTTCTCTACTGTATTGGGAAGATAAGATTCACCATCTTCGATCTACTCCACT
        196 TGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGAAAACATTCACCATCTTCGATCTACTCCACT

                
        261 ACTG
        261 ACTG

                              *   *                              *    *      
        265 CTTAGGGTGACAGAATCTACAAACTTCAACCTACTCCACTACTGCTTAGGGTGGTAGGCCTAATG
          1 CTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTGCTTAGGGTGATAGGACTAATG

                               * *       *  *                 *              
        330 GCTTAAATCTGCTTCTCCATTATATTGGGGAGGTAAGATTCATCATATTCAATCTGCTCCACTAC
         66 GCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCATCATATTCGATCTGCTCCACTAC

                                                               *             
        395 TGTTTAGGGTGACAG-ATCTGCAATCTTCAACCTACTCCACTACTGCTTAGTGTGATAGGACTAA
        131 TGTTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTGCTTAGGGTGATAGGACTAA

              *         *                                            *       
        459 TGACTTAAATCTACTTCTCCACTGTATTGGGAAGAAAACATTCACCATCTTCGATCTCCAT-CAC
        196 TGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGAAAACATTCACCATCTTCGATCTAC-TCCAC

                  
        523 TACTAG
        260 TACT-G

                                           *                  * *      *     
        529 -TTAGGGTGACAGAATCTGCAATCTTCAACCGACTCCACTACTGCTTAGGATAATAGGAGTAATG
          1 CTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTGCTTAGGGTGATAGGACTAATG

                       *             *                *                      
        593 GCTTAAATCTGGTTCTCCACTGTATAGGGAAGATAAGATTCACCA-ACTTCGATCTGCTCCACTA
         66 GCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCATCATA-TTCGATCTGCTCCACTA

               *                                                             
        657 CTGCTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCC-CGTACTGCTTAGGGTGATAGGACT
        130 CTGTTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCAC-TACTGCTTAGGGTGATAGGACT

                               
        721 AATGGCTTAAATCTGCTTC
        194 AATGGCTTAAATCTGCTTC

        740 NNNNNNNNNN


Statistics
Matches: 423,  Mismatches: 47, Indels: 10
        0.88            0.10        0.02

Matches are distributed among these distances:
 262    1  0.00
 263  228  0.54
 264  194  0.46

ACGTcount: A:0.27, C:0.23, G:0.18, T:0.31


Consensus pattern (264 bp):   
CTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTGCTTAGGGTGATAGGACTAATG
GCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCATCATATTCGATCTGCTCCACTAC
TGTTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACTGCTTAGGGTGATAGGACTAA
TGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGAAAACATTCACCATCTTCGATCTACTCCACT
ACTG

Found at i:2290 original size:132 final size:132

Alignment explanation


    Indices: 2049--3017  Score: 1521
    Period size: 132  Copynumber: 7.3  Consensus size: 132

       2039 NNNNNNNNNN

                   *   *                          *      *                   
       2049 AAATCTGGTTCGCCACTGTATTGGGAAGATAAGATTCAGCATCTTGGATCTGCTCCACTACTGCT
          1 AAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGCT

                             *                     *                         
       2114 TAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTATTGCTTAGGGTGATAGGACTAATGGC
         66 TAGGGTGACAGAATCTGTAATCTTCAACCTACTCCACTACTGCTTAGGGTGATAGGACTAATGGC

              
       2179 TT
        131 TT

                   *                              *   *                    * 
       2181 AAATCTGTTTCTCCACTGTATTGGGAAGATAAGATTCATCATATTCGATCTGCTCCACTACTGTT
          1 AAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGCT

                                                         *   *      *        
       2246 TAGGGTGACAGAATCTGTAATCTTCAACCTACTCCACTACTGCTTTGGGAGATAGGTCTAATGGC
         66 TAGGGTGACAGAATCTGTAATCTTCAACCTACTCCACTACTGCTTAGGGTGATAGGACTAATGGC

              
       2311 TT
        131 TT

                                                                 *           
       2313 AAATCTGCTTCTCCACTGTATTGGGAAGATATA-ATTCACCATCTTCGATCTGGTCCACTACTG-
          1 AAATCTGCTTCTCCACTGTATTGGGAAGATA-AGATTCACCATCTTCGATCTGCTCCACTACTGC

                                                                 *           
       2376 TTGAGGGTGACAGAATCTGTAATCTTCAACCTACTCC-CGTACTGCTTAGGGTTATAGGACTAAT
         65 TT-AGGGTGACAGAATCTGTAATCTTCAACCTACTCCAC-TACTGCTTAGGGTGATAGGACTAAT

                 
       2440 GGCTT
        128 GGCTT

                             *    *                               *          
       2445 AAATCTGCTTCTCCACTATATTAGGAAGATAAGATTCACCATCTTCGATCTGCTTCACTACTGCT
          1 AAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGCT

                             *                *           *                  
       2510 TAGGGTGACAGAATCTGCAATCTTCAACCTACTCAACTACTGCTTAAGGTGATAGGACTAATGGC
         66 TAGGGTGACAGAATCTGTAATCTTCAACCTACTCCACTACTGCTTAGGGTGATAGGACTAATGGC

              
       2575 TT
        131 TT

                                  *             *        *                 * 
       2577 AAATCTGCTTCTCCACTGTATTAGGAAGATAAGATTAACCATCTTTGATCTGCTCCACTACTGAT
          1 AAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGCT

                                                **   *                      *
       2642 TAGGGTGACAGAATCTGTAATCTTCAACCTACTCCAAAACTACTTAGGGTGATAGGACTAATGGT
         66 TAGGGTGACAGAATCTGTAATCTTCAACCTACTCCACTACTGCTTAGGGTGATAGGACTAATGGC

              
       2707 TT
        131 TT

                                                                *            
       2709 AAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCATCTTCGATCTGGTCCACTACTGCT
          1 AAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGCT

                          *  *       *                                   *   
       2774 TAGGGTGACAGAATTTGCAATCTTCGACCTACTCCACTACTGCTTAGGGTGATAGGACTAAAGGC
         66 TAGGGTGACAGAATCTGTAATCTTCAACCTACTCCACTACTGCTTAGGGTGATAGGACTAATGGC

              
       2839 TT
        131 TT

                                                      *  *                  *
       2841 AAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCAGCTGCGATCTGCTCCACTACTGA
          1 -AAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGC

                                      *                                      
       2906 TTAGGGTGACAGAATCTGTAATCTTCGACCTACTCCACTACTGCTTAGGGTGATAGGACTAATGG
         65 TTAGGGTGACAGAATCTGTAATCTTCAACCTACTCCACTACTGCTTAGGGTGATAGGACTAATGG

               
       2971 CTT
        130 CTT

                                  *             *       
       2974 AAATCTGCTTCTCCACTGTATTAGGAAGATAAGATTAACCATCT
          1 AAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCATCT


Statistics
Matches: 768,  Mismatches: 62, Indels: 14
        0.91            0.07        0.02

Matches are distributed among these distances:
 131    4  0.01
 132  635  0.83
 133  129  0.17

ACGTcount: A:0.27, C:0.22, G:0.19, T:0.31


Consensus pattern (132 bp):   
AAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGCT
TAGGGTGACAGAATCTGTAATCTTCAACCTACTCCACTACTGCTTAGGGTGATAGGACTAATGGC
TT

Done.