Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_388 ID=scaffold_388-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: 7577
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.33


Found at i:1193 original size:44 final size:45

Alignment explanation


    Indices: 1075--1196  Score: 133
    Period size: 45  Copynumber: 2.7  Consensus size: 45

       1065 ATCGGCTTCA

                                            **         * 
       1075 ATCTGCTCCACTGCAACCTCAGGGAGATAAGATTTGCCATCTCTG
          1 ATCTGCTCCACTGCAACCTCAGGGAGATAAGACCTGCCATCTCAG

                 *            *      *             *       
       1120 ATCT-ATCCCACTGCAACTTCAGGGGGATAAGACCTG-CTTACTCAG
          1 ATCTGCT-CCACTGCAACCTCAGGGAGATAAGACCTGCCAT-CTCAG

                        *                    
       1165 -TCTGCTCCACTACAACCTCAGGGAGATAAGAC
          1 ATCTGCTCCACTGCAACCTCAGGGAGATAAGAC

       1197 ATGATGTGAT


Statistics
Matches: 63,  Mismatches: 11, Indels: 7
        0.78            0.14        0.09

Matches are distributed among these distances:
  44   29  0.46
  45   34  0.54

ACGTcount: A:0.27, C:0.30, G:0.20, T:0.24


Consensus pattern (45 bp):   
ATCTGCTCCACTGCAACCTCAGGGAGATAAGACCTGCCATCTCAG

Found at i:1295 original size:218 final size:218

Alignment explanation


    Indices: 917--1374  Score: 756
    Period size: 218  Copynumber: 2.1  Consensus size: 218

        907 ATAATTGGGT

                      *                           *  *                    *  
        917 ACTTCAGGGGAATAAGACCTGCTTACTCAGTCTGCTCCGCTGCAACCTCAAGGAGATAAGACCTA
          1 ACTTCAGGGGGATAAGACCTGCTTACTCAGTCTGCTCCACTACAACCTCAAGGAGATAAGACATA

                   *                                                 *       
        982 ATGCGATTCACTCTACTGCAACTTCAGAAAGATAAGATCCATTACTTTAATCCGCTCCACTACAA
         66 ATGCGATCCACTCTACTGCAACTTCAGAAAGATAAGATCCATTACTTTAATCCGCTCAACTACAA

                                 *                             *             
       1047 TTTCAGGGAGATAGGATTATCGGCTTCAATCTGCTCCACTGCAACCTCAGGGAGATAAGATTTGC
        131 TTTCAGGGAGATAGGATTATCAGCTTCAATCTGCTCCACTGCAACCTCAGGAAGATAAGATTTGC

                    *               
       1112 CATC-TCTGATCTATCCCACTGCA
        196 CATCTTC-AATCTATCCCACTGCA

                                                              *             *
       1135 ACTTCAGGGGGATAAGACCTGCTTACTCAGTCTGCTCCACTACAACCTCAGGGAGATAAGACATG
          1 ACTTCAGGGGGATAAGACCTGCTTACTCAGTCTGCTCCACTACAACCTCAAGGAGATAAGACATA

               *              *         *                                    
       1200 ATGTGATCCACTCTACTGTAACTTCAGAGAGATAAGATCCATTACTTTAATCCGCTCAACTACAA
         66 ATGCGATCCACTCTACTGCAACTTCAGAAAGATAAGATCCATTACTTTAATCCGCTCAACTACAA

                                                                             
       1265 TTTCAGGGAGATAGGATTATCAGCTTCAATCTGCTCCACTGCAACCTCAGGAAGATAAGATTTGC
        131 TTTCAGGGAGATAGGATTATCAGCTTCAATCTGCTCCACTGCAACCTCAGGAAGATAAGATTTGC

                        *     *    
       1330 CATCTTCAATCTGTCCCATTGCA
        196 CATCTTCAATCTATCCCACTGCA

                                  
       1353 ACTTCAGGGGGATAAGACCTGC
          1 ACTTCAGGGGGATAAGACCTGC

       1375 GATTTCCCAA


Statistics
Matches: 223,  Mismatches: 16, Indels: 2
        0.93            0.07        0.01

Matches are distributed among these distances:
 218  221  0.99
 219    2  0.01

ACGTcount: A:0.29, C:0.26, G:0.19, T:0.26


Consensus pattern (218 bp):   
ACTTCAGGGGGATAAGACCTGCTTACTCAGTCTGCTCCACTACAACCTCAAGGAGATAAGACATA
ATGCGATCCACTCTACTGCAACTTCAGAAAGATAAGATCCATTACTTTAATCCGCTCAACTACAA
TTTCAGGGAGATAGGATTATCAGCTTCAATCTGCTCCACTGCAACCTCAGGAAGATAAGATTTGC
CATCTTCAATCTATCCCACTGCA

Found at i:1342 original size:45 final size:44

Alignment explanation


    Indices: 996--1369  Score: 180
    Period size: 44  Copynumber: 8.5  Consensus size: 44

        986 GATTCACTCT

                         **           *        *    *     
        996 ACTGCAACTTCAGAAAGATAAGA--TCCATTACTTTAATCCGCTCC
          1 ACTGCAACTTCAGGGAGATAAGATTTGCA-T-CTTCAATCTGCTCC

               *   *            *        **              
       1040 ACTACAATTTCAGGGAGATAGGATTAT-CGGCTTCAATCTGCTCC
          1 ACTGCAACTTCAGGGAGATAAGATT-TGCATCTTCAATCTGCTCC

                    *                           *     *    
       1084 ACTGCAACCTCAGGGAGATAAGATTTGCCATC-TCTGATCT-ATCCC
          1 ACTGCAACTTCAGGGAGATAAGATTTG-CATCTTC-AATCTGCT-CC

                           *       **   *       *        
       1129 ACTGCAACTTCAGGGGGATAAGACCTGCTTAC-TCAGTCTGCTCC
          1 ACTGCAACTTCAGGGAGATAAGATTTGCAT-CTTCAATCTGCTCC

               *    *              **      *  *   **   *
       1173 ACTACAACCTCAGGGAGATAAGACATG-AT-GT-GATCCACTCT
          1 ACTGCAACTTCAGGGAGATAAGATTTGCATCTTCAATCTGCTCC

                *        *            *        *    *    *
       1214 ACTGTAACTTCAGAGAGATAAGA--TCCATTACTTTAATCCGCTCA
          1 ACTGCAACTTCAGGGAGATAAGATTTGCA-T-CTTCAATCTGCTCC

               *   *            *         *              
       1258 ACTACAATTTCAGGGAGATAGGATTAT-CAGCTTCAATCTGCTCC
          1 ACTGCAACTTCAGGGAGATAAGATT-TGCATCTTCAATCTGCTCC

                    *     *                               
       1302 ACTGCAACCTCAGGAAGATAAGATTTGCCATCTTCAATCTG-TCCC
          1 ACTGCAACTTCAGGGAGATAAGATTTG-CATCTTCAATCTGCT-CC

             *             *       
       1347 ATTGCAACTTCAGGGGGATAAGA
          1 ACTGCAACTTCAGGGAGATAAGA

       1370 CCTGCGATTT


Statistics
Matches: 246,  Mismatches: 63, Indels: 41
        0.70            0.18        0.12

Matches are distributed among these distances:
  39    1  0.00
  40    1  0.00
  41   25  0.10
  42    1  0.00
  43    4  0.02
  44  141  0.57
  45   68  0.28
  46    3  0.01
  47    2  0.01

ACGTcount: A:0.30, C:0.25, G:0.18, T:0.27


Consensus pattern (44 bp):   
ACTGCAACTTCAGGGAGATAAGATTTGCATCTTCAATCTGCTCC

Done.