Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga11g01077.C4

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: 2607
ACGTcount: A:0.29, C:0.22, G:0.20, T:0.29


Found at i:397 original size:33 final size:33

Alignment explanation


    Indices: 355--729  Score: 417
    Period size: 33  Copynumber: 11.0  Consensus size: 33

        345 GGCATCATCC

                            *               *
        355 CCTGCTACCTCTCCTCTGGAAAAAGAAACGACA
          1 CCTGCTACCTCTCCTCCGGAAAAAGAAACGACT

                                   * *       
        388 CCTGCTACCTCTCCTCCGGAAAAGGTAACGACT
          1 CCTGCTACCTCTCCTCCGGAAAAAGAAACGACT

              *                      *       
        421 CCAGCTACCTCTCCTCCGGAAAAAGGAACGACT
          1 CCTGCTACCTCTCCTCCGGAAAAAGAAACGACT

                                   *         
        454 CCTGCTACCTCTCCTCCGGAAAATGAAACGACT
          1 CCTGCTACCTCTCCTCCGGAAAAAGAAACGACT

                           *                 
        487 CCTGCTACCTCTCCTTCGGAAAAAGAAACGACT
          1 CCTGCTACCTCTCCTCCGGAAAAAGAAACGACT

                *     *            * *       
        520 CCTGTTACCTTTCCTCCGGAAAAGGTAACGACT
          1 CCTGCTACCTCTCCTCCGGAAAAAGAAACGACT

            *  * *          *               **  
        553 TCTTCGACCTCTCCTCTGGAAAAAGTAACAACTCCT
          1 CCTGCTACCTCTCCTCCGGAAAAAG--A-AACGACT

                                        *   *   
        589 GCTACTGCTACCTCTCCTCCGGAAAAAGTAACCACT
          1 -C--CTGCTACCTCTCCTCCGGAAAAAGAAACGACT

                                     **            
        625 CCTGCTACTGCCACCTCTCCTCCGGCGAAAGAAACGACT
          1 CCTG---CT---ACCTCTCCTCCGGAAAAAGAAACGACT

                               *             
        664 CCTGCTACCTCTCCTCCGGCAAAAGAAACGACT
          1 CCTGCTACCTCTCCTCCGGAAAAAGAAACGACT

                           *         *       
        697 CCTGCTACCTCTCCTTCGGAAAAAGTAACGACT
          1 CCTGCTACCTCTCCTCCGGAAAAAGAAACGACT

        730 TCTGAAAAAA


Statistics
Matches: 288,  Mismatches: 42, Indels: 24
        0.81            0.12        0.07

Matches are distributed among these distances:
  33  225  0.78
  35    1  0.00
  36   14  0.05
  39   48  0.17

ACGTcount: A:0.27, C:0.35, G:0.16, T:0.21


Consensus pattern (33 bp):   
CCTGCTACCTCTCCTCCGGAAAAAGAAACGACT

Found at i:1244 original size:183 final size:183

Alignment explanation


    Indices: 936--1305  Score: 695
    Period size: 183  Copynumber: 2.0  Consensus size: 183

        926 GTGGGTCAAG

                                                                          *  
        936 TTCAAATGGTCACAACCAAGACGATTCTATGATAAAAAATGGTAAATACTGGGCTCCACATGGTG
          1 TTCAAATGGTCACAACCAAGACGATTCTATGATAAAAAATGGTAAATACTGGGCTCCACATGATG

                                                                             
       1001 AAACACGTGGTGCTTGTTTCAATACTTCAGAAGTGACGACTGAAAAAACTAAGGATAACGCAAAT
         66 AAACACGTGGTGCTTGTTTCAATACTTCAGAAGTGACGACTGAAAAAACTAAGGATAACGCAAAT

                                                                 
       1066 GATGGCGTGGTTGAGATTTCCGGTGATGAAAGGTGGCGTAGGATGTTGGATTT
        131 GATGGCGTGGTTGAGATTTCCGGTGATGAAAGGTGGCGTAGGATGTTGGATTT

                                *                      *                     
       1119 TTCAAATGGTCACAACCAAGGCGATTCTATGATAAAAAATGGTGAATACTGGGCTCCACATGATG
          1 TTCAAATGGTCACAACCAAGACGATTCTATGATAAAAAATGGTAAATACTGGGCTCCACATGATG

                                   *                                         
       1184 AAACACGTGGTGCTTGTTTCAATGCTTCAGAAGTGACGACTGAAAAAACTAAGGATAACGCAAAT
         66 AAACACGTGGTGCTTGTTTCAATACTTCAGAAGTGACGACTGAAAAAACTAAGGATAACGCAAAT

                                                *                
       1249 GATGGCGTGGTTGAGATTTCCGGTGATGAAAGGTGGTGTAGGATGTTGGATTT
        131 GATGGCGTGGTTGAGATTTCCGGTGATGAAAGGTGGCGTAGGATGTTGGATTT

                
       1302 TTCA
          1 TTCA

       1306 TCTAAAAACA


Statistics
Matches: 182,  Mismatches: 5, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
 183  182  1.00

ACGTcount: A:0.32, C:0.15, G:0.26, T:0.27


Consensus pattern (183 bp):   
TTCAAATGGTCACAACCAAGACGATTCTATGATAAAAAATGGTAAATACTGGGCTCCACATGATG
AAACACGTGGTGCTTGTTTCAATACTTCAGAAGTGACGACTGAAAAAACTAAGGATAACGCAAAT
GATGGCGTGGTTGAGATTTCCGGTGATGAAAGGTGGCGTAGGATGTTGGATTT

Found at i:1483 original size:45 final size:45

Alignment explanation


    Indices: 1433--1521  Score: 160
    Period size: 45  Copynumber: 2.0  Consensus size: 45

       1423 TCTTATATTC

                               *                  *      
       1433 TACCATTAAACCATCATCCTTTCATTTCACCAGCTGGGGGAGTCG
          1 TACCATTAAACCATCATCCCTTCATTTCACCAGCTGGGAGAGTCG

                                                        
       1478 TACCATTAAACCATCATCCCTTCATTTCACCAGCTGGGAGAGTC
          1 TACCATTAAACCATCATCCCTTCATTTCACCAGCTGGGAGAGTC

       1522 AGTGATCATG


Statistics
Matches: 42,  Mismatches: 2, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  45   42  1.00

ACGTcount: A:0.26, C:0.30, G:0.16, T:0.28


Consensus pattern (45 bp):   
TACCATTAAACCATCATCCCTTCATTTCACCAGCTGGGAGAGTCG
Done.