Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga07g02357.M4

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: 21770
ACGTcount: A:0.40, C:0.16, G:0.24, T:0.19


Found at i:164 original size:51 final size:51

Alignment explanation


    Indices: 88--238  Score: 223
    Period size: 51  Copynumber: 3.0  Consensus size: 51

         78 GGAAAAGTAG

                            *               **                 
         88 ATGGCAACTGAAGCAGCGATCATTCAAGAACCTGTTTCCATAGTGGAAAAA
          1 ATGGCAACTGAAGCAGTGATCATTCAAGAACCCATTTCCATAGTGGAAAAA

              *         *       *                              
        139 ATTGCAACTGAATCAGTGATTATTCAAGAACCCATTTCCATAGTGGAAAAA
          1 ATGGCAACTGAAGCAGTGATCATTCAAGAACCCATTTCCATAGTGGAAAAA

                      *                           *           
        190 ATGGCAACTGGAGCAGTGATCATTCAAGAACCCATTTCAATAGT-GAAAA
          1 ATGGCAACTGAAGCAGTGATCATTCAAGAACCCATTTCCATAGTGGAAAA

        239 CAGCAGAGAG


Statistics
Matches: 89,  Mismatches: 11, Indels: 1
        0.88            0.11        0.01

Matches are distributed among these distances:
  50    5  0.06
  51   84  0.94

ACGTcount: A:0.38, C:0.19, G:0.19, T:0.24


Consensus pattern (51 bp):   
ATGGCAACTGAAGCAGTGATCATTCAAGAACCCATTTCCATAGTGGAAAAA

Found at i:7530 original size:6 final size:6

Alignment explanation


    Indices: 7519--7605  Score: 120
    Period size: 6  Copynumber: 14.5  Consensus size: 6

       7509 AGACATAAAG

                                   *      *               *        
       7519 GAAGCT GAAGCT GAAGCT GATGCT GATGCT GAAGCT GAAGAT GAAGCT
          1 GAAGCT GAAGCT GAAGCT GAAGCT GAAGCT GAAGCT GAAGCT GAAGCT

              *      *      *                            
       7567 GATGCT GATGCT GATGCT GAAGCT GAAGCT GAAGCT GAA
          1 GAAGCT GAAGCT GAAGCT GAAGCT GAAGCT GAAGCT GAA

       7606 AGAGAAAAGA


Statistics
Matches: 75,  Mismatches: 6, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
   6   75  1.00

ACGTcount: A:0.30, C:0.15, G:0.33, T:0.22


Consensus pattern (6 bp):   
GAAGCT

Found at i:7555 original size:30 final size:30

Alignment explanation


    Indices: 7519--7604  Score: 145
    Period size: 30  Copynumber: 2.9  Consensus size: 30

       7509 AGACATAAAG

                                          
       7519 GAAGCTGAAGCTGAAGCTGATGCTGATGCT
          1 GAAGCTGAAGCTGAAGCTGATGCTGATGCT

                      *                   
       7549 GAAGCTGAAGATGAAGCTGATGCTGATGCT
          1 GAAGCTGAAGCTGAAGCTGATGCTGATGCT

              *                 *     
       7579 GATGCTGAAGCTGAAGCTGAAGCTGA
          1 GAAGCTGAAGCTGAAGCTGATGCTGA

       7605 AAGAGAAAAG


Statistics
Matches: 52,  Mismatches: 4, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  30   52  1.00

ACGTcount: A:0.29, C:0.15, G:0.34, T:0.22


Consensus pattern (30 bp):   
GAAGCTGAAGCTGAAGCTGATGCTGATGCT

Found at i:16098 original size:312 final size:312

Alignment explanation


    Indices: 15532--16160  Score: 945
    Period size: 312  Copynumber: 2.0  Consensus size: 312

      15522 ATCTTTGCCT

                         **             *              *                     
      15532 TCAGAATTGACTGTTGAGAACCCAAAGCGTGGAGCTGAGGCCAGTGAAGAAGAGGAAGAAAAGGT
          1 TCAGAATTGACTGAAGAGAACCCAAAGCATGGAGCTGAGGCCAATGAAGAAGAGGAAGAAAAGGT

                                                       *          *          
      15597 GAAGGAAGTGGAAATTCTCGAAAAGGAAAGACCTCAGGAGCCTGAAGCTGTTATGGATCAAGAAA
         66 GAAGGAAGTGGAAATTCTCGAAAAGGAAAGACCTCAGGAGCCTAAAGCTGTTATAGATCAAGAAA

                     *                                           *           
      15662 CCATTATAGTTCAGGCTTCAATAACAGAGGAATCACAAAAGATTGAAGCAAACGAAGAGAAAAGG
        131 CCATTATAGCTCAGGCTTCAATAACAGAGGAATCACAAAAGATTGAAGCAAACAAAGAGAAAAGG

                  *           *  *         *         *                       
      15727 AAAGAAGCCAAAAAGCTTGACGATGGGAACCGTGAAGACTCGTCAGCTGGAGAAACAGAAAAGCT
        196 AAAGAAACCAAAAAGCTTCACAATGGGAACCATGAAGACTCATCAGCTGGAGAAACAGAAAAGCT

                    *           ** *                 *          
      15792 AAATGAGCTTCAATTAGTTACTAGAGAAGAAATTGCTTCTGGTCAGTCTTCC
        261 AAATGAGCGTCAATTAGTTAAAAAAGAAGAAATTGCTTCTGATCAGTCTTCC

                                  *                                **        
      15844 TCAGAATTGACTGAAGAGAACCTAAAGCATGGAGCTGAGGCCAATGAAGAAGAGGGGGAAAAGGT
          1 TCAGAATTGACTGAAGAGAACCCAAAGCATGGAGCTGAGGCCAATGAAGAAGAGGAAGAAAAGGT

                         *              *                                    
      15909 GAAGGAAGTGGAACTTCTCGAAAAGGAAGGACCTCAGGAGCCTAAAGCTGTTATAGATCAAGAAA
         66 GAAGGAAGTGGAAATTCTCGAAAAGGAAAGACCTCAGGAGCCTAAAGCTGTTATAGATCAAGAAA

                   *           **    *            *                          
      15974 CCATTATTGCTCAGGCTTCCTTAACTGAGGAATCACAAGAGATTGAAGCAAACAAAGA-AAAAGG
        131 CCATTATAGCTCAGGCTTCAATAACAGAGGAATCACAAAAGATTGAAGCAAACAAAGAGAAAA-G

                     **                                          *       *   
      16038 GAAAGAAACTGAAAAGCTTCACAATGGGAACCATGAAGACTCATCAGCTGGAGTAACAGAAGAGC
        195 GAAAGAAACCAAAAAGCTTCACAATGGGAACCATGAAGACTCATCAGCTGGAGAAACAGAAAAGC

                         *                                       
      16103 TAAATGAGCGTCAGTTAGTTAAAAAAGAAGAAATTGCTTCTGATCAGTCTTCC
        260 TAAATGAGCGTCAATTAGTTAAAAAAGAAGAAATTGCTTCTGATCAGTCTTCC

                 
      16156 TCAGA
          1 TCAGA

      16161 CAAGCAACTT


Statistics
Matches: 283,  Mismatches: 33, Indels: 2
        0.89            0.10        0.01

Matches are distributed among these distances:
 311    4  0.01
 312  279  0.99

ACGTcount: A:0.40, C:0.16, G:0.26, T:0.18


Consensus pattern (312 bp):   
TCAGAATTGACTGAAGAGAACCCAAAGCATGGAGCTGAGGCCAATGAAGAAGAGGAAGAAAAGGT
GAAGGAAGTGGAAATTCTCGAAAAGGAAAGACCTCAGGAGCCTAAAGCTGTTATAGATCAAGAAA
CCATTATAGCTCAGGCTTCAATAACAGAGGAATCACAAAAGATTGAAGCAAACAAAGAGAAAAGG
AAAGAAACCAAAAAGCTTCACAATGGGAACCATGAAGACTCATCAGCTGGAGAAACAGAAAAGCT
AAATGAGCGTCAATTAGTTAAAAAAGAAGAAATTGCTTCTGATCAGTCTTCC
Done.