Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga01g01391.F5

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: 4396
ACGTcount: A:0.31, C:0.18, G:0.24, T:0.27


Found at i:1789 original size:21 final size:20

Alignment explanation


    Indices: 1751--1809  Score: 59
    Period size: 21  Copynumber: 3.0  Consensus size: 20

       1741 AGCTTCTCGA

                          *       
       1751 AGAAGAAG-AGAAGGAAAAGCG
          1 AGAAGAAGAAGAA-CAAAAG-G

            *                   
       1772 TGAAGAAGAAGAACAAAAGG
          1 AGAAGAAGAAGAACAAAAGG

               *               
       1792 AGAGGAA-AAGAACAAAAG
          1 AGAAGAAGAAGAACAAAAG

       1810 AACGAGAGAA


Statistics
Matches: 33,  Mismatches: 4, Indels: 4
        0.80            0.10        0.10

Matches are distributed among these distances:
  19   11  0.33
  20    6  0.18
  21   12  0.36
  22    4  0.12

ACGTcount: A:0.61, C:0.05, G:0.32, T:0.02


Consensus pattern (20 bp):   
AGAAGAAGAAGAACAAAAGG

Found at i:1816 original size:22 final size:19

Alignment explanation


    Indices: 1775--1823  Score: 53
    Period size: 19  Copynumber: 2.4  Consensus size: 19

       1765 AAAAGCGTGA

                *              
       1775 AGAAGAAGAACAAAAGGAG
          1 AGAAAAAGAACAAAAGGAG

              *                   
       1794 AGGAAAAGAACAAAAGAACGAG
          1 AGAAAAAGAACAAAAG---GAG

                    
       1816 AGAAAAAG
          1 AGAAAAAG

       1824 CTCAGGAGAA


Statistics
Matches: 24,  Mismatches: 3, Indels: 3
        0.80            0.10        0.10

Matches are distributed among these distances:
  19   14  0.58
  22   10  0.42

ACGTcount: A:0.65, C:0.06, G:0.29, T:0.00


Consensus pattern (19 bp):   
AGAAAAAGAACAAAAGGAG

Found at i:3350 original size:129 final size:129

Alignment explanation


    Indices: 3120--3376  Score: 347
    Period size: 129  Copynumber: 2.0  Consensus size: 129

       3110 TCAACGATCA

                                    *          *                    *     *  
       3120 GATGGGAGAGATACTTCAAGCTGCGTTCAAAATGGTTTCTCCGAGTGTCAGGTGAAGGGAATTGA
          1 GATGGGAGAGATACTTCAAGCTGCATTCAAAATGGCTTCTCCGAGTGTCAGGTGAAAGGAATCGA

            *      *                                 *                       
       3185 TAAAAAAGAGGATGTCAATGGAGGCATTGCTTTGGAA-AGCGAGGCATTGTTTGGACATTCACCT
         66 AAAAAAACAGGATGTCAATGGAGGCATTGCTTTGGAATA-CCAGGCATTGTTTGGACATTCACCT

                        *                  *          *           *          
       3249 GATGGGAGAGATTCTTC-AGTCTGCATTCAAGATGGCTTCTCTGAGTGTCAGGTTAAAGGAATCG
          1 GATGGGAGAGATACTTCAAG-CTGCATTCAAAATGGCTTCTCCGAGTGTCAGGTGAAAGGAATCG

                                  *  **                            *        
       3313 AAAAAAAACAGGATGTCAATGGGGGGGTTGCTTTGGAATACCAGGCATTGTTTGGGCATTCACC
         65 AAAAAAAACAGGATGTCAATGGAGGCATTGCTTTGGAATACCAGGCATTGTTTGGACATTCACC

       3377 AGACAGTAGA


Statistics
Matches: 111,  Mismatches: 15, Indels: 4
        0.85            0.12        0.03

Matches are distributed among these distances:
 128    2  0.02
 129  108  0.97
 130    1  0.01

ACGTcount: A:0.28, C:0.15, G:0.30, T:0.27


Consensus pattern (129 bp):   
GATGGGAGAGATACTTCAAGCTGCATTCAAAATGGCTTCTCCGAGTGTCAGGTGAAAGGAATCGA
AAAAAAACAGGATGTCAATGGAGGCATTGCTTTGGAATACCAGGCATTGTTTGGACATTCACCT
Done.