Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold692

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: 9837
ACGTcount: A:0.33, C:0.12, G:0.13, T:0.34

Warning! 760 characters in sequence are not A, C, G, or T


Found at i:287 original size:43 final size:43

Alignment explanation


    Indices: 238--573  Score: 458
    Period size: 43  Copynumber: 7.8  Consensus size: 43

        228 AAAGGTTTAT

                              **                      *
        238 TCTTTAGCGGCGTTTGTGATAAAAGCGCCGCTAAAGGTCATGT
          1 TCTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGG

                   *                *                * 
        281 TCTTTAGAGGCGTTTGTGGGAAAATCGCCGCTAAAGGTCATAG
          1 TCTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGG

                                                    *   
        324 TCTTTAGCGGCGTTTGT-GGAAGAAGCGCCGCTAAAGGTCTTGG
          1 TCTTTAGCGGCGTTTGTGGGAA-AAGCGCCGCTAAAGGTCATGG

                            **   *    *           **   
        367 TCTTTAGCGGCGTTTGCAGGAGAAGCACCGCTAAAGGTTTTGG
          1 TCTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGG

                                         *             
        410 TCTTTAGCGGCGTTTGTGGGAAAAGCGCCACTAAAGGTCATGG
          1 TCTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGG

                     *                    *            
        453 TCTTTAGCGACGTTTGTGGGAAAAGCGCCGTTAAAGGTCATGG
          1 TCTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGG

                               *                       
        496 TCTTTAGCGGCGTTTGTGGTAAAAGCGCCGCTAAAGGTCATGG
          1 TCTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGG

            *   *            *    *    *       
        539 GCTTCAGCGGCGTTTGTTGGAATAGCGTCGCTAAA
          1 TCTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAA

        574 TTTCTTTAGC


Statistics
Matches: 258,  Mismatches: 33, Indels: 4
        0.87            0.11        0.01

Matches are distributed among these distances:
  42    4  0.02
  43  251  0.97
  44    3  0.01

ACGTcount: A:0.22, C:0.18, G:0.32, T:0.28


Consensus pattern (43 bp):   
TCTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGG

Found at i:5281 original size:20 final size:21

Alignment explanation


    Indices: 5237--5279  Score: 77
    Period size: 21  Copynumber: 2.0  Consensus size: 21

       5227 AACAACTCAC

                      *          
       5237 TTAGTTTAATGAATAAAAAGT
          1 TTAGTTTAATCAATAAAAAGT

                                 
       5258 TTAGTTTAATCAATAAAAAGT
          1 TTAGTTTAATCAATAAAAAGT

             
       5279 T
          1 T

       5280 AGAATCTCAC


Statistics
Matches: 21,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  21   21  1.00

ACGTcount: A:0.47, C:0.02, G:0.12, T:0.40


Consensus pattern (21 bp):   
TTAGTTTAATCAATAAAAAGT

Found at i:8105 original size:137 final size:137

Alignment explanation


    Indices: 7859--8168  Score: 604
    Period size: 137  Copynumber: 2.3  Consensus size: 137

       7849 GCGCAGTTGT

                                                                             
       7859 AGGATTTTGAAATGGGAGAAGTTGGA-CTCGTTTGGGTGTGGTTGAAATTGGTCATAAGAATTTG
          1 AGGATTTTGAAATGGGAGAAGTTGGAGC-CGTTTGGGTGTGGTTGAAATTGGTCATAAGAATTTG

                                                                             
       7923 AATTGAATTTGAATGGGGAGTTGGAGTAAATCAAGGAGAAAATTTCAGTGGAAGGGATTGGTGGA
         65 AATTGAATTTGAATGGGGAGTTGGAGTAAATCAAGGAGAAAATTTCAGTGGAAGGGATTGGTGGA

                    
       7988 GTTTTTGA
        130 GTTTTTGA

                                                                             
       7996 AGGATTTTGAAATGGGAGAAGTTGGAGCCGTTTGGGTGTGGTTGAAATTGGTCATAAGAATTTGA
          1 AGGATTTTGAAATGGGAGAAGTTGGAGCCGTTTGGGTGTGGTTGAAATTGGTCATAAGAATTTGA

                                                                             
       8061 ATTGAATTTGAATGGGGAGTTGGAGTAAATCAAGGAGAAAATTTCAGTGGAAGGGATTGGTGGAG
         66 ATTGAATTTGAATGGGGAGTTGGAGTAAATCAAGGAGAAAATTTCAGTGGAAGGGATTGGTGGAG

                   
       8126 TTTTTGA
        131 TTTTTGA

                                                
       8133 AGGATTTTGAAATGGGAGAAGTTGGAGCCGTTTGGG
          1 AGGATTTTGAAATGGGAGAAGTTGGAGCCGTTTGGG

       8169 GGGAGTTTTG


Statistics
Matches: 172,  Mismatches: 0, Indels: 2
        0.99            0.00        0.01

Matches are distributed among these distances:
 137  171  0.99
 138    1  0.01

ACGTcount: A:0.29, C:0.04, G:0.35, T:0.31


Consensus pattern (137 bp):   
AGGATTTTGAAATGGGAGAAGTTGGAGCCGTTTGGGTGTGGTTGAAATTGGTCATAAGAATTTGA
ATTGAATTTGAATGGGGAGTTGGAGTAAATCAAGGAGAAAATTTCAGTGGAAGGGATTGGTGGAG
TTTTTGA
Done.