Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold616

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: 10486
ACGTcount: A:0.32, C:0.23, G:0.15, T:0.30


Found at i:97 original size:39 final size:39

Alignment explanation


    Indices: 1--163  Score: 183
    Period size: 38  Copynumber: 4.3  Consensus size: 39

                           *                 *     
          1 CCGGATATAGCAACTCGCACAAATGCC-T-GGGTCTTAG
          1 CCGGATATAGCAACTAGCACAAATGCCTTCGGGACTTAG

                                     *      *        
         38 CCCGGATATAGTC-AC-AGCACAAAAGCCTTCAGGACTTAG
          1 -CCGGATATAG-CAACTAGCACAAATGCCTTCGGGACTTAG

                           *       *               
         77 CCGGATATAGCAACTCGCACAAACGCCTTCGGGACTTAG
          1 CCGGATATAGCAACTAGCACAAATGCCTTCGGGACTTAG

              *       *           *           *    
        116 CCCGATATAGTAA-TAGCACAACTGCCTTCGGGATTTAG
          1 CCGGATATAGCAACTAGCACAAATGCCTTCGGGACTTAG

                      
        154 CCGGATATAG
          1 CCGGATATAG

        164 TCTATTGCCA


Statistics
Matches: 106,  Mismatches: 14, Indels: 10
        0.82            0.11        0.08

Matches are distributed among these distances:
  37   11  0.10
  38   55  0.52
  39   40  0.38

ACGTcount: A:0.29, C:0.27, G:0.23, T:0.21


Consensus pattern (39 bp):   
CCGGATATAGCAACTAGCACAAATGCCTTCGGGACTTAG

Found at i:154 original size:77 final size:76

Alignment explanation


    Indices: 1--163  Score: 229
    Period size: 77  Copynumber: 2.1  Consensus size: 76

                                   *       *                 *               
          1 CCGGATATAGCAACTCGCACAAATGCCTGGGTCTTAGCCCGGATATAGTCACAGCACAAAAGCCT
          1 CCGGATATAGCAACTCGCACAAACGCCTGGGACTTAGCCCGGATATAGTAACAGCACAAAAGCCT

                       
         66 TCAGGACTTAG
         66 TCAGGACTTAG

                                                                 *       **  
         77 CCGGATATAGCAACTCGCACAAACGCCTTCGGGACTTAGCCC-GATATAGTAATAGCACAACTGC
          1 CCGGATATAGCAACTCGCACAAACGCC-T-GGGACTTAGCCCGGATATAGTAACAGCACAAAAGC

                *   *    
        141 CTTCGGGATTTAG
         64 CTTCAGGACTTAG

                      
        154 CCGGATATAG
          1 CCGGATATAG

        164 TCTATTGCCA


Statistics
Matches: 77,  Mismatches: 8, Indels: 3
        0.88            0.09        0.03

Matches are distributed among these distances:
  76   26  0.34
  77   40  0.52
  78   11  0.14

ACGTcount: A:0.29, C:0.27, G:0.23, T:0.21


Consensus pattern (76 bp):   
CCGGATATAGCAACTCGCACAAACGCCTGGGACTTAGCCCGGATATAGTAACAGCACAAAAGCCT
TCAGGACTTAG

Found at i:8425 original size:40 final size:40

Alignment explanation


    Indices: 8264--8480  Score: 331
    Period size: 39  Copynumber: 5.6  Consensus size: 40

       8254 AACCCAAGTA

                     *                     *         
       8264 CCTTCGGGATTTAG-CCGGATATAG-CAACTCGCACAAATG
          1 CCTTCGGGACTTAGCCCGGATATAGTC-ACTAGCACAAATG

                    *                               
       8303 CCTTCGGGTCTTAG-CCGGATATAGTCACTAGCACAAA-G
          1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG

                                                  * 
       8341 CCTTCGGGACTTAGCCCGGATATAG-CACT-GCACAAAAG
          1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG

                                        *           
       8379 CCTTCGGGACTTAGCCCGGATATAGTCAATAGCACAAATG
          1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG

                                                    
       8419 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
          1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG

                                   
       8459 CCTTC-GGACTTAGCCCGGATAT
          1 CCTTCGGGACTTAGCCCGGATAT

       8481 CATCGAATAA


Statistics
Matches: 166,  Mismatches: 7, Indels: 10
        0.91            0.04        0.05

Matches are distributed among these distances:
  37    7  0.04
  38   44  0.27
  39   62  0.37
  40   53  0.32

ACGTcount: A:0.27, C:0.27, G:0.23, T:0.23


Consensus pattern (40 bp):   
CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
Done.