Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold3604

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, 427

Length: 712
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.32


Found at i:103 original size:45 final size:45

Alignment explanation


    Indices: 51--196  Score: 154
    Period size: 45  Copynumber: 3.3  Consensus size: 45

         41 GTCAGTACAT

                       * *                               
         51 GAAGACAAGATTTACTTTCTTCGATCTACTCCGCCACCAGTATGG
          1 GAAGACAAGATCTGCTTTCTTCGATCTACTCCGCCACCAGTATGG

                            *    *     *          *    ***
         96 GAAGACAAGATCTGCTATCTTTGATCTGCTCACG---CTAGTACAT
          1 GAAGACAAGATCTGCTTTCTTCGATCTACTC-CGCCACCAGTATGG

                 *               *        *              
        139 GAAGATAAGATCTGCTTTCTTGGATCTACTTCGCCACCAGTATGG
          1 GAAGACAAGATCTGCTTTCTTCGATCTACTCCGCCACCAGTATGG

                         
        184 GAAGACAAGATCT
          1 GAAGACAAGATCT

        197 TTTGTATTCA


Statistics
Matches: 78,  Mismatches: 19, Indels: 8
        0.74            0.18        0.08

Matches are distributed among these distances:
  42    2  0.03
  43   31  0.40
  45   43  0.55
  46    2  0.03

ACGTcount: A:0.28, C:0.23, G:0.20, T:0.29


Consensus pattern (45 bp):   
GAAGACAAGATCTGCTTTCTTCGATCTACTCCGCCACCAGTATGG

Found at i:157 original size:88 final size:89

Alignment explanation


    Indices: 6--196  Score: 287
    Period size: 88  Copynumber: 2.2  Consensus size: 89

          1 ATATA

                    *   *                                           *        
          6 GGAAGACAGGATTTGCTATCTTTGATCTACTTCACGTCAGTACATGAAGACAAGATTTACTTTCT
          1 GGAAGACAAGATCTGCTATCTTTGATCTACTTCACGTCAGTACATGAAGACAAGATCTACTTTCT

                                    
         71 TCGATCTACTCCGCCACCAGTATG
         66 TCGATCTACTCCGCCACCAGTATG

                                        *                      *       *     
         95 GGAAGACAAGATCTGCTATCTTTGATCTGC-TCACG-CTAGTACATGAAGATAAGATCTGCTTTC
          1 GGAAGACAAGATCTGCTATCTTTGATCTACTTCACGTC-AGTACATGAAGACAAGATCTACTTTC

              *        *             
        158 TTGGATCTACTTCGCCACCAGTATG
         65 TTCGATCTACTCCGCCACCAGTATG

                          
        183 GGAAGACAAGATCT
          1 GGAAGACAAGATCT

        197 TTTGTATTCA


Statistics
Matches: 93,  Mismatches: 8, Indels: 3
        0.89            0.08        0.03

Matches are distributed among these distances:
  87    1  0.01
  88   65  0.70
  89   27  0.29

ACGTcount: A:0.28, C:0.23, G:0.20, T:0.30


Consensus pattern (89 bp):   
GGAAGACAAGATCTGCTATCTTTGATCTACTTCACGTCAGTACATGAAGACAAGATCTACTTTCT
TCGATCTACTCCGCCACCAGTATG

Found at i:213 original size:88 final size:88

Alignment explanation


    Indices: 44--214  Score: 234
    Period size: 88  Copynumber: 1.9  Consensus size: 88

         34 ACTTCACGTC

                              *                                              
         44 AGTACATGAAGACAAGATTTACTTTCTTCGATCTACTCCGCCACCAGTATGGGAAGACAAGATCT
          1 AGTACATGAAGACAAGATCTACTTTCTTCGATCTACTCCGCCACCAGTATGGGAAGACAAGATCT

                 *  ** *           
        109 GCTATCTTTGATCTGCTCACGCT
         66 GCTATATTCAACCTGCTCACGCT

                        *       *       *        *                           
        132 AGTACATGAAGATAAGATCTGCTTTCTTGGATCTACTTCGCCACCAGTATGGGAAGACAAGATCT
          1 AGTACATGAAGACAAGATCTACTTTCTTCGATCTACTCCGCCACCAGTATGGGAAGACAAGATCT

            ** *              
        197 TTTGTATTCAACCTGCTC
         66 GCTATATTCAACCTGCTC

        215 CACTGTTGCT


Statistics
Matches: 71,  Mismatches: 12, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  88   71  1.00

ACGTcount: A:0.27, C:0.23, G:0.19, T:0.30


Consensus pattern (88 bp):   
AGTACATGAAGACAAGATCTACTTTCTTCGATCTACTCCGCCACCAGTATGGGAAGACAAGATCT
GCTATATTCAACCTGCTCACGCT
Done.