Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: CotAD_71151

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, 217

Length: 363
ACGTcount: A:0.31, C:0.22, G:0.23, T:0.23


Found at i:225 original size:43 final size:44

Alignment explanation


    Indices: 94--281  Score: 161
    Period size: 44  Copynumber: 4.3  Consensus size: 44

         84 TATTTTCCCA

                                                        
         94 AGTAGTGGAGCAGATCGAAAGCA-CCAGCCTTATCTCCCTGAGC
          1 AGTAGTGGAGCAGATCGAAAGCATCCAGCCTTATCTCCCTGAGC

              *  *    *  *           **   *           *   
        137 AGCAGCGGAGTAGGTCG-AAG-ATTGTAGATCTTATCTCCCTAAGC
          1 AGTAGTGGAGCAGATCGAAAGCA-TCCAG-CCTTATCTCCCTGAGC

                                                        
        181 AGTAGTGGAGCAGATCGAAAGCA-CCAGCCTTATCTCCCTGAGC
          1 AGTAGTGGAGCAGATCGAAAGCATCCAGCCTTATCTCCCTGAGC

              *  *    *   *    ** *      *              *
        224 AGCAGCGGA-TAGAGCAGATCGTATCCAGTCTTATCTCCCTGAGA
          1 AGTAGTGGAGCAGATC-GAAAGCATCCAGCCTTATCTCCCTGAGC

                          
        268 AGTAGTGGAGCAGA
          1 AGTAGTGGAGCAGA

        282 CAGAAGAAAC


Statistics
Matches: 109,  Mismatches: 28, Indels: 14
        0.72            0.19        0.09

Matches are distributed among these distances:
  41    1  0.01
  42    7  0.06
  43   40  0.37
  44   54  0.50
  45    6  0.06
  46    1  0.01

ACGTcount: A:0.28, C:0.24, G:0.27, T:0.21


Consensus pattern (44 bp):   
AGTAGTGGAGCAGATCGAAAGCATCCAGCCTTATCTCCCTGAGC

Found at i:256 original size:87 final size:86

Alignment explanation


    Indices: 93--281  Score: 276
    Period size: 87  Copynumber: 2.2  Consensus size: 86

         83 TTATTTTCCC

                                                                             
         93 AAGTAGTGGAGCAGATCGAAAGCACCAGCCTTATCTCCCTGAGCAGCAGCGGAGTAGGTCGAAGA
          1 AAGTAGTGGAGCAGATCGAAAGCACCAGCCTTATCTCCCTGAGCAGCAGCGGAGTAGGTC-AAGA

             *   *                
        158 TTGTAGATCTTATCTCCCTAAG
         65 TCGTACATCTTATCTCCCTAAG

            *                                                                
        180 CAGTAGTGGAGCAGATCGAAAGCACCAGCCTTATCTCCCTGAGCAGCAGCGGA-TAGAG-C-AGA
          1 AAGTAGTGGAGCAGATCGAAAGCACCAGCCTTATCTCCCTGAGCAGCAGCGGAGTAG-GTCAAGA

                                  *  
        242 TCGTATCCAGTCTTATCTCCCTGAG
         65 TCGTA--CA-TCTTATCTCCCTAAG

                           
        267 AAGTAGTGGAGCAGA
          1 AAGTAGTGGAGCAGA

        282 CAGAAGAAAC


Statistics
Matches: 93,  Mismatches: 5, Indels: 8
        0.88            0.05        0.08

Matches are distributed among these distances:
  84    7  0.08
  86    5  0.05
  87   81  0.87

ACGTcount: A:0.29, C:0.24, G:0.27, T:0.21


Consensus pattern (86 bp):   
AAGTAGTGGAGCAGATCGAAAGCACCAGCCTTATCTCCCTGAGCAGCAGCGGAGTAGGTCAAGAT
CGTACATCTTATCTCCCTAAG

Found at i:302 original size:87 final size:86

Alignment explanation


    Indices: 93--308  Score: 235
    Period size: 87  Copynumber: 2.5  Consensus size: 86

         83 TTATTTTCCC

                                  *    *  *                                  
         93 AAGTAGTGGAGCAGATCGAAAGCACCAGCCTTATCTCCCTGAGCAGCAGCGGAGTAGGTCGAAGA
          1 AAGTAGTGGAGCAGATCGAAAGAACCAACCATATCTCCCTGAGCAGCAGCGGAGTAGGTC-AAGA

             *   *                
        158 TTGTAGATCTTATCTCCCTAAG
         65 TCGTACATCTTATCTCCCTAAG

            *                     *    *  *                                  
        180 CAGTAGTGGAGCAGATCGAAAGCACCAGCCTTATCTCCCTGAGCAGCAGCGGA-TAGAG-C-AGA
          1 AAGTAGTGGAGCAGATCGAAAGAACCAACCATATCTCCCTGAGCAGCAGCGGAGTAG-GTCAAGA

                                  *  
        242 TCGTATCCAGTCTTATCTCCCTGAG
         65 TCGTA--CA-TCTTATCTCCCTAAG

                                          *             
        267 AAGTAGTGGAGCAGA-C-AGAAGAAACCAATCATATCTCCCTGA
          1 AAGTAGTGGAGCAGATCGA-AAG-AACCAACCATATCTCCCTGA

        309 AGTAGCAGTG


Statistics
Matches: 114,  Mismatches: 9, Indels: 12
        0.84            0.07        0.09

Matches are distributed among these distances:
  84    7  0.06
  85    1  0.01
  86    9  0.08
  87   97  0.85

ACGTcount: A:0.30, C:0.25, G:0.25, T:0.20


Consensus pattern (86 bp):   
AAGTAGTGGAGCAGATCGAAAGAACCAACCATATCTCCCTGAGCAGCAGCGGAGTAGGTCAAGAT
CGTACATCTTATCTCCCTAAG
Done.