Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: CotAD_43571

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: 2232
ACGTcount: A:0.33, C:0.23, G:0.21, T:0.23


Found at i:551 original size:159 final size:159

Alignment explanation


    Indices: 388--1050  Score: 1086
    Period size: 159  Copynumber: 4.2  Consensus size: 159

        378 CTTTTGGGAA

                                                                             
        388 CATCCTCAACCAACAAGCCAACCTCAATTGAATGAAACACGTCAGAACCAGACTCTGATTCATCA
          1 CATCCTCAACCAACAAGCCAACCTCAATTGAATGAAACACGTCAGAACCAGACTCTGATTCATCA

            * *         *                            *                       
        453 GTTAAACTCTCAGCATACTGGGCAATTTCAATCGAATGTAGTAGGTCAGAGTCAAACAGATCTAA
         66 CTCAAACTCTCACCATACTGGGCAATTTCAATCGAATGTAGCAGGTCAGAGTCAAACAGATCTAA

             *  *  *                     
        518 CAAATTCTGTGCCGAGTGACAGCTTGGTG
        131 CGAACTCAGTGCCGAGTGACAGCTTGGTG

                                                 *                           
        547 CATCCTCAACCAACAAGCCAACCTCAATTGAATGAAAGACGTCAGAACCAGACTCTGATTCATCA
          1 CATCCTCAACCAACAAGCCAACCTCAATTGAATGAAACACGTCAGAACCAGACTCTGATTCATCA

                                  *                                          
        612 CTCAAACTCTCACCATACTGGGAAATTTCAATCGAATGT---A-G-CAG-GTCAAACAGATCTAA
         66 CTCAAACTCTCACCATACTGGGCAATTTCAATCGAATGTAGCAGGTCAGAGTCAAACAGATCTAA

                                         
        671 CGAACTCAGTGCCGAGTGACAGCTTGGTG
        131 CGAACTCAGTGCCGAGTGACAGCTTGGTG

                                                                             
        700 CATCCTCAACCAACAAGCCAACCTCAATTGAATGAAACACGTCAGAACCAGACTCTGATTCATCA
          1 CATCCTCAACCAACAAGCCAACCTCAATTGAATGAAACACGTCAGAACCAGACTCTGATTCATCA

               *                          *            *                     
        765 CTCGAACTCTCACCATACTGGGCAATTTCATTCGAATGTAGCACGTCAGAGTCAAACAGATCTAA
         66 CTCAAACTCTCACCATACTGGGCAATTTCAATCGAATGTAGCAGGTCAGAGTCAAACAGATCTAA

                *                    *   
        830 CGAATTCAGTGCCGAGTGACAGCTTTGTG
        131 CGAACTCAGTGCCGAGTGACAGCTTGGTG

                             *                                               
        859 CATCCTCAACCAACAAGTCAACCTCAATTGAATGAAACACGTCAGAACCAGACTCTGATTCATCA
          1 CATCCTCAACCAACAAGCCAACCTCAATTGAATGAAACACGTCAGAACCAGACTCTGATTCATCA

               *        *                *          *              *         
        924 CTCGAACTCTCAGCATACTGGGCAATTTCGATCGAATGTACCAGGTCAGAGTCAAGCAGATCTAA
         66 CTCAAACTCTCACCATACTGGGCAATTTCAATCGAATGTAGCAGGTCAGAGTCAAACAGATCTAA

                        *                
        989 CGAACTCAGTGCAGAGTGACAGCTTGGTG
        131 CGAACTCAGTGCCGAGTGACAGCTTGGTG

            *                                
       1018 TATCCTCAACCAACAAGCCAACCTCAATTGAAT
          1 CATCCTCAACCAACAAGCCAACCTCAATTGAAT

       1051 CACGGATACT


Statistics
Matches: 472,  Mismatches: 26, Indels: 12
        0.93            0.05        0.02

Matches are distributed among these distances:
 153  141  0.30
 154    3  0.01
 155    1  0.00
 156    2  0.00
 157    1  0.00
 158    3  0.01
 159  321  0.68

ACGTcount: A:0.34, C:0.27, G:0.17, T:0.22


Consensus pattern (159 bp):   
CATCCTCAACCAACAAGCCAACCTCAATTGAATGAAACACGTCAGAACCAGACTCTGATTCATCA
CTCAAACTCTCACCATACTGGGCAATTTCAATCGAATGTAGCAGGTCAGAGTCAAACAGATCTAA
CGAACTCAGTGCCGAGTGACAGCTTGGTG

Found at i:815 original size:312 final size:316

Alignment explanation


    Indices: 388--1050  Score: 1109
    Period size: 312  Copynumber: 2.1  Consensus size: 316

        378 CTTTTGGGAA

                                                                             
        388 CATCCTCAACCAACAAGCCAACCTCAATTGAATGAAACACGTCAGAACCAGACTCTGATTCATCA
          1 CATCCTCAACCAACAAGCCAACCTCAATTGAATGAAACACGTCAGAACCAGACTCTGATTCATCA

            * *         *                            * *                     
        453 GTTAAACTCTCAGCATACTGGGCAATTTCAATCGAATGTAGTAGGTCAGAGTCAAACAGATCTAA
         66 CTCAAACTCTCACCATACTGGGCAATTTCAATCGAATGTAGCACGTCAGAGTCAAACAGATCTAA

                   *                                                         
        518 CAAATTCTGTGCCGAGTGACAGCTTGGTGCATCCTCAACCAACAAGCCAACCTCAATTGAATGAA
        131 CAAATTCAGTGCCGAGTGACAGCTTGGTGCATCCTCAACCAACAAGCCAACCTCAATTGAATGAA

             *                                                               
        583 AGACGTCAGAACCAGACTCTGATTCATCACTCAAACTCTCACCATACTGGGAAATTTCAATCGAA
        196 ACACGTCAGAACCAGACTCTGATTCATCACTCAAACTCTCACCATACTGGGAAATTTCAATCGAA

                                                   *                
        648 TGT-A-G-CAG-GTCAAACAGATCTAACGAACTCAGTGCCGAGTGACAGCTTGGTG
        261 TGTCAGGTCAGAGTCAAACAGATCTAACGAACTCAGTGCAGAGTGACAGCTTGGTG

                                                                             
        700 CATCCTCAACCAACAAGCCAACCTCAATTGAATGAAACACGTCAGAACCAGACTCTGATTCATCA
          1 CATCCTCAACCAACAAGCCAACCTCAATTGAATGAAACACGTCAGAACCAGACTCTGATTCATCA

               *                          *                                  
        765 CTCGAACTCTCACCATACTGGGCAATTTCATTCGAATGTAGCACGTCAGAGTCAAACAGATCTAA
         66 CTCAAACTCTCACCATACTGGGCAATTTCAATCGAATGTAGCACGTCAGAGTCAAACAGATCTAA

             *                       *                    *                  
        830 CGAATTCAGTGCCGAGTGACAGCTTTGTGCATCCTCAACCAACAAGTCAACCTCAATTGAATGAA
        131 CAAATTCAGTGCCGAGTGACAGCTTGGTGCATCCTCAACCAACAAGCCAACCTCAATTGAATGAA

                                            *        *         *      *      
        895 ACACGTCAGAACCAGACTCTGATTCATCACTCGAACTCTCAGCATACTGGGCAATTTCGATCGAA
        196 ACACGTCAGAACCAGACTCTGATTCATCACTCAAACTCTCACCATACTGGGAAATTTCAATCGAA

                               *                                      
        960 TGTACCAGGTCAGAGTCAAGCAGATCTAACGAACTCAGTGCAGAGTGACAGCTTGGTG
        261 TGT--CAGGTCAGAGTCAAACAGATCTAACGAACTCAGTGCAGAGTGACAGCTTGGTG

            *                                
       1018 TATCCTCAACCAACAAGCCAACCTCAATTGAAT
          1 CATCCTCAACCAACAAGCCAACCTCAATTGAAT

       1051 CACGGATACT


Statistics
Matches: 326,  Mismatches: 19, Indels: 6
        0.93            0.05        0.02

Matches are distributed among these distances:
 312  247  0.76
 315    1  0.00
 316    1  0.00
 317    3  0.01
 318   74  0.23

ACGTcount: A:0.34, C:0.27, G:0.17, T:0.22


Consensus pattern (316 bp):   
CATCCTCAACCAACAAGCCAACCTCAATTGAATGAAACACGTCAGAACCAGACTCTGATTCATCA
CTCAAACTCTCACCATACTGGGCAATTTCAATCGAATGTAGCACGTCAGAGTCAAACAGATCTAA
CAAATTCAGTGCCGAGTGACAGCTTGGTGCATCCTCAACCAACAAGCCAACCTCAATTGAATGAA
ACACGTCAGAACCAGACTCTGATTCATCACTCAAACTCTCACCATACTGGGAAATTTCAATCGAA
TGTCAGGTCAGAGTCAAACAGATCTAACGAACTCAGTGCAGAGTGACAGCTTGGTG
Done.