Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: CotAD_61055

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, 349

Length: 582
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26


Found at i:393 original size:198 final size:198

Alignment explanation


    Indices: 47--404  Score: 583
    Period size: 198  Copynumber: 1.8  Consensus size: 198

         37 GAAGTTCACA

                                                      *          *           
         47 CGGAGCAGATTGAAGCCACGACGGCGAATCTTATCTCCCTGGTGTTAAGGCTTGGATTAGCTGAA
          1 CGGAGCAGATTGAAGCCACGACGGCGAATCTTATCTCCCTGGCGTTAAGGCTTAGATTAGCTGAA

                  *                * *                            * **       
        112 GTGGAGTGGATTGAAGCTGTGGGTAGCGAATCCTATCTCTTTGGCATTACAGTGGAGCAGATTAA
         66 GTGGAGCGGATTGAAGCTGTGGGCAACGAATCCTATCTCTTTGGCATTACAGTGAAAAAGATTAA

                       *                                                     
        177 GGCCGCAACAGTGAATCTTACTCCCCTGGCAGTCCGCAACGACGAATCTTACTTCCCTGGCGTTG
        131 GGCCGCAACAGCGAATCTTACTCCCCTGGCAGTCCGCAACGACGAATCTTACTTCCCTGGCGTTG

               
        242 TAG
        196 TAG

                                    *                                        
        245 CGGAGCAGATTGAAGCCACGACGGTGAATCTTATCTCCCTGGCGTTAAGGCTTAGATTAGCTGAA
          1 CGGAGCAGATTGAAGCCACGACGGCGAATCTTATCTCCCTGGCGTTAAGGCTTAGATTAGCTGAA

                            *                                                
        310 GTGGAGCGGATTGAAGTTGTGGGCAACGAATCCTATCTCTTTGGCATTACAGTGAAAAAGATTGA
         66 GTGGAGCGGATTGAAGCTGTGGGCAACGAATCCTATCTCTTTGGCATTACAGTGAAAAAGATT-A

                      *            *       
        375 A-GCCGCAACGGCGAATCTTACTTCCCTGGC
        130 AGGCCGCAACAGCGAATCTTACTCCCCTGGC

        405 GGTCATTGTA


Statistics
Matches: 146,  Mismatches: 13, Indels: 2
        0.91            0.08        0.01

Matches are distributed among these distances:
 198  144  0.99
 199    2  0.01

ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25


Consensus pattern (198 bp):   
CGGAGCAGATTGAAGCCACGACGGCGAATCTTATCTCCCTGGCGTTAAGGCTTAGATTAGCTGAA
GTGGAGCGGATTGAAGCTGTGGGCAACGAATCCTATCTCTTTGGCATTACAGTGAAAAAGATTAA
GGCCGCAACAGCGAATCTTACTCCCCTGGCAGTCCGCAACGACGAATCTTACTTCCCTGGCGTTG
TAG

Found at i:504 original size:171 final size:167

Alignment explanation


    Indices: 210--570  Score: 605
    Period size: 171  Copynumber: 2.1  Consensus size: 167

        200 CCCTGGCAGT

                    *                                                  *     
        210 CCGCAACGACGAATCTTACTTCCCTGGCGTTGTAGCGGAGCAGATTGAAGCCACGACGGTGAATC
          1 CCGCAACGGCGAATCTTACTTCCCTGGCGTTGTAGCGGAGCAGATTGAAGCCACGACGGCGAATC

                       *                                 *     *             
        275 TTATCTCCCTGGCGTTAAGGCTTAGATTAGCTGAAGTGGAGCGGATTGAAGTTGTGGGCAACGAA
         66 TTATCTCCCTGACGTTAAGGCTTAGATTAGCTGAAGTGGAGCGGAATGAAGCTGTGGGCAACGAA

                       *                         
        340 TCCTATCTCTTTGGCATTACAGTGAAAAAGATTGAAG
        131 TCCTATCTCTTCGGCATTACAGTGAAAAAGATTGAAG

                                                                             
        377 CCGCAACGGCGAATCTTACTTCCCTGGCGGTCATTGTAGCGGAGCAGATTGAAGCCACGACGGCG
          1 CCGCAACGGCGAATCTTACTTCCCTGGC-G---TTGTAGCGGAGCAGATTGAAGCCACGACGGCG

                                       *                                    *
        442 AATCTTATCTCCCTGACGTTAAGGCTTGGATTAGCTGAAGTGGAGCGGAATGAAGCTGTGGGCAG
         62 AATCTTATCTCCCTGACGTTAAGGCTTAGATTAGCTGAAGTGGAGCGGAATGAAGCTGTGGGCAA

                                                     
        507 CGAATCCTATCTCTTCGGCATTACAGTGAAAAAGATTGAAG
        127 CGAATCCTATCTCTTCGGCATTACAGTGAAAAAGATTGAAG

                  *                
        548 CCGCAATGGCGAATCTTACTTCC
          1 CCGCAACGGCGAATCTTACTTCC

        571 TTGGTAGTGT


Statistics
Matches: 181,  Mismatches: 9, Indels: 4
        0.93            0.05        0.02

Matches are distributed among these distances:
 167   27  0.15
 168    1  0.01
 171  153  0.85

ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25


Consensus pattern (167 bp):   
CCGCAACGGCGAATCTTACTTCCCTGGCGTTGTAGCGGAGCAGATTGAAGCCACGACGGCGAATC
TTATCTCCCTGACGTTAAGGCTTAGATTAGCTGAAGTGGAGCGGAATGAAGCTGTGGGCAACGAA
TCCTATCTCTTCGGCATTACAGTGAAAAAGATTGAAG
Done.