Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: CotAD_73839

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: 2613
ACGTcount: A:0.28, C:0.18, G:0.27, T:0.27


Found at i:2310 original size:117 final size:117

Alignment explanation


    Indices: 2153--2375  Score: 365
    Period size: 117  Copynumber: 1.9  Consensus size: 117

       2143 GGTGGCTGCA

                                      *                *                     
       2153 GTGGTTGTGGCGCTGGATGTGGAAACGTGGTGAAGAGTGGTGGTTGTGGTAGTGGTTGCGGCAGT
          1 GTGGTTGTGGCGCTGGATGTGGAAACATGGTGAAGAGTGGTGGCTGTGGTAGTGGTTGCGGCAGT

                 *                             *                
       2218 GGATGTGGGGGTGGTTGTGGAAGCATAGTGAATAGTGGCAGCTGCGGTGCCG
         66 GGATGCGGGGGTGGTTGTGGAAGCATAGTGAATAGCGGCAGCTGCGGTGCCG

                      *                                       *          **  
       2270 GTGGTTGTGGTGCTGGATGTGGAAACATGGTGAAGAGTGGTGGCTGTGGTGGTGGTTGCGGGGGT
          1 GTGGTTGTGGCGCTGGATGTGGAAACATGGTGAAGAGTGGTGGCTGTGGTAGTGGTTGCGGCAGT

              *                                      
       2335 GGGTGCGGGGGTGGTTGTGGAAGCATAGTGAATAGCGGCAG
         66 GGATGCGGGGGTGGTTGTGGAAGCATAGTGAATAGCGGCAG

       2376 TTGTGGCTCT


Statistics
Matches: 97,  Mismatches: 9, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
 117   97  1.00

ACGTcount: A:0.15, C:0.09, G:0.50, T:0.26


Consensus pattern (117 bp):   
GTGGTTGTGGCGCTGGATGTGGAAACATGGTGAAGAGTGGTGGCTGTGGTAGTGGTTGCGGCAGT
GGATGCGGGGGTGGTTGTGGAAGCATAGTGAATAGCGGCAGCTGCGGTGCCG

Found at i:2335 original size:12 final size:12

Alignment explanation


    Indices: 2320--2351  Score: 55
    Period size: 12  Copynumber: 2.7  Consensus size: 12

       2310 TGGCTGTGGT

                        
       2320 GGTGGTTGCGGG
          1 GGTGGTTGCGGG

                 *      
       2332 GGTGGGTGCGGG
          1 GGTGGTTGCGGG

                    
       2344 GGTGGTTG
          1 GGTGGTTG

       2352 TGGAAGCATA


Statistics
Matches: 18,  Mismatches: 2, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  12   18  1.00

ACGTcount: A:0.00, C:0.06, G:0.69, T:0.25


Consensus pattern (12 bp):   
GGTGGTTGCGGG

Found at i:2481 original size:15 final size:15

Alignment explanation


    Indices: 2461--2498  Score: 76
    Period size: 15  Copynumber: 2.5  Consensus size: 15

       2451 GGAGAACAGT

                           
       2461 GGTTGTGGCGGTGGC
          1 GGTTGTGGCGGTGGC

                           
       2476 GGTTGTGGCGGTGGC
          1 GGTTGTGGCGGTGGC

                    
       2491 GGTTGTGG
          1 GGTTGTGG

       2499 TGGTTGTGGC


Statistics
Matches: 23,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  15   23  1.00

ACGTcount: A:0.00, C:0.11, G:0.61, T:0.29


Consensus pattern (15 bp):   
GGTTGTGGCGGTGGC
Done.