Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold4618

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, 304

Length: 508
ACGTcount: A:0.36, C:0.23, G:0.18, T:0.23


Found at i:171 original size:45 final size:45

Alignment explanation


    Indices: 105--400  Score: 412
    Period size: 45  Copynumber: 6.6  Consensus size: 45

         95 AGTATACAGT

                *     *   *              *             * 
        105 AATCAGTAACGGTAGCAGTAACAGTATTCAACACACAAAGTGCTG
          1 AATCGGTAACAGTAACAGTAACAGTATTCGACACACAAAGTGCCG

                *           *                            
        150 AATCTGTAACAGTAACGGTAACAGTATTCGACACACAAAGTGCCG
          1 AATCGGTAACAGTAACAGTAACAGTATTCGACACACAAAGTGCCG

             *   *                       *             * 
        195 AGTCGATAACAGTAACAGTAACAGTATTCAACACACAAAGTGCTG
          1 AATCGGTAACAGTAACAGTAACAGTATTCGACACACAAAGTGCCG

                *           *                            
        240 AATCTGTAACAGTAACGGTAACAGTATTCGACACACAAAGTGCCG
          1 AATCGGTAACAGTAACAGTAACAGTATTCGACACACAAAGTGCCG

             *         *                                 
        285 AGTCGGTAACAATAACAGTAACAGTATTCGACACACAAAGTGCCG
          1 AATCGGTAACAGTAACAGTAACAGTATTCGACACACAAAGTGCCG

             *                   *                       
        330 AGTCGGTAACAGTAACAGTAATAGTATTCGACACACAAAGTGCCG
          1 AATCGGTAACAGTAACAGTAACAGTATTCGACACACAAAGTGCCG

                *      *    *         
        375 AATCAGTAACAATAACGGTAACAGTA
          1 AATCGGTAACAGTAACAGTAACAGTA

        401 ACAGTAGTCG


Statistics
Matches: 222,  Mismatches: 29, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  45  222  1.00

ACGTcount: A:0.40, C:0.21, G:0.20, T:0.20


Consensus pattern (45 bp):   
AATCGGTAACAGTAACAGTAACAGTATTCGACACACAAAGTGCCG

Found at i:243 original size:90 final size:90

Alignment explanation


    Indices: 120--400  Score: 456
    Period size: 90  Copynumber: 3.1  Consensus size: 90

        110 GTAACGGTAG

                                                                             
        120 CAGTAACAGTATTCAACACACAAAGTGCTGAATCTGTAACAGTAACGGTAACAGTATTCGACACA
          1 CAGTAACAGTATTCAACACACAAAGTGCTGAATCTGTAACAGTAACGGTAACAGTATTCGACACA

                                 *   
        185 CAAAGTGCCGAGTCGATAACAGTAA
         66 CAAAGTGCCGAGTCGATAACAATAA

                                                                             
        210 CAGTAACAGTATTCAACACACAAAGTGCTGAATCTGTAACAGTAACGGTAACAGTATTCGACACA
          1 CAGTAACAGTATTCAACACACAAAGTGCTGAATCTGTAACAGTAACGGTAACAGTATTCGACACA

                           *         
        275 CAAAGTGCCGAGTCGGTAACAATAA
         66 CAAAGTGCCGAGTCGATAACAATAA

                          *             *  *  *           *    *             
        300 CAGTAACAGTATTCGACACACAAAGTGCCGAGTCGGTAACAGTAACAGTAATAGTATTCGACACA
          1 CAGTAACAGTATTCAACACACAAAGTGCTGAATCTGTAACAGTAACGGTAACAGTATTCGACACA

                       *              
        365 CAAAGTGCCGAATC-AGTAACAATAA
         66 CAAAGTGCCGAGTCGA-TAACAATAA

             *         
        390 CGGTAACAGTA
          1 CAGTAACAGTA

        401 ACAGTAGTCG


Statistics
Matches: 179,  Mismatches: 11, Indels: 2
        0.93            0.06        0.01

Matches are distributed among these distances:
  90  179  1.00

ACGTcount: A:0.40, C:0.21, G:0.19, T:0.20


Consensus pattern (90 bp):   
CAGTAACAGTATTCAACACACAAAGTGCTGAATCTGTAACAGTAACGGTAACAGTATTCGACACA
CAAAGTGCCGAGTCGATAACAATAA

Done.