Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold3694

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, 410

Length: 684
ACGTcount: A:0.27, C:0.16, G:0.16, T:0.41


Found at i:303 original size:13 final size:14

Alignment explanation


    Indices: 284--314  Score: 53
    Period size: 14  Copynumber: 2.2  Consensus size: 14

        274 GCTTATATAA

                          
        284 TTTTTTTTACGGCG
          1 TTTTTTTTACGGCG

                    *     
        298 TTTTTTTTGCGGCG
          1 TTTTTTTTACGGCG

               
        312 TTT
          1 TTT

        315 ATTAAAAAAA


Statistics
Matches: 16,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  14   16  1.00

ACGTcount: A:0.03, C:0.13, G:0.23, T:0.61


Consensus pattern (14 bp):   
TTTTTTTTACGGCG

Found at i:500 original size:153 final size:154

Alignment explanation


    Indices: 326--614  Score: 429
    Period size: 153  Copynumber: 1.9  Consensus size: 154

        316 TTAAAAAAAC

                           *                             *     ***         * 
        326 GCCGCTATTGCTTACTTTTAGCGGCGCTTTTACGAGAAGCG-TCGTAAAAATTTTTTCATTTTGA
          1 GCCGCTATTGCTTACCTTTAGCGGCGCTTTTACGAGAAGCGCT-GCAAAAAAAATTTCATTTTAA

                        *          *                         *               
        390 ACAAAATGACGCTGTTTTGCTATTCTAAAAATTTTTTATTTTAT-TTTTTTATATATTGATTTAT
         65 ACAAAATGACGCCGTTTTGCTATGCTAAAAATTTTTTATTTTATATTTTATATATATTGATTTAT

                                     
        454 TCTTTGCCGTGTTTTTTTAACAAAT
        130 TCTTTGCCGTGTTTTTTTAACAAAT

                                      *     *   *                            
        479 GCCGCTATTGCTTACCTTTAGCGGCGTTTTTATGAGGAGCGCTGCAAAAAAAATTTCATTTTAAA
          1 GCCGCTATTGCTTACCTTTAGCGGCGCTTTTACGAGAAGCGCTGCAAAAAAAATTTCATTTTAAA

                                                                          *  
        544 CAAAATGACGCCGTTTTGCTATGCTAAAAATTTTTTATTTTATATTTTATATATATTGATTTGTT
         66 CAAAATGACGCCGTTTTGCTATGCTAAAAATTTTTTATTTTATATTTTATATATATTGATTTATT

            *     
        609 TTTTGC
        131 CTTTGC

        615 GGCGTGAAAA


Statistics
Matches: 120,  Mismatches: 14, Indels: 3
        0.88            0.10        0.02

Matches are distributed among these distances:
 153   95  0.79
 154   25  0.21

ACGTcount: A:0.26, C:0.14, G:0.15, T:0.46


Consensus pattern (154 bp):   
GCCGCTATTGCTTACCTTTAGCGGCGCTTTTACGAGAAGCGCTGCAAAAAAAATTTCATTTTAAA
CAAAATGACGCCGTTTTGCTATGCTAAAAATTTTTTATTTTATATTTTATATATATTGATTTATT
CTTTGCCGTGTTTTTTTAACAAAT
Done.