Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold3675

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, 414

Length: 691
ACGTcount: A:0.30, C:0.15, G:0.14, T:0.41


Found at i:168 original size:24 final size:23

Alignment explanation


    Indices: 135--204  Score: 63
    Period size: 25  Copynumber: 3.0  Consensus size: 23

        125 AAATAAAAAT

                               *      
        135 TTTTAATTTTCCTATTATTGTTATTA
          1 TTTT-ATTTTCCTATT-TTATT-TTA

                      *             
        161 -TTTATTTTTACTATTTTATTTTA
          1 TTTTA-TTTTCCTATTTTATTTTA

                      *           
        184 TTTTATTTTCAT-TTTTATTTT
          1 TTTTATTTTCCTATTTTATTTT

        205 TGCAGGAAAA


Statistics
Matches: 38,  Mismatches: 4, Indels: 8
        0.76            0.08        0.16

Matches are distributed among these distances:
  22    9  0.24
  23    8  0.21
  24    9  0.24
  25   12  0.32

ACGTcount: A:0.20, C:0.06, G:0.01, T:0.73


Consensus pattern (23 bp):   
TTTTATTTTCCTATTTTATTTTA

Found at i:169 original size:25 final size:24

Alignment explanation


    Indices: 135--204  Score: 65
    Period size: 24  Copynumber: 3.0  Consensus size: 24

        125 AAATAAAAAT

                 *    *        *      
        135 TTTTAATTTTCCTATTATTGTTATTA
          1 TTTTATTTTTACTATT-TTATT-TTA

                                    
        161 -TTTATTTTTACTATTTTATTTTA
          1 TTTTATTTTTACTATTTTATTTTA

                     *             
        184 TTTTATTTTCA-T-TTTTATTTT
          1 TTTTATTTTTACTATTTTATTTT

        205 TGCAGGAAAA


Statistics
Matches: 39,  Mismatches: 4, Indels: 6
        0.80            0.08        0.12

Matches are distributed among these distances:
  22    9  0.23
  23    4  0.10
  24   13  0.33
  25   13  0.33

ACGTcount: A:0.20, C:0.06, G:0.01, T:0.73


Consensus pattern (24 bp):   
TTTTATTTTTACTATTTTATTTTA

Found at i:170 original size:6 final size:6

Alignment explanation


    Indices: 149--205  Score: 55
    Period size: 6  Copynumber: 9.3  Consensus size: 6

        139 AATTTTCCTA

                 *                                               *    
        149 TTATTG TTATTAT TTATTT TTACTATT TTA-TT TTA-TT TTATTT TCATTT
          1 TTATTT TTATT-T TTATTT TTA-T-TT TTATTT TTATTT TTATTT TTATTT

                     
        198 TTATTT TT
          1 TTATTT TT

        206 GCAGGAAAAC


Statistics
Matches: 44,  Mismatches: 3, Indels: 8
        0.80            0.05        0.15

Matches are distributed among these distances:
   5   10  0.23
   6   23  0.52
   7    6  0.14
   8    5  0.11

ACGTcount: A:0.19, C:0.04, G:0.02, T:0.75


Consensus pattern (6 bp):   
TTATTT
Done.