Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold5630.1

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: 20066
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.34


Found at i:178 original size:99 final size:99

Alignment explanation


    Indices: 7--203  Score: 358
    Period size: 99  Copynumber: 2.0  Consensus size: 99

          1 ATCAAA

                                                                        *    
          7 TTTCAGATTTGTTGAGTGCAGAATTTTTTTTGGGGTTTTCTCCAAGAATTCTCTCTTGAATTTTC
          1 TTTCAGATTTGTTGAGTGCAGAATTTTTTTTGGGGTTTTCTCCAAGAATTCTCTCTTGAACTTTC

                                   *          
         72 TTTAGAAGTTGTTTTAACAATCTTTTGACTGTGT
         66 TTTAGAAGTTGTTTTAACAATCTCTTGACTGTGT

                                                                       *     
        106 TTTCAGATTTGTTGAGTGCAGAATTTTTTTTGGGGTTTTCTCCAAGAATTCTCTCTTGAGCTTTC
          1 TTTCAGATTTGTTGAGTGCAGAATTTTTTTTGGGGTTTTCTCCAAGAATTCTCTCTTGAACTTTC

                                        *    
        171 TTTAGAAGTTGTTTTAACAATCTCTTGATTGTG
         66 TTTAGAAGTTGTTTTAACAATCTCTTGACTGTG

        204 GGAGCCATCT


Statistics
Matches: 94,  Mismatches: 4, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  99   94  1.00

ACGTcount: A:0.20, C:0.13, G:0.19, T:0.49


Consensus pattern (99 bp):   
TTTCAGATTTGTTGAGTGCAGAATTTTTTTTGGGGTTTTCTCCAAGAATTCTCTCTTGAACTTTC
TTTAGAAGTTGTTTTAACAATCTCTTGACTGTGT

Found at i:1043 original size:21 final size:20

Alignment explanation


    Indices: 1016--1064  Score: 62
    Period size: 21  Copynumber: 2.4  Consensus size: 20

       1006 ATTAATCCCA

                     *            
       1016 CAAAAAAATCAGTCAAAAAAGT
          1 CAAAAAAA-AAGTCAAAAAA-T

                        *       
       1038 CAAAAAAAAAGTGAAAAAAT
          1 CAAAAAAAAAGTCAAAAAAT

                   
       1058 CAAAAAA
          1 CAAAAAA

       1065 GACGAAAGTC


Statistics
Matches: 25,  Mismatches: 2, Indels: 2
        0.86            0.07        0.07

Matches are distributed among these distances:
  20    8  0.32
  21    9  0.36
  22    8  0.32

ACGTcount: A:0.71, C:0.10, G:0.08, T:0.10


Consensus pattern (20 bp):   
CAAAAAAAAAGTCAAAAAAT

Found at i:11245 original size:21 final size:20

Alignment explanation


    Indices: 11218--11266  Score: 62
    Period size: 21  Copynumber: 2.4  Consensus size: 20

      11208 ATTAATCCCA

                     *            
      11218 CAAAAAAATCAGTCAAAAAAGT
          1 CAAAAAAA-AAGTCAAAAAA-T

                        *       
      11240 CAAAAAAAAAGTGAAAAAAT
          1 CAAAAAAAAAGTCAAAAAAT

                   
      11260 CAAAAAA
          1 CAAAAAA

      11267 GACGAAAGTC


Statistics
Matches: 25,  Mismatches: 2, Indels: 2
        0.86            0.07        0.07

Matches are distributed among these distances:
  20    8  0.32
  21    9  0.36
  22    8  0.32

ACGTcount: A:0.71, C:0.10, G:0.08, T:0.10


Consensus pattern (20 bp):   
CAAAAAAAAAGTCAAAAAAT
Done.