Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold3416

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: 30781
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.31


Found at i:6285 original size:13 final size:12

Alignment explanation


    Indices: 6235--6282  Score: 78
    Period size: 12  Copynumber: 4.0  Consensus size: 12

       6225 TAGTAGTTTC

                       *
       6235 TTCAAAAAAAAT
          1 TTCAAAAAAAAA

               *        
       6247 TTCGAAAAAAAA
          1 TTCAAAAAAAAA

                        
       6259 TTCAAAAAAAAA
          1 TTCAAAAAAAAA

                        
       6271 TTCAAAAAAAAA
          1 TTCAAAAAAAAA

       6283 ATTTGGTTTC


Statistics
Matches: 33,  Mismatches: 3, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  12   33  1.00

ACGTcount: A:0.71, C:0.08, G:0.02, T:0.19


Consensus pattern (12 bp):   
TTCAAAAAAAAA

Found at i:6343 original size:15 final size:15

Alignment explanation


    Indices: 6323--6377  Score: 110
    Period size: 15  Copynumber: 3.7  Consensus size: 15

       6313 GATATCAAGT

                           
       6323 TGAAAAAAAAATTCG
          1 TGAAAAAAAAATTCG

                           
       6338 TGAAAAAAAAATTCG
          1 TGAAAAAAAAATTCG

                           
       6353 TGAAAAAAAAATTCG
          1 TGAAAAAAAAATTCG

                      
       6368 TGAAAAAAAA
          1 TGAAAAAAAA

       6378 GAAGAAGCTA


Statistics
Matches: 40,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  15   40  1.00

ACGTcount: A:0.64, C:0.05, G:0.13, T:0.18


Consensus pattern (15 bp):   
TGAAAAAAAAATTCG

Found at i:12340 original size:23 final size:22

Alignment explanation


    Indices: 12289--12340  Score: 54
    Period size: 23  Copynumber: 2.3  Consensus size: 22

      12279 CCTCGTCTTT

                   *              
      12289 TTCTTTTGTTTCTTTTTCTAAC
          1 TTCTTTTCTTTCTTTTTCTAAC

                                     
      12311 -TCATTTTCTCTTCTTTCTTC-AAC
          1 TTC-TTTTCT-TTCTTT-TTCTAAC

                   
      12334 TTCTTTT
          1 TTCTTTT

      12341 TCAATTTTCT


Statistics
Matches: 25,  Mismatches: 1, Indels: 7
        0.76            0.03        0.21

Matches are distributed among these distances:
  21    2  0.08
  22    5  0.20
  23   13  0.52
  24    5  0.20

ACGTcount: A:0.10, C:0.23, G:0.02, T:0.65


Consensus pattern (22 bp):   
TTCTTTTCTTTCTTTTTCTAAC
Done.