Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold1889

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, 735

Length: 1225
ACGTcount: A:0.30, C:0.19, G:0.16, T:0.35


Found at i:276 original size:6 final size:6

Alignment explanation


    Indices: 265--347  Score: 59
    Period size: 6  Copynumber: 14.3  Consensus size: 6

        255 CCCAGCGAGG

                                                          ***       
        265 TTCTTT TTCTTT TTCTTT TTCTCTT TT-TTT TTC-TT TTCCCC TT-TTT
          1 TTCTTT TTCTTT TTCTTT TTCT-TT TTCTTT TTCTTT TTCTTT TTCTTT

              *      *             *                     
        311 TTGTTT TTGTTT TT-TTT TTGTTT TCTCTTT TT-TTT TT
          1 TTCTTT TTCTTT TTCTTT TTCTTT T-TCTTT TTCTTT TT

        348 GGATTAAATC


Statistics
Matches: 65,  Mismatches: 6, Indels: 13
        0.77            0.07        0.15

Matches are distributed among these distances:
   5   21  0.32
   6   35  0.54
   7    9  0.14

ACGTcount: A:0.00, C:0.14, G:0.04, T:0.82


Consensus pattern (6 bp):   
TTCTTT

Found at i:301 original size:17 final size:17

Alignment explanation


    Indices: 265--346  Score: 80
    Period size: 18  Copynumber: 4.8  Consensus size: 17

        255 CCCAGCGAGG

                               
        265 TTCT-TTTTCTTTTTCTTT
          1 TTCTCTTTT-TTTTTC-TT

                             
        283 TTCTCTTTTTTTTTCTT
          1 TTCTCTTTTTTTTTCTT

                *        *    
        300 TTCCCCTTTTTTTGT-TT
          1 TT-CTCTTTTTTTTTCTT

              *           *  
        317 TTGT-TTTTTTTTTGTT
          1 TTCTCTTTTTTTTTCTT

                          
        333 TTCTCTTTTTTTTT
          1 TTCTCTTTTTTTTT

        347 TGGATTAAAT


Statistics
Matches: 54,  Mismatches: 6, Indels: 9
        0.78            0.09        0.13

Matches are distributed among these distances:
  15    8  0.15
  16    5  0.09
  17   17  0.31
  18   20  0.37
  19    4  0.07

ACGTcount: A:0.00, C:0.15, G:0.04, T:0.82


Consensus pattern (17 bp):   
TTCTCTTTTTTTTTCTT

Found at i:347 original size:18 final size:17

Alignment explanation


    Indices: 265--348  Score: 80
    Period size: 17  Copynumber: 4.8  Consensus size: 17

        255 CCCAGCGAGG

                          *   
        265 TTCTTTTTCTTTTTCTTT
          1 TTCTTTTT-TTTTTGTTT

                           *  
        283 TTCTCTTTTTTTTT-CTT
          1 TTCT-TTTTTTTTTGTTT

               ***           
        300 TTCCCCTTTTTTTGTTT
          1 TTCTTTTTTTTTTGTTT

              *              
        317 TTGTTTTTTTTTTGTTT
          1 TTCTTTTTTTTTTGTTT

                           
        334 TCTCTTTTTTTTTTG
          1 T-TCTTTTTTTTTTG

        349 GATTAAATCT


Statistics
Matches: 53,  Mismatches: 10, Indels: 6
        0.77            0.14        0.09

Matches are distributed among these distances:
  16    7  0.13
  17   21  0.40
  18   21  0.40
  19    4  0.08

ACGTcount: A:0.00, C:0.14, G:0.05, T:0.81


Consensus pattern (17 bp):   
TTCTTTTTTTTTTGTTT
Done.