Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold1920

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, 723

Length: 1206
ACGTcount: A:0.24, C:0.21, G:0.17, T:0.38


Found at i:169 original size:12 final size:11

Alignment explanation


    Indices: 152--194  Score: 52
    Period size: 12  Copynumber: 3.8  Consensus size: 11

        142 CCTCTCCTTT

                        
        152 TTCTTTTTGTTA
          1 TTCTTTTT-TTA

                   *   
        164 TTCTTTTCTT-
          1 TTCTTTTTTTA

                       
        174 TTCTTTTTTTA
          1 TTCTTTTTTTA

                      
        185 TTTCTTTTTT
          1 -TTCTTTTTT

        195 CAAGTGAAGT


Statistics
Matches: 27,  Mismatches: 2, Indels: 4
        0.82            0.06        0.12

Matches are distributed among these distances:
  10    9  0.33
  11    2  0.07
  12   16  0.59

ACGTcount: A:0.05, C:0.12, G:0.02, T:0.81


Consensus pattern (11 bp):   
TTCTTTTTTTA

Found at i:175 original size:22 final size:22

Alignment explanation


    Indices: 150--192  Score: 70
    Period size: 22  Copynumber: 2.0  Consensus size: 22

        140 GGCCTCTCCT

                                   
        150 TTTTCTTTTTGTTA-TTCTTTTC
          1 TTTTCTTTTT-TTATTTCTTTTC

                                 
        172 TTTTCTTTTTTTATTTCTTTT
          1 TTTTCTTTTTTTATTTCTTTT

        193 TTCAAGTGAA


Statistics
Matches: 20,  Mismatches: 0, Indels: 2
        0.91            0.00        0.09

Matches are distributed among these distances:
  21    3  0.15
  22   17  0.85

ACGTcount: A:0.05, C:0.12, G:0.02, T:0.81


Consensus pattern (22 bp):   
TTTTCTTTTTTTATTTCTTTTC

Found at i:672 original size:33 final size:29

Alignment explanation


    Indices: 635--710  Score: 91
    Period size: 33  Copynumber: 2.5  Consensus size: 29

        625 TATTCTTTTA

                                     *      
        635 TTTTTGTTTTTTTTTGCTTTTGTTTTCTCGTT
          1 TTTTTGTTTTTTTTTGC-TTT-TTTGCTC-TT

                                           
        667 TTTTT-TACTTTTTTTTGCTTTTTTGCTCTT
          1 TTTTTGT--TTTTTTTTGCTTTTTTGCTCTT

                          
        697 TTTTTGTTTTTTTT
          1 TTTTTGTTTTTTTT

        711 ATTTTTGCCT


Statistics
Matches: 40,  Mismatches: 1, Indels: 9
        0.80            0.02        0.18

Matches are distributed among these distances:
  29    7  0.17
  30    7  0.17
  31    8  0.20
  32    8  0.20
  33   10  0.25

ACGTcount: A:0.01, C:0.09, G:0.09, T:0.80


Consensus pattern (29 bp):   
TTTTTGTTTTTTTTTGCTTTTTTGCTCTT
Done.