Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga12g02552.F1

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: 3982
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34


Found at i:2188 original size:26 final size:26

Alignment explanation


    Indices: 2140--2190  Score: 68
    Period size: 26  Copynumber: 2.0  Consensus size: 26

       2130 CTCGTTATAT

                          *           
       2140 GGCTTTTCGTGAGTTTTCCAATTAAA
          1 GGCTTTTCGTGAGTCTTCCAATTAAA

                   *                  
       2166 GGCTTTTTGTGAG-CTTCCTAATTAA
          1 GGCTTTTCGTGAGTCTTCC-AATTAA

       2191 TGAATCTCAG


Statistics
Matches: 22,  Mismatches: 2, Indels: 2
        0.85            0.08        0.08

Matches are distributed among these distances:
  25    4  0.18
  26   18  0.82

ACGTcount: A:0.22, C:0.16, G:0.20, T:0.43


Consensus pattern (26 bp):   
GGCTTTTCGTGAGTCTTCCAATTAAA

Found at i:2260 original size:25 final size:26

Alignment explanation


    Indices: 2227--2278  Score: 72
    Period size: 25  Copynumber: 2.0  Consensus size: 26

       2217 CTCGCTTGAA

                                       
       2227 TTTCTCGA-TACATGGCTATTTGGAGC
          1 TTTCTCGATTA-ATGGCTATTTGGAGC

                             *        
       2253 TTTC-CGATTAATGGCTCTTTGGAGC
          1 TTTCTCGATTAATGGCTATTTGGAGC

             
       2278 T
          1 T

       2279 ACCGGTTATT


Statistics
Matches: 24,  Mismatches: 1, Indels: 3
        0.86            0.04        0.11

Matches are distributed among these distances:
  25   18  0.75
  26    6  0.25

ACGTcount: A:0.17, C:0.19, G:0.23, T:0.40


Consensus pattern (26 bp):   
TTTCTCGATTAATGGCTATTTGGAGC

Found at i:2327 original size:24 final size:24

Alignment explanation


    Indices: 2249--2328  Score: 83
    Period size: 24  Copynumber: 3.3  Consensus size: 24

       2239 TGGCTATTTG

                  *                  
       2249 GAGCTTTCCGATTAATGGCTCTT-T
          1 GAGCTTCCCGATT-ATGGCTCTTAT

                   *   *           *  
       2273 GGAGC-TACCGGTTATTGGCTCTCAT
          1 -GAGCTTCCCGATTA-TGGCTCTTAT

                                    
       2298 GAGCTTCCCGATTATGGCTCTTAT
          1 GAGCTTCCCGATTATGGCTCTTAT

                   
       2322 GAGCTTC
          1 GAGCTTC

       2329 TCGTTATATA


Statistics
Matches: 46,  Mismatches: 6, Indels: 7
        0.78            0.10        0.12

Matches are distributed among these distances:
  23    1  0.02
  24   33  0.72
  25   12  0.26

ACGTcount: A:0.16, C:0.24, G:0.24, T:0.36


Consensus pattern (24 bp):   
GAGCTTCCCGATTATGGCTCTTAT
Done.