Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga13g00945.N1

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, 200

Length: 229
ACGTcount: A:0.45, C:0.17, G:0.14, T:0.24


Found at i:104 original size:6 final size:6

Alignment explanation


    Indices: 93--171  Score: 66
    Period size: 5  Copynumber: 14.2  Consensus size: 6

         83 GGGATCACTA

                                                                   
         93 ACTAAT ACTAAT -CTAAT -CT-A- ACTAAT ACTAAT -CTAAT ACTAAT
          1 ACTAAT ACTAAT ACTAAT ACTAAT ACTAAT ACTAAT ACTAAT ACTAAT

              *      *                                   
        136 A-GAAT A-GAAT ACTAAT -CTAAT ACTCTAAT ACTAAT A
          1 ACTAAT ACTAAT ACTAAT ACTAAT A--CTAAT ACTAAT A

        172 GAATAGAAAA


Statistics
Matches: 63,  Mismatches: 2, Indels: 16
        0.78            0.02        0.20

Matches are distributed among these distances:
   4    3  0.05
   5   27  0.43
   6   27  0.43
   8    6  0.10

ACGTcount: A:0.48, C:0.16, G:0.03, T:0.33


Consensus pattern (6 bp):   
ACTAAT

Found at i:115 original size:20 final size:21

Alignment explanation


    Indices: 89--134  Score: 85
    Period size: 20  Copynumber: 2.2  Consensus size: 21

         79 AGCCGGGATC

                                 
         89 ACTAACTAATACTAATCTAAT
          1 ACTAACTAATACTAATCTAAT

                                 
        110 -CTAACTAATACTAATCTAAT
          1 ACTAACTAATACTAATCTAAT

                 
        130 ACTAA
          1 ACTAA

        135 TAGAATAGAA


Statistics
Matches: 24,  Mismatches: 0, Indels: 2
        0.92            0.00        0.08

Matches are distributed among these distances:
  20   20  0.83
  21    4  0.17

ACGTcount: A:0.48, C:0.20, G:0.00, T:0.33


Consensus pattern (21 bp):   
ACTAACTAATACTAATCTAAT

Found at i:159 original size:11 final size:11

Alignment explanation


    Indices: 89--135  Score: 73
    Period size: 11  Copynumber: 4.5  Consensus size: 11

         79 AGCCGGGATC

                       
         89 ACTAA-CTAAT
          1 ACTAATCTAAT

                       
         99 ACTAATCTAAT
          1 ACTAATCTAAT

                       
        110 -CTAA-CTAAT
          1 ACTAATCTAAT

                       
        119 ACTAATCTAAT
          1 ACTAATCTAAT

                  
        130 ACTAAT
          1 ACTAAT

        136 AGAATAGAAT


Statistics
Matches: 34,  Mismatches: 0, Indels: 5
        0.87            0.00        0.13

Matches are distributed among these distances:
   9    5  0.15
  10   13  0.38
  11   16  0.47

ACGTcount: A:0.47, C:0.19, G:0.00, T:0.34


Consensus pattern (11 bp):   
ACTAATCTAAT

Found at i:185 original size:14 final size:14

Alignment explanation


    Indices: 168--195  Score: 56
    Period size: 14  Copynumber: 2.0  Consensus size: 14

        158 CTCTAATACT

                          
        168 AATAGAATAGAAAA
          1 AATAGAATAGAAAA

                          
        182 AATAGAATAGAAAA
          1 AATAGAATAGAAAA

        196 TACTAATATA


Statistics
Matches: 14,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  14   14  1.00

ACGTcount: A:0.71, C:0.00, G:0.14, T:0.14


Consensus pattern (14 bp):   
AATAGAATAGAAAA
Done.