Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_676 ID=scaffold_676-JGI_221_v2.0

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: 4838
ACGTcount: A:0.30, C:0.15, G:0.18, T:0.35

Warning! 119 characters in sequence are not A, C, G, or T


Found at i:279 original size:10 final size:10

Alignment explanation


    Indices: 266--290  Score: 50
    Period size: 10  Copynumber: 2.5  Consensus size: 10

        256 AAGTTTAGTT

                      
        266 TGTTTTAATG
          1 TGTTTTAATG

                      
        276 TGTTTTAATG
          1 TGTTTTAATG

                 
        286 TGTTT
          1 TGTTT

        291 GTTCATAAAT


Statistics
Matches: 15,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  10   15  1.00

ACGTcount: A:0.16, C:0.00, G:0.20, T:0.64


Consensus pattern (10 bp):   
TGTTTTAATG

Found at i:4087 original size:19 final size:19

Alignment explanation


    Indices: 4063--4101  Score: 69
    Period size: 19  Copynumber: 2.1  Consensus size: 19

       4053 AATAAATTTC

                               
       4063 TCATCTTAGTTAATTGAGT
          1 TCATCTTAGTTAATTGAGT

                           *   
       4082 TCATCTTAGTTAATTTAGT
          1 TCATCTTAGTTAATTGAGT

             
       4101 T
          1 T

       4102 GTTGGAATAA


Statistics
Matches: 19,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  19   19  1.00

ACGTcount: A:0.26, C:0.10, G:0.13, T:0.51


Consensus pattern (19 bp):   
TCATCTTAGTTAATTGAGT

Found at i:4217 original size:10 final size:10

Alignment explanation


    Indices: 4199--4245  Score: 69
    Period size: 10  Copynumber: 4.8  Consensus size: 10

       4189 TAAGTCTAAT

                      
       4199 ATGTGTTTAA
          1 ATGTGTTTAA

                *     
       4209 ATGTATTT-A
          1 ATGTGTTTAA

                      
       4218 ATGTGTTTAA
          1 ATGTGTTTAA

                    * 
       4228 ATGTGTTTTA
          1 ATGTGTTTAA

                    
       4238 ATGTGTTT
          1 ATGTGTTT

       4246 GCTAATAAAT


Statistics
Matches: 33,  Mismatches: 3, Indels: 2
        0.87            0.08        0.05

Matches are distributed among these distances:
   9    8  0.24
  10   25  0.76

ACGTcount: A:0.26, C:0.00, G:0.19, T:0.55


Consensus pattern (10 bp):   
ATGTGTTTAA

Found at i:4223 original size:19 final size:20

Alignment explanation


    Indices: 4199--4245  Score: 78
    Period size: 19  Copynumber: 2.4  Consensus size: 20

       4189 TAAGTCTAAT

                                
       4199 ATGTGTTTAAATGT-ATTTA
          1 ATGTGTTTAAATGTGATTTA

                           *    
       4218 ATGTGTTTAAATGTGTTTTA
          1 ATGTGTTTAAATGTGATTTA

                    
       4238 ATGTGTTT
          1 ATGTGTTT

       4246 GCTAATAAAT


Statistics
Matches: 26,  Mismatches: 1, Indels: 1
        0.93            0.04        0.04

Matches are distributed among these distances:
  19   14  0.54
  20   12  0.46

ACGTcount: A:0.26, C:0.00, G:0.19, T:0.55


Consensus pattern (20 bp):   
ATGTGTTTAAATGTGATTTA

Found at i:4306 original size:74 final size:74

Alignment explanation


    Indices: 4214--4352  Score: 215
    Period size: 74  Copynumber: 1.9  Consensus size: 74

       4204 TTTAAATGTA

                                  *  *                *                      
       4214 TTTAATGTGTTTAAATGTGTTTTAATGTGTTTGCTAATAAATGCTTGCAGGTGACTATTTAGTTG
          1 TTTAATGTGTTTAAATGTGTTTAAAGGTGTTTGCTAATAAATACTTGCAGGTGACTATTTAGTTG

                     
       4279 CTTATTAAG
         66 CTTATTAAG

                *                            *         *  *                  
       4288 TTTAGTGTGTTTAAATGTGTTTAAAGGTGTTTGTTAATAAATATTTTCAGGTGACTATTTAGTTG
          1 TTTAATGTGTTTAAATGTGTTTAAAGGTGTTTGCTAATAAATACTTGCAGGTGACTATTTAGTTG

       4353 GAATCAGTTA


Statistics
Matches: 58,  Mismatches: 7, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  74   58  1.00

ACGTcount: A:0.26, C:0.05, G:0.21, T:0.48


Consensus pattern (74 bp):   
TTTAATGTGTTTAAATGTGTTTAAAGGTGTTTGCTAATAAATACTTGCAGGTGACTATTTAGTTG
CTTATTAAG
Done.