Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_599 ID=scaffold_599-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: 5702
ACGTcount: A:0.28, C:0.16, G:0.18, T:0.31

Warning! 354 characters in sequence are not A, C, G, or T


Found at i:3399 original size:84 final size:84

Alignment explanation


    Indices: 3301--3465  Score: 303
    Period size: 84  Copynumber: 2.0  Consensus size: 84

       3291 GGAGAAAAAA

                                 *                                           
       3301 AATCGACGAAACCAATGAAAATTGTTTTTGGTATTTTGACTCGTTTCGGATATGATTTTAACTTC
          1 AATCGACGAAACCAATGAAAAGTGTTTTTGGTATTTTGACTCGTTTCGGATATGATTTTAACTTC

                               
       3366 AAAAATAACACCGAATGGC
         66 AAAAATAACACCGAATGGC

                            *                                           *    
       3385 AATCGACGAAACCAATTAAAAGTGTTTTTGGTATTTTGACTCGTTTCGGATATGATTTTAGCTTC
          1 AATCGACGAAACCAATGAAAAGTGTTTTTGGTATTTTGACTCGTTTCGGATATGATTTTAACTTC

                            
       3450 AAAAATAACACCGAAT
         66 AAAAATAACACCGAAT

       3466 TGCCTGAAAC


Statistics
Matches: 78,  Mismatches: 3, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  84   78  1.00

ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34


Consensus pattern (84 bp):   
AATCGACGAAACCAATGAAAAGTGTTTTTGGTATTTTGACTCGTTTCGGATATGATTTTAACTTC
AAAAATAACACCGAATGGC

Found at i:5476 original size:16 final size:16

Alignment explanation


    Indices: 5455--5511  Score: 78
    Period size: 16  Copynumber: 3.6  Consensus size: 16

       5445 TTTGGTTCGC

                  *         
       5455 TGTATTAGATTAGAGG
          1 TGTATTGGATTAGAGG

                            
       5471 TGTATTGGATTAGAGG
          1 TGTATTGGATTAGAGG

                *    *      
       5487 TGTAATGGAATAGAGG
          1 TGTATTGGATTAGAGG

                *    
       5503 TGTAATGGA
          1 TGTATTGGA

       5512 ATAAATGTGT


Statistics
Matches: 38,  Mismatches: 3, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  16   38  1.00

ACGTcount: A:0.32, C:0.00, G:0.35, T:0.33


Consensus pattern (16 bp):   
TGTATTGGATTAGAGG

Found at i:5512 original size:16 final size:16

Alignment explanation


    Indices: 5465--5524  Score: 84
    Period size: 16  Copynumber: 3.8  Consensus size: 16

       5455 TGTATTAGAT

                      *    *
       5465 TAGAGGTGTATTGGAT
          1 TAGAGGTGTAATGGAA

                            
       5481 TAGAGGTGTAATGGAA
          1 TAGAGGTGTAATGGAA

                            
       5497 TAGAGGTGTAATGGAA
          1 TAGAGGTGTAATGGAA

              * *       
       5513 TAAATGTGTAAT
          1 TAGAGGTGTAAT

       5525 AGCAAATCAA


Statistics
Matches: 40,  Mismatches: 4, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  16   40  1.00

ACGTcount: A:0.35, C:0.00, G:0.33, T:0.32


Consensus pattern (16 bp):   
TAGAGGTGTAATGGAA
Done.