Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_129 ID=scaffold_129-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: 11749
ACGTcount: A:0.36, C:0.15, G:0.16, T:0.32


Found at i:6387 original size:12 final size:11

Alignment explanation


    Indices: 6372--6440  Score: 58
    Period size: 12  Copynumber: 6.5  Consensus size: 11

       6362 ATAAACAGAA

                        
       6372 AATAAAGCTAAT
          1 AATAAAG-TAAT

                  *    
       6384 AAT-AATTAAT
          1 AATAAAGTAAT

                 *      
       6394 AATAGTAGTAAT
          1 AATA-AAGTAAT

                       
       6406 AAT-AA-TAAT
          1 AATAAAGTAAT

                        
       6415 AATAATAGTAAT
          1 AATAA-AGTAAT

                       
       6427 AAT-AA-TAAT
          1 AATAAAGTAAT

                 
       6436 AATAA
          1 AATAA

       6441 CACTAAAATA


Statistics
Matches: 47,  Mismatches: 4, Indels: 14
        0.72            0.06        0.22

Matches are distributed among these distances:
   9   14  0.30
  10   11  0.23
  11    4  0.09
  12   18  0.38

ACGTcount: A:0.61, C:0.01, G:0.06, T:0.32


Consensus pattern (11 bp):   
AATAAAGTAAT

Found at i:6388 original size:3 final size:3

Alignment explanation


    Indices: 6380--6440  Score: 86
    Period size: 3  Copynumber: 20.0  Consensus size: 3

       6370 AAAATAAAGC

                                   *   *                           *    
       6380 TAA TAA TAA TTAA TAA TAG TAG TAA TAA TAA TAA TAA TAA TAG TAA
          1 TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA

                               
       6426 TAA TAA TAA TAA TAA
          1 TAA TAA TAA TAA TAA

       6441 CACTAAAATA


Statistics
Matches: 53,  Mismatches: 4, Indels: 2
        0.90            0.07        0.03

Matches are distributed among these distances:
   3   50  0.94
   4    3  0.06

ACGTcount: A:0.61, C:0.00, G:0.05, T:0.34


Consensus pattern (3 bp):   
TAA

Done.