Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_359 ID=scaffold_359-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: 7894
ACGTcount: A:0.31, C:0.14, G:0.21, T:0.33


Found at i:554 original size:40 final size:40

Alignment explanation


    Indices: 491--622  Score: 142
    Period size: 40  Copynumber: 3.3  Consensus size: 40

        481 TATGTCTAGA

                                             *      
        491 ACTTAGTGTGCGATTCGAGATAGCTTCGGCTATTTATGGC
          1 ACTTAGTGTGCGATTCGAGATAGCTTCGGCTATATATGGC

                             *                      *
        531 ACTTAGTGTGCGATT-GGGAATAGCTTCGGCTATATATGGT
          1 ACTTAGTGTGCGATTCGAG-ATAGCTTCGGCTATATATGGC

                      *   *        *      *    *  *   
        571 ACTTAGTGTGTGATACTGAGATAACATT-GTCTATGTAAGGC
          1 ACTTAGTGTGCGATTC-GAGATAGC-TTCGGCTATATATGGC

                       
        612 ACTTAGTGTGC
          1 ACTTAGTGTGC

        623 AGAATTATAA


Statistics
Matches: 76,  Mismatches: 12, Indels: 7
        0.80            0.13        0.07

Matches are distributed among these distances:
  39    2  0.03
  40   47  0.62
  41   23  0.30
  42    4  0.05

ACGTcount: A:0.23, C:0.14, G:0.27, T:0.35


Consensus pattern (40 bp):   
ACTTAGTGTGCGATTCGAGATAGCTTCGGCTATATATGGC

Found at i:2905 original size:18 final size:18

Alignment explanation


    Indices: 2882--2919  Score: 51
    Period size: 18  Copynumber: 2.1  Consensus size: 18

       2872 TCGTTGTTTT

                               
       2882 AGTTGAAAGAGCTT-GCAA
          1 AGTTG-AAGAGCTTAGCAA

                  *           
       2900 AGTTGAGGAGCTTAGCAA
          1 AGTTGAAGAGCTTAGCAA

              
       2918 AG
          1 AG

       2920 AAAGAAGAAA


Statistics
Matches: 18,  Mismatches: 1, Indels: 2
        0.86            0.05        0.10

Matches are distributed among these distances:
  17    7  0.39
  18   11  0.61

ACGTcount: A:0.37, C:0.11, G:0.32, T:0.21


Consensus pattern (18 bp):   
AGTTGAAGAGCTTAGCAA

Found at i:5505 original size:29 final size:29

Alignment explanation


    Indices: 5468--5533  Score: 123
    Period size: 29  Copynumber: 2.3  Consensus size: 29

       5458 ATTATTTAAG

                                         
       5468 ATTCAGAGGTCGAATATGTGTACCAAGAA
          1 ATTCAGAGGTCGAATATGTGTACCAAGAA

                                    *    
       5497 ATTCAGAGGTCGAATATGTGTACCGAGAA
          1 ATTCAGAGGTCGAATATGTGTACCAAGAA

                    
       5526 ATTCAGAG
          1 ATTCAGAG

       5534 TTAATTCAGA


Statistics
Matches: 36,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  29   36  1.00

ACGTcount: A:0.36, C:0.14, G:0.26, T:0.24


Consensus pattern (29 bp):   
ATTCAGAGGTCGAATATGTGTACCAAGAA

Found at i:7588 original size:9 final size:9

Alignment explanation


    Indices: 7562--7598  Score: 56
    Period size: 9  Copynumber: 4.1  Consensus size: 9

       7552 TGAGTTTTCG

                     
       7562 AATTCGAAT
          1 AATTCGAAT

              * *    
       7571 AACTGGAAT
          1 AATTCGAAT

                     
       7580 AATTCGAAT
          1 AATTCGAAT

                     
       7589 AATTCGAAT
          1 AATTCGAAT

             
       7598 A
          1 A

       7599 TCAAACTATA


Statistics
Matches: 24,  Mismatches: 4, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
   9   24  1.00

ACGTcount: A:0.46, C:0.11, G:0.14, T:0.30


Consensus pattern (9 bp):   
AATTCGAAT

Found at i:7866 original size:30 final size:31

Alignment explanation


    Indices: 7812--7871  Score: 77
    Period size: 30  Copynumber: 2.0  Consensus size: 31

       7802 AAACCTTTTA

                         *    *            
       7812 TTTTCCCCCAAAATTTTTCCTCCC-TCCCAC
          1 TTTTCCCCCAAAACTTTTACTCCCTTCCCAC

                    *          *          
       7842 TTTTCCCCTAAAACTTTTATTCCCTTCCCA
          1 TTTTCCCCCAAAACTTTTACTCCCTTCCCA

       7872 TCTCTCCTCT


Statistics
Matches: 25,  Mismatches: 4, Indels: 1
        0.83            0.13        0.03

Matches are distributed among these distances:
  30   20  0.80
  31    5  0.20

ACGTcount: A:0.18, C:0.42, G:0.00, T:0.40


Consensus pattern (31 bp):   
TTTTCCCCCAAAACTTTTACTCCCTTCCCAC
Done.