Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_375 ID=scaffold_375-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: 7857
ACGTcount: A:0.32, C:0.15, G:0.17, T:0.34

Warning! 117 characters in sequence are not A, C, G, or T


Found at i:6033 original size:17 final size:17

Alignment explanation


    Indices: 5991--6071  Score: 78
    Period size: 17  Copynumber: 4.6  Consensus size: 17

       5981 AATTTAATTT

                             
       5991 TAATATAAAT-ATTTAA
          1 TAATATAAATAATTTAA

                               
       6007 T-ATGACTAAATAATTTAA
          1 TAAT-A-TAAATAATTTAA

                         *   
       6025 TAATATAAATAATATAA
          1 TAATATAAATAATTTAA

                *               
       6042 -AATGTGAAATTTAATTTAA
          1 TAATAT-AAA--TAATTTAA

                       
       6061 TAATATAAATA
          1 TAATATAAATA

       6072 GTAGATATAA


Statistics
Matches: 53,  Mismatches: 4, Indels: 15
        0.74            0.06        0.21

Matches are distributed among these distances:
  15    2  0.04
  16    6  0.11
  17   21  0.40
  18    8  0.15
  19   12  0.23
  20    4  0.08

ACGTcount: A:0.56, C:0.01, G:0.04, T:0.40


Consensus pattern (17 bp):   
TAATATAAATAATTTAA

Found at i:6570 original size:9 final size:9

Alignment explanation


    Indices: 6556--6583  Score: 56
    Period size: 9  Copynumber: 3.1  Consensus size: 9

       6546 TATAGTTTGA

                     
       6556 TATTCGAAT
          1 TATTCGAAT

                     
       6565 TATTCGAAT
          1 TATTCGAAT

                     
       6574 TATTCGAAT
          1 TATTCGAAT

             
       6583 T
          1 T

       6584 CGAATTCGAA


Statistics
Matches: 19,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   9   19  1.00

ACGTcount: A:0.32, C:0.11, G:0.11, T:0.46


Consensus pattern (9 bp):   
TATTCGAAT

Found at i:7761 original size:12 final size:12

Alignment explanation


    Indices: 7744--7769  Score: 52
    Period size: 12  Copynumber: 2.2  Consensus size: 12

       7734 CAAAACAAGC

                        
       7744 TTTTAGCGGCGT
          1 TTTTAGCGGCGT

                        
       7756 TTTTAGCGGCGT
          1 TTTTAGCGGCGT

              
       7768 TT
          1 TT

       7770 AGATAAAAAA


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

Matches are distributed among these distances:
  12   14  1.00

ACGTcount: A:0.08, C:0.15, G:0.31, T:0.46


Consensus pattern (12 bp):   
TTTTAGCGGCGT
Done.