Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_687 ID=scaffold_687-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: 5938
ACGTcount: A:0.27, C:0.12, G:0.14, T:0.25

Warning! 1303 characters in sequence are not A, C, G, or T


Found at i:3665 original size:26 final size:26

Alignment explanation


    Indices: 3635--3686  Score: 77
    Period size: 26  Copynumber: 2.0  Consensus size: 26

       3625 AATAAAATAA

                      * *             
       3635 AACATTCAATGTTTCAGTTTAATTAG
          1 AACATTCAATATATCAGTTTAATTAG

                                *     
       3661 AACATTCAATATATCAGTTTTATTAG
          1 AACATTCAATATATCAGTTTAATTAG

       3687 CATTATTTTT


Statistics
Matches: 23,  Mismatches: 3, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  26   23  1.00

ACGTcount: A:0.37, C:0.12, G:0.10, T:0.42


Consensus pattern (26 bp):   
AACATTCAATATATCAGTTTAATTAG

Found at i:5033 original size:45 final size:45

Alignment explanation


    Indices: 4969--5062  Score: 188
    Period size: 45  Copynumber: 2.1  Consensus size: 45

       4959 AAGAATTGAG

                                                         
       4969 ATTGTTTCAATCCCACACCACGCTAGAACATTCCAATTCCACATT
          1 ATTGTTTCAATCCCACACCACGCTAGAACATTCCAATTCCACATT

                                                         
       5014 ATTGTTTCAATCCCACACCACGCTAGAACATTCCAATTCCACATT
          1 ATTGTTTCAATCCCACACCACGCTAGAACATTCCAATTCCACATT

                
       5059 ATTG
          1 ATTG

       5063 AAATGAACTT


Statistics
Matches: 49,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  45   49  1.00

ACGTcount: A:0.31, C:0.32, G:0.07, T:0.30


Consensus pattern (45 bp):   
ATTGTTTCAATCCCACACCACGCTAGAACATTCCAATTCCACATT

Found at i:5633 original size:26 final size:26

Alignment explanation


    Indices: 5603--5654  Score: 77
    Period size: 26  Copynumber: 2.0  Consensus size: 26

       5593 AATAAAATAA

                      * *             
       5603 AACATTCAATGTTTCAGTTTAATTAG
          1 AACATTCAATATATCAGTTTAATTAG

                                *     
       5629 AACATTCAATATATCAGTTTTATTAG
          1 AACATTCAATATATCAGTTTAATTAG

       5655 CATTATTTTT


Statistics
Matches: 23,  Mismatches: 3, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  26   23  1.00

ACGTcount: A:0.37, C:0.12, G:0.10, T:0.42


Consensus pattern (26 bp):   
AACATTCAATATATCAGTTTAATTAG
Done.