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[Guy Bottu]

	Dear friends,
	
I am puzzled by pscan outputs. I do not see the difference between "Not all 
elements match but those that do are in order" and "Remaining partial matches", 
since in both cases there are two matches with the same element. And, in 
general, how does pscan handle cases where you the protein really contains 
several times the same motif (e.g. proteins with kringles). Can Alan or someone 
else anwer this ?

	Regards,
	Guy Bottu
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CLASS 1
Fingerprints with all elements in order



CLASS 2
All elements match but not all in the correct order

Fingerprint HTHREPRESSR Elements 2
    Accession number PR00031
    Lambda and other repressor helix-turn-helix signature
  Element 1 Threshold 50% Score 73%
             Start position 135 Length 10
  Element 2 Threshold 32% Score 32%
             Start position 74 Length 17


CLASS 3
Not all elements match but those that do are in order

Fingerprint GEMCOATBR1 Elements 7
    Accession number PR00225
    Geminivirus BR1 coat protein signature
  Element 3 Threshold 30% Score 37%
             Start position 281 Length 15
  Element 3 Threshold 30% Score 31%
             Start position 196 Length 15


CLASS 4
Remaining partial matches

Fingerprint GABAARBETA Elements 4
    Accession number PR01160
    Gamma-aminobutyric-acid A receptor beta subunit signature
  Element 1 Threshold 33% Score 34%
             Start position 275 Length 15
  Element 1 Threshold 33% Score 33%
             Start position 187 Length 15