#--------------------- PRIMER 3  (3/28/10) -----------------------
item:PRIMER 3
itemlabel:PRIMER 3
itemmethod: (primer3b.sh in1 $MAXPRIMERS $OPTLEN $MINLEN $MAXLEN $OPTTEMP $MINTEMP $MAXTEMP $MINGC $MAXGC $SALTCONC $DNACONC $MAXUNK $MAXSELF $MAX3PSELF $GCCLAMP $MINPROD $MAXPROD $intoligo $ioptlen $iminlen $imaxlen $iopttemp $imintemp $imaxtemp $imingc $imaxgc $isaltconc $idnaconc $imaxunk $imaxself $imax3pself > in1.in; $RM_CMD in1; primer3brun.sh in1.in)& 
itemhelp:doc/primer/primer3_manual.htm
itemopen:gde_help_viewer.csh

arg:MAXPRIMERS
argtype:slider
arglabel: Find the N best primer pairs/internal oligos (N):
argmin:1
argmax:30
argvalue:5

arg:OPTLEN
argtype:slider
arglabel:optimal    PRIMER LENGTH
argmin:10
argmax:50
argvalue:20

arg:MINLEN
argtype:slider
arglabel:minimum    PRIMER LENGTH
argmin:10
argmax:50
argvalue:18

arg:MAXLEN
argtype:slider
arglabel:maximum    PRIMER LENGTH
argmin:10
argmax:50
argvalue:22

arg:OPTTEMP
argtype:slider
arglabel:optimal    PRIMER Tm
argmin:30
argmax:100
argvalue:60

arg:MINTEMP
argtype:slider
arglabel:minimum    PRIMER Tm
argmin:30
argmax:100
argvalue:57

arg:MAXTEMP
argtype:slider
arglabel:maximum    PRIMER Tm
argmin:30
argmax:100
argvalue:63

arg:MINGC
argtype:slider
arglabel:minimum    %GC
argmin:20
argmax:80
argvalue:20

arg:MAXGC
argtype:slider
arglabel:maximum    %GC
argmin:20
argmax:80
argvalue:80

arg:SALTCONC
argtype:slider
arglabel:SALT concentration (mM)
argmin:10
argmax:500
argvalue:50

arg:DNACONC
argtype:slider
arglabel:DNA   concentration (nM)
argmin:1
argmax:100
argvalue:50

arg:MAXUNK
argtype:slider
arglabel:maximum UNKNOWN BASES (Ns) allowed in primer
argmin:0
argmax:5
argvalue:0

arg:MAXSELF
argtype:slider
arglabel:maximum primer SELF-COMPLEMENTARITY
argmin:0
argmax:20
argvalue:12

arg:MAX3PSELF
argtype:slider
arglabel:maximum primer 3' END SELF-COMPLEMENTARITY
argmin:0
argmax:20
argvalue:8

arg:GCCLAMP
argtype:slider
arglabel:GC CLAMP (how many 3' bases?)
argmin:0
argmax:5
argvalue:0

arg:MINPROD
argtype:slider
arglabel:minimum PRODUCT LENGTH
argmin:100
argmax:3000
argvalue:100

arg:MAXPROD
argtype:slider
arglabel:maximum PRODUCT LENGTH
argmin:100
argmax:3000
argvalue:500

arg:intoligo
argtype:chooser
arglabel:===========FIND AN OLIGO INTERNAL TO PCR FRAGMENT?========
argchoice:Yes:1
argchoice:No:0
argvalue:1

arg:ioptlen
argtype:slider
arglabel:optimal    OLIGO LENGTH
argmin:10
argmax:50
argvalue:20

arg:iminlen
argtype:slider
arglabel:minimum    OLIGO LENGTH
argmin:10
argmax:50
argvalue:18

arg:imaxlen
argtype:slider
arglabel:maximum    OLIGO LENGTH
argmin:10
argmax:50
argvalue:27

arg:iopttemp
argtype:slider
arglabel:optimal    OLIGO Tm
argmin:30
argmax:100
argvalue:60

arg:imintemp
argtype:slider
arglabel:minimum    OLIGO Tm
argmin:30
argmax:100
argvalue:57

arg:imaxtemp
argtype:slider
arglabel:maximum    OLIGO Tm
argmin:30
argmax:100
argvalue:63

arg:imingc
argtype:slider
arglabel:minimum    %GC
argmin:20
argmax:80
argvalue:20

arg:imaxgc
argtype:slider
arglabel:maximum    %GC
argmin:20
argmax:80
argvalue:80

arg:isaltconc
argtype:slider
arglabel:SALT concentration (mM)
argmin:10
argmax:500
argvalue:50

arg:idnaconc
argtype:slider
arglabel:DNA   concentration (nM)
argmin:1
argmax:100
argvalue:50

arg:imaxunk
argtype:slider
arglabel:maximum UNKNOWN BASES (Ns) allowed in OLIGO
argmin:0
argmax:5
argvalue:0

arg:imaxself
argtype:slider
arglabel:maximum OLIGO SELF-COMPLEMENTARITY
argmin:0
argmax:20
argvalue:12

arg:imax3pself
argtype:slider
arglabel:maximum OLIGO 3' END SELF-COMPLEMENTARITY
argmin:0
argmax:20
argvalue:12

in:in1
informat:flat
insave: