#--------------------- 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: