staden-common 2.0.0+b11-2 / usr / share / staden / etc / config.prefinish

{::Params { -external_seq_file {} -dust_level 18 -skip_template_file skip_templates -avail_template_file avail_templates -find_dup_templates 1 -use_avg_insert 0 -min_template_score 0.4 -min_score 0.6 -max_score_drop 0.2 -mandatory_ratio 0.4 -min_extension 50} {{::ParamWalk { -pwalk_search_dist 100 -pwalk_max_match 9 -pwalk_noligos 4 -pwalk_ntemplates 4 -pwalk_offset1 130 -pwalk_offset2 60 -pwalk_seq_gap 60 -pwalk_consistent_only 0 -pwalk_max_err 0.02 -pwalk_min_qual 30 -pwalk_max_err2 0.1 -pwalk_min_qual2 15 -pwalk_end_dist 700 -pwalk_use_template 1 -pwalk_use_template_score 0 -pwalk_tag_cons 0 -pwalk_tag_type {}} {}} {::ParamPrimer3 { -primer_min_tm 50 -primer_max_tm 55 -primer_opt_tm 53 -primer_min_len 17 -primer_max_len 23 -primer_opt_len 20 -primer_min_gc 30 -primer_opt_gc 0 -primer_max_gc 70 -primer_salt_conc 50 -primer_dna_conc 50 -primer_max_end_stability 100 -primer_self_any 8 -primer_self_end 3 -primer_gc_clamp 1 -primer_max_poly_x 5} {}} {::ParamCosts { -reseq_cost 1.2 -vpwalk_cost 2.0 -cpwalk_cost 8.0 -long_cost 2.0 -reverse_cost 1.0 -reseq_length 400 -pwalk_length 400 -long_length 700 -reseq_nsolutions 4 -long_nsolutions 4 -pwalk_nsolutions 4} {}}}} {::Pass {} {{::Rule {-name {Extend contig leftwards} -mandatory 1 -pweight 0.5 -mweight 10 -avoid_primers 1 -expression <contig_left_end>} {{::Solution {-experiments vpwalk -chemistry 17 -strand 2} {}}}} {::Rule {-name {Extend contig rightwards} -mandatory 1 -pweight 0.5 -mweight 10 -avoid_primers 1 -expression <contig_right_end>} {{::Solution {-experiments vpwalk -chemistry 17 -strand 1} {}}}} {::Rule {-name {Double stranded} -mandatory 0 -pweight 0.1 -mweight 0.1 -avoid_primers 0 -expression {<strand_top> && <strand_bottom>}} {}} {::Rule {-name {Minimum template depth} -mandatory 1 -pweight 1.0 -mweight 1.0 -avoid_primers 1 -expression {<template_depth_ge 2>}} {{::Solution {-experiments vpwalk -chemistry 17 -strand 0} {}}}}}} {::Pass {} {{::Rule {-name {Minimum consensus confidence} -mandatory 0 -pweight 0.7 -mweight 0.7 -avoid_primers 0 -expression {<confidence_ge 30>}} {{::Solution {-experiments vpwalk -chemistry 17 -strand 0} {}}}}}}