diff --git a/circRNA.py b/circRNA.py new file mode 100644 index 0000000..4da7504 --- /dev/null +++ b/circRNA.py @@ -0,0 +1,145 @@ +import sys +import requests +import os +import uuid +import json + +SPECIES = 'homo_sapiens' +ASSEMBLY = 'GRCh38' +OFFSET = 200 + +def get_input(): + try: + coord = sys.argv[1].rstrip('\n') + strand = sys.argv[2].rstrip('\n') + outfile = sys.argv[3].rstrip('\n') + except IndexError: + print "USAGE:\npython circRNA.py coordinates strand outfile\n" + print "\t'coordinates': chrom:start-end format (exp: 10:25000000-25001000)" + print "\t'strand' : can be '+' or '-'" + print "\t'outfile' : Give a name where the output will be saved in CSV format" + sys.exit() + coord = coord.rstrip('\n').rstrip('\r') + strand = strand.rstrip('\n').rstrip('\r') + try: + chrom, start, end = parse_coords(coord) + except: + print "ERROR: Please provide coordinate in chrom:start-end format (exp: 10:25000000-25001000)" + sys.exit() + if strand not in ['+', '-']: + print "ERROR: Strand should be either '+' or '-'" + sys.exit() + return chrom.upper().replace('CHR', ''), start, end, strand, outfile + +def parse_coords(coord): + chrom = coord.split(":")[0] + start = coord.split(":")[1].split("-")[0] + end = coord.split(":")[1].split("-")[1] + print "INFO: Input coordinates successfully parsed as following:" + print "INFO: Chrom:%s Start:%s End:%s" % (chrom, start, end) + return chrom, start, end + +def get_circ_coordinates(start, end, strand, offset=OFFSET): + # if its positive strand the offset is subtracted from end and add to the start sequence + if strand == "+": + start1 = int(end) - offset + end1 = int(end) + start2 = int(start) + end2 = int(start) + offset + # if its negative strand, reverse complement of the obtained sequence is joined together + elif strand == "-": + start1 = int(start) + end1 = int(start) + offset + start2 = int(end) - offset + end2 = int(end) + else: + return False + print "INFO: Calculation of backspliced coordinates with offset of %dbp complete" % offset + return ((start1, end1), (start2, end2)) + +def fetch_ensembl(chrom, start, end, strand, species=SPECIES, assembly=ASSEMBLY): + print "INFO: Will connect to ENSEMBL for species: %s and assembly:%s" % (species, assembly) + server = "https://rest.ensembl.org" + s = '1' if strand == '+' else '-1' + ext = "/sequence/region/%s/%s:%s..%s:%s?coord_system_version=%s" % ( + species, chrom, str(start), str(end), s, assembly) + print "INFO:", server+ext + r = requests.get(server+ext, headers={ "Content-Type" : "text/plain"}) + if not r.ok: + print "ERROR: Unable to contact Ensembl to fetch sequences. Exiting now.." + sys.exit() + print "INFO: Ensembl query successful" + return r.text + +def get_backspliced_seq(circ_cords): + print "INFO: Connecting to Ensembl for fetching 5' sequence" + seq1 = fetch_ensembl(chrom, circ_cords[0][0], circ_cords[0][1], strand) + print "INFO: Connecting to Ensembl for fetching 3' sequence" + seq2 = fetch_ensembl(chrom, circ_cords[1][0], circ_cords[1][1], strand) + # Strand info is allow implicit in seq1 and seq2 + return seq1+seq2 + +def run_primer3(seq): + print "INFO: Creating template file for Primer3 with template length of: %d" % len(seq) + temp_fn = str(uuid.uuid4()) + with open(temp_fn, 'w') as OUT: + OUT.write("SEQUENCE_ID=sequence\nSEQUENCE_TEMPLATE=%s\n=\n" % seq) + script_dir = os.path.dirname(os.path.realpath(__file__)) + exe = "%s/primer3_bin/primer3_core" % script_dir + settings_fn = "%s/primer3_bin/circrna_primers_settings.p3" % script_dir + print "INFO: Using Primer3 settings file: %s" % settings_fn + cmd = "%s -p3_settings_file=%s -echo_settings_file %s" % (exe, settings_fn, temp_fn) + print "INFO: Running Primer3..." + print "INFO: ", cmd + output = os.popen(cmd).read() + os.system('rm %s' % temp_fn) + print "INFO: Removed temporary input file for Primer3" + return output + +def prep_output(raw_output): + output_dict = {} + for line in raw_output.split('\n'): + cols = line.rstrip('\n').split('=') + try: + output_dict[cols[0]] = cols[1] + except IndexError: + pass + num_primers = int(output_dict['PRIMER_PAIR_NUM_RETURNED']) + valid_primers = 0 + if num_primers > 0: + parsed = [','.join([ + "Primer ID", "Product size", "Left primer", "Right primer", + "Left GC", "Right GC", "Left TM", "Right TM", + "Left pos", "Right pos", "Left size", "Right size" + ])] + for i in range(num_primers): + left_pos = output_dict['PRIMER_LEFT_%d' % i].split(',')[0] + right_pos = output_dict['PRIMER_RIGHT_%d' % i].split(',')[0] + if int(left_pos) < 195 and int(right_pos) > 205: + valid_primers += 1 + parsed.append(",".join([ + str(i), output_dict['PRIMER_PAIR_%d_PRODUCT_SIZE' % i], + output_dict['PRIMER_LEFT_%d_SEQUENCE' % i], output_dict['PRIMER_RIGHT_%d_SEQUENCE' % i], + output_dict['PRIMER_LEFT_%d_GC_PERCENT' % i], output_dict['PRIMER_RIGHT_%d_GC_PERCENT' % i], + output_dict['PRIMER_LEFT_%d_TM' % i], output_dict['PRIMER_RIGHT_%d_TM' % i], + left_pos, right_pos, + output_dict['PRIMER_LEFT_%d' % i].split(',')[1], output_dict['PRIMER_RIGHT_%d' % i].split(',')[1] + ])) + else: + print "WARNING: No primers found" + return "No primers found" + print "INFO: %d primers found" % valid_primers + return '\n'.join(parsed) + +if __name__ == '__main__': + print "Welcome to CircPrimer" + chrom, start, end, strand, outfile = get_input() + cc = get_circ_coordinates(start, end, strand) + back_seq = get_backspliced_seq(cc) + primer3_output = run_primer3(back_seq) + with open("%s_raw_primer3.csv" % outfile, 'w') as OUT: + OUT.write(primer3_output) + primers_table = prep_output(primer3_output) + with open("%s.csv" % outfile, 'w') as OUT: + OUT.write(primers_table) + print "SUCCESS: Analysis complete.. Primers are saved in %s.csv" % outfile diff --git a/primer3_bin/circrna_primers_settings.p3 b/primer3_bin/circrna_primers_settings.p3 new file mode 100644 index 0000000..325f527 --- /dev/null +++ b/primer3_bin/circrna_primers_settings.p3 @@ -0,0 +1,37 @@ +Primer3 File - http://primer3.sourceforge.net +P3_FILE_TYPE=settings + +SEQUENCE_TARGET=195,10 +PRIMER_NUM_RETURN=20 +PRIMER_TASK=generic +PRIMER_PICK_LEFT_PRIMER=1 +PRIMER_PICK_RIGHT_PRIMER=1 +PRIMER_PRODUCT_SIZE_RANGE=100-400 +PRIMER_OPT_SIZE=20 +PRIMER_MIN_SIZE=18 +PRIMER_MAX_SIZE=23 +PRIMER_MIN_TM=57.0 +PRIMER_OPT_TM=59.0 +PRIMER_MAX_TM=63.0 +PRIMER_PAIR_MAX_DIFF_TM=3.0 +PRIMER_MIN_GC=30.0 +PRIMER_MAX_GC=70.0 +PRIMER_EXPLAIN_FLAG=1 +PRIMER_THERMODYNAMIC_PARAMETERS_PATH=primer3_bin/primer3_config/ +PRIMER_MIN_THREE_PRIME_DISTANCE=3 +PRIMER_MAX_END_STABILITY=9.0 +PRIMER_MAX_SELF_ANY_TH=45.00 +PRIMER_MAX_SELF_END_TH=35.00 +PRIMER_PAIR_MAX_COMPL_ANY_TH=45.00 +PRIMER_PAIR_MAX_COMPL_END_TH=35.00 +PRIMER_MAX_HAIRPIN_TH=24.00 +PRIMER_MAX_TEMPLATE_MISPRIMING_TH=40.00 +PRIMER_PAIR_MAX_TEMPLATE_MISPRIMING_TH=70.00 +PRIMER_MAX_POLY_X=4 +PRIMER_LIBERAL_BASE=1 +PRIMER_LIB_AMBIGUITY_CODES_CONSENSUS=0 +PRIMER_WT_POS_PENALTY=0.0 +PRIMER_INTERNAL_SALT_DIVALENT=1.5 +PRIMER_MAX_TEMPLATE_MISPRIMING=12.00 +PRIMER_PAIR_MAX_TEMPLATE_MISPRIMING=24.00 += \ No newline at end of file diff --git a/primer3_bin/long_seq_tm_test b/primer3_bin/long_seq_tm_test new file mode 100755 index 0000000..6626169 Binary files /dev/null and b/primer3_bin/long_seq_tm_test differ diff --git a/primer3_bin/ntdpal b/primer3_bin/ntdpal new file mode 100755 index 0000000..19225b7 Binary files /dev/null and b/primer3_bin/ntdpal differ diff --git a/primer3_bin/ntthal b/primer3_bin/ntthal new file mode 100755 index 0000000..7a943bb Binary files /dev/null and b/primer3_bin/ntthal differ diff --git a/primer3_bin/oligotm b/primer3_bin/oligotm new file mode 100755 index 0000000..5109a6b Binary files /dev/null and b/primer3_bin/oligotm differ diff --git a/primer3_bin/primer3_config/dangle.dh b/primer3_bin/primer3_config/dangle.dh new file mode 100644 index 0000000..2e02981 --- /dev/null +++ b/primer3_bin/primer3_config/dangle.dh @@ -0,0 +1,128 @@ +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +-500 +4700 +-4100 +-3800 +0 +0 +0 +0 +0 +0 +0 +0 +-5900 +-2600 +-3200 +-5200 +0 +0 +0 +0 +0 +0 +0 +0 +-2100 +-200 +-3900 +-4400 +0 +0 +0 +0 +0 +0 +0 +0 +-700 +4400 +-1600 +2900 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +-2900 +-4100 +-4200 +-200 +0 +0 +0 +0 +0 +0 +0 +0 +-3700 +-4000 +-3900 +-4900 +0 +0 +0 +0 +0 +0 +0 +0 +-6300 +-4400 +-5100 +-4000 +0 +0 +0 +0 +0 +0 +0 +0 +200 +600 +-1100 +-6900 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 diff --git a/primer3_bin/primer3_config/dangle.ds b/primer3_bin/primer3_config/dangle.ds new file mode 100644 index 0000000..6147d48 --- /dev/null +++ b/primer3_bin/primer3_config/dangle.ds @@ -0,0 +1,128 @@ +inf +inf +inf +inf +inf +inf +inf +inf +inf +inf +inf +inf +-1.1 +14.2 +-13.1 +-12.6 +inf +inf +inf +inf +inf +inf +inf +inf +-16.5 +-7.4 +-10.4 +-15 +inf +inf +inf +inf +inf +inf +inf +inf +-3.9 +-0.1 +-11.2 +-13.1 +inf +inf +inf +inf +inf +inf +inf +inf +-0.8 +14.9 +-3.6 +10.4 +inf +inf +inf +inf +inf +inf +inf +inf +inf +inf +inf +inf +inf +inf +inf +inf +inf +inf +inf +inf +inf +inf +inf +inf +-7.6 +-13 +-15 +-0.5 +inf +inf +inf +inf +inf +inf +inf +inf +-10 +-11.9 +-10.9 +-13.8 +inf +inf +inf +inf +inf +inf +inf +inf +-17.1 +-12.6 +-14 +-10.9 +inf +inf +inf +inf +inf +inf +inf +inf +2.3 +3.3 +-1.6 +-20 +inf +inf +inf +inf +inf +inf +inf +inf +inf +inf +inf +inf diff --git a/primer3_bin/primer3_config/interpretations/dangle_i.dh b/primer3_bin/primer3_config/interpretations/dangle_i.dh new file mode 100644 index 0000000..8ae2fc8 --- /dev/null +++ b/primer3_bin/primer3_config/interpretations/dangle_i.dh @@ -0,0 +1,131 @@ +/* Enthalpy of dangling end */ +/* 3' dangling */ +AA_A 0 +AC_A 0 +AG_A 0 +AT_A 0 +AA_C 0 +AC_C 0 +AG_C 0 +AT_C 0 +AA_G 0 +AC_G 0 +AG_G 0 +AT_G 0 +AA_T 5 +AC_T -47 +AG_T 41 +AT_T 38 +CA_A 0 +CC_A 0 +CG_A 0 +CT_A 0 +CA_C 0 +CC_C 0 +CG_C 0 +CT_C 0 +CA_G 59 +CC_G 26 +CG_G 32 +CT_G 52 +CA_T 0 +CC_T 0 +CG_T 0 +CT_T 0 +GA_A 0 +GC_A 0 +GG_A 0 +GT_A 0 +GA_C 21 +GC_C 2 +GG_C 39 +GT_C 44 +GA_G 0 +GC_G 0 +GG_G 0 +GT_G 0 +GA_T 0 +GC_T 0 +GG_T 0 +GT_T 0 +TA_A 7 +TC_A -44 +TG_A 16 +TT_A -29 +TA_C 0 +TC_C 0 +TG_C 0 +TT_C 0 +TA_G 0 +TC_G 0 +TG_G 0 +TT_G 0 +TA_T 0 +TC_T 0 +TG_T 0 +TT_T 0 +/* 5' dangling */ +A_AA 0 +A_AC 0 +A_AG 0 +A_AT 0 +A_CA 0 +A_CC 0 +A_CG 0 +A_CT 0 +A_GA 0 +A_GC 0 +A_GG 0 +A_GT 0 +A_TA 29 +A_TC 41 +A_TG 42 +A_TT 2 +C_AA 0 +C_AC 0 +C_AG 0 +C_AT 0 +C_CA 0 +C_CC 0 +C_CG 0 +C_CT 0 +C_GA 37 +C_GC 40 +C_GG 39 +C_GT 49 +C_TA 0 +C_TC 0 +C_TG 0 +C_TT 0 +G_AA 0 +G_AC 0 +G_AG 0 +G_AT 0 +G_CA 63 +G_CC 44 +G_CG 51 +G_CT 40 +G_GA 0 +G_GC 0 +G_GG 0 +G_GT 0 +G_TA 0 +G_TC 0 +G_TG 0 +G_TT 0 +T_AA -2 +T_AC -6 +T_AG 11 +T_AT 69 +T_CA 0 +T_CC 0 +T_CG 0 +T_CT 0 +T_GA 0 +T_GC 0 +T_GG 0 +T_GT 0 +T_TA 0 +T_TC 0 +T_TG 0 +T_TT 0 diff --git a/primer3_bin/primer3_config/interpretations/dangle_i.ds b/primer3_bin/primer3_config/interpretations/dangle_i.ds new file mode 100644 index 0000000..2027921 --- /dev/null +++ b/primer3_bin/primer3_config/interpretations/dangle_i.ds @@ -0,0 +1,131 @@ +/* Entropy of dangling end */ +/* 3' dangling */ +AA_A 0 +AC_A 0 +AG_A 0 +AT_A 0 +AA_C 0 +AC_C 0 +AG_C 0 +AT_C 0 +AA_G 0 +AC_G 0 +AG_G 0 +AT_G 0 +AA_T 11 +AC_T -142 +AG_T 131 +AT_T 126 +CA_A 0 +CC_A 0 +CG_A 0 +CT_A 0 +CA_C 0 +CC_C 0 +CG_C 0 +CT_C 0 +CA_G 165 +CC_G 74 +CG_G 104 +CT_G 150 +CA_T 0 +CC_T 0 +CG_T 0 +CT_T 0 +GA_A 0 +GC_A 0 +GG_A 0 +GT_A 0 +GA_C 39 +GC_C 1 +GG_C 112 +GT_C 131 +GA_G 0 +GC_G 0 +GG_G 0 +GT_G 0 +GA_T 0 +GC_T 0 +GG_T 0 +GT_T 0 +TA_A 8 +TC_A -149 +TG_A 36 +TT_A -104 +TA_C 0 +TC_C 0 +TG_C 0 +TT_C 0 +TA_G 0 +TC_G 0 +TG_G 0 +TT_G 0 +TA_T 0 +TC_T 0 +TG_T 0 +TT_T 0 +/* 5' dangling */ +A_AA 0 +A_AC 0 +A_AG 0 +A_AT 0 +A_CA 0 +A_CC 0 +A_CG 0 +A_CT 0 +A_GA 0 +A_GC 0 +A_GG 0 +A_GT 0 +A_TA 76 +A_TC 130 +A_TG 150 +A_TT 5 +C_AA 0 +C_AC 0 +C_AG 0 +C_AT 0 +C_CA 0 +C_CC 0 +C_CG 0 +C_CT 0 +C_GA 100 +C_GC 119 +C_GG 109 +C_GT 138 +C_TA 0 +C_TC 0 +C_TG 0 +C_TT 0 +G_AA 0 +G_AC 0 +G_AG 0 +G_AT 0 +G_CA 171 +G_CC 126 +G_CG 140 +G_CT 109 +G_GA 0 +G_GC 0 +G_GG 0 +G_GT 0 +G_TA 0 +G_TC 0 +G_TG 0 +G_TT 0 +T_AA -23 +T_AC -33 +T_AG 16 +T_AT 200 +T_CA 0 +T_CC 0 +T_CG 0 +T_CT 0 +T_GA 0 +T_GC 0 +T_GG 0 +T_GT 0 +T_TA 0 +T_TC 0 +T_TG 0 +T_TT 0 diff --git a/primer3_bin/primer3_config/interpretations/loops_i.dh b/primer3_bin/primer3_config/interpretations/loops_i.dh new file mode 100644 index 0000000..8ef2b51 --- /dev/null +++ b/primer3_bin/primer3_config/interpretations/loops_i.dh @@ -0,0 +1,34 @@ +DESTABILIZING ENTHALPIES BY SIZE OF LOOP (INTERPOLATE WHERE NEEDED) +hp3 ave calc no tmm;hp4 ave calc with tmm; ave all bulges +SIZE INTERNAL BULGE HAIRPIN +------------------------------------------------------- +1 . 0.0 . +2 0.0 0.0 . +3 0.0 0.0 0.0 +4 0.0 0.0 0.0 +5 0.0 0.0 0.0 +6 0.0 0.0 0.0 +7 0.0 0.0 0.0 +8 0.0 0.0 0.0 +9 0.0 0.0 0.0 +10 0.0 0.0 0.0 +11 0.0 0.0 0.0 +12 0.0 0.0 0.0 +13 0.0 0.0 0.0 +14 0.0 0.0 0.0 +15 0.0 0.0 0.0 +16 0.0 0.0 0.0 +17 0.0 0.0 0.0 +18 0.0 0.0 0.0 +19 0.0 0.0 0.0 +20 0.0 0.0 0.0 +21 0.0 0.0 0.0 +22 0.0 0.0 0.0 +23 0.0 0.0 0.0 +24 0.0 0.0 0.0 +25 0.0 0.0 0.0 +26 0.0 0.0 0.0 +27 0.0 0.0 0.0 +28 0.0 0.0 0.0 +29 0.0 0.0 0.0 +30 0.0 0.0 0.0 diff --git a/primer3_bin/primer3_config/interpretations/loops_i.ds b/primer3_bin/primer3_config/interpretations/loops_i.ds new file mode 100644 index 0000000..632a027 --- /dev/null +++ b/primer3_bin/primer3_config/interpretations/loops_i.ds @@ -0,0 +1,31 @@ +SIZE INTERNAL BULGE HAIRPIN +1 . -128.9 . +2 . -93.5 . +3 -103.1 -99.9 -112.8 +4 -116 -103.1 -112.8 +5 -128.9 -106.4 -106.4 +6 -141.8 -112.8 -128.9 +7 -148.3 -119.2 -135.4 +8 -154.7 -125.7 -138.6 +9 -157.9 -132.1 -145 +10 -157.9 -138.6 -148.3 +11 -162.6 -143.2 -152.9 +12 -167.6 -145 -161.2 +13 -171.5 -148.9 -165 +14 -174.1 -154.7 -164.4 +15 -177.4 -158.1 -167.7 +16 -180.5 -161.2 -170.8 +17 -183.4 -164.1 -173.8 +18 -187 -167.6 -177.3 +19 -189.6 -170.2 -179.9 +20 -190.2 -170.8 -183.7 +21 -192.5 -173.2 -186.1 +22 -194.8 -175.5 -188.4 +23 -197 -177.6 -190.5 +24 -199 -179.7 -192.6 +25 -203.1 -180.5 -196.6 +26 -205 -182.4 -198.5 +27 -206.8 -184.2 -200.4 +28 -208.6 -186 -202.1 +29 -210.3 -187.7 -203.8 +30 -212.8 -190.2 -203.1 diff --git a/primer3_bin/primer3_config/interpretations/stack_i.dh b/primer3_bin/primer3_config/interpretations/stack_i.dh new file mode 100644 index 0000000..993e19c --- /dev/null +++ b/primer3_bin/primer3_config/interpretations/stack_i.dh @@ -0,0 +1,257 @@ +/* values in articles are modified as follows: dS *(-10) and dH *(-10) */ +AA_AA inf +AA_AC inf +AA_AG inf +AA_AT inf +AA_CA inf +AA_CC inf +AA_CG inf +AA_CT inf +AA_GA inf +AA_GC inf +AA_GG inf +AA_GT inf +AA_TA inf +AA_TC inf +AA_TG inf +AA_TT -7900 +AC_AA inf +AC_AC inf +AC_AG inf +AC_AT inf +AC_CA inf +AC_CC inf +AC_CG inf +AC_CT inf +AC_GA inf +AC_GC inf +AC_GG inf +AC_GT inf +AC_TA inf +AC_TC inf +AC_TG -8400 +AC_TT inf +AG_AA inf +AG_AC inf +AG_AG inf +AG_AT inf +AG_CA inf +AG_CC inf +AG_CG inf +AG_CT inf +AG_GA inf +AG_GC inf +AG_GG inf +AG_GT inf +AG_TA inf +AG_TC -7800 +AG_TG inf +AG_TT inf +AT_AA inf +AT_AC inf +AT_AG inf +AT_AT inf +AT_CA inf +AT_CC inf +AT_CG inf +AT_CT inf +AT_GA inf +AT_GC inf +AT_GG inf +AT_GT inf +AT_TA -7200 +AT_TC inf +AT_TG inf +AT_TT inf +CA_AA inf +CA_AC inf +CA_AG inf +CA_AT inf +CA_CA inf +CA_CC inf +CA_CG inf +CA_CT inf +CA_GA inf +CA_GC inf +CA_GG inf +CA_GT -8500 +CA_TA inf +CA_TC inf +CA_TG inf +CA_TT inf +CC_AA inf +CC_AC inf +CC_AG -52 +CC_AT inf +CC_CA inf +CC_CC inf +CC_CG -36 +CC_CT inf +CC_GA inf +CC_GC inf +CC_GG -8000 +CC_GT inf +CC_TA inf +CC_TC inf +CC_TG inf +CC_TT inf +CG_AA inf +CG_AC inf +CG_AG inf +CG_AT inf +CG_CA inf +CG_CC inf +CG_CG inf +CG_CT inf +CG_GA inf +CG_GC -10600 +CG_GG inf +CG_GT inf +CG_TA inf +CG_TC inf +CG_TG inf +CG_TT inf +CT_AA inf +CT_AC inf +CT_AG inf +CT_AT inf +CT_CA inf +CT_CC inf +CT_CG inf +CT_CT inf +CT_GA -7800 +CT_GC inf +CT_GG inf +CT_GT inf +CT_TA inf +CT_TC inf +CT_TG inf +CT_TT inf +GA_AA inf +GA_AC inf +GA_AG inf +GA_AT inf +GA_CA inf +GA_CC inf +GA_CG inf +GA_CT -8200 +GA_GA inf +GA_GC inf +GA_GG inf +GA_GT inf +GA_TA inf +GA_TC inf +GA_TG inf +GA_TT inf +GC_AA inf +GC_AC inf +GC_AG inf +GC_AT inf +GC_CA inf +GC_CC inf +GC_CG -9800 +GC_CT inf +GC_GA inf +GC_GC inf +GC_GG inf +GC_GT inf +GC_TA inf +GC_TC inf +GC_TG inf +GC_TT inf +GG_AA inf +GG_AC inf +GG_AG inf +GG_AT inf +GG_CA inf +GG_CC -8000 +GG_CG inf +GG_CT inf +GG_GA inf +GG_GC inf +GG_GG inf +GG_GT inf +GG_TA inf +GG_TC inf +GG_TG inf +GG_TT inf +GT_AA inf +GT_AC inf +GT_AG inf +GT_AT inf +GT_CA -8400 +GT_CC inf +GT_CG inf +GT_CT inf +GT_GA inf +GT_GC inf +GT_GG inf +GT_GT inf +GT_TA inf +GT_TC inf +GT_TG inf +GT_TT inf +TA_AA inf +TA_AC inf +TA_AG inf +TA_AT -7200 +TA_CA inf +TA_CC inf +TA_CG inf +TA_CT inf +TA_GA inf +TA_GC inf +TA_GG inf +TA_GT inf +TA_TA inf +TA_TC inf +TA_TG inf +TA_TT inf +TC_AA inf +TC_AC inf +TC_AG -8200 +TC_AT inf +TC_CA inf +TC_CC inf +TC_CG inf +TC_CT inf +TC_GA inf +TC_GC inf +TC_GG inf +TC_GT inf +TC_TA inf +TC_TC inf +TC_TG inf +TC_TT inf +TG_AA inf +TG_AC -8500 +TG_AG inf +TG_AT inf +TG_CA inf +TG_CC inf +TG_CG inf +TG_CT inf +TG_GA inf +TG_GC inf +TG_GG inf +TG_GT inf +TG_TA inf +TG_TC inf +TG_TG inf +TG_TT inf +TT_AA -7900 +TT_AC inf +TT_AG inf +TT_AT inf +TT_CA inf +TT_CC inf +TT_CG inf +TT_CT inf +TT_GA inf +TT_GC inf +TT_GG inf +TT_GT inf +TT_TA inf +TT_TC inf +TT_TG inf +TT_TT inf diff --git a/primer3_bin/primer3_config/interpretations/stack_i.ds b/primer3_bin/primer3_config/interpretations/stack_i.ds new file mode 100644 index 0000000..0c40496 --- /dev/null +++ b/primer3_bin/primer3_config/interpretations/stack_i.ds @@ -0,0 +1,256 @@ +AA_AA inf +AA_AC inf +AA_AG inf +AA_AT inf +AA_CA inf +AA_CC inf +AA_CG inf +AA_CT inf +AA_GA inf +AA_GC inf +AA_GG inf +AA_GT inf +AA_TA inf +AA_TC inf +AA_TG inf +AA_TT -22.2 +AC_AA inf +AC_AC inf +AC_AG inf +AC_AT inf +AC_CA inf +AC_CC inf +AC_CG inf +AC_CT inf +AC_GA inf +AC_GC inf +AC_GG inf +AC_GT inf +AC_TA inf +AC_TC inf +AC_TG -22.4 +AC_TT inf +AG_AA inf +AG_AC inf +AG_AG inf +AG_AT inf +AG_CA inf +AG_CC inf +AG_CG inf +AG_CT inf +AG_GA inf +AG_GC -13.2 +AG_GG inf +AG_GT inf +AG_TA inf +AG_TC -21.0 +AG_TG inf +AG_TT inf +AT_AA inf +AT_AC inf +AT_AG inf +AT_AT inf +AT_CA inf +AT_CC inf +AT_CG inf +AT_CT inf +AT_GA inf +AT_GC inf +AT_GG inf +AT_GT inf +AT_TA -20.4 +AT_TC inf +AT_TG inf +AT_TT inf +CA_AA inf +CA_AC inf +CA_AG inf +CA_AT inf +CA_CA inf +CA_CC inf +CA_CG inf +CA_CT inf +CA_GA inf +CA_GC inf +CA_GG inf +CA_GT -22.7 +CA_TA inf +CA_TC inf +CA_TG inf +CA_TT inf +CC_AA inf +CC_AC inf +CC_AG inf +CC_AT inf +CC_CA inf +CC_CC inf +CC_CG inf +CC_CT inf +CC_GA inf +CC_GC inf +CC_GG -19.9 +CC_GT inf +CC_TA inf +CC_TC inf +CC_TG inf +CC_TT inf +CG_AA inf +CG_AC inf +CG_AG inf +CG_AT inf +CG_CA inf +CG_CC inf +CG_CG inf +CG_CT inf +CG_GA inf +CG_GC -27.2 +CG_GG inf +CG_GT inf +CG_TA inf +CG_TC inf +CG_TG inf +CG_TT inf +CT_AA inf +CT_AC inf +CT_AG inf +CT_AT inf +CT_CA inf +CT_CC inf +CT_CG inf +CT_CT inf +CT_GA -21.0 +CT_GC inf +CT_GG inf +CT_GT -15.8 +CT_TA inf +CT_TC inf +CT_TG inf +CT_TT inf +GA_AA inf +GA_AC inf +GA_AG inf +GA_AT inf +GA_CA inf +GA_CC inf +GA_CG inf +GA_CT -22.2 +GA_GA inf +GA_GC inf +GA_GG inf +GA_GT inf +GA_TA inf +GA_TC inf +GA_TG inf +GA_TT inf +GC_AA inf +GC_AC inf +GC_AG inf +GC_AT inf +GC_CA inf +GC_CC inf +GC_CG -24.4 +GC_CT inf +GC_GA inf +GC_GC inf +GC_GG inf +GC_GT inf +GC_TA inf +GC_TC inf +GC_TG inf +GC_TT inf +GG_AA inf +GG_AC inf +GG_AG inf +GG_AT inf +GG_CA inf +GG_CC -19.9 +GG_CG -15.8 +GG_CT inf +GG_GA inf +GG_GC inf +GG_GG inf +GG_GT inf +GG_TA inf +GG_TC inf +GG_TG inf +GG_TT inf +GT_AA inf +GT_AC inf +GT_AG inf +GT_AT inf +GT_CA -22.4 +GT_CC inf +GT_CG inf +GT_CT inf +GT_GA inf +GT_GC inf +GT_GG inf +GT_GT inf +GT_TA inf +GT_TC inf +GT_TG inf +GT_TT inf +TA_AA inf +TA_AC inf +TA_AG inf +TA_AT -21.3 +TA_CA inf +TA_CC inf +TA_CG inf +TA_CT inf +TA_GA inf +TA_GC inf +TA_GG inf +TA_GT inf +TA_TA inf +TA_TC inf +TA_TG inf +TA_TT inf +TC_AA inf +TC_AC inf +TC_AG -22.2 +TC_AT inf +TC_CA inf +TC_CC inf +TC_CG inf +TC_CT inf +TC_GA inf +TC_GC inf +TC_GG inf +TC_GT inf +TC_TA inf +TC_TC inf +TC_TG inf +TC_TT inf +TG_AA inf +TG_AC -22.7 +TG_AG inf +TG_AT inf +TG_CA inf +TG_CC inf +TG_CG inf +TG_CT inf +TG_GA inf +TG_GC inf +TG_GG inf +TG_GT inf +TG_TA inf +TG_TC inf +TG_TG inf +TG_TT inf +TT_AA -22.2 +TT_AC inf +TT_AG inf +TT_AT inf +TT_CA inf +TT_CC inf +TT_CG inf +TT_CT inf +TT_GA -9 +TT_GC inf +TT_GG inf +TT_GT inf +TT_TA inf +TT_TC inf +TT_TG inf +TT_TT inf diff --git a/primer3_bin/primer3_config/interpretations/stackmm_i_mm.dh b/primer3_bin/primer3_config/interpretations/stackmm_i_mm.dh new file mode 100644 index 0000000..81380da --- /dev/null +++ b/primer3_bin/primer3_config/interpretations/stackmm_i_mm.dh @@ -0,0 +1,257 @@ +/* values in articles are modified as follows: dS *(-10) and dH *(-10) */ +AA_AA inf +AA_AC inf +AA_AG inf +AA_AT inf +AA_CA inf +AA_CC inf +AA_CG inf +AA_CT 7600 +AA_GA inf +AA_GC inf +AA_GG inf +AA_GT 3000 +AA_TA 1200 +AA_TC 2300 +AA_TG -600 +AA_TT inf +AC_AA inf +AC_AC inf +AC_AG -2900 +AC_AT inf +AC_CA inf +AC_CC inf +AC_CG -700 +AC_CT inf +AC_GA inf +AC_GC inf +AC_GG 500 +AC_GT inf +AC_TA 5300 +AC_TC 0 +AC_TG -8400 +AC_TT 700 +AG_AA inf +AG_AC -900 +AG_AG inf +AG_AT inf +AG_CA inf +AG_CC 600 +AG_CG inf +AG_CT inf +AG_GA inf +AG_GC -4000 +AG_GG inf +AG_GT inf +AG_TA -700 +AG_TC inf +AG_TG -3100 +AG_TT -1000 +AT_AA 1200 +AT_AC inf +AT_AG inf +AT_AT inf +AT_CA 5300 +AT_CC inf +AT_CG inf +AT_CT inf +AT_GA -700 +AT_GC inf +AT_GG inf +AT_GT inf +AT_TA -7200 +AT_TC -1200 +AT_TG -2500 +AT_TT -2700 +CA_AA inf +CA_AC inf +CA_AG inf +CA_AT 3400 +CA_CA inf +CA_CC inf +CA_CG inf +CA_CT 6100 +CA_GA -900 +CA_GC 1900 +CA_GG -700 +CA_GT inf +CA_TA inf +CA_TC inf +CA_TG inf +CA_TT 1000 +CC_AA inf +CC_AC inf +CC_AG 5200 +CC_AT inf +CC_CA inf +CC_CC inf +CC_CG 3600 +CC_CT inf +CC_GA 600 +CC_GC -1500 +CC_GG inf +CC_GT -800 +CC_TA inf +CC_TC inf +CC_TG 5200 +CC_TT inf +CG_AA inf +CG_AC 1900 +CG_AG inf +CG_AT inf +CG_CA inf +CG_CC -1500 +CG_CG inf +CG_CT inf +CG_GA -4000 +CG_GC inf +CG_GG -4900 +CG_GT -4100 +CG_TA inf +CG_TC -1500 +CG_TG inf +CG_TT inf +CT_AA 2300 +CT_AC inf +CT_AG inf +CT_AT inf +CT_CA 0 +CT_CC inf +CT_CG inf +CT_CT inf +CT_GA inf +CT_GC -1500 +CT_GG -2800 +CT_GT -5000 +CT_TA -1200 +CT_TC inf +CT_TG inf +CT_TT inf +GA_AA inf +GA_AC inf +GA_AG inf +GA_AT 700 +GA_CA -2900 +GA_CC 5200 +GA_CG -600 +GA_CT inf +GA_GA inf +GA_GC inf +GA_GG inf +GA_GT 1600 +GA_TA inf +GA_TC inf +GA_TG inf +GA_TT -1300 +GC_AA inf +GC_AC inf +GC_AG -600 +GC_AT inf +GC_CA -700 +GC_CC 3600 +GC_CG inf +GC_CT 2300 +GC_GA inf +GC_GC inf +GC_GG -6000 +GC_GT inf +GC_TA inf +GC_TC inf +GC_TG -4400 +GC_TT inf +GG_AA inf +GG_AC -700 +GG_AG inf +GG_AT inf +GG_CA 500 +GG_CC inf +GG_CG -6000 +GG_CT 3300 +GG_GA inf +GG_GC -4900 +GG_GG inf +GG_GT inf +GG_TA inf +GG_TC -2800 +GG_TG inf +GG_TT 5800 +GT_AA -600 +GT_AC inf +GT_AG inf +GT_AT inf +GT_CA inf +GT_CC 5200 +GT_CG -4400 +GT_CT -2200 +GT_GA -3100 +GT_GC inf +GT_GG inf +GT_GT inf +GT_TA -2500 +GT_TC inf +GT_TG 4100 +GT_TT inf +TA_AA 4700 +TA_AC 3400 +TA_AG 700 +TA_AT inf +TA_CA inf +TA_CC inf +TA_CG inf +TA_CT 1200 +TA_GA inf +TA_GC inf +TA_GG inf +TA_GT -100 +TA_TA inf +TA_TC inf +TA_TG inf +TA_TT 200 +TC_AA 7600 +TC_AC 6100 +TC_AG inf +TC_AT 1200 +TC_CA inf +TC_CC inf +TC_CG 2300 +TC_CT inf +TC_GA inf +TC_GC inf +TC_GG 3300 +TC_GT inf +TC_TA inf +TC_TC inf +TC_TG -2200 +TC_TT inf +TG_AA 3000 +TG_AC inf +TG_AG 1600 +TG_AT -100 +TG_CA inf +TG_CC -800 +TG_CG inf +TG_CT inf +TG_GA inf +TG_GC -4100 +TG_GG inf +TG_GT -1400 +TG_TA inf +TG_TC -5000 +TG_TG inf +TG_TT inf +TT_AA inf +TT_AC 1000 +TT_AG -1300 +TT_AT 200 +TT_CA 700 +TT_CC inf +TT_CG inf +TT_CT inf +TT_GA -100 +TT_GC inf +TT_GG 5800 +TT_GT inf +TT_TA -2700 +TT_TC inf +TT_TG inf +TT_TT inf diff --git a/primer3_bin/primer3_config/interpretations/stackmm_i_mm.ds b/primer3_bin/primer3_config/interpretations/stackmm_i_mm.ds new file mode 100644 index 0000000..a14b34d --- /dev/null +++ b/primer3_bin/primer3_config/interpretations/stackmm_i_mm.ds @@ -0,0 +1,256 @@ +AA_AA inf +AA_AC inf +AA_AG inf +AA_AT 12.9 +AA_CA inf +AA_CC inf +AA_CG inf +AA_CT 20.2 +AA_GA inf +AA_GC inf +AA_GG inf +AA_GT 7.4 +AA_TA 1.7 +AA_TC 4.6 +AA_TG -2.3 +AA_TT inf +AC_AA inf +AC_AC inf +AC_AG -9.8 +AC_AT inf +AC_CA inf +AC_CC inf +AC_CG -3.8 +AC_CT inf +AC_GA inf +AC_GC inf +AC_GG 3.2 +AC_GT inf +AC_TA 14.6 +AC_TC -4.4 +AC_TG inf +AC_TT 0.2 +AG_AA inf +AG_AC -4.2 +AG_AG inf +AG_AT inf +AG_CA inf +AG_CC 0.6 +AG_CG inf +AG_CT inf +AG_GA inf +AG_GC -13.2 +AG_GG inf +AG_GT inf +AG_TA -2.3 +AG_TC inf +AG_TG -9.5 +AG_TT 0.9 +AT_AA 1.7 +AT_AC inf +AT_AG inf +AT_AT inf +AT_CA 14.6 +AT_CC inf +AT_CG inf +AT_CT inf +AT_GA -2.3 +AT_GC inf +AT_GG inf +AT_GT inf +AT_TA inf +AT_TC -6.2 +AT_TG -8.3 +AT_TT -10.8 +CA_AA inf +CA_AC inf +CA_AG inf +CA_AT 8.0 +CA_CA inf +CA_CC inf +CA_CG inf +CA_CT 16.4 +CA_GA -4.2 +CA_GC 3.7 +CA_GG -2.3 +CA_GT inf +CA_TA inf +CA_TC inf +CA_TG inf +CA_TT 0.7 +CC_AA inf +CC_AC inf +CC_AG 14.2 +CC_AT inf +CC_CA inf +CC_CC inf +CC_CG 8.9 +CC_CT inf +CC_GA -0.6 +CC_GC -7.2 +CC_GG -19.9 +CC_GT -4.5 +CC_TA inf +CC_TC inf +CC_TG 13.5 +CC_TT inf +CG_AA inf +CG_AC 3.7 +CG_AG inf +CG_AT inf +CG_CA inf +CG_CC -7.2 +CG_CG inf +CG_CT inf +CG_GA -13.2 +CG_GC inf +CG_GG -15.3 +CG_GT -11.7 +CG_TA inf +CG_TC -6.1 +CG_TG inf +CG_TT inf +CT_AA 4.6 +CT_AC inf +CT_AG inf +CT_AT inf +CT_CA -4.4 +CT_CC inf +CT_CG inf +CT_CT inf +CT_GA inf +CT_GC -6.1 +CT_GG -8.0 +CT_GT -15.8 +CT_TA -6.2 +CT_TC inf +CT_TG inf +CT_TT inf +GA_AA inf +GA_AC inf +GA_AG inf +GA_AT 0.7 +GA_CA -9.8 +GA_CC 14.2 +GA_CG -1.0 +GA_CT inf +GA_GA inf +GA_GC inf +GA_GG inf +GA_GT 3.6 +GA_TA inf +GA_TC inf +GA_TG inf +GA_TT -5.3 +GC_AA inf +GC_AC inf +GC_AG -1.0 +GC_AT inf +GC_CA -3.8 +GC_CC 8.9 +GC_CG inf +GC_CT 5.4 +GC_GA inf +GC_GC inf +GC_GG -15.8 +GC_GT inf +GC_TA inf +GC_TC inf +GC_TG -12.3 +GC_TT inf +GG_AA inf +GG_AC -2.3 +GG_AG inf +GG_AT inf +GG_CA 3.2 +GG_CC -19.9 +GG_CG -15.8 +GG_CT 10.4 +GG_GA inf +GG_GC -15.3 +GG_GG inf +GG_GT inf +GG_TA inf +GG_TC 80 +GG_TG inf +GG_TT 16.3 +GT_AA 23 +GT_AC inf +GT_AG inf +GT_AT inf +GT_CA inf +GT_CC 13.5 +GT_CG -12.3 +GT_CT -8.4 +GT_GA -9.5 +GT_GC inf +GT_GG inf +GT_GT inf +GT_TA -8.3 +GT_TC inf +GT_TG 9.5 +GT_TT inf +TA_AA 12.9 +TA_AC 8.0 +TA_AG 0.7 +TA_AT inf +TA_CA inf +TA_CC inf +TA_CG inf +TA_CT 0.7 +TA_GA inf +TA_GC inf +TA_GG inf +TA_GT -1.7 +TA_TA inf +TA_TC inf +TA_TG inf +TA_TT -1.5 +TC_AA 20.2 +TC_AC 16.4 +TC_AG inf +TC_AT 0.7 +TC_CA inf +TC_CC inf +TC_CG 5.4 +TC_CT inf +TC_GA inf +TC_GC inf +TC_GG 10.4 +TC_GT inf +TC_TA inf +TC_TC inf +TC_TG -8.4 +TC_TT inf +TG_AA 7.4 +TG_AC inf +TG_AG 3.6 +TG_AT -1.7 +TG_CA inf +TG_CC -4.5 +TG_CG inf +TG_CT inf +TG_GA inf +TG_GC -11.7 +TG_GG inf +TG_GT -6.2 +TG_TA inf +TG_TC -15.8 +TG_TG inf +TG_TT inf +TT_AA inf +TT_AC -7 +TT_AG -5.3 +TT_AT -1.5 +TT_CA 0.2 +TT_CC inf +TT_CG inf +TT_CT inf +TT_GA 0.9 +TT_GC inf +TT_GG 16.3 +TT_GT inf +TT_TA -10.8 +TT_TC inf +TT_TG inf +TT_TT inf diff --git a/primer3_bin/primer3_config/interpretations/tetraloop_i.dh b/primer3_bin/primer3_config/interpretations/tetraloop_i.dh new file mode 100644 index 0000000..9ce63c6 --- /dev/null +++ b/primer3_bin/primer3_config/interpretations/tetraloop_i.dh @@ -0,0 +1,79 @@ +/* tetraloop bonuses for GNRA and GNAB kcal/mol*(-10) */ + +AAAAAT -5 +AAAACT -7 +AAACAT -10 +ACTTGT 0 +AGAAAT 11 +AGAGAT 11 +AGATAT 15 +AGCAAT 16 +AGCGAT 11 +AGCTTT -2 +AGGAAT 11 +AGGGAT 11 +AGGGGT -5 +AGTAAT 16 +AGTGAT 11 +AGTTCT -8 +ATTCGT 2 +ATTTGT 0 +ATTTTT 5 +CAAAAG -5 +CAAACG -7 +CAACAG -10 +CAACCG 0 +CCTTGG 0 +CGAAAG 11 +CGAGAG 11 +CGATAG 15 +CGCAAG 16 +CGCGAG 11 +CGCTTG -2 +CGGAAG 11 +CGGGAG 10 +CGGGGG -5 +CGTAAG 16 +CGTGAG 11 +CGTTCG -8 +CTTCGG 2 +CTTTGG 0 +CTTTTG 5 +GAAAAC -5 +GAAACC -7 +GAACAC -10 +GCTTGC 0 +GGAAAC 11 +GGAGAC 11 +GGATAC 16 +GGCAAC 16 +GGCGAC 11 +GGCTTC -2 +GGGAAC 11 +GGGGAC 11 +GGGGGC -5 +GGTAAC 16 +GGTGAC 11 +GGTTCC -8 +GTTCGC 2 +GTTTGC 0 +GTTTTC 5 +TAAAAA -5 +TAAACA -7 +TAACAA -10 +TCTTGA 0 +TGAAAA 11 +TGAGAA 11 +TGATAA 16 +TGCAAA 16 +TGCGAA 11 +TGCTTA -2 +TGGAAA 11 +TGGGAA 11 +TGGGGA -5 +TGTAAA 16 +TGTGAA 11 +TGTTCA -8 +TTTCGA 2 +TTTTGA 0 +TTTTTA 5 diff --git a/primer3_bin/primer3_config/interpretations/tetraloop_i.ds b/primer3_bin/primer3_config/interpretations/tetraloop_i.ds new file mode 100644 index 0000000..2fdcfd5 --- /dev/null +++ b/primer3_bin/primer3_config/interpretations/tetraloop_i.ds @@ -0,0 +1,81 @@ +/* +VIIDE + */ + +AAAAAT 6.5 +AAAACT -16.1 +AAACAT -16.1 +ACTTGT -41.9 +AGAAAT -16.1 +AGAGAT -16.1 +AGATAT -16.1 +AGCAAT -16.1 +AGCGAT -16.1 +AGCTTT -16.1 +AGGAAT -16.1 +AGGGAT -16.1 +AGGGGT -6.4 +AGTAAT -16.1 +AGTGAT -16.1 +AGTTCT -16.1 +ATTCGT -16.1 +ATTTGT -16.1 +ATTTTT -16.1 +CAAAAG 12.9 +CAAACG 0 +CAACAG 0 +CAACCG 0 +CCTTGG -25.7 +CGAAAG 0 +CGAGAG 0 +CGATAG 0 +CGCAAG 0 +CGCGAG 0 +CGCTTG 0 +CGGAAG 0 +CGGGAG 0 +CGGGGG 9.7 +CGTAAG 0 +CGTGAG 0 +CGTTCG 0 +CTTCGG 0 +CTTTGG 0 +CTTTTG 0 +GAAAAC 32.3 +GAAACC 0 +GAACAC 0 +GCTTGC -25.7 +GGAAAC 0 +GGAGAC 0 +GGATAC 0 +GGCAAC 0 +GGCGAC 0 +GGCTTC 0 +GGGAAC 0 +GGGGAC 0 +GGGGGC 9.7 +GGTAAC 0 +GGTGAC 0 +GGTTCC 0 +GTTCGC 0 +GTTTGC 0 +GTTTTC 0 +TAAAAA -3.2 +TAAACA -16.1 +TAACAA -16.1 +TCTTGA -41.9 +TGAAAA -16.1 +TGAGAA -16.1 +TGATAA -16.1 +TGCAAA -16.1 +TGCGAA -16.1 +TGCTTA -16.1 +TGGAAA -16.1 +TGGGAA -16.1 +TGGGGA -6.4 +TGTAAA -16.1 +TGTGAA -16.1 +TGTTCA -16.1 +TTTCGA -16.1 +TTTTGA -16.1 +TTTTTA -16.1 diff --git a/primer3_bin/primer3_config/interpretations/triloop_i.dh b/primer3_bin/primer3_config/interpretations/triloop_i.dh new file mode 100644 index 0000000..e686148 --- /dev/null +++ b/primer3_bin/primer3_config/interpretations/triloop_i.dh @@ -0,0 +1,21 @@ + +/* triloop bonus*/ + +/* Enthalpy Hairpin loop */ + +AGAAT 15 +AGCAT 15 +AGGAT 15 +AGTAT 15 +CGAAG 20 +CGCAG 20 +CGGAG 20 +CGTAG 20 +GGAAC 20 +GGCAC 20 +GGGAC 20 +GGTAC 20 +TGAAA 15 +TGCAA 15 +TGGAA 15 +TGTAA 15 diff --git a/primer3_bin/primer3_config/interpretations/triloop_i.ds b/primer3_bin/primer3_config/interpretations/triloop_i.ds new file mode 100644 index 0000000..f7457a0 --- /dev/null +++ b/primer3_bin/primer3_config/interpretations/triloop_i.ds @@ -0,0 +1,18 @@ +/* bonuses for GNA triloops */ + +AGAAT 0 +AGCAT 0 +AGGAT 0 +AGTAT 0 +CGAAG 0 +CGCAG 0 +CGGAG 0 +CGTAG 0 +GGAAC 0 +GGCAC 0 +GGGAC 0 +GGTAC 0 +TGAAA 0 +TGCAA 0 +TGGAA 0 +TGTAA 0 diff --git a/primer3_bin/primer3_config/interpretations/tstack2_i.dh b/primer3_bin/primer3_config/interpretations/tstack2_i.dh new file mode 100644 index 0000000..05fc6db --- /dev/null +++ b/primer3_bin/primer3_config/interpretations/tstack2_i.dh @@ -0,0 +1,256 @@ +AA_AA 0 +AA_AC 0 +AA_AG 0 +AA_AT -2500 +AA_CA 0 +AA_CC 0 +AA_CG 0 +AA_CT -2700 +AA_GA 0 +AA_GC 0 +AA_GG 0 +AA_GT -2400 +AA_TA -3100 +AA_TC -1600 +AA_TG -1900 +AA_TT -5000 +AC_AA 0 +AC_AC 0 +AC_AG -8000 +AC_AT 0 +AC_CA 0 +AC_CC 0 +AC_CG -3200 +AC_CT 0 +AC_GA 0 +AC_GC 0 +AC_GG -4600 +AC_GT 0 +AC_TA -1800 +AC_TC -100 +AC_TG -6000 +AC_TT -900 +AG_AA 0 +AG_AC -4300 +AG_AG 0 +AG_AT 0 +AG_CA 0 +AG_CC -2700 +AG_CG 0 +AG_CT 0 +AG_GA 0 +AG_GC -6000 +AG_GG 0 +AG_GT 0 +AG_TA -2500 +AG_TC -6000 +AG_TG -1100 +AG_TT -3200 +AT_AA -3100 +AT_AC 0 +AT_AG 0 +AT_AT 0 +AT_CA -1800 +AT_CC 0 +AT_CG 0 +AT_CT 0 +AT_GA -2500 +AT_GC 0 +AT_GG 0 +AT_GT 0 +AT_TA -5000 +AT_TC -2300 +AT_TG -3500 +AT_TT -2400 +CA_AA 0 +CA_AC 0 +CA_AG 0 +CA_AT -2300 +CA_CA 0 +CA_CC 0 +CA_CG 0 +CA_CT -700 +CA_GA -4300 +CA_GC -2600 +CA_GG -3900 +CA_GT -6000 +CA_TA 0 +CA_TC 0 +CA_TG 0 +CA_TT -700 +CC_AA 0 +CC_AC 0 +CC_AG -5000 +CC_AT 0 +CC_CA 0 +CC_CC 0 +CC_CG -3900 +CC_CT 0 +CC_GA -2700 +CC_GC -2100 +CC_GG -7000 +CC_GT -3200 +CC_TA 0 +CC_TC 0 +CC_TG -3000 +CC_TT 0 +CG_AA 0 +CG_AC -2600 +CG_AG 0 +CG_AT 0 +CG_CA 0 +CG_CC -2100 +CG_CG 0 +CG_CT 0 +CG_GA -6000 +CG_GC -7000 +CG_GG -3800 +CG_GT -3800 +CG_TA 0 +CG_TC -3900 +CG_TG 0 +CG_TT 0 +CT_AA -1600 +CT_AC 0 +CT_AG 0 +CT_AT 0 +CT_CA -100 +CT_CC 0 +CT_CG 0 +CT_CT 0 +CT_GA -6000 +CT_GC -3900 +CT_GG -6600 +CT_GT -6100 +CT_TA -2300 +CT_TC 0 +CT_TG 0 +CT_TT 0 +GA_AA 0 +GA_AC 0 +GA_AG 0 +GA_AT -2000 +GA_CA -8000 +GA_CC -5000 +GA_CG -4300 +GA_CT -6000 +GA_GA 0 +GA_GC 0 +GA_GG 0 +GA_GT -1100 +GA_TA 0 +GA_TC 0 +GA_TG 0 +GA_TT -3600 +GC_AA 0 +GC_AC 0 +GC_AG -4300 +GC_AT 0 +GC_CA -3200 +GC_CC -3900 +GC_CG -7000 +GC_CT -4900 +GC_GA 0 +GC_GC 0 +GC_GG -700 +GC_GT 0 +GC_TA 0 +GC_TC 0 +GC_TG -5900 +GC_TT 0 +GG_AA 0 +GG_AC -3900 +GG_AG 0 +GG_AT 0 +GG_CA -4600 +GG_CC -7000 +GG_CG -700 +GG_CT -5700 +GG_GA 0 +GG_GC -3800 +GG_GG 0 +GG_GT 0 +GG_TA 0 +GG_TC -6600 +GG_TG 0 +GG_TT 0 +GT_AA -1900 +GT_AC 0 +GT_AG 0 +GT_AT 0 +GT_CA -6000 +GT_CC -3000 +GT_CG -5900 +GT_CT -7400 +GT_GA -1100 +GT_GC 0 +GT_GG 0 +GT_GT 0 +GT_TA -3500 +GT_TC 0 +GT_TG 0 +GT_TT 0 +TA_AA -2500 +TA_AC -2300 +TA_AG -2000 +TA_AT -5000 +TA_CA 0 +TA_CC 0 +TA_CG 0 +TA_CT -2500 +TA_GA 0 +TA_GC 0 +TA_GG 0 +TA_GT -3900 +TA_TA 0 +TA_TC 0 +TA_TG 0 +TA_TT -3200 +TC_AA -2700 +TC_AC -700 +TC_AG -6000 +TC_AT -2500 +TC_CA 0 +TC_CC 0 +TC_CG -4900 +TC_CT 0 +TC_GA 0 +TC_GC 0 +TC_GG -5700 +TC_GT 0 +TC_TA 0 +TC_TC 0 +TC_TG -7400 +TC_TT 0 +TG_AA -2400 +TG_AC -6000 +TG_AG -1100 +TG_AT -3900 +TG_CA 0 +TG_CC -3200 +TG_CG 0 +TG_CT 0 +TG_GA 0 +TG_GC -3800 +TG_GG 0 +TG_GT 0 +TG_TA 0 +TG_TC -6100 +TG_TG 0 +TG_TT 0 +TT_AA -5000 +TT_AC -700 +TT_AG -3600 +TT_AT -3200 +TT_CA -900 +TT_CC 0 +TT_CG 0 +TT_CT 0 +TT_GA -3200 +TT_GC 0 +TT_GG 0 +TT_GT 0 +TT_TA -2400 +TT_TC 0 +TT_TG 0 +TT_TT 0 diff --git a/primer3_bin/primer3_config/interpretations/tstack2_i.ds b/primer3_bin/primer3_config/interpretations/tstack2_i.ds new file mode 100644 index 0000000..13b0d97 --- /dev/null +++ b/primer3_bin/primer3_config/interpretations/tstack2_i.ds @@ -0,0 +1,256 @@ +AA_AA inf +AA_AC inf +AA_AG inf +AA_AT -6.3 +AA_CA inf +AA_CC inf +AA_CG inf +AA_CT -7.0 +AA_GA inf +AA_GC inf +AA_GG inf +AA_GT -5.8 +AA_TA -7.8 +AA_TC -4.0 +AA_TG -4.4 +AA_TT -13.2 +AC_AA inf +AC_AC inf +AC_AG -22.5 +AC_AT inf +AC_CA inf 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+TA_AA -6.3 +TA_AC -5.9 +TA_AG -4.7 +TA_AT -14.2 +TA_CA inf +TA_CC inf +TA_CG inf +TA_CT -6.3 +TA_GA inf +TA_GC inf +TA_GG inf +TA_GT -10.5 +TA_TA inf +TA_TC inf +TA_TG inf +TA_TT -8.9 +TC_AA -7.0 +TC_AC -1.3 +TC_AG -16.1 +TC_AT -6.3 +TC_CA inf +TC_CC inf +TC_CG -13.5 +TC_CT inf +TC_GA inf +TC_GC inf +TC_GG -15.9 +TC_GT inf +TC_TA inf +TC_TC inf +TC_TG -21.2 +TC_TT inf +TG_AA -5.8 +TG_AC -16.1 +TG_AG -2.7 +TG_AT -10.5 +TG_CA inf +TG_CC -8.0 +TG_CG inf +TG_CT inf +TG_GA inf +TG_GC -9.0 +TG_GG inf +TG_GT inf +TG_TA inf +TG_TC -16.9 +TG_TG inf +TG_TT inf +TT_AA -13.5 +TT_AC -1.2 +TT_AG -9.8 +TT_AT -8.9 +TT_CA -1.7 +TT_CC inf +TT_CG inf +TT_CT inf +TT_GA -8.7 +TT_GC inf +TT_GG inf +TT_GT inf +TT_TA -6.5 +TT_TC inf +TT_TG inf +TT_TT inf diff --git a/primer3_bin/primer3_config/interpretations/tstack_i.dh b/primer3_bin/primer3_config/interpretations/tstack_i.dh new file mode 100644 index 0000000..a257d9f --- /dev/null +++ b/primer3_bin/primer3_config/interpretations/tstack_i.dh @@ -0,0 +1,256 @@ +AA_AA 0 +AA_AC 0 +AA_AG 0 +AA_AT 25 +AA_CA 0 +AA_CC 0 +AA_CG 0 +AA_CT 27 +AA_GA 0 +AA_GC 0 +AA_GG 0 +AA_GT 24 +AA_TA 31 +AA_TC 16 +AA_TG 19 +AA_TT 0 +AC_AA 0 +AC_AC 0 +AC_AG 80 +AC_AT 0 +AC_CA 0 +AC_CC 0 +AC_CG 32 +AC_CT 0 +AC_GA 0 +AC_GC 0 +AC_GG 46 +AC_GT 0 +AC_TA 18 +AC_TC 1 +AC_TG 0 +AC_TT 9 +AG_AA 0 +AG_AC 43 +AG_AG 0 +AG_AT 0 +AG_CA 0 +AG_CC 27 +AG_CG 0 +AG_CT 0 +AG_GA 0 +AG_GC 60 +AG_GG 0 +AG_GT 0 +AG_TA 25 +AG_TC 0 +AG_TG 11 +AG_TT 32 +AT_AA 31 +AT_AC 0 +AT_AG 0 +AT_AT 0 +AT_CA 18 +AT_CC 0 +AT_CG 0 +AT_CT 0 +AT_GA 25 +AT_GC 0 +AT_GG 0 +AT_GT 0 +AT_TA 0 +AT_TC 23 +AT_TG 35 +AT_TT 24 +CA_AA 0 +CA_AC 0 +CA_AG 0 +CA_AT 23 +CA_CA 0 +CA_CC 0 +CA_CG 0 +CA_CT 7 +CA_GA 43 +CA_GC 26 +CA_GG 39 +CA_GT 0 +CA_TA 0 +CA_TC 0 +CA_TG 0 +CA_TT 7 +CC_AA 0 +CC_AC 0 +CC_AG 50 +CC_AT 0 +CC_CA 0 +CC_CC 0 +CC_CG 39 +CC_CT 0 +CC_GA 27 +CC_GC 21 +CC_GG 0 +CC_GT 32 +CC_TA 0 +CC_TC 0 +CC_TG 30 +CC_TT 0 +CG_AA 0 +CG_AC 26 +CG_AG 0 +CG_AT 0 +CG_CA 0 +CG_CC 21 +CG_CG 0 +CG_CT 0 +CG_GA 60 +CG_GC 0 +CG_GG 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inf +TC_TA inf +TC_TC inf +TC_TG 212 +TC_TT inf +TG_AA 58 +TG_AC 0 +TG_AG 27 +TG_AT 105 +TG_CA inf +TG_CC 80 +TG_CG inf +TG_CT inf +TG_GA inf +TG_GC 90 +TG_GG inf +TG_GT inf +TG_TA inf +TG_TC 169 +TG_TG inf +TG_TT inf +TT_AA 0 +TT_AC 12 +TT_AG 98 +TT_AT 89 +TT_CA 17 +TT_CC inf +TT_CG inf +TT_CT inf +TT_GA 87 +TT_GC inf +TT_GG inf +TT_GT inf +TT_TA 65 +TT_TC inf +TT_TG inf +TT_TT inf diff --git a/primer3_bin/primer3_config/interpretations/tstack_tm_inf_i.dh b/primer3_bin/primer3_config/interpretations/tstack_tm_inf_i.dh new file mode 100644 index 0000000..a257d9f --- /dev/null +++ b/primer3_bin/primer3_config/interpretations/tstack_tm_inf_i.dh @@ -0,0 +1,256 @@ +AA_AA 0 +AA_AC 0 +AA_AG 0 +AA_AT 25 +AA_CA 0 +AA_CC 0 +AA_CG 0 +AA_CT 27 +AA_GA 0 +AA_GC 0 +AA_GG 0 +AA_GT 24 +AA_TA 31 +AA_TC 16 +AA_TG 19 +AA_TT 0 +AC_AA 0 +AC_AC 0 +AC_AG 80 +AC_AT 0 +AC_CA 0 +AC_CC 0 +AC_CG 32 +AC_CT 0 +AC_GA 0 +AC_GC 0 +AC_GG 46 +AC_GT 0 +AC_TA 18 +AC_TC 1 +AC_TG 0 +AC_TT 9 +AG_AA 0 +AG_AC 43 +AG_AG 0 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+TT_GC 0 +TT_GG 0 +TT_GT 0 +TT_TA 24 +TT_TC 0 +TT_TG 0 +TT_TT 0 diff --git a/primer3_bin/primer3_config/interpretations/tstack_tm_inf_i.ds b/primer3_bin/primer3_config/interpretations/tstack_tm_inf_i.ds new file mode 100644 index 0000000..9ed4328 --- /dev/null +++ b/primer3_bin/primer3_config/interpretations/tstack_tm_inf_i.ds @@ -0,0 +1,256 @@ +AA_AA inf +AA_AC inf +AA_AG inf +AA_AT 63 +AA_CA inf +AA_CC inf +AA_CG inf +AA_CT 70 +AA_GA inf +AA_GC inf +AA_GG inf +AA_GT 58 +AA_TA 78 +AA_TC 40 +AA_TG 44 +AA_TT inf +AC_AA inf +AC_AC inf +AC_AG 225 +AC_AT inf +AC_CA inf +AC_CC inf +AC_CG 71 +AC_CT inf +AC_GA inf +AC_GC inf +AC_GG 114 +AC_GT inf +AC_TA 38 +AC_TC 5 +AC_TG inf +AC_TT 17 +AG_AA inf +AG_AC 107 +AG_AG inf +AG_AT inf +AG_CA inf +AG_CC 60 +AG_CG inf +AG_CT inf +AG_GA inf +AG_GC 155 +AG_GG inf +AG_GT inf +AG_TA 59 +AG_TC inf +AG_TG 21 +AG_TT 87 +AT_AA 78 +AT_AC inf +AT_AG inf +AT_AT inf +AT_CA 38 +AT_CC inf +AT_CG inf +AT_CT inf +AT_GA 59 +AT_GC inf +AT_GG inf +AT_GT inf +AT_TA inf 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+GC_GG 192 +GC_GT inf +GC_TA inf +GC_TC inf +GC_TG 161 +GC_TT inf +GG_AA inf +GG_AC 96 +GG_AG inf +GG_AT inf +GG_CA 114 +GG_CC inf +GG_CG 192 +GG_CT 159 +GG_GA inf +GG_GC 95 +GG_GG inf +GG_GT inf +GG_TA inf +GG_TC 187 +GG_TG inf +GG_TT inf +GT_AA 44 +GT_AC inf +GT_AG inf +GT_AT inf +GT_CA inf +GT_CC 78 +GT_CG 161 +GT_CT 212 +GT_GA 21 +GT_GC inf +GT_GG inf +GT_GT inf +GT_TA 94 +GT_TC inf +GT_TG inf +GT_TT inf +TA_AA 63 +TA_AC 59 +TA_AG 47 +TA_AT inf +TA_CA inf +TA_CC inf +TA_CG inf +TA_CT 63 +TA_GA inf +TA_GC inf +TA_GG inf +TA_GT 105 +TA_TA inf +TA_TC inf +TA_TG inf +TA_TT 89 +TC_AA 70 +TC_AC 13 +TC_AG inf +TC_AT 63 +TC_CA inf +TC_CC inf +TC_CG 135 +TC_CT inf +TC_GA inf +TC_GC inf +TC_GG 159 +TC_GT inf +TC_TA inf +TC_TC inf +TC_TG 212 +TC_TT inf +TG_AA 58 +TG_AC inf +TG_AG 27 +TG_AT 105 +TG_CA inf +TG_CC 80 +TG_CG inf +TG_CT inf +TG_GA inf +TG_GC 90 +TG_GG inf +TG_GT inf +TG_TA inf +TG_TC 169 +TG_TG inf +TG_TT inf +TT_AA inf +TT_AC 12 +TT_AG 98 +TT_AT 89 +TT_CA 17 +TT_CC inf +TT_CG inf +TT_CT inf +TT_GA 87 +TT_GC inf +TT_GG inf +TT_GT inf +TT_TA 65 +TT_TC inf +TT_TG inf +TT_TT inf diff --git a/primer3_bin/primer3_config/loops.dh b/primer3_bin/primer3_config/loops.dh new file mode 100644 index 0000000..3c3fd84 --- /dev/null +++ b/primer3_bin/primer3_config/loops.dh @@ -0,0 +1,30 @@ +1 inf 0.0 inf +2 inf 0.0 inf +3 0.0 0.0 0.0 +4 0.0 0.0 0.0 +5 0.0 0.0 0.0 +6 0.0 0.0 0.0 +7 0.0 0.0 0.0 +8 0.0 0.0 0.0 +9 0.0 0.0 0.0 +10 0.0 0.0 0.0 +11 0.0 0.0 0.0 +12 0.0 0.0 0.0 +13 0.0 0.0 0.0 +14 0.0 0.0 0.0 +15 0.0 0.0 0.0 +16 0.0 0.0 0.0 +17 0.0 0.0 0.0 +18 0.0 0.0 0.0 +19 0.0 0.0 0.0 +20 0.0 0.0 0.0 +21 0.0 0.0 0.0 +22 0.0 0.0 0.0 +23 0.0 0.0 0.0 +24 0.0 0.0 0.0 +25 0.0 0.0 0.0 +26 0.0 0.0 0.0 +27 0.0 0.0 0.0 +28 0.0 0.0 0.0 +29 0.0 0.0 0.0 +30 0.0 0.0 0.0 diff --git a/primer3_bin/primer3_config/loops.ds b/primer3_bin/primer3_config/loops.ds new file mode 100644 index 0000000..141101c --- /dev/null +++ b/primer3_bin/primer3_config/loops.ds @@ -0,0 +1,30 @@ +1 -1.0 -12.89 -1.0 +2 -1.0 -9.35 -1.0 +3 -10.31 -9.99 -11.28 +4 -11.6 -10.31 -11.28 +5 -12.89 -10.64 -10.64 +6 -14.18 -11.28 -12.89 +7 -14.83 -11.92 -13.54 +8 -15.47 -12.57 -13.86 +9 -15.79 -13.21 -14.5 +10 -15.79 -13.86 -14.83 +11 -16.26 -14.32 -15.29 +12 -16.76 -14.5 -16.12 +13 -17.15 -14.89 -16.5 +14 -17.41 -15.47 -16.44 +15 -17.74 -15.81 -16.77 +16 -18.05 -16.12 -17.08 +17 -18.34 -16.41 -17.38 +18 -18.7 -16.76 -17.73 +19 -18.96 -17.02 -17.99 +20 -19.02 -17.08 -18.37 +21 -19.25 -17.32 -18.61 +22 -19.48 -17.55 -18.84 +23 -19.7 -17.76 -19.05 +24 -19.9 -17.97 -19.26 +25 -20.31 -18.05 -19.66 +26 -20.5 -18.24 -19.85 +27 -20.68 -18.42 -20.04 +28 -20.86 -18.6 -20.21 +29 -21.03 -18.77 -20.38 +30 -21.28 -19.02 -20.31 diff --git a/primer3_bin/primer3_config/stack.dh b/primer3_bin/primer3_config/stack.dh new file mode 100644 index 0000000..74124ab --- /dev/null +++ b/primer3_bin/primer3_config/stack.dh @@ -0,0 +1,256 @@ +inf +inf +inf +inf +inf +inf +inf +inf +inf +inf +inf +inf +inf +inf +inf +-7900 +inf +inf +inf 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+inf +inf +inf +inf +inf +inf +inf +inf +-21.0 +inf +inf +inf +inf +inf +inf +inf +inf +inf +inf +inf +inf +inf +inf +-22.2 +inf +inf +inf +inf +inf +inf +inf +inf +inf +inf +inf +inf +inf +inf +-24.4 +inf +inf +inf +inf +inf +inf +inf +inf +inf +inf +inf +inf +inf +inf +-19.9 +inf +inf +inf +inf +inf +inf +inf +inf +inf +inf +inf +inf +inf +inf +-22.4 +inf +inf +inf +inf +inf +inf +inf +inf +inf +inf +inf +inf +inf +inf +-21.3 +inf +inf +inf +inf +inf +inf +inf +inf +inf +inf +inf +inf +inf +inf +-22.2 +inf +inf +inf +inf +inf +inf +inf +inf +inf +inf +inf +inf +inf +inf +-22.7 +inf +inf +inf +inf +inf +inf +inf +inf +inf +inf +inf +inf +inf +inf +-22.2 +inf +inf +inf +inf +inf +inf +inf +inf +inf +inf +inf +inf +inf +inf +inf diff --git a/primer3_bin/primer3_config/stackmm.dh b/primer3_bin/primer3_config/stackmm.dh new file mode 100644 index 0000000..c86ae64 --- /dev/null +++ b/primer3_bin/primer3_config/stackmm.dh @@ -0,0 +1,256 @@ +inf +inf +inf +4700 +inf +inf +inf +7600 +inf +inf 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+4700 +3400 +700 +inf +inf +inf +inf +1200 +inf +inf +inf +-100 +inf +inf +inf +200 +7600 +6100 +inf +1200 +inf +inf +2300 +inf +inf +inf +3300 +inf +inf +inf +-2200 +inf +3000 +inf +1600 +-100 +inf +-800 +inf +inf +inf +-4100 +inf +-1400 +inf +-5000 +inf +inf +inf +1000 +-1300 +200 +700 +inf +inf +inf +1000 +inf +5800 +inf +-2700 +inf +inf +inf diff --git a/primer3_bin/primer3_config/stackmm.ds b/primer3_bin/primer3_config/stackmm.ds new file mode 100644 index 0000000..5aa3c1f --- /dev/null +++ b/primer3_bin/primer3_config/stackmm.ds @@ -0,0 +1,256 @@ +inf +inf +inf +12.9 +inf +inf +inf +20.2 +inf +inf +inf +7.4 +1.7 +4.6 +-2.3 +inf +inf +inf +-9.8 +inf +inf +inf +-3.8 +inf +inf +inf +3.2 +inf +14.6 +-4.4 +inf +0.2 +inf +-4.2 +inf +inf +inf +0.6 +inf +inf +inf +-13.2 +inf +inf +-2.3 +inf +-9.5 +0.9 +1.7 +inf +inf +inf +14.6 +inf +inf +inf +-2.3 +inf +inf +inf +inf +-6.2 +-8.3 +-10.8 +inf +inf +inf +8.0 +inf +inf +inf +16.4 +-4.2 +3.7 +-2.3 +inf +inf +inf +inf +0.7 +inf +inf +14.2 +inf +inf +inf +8.9 +inf +-0.6 +-7.2 +inf +-4.5 +inf +inf +13.5 +inf +inf +3.7 +inf +inf +inf +-7.2 +inf +inf +-13.2 +inf +-15.3 +-11.7 +inf +-6.1 +inf +inf +4.6 +inf +inf +inf +-4.4 +inf +inf +inf +inf +-6.1 +-8.0 +-15.8 +-6.2 +inf +inf +inf +inf +inf +inf +0.7 +-9.8 +14.2 +-1.0 +inf +inf +inf +inf +3.6 +inf +inf +inf +-5.3 +inf +inf +-1.0 +inf +-3.8 +8.9 +inf +5.4 +inf +inf +-15.8 +inf +inf +inf +-12.3 +inf +inf +-2.3 +inf +inf +3.2 +inf +-15.8 +10.4 +inf +-15.3 +inf +inf +inf +80 +inf +16.3 +23 +inf +inf +inf +inf +13.5 +-12.3 +-8.4 +-9.5 +inf +inf +inf +-8.3 +inf +9.5 +inf +12.9 +8.0 +0.7 +inf +inf +inf +inf +0.7 +inf +inf +inf +-1.7 +inf +inf +inf +-1.5 +20.2 +16.4 +inf +0.7 +inf +inf +5.4 +inf +inf +inf +10.4 +inf +inf +inf +-8.4 +inf +7.4 +inf +3.6 +-1.7 +inf +-4.5 +inf +inf +inf +-11.7 +inf +-6.2 +inf +-15.8 +inf +inf +inf +-7 +-5.3 +-1.5 +0.2 +inf +inf +inf +0.9 +inf +16.3 +inf +-10.8 +inf +inf +inf diff --git a/primer3_bin/primer3_config/tetraloop.dh b/primer3_bin/primer3_config/tetraloop.dh new file mode 100644 index 0000000..408a789 --- /dev/null +++ b/primer3_bin/primer3_config/tetraloop.dh @@ -0,0 +1,77 @@ +AAAAAT 500 +AAAACT 700 +AAACAT 1000 +ACTTGT 0 +AGAAAT -1100 +AGAGAT -1100 +AGATAT -1500 +AGCAAT -1600 +AGCGAT -1100 +AGCTTT 200 +AGGAAT -1100 +AGGGAT -1100 +AGGGGT 500 +AGTAAT -1600 +AGTGAT -1100 +AGTTCT 800 +ATTCGT -200 +ATTTGT 0 +ATTTTT -500 +CAAAAG 500 +CAAACG 700 +CAACAG 1000 +CAACCG 0 +CCTTGG 0 +CGAAAG -1100 +CGAGAG -1100 +CGATAG -1500 +CGCAAG -1600 +CGCGAG -1100 +CGCTTG 200 +CGGAAG -1100 +CGGGAG -1000 +CGGGGG 500 +CGTAAG -1600 +CGTGAG -1100 +CGTTCG 800 +CTTCGG -200 +CTTTGG 0 +CTTTTG -500 +GAAAAC 500 +GAAACC 700 +GAACAC 1000 +GCTTGC 0 +GGAAAC -1100 +GGAGAC -1100 +GGATAC -1600 +GGCAAC -1600 +GGCGAC -1100 +GGCTTC 200 +GGGAAC -1100 +GGGGAC -1100 +GGGGGC 500 +GGTAAC -1600 +GGTGAC -1100 +GGTTCC 800 +GTTCGC -200 +GTTTGC 0 +GTTTTC -500 +TAAAAA 500 +TAAACA 700 +TAACAA 1000 +TCTTGA 0 +TGAAAA -1100 +TGAGAA -1100 +TGATAA -1600 +TGCAAA -1600 +TGCGAA -1100 +TGCTTA 200 +TGGAAA -1100 +TGGGAA -1100 +TGGGGA 500 +TGTAAA -1600 +TGTGAA -1100 +TGTTCA 800 +TTTCGA -200 +TTTTGA 0 +TTTTTA -500 diff --git a/primer3_bin/primer3_config/tetraloop.ds b/primer3_bin/primer3_config/tetraloop.ds new file mode 100644 index 0000000..bd8598b --- /dev/null +++ b/primer3_bin/primer3_config/tetraloop.ds @@ -0,0 +1,77 @@ +AAAAAT -650 +AAAACT 1610 +AAACAT 1610 +ACTTGT 4190 +AGAAAT 1610 +AGAGAT 1610 +AGATAT 1610 +AGCAAT 1610 +AGCGAT 1610 +AGCTTT 1610 +AGGAAT 1610 +AGGGAT 1610 +AGGGGT 640 +AGTAAT 1610 +AGTGAT 1610 +AGTTCT 1610 +ATTCGT 1610 +ATTTGT 1610 +ATTTTT 1610 +CAAAAG -1290 +CAAACG 0 +CAACAG 0 +CAACCG 0 +CCTTGG 2570 +CGAAAG 0 +CGAGAG 0 +CGATAG 0 +CGCAAG 0 +CGCGAG 0 +CGCTTG 0 +CGGAAG 0 +CGGGAG 0 +CGGGGG -970 +CGTAAG 0 +CGTGAG 0 +CGTTCG 0 +CTTCGG 0 +CTTTGG 0 +CTTTTG 0 +GAAAAC -3230 +GAAACC 0 +GAACAC 0 +GCTTGC 2570 +GGAAAC 0 +GGAGAC 0 +GGATAC 0 +GGCAAC 0 +GGCGAC 0 +GGCTTC 0 +GGGAAC 0 +GGGGAC 0 +GGGGGC -970 +GGTAAC 0 +GGTGAC 0 +GGTTCC 0 +GTTCGC 0 +GTTTGC 0 +GTTTTC 0 +TAAAAA 320 +TAAACA 1610 +TAACAA 1610 +TCTTGA 4190 +TGAAAA 1610 +TGAGAA 1610 +TGATAA 1610 +TGCAAA 1610 +TGCGAA 1610 +TGCTTA 1610 +TGGAAA 1610 +TGGGAA 1610 +TGGGGA 640 +TGTAAA 1610 +TGTGAA 1610 +TGTTCA 1610 +TTTCGA 1610 +TTTTGA 1610 +TTTTTA 1610 diff --git a/primer3_bin/primer3_config/triloop.dh b/primer3_bin/primer3_config/triloop.dh new file mode 100644 index 0000000..acbd974 --- /dev/null +++ b/primer3_bin/primer3_config/triloop.dh @@ -0,0 +1,16 @@ +AGAAT -1500 +AGCAT -1500 +AGGAT -1500 +AGTAT -1500 +CGAAG -2000 +CGCAG -2000 +CGGAG -2000 +CGTAG -2000 +GGAAC -2000 +GGCAC -2000 +GGGAC -2000 +GGTAC -2000 +TGAAA -1500 +TGCAA -1500 +TGGAA -1500 +TGTAA -1500 diff --git a/primer3_bin/primer3_config/triloop.ds b/primer3_bin/primer3_config/triloop.ds new file mode 100644 index 0000000..5bcbd4e --- /dev/null +++ b/primer3_bin/primer3_config/triloop.ds @@ -0,0 +1,16 @@ +AGAAT 0 +AGCAT 0 +AGGAT 0 +AGTAT 0 +CGAAG 0 +CGCAG 0 +CGGAG 0 +CGTAG 0 +GGAAC 0 +GGCAC 0 +GGGAC 0 +GGTAC 0 +TGAAA 0 +TGCAA 0 +TGGAA 0 +TGTAA 0 diff --git a/primer3_bin/primer3_config/tstack.dh b/primer3_bin/primer3_config/tstack.dh new file mode 100644 index 0000000..41dd41e --- /dev/null +++ b/primer3_bin/primer3_config/tstack.dh @@ -0,0 +1,256 @@ +0 +0 +0 +-2500 +0 +0 +0 +-2700 +0 +0 +0 +-2400 +-3100 +-1600 +-1900 +0 +0 +0 +-8000 +0 +0 +0 +-3200 +0 +0 +0 +-4600 +0 +-1800 +-100 +0 +-900 +0 +-4300 +0 +0 +0 +-2700 +0 +0 +0 +-6000 +0 +0 +-2500 +0 +-1100 +-3200 +-3100 +0 +0 +0 +-1800 +0 +0 +0 +-2500 +0 +0 +0 +0 +-2300 +-3500 +-2400 +0 +0 +0 +-2300 +0 +0 +0 +-700 +-4300 +-2600 +-3900 +0 +0 +0 +0 +-700 +0 +0 +-5000 +0 +0 +0 +-3900 +0 +-2700 +-2100 +0 +-3200 +0 +0 +-3000 +0 +0 +-2600 +0 +0 +0 +-2100 +0 +0 +-6000 +0 +-3800 +-3800 +0 +-3900 +0 +0 +-1600 +0 +0 +0 +-100 +0 +0 +0 +0 +-3900 +-6600 +-6100 +-2300 +0 +0 +0 +0 +0 +0 +-2000 +-8000 +-5000 +-4300 +0 +0 +0 +0 +-1100 +0 +0 +0 +-3600 +0 +0 +-4300 +0 +-3200 +-3900 +0 +-4900 +0 +0 +-700 +0 +0 +0 +-5900 +0 +0 +-3900 +0 +0 +-4600 +0 +-700 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