{
"generator": "primer3-py",
"primer3_py_version": "2.3.0",
"tm_tests": [
{
"name": "M13_forward",
"seq": "GTAAAACGACGGCCAGT",
"params": "default",
"expected_tm": 54.695494691112515
},
{
"name": "M13_reverse",
"seq": "CAGGAAACAGCTATGAC",
"params": "default",
"expected_tm": 49.095322907921854
},
{
"name": "T7_promoter",
"seq": "TAATACGACTCACTATAGGG",
"params": "default",
"expected_tm": 50.32403821708397
},
{
"name": "SP6_promoter",
"seq": "ATTTAGGTGACACTATAG",
"params": "default",
"expected_tm": 44.545014772856405
},
{
"name": "GC_rich_20mer",
"seq": "GCGCGCGCGCGCGCGCGCGC",
"params": "default",
"expected_tm": 83.40529626638005
},
{
"name": "AT_rich_19mer",
"seq": "AAAAAAAAAAAAAAAAAAA",
"params": "default",
"expected_tm": 39.904309851471965
},
{
"name": "balanced_20mer",
"seq": "ATCGATCGATCGATCGATCG",
"params": "default",
"expected_tm": 57.363116239639965
},
{
"name": "short_10mer",
"seq": "ATCGATCGAT",
"params": "default",
"expected_tm": 26.43455660044998
},
{
"name": "long_40mer",
"seq": "ATCGATCGATCGATCGATCGATCGATCGATCGATCGATCG",
"params": "default",
"expected_tm": 72.5555871909819
},
{
"name": "method_breslauer_salt_schildkraut",
"seq": "GTAAAACGACGGCCAGT",
"params": {
"tm_method": "breslauer",
"salt_correction": "schildkraut"
},
"expected_tm": 62.99586675305511
},
{
"name": "method_breslauer_salt_santalucia",
"seq": "GTAAAACGACGGCCAGT",
"params": {
"tm_method": "breslauer",
"salt_correction": "santalucia"
},
"expected_tm": 66.70173356709859
},
{
"name": "method_breslauer_salt_owczarzy",
"seq": "GTAAAACGACGGCCAGT",
"params": {
"tm_method": "breslauer",
"salt_correction": "owczarzy"
},
"expected_tm": 67.11597941468256
},
{
"name": "method_santalucia_salt_schildkraut",
"seq": "GTAAAACGACGGCCAGT",
"params": {
"tm_method": "santalucia",
"salt_correction": "schildkraut"
},
"expected_tm": 50.453370543468225
},
{
"name": "method_santalucia_salt_santalucia",
"seq": "GTAAAACGACGGCCAGT",
"params": {
"tm_method": "santalucia",
"salt_correction": "santalucia"
},
"expected_tm": 54.695494691112515
},
{
"name": "method_santalucia_salt_owczarzy",
"seq": "GTAAAACGACGGCCAGT",
"params": {
"tm_method": "santalucia",
"salt_correction": "owczarzy"
},
"expected_tm": 55.195149488500874
},
{
"name": "conditions_high_mv",
"seq": "GTAAAACGACGGCCAGT",
"params": {
"conditions": {
"mv_conc": 200.0
}
},
"expected_tm": 57.80364848002341
},
{
"name": "conditions_low_mv",
"seq": "GTAAAACGACGGCCAGT",
"params": {
"conditions": {
"mv_conc": 10.0
}
},
"expected_tm": 53.37497871107513
},
{
"name": "conditions_high_dv",
"seq": "GTAAAACGACGGCCAGT",
"params": {
"conditions": {
"dv_conc": 5.0
}
},
"expected_tm": 57.613519079344485
},
{
"name": "conditions_high_dntp",
"seq": "GTAAAACGACGGCCAGT",
"params": {
"conditions": {
"dntp_conc": 2.0
}
},
"expected_tm": 49.16808228911765
},
{
"name": "conditions_high_dna",
"seq": "GTAAAACGACGGCCAGT",
"params": {
"conditions": {
"dna_conc": 500.0
}
},
"expected_tm": 58.41811790862431
},
{
"name": "conditions_dmso_5pct",
"seq": "GTAAAACGACGGCCAGT",
"params": {
"conditions": {
"dmso_conc": 5.0,
"dmso_fact": 0.6
}
},
"expected_tm": 51.695494571903225
},
{
"name": "conditions_formamide_1M",
"seq": "GTAAAACGACGGCCAGT",
"params": {
"conditions": {
"formamide_conc": 1.0
}
},
"expected_tm": 52.05531822052428
},
{
"name": "conditions_combined",
"seq": "GTAAAACGACGGCCAGT",
"params": {
"conditions": {
"mv_conc": 100.0,
"dv_conc": 3.0,
"dntp_conc": 1.0,
"dna_conc": 200.0
}
},
"expected_tm": 59.337417404450605
}
],
"thermo_tests": [
{
"type": "hairpin",
"name": "strong_hairpin",
"seq1": "CCCCCATCCGATCAGGGGG",
"expected": {
"structure_found": true,
"tm": 66.7472726460212,
"dg": -3176.9186867678436,
"dh": -36300.0,
"ds": -106.7969734426315
}
},
{
"type": "hairpin",
"name": "palindrome",
"seq1": "AATTAATTAATT",
"expected": {
"structure_found": false,
"tm": 0.0,
"dg": 0.0,
"dh": 0.0,
"ds": 0.0
}
},
{
"type": "hairpin",
"name": "no_structure",
"seq1": "AAAAAAAAAA",
"expected": {
"structure_found": false,
"tm": 0.0,
"dg": 0.0,
"dh": 0.0,
"ds": 0.0
}
},
{
"type": "hairpin",
"name": "gc_hairpin",
"seq1": "GCGCGCATATATGCGCGC",
"expected": {
"structure_found": true,
"tm": 85.93696640122744,
"dg": -8735.654144611017,
"dh": -64100.0,
"ds": -178.50828907105912
}
},
{
"type": "hairpin_structure",
"name": "strong_hairpin_with_structure",
"seq1": "CCCCCATCCGATCAGGGGG",
"expected": {
"structure_found": true,
"tm": 66.7472726460212,
"dg": -3176.9186867678436,
"dh": -36300.0,
"ds": -106.7969734426315,
"ascii_structure": "SEQ\t/////---------\\\\\\\\\\\nSTR\tCCCCCATCCGATCAGGGGG\n"
}
},
{
"type": "hairpin",
"name": "custom_conditions",
"seq1": "CCCCCATCCGATCAGGGGG",
"params": {
"mv_conc": 100.0,
"dv_conc": 3.0,
"temp_c": 25.0
},
"expected": {
"structure_found": true,
"tm": 68.71482079007984,
"dg": -4641.741115720983,
"dh": -36300.0,
"ds": -106.18232059124273
}
},
{
"type": "homodimer",
"name": "self_comp",
"seq1": "AGTCTAGTCTATCGATCG",
"expected": {
"structure_found": true,
"tm": 9.356456390075891,
"dg": -6068.7261446141065,
"dh": -52600.0,
"ds": -150.02828907104916
}
},
{
"type": "homodimer",
"name": "poly_a",
"seq1": "AAAAAAAAAA",
"expected": {
"structure_found": false,
"tm": 0.0,
"dg": 0.0,
"dh": 0.0,
"ds": 0.0
}
},
{
"type": "homodimer",
"name": "gc_rich",
"seq1": "GCGCGCGCGCGCGCGCGCGC",
"expected": {
"structure_found": true,
"tm": 84.26057136046398,
"dg": -35908.203349516305,
"dh": -193200.0,
"ds": -507.1474984700426
}
},
{
"type": "homodimer",
"name": "no_dimer",
"seq1": "ATCGATCGAT",
"expected": {
"structure_found": true,
"tm": 28.082649837650365,
"dg": -8259.471060294236,
"dh": -71000.0,
"ds": -202.29092032792445
}
},
{
"type": "heterodimer",
"name": "comp_10",
"seq1": "AAAAAAAAAA",
"seq2": "TTTTTTTTTT",
"expected": {
"structure_found": true,
"tm": 11.216594246691386,
"dg": -5186.161060294242,
"dh": -66500.0,
"ds": -197.69092032792443
}
},
{
"type": "heterodimer",
"name": "partial_comp",
"seq1": "ATCGATCGATCG",
"seq2": "CGATCGATCGAT",
"expected": {
"structure_found": true,
"tm": 37.57223202159912,
"dg": -11385.118518140505,
"dh": -92000.0,
"ds": -259.9222359563421
}
},
{
"type": "heterodimer",
"name": "no_comp",
"seq1": "AAAAAAAAAA",
"seq2": "AAAAAAAAAA",
"expected": {
"structure_found": false,
"tm": 0.0,
"dg": 0.0,
"dh": 0.0,
"ds": 0.0
}
},
{
"type": "heterodimer",
"name": "gc_at_mix",
"seq1": "GCGCGCGCGC",
"seq2": "ATATATATAT",
"expected": {
"structure_found": false,
"tm": 0.0,
"dg": 0.0,
"dh": 0.0,
"ds": 0.0
}
},
{
"type": "end_stability",
"name": "at_end",
"seq1": "AGCTATTTTTTTTTTT",
"seq2": "CATGATTTTTTTTTTTTTT",
"expected": {
"structure_found": true,
"tm": -303.56854879856087,
"dg": 1099.9999999999998,
"dh": 1100.0,
"ds": 8.881784197001252e-16
}
},
{
"type": "end_stability",
"name": "gc_end",
"seq1": "AGCTAGCGCGCGCGCG",
"seq2": "CATGATGCGCGCGCGCGCG",
"expected": {
"structure_found": true,
"tm": 60.65390096399119,
"dg": -19279.74728922203,
"dh": -113800.0,
"ds": -304.75657814211826
}
},
{
"type": "end_stability",
"name": "mixed",
"seq1": "ATCGATCGATCG",
"seq2": "CGATCGATCGAT",
"expected": {
"structure_found": true,
"tm": 37.57223202159912,
"dg": -11385.118518140505,
"dh": -92000.0,
"ds": -259.9222359563421
}
}
],
"design_tests": [
{
"name": "basic_design",
"num_pairs": 5,
"pairs": [
{
"left_seq": "CCTGGGGTGCCTAATGAGTG",
"right_seq": "TACCGCCTTTGAGTGAGCTG",
"left_tm": 60.10701692078908,
"right_tm": 60.0373256491867,
"left_pos": [
144,
20
],
"right_pos": [
364,
20
],
"product_size": 221,
"pair_penalty": 0.14434256997577677
},
{
"left_seq": "TCCGCTCACAATTCCACACA",
"right_seq": "TACCGCCTTTGAGTGAGCTG",
"left_tm": 59.892356747650354,
"right_tm": 60.0373256491867,
"left_pos": [
94,
20
],
"right_pos": [
364,
20
],
"product_size": 271,
"pair_penalty": 0.14496890153634467
},
{
"left_seq": "CCTGGGGTGCCTAATGAGTG",
"right_seq": "TTTGCTGGCCTTTTGCTCAC",
"left_tm": 60.10701692078908,
"right_tm": 59.89532901784224,
"left_pos": [
144,
20
],
"right_pos": [
428,
20
],
"product_size": 285,
"pair_penalty": 0.21168790294683504
},
{
"left_seq": "CCTGGGGTGCCTAATGAGTG",
"right_seq": "CCTTTTGCTGGCCTTTTGCT",
"left_tm": 60.10701692078908,
"right_tm": 59.89273163212596,
"left_pos": [
144,
20
],
"right_pos": [
431,
20
],
"product_size": 288,
"pair_penalty": 0.21428528866312035
},
{
"left_seq": "GGTACCGAGCTCGAATTCGT",
"right_seq": "CGAGTCAGTGAGCGAGGAAG",
"left_tm": 59.8998535364787,
"right_tm": 60.179176326100446,
"left_pos": [
37,
20
],
"right_pos": [
310,
20
],
"product_size": 274,
"pair_penalty": 0.2793227896217445
}
]
},
{
"name": "pick_left_only",
"num_left": 3,
"left_primers": [
{
"seq": "CAGCTCACTCAAAGGCGGTA",
"tm": 60.0373256491867,
"pos": [
345,
20
],
"gc": 55.0
},
{
"seq": "GGTACCGAGCTCGAATTCGT",
"tm": 59.8998535364787,
"pos": [
37,
20
],
"gc": 55.0
},
{
"seq": "GTGAGCAAAAGGCCAGCAAA",
"tm": 59.89532901784224,
"pos": [
409,
20
],
"gc": 50.0
}
]
},
{
"name": "pick_right_only",
"num_right": 3,
"right_primers": [
{
"seq": "TACCGCCTTTGAGTGAGCTG",
"tm": 60.0373256491867,
"pos": [
364,
20
],
"gc": 55.0
},
{
"seq": "ACGAATTCGAGCTCGGTACC",
"tm": 59.8998535364787,
"pos": [
56,
20
],
"gc": 55.0
},
{
"seq": "TTTGCTGGCCTTTTGCTCAC",
"tm": 59.89532901784224,
"pos": [
428,
20
],
"gc": 50.0
}
]
},
{
"name": "excluded_region",
"num_pairs": 3,
"pairs": [
{
"left_seq": "CCTGGGGTGCCTAATGAGTG",
"right_seq": "TACCGCCTTTGAGTGAGCTG",
"left_pos": [
144,
20
],
"right_pos": [
364,
20
],
"product_size": 221
},
{
"left_seq": "CCTGGGGTGCCTAATGAGTG",
"right_seq": "TTTGCTGGCCTTTTGCTCAC",
"left_pos": [
144,
20
],
"right_pos": [
428,
20
],
"product_size": 285
},
{
"left_seq": "CCTGGGGTGCCTAATGAGTG",
"right_seq": "CCTTTTGCTGGCCTTTTGCT",
"left_pos": [
144,
20
],
"right_pos": [
431,
20
],
"product_size": 288
}
]
},
{
"name": "included_region",
"num_pairs": 3,
"pairs": [
{
"left_seq": "CCTGGGGTGCCTAATGAGTG",
"right_seq": "CGAGTCAGTGAGCGAGGAAG",
"left_pos": [
144,
20
],
"right_pos": [
310,
20
],
"product_size": 167
},
{
"left_seq": "TTAATGAATCGGCCAACGCG",
"right_seq": "TACCGCCTTTGAGTGAGCTG",
"left_pos": [
235,
20
],
"right_pos": [
364,
20
],
"product_size": 130
},
{
"left_seq": "CCTGGGGTGCCTAATGAGTG",
"right_seq": "CAATACGCAAACCGCCTCTC",
"left_pos": [
144,
20
],
"right_pos": [
278,
20
],
"product_size": 135
}
]
},
{
"name": "gc_constraints",
"num_pairs": 3,
"pairs": [
{
"left_seq": "TCCGCTCACAATTCCACACA",
"right_seq": "TACCGCCTTTGAGTGAGCTG",
"left_gc": 50.0,
"right_gc": 55.0
},
{
"left_seq": "ACACAACATACGAGCCGGAA",
"right_seq": "TACCGCCTTTGAGTGAGCTG",
"left_gc": 50.0,
"right_gc": 55.0
},
{
"left_seq": "AAAGCCTGGGGTGCCTAATG",
"right_seq": "TACCGCCTTTGAGTGAGCTG",
"left_gc": 55.0,
"right_gc": 55.0
}
]
},
{
"name": "check_primers",
"num_pairs": 1,
"left_tm": 60.10701692078908,
"right_tm": 60.0373256491867,
"product_size": 221,
"pair_penalty": 0.14434256997577677
},
{
"name": "breslauer_schildkraut",
"num_pairs": 3,
"pairs": [
{
"left_seq": "GCCTAATGAGTGAGCTAACT",
"right_seq": "GATTCTGTGGATAACCGTAT",
"left_tm": 59.98810582125742,
"right_tm": 60.09808844389033,
"product_size": 233
},
{
"left_seq": "GCCTAATGAGTGAGCTAACT",
"right_seq": "ATTCTGTGGATAACCGTATT",
"left_tm": 59.98810582125742,
"right_tm": 59.78244178849178,
"product_size": 232
},
{
"left_seq": "AAGCATAAAGTGTAAAGCCT",
"right_seq": "GATTCTGTGGATAACCGTAT",
"left_tm": 59.81516262759163,
"right_tm": 60.09808844389033,
"product_size": 258
}
]
},
{
"name": "custom_size_range",
"num_pairs": 3,
"pairs": [
{
"left_seq": "TATCCGCTCACAATTCCACACA",
"right_seq": "AACCGTATTACCGCCTTTGAGT",
"left_len": 22,
"right_len": 22,
"left_tm": 60.02765330309484,
"right_tm": 60.02783691065491
},
{
"left_seq": "CGCTCACAATTCCACACAACAT",
"right_seq": "AACCGTATTACCGCCTTTGAGT",
"left_len": 22,
"right_len": 22,
"left_tm": 60.03089327883015,
"right_tm": 60.02783691065491
},
{
"left_seq": "TATCCGCTCACAATTCCACACA",
"right_seq": "GTGGATAACCGTATTACCGCCT",
"left_len": 22,
"right_len": 22,
"left_tm": 60.02765330309484,
"right_tm": 59.96365383312758
}
]
}
]
}