Louis BECQUEY / biorseo

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Louis BECQUEY
1d43ff8f 1 parent 350f4e49

Pseudoknots types data

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Showing 2 changed files with 817 additions and 19 deletions
......@@ -276,25 +276,6 @@ SecondaryStructure MOIP::solve_objective(int o, double min, double max)
void MOIP::define_problem_constraints(void)
{
// Force basepairs between the end of a component and the beginning of the next
if (verbose_) cout << "\t>forcing basepairs between bounds of inserted components..." << endl;
for (size_t i = 0; i < insertion_sites_.size(); i++) {
Motif& x = insertion_sites_[i];
IloExpr c6p = IloExpr(env_);
if (allowed_basepair(x.comp[0].pos.first, x.comp.back().pos.second))
c6p += y(x.comp[0].pos.first, x.comp.back().pos.second);
if (verbose_) cout << "\t\t" << (C(i, 0) <= c6p) << endl;
model_.add(C(i, 0) <= c6p);
if (x.comp.size() == 1) // This constraint is for multi-component motives.
continue;
for (size_t j = 0; j < x.comp.size() - 1; j++) {
IloExpr c6 = IloExpr(env_);
if (allowed_basepair(x.comp[j].pos.second, x.comp[j + 1].pos.first))
c6 += y(x.comp[j].pos.second, x.comp[j + 1].pos.first);
model_.add(C(i, j) <= c6);
if (verbose_) cout << "\t\t" << (C(i, j) <= c6) << endl;
}
}
// ensure there only is 0 or 1 pairing by nucleotide:
if (verbose_) cout << "\t>ensuring there are at most 1 pairing by nucleotide..." << endl;
......@@ -391,6 +372,25 @@ void MOIP::define_problem_constraints(void)
model_.add(c5 == jm1 * C(i, 0));
if (verbose_) cout << "\t\t>motif " << i << " : " << (c5 == jm1 * C(i, 0)) << endl;
}
// Force basepairs between the end of a component and the beginning of the next
if (verbose_) cout << "\t>forcing basepairs between bounds of inserted components..." << endl;
for (size_t i = 0; i < insertion_sites_.size(); i++) {
Motif& x = insertion_sites_[i];
IloExpr c6p = IloExpr(env_);
if (allowed_basepair(x.comp[0].pos.first, x.comp.back().pos.second))
c6p += y(x.comp[0].pos.first, x.comp.back().pos.second);
if (verbose_) cout << "\t\t" << (C(i, 0) <= c6p) << endl;
model_.add(C(i, 0) <= c6p);
if (x.comp.size() == 1) // This constraint is for multi-component motives.
continue;
for (size_t j = 0; j < x.comp.size() - 1; j++) {
IloExpr c6 = IloExpr(env_);
if (allowed_basepair(x.comp[j].pos.second, x.comp[j + 1].pos.first))
c6 += y(x.comp[j].pos.second, x.comp[j + 1].pos.first);
model_.add(C(i, j) <= c6);
if (verbose_) cout << "\t\t" << (C(i, j) <= c6) << endl;
}
}
// Forbid pseudoknots
if (!this->allow_pk_) {
if (verbose_) cout << "\t>forbidding pseudoknots..." << endl;
......
>_PKB1:_Bovine_Leukemia_Virus_(BLV)
AAAAAACUAAUAGAGGGGGGACUUAGCGCCCCCCAAACCGUAACCCC
..............[[[[[[.....(((]]]]]]....)))......
>_PKB2:_Beet_Western-Yellows_Virus_(BWYV)
GGGAAACGGAGUGCGCGGCACCGUCCGCGGAACAAACGGAGAAGGCAGCU
.............[[[[[..((((]]]]]......))))...........
>_PKB3:_Equine_Infectious_Anemic_Virus_(EIAV)
AAAAAACGGGAAGCAAGGGGCUCAAGGGAGGCCCCAGAAACAAACUUUCCCGAU
................[[[[[[...((((]]]]]]............))))...
>_PKB4:_Feline_Immunodeficiency_Virus_(FIV)
GGGAAACUGGAAGGCGGGGCGAGCUGCAGCCCCAGUGAAUCAAAUGCAGC
...............[[[[[..((((((]]]]]...........))))))
>_PKB5:_turnip_yellow_mosaic_virus_(TYMV)
CGGGUGCAACUCCCGCCCCUCUUCCGAGGGUCAUCGGAACC
...............(((....[[[[[)))...]]]]]...
>_PKB6:_kennedya_yellow_mosaic_virus_(KYMV-BP)
GGGGUGCAACUCCCCCGUCUAUCCUGGACGUCACCAGGACCA
...............(((...[[[[[[)))...]]]]]]...
>_PKB7:_cacao_yellow_mosaic_virus_(CaYMV)
GGUGGUGCAACUCCCCCGUCCUCCCGAACGUCAUCGGGACCA
................(((..[[[[[[)))...]]]]]]...
>_PKB8:_physalis_mottle_virus_(PhyMV)
UGGGUGCAACUCCCCCCCCUUCCGUGGGUAACGGAAACCA
..............(((..[[[[[[)))..]]]]]]....
>_PKB9:_desmodium_yellow_mottle_virus_(DYMV)
GGGGUGCAACUCCCCCGUCUAUCCUGGACGUCACCAGGACCA
...............(((...[[[[[[)))...]]]]]]...
>_PKB10:_ononis_yellow_mosaic_virus_(OYMV)
UGGGUUCAACUCCCCCCCUUUUCCGAGGGUAUCGGAAACC
..............(((...[[[[[[)))..]]]]]]...
>_PKB11:_clitoria_yellow_vein_virus_(CYVV)
UGGGUGCAACCCCCCCGUCCAUCUCGAACGUCAUCGAGACCA
...............(((...[[[[[[)))...]]]]]]...
>_PKB12:_wild_cucumber_mosaic_virus_(WCMV)
CGGGUGCAACCCCCCCUCCCCCCGUAGGUUAACGGGACCA
..............(((...[[[[[)))...]]]]]....
>_PKB13:_calopogonium_yellow_vein_virus_(CaYVV)
GGGGUGCGACUCCCCCGUCUAUCCUGAACGUCAUCAGGACCA
...............(((...[[[[[[)))...]]]]]]...
>_PKB14:_andean_potato_latent_virus_(APLV)
CGGGUGCGACUCCCCCCCCUCCUGUGGGCUACAGGAACCA
..............(((..[[[[[[)))..]]]]]]....
>_PKB15:_eggplant_mosaic_virus_(EMV)
UGGGUGCGACUCCCCCCCCUCCCGUGGGUCAACGGGAACCA
..............(((..[[[[[[)))...]]]]]]....
>_PKB16:_okra_mosaic_virus_(OMV)
GGGGUGCAACUCCCCCGCCCAUCUCGAGCGUCAUCGAGACCA
...............(((...[[[[[[)))...]]]]]]...
>_PKB17:_tobacco_mosaic_virus_(CcTMV)
GGGGAGCAUUACCCCCCCAAAACCCUGGGGAUACAGGGCCCA
...............(((....[[[[[)))...]]]]]....
>_PKB18:_tobacco_mosaic_virus_(TMV)
GGGGUUCGAAUCCCCCCGUUACCCCCGGUAGGGGCCCA
...............(((...[[[[)))..]]]]....
>_PKB19:_pepper_mild_mottle_virus_(PMMV-I)
GGGGUUCGAAUCCCCCCCGAACCGCGGGUAGCGGCCCA
...............(((...[[[[)))..]]]]....
>_PKB20:_cucumber_green_mottle_mosaic_virus_(CGMMV)
GGGGUUCGAAUCCCCCCUUUUCCCCGGGUAGGGGCCCA
...............(((...[[[[)))..]]]]....
>_PKB21:_tobacco_mosaic_virus_(TMV-L)
GGGAUUCGAAUUCCCCCGGAACCCCCGGUUGGGGCCCA
...............(((...[[[[)))..]]]]....
>_PKB22:_satellite_tobacco_mosaic_virus_(STMV)
GGGGUUCGAAUCCCUCCCUAACCGCGGGUAAGCGGCCCA
...............(((...[[[[)))...]]]]....
>_PKB23:_tobacco_mild_green_mosaic_virus_(TMGMV)
GAGGUUCGAAUCCUCCCGUAACCGCCGGUAGCGGCCCA
...............(((...[[[[)))..]]]]....
>_PKB24:_paprika_mild_mottle_virus_(PaMMV)
GGGGUUCGAAUCCCCCCUUUACCCCGGGUAUGGGGCCCA
...............(((...[[[[)))...]]]]....
>_PKB25:_turnip_vein-clearing_virus_(TVCV)
GAGGUUCGAAUCCUCCCUAACCCCGGGUAGGGGCCCA
...............(((..[[[[)))..]]]]....
>_PKB26:_oilseed_rape_mosaic_virus_(ORMV)
GAGGUUCGAAUCCUCCCUAACCCCGGGUAGGGGCCCA
...............(((..[[[[)))..]]]]....
>_PKB27:_pepper_mild_mottle_virus_(PMMV-S)
GGGGUUCGAAUCCCCCCCGAACCGCGGGUAGCGGCCCA
...............(((...[[[[)))..]]]]....
>_PKB28:_odontoglossum_ringspot_virus_(ORSV-S1)
GGGAUUCGAAUUCCCCCUUACCUCGGGUAGAGGCCCA
...............(((..[[[[)))..]]]]....
>_PKB29:_tobacco_mosaic_virus_(TMVcg)
GAGGUUCGAAUCCUCCCUAACCCCGGGUAGGGGCCCA
...............(((..[[[[)))..]]]]....
>_PKB30:_soil-borne_wheat_mosaic_virus_(SBWMV1)
GGGGUUCAAAUCCCCCCCGAACCGGAGGGUUAUCCGGCCCA
...............(((...[[[[[)))...]]]]]....
>_PKB31:_soil-borne_wheat_mosaic_virus_(SBWMV2)
GGGGUUCAAUUCCCCCCCCAUCCGGAGGGUUAUCCGGCCC
...............(((...[[[[[)))...]]]]]...
>_PKB32:_potato_mop-top_virus_(PMTV2)
GGGUGCAACUCCCCCCCCCUUGGAGGGUAUCCAAGACC
.............(((..[[[[[[)))..]]]]]]...
>_PKB33:_peanut_clump_virus_(PCV1)
GGUGCAAAUCCCCCGCUGAAACGGAGCGAUAUCCGUCCCA
.............(((....[[[[[)))...]]]]]....
>_PKB34:_peanut_clump_virus_(PCV2)
GGUGCAAAUCCCCCGCUGAAACGGAGCGAUAUCCGUCCCA
.............(((....[[[[[)))...]]]]]....
>_PKB35:_Indian_peanut_clump_virus_(IPCV1)
GGUGCAAAUCCCCCGCCGAUACGGAGCGAUAUCCGUCCCA
.............(((....[[[[[)))...]]]]]....
>_PKB36:_beet_soil-borne_virus_(BSBV1)
GGGGUGCAAAUCCCCCCCUUUACUUGAGGGAAAUCAAGCCC
...............(((....[[[[[)))...]]]]]...
>_PKB37:_beet_soil-borne_virus_(BSBV2)
GGGGUGCAAAUCCCCCCCUUAACUUGAGGGAAAUCAAGCCC
...............(((....[[[[[)))...]]]]]...
>_PKB38:_beet_soil-borne_virus_(BSBV3)
GGGGUGCAACUCCCCCCCUUAACUAGAGGGAAAUCUAGCCC
...............(((....[[[[[)))...]]]]]...
>_PKB39:_beet_virus_Q_(BVQ1)
GGGGUGCAAAUCCCCCCCUAACUUGAGGGAAAUCAAGCCCC
...............(((...[[[[[)))...]]]]]....
>_PKB40:_beet_virus_Q_(BVQ2)
GGGGUGCAAAUCCCCCCCUAACUUGAGGGAAAUCAAGCCC
...............(((...[[[[[)))...]]]]]...
>_PKB41:_beet_virus_Q_(BVQ3)
GGGGUGCAAAUCCCCCCCUAACUUGAGGGAAAUCAAGCCCC
...............(((...[[[[[)))...]]]]]....
>_PKB42:_potato_leafroll_virus_(PLRV-W)
UUUAAAUGGGCGAGCGGCACCGCCCGCCAAAACAAACGG
.............((((..[[[.)))).........]]]
>_PKB43:_potato_leafroll_virus_(PLRV-S)
UUUAAAUGGGCAAGCGGCACCGUCCGCCAAAACAAACGG
.............((((..[[[[))))........]]]]
>_PKB44:_cucurbit_aphid-borne_yellows_virus_(CABYV)
GGGAAACGGGCAGGCGGCGGCGACCGCCGAAACAACCGC
............(((((..[[[.)))))........]]]
>_PKB45:_pea_enation_mosaic_virus_(PEMV)
GGGAAACGGAUUAUUCCGGUCGACUCCGGAGAAACAAAGUC
.............((((((..[[[[))))))......]]]]
>_PKB46:_barley_yellow_dwarf_virus_(BYDV-NY-RPV)
GGGAAACGGGAAGGCGGCGGCGUCCGCCGUAACAAACGC
............(((((..[[[[))))).......]]]]
>_PKB47:_Moloney_murine_leukemia_virus_(Mo-MuLV)
UAGGGAGGUCAGGGUCAGGAGCCCCCCCCUGAACCCAGGAUAACCCUCAAAGUCGGGGGGC
...........((((((((.[[[[[[[)))).))))..................]]]]]]]
>_PKB48:_spleen_necrosis_virus_(SNV)
UAGGGCCGUCAGGGUUCUCCCGCCCUCCGUGAACCCAGGCUAAAAGUUAAGGUAGGGGGGC
...........((((((.(..[[[[[[[).))))))..................]]]]]]]
>_PKB49:_E.coli_(Ec_PK1)
CGAGGGGCGGUUGGCCUCGUAAAAAGCCGC
(((((.[[[[[[..))))).....]]]]]]
>_PKB50:_E.coli_(Ec_PK2)
CCUCUCUCCCUAGCCUCCGCUCUUAGGACGGGGAUCAAGAGAGGUCAAACCCAAAAGAG
(((((((((((..(((...[[[[[)))..))))....)))))))..........]]]]]
>_PKB51:_E.coli_(Ec_PK3)
GCGUGGAAGCCCUGCCUGGGGUUGAAGCGUUAAAACUUAAUCAGGC
((((...(((((.[[[[[)))))...))))...........]]]]]
>_PKB52:_E.coli_(Ec_PK4)
GUUUGUUAGUGGCGUGUCCGUCCGCAGCUGGCAAGCGAAUGUAAAGACUGAC
((((((((((.(((.[[[.[[[))).)))))))))).........]]].]]]
>_PKB53:_tobacco_mosaic_virus_(TMV_UPD-PK1)
ACGGAUUGUGUCCGUAAUCACA
..(((.[[[[))).....]]]]
>_PKB54:_tobacco_mosaic_virus_(TMV_UPD-PK2)
CGUGGUGCGUACGAUAACGCAU
(((.[[[[[[)))...]]]]]]
>_PKB55:_tobacco_mosaic_virus_(TMV_UPD-PK3)
AGUGUUUUUCCCUCCACUUAAAUCGAAGGG
((((.....[[[[[))))......].]]]]
>_PKB56:_odontoglossum_ringspot_virus_(ORSV-S1_UPD3-PK1)
UAACGUUGAUAGUGUUGAACUAUC
((((((.[[[[))))))...]]]]
>_PKB57:_tobacco_mosaic_virus_(TMV_PKbulge)
UGUGUCUUGGAUCGCGCGGGUCAAAUGUAUAUGGUUCAUAUACAUCCGCAGGCACGUAAUAAAGCGA
(((((((....[[[[((((.....((((((((.....))))))))))))))))))).......]]]]
>_PKB58:_odontoglossum_ringspot_virus_(ORSV-S1_UPD1-PK3)
AGUGUUUGUCCCUCCACUUAAAUCGAAGGG
((((.....[[[[[))))......].]]]]
>_PKB59:_odontoglossum_ringspot_virus_(ORSV-S1_UPD1-PK2)
CGUGGUGCAUACGAUAAUGCAU
(((.[[[[[[)))...]]]]]]
>_PKB60:_odontoglossum_ringspot_virus_(ORSV-S1_UPD2-PK3)
AGUGUUUAUCCCUCCACUUGAAUCGAAGGG
((((.....[[[[[))))......].]]]]
>_PKB61:_odontoglossum_ringspot_virus_(ORSV-S1_UPD2-PK2)
CGUUGUGUACACGAUAGUACAU
(((.[[[[[[)))...]]]]]]
>_PKB62:_odontoglossum_ringspot_virus_(ORSV-S1_UPD3-PK3)
AGUGGUUAUCCCUCCACUUAAAUCGAAGGG
((((.....[[[[[))))......].]]]]
>_PKB63:_odontoglossum_ringspot_virus_(ORSV-S1_UPD3-PK2)
CGUGGUGCAUACGAUAAUGCAU
(((.[[[[[[)))...]]]]]]
>_PKB65:_E.coli_(Ec_16S-PK505/526)
GCACCGGCUAACUCCGUGCCAGCAGCCGCGGUAAUACGGAGGGUGC
((((((((...[[[[[[[......))).......]]]]]]])))))
>_PKB66:__(TPK-70.28)
CAAGAACCGGACGGGUGAGAACCGAGACAAACACCCACCA
.......(((..[[[[[....))).......]]]]]....
>_PKB67:_Legionella_pneumophila_(Lp_PK1)
CGAGAAGGAGAUCUCUCGUAAAUAAGACUC
(((((..[[[.[[))))).......]]]]]
>_PKB68:_Legionella_pneumophila_(Lp_PK2)
GUUAAACCAUCACUGUGUACUGGCCAAUAAACCCAGUAUCCCGUUCGACCGAGCCCGCUUAUCGGUAU
(((.(((....((((.[[[[[[[..........)))).....))).)))............]]]]]]]
>_PKB69:_Legionella_pneumophila_(Lp_PK3)
CGGUCAUAAGAGAUAAGCUAGCGUCCUAAUCUAUCCCGGGUUAUGGCGCGAAACUCAGGGA
(((((((((........................[[[[[[[))))))).))...]]].]]]]
>_PKB70:_Legionella_pneumophila_(Lp_PK4)
GCUGUGUAUCAUCCUGCCCGUCGGAGGAGCCACAGUUAAAUUCAAAAGACAAGGC
((((((..((.(((.[[[.[[[))).))..))))))...........]]]..]]]
>_PKB72:_E.coli_(Ec_S15)
GGGAUCGCUGAAUUAGAGAUCGGCGUCCUUUCAUUCUAUAUACUUUGGAGUUUUAAAAUGUCUCUAA
((((.((((((.[[[[[[[))))))))))...............................]]]]]]]
>_PKB73:_T2_bacteriophage_(T2_gene32)
CUGACCAGCUAUGAGGUCAUACAUCGUCAUAGC
.(((((.[[[[[[[))))).......]]]]]]]
>_PKB74:_bacteriophage_T4_(T4_gene32)
UGCCAGCUAUGAGGUAAAGUGUCAUAGC
((((.[[[[[[[)))).....]]]]]]]
>_PKB75:_hepatitis_delta_virus_("Italy"_variant)_(HDV-It_g)
UGGCCGGCAUGGUCCCAGCCUCCUCGCUGGCGCCGGCUGGGCAACAUUCCGAGGGGACCGUCCCCUCGGUAAUGGCGAAUGGGACCCA
.(((((((..[[[[[[[{{{.[[.....}}})))))))]]....(((((((((((((...))))))))).)))).....]]]]]]]..
>_PKB76:_hepatitis_delta_virus_("Italy"_variant)_(HDV-It_ag)
GGGUCGGCAUGGCAUCUCCACCUCCUCGCGGUCCGACCUGGGCAUCCGAAGGAGGACGCACGUCCACUCGGAUGGCUAAGGGAGAGCCA
(((((((........[[[[(((.......))))))))))...(((((((....((((....))))..)))))))......]]]].....
>_PKB78:_AKV_murine_leukemia_virus_(AKV-MuLV)
UAGGGGGGUCAGGGUCAGGAGCCCCCCCCUGAACCCAGGAUAACCCUCACUGUCGGGGGGCA
...........((((((((.[[[[[[[)))).))))..................]]]]]]].
>_PKB79:_gibbon_ape_leukemia_virus_(GaLV)
UAGGGGAGUCAGGGUUCGGACCCCCUCCCCGAACCUAGGGUAACACUGACUGUGGAGGGGA
...........((((((((..[[[[[[[)))))))).................]]]]]]].
>_PKB80:_mouse_mammary_tumor_virus_(MMTV_gag/pro)
AAAAAACUUGUAAAGGGGCAGUCCCCUAGCCCCGCUCAAAAGGGGGAUG
..............(((((.[[[[[[[.)))))........]]]]]]].
>_PKB81:__(oligo_PK5)
GCGAUUUCUGACCGCUUUUUUGUCAG
(((....[[[[[)))......]]]]]
>_PKB82:_tobacco_mosaic_virus_(TMV-L_UPD-PK1)
AUAAAGUUUGUGUUUCUAAAACACAC
..(((...[[[[)))......]]]].
>_PKB83:_tobacco_mosaic_virus_(TMV-L_UPD-PK2)
ACGUGGUACGUACGAUAACGUACA
.(((.[[[[[[)))...]]]]]].
>_PKB84:_tobacco_mosaic_virus_(TMV-L_UPD-PK3)
CAGUGUUUUUCCCUCCACUUAAAUCGAAGGGU
.((((.....[[[[[))))......].]]]].
>_PKB85:_tobacco_mosaic_virus_(CcTMV_UPD-PK1)
AAGUUUGGUCGUACUUAACGACCU
.(((..[[[[[[)))..]]]]]].
>_PKB86:_tobacco_mosaic_virus_(CcTMV_UPD-PK2)
UAGGGGCUUACCGAAAUAAGCC
.(((.[[[[[)))...]]]]].
>_PKB87:_tobacco_mosaic_virus_(CcTMV_UPD-PK3)
CCGUGUUUAAGAGUCCACGCAAAUCGAACUCU
.((((.....[[[[[))))......].]]]].
>_PKB88:_Feline_leukemia_virus_(FeLV)
UAGGAGAGUCAGGGCCAGGACCCCCCCCCCUGAGCCCAGGAUAACCUUAAGAAUAGGGGGGC
...........((((((((...[[[[[[)))).))))..................]]]]]].
>_PKB89:_cucumber_green_mottle_mosaic_virus_(CGMMV_UPD-PK1)
ACCUCGAAAGCUUAGUUUCGAGGGUCUUCUGAU
.((((((((..[[[[)))))))).....]]]].
>_PKB90:_cucumber_green_mottle_mosaic_virus_(CGMMV_UPD-PK2)
UGGUGGUGCACACCAAAGUGCAUA
.(((.[[[[[[)))...]]]]]].
>_PKB91:_cucumber_green_mottle_mosaic_virus_(CGMMV_UPD-PK3)
UAGUGCUUUCCCGUUCACUUAAAUCGAACGGUU
.((((.....[[[[[))))......].]]]]..
>_PKB92:_tobacco_mild_green_mosaic_virus_(TMGMV_UPD-PK1)
AAAGUCGCUGAAGACUUAAAAUUCAGG
.(((((.[[[[[)))))....]]]]].
>_PKB93:_tobacco_mild_green_mosaic_virus_(TMGMV_UPD-PK2)
GGGUGGCUGAUACCAAAAUCAGCA
.(((.[[[[[[)))...]]]]]].
>_PKB94:_tobacco_mild_green_mosaic_virus_(TMGMV_UPD-PK3)
CAGUGGUUGUUCGUCCACUUAAAUAUAACGAUU
.((((.....[[[[.))))........]]]]..
>_PKB95:_pepper_mild_mottle_virus_(PMMV-S_UPD-PK1)
AGUUGGACGAACAUUAAACGUCC
.(((.[[[[)))......]]]].
>_PKB96:_pepper_mild_mottle_virus_(PMMV-S_UPD-PK2)
CCGUGGCGAGUACGAUAACUCGUA
.(((.[[[[[[)))...]]]]]].
>_PKB97:_pepper_mild_mottle_virus_(PMMV-S_UPD-PK3)
UAGUGUUUUUCCCUCCACUUAAAUCGAAGGGU
.((((.....[[[[[))))......].]]]].
>_PKB98:_baboon_endogenous_virus_(BaEV)
UAGGGGUGUCAGGGCUCUGGAGCCCCCCCCGAGCCCCGGCUAACUCUAUCUGUAGGGGGGCA
...........((((((.((.[[[[[[[))))))))..................]]]]]]].
>_PKB99:_Cas-Br-E_murine_leukemia_virus_(Cas-Br-E-MuLV)
UAGGGGGGUCGGGGUCAGGAGCCCCCCCCUGAACCCAGGAUAACCCUCAAAGUCGGGGGGCAA
...........((((((((.[[[[[[[)))).))))..................]]]]]]]..
>_PKB100:_satellite_tobacco_mosaic_virus_(STMV_UPD2-PK1)
AAGCCUUUUGGAUCGAAGGUUAAACGAUCCG
.((((((..[[[[[[))))))...]]]]]].
>_PKB101:_satellite_tobacco_mosaic_virus_(STMV_UPD2-PK2)
CGCUCCUCGCUUGAGCUUGAGGCGGC
.((((.[[[[[[))))...]]]]]].
>_PKB102:_satellite_tobacco_mosaic_virus_(STMV_UPD2-PK3)
GCGUAUCUCUUAUGUCAACAGAGA
.((((.[[[[)))).....]]]].
>_PKB103:_satellite_tobacco_mosaic_virus_(STMV_UPD1-PK1)
CGCCGACGUGGCUGUAUAAUACGUC
.(((.[[[[)))........]]]].
>_PKB104:_satellite_tobacco_mosaic_virus_(STMV_UPD1-PK2)
UCGUUGACAAGUACGAAAUCUUGUUA
.(((.[[[[[[.)))....]]]]]].
>_PKB105:_satellite_tobacco_mosaic_virus_(STMV_UPD1-PK3)
UAGUGUUUUUCCCUCCACUUAAAUCGAAGGGU
.((((.....[[[[[))))......].]]]].
>_PKB107:_simian_retrovirus-1_(SRV1_gag/pro)
GGGAAACGGACUGAGGGGCCAGCCCCAGGCCCCGAAACAAGCUUAUGGGGCG
..............((((((.[[[[[[))))))............]]]]]].
>_PKB108:_Tetrahymena_thermophila_(T.the_telo)
UAUAACCUUCACCAAUUAGGUUCAAAUAAGUGGUA
...((((...[[[[[[[[))))....]]]]]]]].
>_PKB109:_beet_virus_Q_(BVQ1_UPD-PKc)
UUGUGGUGCAUACAAUAAUGCAUA
.(((.[[[[[[)))...]]]]]].
>_PKB110:_beet_virus_Q_(BVQ1_UPD-PKb)
UAGUGUUUGCCGUUCCACUUAAAUCGAAACGGA
.((((....[[[[[[))))......].]]]]].
>_PKB111:_beet_virus_Q_(BVQ2_UPD-PKc)
ACGUGGUGCAUACGUUAAUGCAUA
.(((.[[[[[[)))...]]]]]].
>_PKB112:_beet_virus_Q_(BVQ2_UPD-PKb)
UAGUGUUUUUCGUUCCACUUAAAUCGAAACGAU
.((((....[[[[[[))))......].]]]]].
>_PKB113:_beet_virus_Q_(BVQ3_UPD-PKc)
UCGUGGUGCAUACGAAAAUGCAUA
.(((.[[[[[[)))...]]]]]].
>_PKB114:_beet_virus_Q_(BVQ3_UPD-PKb)
UAGUGUUUACCGUUCCACUUAAAUCGAAACGGA
.((((....[[[[[[))))......].]]]]].
>_PKB115:_beet_soil-borne_virus_(BSBV1_UPD-PKc)
CGGUAGCGCGAACCUUAUCGCGCA
.(((.[[[[[[)))...]]]]]].
>_PKB116:_beet_soil-borne_virus_(BSBV1_UPD-PKb)
CAGUGUUUUGAAGUCCACUUAAAUAGAACUUCU
.((((....[[[[[[))))......].]]]]].
>_PKB117:_beet_soil-borne_virus_(BSBV2_UPD-PKc)
ACGUGGGUUAUACGAUAAUAACCG
.(((.[[[[[[)))...]]]]]].
>_PKB118:_beet_soil-borne_virus_(BSBV2_UPD-PKb)
CGGUGCUUUUAUGUUCACCGAAAUCGAACAUAC
.((((....[[[[[[))))......].]]]]].
>_PKB119:_beet_soil-borne_virus_(BSBV3_UPD-PKc)
ACGUGGCGAAUACGAUAAUUCGUA
.(((.[[[[[[)))...]]]]]].
>_PKB120:_beet_soil-borne_virus_(BSBV3_UPD-PKb)
UAGUGUUCGUGGAUAACACUUUAAUUAAGAUUCAUA
.((((((.[[[[[[)))))).........]]]]]].
>_PKB121:_satellite_tobacco_necrosis_virus_1_(STNV1_PK1)
AAGCAGUCCCAGCUCUGCAUUGGGAA
.(((..[[[[[)))......]]]]].
>_PKB122:_satellite_tobacco_necrosis_virus_1_(STNV1_PK2)
UACUACUUGCUCAUUUGUAGUCUAAAUGAGA
.(((((...[[[[[[[)))))..]]]]]]].
>_PKB123:_satellite_tobacco_necrosis_virus_1_(STNV1_PK3)
GACGUUGGCCUCGACGUGUCGAGGUG
.((((..[[[[[[))))..]]]]]].
>_PKB124:_satellite_tobacco_necrosis_virus_2_(STNV2_PK1)
CAGUAGUCCUGAACUAGUAAAUCAGGACC
.(((.[[[[[[[)))......]]]]]]].
>_PKB125:_satellite_tobacco_necrosis_virus_2_(STNV2_PK2)
CCAUUCCCACUAGUGUAUUAGUGGA
.(((..[[[[[[)))...]]]]]].
>_PKB126:_satellite_tobacco_necrosis_virus_2_(STNV2_PK3)
GAACGAGGCCCCGCGUGAAUUGGGGUG
..(((..[[[[[[)))....]]]]]].
>_PKB130:_tobacco_rattle_virus_(TRV-PSG)
AGGGGUAAAACCCCUCGCCUACGUAAGCGUUAUUACGCCC
...............(((...[[[[[)))...]]]]]...
>_PKB131:__(NGF-H1)
CGCUCAACUCAUGGAGCGCAAGACGAAUAGCUACAUAUUCGACAUGAG
(((((..[[[[[[))))).....((((((......)))))).]]]]]]
>_PKB132:__(NGF-L2)
CGCUCAACCUCAGAGCGCAAGAGUCGAACGAAUACAGUUCGACAUGAGG
(((((..[[[[[))))).....(((((((.......))))))).]]]]]
>_PKB133:__(NGF-L6)
CGCUCAACUCAUGGAGCGCACGACGGAUCACCAUCGAUUCGACAUGAG
(((((..[[[[[[))))).....((((((......)))))).]]]]]]
>_PKB138:_barley_stripe_mosaic_virus_(BSMVbeta)
AUUGGUAUGUAAGCUACAACUUCCGGUAGCUGCGUCACACUUUAAGAGUGUGCAUACUGAGCCGAAGCUCAGCUUCGGUCCCCCAAGGGAAGACCA
.((((((((..((((((..[[[[[.))))))....((((((.....)))))))))))))).((((((.....)))))).........]]]]]....
>_PKB139:_tobacco_mosaic_virus_(TMV-L_PKbulge)
UAGUGUCUUGGAGCGCGCGGAGUAAACAUAUAUGGUUCAUAUAUGUCCGUAGGCACGUAAAAAAAGCGAG
..((((((....[[[[((((.....((((((((.....)))))))))))))))))).........]]]].
>_PKB140:_cucumber_green_mottle_mosaic_virus_(CGMMV_PKbulge)
UUUGCUCAUUGGUUUGCGGAAACCUCUCACGUGUGACGUUGAAGUUUCUAUGGGCAGUAAUUCUGCAAG
.((((((((....[[[[((((((.((..(((.....))).)).)))))))))))))).......]]]].
>_PKB141:_tobacco_mild_green_mosaic_virus_(TMGMV_PKbulge)
UUGUCAUAUCUGGAUCCAACAGUUAAACCAUGUGAUGGUGUAUACUGUGGUAUGGCGUAAAACAUCGGAG
.(((((((((....[[[.(((((...((((.....))))....)))))))))))))).........]]].
>_PKB142:_satellite_tobacco_mosaic_virus_(STMV_PKbulge)
UUUUGUUUUGGUCUUCCCGAACGCAUACGUUAGUGUGACUACCGUUGUUCGAAACAAGUAAAACAGGAAGG
.(((((((....[[[[[((((((...(((.(((.....))).)))))))))))))))).......]]]]].
>_PKB143:_pepper_mild_mottle_virus_(PMMV-S_PKbulge)
UUGUCGUUGGGAUGGAACGCAAUUAAAUACAUGUGUGACGUGUAUUUGCGAACGACGUAAUUAUUUUUCAG
.(((((((....[[[[[(((....(((((((((.....)))))))))))))))))))........]]]]].
>_PKB144:_odontoglossum_ringspot_virus_(ORSV-S1_PKbulge1)
UUGUGUAUAUGGAUCAUGCGGAUAAAGUUAUACUGGUGCAGUAUAACCCGUUAUACACAUAAAAUUAUGAG
.((((((((....[[[[((((.....((((((((.....)))))))))))))))))))).......]]]].
>_PKB145:_odontoglossum_ringspot_virus_(ORSV-S1_PKbulge2)
UUGUGUCAGACGCGUGUAAGGAGUGGUCAACCUUACGACACAUUUAAAUAAUGCGUCC
.(((((..[[[[[[(((((((.........)))))))))))).........]]]]]].
>_PKB146:_odontoglossum_ringspot_virus_(ORSV-S1_PKbulge3)
UUUCACUGCGGAUAUGUAGGUUUCCUCGGUGAAUAUAAAACUUAUAUCCC
.(((((...[[[[[((.(((...))))))))))...........]]]]].
>_PKB147:_Saccharomyces_cerevisiae_(Sc_18S-PKE21-7/8)
AUAAUAGAAUAGGACGUUUGGUUCUAUUUUGUUGGUUUCUAGGACCAUCGU
.((((((((((...[[..[[[[[[)))))))))).......]]]]]].]].
>_PKB151:_barley_stripe_mosaic_virus_(BSMVbeta_UPD-PK1)
AAAUGUUUGAUCAGAUCAUUCAAAUCUGAUGG
.((((....[[[[[[[))))...]]]]]]]..
>_PKB152:_barley_stripe_mosaic_virus_(BSMVbeta_UPD-PK2)
UGGUGCCCAUCAACCAUAUGAUGGGA
.(((.[[[[[[[)))...]]]]]]].
>_PKB153:_barley_stripe_mosaic_virus_(BSMVbeta_UPD-PK3)
GAGUGUUUGCAAGUCCACUAUAAUCGAACUUGA
.((((....[[[[[[))))......].]]]]].
>_PKB154:_brome_mosaic_virus_(BMV3_UPD-PK1)
GAGCCCCUGACUGGGUUAAAGUCACA
.(((((.[[[[[)))))..]]]]]..
>_PKB155:_brome_mosaic_virus_(BMV3_UPD-PK2)
CCCUUGUCUCAGGUAGAGACC
.(((.[[[[[)))..]]]]].
>_PKB156:_brome_mosaic_virus_(BMV3_UPD-PK3)
ACUUUGGCUAAGGUUAAAAGCUU
.(((.[[[[)))......]]]].
>_PKB157:_brome_mosaic_virus_(BMV3_UPD-PK4)
UUGUUGAAUCAGUACAAUAACUGAUA
.(((...[[[[[[)))...]]]]]].
>_PKB158:_tobacco_rattle_virus,_strain_PSG_(TRV-PSG2_PK1)
CUUUAAGGGACCUUGUGAAAUUCAAGGG
.((((.....[[[[[))))...]]]]].
>_PKB159:_tobacco_rattle_virus,_strain_PSG_(TRV-PSG2_PK2)
GGGCGGGUGUCGCCAGAAAUCACCG
.(((.[[[[[.)))....].]]]].
>_PKB160:_tobacco_rattle_virus,_strain_PSG_(TRV-PSG2_PK3)
CGAUACUACUAGUUGUAUCAAAACAAAACUAA
.(((((...[[[[[))))).......]]]]].
>_PKB161:_tobacco_rattle_virus,_strain_PSG_(TRV-PSG2_PK4)
AGGUGGAUGUUACCAUAAACAUUA
.(((.[[[[[[)))...]]]]]].
>_PKB162:_tobacco_rattle_virus,_strain_PSG_(TRV-PSG2_PK5)
UAAUGUCGCAGGUGGCAUUUUAAAAUAAGACCUGA
.((((((.[[[[[))))))..........]]]]].
>_PKB163:_Homo_sapiens_(Hs_SRP-pkn)
GCCGGGCGCGGUGGCGCGUGCCUGUAGUCCCAGCUACUCGGGAGGCU
(((.((((((.[[[[.)))))).....((((.]]]]...))))))).
>_PKB164:_poa_semilatent_virus_(PSLVbeta)
AUUGGUAUGUAAGCUACUUCUUCCAGUAGCUGCGUCAUAACAUCAAGGUUAUGCAUACUGAGCCGAAGCUCAGCUUCGGUCCUCCAAGGAAGACCA
.((((((((..((((((..[[[[[.))))))....((((((......)))))))))))))).((((((.....))))))........]]]]]....
>_PKB165:_poa_semilatent_virus_(PSLVbeta_UPD-PK1)
AUUGCCACUGUGGAAAUCAGUGA
.(((.[[[[[)))....]]]]].
>_PKB166:_poa_semilatent_virus_(PSLVbeta_UPD-PK2)
CGGUUUUAUCUACCAUAAGAUAAA
.(((.[[[[[[)))...]]]]]].
>_PKB167:_poa_semilatent_virus_(PSLVbeta_UPD-PK3)
AAGUGUUUUCAUGUCCACUUAAAUCGAACAUGAAC
.((((..[[[[[[[[))))......].]]]]]]].
>_PKB169:_Coxsackie_B_virus_(CoxB3)
ACCCUACUGUGCUAACCGAACCAGAUAACGGUACAGUAGGGGUAAAUUCUCCGCAUUCGGUGCGGAAAAAAAA
.((((((((((((.[[[[[[.........)))))))))))).....((.(((((.]]]]]]))))).))....
>_PKB172:_bamboo_mosaic_virus_(BaMV)
CUUUUGGUUUCUACAGUUUUUUCCAAAAAAAAAAAAAAA
.((((((.........[[[[[[))))))...]]]]]]..
>_PKB173:_Satellite_cereal_yellow_dwarf_virus-RPV_RNA_(satRPV)
ACAGAGCGCGUACUGUCUGACGACGUAUCCGCGCGGACUAGAAGGCUGGUGCCUCGUCCAACAAAUAGAUACA
((((.[[[[[..))))........(((((]]]]]((((....((((....)))).))))........))))).
>_PKB175:__(biotin-PK)
CACCGACCAUAGGCUCGGGUUGCCAGAGGUUCCACACUUUCAUCGAAAAGCCUAUGC
.(((((.[[[[[[[)))))..............................]]]]]]].
>_PKB176:__(biotin-PK-AN69.1)
GGACCGUCAGAGGACACGGUUAAAAAGUCCUCU
..(((((..[[[[[[)))))......]]]]]].
>_PKB177:_Rattus_rattus_(black_rat)_(Rr_ODCanti)
UGCUCCUGAUGUCCCUCACCCACCCCUGAAGAUCCCAGGUGGGCGAGGGAACAGUCAGCGGGAUCACAGU
............(((((.((((((......[[[[[[.)))))).)))))..........]]]]]].....
>_PKB182:_soil-borne_rye_mosaic_virus_(SBRMV1-PKa)
GGGGUUCAAAUCCCCCCCCGAACCGGAGGGUUAUCCGGCCCA
...............(((....[[[[[)))...]]]]]....
>_PKB183:_soil-borne_rye_mosaic_virus_(SBRMV1-UPD-PKb)
ACGUCGUGCAGUACGGUAAACUGCACA
.(((.[[[[[[[)))....]]]]]]].
>_PKB184:_soil-borne_rye_mosaic_virus_(SBRMV1_UPD-PKc)
UUCUGUUUUUCGAACAGAUGUAAAUCGAAGA
.(((((.[[[[[[)))))......]]]]]].
>_PKB185:_soil-borne_rye_mosaic_virus_(SBRMV1_UPD-PKd)
ACGUGGCCAUCACGAUAGAUGGUU
.(((.[[[[[[)))...]]]]]].
>_PKB186:_soil-borne_rye_mosaic_virus_(SBRMV1_UPD-PKe)
AAGCCUAUUUGUACGGGUUGAGUACAAAC
.(((((.[[[[[..)))))....]]]]].
>_PKB187:_soil-borne_rye_mosaic_virus_(SBRMV1_UPD-PKf)
GCCGCUGGGAUUGCGGAUUAUAAAUCG
.((((...[[[[))))......]]]].
>_PKB188:_soil-borne_rye_mosaic_virus_(SBRMV1_UPD-PKg)
UCGUUGCCGUCACGAUAGACGGA
.(((..[[[[[)))...]]]]].
>_PKB189:_soil-borne_rye_mosaic_virus_(SBRMV1_UPD-PKh)
AGUCUAACAUGUCGGGCUGAGACAUGUC
.((((.[[[[[[[))))...]]]]]]].
>_PKB190:_Plautia_stali_intestine_virus_(PSIV_IRES)
CUCGCUCAAACAUUAAGUGGUGUUGUGCGAAAAGAAUCUCACUUCAA
.((((...(((((.[[[[[)))))..)))).........]]]]]...
>_PKB194:_soil-borne_wheat_mosaic_virus_(SBWMV1_UPD-PKb)
UACGCUGUACAGUGCGUUAAACUGUACA
..(((.[[[[[[[)))....]]]]]]].
>_PKB195:_soil-borne_wheat_mosaic_virus_(SBWMV1_UPD-PKc)
CUCUGUUGAUCAAACAGAAAUAAAUUGAUUA
.(((((.[[[[[[)))))......]]]]]].
>_PKB196:_soil-borne_wheat_mosaic_virus_(SBWMV1_UPD-PKd)
ACGCGGUCAUUGCGAUAAAUGACU
.(((.[[[[[[)))...]]]]]].
>_PKB197:_soil-borne_wheat_mosaic_virus_(SBWMV1_UPD-PKe)
GAACCUAUUUGCUCGGGUUGAGUGCAAAC
..((((.[[[[[..)))).....]]]]].
>_PKB198:_soil-borne_wheat_mosaic_virus_(SBWMV1_UPD-PKf)
ACCGCCUGAUUAGCGGUCUACAAGUUAAUCGA
.((((..[[[[[)))).........]]]]]..
>_PKB199:_soil-borne_wheat_mosaic_virus_(SBWMV1_UPD-PKg)
UCGUGGUCAGUACGAUAACUGAU
.(((..[[[[[)))...]]]]].
>_PKB200:_soil-borne_wheat_mosaic_virus_(SBWMV1_UPD-PKh)
AGUCUAAUUUGUCGGGCUGAGACAAAUC
.((((.[[[[[[[))))...]]]]]]].
>_PKB201:_soil-borne_wheat_mosaic_virus_(SBWMV2_UPD-PKb)
GGCGUUCUACAGUACGUUUAAACUGUAGG
..(((.[[[[[[[))).....]]]]]]].
>_PKB202:_soil-borne_wheat_mosaic_virus_(SBWMV2_UPD-PKi)
UGGUGCUUGUUAUUUCACCUAAAUCGAAAUAACG
.((((...[[[[[[[)))).......]]]]]]].
>_PKB203:_soil-borne_wheat_mosaic_virus_(SBWMV2_UPD-PKk)
ACGUGGUCUUCACGAUAGAAGAUG
.(((.[[[[[[)))...]]]]]].
>_PKB204:_soil-borne_wheat_mosaic_virus_(SBWMV2_UPD-PKl)
CAGAGUUAUCAUACUCUAUAAACUAUGAC
.((((...[[[[[))))......]]]]].
>_PKB205:_Palmaria_palmata_(Pp_18S-PKE23-9/12)
UUAGAGUGUUCAAAGCCAGGCGUUUGCCGUGAAUACAUUAGCAUGGAA
.((..((.[[[[..))(((((....))).))..))........]]]].
>_PKB206:_Homo_sapiens_(Hs_PrP)
GCCUCAUGGUGGUGGCUGGGGGCAGCCUCAUGGUGGUGGCUGGGG
...((((((.............[[[[[))))))....]]]]]...
>_PKB207:_Bos_Taurus_(cow)_(Bt_PrP)
GCCCCAUGGAGGUGGCUGGGGCCAGCCUCAUGGAGGUGGCUGGGG
...((((((............[[[[[[))))))....]]]]]]..
>_PKB210:_Bordetella_pertussis_(Bp_PK2)
CCGCUGCACUGAUCUGUCCUUGGGUCAGGCGGGGGAAGGCAACUUCCCAGGGGGCAACCCCGAACCGCAGCAGCGACAUUCACAAGGAAU
.((((((..(((...[[[[[[[..))).((((((((((....)))))).((((....))))...)))).)))))).......]]]]]]].
>_PKB212:_Plautia_stali_intestine_virus_(PSIV_IRES-PKIII)
AGGUCUUGUAUAUUUAUACUUACCACACAAGAUGGACCGGAGCAGCCCUCCAAUAUCUAGUGUA
.((((..((((....)))).....[[[[.[[[[[))))((((.....))))..]]]]].]]]].
>_PKB213:_Himetobi_P_virus_(HiPV_IRES-PKI)
CAGCCUUGUAGUUUUAGUGGACUUUAGGCUAAAGAAUUUCACUAG
.(((((...((((.[[[[[))))..))))).........]]]]].
>_PKB215:_Himetobi_P_virus_(HiPV_IRES-PKIII)
GACCCUUAGUUAUUUAGCUUUACCGCCCAGGAUGGGGUGCAGCGUUCCUGCAAUAUCCAGGGCA
.((((..((((....)))).....[[[[.[[[[[))))((((.....))))..]]]]].]]]].
>_PKB216:_Drosophila_C_virus_(DCV_IRES-PKI)
CUUCUUAUAUGAUUAGGUUGUCAUUUAGAAUAAGAAAAUAACCUG
.((((...(((((.[[[[[)))))..)))).........]]]]].
>_PKB217:_lactate_dehydrogenase-elevating_virus,_strain_C_(LDV-C)
UUUAAACUGCUAGCCACCUCUGGUCUCGACCGCUGUACUAGAGGUGGGCUGACGGUGUYUGGCGAUGCGGUCA
.............(((((((((((...[[[[[[...)))))))))))...................]]]]]].
>_PKB218:_Porcine_reproductive_and_respiratory_syndrome_virus,_North_American_isolate_(16244B)_(PRRSV-16244B)
UUUAAACUGCUAGCCGCCAGCGGCUUGACCCGCUGUGGUCGCGGCGGCUUGGUUGUUACUGAGACAGCGGUA
............((((((.((((((....[[[[[[[))))))))))))...............]]]]]]]..
>_PKB220:_Drosophila_C_virus_(DCV_IRES-PKIII)
UUAGGUUAACUAUUUAGUUUUACUGUUCAGGAUGCCUAUUGGCAGCCCCAUAAUAUCCAGGACA
.((((..((((....)))).....[[[[.[[[[[)))).(((.....)))...]]]]].]]]].
>_PKB221:_Cricket_paralysis_virus_(CrPV_IRES-PKI)
CGGUUUUUCAGAUUAGGUAGUCGAAAAACCUAAGAAAUUUACCUG
.((((((...(((.[[[[[)))..)))))).........]]]]].
>_PKB223:_Cricket_paralysis_virus_(CrPV_IRES-PKIII)
UUAGGUUAGCUAUUUAGCUUUACGUUCCAGGAUGCCUAGUGGCAGCCCCACAAUAUCCAGGAAG
.((((..((((....)))).....[[[[.[[[[[))))((((.....))))..]]]]].]]]].
>_PKB224:_Triatoma_virus_(TrV_IRES-PKI)
UUUCCUAUACCUCGAGUCGGGUUUGGAAUCUAAGGUUGACUCG
.((((...((((.[[[[[))))..)))).........]]]]].
>_PKB226:_Triatoma_virus_(TrV_IRES-PKIII)
UGCGCUUGCCUAUUUAGGCAUACUUCUCAGGAUGGCGCGUUGCAGUCCAACAAGAUCCAGGGAC
.((((..((((....)))).....[[[[.[[[[.))))((((.....))))...]]]].]]]].
>_PKB227:_Black_queen_cell_virus_(BQCV_IRES-PKI)
AUGUUUAGAAGAUUAGGUAGUCUCUAAACAGAACAAUUUACCUG
.(((((...((((.[[[[[))))..)))))........]]]]].
>_PKB229:_Black_queen_cell_virus_(BQCV_IRES-PKIII)
AUCACCGUACCUAUUUAGGUUUACGCUCCAAGAUCGGUGGAUAGCAGCCCUAUCAAUAUCUAGGAGA
..((((..((((....)))).....[[[[.[[[[.))))(((((.....)))))...]]]].]]]].
>_PKB230:_Rhopalosiphum_padi_virus_(RhPV_IRES-PKI)
CAGGAGAGCAUACGCUAGGUCGCGUUGACUAUCCUUAUAUAUGACCUG
.((((.((((.((((.[[[[[)))))).)).)))).......]]]]].
>_PKB232:_Rhopalosiphum_padi_virus_(RhPV_IRES-PKIII)
UUGGUUAGCUAUUUAGCUUUACUAAUCAAGACGCCGUCGUGCAGCCCACAAAAGUCUAGAUA
.(((..((((....))))......[[[.[[[[.)))..(((.....)))....]]]].]]].
>_PKB233:_Porcine_reproductive_and_respiratory_syndrome_virus,_European_Lelystad_strain_(LV)_(PRRSV-LV)
UUUAAACUGUUAGCCGCCAGCGGCUUGACCCGCUGUGGCCGCGGCGGCCUAGUUGUGACUGAAACGGCGGU
............((((((.((((((....[[[[[[[))))))))))))...............]]]]]]].
>_PKB234:_Variovorax_paradoxus_(Vp_PK2)
GCCUUGCAACAGUUGGCCGAUGGGCUGGGCAAGGGGGUCUGGAGCAAUCCUGACCUCCCGGCUGCAAGGAUAACUACAUGGGCU
.((((((..(((...[[[[[[[..))).(((((((((((((((....))))))))))))))).)))))).......]]]]]]].
>_PKB235:_Giardiavirus_(GLV_IRES)
GGAGACCCAUGGAGAGUCUCCAGAGGUUCCUAAGGCCUCGAUCGCGCCUGCCGGGAGGCAGAAUGUCCCGGUUCUCC
((((((....[[[[[)))))).(((((.......)))))..........(((((((.........)))))))]]]]]
>_PKB237:_West_Nile_virus_(WNV_PK3end)
ACCUGGGAUAGACUAGGGGAUCUUCUGCUCUGCACAACCAGCCACACGGCACAGUGCGCCGACAUAGGUGGCUGGUGGUGCUAGAACACAGGAUCU
.(((((..[[[[)))))......]]]].(((((((.(((((((((.((((.......))))......))))))))).)))).)))...........
>_PKB238:_Dengue_virus_type_2_(DEN2_PK1)
AUGGGGGCCCAAGGUGAGAUGAAGCUGUAGUCUCACUGGAAGGACUAGAGGUUAGAGGAGACCCCCCCAAAACAAAAAACAGCA
.((((((((...((((((((...[[[[[.))))))))....))......((((......)))))))))).........]]]]].
>_PKB240:_beet_chlorosis_virus_(BChV)
GGGAAAUGGACUGAGCGGCGCCGACCGCCAAACAACCGGCA
..............((((.[[[[.))))........]]]].
>_PKB241:_Montana_Myotis_leukoencephalitis_virus_(MMLV_PKb)
AGAGAGUUAUUCGCUCCUCUCGAGAUUGAGCGGC
.(((((....[[[[[[)))))......]]]]]].
>_PKB242:_Rio_Bravo_virus_(RBV_PKb)
UGAGGUUUUUCCCCUCCCUCAUGAUGAGGGGAAG
.((((...[[[[[[[[)))).....]]]]]]]].
>_PKB244:_hepatitis_A_virus_(HAV)
UUAAACAAAUUUUCUUAAAAUUUCUGAGGUUUGUUUAUUUCUUUUAUCAGUAAAU
.((((((((((.........[[[[[[[)))))))))).........]]]].]]].
>_PKB245:_Human_Parechovirus_1_(HPeV1)
CCCAGCCUUGGGGUGGCUGGUCAAUAAAAACCCCC
.((((((..[[[[[)))))).........]]]]].
>_PKB246:_Hepatitis_C_Virus_(HCV)
GACCGTGCACCATGAGCACGAATCCTAAACCTCA
((.((((.....[[[[))))..))......]]]]
>_PKB247:_Nemesia_ring_necrosis_virus_(NeRNV_PKa)
CCCCUGUCCCGGGUAGGGAACC
.(((..[[[[)))..]]]]...
>_PKB248:_Nemesia_ring_necrosis_virus_(NeRNV_PKb)
UGUUCCUUGGAUUGCUACGUUCACCAGAUUUGUGUAAUCUGGCCGUUAGGAACUUAAAAUUGCGCG
.((((((.....[[[((((....(((((((.....))))))).))))))))))........]]]..
>_PKB249:_Nemesia_ring_necrosis_virus_(NeRNV_UPD-PK1)
UAGUGUUUCGGCUUCCACUUAAAUCGAAAGCCA
.((((....[[[[[[))))......].]]]]].
>_PKB250:_Nemesia_ring_necrosis_virus_(NeRNV_UPD-PK2)
GGGUGGCGCACACCACAGUGCGUA
.(((.[[[[[[)))...]]]]]].
>_PKB251:_Nemesia_ring_necrosis_virus_(NeRNV_UPD-PK3)
CAGCCUCUCACAGCUUCCUCGUGAGG
.(((..[[[[[.))).....]]]]].
>_PKB253:_White_Bream_Virus_(WBV)
UUUAAACUGGUGGGGCAGUGUCUAGGAUUGACGUUAGACACUGCUUUUUGCCCGUUUCAAACAGGUGAAUACAAACCGUCAU
...........((((((((((((((...[[[[[)))))))))))))).............................]]]]].
>_PKB254:_SARS_coronavirus_(SARS-CoV)
UUUAAACGGGUUUGCGGUGUAAGUGCAGCCCGUCUUACACCGUGCGGCACAGGCACUAGUACUGAUGUCGUCUACAGGGCUU
............(((((((((((...[[[[[[[)))))))))))((((((((.........))).)))))...]].]]]]].
>_PKB255:_mouse_hepatitis_virus_(MHV)
CUCUCUAUCAGAAUGGAUGUCUUGCUGUCAUAACAGAUAGAGAAGGUUGUGGCAGA
.((((((((...............[[[[[[[[[[.))))))))..]]]]]]]]]].
>_PKB256:_bovine_coronavirus_(BCV)
CUCUCUAUCAGAAUGGAUGUCUUGCUGCUAUAAUAGAUAGAGAAGGUUAUAGCAGA
.((((((((...............[[[[[[[[[[.))))))))..]]]]]]]]]].
>_PKB257:_Mus_musculus_(mouse)_(Mm_Edr)
GGGAAACUCCCCGGCCCCGCUGUAGGGGGACCUUCAGCGACAGGGCCAGAACGAAUAAGGUCCCCA
............((((((((((...[[[[[[[[[)))))...))))).........]]]]]]]]].
>_PKB258:_Homo_sapiens_(Hs_Ma3)
GGGAAACGGGAACUGGGCUUGGGACAAGAGCCAUCCCAAGUCCAAGGCCAAGUAGGCUCG
.............(((((((((((...[[[[[.)))))))))))..........]]]]].
>_PKB259:_potato_yellow_vein_virus_(PYVV1)
CGGUAGAAAAGAUGGUUUAAACCACGCCUUCUACCAAGUUAGUAAAUAAAUAGGCGG
.((((((.....((((....))))[[[[[))))))................]]]]].
>_PKB260:_potato_yellow_vein_virus_(PYVV2)
AGUAGAAAAGUUGGUGCUUAGACCACGCCCUCUACCGUAAUAAUAGAUAAAUAGGCG
.(((((.....((((......))))[[[[.)))))..................]]]]
>_PKB261:_potato_yellow_vein_virus_(PYVV3)
CGGUAGAAAAGAUGGUUUGAAAACCACGCCUUCUACCAAUAUAGUAAAUAAAUAGGCGG
.((((((.....(((((....)))))[[[[[))))))................]]]]].
>_PKB262:_cucumber_yellows_virus_(CuYV1)
CGUUUGGUCGAAUGCUACUAGAGCAGCCUGACCAAACUAGUAUUAGUAAAUAAAGG
.((((((((...((((.....)))).[[[))))))))................]]]
>_PKB263:_cucurbit_yellow_stunting_disorder_virus_(CYSDV1)
CGACACUCUAAAGAGUUCCGUGAGGAACCACCUUGAGUGUCUAGUUAUAAAUAAACUAGGUC
.(((((((......(((((....))))).[[[[.)))))))................]]]].
>_PKB264:_cucurbit_yellow_stunting_disorder_virus_(CYSDV2)
CGACACUCUAAAGUGUUCCAAGAGGAACCACCUUGAGUGUCUAGUUAUAAAUAAACUAGGUC
.(((((((......(((((....))))).[[[[.)))))))................]]]].
>_PKB265:_sweet_potato_chlorotic_stunt_virus_(SPCSV1)
CGGUUUUCCUAAAUCGUCGUGAGACGGACCUUGGAAAACCUAGUAUUUAAAUAACUAGGUC
.((((((((.....((((....))))[[[[[.))))))))................]]]]]
>_PKB266:_lettuce_infectious_yellows_virus_(LIYV1)
UGUCUUCCUAAAAUCCUUGGAAGACUGUAUAUAUAGAAUAAAGGUCG
.(((((((......[[[[)))))))...............]]]]...
>_PKB267:_little_cherry_virus_1_(LChV-1)
AAUGCAACUUUUAAAUAGUUUAUCUGUUAAGAUAAACCACCUAGGUUGCAUAUAUAAAAAAUAAAAGGUGCC
.(((((((((.......((((((((....))))))))[[[[[)))))))))..............]]]]]..
>_PKB268:_beet_yellows_virus_(BYV)
CUCCUAGCGAAGUCCCGCUAGGAAGAAAAAAUAAGGGCCG
.(((((((...[[[[.)))))))...........]]]]..
>_PKB269:_citrus_tristeza_virus_(CTV)
AGUUCUCCUUAGAGUGUGUGUUGUUUACCCAACGCACUGUCCCUAUGGGGGGCCAACAUAGGUCCA
.(((((((.......((((((((......))))))))....[[[[[)))))))....]]]]]....
>_PKB270:_Pineapple_mealybug_wilt_associated_virus_-_2_(PMWaV-2)
CAAAGUCCUAUAAACCUCAAUAAUCCCUCGUUAGGAGGGACACGCGAGGACUUUGGCGUGCC
.((((((((..............((((((.....))))))[[[[[.)))))))).]]]]]..
>_PKB271:_Grapevine_leafroll-associated_virus_-_2_(GLRaV-3)
ACGCCAAAAUCCAAUUAAAGUUUGGGACCUAGGCGGGCCUCUUACGAGGCUAACUUAUCGACAAUAAGUUAGGUC
.((((.....((((.......))))[[[[[[))))((((((....))))))..................]]]]]]
>_PKB272:_strawberry_chlorotic_fleck_associated_virus_(SCFaV)
ACUGUGAUUAUAAAAGUGGAGUACUAAAGUACCCACUACCUUUAAUCACAGACAAUAAAGGUCCAU
.((((((((.....(((((.((((....)))))))))[[[[[[)))))))).....]]]]]]....
>_PKB273:_influenza_A_virus,_strain_A/PR/8/34_(IAV_PK_NS)
UUCCAGGACAUACUGCUGAGGAUGUCAAAAAUGCAGUUGGAGUCCUCA
.(((((...........[[[[[[.............)))))]]]]]].
>_PKB274:_influenza_B_virus,_strain_B/Victoria/02/1987_(IBV_PK_NS)
ACUGAUGAUCUUACAGUGGAGGAUGAAGAAGAUGGCCAUCGGAUCCUCA
.((((((...........[[[[[[............))))))]]]]]].
>_PKB275:_Bacillus_subtilis_(Bs_glmS_P3.1)
CCGGCUGAGUGUGCAGAUCACAGCCGUAAGAAUUUCUUCAAACCAAGGGGGUGACUCCUUGAACAAAGAGAAAUCACAUGAUCUU
.((((((.......[[[[[[)))))).....(((((((.....(((((((....)))))))......)))))))....]]]]]].
>_PKB276:_Bacillus_subtilis_(Bs_glmS_P1.1)
CGCCCGAACUAAGCGCCCGGAAAAAGGCUUAGUUGACGAGGAUGGAGGUUAUCGAAUUUCGCGGAUCCUCCCG
.(((((((((((((............)))))))).........[[[[[....(((...))))))))]]]]]..
>_PKB277:_tobacco_etch_virus_(TEV_PK1)
CGAAUCUCAAGCAAUCAAGCAUUCUACUUCUAUUGCA
.((((((...[[[[[..)).)))).......]]]]].
>_PKB278:_tobacco_etch_virus_(TEV_PK2)
AUUUAAAUCAUUUCUUUUAAAGCAAAAGC
.((((((...[[[..))))))....]]].
>_PKB279:_tobacco_etch_virus_(TEV_PK3)
CAAUUUUCUGAAAAUUUUCAC
.(((((..[[[))))).]]].
>_PKB280:_Visna-Maedi_virus_(VMV)
GGGAAACAACAGGAGGGGGCCACGUGUGGUGCCGUCCGCGCCCCCUAUGUUGUAACAGAAGCACCACC
.............(((((((.....[[[[[[[.......)))))))..............]]]]]]].
>_PKB281:_sugarcane_yellow_leaf_virus_(ScYLV)
GGGAAACGAGCCAAGUGGCGCCGACCACUUAAAAACACCGGAA
.............(((((..[[[.))))).........]]]..
>_PKB282:_foot-and-mouth_disease_virus,_serotype_A_(FMDV-A_PKI)
CCGUCGUUUCCGACGUAAAAGGAAGCAA
.((((..[[[[)))).....]]]]....
>_PKB283:_foot-and-mouth_disease_virus,_serotype_A_(FMDV-A_PKII)
CCGCCUGUCCCGGCGUUAAAGGGAAGUAA
.((((..[[[[)))).....]]]].....
>_PKB284:_foot-and-mouth_disease_virus,_serotype_A_(FMDV-A_PKIII)
ACCGCCUACCCCGGCGUUAACGGGGAACAA
..((((..[[[[)))).....]]]].....
>_PKB285:_foot-and-mouth_disease_virus,_serotype_O_(FMDV-O1K_PKI)
ACCGUCGUUCCCGACGUAAAAGGGAGG
..((((..[[[[)))).....]]]]..
>_PKB286:_foot-and-mouth_disease_virus,_serotype_O_(FMDV-O1K_PKII)
ACCGUCCGGCCCGACGUAAAAGGGUGGUAA
..((((...[[[)))).....]]]......
>_PKB287:_foot-and-mouth_disease_virus,_serotype_O_(FMDV-O1K_PKIII)
CCGUCUUUCCCGACGUUAAAGGGAUG
.((((..[[[[)))).....]]]]..
>_PKB288:_foot-and-mouth_disease_virus,_serotype_O_(FMDV-O1K_PKIV)
CCUUCGCUCGGAAGUAAAACGACAA
.((((..[[[)))).....]]]...
>_PKB289:_foot-and-mouth_disease_virus,_serotype_C_(FMDV-C_PKI)
ACCGUCGUUCCCGACGUAAAAGGGAUGU
..((((..[[[[)))).....]]]]...
>_PKB290:_foot-and-mouth_disease_virus,_serotype_C_(FMDV-C_PKII)
ACCGUCUCUCCCGACGUUAAAGGGAUGUAA
..((((..[[[[)))).....]]]].....
>_PKB291:_foot-and-mouth_disease_virus,_serotype_C_(FMDV-C_PKIII)
CCGCCUAUCCCGGCGUUAAUGGGAGG
.((((..[[[[)))).....]]]]..
>_PKB292:_foot-and-mouth_disease_virus,_serotype_C_(FMDV-C_PKIV)
CCUUCACCUGGAAGUAAAACAGCAA
.((((..[[[)))).....]]]...
>_PKB293:_encephalomyocarditis_virus_(EMCV-R_PKB)
ACGUGAAGGCUACGAUAGUGCCAG
.((((..[[[)))).....]]]..
>_PKB294:_encephalomyocarditis_virus_(EMCV-R_PKC)
AGGGCGGGUACUGCCGUAAGUGCCA
..(((.[[[[[[)))...]]]]]].
>_PKB295:_Mengovirus_(Mengo_PKB)
ACGUGAAGGCUACGAUAGUGCCAG
.((((..[[[)))).....]]]..
>_PKB296:_Mengovirus_(Mengo_PKC)
AGGGCGGGUCCUGCCGAAAGUGCCAA
..(((.[[[.[[)))...]].]]]..
>_PKB297:_hepatitis_A_virus_(HAV_PK1)
AAGUCCAUGGUGAGGGGACUUGAUACCUCACCG
.(((((..[[[[[[[))))).....]]]]]]].
>_PKB298:_hepatitis_A_virus_(HAV_PK2)
CGCCGUUUGCCUAGGCUAUAGGCUAAAUU
.(((....[[[[[)))..]]]]]......
>_PKB299:_Theiler's_murine_encephalomyelitis_virus_(TMEV)
ACGCGGGUACUGCGAUAGUGCCACC
.(((.[[[[[[)))..]]]]]]...
>_PKB300:__(antiHIV1-RT_1.1)
UCAAGAAUUCCGUUUUCAGUCGGGAAAAACUGAACAA
.......(((((..[[[[[[)))))...]]]]]]...
>_PKB301:__(antiHIV1-RT_1.3a)
GAAUAUCUUCCGAAGCCGAACGGGAAAACCGGCAUCU
.......(((((..[[[[..)))))....]]]]....
>_PKB302:__(antiHIV1-NC_psi-50-1)
GCCAGUGGUUUGCAAUGCUGGUCCGGUGCGU
(((((((...[[[[.)))))))....]]]].
>_PKB303:_Bombyx_mori_(R2_retroPK)
AGCCCCGAUGGACGGACCGCGAGGACCGUCAAGCCUAGCAGGUACCUUCGGGUGGGGCCUUGCGAUACCUGCGGGC
.(((((....(((((.((....)).)))))...[[[.[[[[[[(((....))))))))........]]]]]]]]].
>_PKB304:_B._subtilis_(SBU)
AGAGGUUCUAGCUACACCCUCUAUAAAAAACUAA
(((((...[[[......)))))........]]].