Origin IGS: tctcccacctcctttcgtttcaaataggataagcaatcagtgtgtccagtaacctgatatctagaaatttgtagttctttttgaattggatgattctgattcctcataaatttcgcactttctacctgatagcttgaaataagcctcaagt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 acttgaggcttatttcaagctatcaggtagaaagtgcgaaatttatgaggaatcagaatcatccaattcaaaaagaactacaaatttctagatatcaggttactggacacactgattgcttatcctatttgaaacgaaaggaggtgggaga Mask Tandem Repeat Region ================================================ tctcccacctcctttcgtttcaaataggataagcaatcagtgtgtccagtaacctgatatctagaaatttgtagttctttttgaattggatgattctgattcctcataaatttcgcactttctacctgatagcttgaaataagcctcaagt Find is-nt database================================================ Query_seq: SSA_1143:SSA_1144|SSA_1143:SSA_1144:Na+-driven multidrug efflux pump, putative:Beta-N-acetylhexosaminidase, putative:<-<-:1173588..1173738 151 tctcccacctcctttcgtttcaaataggataagcaatcagtgtgtccagtaacctgatatctagaaatttgtagttctttttgaattggatgattctgattcctcataaatttcgcactttctacctgatagcttgaaataagcctcaagt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1143:SSA_1144|SSA_1143:SSA_1144:Na+-driven multidrug efflux pump, putative:Beta-N-acetylhexosaminidase, putative:<-<-:1173588..1173738 151 tctcccacctcctttcgtttcaaataggataagcaatcagtgtgtccagtaacctgatatctagaaatttgtagttctttttgaattggatgattctgattcctcataaatttcgcactttctacctgatagcttgaaataagcctcaagt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1143:SSA_1144|SSA_1143:SSA_1144:Na+-driven multidrug efflux pump, putative:Beta-N-acetylhexosaminidase, putative:<-<-:1173588..1173738 151 tctcccacctcctttcgtttcaaataggataagcaatcagtgtgtccagtaacctgatatctagaaatttgtagttctttttgaattggatgattctgattcctcataaatttcgcactttctacctgatagcttgaaataagcctcaagt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tctcccacctcctttcgtttcaaataggataagcaatcagtgtgtccagtaacctgatatctagaaatttgtagttctttttgaattggatgattctgattcctcataaatttcgcactttctacctgatagcttgaaataagcctcaagt Predict ORF larger than 30AA ================================================ Protein_Len: 49 Strand: - Start: 3 End: 149 .. G V E K R K L Y S L C D T H G T V Q Y R S I Q L E K Q I P H N Q N R M F K A S E V Q Y S S I L R M .. tctcccacctcctttcgtttcaaataggataagcaatcagtgtgtccagtaacctgatatctagaaatttgtagttctttttgaattggatgattctgattcctcataaatttcgcactttctacctgatagcttgaaataagcctcaagt Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tctcccacctcctttcgtttcaaataggataagcaatcagtgtgtccagtaacctgatatctagaaatttgtagttctttttgaattggatgattctgattcctcataaatttcgcactttctacctgatagcttgaaataagcctcaagt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_1143:SSA_1144|SSA_1143:SSA_1144:Na+-driven multidrug efflux pump, putative:Beta-N-acetylhexosaminidase, putative:<-<-:1173588..1173738 151 tctcccacctcctttcgtttcaaataggataagcaatcagtgtgtccagtaacctgatatctagaaatttgtagttctttttgaattggatgattctgattcctcataaatttcgcactttctacctgatagcttgaaataagcctcaagt Intra-Species Hit: Count: 1 Min: 1 Max: 151 Len: 151 Subject: NC_009009_SSA_1143_SSA_1144|Na+-driven multidrug efflux pump, putative:Beta-N-acetylhexosaminidase, putative|NEGATIVE:NEGATIVE|[1173588,1173738]|151 HSP 1 e-value: 1.0E-80 bit: 299.0 Len: 151 Query Start:1 Query End:151 Subject Strand: POSITIVE Subject Start: 1 Subject End: 151 tctcccacctcctttcgtttcaaataggataagcaatcagtgtgtccagtaacctgatatctagaaatttgtagttctttttgaattggatgattctgattcctcataaatttcgcactttctacctgatagcttgaaataagcctcaagt tctcccacctcctttcgtttcaaataggataagcaatcagtgtgtccagtaacctgatatctagaaatttgtagttctttttgaattggatgattctgattcctcataaatttcgcactttctacctgatagcttgaaataagcctcaagt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCUCCCACCUCCUUUCGUUUCAAAUAGGAUAAGCAAUCAGUGUGUCCAGUAACCUGAUAUCUAGAAAUUUGUAGUUCUUUUUGAAUUGGAUGAUUCUGAUUCCUCAUAAAUUUCGCACUUUCUACCUGAUAGCUUGAAAUAAGCCUCAAGU ...................(((..(((((...((.(((((.((........))))))).....(((((((((((........((((..((....))..)))))).)))))))))))...)))))..)))..((((((........)))))) (-27.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACUUGAGGCUUAUUUCAAGCUAUCAGGUAGAAAGUGCGAAAUUUAUGAGGAAUCAGAAUCAUCCAAUUCAAAAAGAACUACAAAUUUCUAGAUAUCAGGUUACUGGACACACUGAUUGCUUAUCCUAUUUGAAACGAAAGGAGGUGGGAGA (((((((((((.....))))).)))))).................((((.((((((.................((((........)))).....((((....)))).....)))))).))))((((((((....(....).)))))))).. (-32.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 923 50 1 141 92 NC_009009:SSA_1143|5end_Na+-driven_multidrug_efflux_pump,_putative_1173497..1173727_NEGATIVE 337 129 81 134 85 NC_009009:SSA_1431|5end_hypothetical_protein_1438730..1438960_NEGATIVE 300 45 3 55 13 NC_009009:SSA_1921|5end_hypothetical_protein_1910875..1911105_POSITIVE 296 48 3 225 164 NC_009009:SSA_1009|5end_Galactose-1-phosphate-uridylyltransferase,_putative_1011254..1011484_POSITIVE 290 77 43 214 180 NC_009009:SSA_0897|5end_Two_component_system_histidine_kinase,_putative_888358..888588_POSITIVE 284 48 1 176 125 NC_009009:SSA_1840|5end_RNA_binding_protein,_putative_1834422..1834652_NEGATIVE 279 49 8 146 99 NC_009009:SSA_0584|5end_hypothetical_protein_575806..576036_POSITIVE 274 40 3 158 122 NC_009009:SSA_2159|5end_hypothetical_protein_2159621..2159851_NEGATIVE 274 47 1 138 91 NC_009009:SSA_1444|5end_Imidazole_glycerol-phosphate_synthase_subunit_hisH,_putative_1447267..1447497_NEGATIVE 274 79 32 213 159 NC_009009:SSA_0204|5end_Nisin_biosynthesis_two-component_response_transcriptional_regulator_nisR,_putative_202057..202287_POSITIVE 271 48 5 132 88 NC_009009:SSA_1450|5end_hypothetical_protein_1452710..1452940_NEGATIVE 270 34 2 120 87 NC_009009:SSA_0911|5end_hypothetical_protein_922078..922308_POSITIVE 258 137 91 194 147 NC_009009:SSA_1617|5end_hypothetical_protein_1620651..1620881_NEGATIVE 253 58 11 77 15 NC_009009:SSA_1544|5end_Conserved_uncharacterized_protein_1548796..1549026_NEGATIVE 251 50 4 68 25 NC_009009:SSA_1938|5end_Enoyl-acyl_carrier_protein(ACP)_reductase,_putative_1925738..1925968_NEGATIVE 250 107 61 91 43 NC_009009:SSA_0060|5end_Tagatose-6-phosphate_ketose/aldose_isomerase,_putative_61477..61707_POSITIVE 248 48 1 148 96 NC_009009:SSA_2222|5end_Tyrosine-protein_kinase_Wze,_putative_2223997..2224227_NEGATIVE 248 75 38 204 162 NC_009009:SSA_0231|5end_Conserved_uncharacterized_protein_225713..225943_POSITIVE 247 80 32 72 26 NC_009009:SSA_0925|5end_ABC-type_antimicrobial_peptide_transport_system,_ATPase_component,_putative_934749..934979_POSITIVE 247 79 32 69 9 NC_009009:SSA_0341|5end_hypothetical_protein_334731..334961_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 275 47 1 151 91 NC_009009:SSA_1952|3end_ABC-type_Fe-S_cluster_assembly_transporter,_permease_component,_putative_1948212..1948362_NEGATIVE 274 47 1 103 56 NC_009009:SSA_1445|3end_Imidazole_glycerol-phosphate_dehydratase,_putative_1447302..1447452_NEGATIVE 271 48 5 98 54 NC_009009:SSA_1451|3end_Exonuclease_RexA,_putative_1452744..1452894_NEGATIVE 270 34 2 123 90 NC_009009:SSA_0910|3end_ABC-type_multidrug_transporter,_ATPase_component,_putative_922161..922311_POSITIVE 270 59 12 146 109 NC_009009:SSA_0905|3end_CshA-like_fibrillar_surface_protein_B_909060..909210_POSITIVE 265 50 10 40 4 NC_009009:SSA_0561|3end_RNA:NAD_2'-phosphotransferase,_putative_554255..554405_POSITIVE 258 137 91 125 78 NC_009009:SSA_1618|3end_hypothetical_protein_1620720..1620870_NEGATIVE 256 127 87 115 77 NC_009009:SSA_1336|3end_Conserved_ankyrin_repeat_protein,_putative_1349581..1349731_NEGATIVE 252 79 34 52 14 NC_009009:SSA_1532|3end_Membrane-fusion_protein_/_periplasmic_component_of_efflux_system,_putative_1539460..1539610_NEGATIVE 249 105 61 129 85 NC_009009:SSA_2384|3end_Acetyltransferase,_GNAT_family,_putative_1465468..1465618_NEGATIVE 248 48 1 137 85 NC_009009:SSA_2223|3end_Capsular_polysaccharide_biosynthesis_protein_Wzd_(chain_length_regulator),_putative_2224008..2224158_NEGATIVE 247 80 32 71 25 NC_009009:SSA_0924|3end_ABC-type_antimicrobial_peptide_transport_system,_permease_component,_putative_934828..934978_POSITIVE 246 100 54 95 40 NC_009009:SSA_2242|3end_hypothetical_protein_2238121..2238271_NEGATIVE 242 48 3 136 94 NC_009009:SSA_1100|3end_Hemolysin_exporter,_ATPase_component,_putative_1122088..1122238_POSITIVE 241 133 96 149 116 NC_009009:SSA_2222|3end_Tyrosine-protein_kinase_Wze,_putative_2223299..2223449_NEGATIVE 238 147 110 50 1 NC_009009:SSA_2055|3end_hypothetical_protein_2057936..2058086_NEGATIVE 237 147 110 91 47 NC_009009:SSA_0911|3end_hypothetical_protein_922898..923048_POSITIVE 235 148 114 55 15 NC_009009:SSA_0512|3end_Nicotinate-nucleotide--dimethylbenzimidazole_phosphoribosyltransferase,_putative_511625..511775_POSITIVE 233 80 36 90 33 NC_009009:SSA_1899|3end_hypothetical_protein_1894443..1894593_NEGATIVE 232 134 95 92 65 NC_009009:SSA_1972|3end_Two-component_system_transcriptional_regulator_(CheY_domain_and_HTH-like_DNA-binding_domain),_putative_1967811..1967961_NEGATIVE