Origin IGS: agcagcctcctttcagtttagctaaatttatagtataatgtaatcaaaacggaacaccttgttcagttttcttcatctttattatcccttattctcagaaaggaaacaagaagcaattgaggggcgggtcagttattgaacaatcctgctcttttgttccgaaacgct .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 agcgtttcggaacaaaagagcaggattgttcaataactgacccgcccctcaattgcttcttgtttcctttctgagaataagggataataaagatgaagaaaactgaacaaggtgttccgttttgattacattatactataaatttagctaaactgaaaggaggctgct Mask Tandem Repeat Region ================================================ agcagcctcctttcagtttagctaaatttatagtataatgtaatcaaaacggaacaccttgttcagttttcttcatctttattatcccttattctcagaaaggaaacaagaagcaattgaggggcgggtcagttattgaacaatcctgctcttttgttccgaaacgct Find is-nt database================================================ Query_seq: SSA_2321:SSA_2322|SSA_2321:SSA_2322:Cation (Co/Zn/Cd) efflux protein, putative:Transcriptional regulator, TetR/AcrR family, putative:<-->:2327016..2327183 168 agcagcctcctttcagtttagctaaatttatagtataatgtaatcaaaacggaacaccttgttcagttttcttcatctttattatcccttattctcagaaaggaaacaagaagcaattgaggggcgggtcagttattgaacaatcctgctcttttgttccgaaacgct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_2321:SSA_2322|SSA_2321:SSA_2322:Cation (Co/Zn/Cd) efflux protein, putative:Transcriptional regulator, TetR/AcrR family, putative:<-->:2327016..2327183 168 agcagcctcctttcagtttagctaaatttatagtataatgtaatcaaaacggaacaccttgttcagttttcttcatctttattatcccttattctcagaaaggaaacaagaagcaattgaggggcgggtcagttattgaacaatcctgctcttttgttccgaaacgct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_2321:SSA_2322|SSA_2321:SSA_2322:Cation (Co/Zn/Cd) efflux protein, putative:Transcriptional regulator, TetR/AcrR family, putative:<-->:2327016..2327183 168 agcagcctcctttcagtttagctaaatttatagtataatgtaatcaaaacggaacaccttgttcagttttcttcatctttattatcccttattctcagaaaggaaacaagaagcaattgaggggcgggtcagttattgaacaatcctgctcttttgttccgaaacgct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 agcagcctcctttcagtttagctaaatttatagtataatgtaatcaaaacggaacaccttgttcagttttcttcatctttattatcccttattctcagaaaggaaacaagaagcaattgaggggcgggtcagttattgaacaatcctgctcttttgttccgaaacgct Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: + Start: 75 End: 167 .......................................................................... M F I I P Y S Q K G N K K Q L R G G S V I E Q S C S F V P K R . agcagcctcctttcagtttagctaaatttatagtataatgtaatcaaaacggaacaccttgttcagttttcttcatctttattatcccttattctcagaaaggaaacaagaagcaattgaggggcgggtcagttattgaacaatcctgctcttttgttccgaaacgct Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ PromScan Matrix: RpoD-17 Strand: + Score: 84 Start: 10 End: 39 .........CTTTCAGTTTAGCTAAATTTATAGTATAAT................................................................................................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ agcagcctcctttcagtttagctaaatttatagtataatgtaatcaaaacggaacaccttgttcagttttcttcatctttattatcccttattctcagaaaggaaacaagaagcaattgaggggcgggtcagttattgaacaatcctgctcttttgttccgaaacgct Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 74 HP_score: -5.1 Tail_Score: -4.81163 Start: 50 End: 66 Full_Region: ATAATGTAATCAAAA CGGAACA CCT TGTTCAG TTTTCTTCATCTTTA .................................................CGGAACACCTTGTTCAG...................................................................................................... Find igs database================================================ Query_seq: SSA_2321:SSA_2322|SSA_2321:SSA_2322:Cation (Co/Zn/Cd) efflux protein, putative:Transcriptional regulator, TetR/AcrR family, putative:<-->:2327016..2327183 168 agcagcctcctttcagtttagctaaatttatagtataatgtaatcaaaacggaacaccttgttcagttttcttcatctttattatcccttattctcagaaaggaaacaagaagcaattgaggggcgggtcagttattgaacaatcctgctcttttgttccgaaacgct Intra-Species Hit: Count: 1 Min: 1 Max: 168 Len: 168 Subject: NC_009009_SSA_2321_SSA_2322|Cation (Co/Zn/Cd) efflux protein, putative:Transcriptional regulator, TetR/AcrR family, putative|NEGATIVE:POSITIVE|[2327016,2327183]|168 HSP 1 e-value: 1.0E-90 bit: 333.0 Len: 168 Query Start:1 Query End:168 Subject Strand: POSITIVE Subject Start: 1 Subject End: 168 agcagcctcctttcagtttagctaaatttatagtataatgtaatcaaaacggaacaccttgttcagttttcttcatctttattatcccttattctcagaaaggaaacaagaagcaattgaggggcgggtcagttattgaacaatcctgctcttttgttccgaaacgct agcagcctcctttcagtttagctaaatttatagtataatgtaatcaaaacggaacaccttgttcagttttcttcatctttattatcccttattctcagaaaggaaacaagaagcaattgaggggcgggtcagttattgaacaatcctgctcttttgttccgaaacgct Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGCAGCCUCCUUUCAGUUUAGCUAAAUUUAUAGUAUAAUGUAAUCAAAACGGAACACCUUGUUCAGUUUUCUUCAUCUUUAUUAUCCCUUAUUCUCAGAAAGGAAACAAGAAGCAAUUGAGGGGCGGGUCAGUUAUUGAACAAUCCUGCUCUUUUGUUCCGAAACGCU (((....(((((((......((((......))))...........(((((.((((.....)))).)))))...........................))))))).....(.((((...((((((((((...(((....)))...)))))))))))))).).....))) (-35.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGCGUUUCGGAACAAAAGAGCAGGAUUGUUCAAUAACUGACCCGCCCCUCAAUUGCUUCUUGUUUCCUUUCUGAGAAUAAGGGAUAAUAAAGAUGAAGAAAACUGAACAAGGUGUUCCGUUUUGAUUACAUUAUACUAUAAAUUUAGCUAAACUGAAAGGAGGCUGCU .(((..((((.......((((......)))).....))))..))).........((.....((((((((((.(..................((((((.(((((.((((.....)))).)))))..)).))))...(((......))).....).)))))))))).)). (-32.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 918 130 81 221 172 NC_009009:SSA_2321|5end_Cation_(Co/Zn/Cd)_efflux_protein,_putative_2326925..2327155_NEGATIVE 365 130 81 179 136 NC_009009:SSA_1869|5end_ATP-dependent_RNA_helicase,_putative_1865495..1865725_NEGATIVE 320 156 117 148 114 NC_009009:SSA_1735|5end_UreX,_putative_1721072..1721302_NEGATIVE 309 157 120 231 179 NC_009009:SSA_0241|5end_Ribosomal_protein_L11_methyltransferase,_putative_234021..234251_POSITIVE 307 151 112 182 151 NC_009009:SSA_0633|5end_Anthranilate_synthase_component_II,_putative_622813..623043_POSITIVE 303 130 82 181 129 NC_009009:SSA_1563|5end_Metal-dependent_hydrolase,_beta-lactamase_superfamily_I,_putative_1567256..1567486_NEGATIVE 300 127 87 154 113 NC_009009:SSA_1367|5end_hypothetical_protein_1383593..1383823_POSITIVE 298 150 102 196 147 NC_009009:SSA_1871|5end_Penicillin-binding_protein_2X,_putative_1868873..1869103_NEGATIVE 294 160 112 202 131 NC_009009:SSA_0826|5end_hypothetical_protein_805098..805328_POSITIVE 289 128 97 194 166 NC_009009:SSA_0380|5end_Enzyme_of_poly-gamma-glutamate_biosynthesis_(capsule_formation),_putative_370916..371146_POSITIVE 285 160 112 225 176 NC_009009:SSA_0142|5end_hypothetical_protein_137230..137460_POSITIVE 280 159 111 184 130 NC_009009:SSA_1967|5end_Threonine_desaminase,_putative_1963559..1963789_NEGATIVE 279 159 120 53 15 NC_009009:SSA_2360|5end_tRNA_(5-methylaminomethyl-2-thiouridylate)-methyltransferase,_putative_2363779..2364009_NEGATIVE 275 160 117 214 178 NC_009009:SSA_0495|5end_ABC-type_oligopeptide/nickel_transport_system,_ATPase_component,_putative_495186..495416_POSITIVE 274 130 81 67 17 NC_009009:SSA_0744|5end_S-adenosylmethio_nine:tRNA-ribosyltransferase-isomerase_(queuine_synthetase),_putative_726804..727034_NEGATIVE 274 132 95 225 183 NC_009009:SSA_0424|5end_Exopolysaccharide_biosynthesis_protein,_putative_422233..422463_NEGATIVE 272 153 114 183 139 NC_009009:SSA_2070|5end_Zinc_metalloprotease,_putative_2074574..2074804_NEGATIVE 272 158 114 112 56 NC_009009:SSA_1769|5end_hypothetical_protein_1757490..1757720_NEGATIVE 272 150 114 224 171 NC_009009:SSA_1414|5end_hypothetical_protein_1425412..1425642_NEGATIVE 271 100 56 174 125 NC_009009:SSA_1259|5end_Purine_nucleoside_phosphorylase,_putative_1285722..1285952_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 365 130 81 74 31 NC_009009:SSA_1870|3end_Phospho-N-acetylmuramoyl-pentapeptide-_transferase,_putative_1865600..1865750_NEGATIVE 318 158 120 91 38 NC_009009:SSA_0240|3end_Acetyltransferase,_GNAT_family,_putative_233960..234110_POSITIVE 294 125 82 97 40 NC_009009:SSA_1031|3end_DNA_topology_modulation_protein_FlaR,_putative_1047734..1047884_NEGATIVE 294 160 112 80 9 NC_009009:SSA_0825|3end_DNA-directed_RNA_polymerase,_sigma_subunit_(sigma70/sigma32),_putative_805056..805206_POSITIVE 289 128 97 31 3 NC_009009:SSA_0379|3end_PTS_system,_beta-glucoside-specific_EII_component,_putative_370833..370983_POSITIVE 285 160 112 106 57 NC_009009:SSA_0141|3end_Copper_chaperone,_putative_137191..137341_POSITIVE 280 159 111 84 30 NC_009009:SSA_1968|3end_Ketol-acid_reductoisomerase,_putative_1963659..1963809_NEGATIVE 278 133 105 150 116 NC_009009:SSA_0990|3end_hypothetical_protein_992550..992700_POSITIVE 274 130 81 57 7 NC_009009:SSA_0745|3end_hypothetical_protein_726814..726964_NEGATIVE 272 158 114 118 62 NC_009009:SSA_1770|3end_hypothetical_protein_1757484..1757634_NEGATIVE 271 100 56 144 95 NC_009009:SSA_1260|3end_Phosphopentomutase,_putative_1285752..1285902_NEGATIVE 270 109 62 51 8 NC_009009:SSA_0773|3end_PTS_enzyme_I,_putative_754416..754566_POSITIVE 269 116 73 99 53 NC_009009:SSA_1445|3end_Imidazole_glycerol-phosphate_dehydratase,_putative_1447302..1447452_NEGATIVE 266 156 111 99 60 NC_009009:SSA_2016|3end_Phosphoglycerate_mutase,_putative_2015592..2015742_NEGATIVE 262 160 113 130 73 NC_009009:SSA_1938|3end_Enoyl-acyl_carrier_protein(ACP)_reductase,_putative_1924764..1924914_NEGATIVE 260 160 113 76 26 NC_009009:SSA_0548|3end_Alanine_racemase,_putative_543529..543679_POSITIVE 256 129 84 42 1 NC_009009:SSA_0747|3end_DD-carboxypeptidase,_putative_729371..729521_POSITIVE 255 155 116 36 1 NC_009009:SSA_0671|3end_Methylenetetrahydrofolate_dehydrogenase/methenyltetrahydrofolate_cyclohydrolase,_putative_655274..655424_POSITIVE 253 155 117 106 57 NC_009009:SSA_0494|3end_ABC-type_dipeptide/oligopeptide/nickel_transport_system,_ATPase_component,_putative_495269..495419_POSITIVE 252 158 112 95 52 NC_009009:SSA_0617|3end_Membrane_protease_subunits,_stomatin/prohibitin-like_protein_(SPFH_domain/band_7_family),_putative_611438..611588_POSITIVE