Origin IGS: gcaagaagcaaagactgggaaatgaccttgctctaaaaaatcatcattcagttttgcaggatacaagatctgtttgactgaaagtctatttctatcaagcttttaaaagtttaattatgattgtcgaggtgggaccaagaatcaaaaatcatggattttttagattctgtctcgcctcttttattatagccatttctggaaagattttgctttttggtagctttgtaatataataatcctatatgtttcataaaggcgcttacggcatagggggtgaaaa .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ttttcaccccctatgccgtaagcgcctttatgaaacatataggattattatattacaaagctaccaaaaagcaaaatctttccagaaatggctataataaaagaggcgagacagaatctaaaaaatccatgatttttgattcttggtcccacctcgacaatcataattaaacttttaaaagcttgatagaaatagactttcagtcaaacagatcttgtatcctgcaaaactgaatgatgattttttagagcaaggtcatttcccagtctttgcttcttgc Mask Tandem Repeat Region ================================================ gcaagaagcaaagactgggaaatgaccttgctctaaaaaatcatcattcagttttgcaggatacaagatctgtttgactgaaagtctatttctatcaagcttttaaaagtttaattatgattgtcgaggtgggaccaagaatcaaaaatcatggattttttagattctgtctcgcctcttttattatagccatttctggaaagattttgctttttggtagctttgtaatataataatcctatatgtttcataaaggcgcttacggcatagggggtgaaaa Find is-nt database================================================ Query_seq: SSA_0214:SSA_0215|SSA_0214:SSA_0215:Single-strand DNA-binding protein (conjugal DNA-protein transfer system), putative:Periplasmic sugar-binding protein (ribose porter), putative:->->:210751..211030 280 gcaagaagcaaagactgggaaatgaccttgctctaaaaaatcatcattcagttttgcaggatacaagatctgtttgactgaaagtctatttctatcaagcttttaaaagtttaattatgattgtcgaggtgggaccaagaatcaaaaatcatggattttttagattctgtctcgcctcttttattatagccatttctggaaagattttgctttttggtagctttgtaatataataatcctatatgtttcataaaggcgcttacggcatagggggtgaaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0214:SSA_0215|SSA_0214:SSA_0215:Single-strand DNA-binding protein (conjugal DNA-protein transfer system), putative:Periplasmic sugar-binding protein (ribose porter), putative:->->:210751..211030 280 gcaagaagcaaagactgggaaatgaccttgctctaaaaaatcatcattcagttttgcaggatacaagatctgtttgactgaaagtctatttctatcaagcttttaaaagtttaattatgattgtcgaggtgggaccaagaatcaaaaatcatggattttttagattctgtctcgcctcttttattatagccatttctggaaagattttgctttttggtagctttgtaatataataatcctatatgtttcataaaggcgcttacggcatagggggtgaaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0214:SSA_0215|SSA_0214:SSA_0215:Single-strand DNA-binding protein (conjugal DNA-protein transfer system), putative:Periplasmic sugar-binding protein (ribose porter), putative:->->:210751..211030 280 gcaagaagcaaagactgggaaatgaccttgctctaaaaaatcatcattcagttttgcaggatacaagatctgtttgactgaaagtctatttctatcaagcttttaaaagtttaattatgattgtcgaggtgggaccaagaatcaaaaatcatggattttttagattctgtctcgcctcttttattatagccatttctggaaagattttgctttttggtagctttgtaatataataatcctatatgtttcataaaggcgcttacggcatagggggtgaaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gcaagaagcaaagactgggaaatgaccttgctctaaaaaatcatcattcagttttgcaggatacaagatctgtttgactgaaagtctatttctatcaagcttttaaaagtttaattatgattgtcgaggtgggaccaagaatcaaaaatcatggattttttagattctgtctcgcctcttttattatagccatttctggaaagattttgctttttggtagctttgtaatataataatcctatatgtttcataaaggcgcttacggcatagggggtgaaaa Predict ORF larger than 30AA ================================================ Protein_Len: 51 Strand: + Start: 78 End: 230 ............................................................................. M K V Y F Y Q A F K S L I M I V E V G P R I K N H G F F R F C L A S F I I A I S G K I L L F G S F V I .................................................. Protein_Len: 46 Strand: - Start: 114 End: 251 ................................................................................................................. N H N D L H S W S D F I M S K K S E T E G R K N Y G N R S L N Q K K T A K Y Y L L G I H K M ............................. gcaagaagcaaagactgggaaatgaccttgctctaaaaaatcatcattcagttttgcaggatacaagatctgtttgactgaaagtctatttctatcaagcttttaaaagtttaattatgattgtcgaggtgggaccaagaatcaaaaatcatggattttttagattctgtctcgcctcttttattatagccatttctggaaagattttgctttttggtagctttgtaatataataatcctatatgtttcataaaggcgcttacggcatagggggtgaaaa 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: 83 Start: 158 End: 187 .............................................................................................................................................................TTTTAGATTCTGTCTCGCCTCTTTTATTAT............................................................................................. PromScan Matrix: RpoD-17 Strand: + Score: 83 Start: 205 End: 234 ............................................................................................................................................................................................................TTTTGCTTTTTGGTAGCTTTGTAATATAAT.............................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gcaagaagcaaagactgggaaatgaccttgctctaaaaaatcatcattcagttttgcaggatacaagatctgtttgactgaaagtctatttctatcaagcttttaaaagtttaattatgattgtcgaggtgggaccaagaatcaaaaatcatggattttttagattctgtctcgcctcttttattatagccatttctggaaagattttgctttttggtagctttgtaatataataatcctatatgtttcataaaggcgcttacggcatagggggtgaaaa Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_0214:SSA_0215|SSA_0214:SSA_0215:Single-strand DNA-binding protein (conjugal DNA-protein transfer system), putative:Periplasmic sugar-binding protein (ribose porter), putative:->->:210751..211030 280 gcaagaagcaaagactgggaaatgaccttgctctaaaaaatcatcattcagttttgcaggatacaagatctgtttgactgaaagtctatttctatcaagcttttaaaagtttaattatgattgtcgaggtgggaccaagaatcaaaaatcatggattttttagattctgtctcgcctcttttattatagccatttctggaaagattttgctttttggtagctttgtaatataataatcctatatgtttcataaaggcgcttacggcatagggggtgaaaa Intra-Species Hit: Count: 1 Min: 1 Max: 280 Len: 280 Subject: NC_009009_SSA_0214_SSA_0215|Single-strand DNA-binding protein (conjugal DNA-protein transfer system), putative:Periplasmic sugar-binding protein (ribose porter), putative|POSITIVE:POSITIVE|[210751,211030]|280 HSP 1 e-value: 1.0E-157 bit: 555.0 Len: 280 Query Start:1 Query End:280 Subject Strand: POSITIVE Subject Start: 1 Subject End: 280 gcaagaagcaaagactgggaaatgaccttgctctaaaaaatcatcattcagttttgcaggatacaagatctgtttgactgaaagtctatttctatcaagcttttaaaagtttaattatgattgtcgaggtgggaccaagaatcaaaaatcatggattttttagattctgtctcgcctcttttattatagccatttctggaaagattttgctttttggtagctttgtaatataataatcctatatgtttcataaaggcgcttacggcatagggggtgaaaa gcaagaagcaaagactgggaaatgaccttgctctaaaaaatcatcattcagttttgcaggatacaagatctgtttgactgaaagtctatttctatcaagcttttaaaagtttaattatgattgtcgaggtgggaccaagaatcaaaaatcatggattttttagattctgtctcgcctcttttattatagccatttctggaaagattttgctttttggtagctttgtaatataataatcctatatgtttcataaaggcgcttacggcatagggggtgaaaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GCAAGAAGCAAAGACUGGGAAAUGACCUUGCUCUAAAAAAUCAUCAUUCAGUUUUGCAGGAUACAAGAUCUGUUUGACUGAAAGUCUAUUUCUAUCAAGCUUUUAAAAGUUUAAUUAUGAUUGUCGAGGUGGGACCAAGAAUCAAAAAUCAUGGAUUUUUUAGAUUCUGUCUCGCCUCUUUUAUUAUAGCCAUUUCUGGAAAGAUUUUGCUUUUUGGUAGCUUUGUAAUAUAAUAAUCCUAUAUGUUUCAUAAAGGCGCUUACGGCAUAGGGGGUGAAAA .((((((((((((.((.(((((((.....(((.(((..((((((..(((((((..(((((........)))))..)))))))..............((((((....))))))....))))))...((((((((((..(((((((((((((...)))))))..)))))))))))))))).....))).))))))))))....)).))))))))))))....((((((((((((.........))))))..)))))).((((..(......)..)))).... (-74.10) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUUCACCCCCUAUGCCGUAAGCGCCUUUAUGAAACAUAUAGGAUUAUUAUAUUACAAAGCUACCAAAAAGCAAAAUCUUUCCAGAAAUGGCUAUAAUAAAAGAGGCGAGACAGAAUCUAAAAAAUCCAUGAUUUUUGAUUCUUGGUCCCACCUCGACAAUCAUAAUUAAACUUUUAAAAGCUUGAUAGAAAUAGACUUUCAGUCAAACAGAUCUUGUAUCCUGCAAAACUGAAUGAUGAUUUUUUAGAGCAAGGUCAUUUCCCAGUCUUUGCUUCUUGC .........((((((.((((((....)))))).....)))))).....................(((.(((((((..((.....(((((((((.........((((.(.(((((((((..(((((((...)))))))))))))..))).).)))).........................((((...((((((.....((((((....(((..........)))....)))))).....))))))..))))..)))))))))..))..))))))).))). (-57.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 316 198 152 127 70 NC_009009:SSA_1449|5end_Histidinol-phosphate/aromatic_aminotransferase_and_cobyric_acid_decarboxylase,_putative_1451931..1452161_NEGATIVE 310 216 171 195 149 NC_009009:SSA_0242|5end_hypothetical_protein_234978..235208_POSITIVE 299 94 56 136 101 NC_009009:SSA_1132|5end_TatC,_sec-independent_protein_translocase,_putative_1158645..1158875_POSITIVE 298 178 131 169 122 NC_009009:SSA_0060|5end_Tagatose-6-phosphate_ketose/aldose_isomerase,_putative_61477..61707_POSITIVE 276 207 161 184 137 NC_009009:SSA_0893|5end_ATP-binding_cassette_transporter-like_protein,_putative_884527..884757_POSITIVE 274 196 162 49 20 NC_009009:SSA_0163|5end_hypothetical_protein_162127..162357_POSITIVE 273 274 236 188 151 NC_009009:SSA_0051|5end_Dihydroxyacetone_kinase_phosphotransfer_protein,_putative_55190..55420_POSITIVE 270 155 113 207 165 NC_009009:SSA_1979|5end_Alkaline-shock_protein,_putative_1974301..1974531_NEGATIVE 269 277 244 49 16 NC_009009:SSA_2267|5end_Lactose_operon_transcriptional_repressor,_LacI_family,_putative_2266127..2266357_POSITIVE 267 219 175 177 125 NC_009009:SSA_0419|5end_Alpha-galactosidase,_putative_416213..416443_POSITIVE 265 277 244 117 84 NC_009009:SSA_0967|5end_hypothetical_protein_975872..976102_POSITIVE 261 199 152 168 132 NC_009009:SSA_1414|5end_hypothetical_protein_1425412..1425642_NEGATIVE 261 219 172 149 98 NC_009009:SSA_0464|5end_Cobalamin_biosynthesis_protein_cobD,_putative_468225..468455_POSITIVE 260 160 118 42 1 NC_009009:SSA_0231|5end_Conserved_uncharacterized_protein_225713..225943_POSITIVE 260 209 163 118 70 NC_009009:SSA_0204|5end_Nisin_biosynthesis_two-component_response_transcriptional_regulator_nisR,_putative_202057..202287_POSITIVE 259 218 172 49 9 NC_009009:SSA_1174|5end_Dihydrolipoamide_dehydrogenase,_putative_1202854..1203084_NEGATIVE 259 227 187 44 1 NC_009009:SSA_0553|5end_hypothetical_protein_548911..549141_POSITIVE 256 92 51 175 134 NC_009009:SSA_0895|5end_ATP-binding_cassette_transporter-like_protein,_putative_886466..886696_POSITIVE 256 198 153 187 138 NC_009009:SSA_0605|5end_Methyltransferase_gidB,_putative_593707..593937_NEGATIVE 256 183 146 160 109 NC_009009:SSA_0202|5end_hypothetical_protein_200534..200764_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 353 199 152 109 59 NC_009009:SSA_0349|3end_Transcriptional_regulator,_TetR/AcrR_family,_putative_341828..341978_POSITIVE 322 226 186 60 26 NC_009009:SSA_0597|3end_hypothetical_protein_588563..588713_POSITIVE 303 276 238 151 103 NC_009009:SSA_0587|3end_Metal-dependent_amidase/aminoacylase/carboxypeptidase,_putative_579761..579911_POSITIVE 279 60 13 56 7 NC_009009:SSA_0274|3end_hypothetical_protein_268580..268730_NEGATIVE 279 187 146 72 23 NC_009009:SSA_0205|3end_NisK_(sensor-receptor_histidine_kinase_domain),_putative_203839..203989_POSITIVE 272 220 176 147 103 NC_009009:SSA_0673|3end_hypothetical_protein_656994..657144_POSITIVE 270 155 113 64 22 NC_009009:SSA_1980|3end_50S_ribosomal_protein_L28,_putative_1974444..1974594_NEGATIVE 267 60 11 76 17 NC_009009:SSA_0956|3end_surface_protein_D_965418..965568_POSITIVE 267 219 175 68 16 NC_009009:SSA_0418|3end_AraC-type_DNA-binding_domain-containing_protein,_putative_416184..416334_POSITIVE 261 219 172 147 96 NC_009009:SSA_0463|3end_Cobyrinic_acid_A,C-diamide_synthase,_putative_468303..468453_POSITIVE 260 209 163 105 57 NC_009009:SSA_0203|3end_hypothetical_protein_202124..202274_POSITIVE 259 276 239 135 94 NC_009009:SSA_0611|3end_HtpX_protease,_putative_600515..600665_POSITIVE 258 216 175 139 99 NC_009009:SSA_1611|3end_Era-like_GTP-binding_protein,_putative_1615133..1615283_NEGATIVE 256 198 153 105 56 NC_009009:SSA_0606|3end_ABC-type_antimicrobial_peptide_transport_system,_ATPase_component,_putative_593789..593939_NEGATIVE 256 277 244 50 17 NC_009009:SSA_0445|3end_hypothetical_protein_444776..444926_POSITIVE 256 199 153 146 88 NC_009009:SSA_0416|3end_5-methyltetrahydropteroyltriglutamate--_homocysteine_methyltransferase,_putative_414222..414372_POSITIVE 255 275 238 149 117 NC_009009:SSA_0325|3end_Membrane-anchored_glycerophosphoryl_diester_phosphodiesterase,_putative_319437..319587_POSITIVE 254 221 190 41 10 NC_009009:SSA_1083|3end_Conserved_uncharacterized_protein_1101752..1101902_POSITIVE 253 225 189 45 1 NC_009009:SSA_0480|3end_Cobalt_ABC_transporter,_ATP-binding_protein,_putative_482057..482207_POSITIVE 252 199 161 150 108 NC_009009:SSA_0892|3end_ATP-binding_cassette_lipoprotein,_putative_884578..884728_POSITIVE