Origin IGS: agagtgttggtttgttcctttaggataagtcagtgctctttttttcacaatcttttgttaaaattagattaaaacacgaaaaacgcttacattttttctagtatattgattgtgaaaatgatataataaacataagattatcaagttaagtttttgttaaaataggttaatttttaaaatattgtttgcagttgactttggttttcagtagaaaagcgaggaaactat .........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 atagtttcctcgcttttctactgaaaaccaaagtcaactgcaaacaatattttaaaaattaacctattttaacaaaaacttaacttgataatcttatgtttattatatcattttcacaatcaatatactagaaaaaatgtaagcgtttttcgtgttttaatctaattttaacaaaagattgtgaaaaaaagagcactgacttatcctaaaggaacaaaccaacactct Mask Tandem Repeat Region ================================================ agagtgttggtttgttcctttaggataagtcagtgctctttttttcacaatcttttgttaaaattagattaaaacacgaaaaacgcttacattttttctagtatattgattgtgaaaatgatataataaacataagattatcaagttaagtttttgttaaaataggttaatttttaaaatattgtttgcagttgactttggttttcagtagaaaagcgaggaaactat Find is-nt database================================================ Query_seq: SSA_1135:SSA_1136|SSA_1135:SSA_1136:Na+-driven multidrug efflux pump, putative:ATPases with chaperone activity, ATP-binding subunit, putative:->->:1161836..1162063 228 agagtgttggtttgttcctttaggataagtcagtgctctttttttcacaatcttttgttaaaattagattaaaacacgaaaaacgcttacattttttctagtatattgattgtgaaaatgatataataaacataagattatcaagttaagtttttgttaaaataggttaatttttaaaatattgtttgcagttgactttggttttcagtagaaaagcgaggaaactat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1135:SSA_1136|SSA_1135:SSA_1136:Na+-driven multidrug efflux pump, putative:ATPases with chaperone activity, ATP-binding subunit, putative:->->:1161836..1162063 228 agagtgttggtttgttcctttaggataagtcagtgctctttttttcacaatcttttgttaaaattagattaaaacacgaaaaacgcttacattttttctagtatattgattgtgaaaatgatataataaacataagattatcaagttaagtttttgttaaaataggttaatttttaaaatattgtttgcagttgactttggttttcagtagaaaagcgaggaaactat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1135:SSA_1136|SSA_1135:SSA_1136:Na+-driven multidrug efflux pump, putative:ATPases with chaperone activity, ATP-binding subunit, putative:->->:1161836..1162063 228 agagtgttggtttgttcctttaggataagtcagtgctctttttttcacaatcttttgttaaaattagattaaaacacgaaaaacgcttacattttttctagtatattgattgtgaaaatgatataataaacataagattatcaagttaagtttttgttaaaataggttaatttttaaaatattgtttgcagttgactttggttttcagtagaaaagcgaggaaactat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 agagtgttggtttgttcctttaggataagtcagtgctctttttttcacaatcttttgttaaaattagattaaaacacgaaaaacgcttacattttttctagtatattgattgtgaaaatgatataataaacataagattatcaagttaagtttttgttaaaataggttaatttttaaaatattgtttgcagttgactttggttttcagtagaaaagcgaggaaactat Predict ORF larger than 30AA ================================================ agagtgttggtttgttcctttaggataagtcagtgctctttttttcacaatcttttgttaaaattagattaaaacacgaaaaacgcttacattttttctagtatattgattgtgaaaatgatataataaacataagattatcaagttaagtttttgttaaaataggttaatttttaaaatattgtttgcagttgactttggttttcagtagaaaagcgaggaaactat 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================================================ agagtgttggtttgttcctttaggataagtcagtgctctttttttcacaatcttttgttaaaattagattaaaacacgaaaaacgcttacattttttctagtatattgattgtgaaaatgatataataaacataagattatcaagttaagtttttgttaaaataggttaatttttaaaatattgtttgcagttgactttggttttcagtagaaaagcgaggaaactat Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_1135:SSA_1136|SSA_1135:SSA_1136:Na+-driven multidrug efflux pump, putative:ATPases with chaperone activity, ATP-binding subunit, putative:->->:1161836..1162063 228 agagtgttggtttgttcctttaggataagtcagtgctctttttttcacaatcttttgttaaaattagattaaaacacgaaaaacgcttacattttttctagtatattgattgtgaaaatgatataataaacataagattatcaagttaagtttttgttaaaataggttaatttttaaaatattgtttgcagttgactttggttttcagtagaaaagcgaggaaactat Intra-Species Hit: Count: 1 Min: 1 Max: 228 Len: 228 Subject: NC_009009_SSA_1135_SSA_1136|Na+-driven multidrug efflux pump, putative:ATPases with chaperone activity, ATP-binding subunit, putative|POSITIVE:POSITIVE|[1161836,1162063]|228 HSP 1 e-value: 1.0E-114 bit: 410.0 Len: 228 Query Start:1 Query End:228 Subject Strand: POSITIVE Subject Start: 1 Subject End: 228 agagtgttggtttgttcctttaggataagtcagtgctcnnnnnnncacaatcttttgttaaaattagattaaaacacgaaaaacgcttacattttttctagtatattgattgtgaaaatgatataataaacataagattatcaagttaagtttttgttaaaataggttaatttttaaaatattgtttgcagttgactttggttttcagtagaaaagcgaggaaactat agagtgttggtttgttcctttaggataagtcagtgctctttttttcacaatcttttgttaaaattagattaaaacacgaaaaacgcttacattttttctagtatattgattgtgaaaatgatataataaacataagattatcaagttaagtttttgttaaaataggttaatttttaaaatattgtttgcagttgactttggttttcagtagaaaagcgaggaaactat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGAGUGUUGGUUUGUUCCUUUAGGAUAAGUCAGUGCUCUUUUUUUCACAAUCUUUUGUUAAAAUUAGAUUAAAACACGAAAAACGCUUACAUUUUUUCUAGUAUAUUGAUUGUGAAAAUGAUAUAAUAAACAUAAGAUUAUCAAGUUAAGUUUUUGUUAAAAUAGGUUAAUUUUUAAAAUAUUGUUUGCAGUUGACUUUGGUUUUCAGUAGAAAAGCGAGGAAACUAU ((((..(((..((((((.....))))))..)))..))))..(((((((((((...(((....((((((..(((...((.....))......)))..)))))))))..)))))))))))........((((((.....(((..(((((((.((.((.....)).)).))))))).))).....)))))).((((..(((((.(((((....))))).))))).)))).. (-46.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUAGUUUCCUCGCUUUUCUACUGAAAACCAAAGUCAACUGCAAACAAUAUUUUAAAAAUUAACCUAUUUUAACAAAAACUUAACUUGAUAAUCUUAUGUUUAUUAUAUCAUUUUCACAAUCAAUAUACUAGAAAAAAUGUAAGCGUUUUUCGUGUUUUAAUCUAAUUUUAACAAAAGAUUGUGAAAAAAAGAGCACUGACUUAUCCUAAAGGAACAAACCAACACUCU ...(((((...(.(((((....))))).).((((((..(((............................................((((((........)))))).....(((((((((((.........((((((.((....)))))))).((((..(((...)))..))))...))))))))))).....))).))))))........)))))............. (-34.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 323 37 1 216 175 NC_009009:SSA_1649|5end_hypothetical_protein_1648886..1649116_NEGATIVE 272 59 11 150 110 NC_009009:SSA_2230|5end_Ribonucleotide_reductase,_class_III,_anaerobic,_putative_2231158..2231388_NEGATIVE 266 206 165 195 156 NC_009009:SSA_1559|5end_Conserved_uncharacterized_protein_1561656..1561886_NEGATIVE 265 220 183 53 16 NC_009009:SSA_2050|5end_Arabinose_efflux_permease,_putative_2053255..2053485_POSITIVE 263 46 6 108 62 NC_009009:SSA_1731|5end_ATP-dependent_Clp_protease,_proteolytic_subunit,_putative_1716808..1717038_NEGATIVE 263 50 1 226 165 NC_009009:SSA_0838|5end_GtfB,_putative_825406..825636_POSITIVE 262 212 185 71 44 NC_009009:SSA_0502|5end_Peptide_ABC_transporter,_permease_protein,_putative_501554..501784_POSITIVE 259 50 4 224 179 NC_009009:SSA_1155|5end_Serine_hydroxymethyltransferase,_putative_1183298..1183528_POSITIVE 251 47 3 90 36 NC_009009:SSA_0503|5end_Peptide_ABC_transporter,_ATP-binding_protein,_putative_502231..502461_POSITIVE 249 46 1 157 104 NC_009009:SSA_0454|5end_Lactose_operon_transcriptional_repressor,_LacI_family,_putative_457015..457245_NEGATIVE 249 220 181 182 143 NC_009009:SSA_0065|5end_Low_molecular_weight_phosphotyrosine_protein_phosphatase,_putative_67175..67405_POSITIVE 245 56 11 231 185 NC_009009:SSA_2051|5end_Oligoendopeptidase,_putative_2054731..2054961_POSITIVE 244 50 4 207 159 NC_009009:SSA_0596|5end_hypothetical_protein_586913..587143_POSITIVE 241 212 184 46 9 NC_009009:SSA_0636|5end_N-(5'-phosphoribosyl)anthranilate_isomerase,_putative_625184..625414_POSITIVE 237 46 1 150 102 NC_009009:SSA_2079|5end_Acetyltransferase,_putative_2083971..2084201_POSITIVE 237 42 3 231 192 NC_009009:SSA_1692|5end_Phospho-B-galactosidase_LacG,_putative_1685006..1685236_NEGATIVE 232 47 1 90 42 NC_009009:SSA_0991|5end_Deoxyribonuclease,_putative_993342..993572_NEGATIVE 229 46 1 86 45 NC_009009:SSA_0843|5end_hypothetical_protein_827682..827912_POSITIVE 228 40 1 43 4 NC_009009:SSA_0625|5end_Phosphopantetheine_adenylyltransferase_615608..615838_POSITIVE 227 46 1 68 21 NC_009009:SSA_2222|5end_Tyrosine-protein_kinase_Wze,_putative_2223997..2224227_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 296 41 1 92 52 NC_009009:SSA_1135|3end_Na+-driven_multidrug_efflux_pump,_putative_1161775..1161925_POSITIVE 284 48 3 140 100 NC_009009:SSA_2074|3end_Preprotein_translocase_subunit_YajC,_putative_2076600..2076750_NEGATIVE 252 48 3 140 93 NC_009009:SSA_1693|3end_Phosphotransferase_system_lactose-specific_component_IIBC,_putative_1685105..1685255_NEGATIVE 251 47 3 102 48 NC_009009:SSA_0502|3end_Peptide_ABC_transporter,_permease_protein,_putative_502323..502473_POSITIVE 245 56 11 116 70 NC_009009:SSA_2050|3end_Arabinose_efflux_permease,_putative_2054696..2054846_POSITIVE 235 45 3 128 74 NC_009009:SSA_1479|3end_Transposase,_putative_1483889..1484039_POSITIVE 229 46 1 114 73 NC_009009:SSA_0842|3end_Effector_of_murein_hydrolase_LrgA/holin-like_protein,_putative_827790..827940_POSITIVE 228 40 1 53 14 NC_009009:SSA_0624|3end_hypothetical_protein_615698..615848_POSITIVE 227 46 1 57 10 NC_009009:SSA_2223|3end_Capsular_polysaccharide_biosynthesis_protein_Wzd_(chain_length_regulator),_putative_2224008..2224158_NEGATIVE 225 58 22 94 60 NC_009009:SSA_1319|3end_hypothetical_protein_1336780..1336930_POSITIVE 224 47 1 70 6 NC_009009:SSA_1960|3end_hypothetical_protein_1956571..1956721_NEGATIVE 224 60 16 117 65 NC_009009:SSA_1076|3end_hypothetical_protein_1095047..1095197_POSITIVE 224 59 21 91 55 NC_009009:SSA_0650|3end_GTP-binding_protein_TypA/BipA,_putative_634604..634754_POSITIVE 223 38 4 114 85 NC_009009:SSA_2077|3end_hypothetical_protein_2081352..2081502_NEGATIVE 223 59 22 125 78 NC_009009:SSA_2055|3end_hypothetical_protein_2057936..2058086_NEGATIVE 216 60 12 124 83 NC_009009:SSA_2189|3end_hypothetical_protein_2190279..2190429_NEGATIVE 216 40 1 133 86 NC_009009:SSA_2020|3end_hypothetical_protein_2022471..2022621_POSITIVE 215 38 6 35 8 NC_009009:SSA_2297|3end_hypothetical_protein_2298776..2298926_NEGATIVE 214 53 11 140 97 NC_009009:SSA_1034|3end_Conserved_uncharacterized_protein_1050252..1050402_POSITIVE 214 216 187 100 64 NC_009009:SSA_0642|3end_Type_4_prepilin_peptidase,_putative_629391..629541_NEGATIVE