Origin IGS: tactcaaataaaacatcaggaatgttcgttttcctgatgtttttttaaatttaacagaattgtaaaaattgctcagttttcagcgaaaacgctctaaaacactgactttctccgcagatgctctaggaaaaacttgacagcttttgtcatttatattaaaataaatttaatataagaactgaaaacgaacacaacggagtgtttgaactacatataagtgagcaacggtgctacaaaaaatgaaacttcttttttgtagtgctttttttatcagtgaatctggagtaaagcg .........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 cgctttactccagattcactgataaaaaaagcactacaaaaaagaagtttcattttttgtagcaccgttgctcacttatatgtagttcaaacactccgttgtgttcgttttcagttcttatattaaatttattttaatataaatgacaaaagctgtcaagtttttcctagagcatctgcggagaaagtcagtgttttagagcgttttcgctgaaaactgagcaatttttacaattctgttaaatttaaaaaaacatcaggaaaacgaacattcctgatgttttatttgagta Mask Tandem Repeat Region ================================================ tactcaaataaaacatcaggaatgttcgttttcctgatgtttttttaaatttaacagaattgtaaaaattgctcagttttcagcgaaaacgctctaaaacactgactttctccgcagatgctctaggaaaaacttgacagcttttgtcatttatattaaaataaatttaatataagaactgaaaacgaacacaacggagtgtttgaactacatataagtgagcaacggtgctacaaaaaatgaaacttcttttttgtagtgctttttttatcagtgaatctggagtaaagcg Find is-nt database================================================ Query_seq: SSA_0462:SSA_0463|SSA_0462:SSA_0463:ABC-type multidrug transport system (phospholipid, LPS, lipid A and drug exporter), ATPase and permease components, putative:Cobyrinic acid A,C-diamide synthase, putative:->->:466713..467004 292 tactcaaataaaacatcaggaatgttcgttttcctgatgtttttttaaatttaacagaattgtaaaaattgctcagttttcagcgaaaacgctctaaaacactgactttctccgcagatgctctaggaaaaacttgacagcttttgtcatttatattaaaataaatttaatataagaactgaaaacgaacacaacggagtgtttgaactacatataagtgagcaacggtgctacaaaaaatgaaacttcttttttgtagtgctttttttatcagtgaatctggagtaaagcg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0462:SSA_0463|SSA_0462:SSA_0463:ABC-type multidrug transport system (phospholipid, LPS, lipid A and drug exporter), ATPase and permease components, putative:Cobyrinic acid A,C-diamide synthase, putative:->->:466713..467004 292 tactcaaataaaacatcaggaatgttcgttttcctgatgtttttttaaatttaacagaattgtaaaaattgctcagttttcagcgaaaacgctctaaaacactgactttctccgcagatgctctaggaaaaacttgacagcttttgtcatttatattaaaataaatttaatataagaactgaaaacgaacacaacggagtgtttgaactacatataagtgagcaacggtgctacaaaaaatgaaacttcttttttgtagtgctttttttatcagtgaatctggagtaaagcg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0462:SSA_0463|SSA_0462:SSA_0463:ABC-type multidrug transport system (phospholipid, LPS, lipid A and drug exporter), ATPase and permease components, putative:Cobyrinic acid A,C-diamide synthase, putative:->->:466713..467004 292 tactcaaataaaacatcaggaatgttcgttttcctgatgtttttttaaatttaacagaattgtaaaaattgctcagttttcagcgaaaacgctctaaaacactgactttctccgcagatgctctaggaaaaacttgacagcttttgtcatttatattaaaataaatttaatataagaactgaaaacgaacacaacggagtgtttgaactacatataagtgagcaacggtgctacaaaaaatgaaacttcttttttgtagtgctttttttatcagtgaatctggagtaaagcg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tactcaaataaaacatcaggaatgttcgttttcctgatgtttttttaaatttaacagaattgtaaaaattgctcagttttcagcgaaaacgctctaaaacactgactttctccgcagatgctctaggaaaaacttgacagcttttgtcatttatattaaaataaatttaatataagaactgaaaacgaacacaacggagtgtttgaactacatataagtgagcaacggtgctacaaaaaatgaaacttcttttttgtagtgctttttttatcagtgaatctggagtaaagcg Predict ORF larger than 30AA ================================================ Protein_Len: 35 Strand: - Start: 170 End: 274 ......................................................................................................................................................................... Y L F Q F R V C R L T Q V V Y L H A V T S C F I F S R K Q L A K K I M .................. tactcaaataaaacatcaggaatgttcgttttcctgatgtttttttaaatttaacagaattgtaaaaattgctcagttttcagcgaaaacgctctaaaacactgactttctccgcagatgctctaggaaaaacttgacagcttttgtcatttatattaaaataaatttaatataagaactgaaaacgaacacaacggagtgtttgaactacatataagtgagcaacggtgctacaaaaaatgaaacttcttttttgtagtgctttttttatcagtgaatctggagtaaagcg 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: 92 Start: 133 End: 162 ....................................................................................................................................CTTGACAGCTTTTGTCATTTATATTAAAAT.................................................................................................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tactcaaataaaacatcaggaatgttcgttttcctgatgtttttttaaatttaacagaattgtaaaaattgctcagttttcagcgaaaacgctctaaaacactgactttctccgcagatgctctaggaaaaacttgacagcttttgtcatttatattaaaataaatttaatataagaactgaaaacgaacacaacggagtgtttgaactacatataagtgagcaacggtgctacaaaaaatgaaacttcttttttgtagtgctttttttatcagtgaatctggagtaaagcg Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 46 HP_score: -3.6 Tail_Score: -3.03286 Start: 17 End: 36 Full_Region: aatttaaaaaaacat caggaa aacgaaca ttcctg atgttttatttgagt ................caggaaaacgaacattcctg................................................................................................................................................................................................................................................................ TransTerm Strand: - Conf: 46 HP_score: -4.3 Tail_Score: -2.65504 Start: 135 End: 149 Full_Region: ttattttaatataaa tgaca aaagc tgtca agtttttcctagagc ......................................................................................................................................tgacaaaagctgtca............................................................................................................................................... TransTerm Strand: - Conf: 56 HP_score: -2.1 Tail_Score: -4.37734 Start: 186 End: 205 Full_Region: cacttatatgtagtt caaacac tccgtt gtgttcg ttttcagttcttata .........................................................................................................................................................................................caaacactccgttgtgttcg....................................................................................... TransTerm Strand: + Conf: 90 HP_score: -6.7 Tail_Score: -5.64274 Start: 228 End: 262 Full_Region: TATAAGTGAGCAACG GTGCTACAAAAAATGA AACT TCTTTTTTGTAGTGC TTTTTTTATCAGTGA ...................................................................................................................................................................................................................................GTGCTACAAAAAATGAAACTTCTTTTTTGTAGTGC.............................. Find igs database================================================ Query_seq: SSA_0462:SSA_0463|SSA_0462:SSA_0463:ABC-type multidrug transport system (phospholipid, LPS, lipid A and drug exporter), ATPase and permease components, putative:Cobyrinic acid A,C-diamide synthase, putative:->->:466713..467004 292 tactcaaataaaacatcaggaatgttcgttttcctgatgtttttttaaatttaacagaattgtaaaaattgctcagttttcagcgaaaacgctctaaaacactgactttctccgcagatgctctaggaaaaacttgacagcttttgtcatttatattaaaataaatttaatataagaactgaaaacgaacacaacggagtgtttgaactacatataagtgagcaacggtgctacaaaaaatgaaacttcttttttgtagtgctttttttatcagtgaatctggagtaaagcg Intra-Species Hit: Count: 1 Min: 1 Max: 292 Len: 292 Subject: NC_009009_SSA_0462_SSA_0463|ABC-type multidrug transport system (phospholipid, LPS, lipid A and drug exporter), ATPase and permease components, putative:Cobyrinic acid A,C-diamide synthase, putative|POSITIVE:POSITIVE|[466713,467004]|292 HSP 1 e-value: 1.0E-139 bit: 496.0 Len: 292 Query Start:1 Query End:292 Subject Strand: POSITIVE Subject Start: 1 Subject End: 292 tactcaaataaaacatcaggaatgttcgttttcctgatgnnnnnnnaaatttaacagaattgtaaaaattgctcagttttcagcgaaaacgctctaaaacactgactttctccgcagatgctctaggaaaaacttgacagcttttgtcatttatattaaaataaatttaatataagaactgaaaacgaacacaacggagtgtttgaactacatataagtgagcaacggtgctacaaaaaatgaaacttcttttttgtagtgcnnnnnnnatcagtgaatctggagtaaagcg tactcaaataaaacatcaggaatgttcgttttcctgatgtttttttaaatttaacagaattgtaaaaattgctcagttttcagcgaaaacgctctaaaacactgactttctccgcagatgctctaggaaaaacttgacagcttttgtcatttatattaaaataaatttaatataagaactgaaaacgaacacaacggagtgtttgaactacatataagtgagcaacggtgctacaaaaaatgaaacttcttttttgtagtgctttttttatcagtgaatctggagtaaagcg Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UACUCAAAUAAAACAUCAGGAAUGUUCGUUUUCCUGAUGUUUUUUUAAAUUUAACAGAAUUGUAAAAAUUGCUCAGUUUUCAGCGAAAACGCUCUAAAACACUGACUUUCUCCGCAGAUGCUCUAGGAAAAACUUGACAGCUUUUGUCAUUUAUAUUAAAAUAAAUUUAAUAUAAGAACUGAAAACGAACACAACGGAGUGUUUGAACUACAUAUAAGUGAGCAACGGUGCUACAAAAAAUGAAACUUCUUUUUUGUAGUGCUUUUUUUAUCAGUGAAUCUGGAGUAAAGCG (((((....(((((((((((((........)))))))))))))...........((((((((((((((.(((((((((((.((((....))))..)))))......((((...(((((.(((.((((.....))))..))).)))))..(((((((((((.....)))))))))))....)))).(((((((......))))))).............))))))..((..((((((((((.((....))))))))))))..)).)))))).))))...)))))))))..... (-76.20) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CGCUUUACUCCAGAUUCACUGAUAAAAAAAGCACUACAAAAAAGAAGUUUCAUUUUUUGUAGCACCGUUGCUCACUUAUAUGUAGUUCAAACACUCCGUUGUGUUCGUUUUCAGUUCUUAUAUUAAAUUUAUUUUAAUAUAAAUGACAAAAGCUGUCAAGUUUUUCCUAGAGCAUCUGCGGAGAAAGUCAGUGUUUUAGAGCGUUUUCGCUGAAAACUGAGCAAUUUUUACAAUUCUGUUAAAUUUAAAAAAACAUCAGGAAAACGAACAUUCCUGAUGUUUUAUUUGAGUA .(((((....(((.....)))......))))).((((((((((((....)).))))))))))....(((((((....................((((((.((((((...........((((((((((.....)))))))))).(((((.....)))))...........))))))..)))))).........(((((..((((....)))).))))).))))))).................((((((((((((((((((((........))))))))))))).))))))). (-76.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 323 129 81 51 8 NC_009009:SSA_0956|5end_surface_protein_D_961223..961453_POSITIVE 309 127 81 207 157 NC_009009:SSA_1866|5end_hypothetical_protein_1862182..1862412_NEGATIVE 309 121 82 43 1 NC_009009:SSA_0489|5end_Adenosylcobinamide_kinase_/_adenosylcobinamide_phosphate_guanyltransferase,_putative_489655..489885_POSITIVE 305 139 92 181 136 NC_009009:SSA_1231|5end_hypothetical_protein_1254758..1254988_NEGATIVE 304 149 107 47 4 NC_009009:SSA_1241|5end_Orotidine-5'-phosphate_decarboxylase,_putative_1266201..1266431_NEGATIVE 296 127 81 230 184 NC_009009:SSA_1822|5end_hypothetical_protein_1811125..1811355_NEGATIVE 294 119 75 158 115 NC_009009:SSA_2002|5end_tRNA_pseudouridine_synthase_A,_putative_1998959..1999189_NEGATIVE 289 130 82 205 148 NC_009009:SSA_2070|5end_Zinc_metalloprotease,_putative_2074574..2074804_NEGATIVE 289 115 71 73 19 NC_009009:SSA_1607|5end_Formamidopyrimidine-DNA_glycosylase,_putative_1613255..1613485_NEGATIVE 288 130 81 204 152 NC_009009:SSA_1572|5end_hypothetical_protein_1575908..1576138_NEGATIVE 284 143 102 49 11 NC_009009:SSA_0345|5end_hypothetical_protein_338803..339033_POSITIVE 278 130 81 84 34 NC_009009:SSA_1605|5end_Major_facilitator_superfamily_multi-drug_resistance_efflux_pump_pmrA,_putative_1611732..1611962_NEGATIVE 278 120 71 179 124 NC_009009:SSA_0197|5end_Dihydropteroate_synthase,_putative_195946..196176_POSITIVE 277 120 71 60 13 NC_009009:SSA_0318|5end_Secreted_metalloendopeptidase_Gcp_311701..311931_POSITIVE 275 146 112 36 9 NC_009009:SSA_1743|5end_ABC-type_Fe3+-siderophore_transport_system,_permease_component,_putative_1730170..1730400_POSITIVE 270 78 33 57 16 NC_009009:SSA_0992|5end_hypothetical_protein_993486..993716_POSITIVE 265 146 104 168 123 NC_009009:SSA_1667|5end_hypothetical_protein_1667704..1667934_NEGATIVE 265 150 107 57 12 NC_009009:SSA_0903|5end_NAD(P)H_dehydrogenase_(quinone),_putative_893242..893472_POSITIVE 263 52 18 71 34 NC_009009:SSA_1318|5end_GTP-binding_protein_lepA,_putative_1335821..1336051_NEGATIVE 262 149 106 44 1 NC_009009:SSA_1592|5end_hypothetical_protein_1596397..1596627_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 309 121 82 50 8 NC_009009:SSA_0488|3end_Glutamate-1-semialdehyde_2,1-aminotransferase,_putative_489742..489892_POSITIVE 305 139 92 133 88 NC_009009:SSA_1232|3end_Topoisomerase_IV_subunit_B,_putative_1254806..1254956_NEGATIVE 304 43 1 83 33 NC_009009:SSA_1687|3end_NADH-binding_ferric-oxidoreductase,_putative_1681823..1681973_POSITIVE 300 43 10 81 48 NC_009009:SSA_0462|3end_ABC-type_multidrug_transport_system_(phospholipid,_LPS,_lipid_A_and_drug_exporter),_ATPase_and_permease_components,_putative_466652..466802_POSITIVE 295 117 72 136 97 NC_009009:SSA_0413|3end_Anthranilate/para-aminobenzoate_synthases_component_I/_Chorismate_binding_enzyme,_putative_408315..408465_NEGATIVE 288 130 81 58 6 NC_009009:SSA_1573|3end_hypothetical_protein_1576054..1576204_NEGATIVE 287 149 102 64 16 NC_009009:SSA_1867|3end_ABC-type_polar_amino_acid_transport_system,_ATPase_component,_putative_1862353..1862503_NEGATIVE 286 269 221 146 100 NC_009009:SSA_0708|3end_hypothetical_protein_694757..694907_POSITIVE 285 260 214 114 67 NC_009009:SSA_2354|3end_hypothetical_protein_2355605..2355755_NEGATIVE 280 48 1 94 47 NC_009009:SSA_1027|3end_hypothetical_protein_1045244..1045394_POSITIVE 277 120 71 70 23 NC_009009:SSA_0317|3end_Ribosomal_protein_alanine_acetyl_transferase,_putative_311791..311941_POSITIVE 274 125 83 143 87 NC_009009:SSA_0593|3end_Rhodanese-like_sulfurtransferase,_putative_585551..585701_POSITIVE 269 149 103 51 2 NC_009009:SSA_1593|3end_Dipeptidase,_putative_1596390..1596540_NEGATIVE 265 146 104 134 89 NC_009009:SSA_1668|3end_NrdI_protein,_putative_1667738..1667888_NEGATIVE 262 150 103 64 1 NC_009009:SSA_1924|3end_Transcriptional_regulator,_TetR/AcrR_family,_putative_1912691..1912841_NEGATIVE 260 229 189 140 105 NC_009009:SSA_1550|3end_hypothetical_protein_1552228..1552378_NEGATIVE 260 119 71 51 11 NC_009009:SSA_1477|3end_Truncated_transposase,_putative_1482914..1483064_POSITIVE 259 126 91 145 99 NC_009009:SSA_1024|3end_Alpha-amylase,_putative_1041182..1041332_NEGATIVE 259 93 56 126 95 NC_009009:SSA_0242|3end_hypothetical_protein_235810..235960_POSITIVE 259 149 107 131 88 NC_009009:SSA_0065|3end_Low_molecular_weight_phosphotyrosine_protein_phosphatase,_putative_67677..67827_POSITIVE