Origin IGS: gtctattaagttttaaaatattcaagccggtagaactttctccggctttttactgtttgaaaaaaatgtactagatttgctgttcatcaagcggatttttctcttttccgagctacattatgtttaccagaaaattaccgtagcggatttgtgaaaaatctataagattcatttataatgataaatgaatgaatattctaggtaagaagttagaggagagtaa .........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 ttactctcctctaacttcttacctagaatattcattcatttatcattataaatgaatcttatagatttttcacaaatccgctacggtaattttctggtaaacataatgtagctcggaaaagagaaaaatccgcttgatgaacagcaaatctagtacatttttttcaaacagtaaaaagccggagaaagttctaccggcttgaatattttaaaacttaatagac Mask Tandem Repeat Region ================================================ gtctattaagttttaaaatattcaagccggtagaactttctccggctttttactgtttgaaaaaaatgtactagatttgctgttcatcaagcggatttttctcttttccgagctacattatgtttaccagaaaattaccgtagcggatttgtgaaaaatctataagattcatttataatgataaatgaatgaatattctaggtaagaagttagaggagagtaa Find is-nt database================================================ Query_seq: SSA_1120:SSA_1121|SSA_1120:SSA_1121:Two-component sensor kinase (with C-terminal ATPase domain), putative:Cytochrome C-type biogenesis protein, putative:->->:1147066..1147288 223 gtctattaagttttaaaatattcaagccggtagaactttctccggctttttactgtttgaaaaaaatgtactagatttgctgttcatcaagcggatttttctcttttccgagctacattatgtttaccagaaaattaccgtagcggatttgtgaaaaatctataagattcatttataatgataaatgaatgaatattctaggtaagaagttagaggagagtaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1120:SSA_1121|SSA_1120:SSA_1121:Two-component sensor kinase (with C-terminal ATPase domain), putative:Cytochrome C-type biogenesis protein, putative:->->:1147066..1147288 223 gtctattaagttttaaaatattcaagccggtagaactttctccggctttttactgtttgaaaaaaatgtactagatttgctgttcatcaagcggatttttctcttttccgagctacattatgtttaccagaaaattaccgtagcggatttgtgaaaaatctataagattcatttataatgataaatgaatgaatattctaggtaagaagttagaggagagtaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1120:SSA_1121|SSA_1120:SSA_1121:Two-component sensor kinase (with C-terminal ATPase domain), putative:Cytochrome C-type biogenesis protein, putative:->->:1147066..1147288 223 gtctattaagttttaaaatattcaagccggtagaactttctccggctttttactgtttgaaaaaaatgtactagatttgctgttcatcaagcggatttttctcttttccgagctacattatgtttaccagaaaattaccgtagcggatttgtgaaaaatctataagattcatttataatgataaatgaatgaatattctaggtaagaagttagaggagagtaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gtctattaagttttaaaatattcaagccggtagaactttctccggctttttactgtttgaaaaaaatgtactagatttgctgttcatcaagcggatttttctcttttccgagctacattatgtttaccagaaaattaccgtagcggatttgtgaaaaatctataagattcatttataatgataaatgaatgaatattctaggtaagaagttagaggagagtaa Predict ORF larger than 30AA ================================================ Protein_Len: 44 Strand: + Start: 20 End: 151 ................... M Q A G R T F S G F L L F E K N V L D L L F I K R I F L F S E L H Y V Y Q K I T V A D L ........................................................................ gtctattaagttttaaaatattcaagccggtagaactttctccggctttttactgtttgaaaaaaatgtactagatttgctgttcatcaagcggatttttctcttttccgagctacattatgtttaccagaaaattaccgtagcggatttgtgaaaaatctataagattcatttataatgataaatgaatgaatattctaggtaagaagttagaggagagtaa 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: 85 Start: 150 End: 179 .....................................................................................................................................................TGTGAAAAATCTATAAGATTCATTTATAAT............................................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gtctattaagttttaaaatattcaagccggtagaactttctccggctttttactgtttgaaaaaaatgtactagatttgctgttcatcaagcggatttttctcttttccgagctacattatgtttaccagaaaattaccgtagcggatttgtgaaaaatctataagattcatttataatgataaatgaatgaatattctaggtaagaagttagaggagagtaa Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_1120:SSA_1121|SSA_1120:SSA_1121:Two-component sensor kinase (with C-terminal ATPase domain), putative:Cytochrome C-type biogenesis protein, putative:->->:1147066..1147288 223 gtctattaagttttaaaatattcaagccggtagaactttctccggctttttactgtttgaaaaaaatgtactagatttgctgttcatcaagcggatttttctcttttccgagctacattatgtttaccagaaaattaccgtagcggatttgtgaaaaatctataagattcatttataatgataaatgaatgaatattctaggtaagaagttagaggagagtaa Intra-Species Hit: Count: 1 Min: 1 Max: 223 Len: 223 Subject: NC_009009_SSA_1120_SSA_1121|Two-component sensor kinase (with C-terminal ATPase domain), putative:Cytochrome C-type biogenesis protein, putative|POSITIVE:POSITIVE|[1147066,1147288]|223 HSP 1 e-value: 1.0E-111 bit: 400.0 Len: 223 Query Start:1 Query End:223 Subject Strand: POSITIVE Subject Start: 1 Subject End: 223 gtctattaagttttaaaatattcaagccggtagaactttctccggctttttactgtttgnnnnnnntgtactagatttgctgttcatcaagcggatttttctcttttccgagctacattatgtttaccagaaaattaccgtagcggatttgtgaaaaatctataagattcatttataatgataaatgaatgaatattctaggtaagaagttagaggagagtaa gtctattaagttttaaaatattcaagccggtagaactttctccggctttttactgtttgaaaaaaatgtactagatttgctgttcatcaagcggatttttctcttttccgagctacattatgtttaccagaaaattaccgtagcggatttgtgaaaaatctataagattcatttataatgataaatgaatgaatattctaggtaagaagttagaggagagtaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUCUAUUAAGUUUUAAAAUAUUCAAGCCGGUAGAACUUUCUCCGGCUUUUUACUGUUUGAAAAAAAUGUACUAGAUUUGCUGUUCAUCAAGCGGAUUUUUCUCUUUUCCGAGCUACAUUAUGUUUACCAGAAAAUUACCGUAGCGGAUUUGUGAAAAAUCUAUAAGAUUCAUUUAUAAUGAUAAAUGAAUGAAUAUUCUAGGUAAGAAGUUAGAGGAGAGUAA ((.((((...(((((((......(((((((.(((....)))))))))).......)))))))..)))).)).(((((((((........)))))))))..((((((((..((((........((((((((((............((((((.....)))))).....((((((((((....)))))))))).....)))).)))))).)))).))))))))... (-53.02) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUACUCUCCUCUAACUUCUUACCUAGAAUAUUCAUUCAUUUAUCAUUAUAAAUGAAUCUUAUAGAUUUUUCACAAAUCCGCUACGGUAAUUUUCUGGUAAACAUAAUGUAGCUCGGAAAAGAGAAAAAUCCGCUUGAUGAACAGCAAAUCUAGUACAUUUUUUUCAAACAGUAAAAAGCCGGAGAAAGUUCUACCGGCUUGAAUAUUUUAAAACUUAAUAGAC .......................((((((((((.(((((((((....)))))))))...............((...(((((((((....(((......))).....))))))..)))...(((((((((..(((.(((.........))).)))..))))))))).....))...((((((((((....))).)))))))))))))))))............. (-44.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 321 112 79 180 146 NC_009009:SSA_2005|5end_Chaperone_protein_dnaJ,_putative_2006384..2006614_NEGATIVE 287 113 72 204 141 NC_009009:SSA_0818|5end_SPX_domain-like_protein,_putative_799675..799905_POSITIVE 285 62 28 54 12 NC_009009:SSA_2140|5end_Ribonuclease_P_protein_component,_putative_2140574..2140804_NEGATIVE 276 58 21 221 181 NC_009009:SSA_1720|5end_Initiation-control_protein,_putative_1707113..1707343_NEGATIVE 270 56 25 228 203 NC_009009:SSA_1707|5end_Conserved_uncharacterized_protein_1697782..1698012_POSITIVE 268 61 26 182 146 NC_009009:SSA_2207|5end_hypothetical_protein_2207221..2207451_NEGATIVE 263 50 8 45 1 NC_009009:SSA_1547|5end_HPr_kinase/phosphorylase,_putative_1550980..1551210_NEGATIVE 262 115 73 140 97 NC_009009:SSA_1294|5end_hypothetical_protein_1312581..1312811_NEGATIVE 261 130 86 112 54 NC_009009:SSA_1335|5end_Ankyrin_repeat_protein,_putative_1349663..1349893_NEGATIVE 261 115 79 197 155 NC_009009:SSA_0210|5end_hypothetical_protein_207757..207987_POSITIVE 260 119 73 121 78 NC_009009:SSA_1225|5end_Branched-chain_amino_acid_aminotransferase,_putative_1248608..1248838_NEGATIVE 260 115 73 182 129 NC_009009:SSA_0031|5end_Glutamine_phosphoribosylpyrophosphate_amidotransferase,_putative_36439..36669_POSITIVE 258 88 42 52 1 NC_009009:SSA_2351|5end_ABC-type_nitrate/sulfonate/bicarbonate_transport_system,_ATPase_component,_putative_2353507..2353737_NEGATIVE 257 116 79 113 55 NC_009009:SSA_1460|5end_Transcriptional_attenuator_LytR,_putative_1468915..1469145_NEGATIVE 254 130 82 67 1 NC_009009:SSA_1995|5end_hypothetical_protein_1993358..1993588_NEGATIVE 254 114 73 59 14 NC_009009:SSA_0885|5end_hypothetical_protein_879514..879744_NEGATIVE 253 109 66 164 117 NC_009009:SSA_0536|5end_B12-dependent_diol_dehydratase_small_subunit,_putative_531342..531572_POSITIVE 252 115 72 163 124 NC_009009:SSA_1414|5end_hypothetical_protein_1425412..1425642_NEGATIVE 252 109 68 38 2 NC_009009:SSA_0968|5end_hypothetical_protein_976699..976929_POSITIVE 252 114 71 216 177 NC_009009:SSA_0785|5end_Proton-translocating_ATPase,_F1_sector,_delta_subunit,_putative_768044..768274_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 289 118 74 73 19 NC_009009:SSA_1459|3end_RNA_methyltransferase,_putative_1466111..1466261_NEGATIVE 287 110 72 128 81 NC_009009:SSA_1382|3end_hypothetical_protein_1399797..1399947_NEGATIVE 281 56 19 151 102 NC_009009:SSA_0127|3end_Multispanning_membrane_protein,_translocator_of_proteins,_putative_119107..119257_POSITIVE 274 48 24 67 43 NC_009009:SSA_1120|3end_Two-component_sensor_kinase_(with_C-terminal_ATPase_domain),_putative_1147005..1147155_POSITIVE 262 114 73 141 87 NC_009009:SSA_2321|3end_Cation_(Co/Zn/Cd)_efflux_protein,_putative_2326050..2326200_NEGATIVE 262 115 73 139 96 NC_009009:SSA_1296|3end_hypothetical_protein_1312582..1312732_NEGATIVE 260 115 73 87 34 NC_009009:SSA_0030|3end_Phosphoribosylformylglycinamidine_synthase,_putative_36424..36574_POSITIVE 258 88 42 52 1 NC_009009:SSA_2352|3end_ABC-type_nitrate/sulfonate/bicarbonate_transporter,_periplasmic_component,_putative_2353507..2353657_NEGATIVE 257 116 79 94 36 NC_009009:SSA_1462|3end_Prephenate_dehydratase,_putative_1468934..1469084_NEGATIVE 253 109 66 133 86 NC_009009:SSA_0535|3end_Propanediol_utilization:_dehydratase,_medium_subunit,_putative_531391..531541_POSITIVE 253 110 63 134 85 NC_009009:SSA_0403|3end_CAAX_amino_terminal_protease_family,_putative_401388..401538_POSITIVE 251 56 26 78 53 NC_009009:SSA_0564|3end_Potential_aminotransferase,_putative_556988..557138_POSITIVE 249 46 10 145 103 NC_009009:SSA_0087|3end_V-type_sodium_ATPase,_subunit_E,_putative_88999..89149_POSITIVE 248 56 11 80 33 NC_009009:SSA_1116|3end_hypothetical_protein_1142752..1142902_POSITIVE 245 179 138 76 28 NC_009009:SSA_2114|3end_Transcriptional_repressor_of_purine_operon,_putative_2116714..2116864_NEGATIVE 242 150 103 107 69 NC_009009:SSA_1324|3end_Ceramide_glucosyltransferase,_putative_1340428..1340578_NEGATIVE 240 129 89 104 70 NC_009009:SSA_0193|3end_CAAX_amino_terminal_protease_family_protein,_putative_195075..195225_POSITIVE 238 113 71 129 85 NC_009009:SSA_1801|3end_hypothetical_protein_1782652..1782802_NEGATIVE 237 116 75 146 100 NC_009009:SSA_0937|3end_Arsenate_reductase,_glutaredoxin_family,_putative_946664..946814_POSITIVE 237 57 22 92 60 NC_009009:SSA_0748|3end_Sugar:H+_symporter,_permease_of_the_major_facilitator_superfamily,_putative_730635..730785_POSITIVE