Origin IGS: tgtttttactttgccctttaagtcttttttcttccaatcagtttcaggcataattgctgagtatgaataagaaaaaaccaacaacatcagaattagccctcctaaatattttttcagatatttatagattgtcattttatcaactcctaatgttactggtttttattt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aaataaaaaccagtaacattaggagttgataaaatgacaatctataaatatctgaaaaaatatttaggagggctaattctgatgttgttggttttttcttattcatactcagcaattatgcctgaaactgattggaagaaaaaagacttaaagggcaaagtaaaaaca Mask Tandem Repeat Region ================================================ tgtttttactttgccctttaagtcttttttcttccaatcagtttcaggcataattgctgagtatgaataagaaaaaaccaacaacatcagaattagccctcctaaatattttttcagatatttatagattgtcattttatcaactcctaatgttactggtttttattt Find is-nt database================================================ Query_seq: FN2012:FN2013|FN2012:FN2013:hypothetical protein:GTP-binding protein:<-<-:513990..514157 168 tgtttttactttgccctttaagtcttttttcttccaatcagtttcaggcataattgctgagtatgaataagaaaaaaccaacaacatcagaattagccctcctaaatattttttcagatatttatagattgtcattttatcaactcctaatgttactggtttttattt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN2012:FN2013|FN2012:FN2013:hypothetical protein:GTP-binding protein:<-<-:513990..514157 168 tgtttttactttgccctttaagtcttttttcttccaatcagtttcaggcataattgctgagtatgaataagaaaaaaccaacaacatcagaattagccctcctaaatattttttcagatatttatagattgtcattttatcaactcctaatgttactggtttttattt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN2012:FN2013|FN2012:FN2013:hypothetical protein:GTP-binding protein:<-<-:513990..514157 168 tgtttttactttgccctttaagtcttttttcttccaatcagtttcaggcataattgctgagtatgaataagaaaaaaccaacaacatcagaattagccctcctaaatattttttcagatatttatagattgtcattttatcaactcctaatgttactggtttttattt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgtttttactttgccctttaagtcttttttcttccaatcagtttcaggcataattgctgagtatgaataagaaaaaaccaacaacatcagaattagccctcctaaatattttttcagatatttatagattgtcattttatcaactcctaatgttactggtttttattt Predict ORF larger than 30AA ================================================ Protein_Len: 38 Strand: + Start: 54 End: 167 ..................................................... M L S M N K K K P T T S E L A L L N I F S D I Y R L S F Y Q L L M L L V F I . Protein_Len: 45 Strand: - Start: 1 End: 135 T K V K G K L D K K K W D T E P M I A S Y S Y S F V L L M L I L G G L Y K K L Y K Y I T M ................................. tgtttttactttgccctttaagtcttttttcttccaatcagtttcaggcataattgctgagtatgaataagaaaaaaccaacaacatcagaattagccctcctaaatattttttcagatatttatagattgtcattttatcaactcctaatgttactggtttttattt 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================================================ tgtttttactttgccctttaagtcttttttcttccaatcagtttcaggcataattgctgagtatgaataagaaaaaaccaacaacatcagaattagccctcctaaatattttttcagatatttatagattgtcattttatcaactcctaatgttactggtttttattt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: FN2012:FN2013|FN2012:FN2013:hypothetical protein:GTP-binding protein:<-<-:513990..514157 168 tgtttttactttgccctttaagtcttttttcttccaatcagtttcaggcataattgctgagtatgaataagaaaaaaccaacaacatcagaattagccctcctaaatattttttcagatatttatagattgtcattttatcaactcctaatgttactggtttttattt Intra-Species Hit: Count: 1 Min: 1 Max: 168 Len: 168 Subject: NC_003454_FN2012_FN2013|hypothetical protein:GTP-binding protein|NEGATIVE:NEGATIVE|[513990,514157]|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 tgtttttactttgccctttaagtcttttttcttccaatcagtttcaggcataattgctgagtatgaataagaaaaaaccaacaacatcagaattagccctcctaaatattttttcagatatttatagattgtcattttatcaactcctaatgttactggtttttattt tgtttttactttgccctttaagtcttttttcttccaatcagtttcaggcataattgctgagtatgaataagaaaaaaccaacaacatcagaattagccctcctaaatattttttcagatatttatagattgtcattttatcaactcctaatgttactggtttttattt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGUUUUUACUUUGCCCUUUAAGUCUUUUUUCUUCCAAUCAGUUUCAGGCAUAAUUGCUGAGUAUGAAUAAGAAAAAACCAACAACAUCAGAAUUAGCCCUCCUAAAUAUUUUUUCAGAUAUUUAUAGAUUGUCAUUUUAUCAACUCCUAAUGUUACUGGUUUUUAUUU (((((.(((((.((...(((.((((.....((.......))....)))).)))..)).))))).)))))...((((((((..(((((.((............((((((((......))))))))..(((.........))).....)).)))))..)))))))).... (-26.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAUAAAAACCAGUAACAUUAGGAGUUGAUAAAAUGACAAUCUAUAAAUAUCUGAAAAAAUAUUUAGGAGGGCUAAUUCUGAUGUUGUUGGUUUUUUCUUAUUCAUACUCAGCAAUUAUGCCUGAAACUGAUUGGAAGAAAAAAGACUUAAAGGGCAAAGUAAAAACA .....((((((((((((((((((((((........)))..(((.(((((((.(....).)))))))..))).....)))))))))))))))))))(((((..(((...((((((....)).))))...)))....))))).....((((........))))....... (-32.70) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 828 60 11 151 102 NC_003454:FN2012|5end_hypothetical_protein_513899..514129_NEGATIVE 279 35 1 53 17 NC_003454:FN0682|5end_Fibronectin-binding_protein-like_protein_A_1336794..1337024_POSITIVE 274 49 1 104 50 NC_003454:FN0163|5end_5-methyltetrahydrofolate--homocysteine_methyltransferase_791318..791548_POSITIVE 237 68 23 87 40 NC_003454:FN0551|5end_Bacterial_regulatory_proteins,_crp_family_1203276..1203506_POSITIVE 237 38 1 70 23 NC_003454:FN1764|5end_Enolase_257997..258227_NEGATIVE 232 50 13 194 158 NC_003454:FN0149|5end_Malonyl-CoA-[acyl-carrier-protein]_transacylase_777486..777716_POSITIVE 231 112 79 107 67 NC_003454:FN0357|5end_ATP_synthase_epsilon_chain,_sodium_ion_specific_988276..988506_NEGATIVE 231 68 23 154 98 NC_003454:FN1754|5end_thiazole_synthase_251117..251347_NEGATIVE 230 69 25 163 115 NC_003454:FN1249|5end_Transcriptional_regulator,_DeoR_family_1906241..1906471_NEGATIVE 226 108 63 121 67 NC_003454:FN1450|5end_Integral_membrane_protein_2131410..2131640_NEGATIVE 225 149 101 107 54 NC_003454:FN1020|5end_3-hydroxybutyryl-CoA_dehydratase_1674576..1674806_NEGATIVE 224 57 13 64 19 NC_003454:FN1326|5end_Undecaprenyl_pyrophosphate_synthetase_1981890..1982120_NEGATIVE 223 60 23 107 73 NC_003454:FN0727|5end_hypothetical_protein_1385507..1385737_NEGATIVE 223 61 35 112 89 NC_003454:FN1604|5end_hypothetical_protein_113822..114052_NEGATIVE 222 66 30 104 69 NC_003454:FN0231|5end_hypothetical_protein_857351..857581_NEGATIVE 217 80 31 145 99 NC_003454:FN2041|5end_Transcription_antitermination_protein_nusG_549659..549889_NEGATIVE 216 139 92 164 114 NC_003454:FN1825|5end_hypothetical_protein_313994..314224_POSITIVE 214 32 3 117 92 NC_003454:FN1325|5end_Phosphatidate_cytidylyltransferase_1981205..1981435_NEGATIVE 213 116 83 229 195 NC_003454:FN0740|5end_imidazolonepropionase_1398914..1399144_NEGATIVE 212 130 83 137 87 NC_003454:FN0575|5end_hypothetical_protein_1225331..1225561_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 279 35 1 51 15 NC_003454:FN0681|3end_Transcriptional_regulator,_MarR_family_1336872..1337022_POSITIVE 231 112 79 97 57 NC_003454:FN0358|3end_ATP_synthase_subunit_B_988286..988436_NEGATIVE 230 49 11 50 4 NC_003454:FN0162|3end_Na+_driven_multidrug_efflux_pump_791344..791494_POSITIVE 223 60 23 129 95 NC_003454:FN0728|3end_hypothetical_protein_1385485..1385635_NEGATIVE 217 80 31 148 102 NC_003454:FN2042|3end_Protein_translocase_subunit_SecE_549656..549806_NEGATIVE 214 32 3 124 99 NC_003454:FN1326|3end_Undecaprenyl_pyrophosphate_synthetase_1981198..1981348_NEGATIVE 213 45 1 150 100 NC_003454:FN0063|3end_hypothetical_protein_699394..699544_POSITIVE 211 45 4 48 10 NC_003454:FN0329|3end_50S_ribosomal_protein_L13_964647..964797_POSITIVE 209 58 18 148 96 NC_003454:FN1937|3end_hypothetical_protein_437705..437855_NEGATIVE 209 59 11 149 112 NC_003454:FN1585|3end_hypothetical_protein_96213..96363_NEGATIVE 208 104 61 149 104 NC_003454:FN1375|3end_Citrate-sodium_symport_2023860..2024010_POSITIVE 207 64 32 64 37 NC_003454:FN1183|3end_Hypothetical_cytosolic_protein_1845428..1845578_NEGATIVE 204 111 83 147 118 NC_003454:FN0741|3end_Glutamate_formiminotransferase_1398991..1399141_NEGATIVE 204 38 5 44 1 NC_003454:FN1765|3end_pyruvate_kinase_258023..258173_NEGATIVE 203 126 86 133 93 NC_003454:FN1492|3end_DNA_repair_protein_recO_2172769..2172919_NEGATIVE 200 114 74 92 57 NC_003454:FN1832|3end_TonB_protein_321440..321590_NEGATIVE 198 58 22 40 4 NC_003454:FN1630|3end_SSU_ribosomal_protein_S8P_134533..134683_NEGATIVE 197 50 4 143 89 NC_003454:FN1782|3end_Phosphocarrier_protein_HPr_264221..264371_NEGATIVE 197 107 78 96 54 NC_003454:FN1724|3end_Potassium_uptake_protein_KtrA_222654..222804_NEGATIVE 195 39 1 59 20 NC_003454:FN1056|3end_hypothetical_protein_1704372..1704522_POSITIVE