Origin IGS: acaaacctccttttctttatatattaattttaccataaaaagagaagaacaaataacaagaactcaattaatcatatggaaaattcttcgtatgtatcttttcctaaataaattagtgtt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aacactaatttatttaggaaaagatacatacgaagaattttccatatgattaattgagttcttgttatttgttcttctctttttatggtaaaattaatatataaagaaaaggaggtttgt Mask Tandem Repeat Region ================================================ acaaacctccttttctttatatattaattttaccataaaaagagaagaacaaataacaagaactcaattaatcatatggaaaattcttcgtatgtatcttttcctaaataaattagtgtt Find is-nt database================================================ Query_seq: SSA_1757:SSA_1758|SSA_1757:SSA_1758:hypothetical protein:hypothetical protein:<-<-:1745981..1746100 120 acaaacctccttttctttatatattaattttaccataaaaagagaagaacaaataacaagaactcaattaatcatatggaaaattcttcgtatgtatcttttcctaaataaattagtgtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1757:SSA_1758|SSA_1757:SSA_1758:hypothetical protein:hypothetical protein:<-<-:1745981..1746100 120 acaaacctccttttctttatatattaattttaccataaaaagagaagaacaaataacaagaactcaattaatcatatggaaaattcttcgtatgtatcttttcctaaataaattagtgtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1757:SSA_1758|SSA_1757:SSA_1758:hypothetical protein:hypothetical protein:<-<-:1745981..1746100 120 acaaacctccttttctttatatattaattttaccataaaaagagaagaacaaataacaagaactcaattaatcatatggaaaattcttcgtatgtatcttttcctaaataaattagtgtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 acaaacctccttttctttatatattaattttaccataaaaagagaagaacaaataacaagaactcaattaatcatatggaaaattcttcgtatgtatcttttcctaaataaattagtgtt Predict ORF larger than 30AA ================================================ Protein_Len: 32 Strand: + Start: 23 End: 118 ...................... M N F T I K R E E Q I T R T Q L I I W K I L R M Y L F L N K L V .. acaaacctccttttctttatatattaattttaccataaaaagagaagaacaaataacaagaactcaattaatcatatggaaaattcttcgtatgtatcttttcctaaataaattagtgtt 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================================================ acaaacctccttttctttatatattaattttaccataaaaagagaagaacaaataacaagaactcaattaatcatatggaaaattcttcgtatgtatcttttcctaaataaattagtgtt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_1757:SSA_1758|SSA_1757:SSA_1758:hypothetical protein:hypothetical protein:<-<-:1745981..1746100 120 acaaacctccttttctttatatattaattttaccataaaaagagaagaacaaataacaagaactcaattaatcatatggaaaattcttcgtatgtatcttttcctaaataaattagtgtt Intra-Species Hit: Count: 1 Min: 1 Max: 120 Len: 120 Subject: NC_009009_SSA_1757_SSA_1758|hypothetical protein:hypothetical protein|NEGATIVE:NEGATIVE|[1745981,1746100]|120 HSP 1 e-value: 3.0E-62 bit: 238.0 Len: 120 Query Start:1 Query End:120 Subject Strand: POSITIVE Subject Start: 1 Subject End: 120 acaaacctccttttctttatatattaattttaccataaaaagagaagaacaaataacaagaactcaattaatcatatggaaaattcttcgtatgtatcttttcctaaataaattagtgtt acaaacctccttttctttatatattaattttaccataaaaagagaagaacaaataacaagaactcaattaatcatatggaaaattcttcgtatgtatcttttcctaaataaattagtgtt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACAAACCUCCUUUUCUUUAUAUAUUAAUUUUACCAUAAAAAGAGAAGAACAAAUAACAAGAACUCAAUUAAUCAUAUGGAAAAUUCUUCGUAUGUAUCUUUUCCUAAAUAAAUUAGUGUU ....................((((((((((...........(((((((...........(....).......((((((((......))))))))..)))))))......)))))))))). (-13.73) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AACACUAAUUUAUUUAGGAAAAGAUACAUACGAAGAAUUUUCCAUAUGAUUAAUUGAGUUCUUGUUAUUUGUUCUUCUCUUUUUAUGGUAAAAUUAAUAUAUAAAGAAAAGGAGGUUUGU ....((((.....))))...((((.(((.((.((((((((...............))))))))))....)))))))((((((((...(((.........)))....))))))))...... (-14.76) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 732 90 41 181 132 NC_009009:SSA_1757|5end_hypothetical_protein_1745890..1746120_NEGATIVE 257 48 6 142 92 NC_009009:SSA_0553|5end_hypothetical_protein_548911..549141_POSITIVE 235 105 62 108 58 NC_009009:SSA_0871|5end_Cell_division_protein_FtsX,_putative_863621..863851_POSITIVE 228 48 6 156 98 NC_009009:SSA_0135|5end_Multiple_antibiotic_resistance_operon_transcriptional_repressor_(MarR),_putative_130574..130804_POSITIVE 220 49 5 143 98 NC_009009:SSA_0009|5end_Ribosome-associated_heat_shock_protein_(S4),_putative_9165..9395_POSITIVE 195 105 68 102 69 NC_009009:SSA_0343|5end_DNA-damage-inducible_protein_P,_putative_337525..337755_POSITIVE 194 116 76 223 179 NC_009009:SSA_2021|5end_hypothetical_protein_2023534..2023764_NEGATIVE 194 83 41 216 180 NC_009009:SSA_1851|5end_Guanylate_kinase,_putative_1846682..1846912_NEGATIVE 193 65 32 40 3 NC_009009:SSA_0231|5end_Conserved_uncharacterized_protein_225713..225943_POSITIVE 187 50 8 114 69 NC_009009:SSA_1068|5end_Transcriptional_regulator,_LysR_family_(capsular_polysaccharide_biosynthesis_regulation),_putative_1087355..1087585_POSITIVE 186 37 1 134 94 NC_009009:SSA_1985|5end_hypothetical_protein_1981773..1982003_NEGATIVE 186 47 7 142 99 NC_009009:SSA_1921|5end_hypothetical_protein_1910875..1911105_POSITIVE 186 105 74 196 164 NC_009009:SSA_1498|5end_50S_ribosomal_protein_L20,_putative_1504112..1504342_NEGATIVE 186 37 6 135 99 NC_009009:SSA_0384|5end_hypothetical_protein_376240..376470_POSITIVE 183 38 1 134 90 NC_009009:SSA_1984|5end_Cell_surface_SD_repeat_antigen_precursor,_putative_1979035..1979265_NEGATIVE 183 49 5 146 97 NC_009009:SSA_1464|5end_3-phosphoshikimate_1-carboxyvinyltransferase,_putative_1471516..1471746_NEGATIVE 181 112 80 114 80 NC_009009:SSA_2205|5end_Transcription_antitermination_factor_NusG,_putative_2206100..2206330_NEGATIVE 181 65 27 127 90 NC_009009:SSA_1770|5end_hypothetical_protein_1758431..1758661_NEGATIVE 181 114 85 218 180 NC_009009:SSA_1075|5end_Coproporphyrinogen_III_oxidase,_putative_1093093..1093323_POSITIVE 181 48 7 147 100 NC_009009:SSA_0820|5end_Ribosomal_protein_S21,_putative_801249..801479_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 257 48 6 52 2 NC_009009:SSA_0552|3end_Cof_family_protein,_putative_548901..549051_POSITIVE 243 35 1 80 47 NC_009009:SSA_1759|3end_hypothetical_protein_1746664..1746814_NEGATIVE 235 105 62 115 65 NC_009009:SSA_0870|3end_Cell_division_protein_FtsE,_putative_863708..863858_POSITIVE 220 49 5 52 7 NC_009009:SSA_0008|3end_Transcription-repair_coupling_factor,_putative_9154..9304_POSITIVE 196 118 75 40 7 NC_009009:SSA_1783|3end_Xanthosine_triphosphate_pyrophosphatase_(NTPase/HAM1_family),_putative_1768102..1768252_NEGATIVE 186 47 7 71 28 NC_009009:SSA_1920|3end_Phosphotransferase_system,_mannose-specific_EIID,_putative_1910884..1911034_POSITIVE 186 105 74 151 119 NC_009009:SSA_1499|3end_50S_ribosomal_protein_L35,_putative_1504157..1504307_NEGATIVE 181 65 27 67 30 NC_009009:SSA_1771|3end_Conserved_DNA_methyltransferase_protein,_putative_1758491..1758641_NEGATIVE 181 114 85 79 41 NC_009009:SSA_1074|3end_Pyrroline-5-carboxylate_reductase,_putative_1093034..1093184_POSITIVE 174 86 42 61 9 NC_009009:SSA_0032|3end_Phosphoribosylformylglycinamidine_cyclo-ligase,_putative_39040..39190_POSITIVE 171 106 67 107 77 NC_009009:SSA_0632|3end_Anthranilate_synthase_component_I,_putative_622896..623046_POSITIVE 170 23 1 97 68 NC_009009:SSA_1897|3end_Ribosomal_protein_HS6-type_(S12/L30/L7a),_putative_1894154..1894304_NEGATIVE 167 118 72 118 71 NC_009009:SSA_2369|3end_hypothetical_protein_2370239..2370389_NEGATIVE 166 107 63 110 63 NC_009009:SSA_0914|3end_Phenylalanyl-tRNA_synthetase_beta_chain,_putative_927437..927587_POSITIVE 165 104 72 119 91 NC_009009:SSA_1712|3end_Arsenate_reductase_(ArsC),_glutaredoxin_family,_putative_1699731..1699881_NEGATIVE 165 106 70 146 103 NC_009009:SSA_0556|3end_hypothetical_protein_551922..552072_POSITIVE 164 47 6 133 102 NC_009009:SSA_0075|3end_ABC_sugar_transporter,_permease_protein,_putative_79927..80077_POSITIVE 159 30 2 84 51 NC_009009:SSA_1328|3end_hypothetical_protein_1344342..1344492_NEGATIVE 159 46 1 128 85 NC_009009:SSA_0967|3end_hypothetical_protein_976620..976770_POSITIVE 156 34 5 117 88 NC_009009:SSA_1728|3end_ABC_transporter_membrane-spanning_permease-branched_chain_amino_acid_transport,_putative_1713424..1713574_NEGATIVE