Origin IGS: aacttgaatacttgataagaatttcttataattttataggaatgttaagtgaaacaaagttgaatttgtaattaaaattttttgtattttacgaaaggagaatagtgattt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aaatcactattctcctttcgtaaaatacaaaaaattttaattacaaattcaactttgtttcacttaacattcctataaaattataagaaattcttatcaagtattcaagtt Mask Tandem Repeat Region ================================================ aacttgaatacttgataagaatttcttataattttataggaatgttaagtgaaacaaagttgaatttgtaattaaaattttttgtattttacgaaaggagaatagtgattt Find is-nt database================================================ Query_seq: SSA_1764:SSA_2385|SSA_1764:SSA_2385:hypothetical protein:hypothetical protein:->->:1752571..1752681 111 aacttgaatacttgataagaatttcttataattttataggaatgttaagtgaaacaaagttgaatttgtaattaaaattttttgtattttacgaaaggagaatagtgattt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1764:SSA_2385|SSA_1764:SSA_2385:hypothetical protein:hypothetical protein:->->:1752571..1752681 111 aacttgaatacttgataagaatttcttataattttataggaatgttaagtgaaacaaagttgaatttgtaattaaaattttttgtattttacgaaaggagaatagtgattt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1764:SSA_2385|SSA_1764:SSA_2385:hypothetical protein:hypothetical protein:->->:1752571..1752681 111 aacttgaatacttgataagaatttcttataattttataggaatgttaagtgaaacaaagttgaatttgtaattaaaattttttgtattttacgaaaggagaatagtgattt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aacttgaatacttgataagaatttcttataattttataggaatgttaagtgaaacaaagttgaatttgtaattaaaattttttgtattttacgaaaggagaatagtgattt Predict ORF larger than 30AA ================================================ aacttgaatacttgataagaatttcttataattttataggaatgttaagtgaaacaaagttgaatttgtaattaaaattttttgtattttacgaaaggagaatagtgattt 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: 88 Start: 3 End: 32 ..CTTGAATACTTGATAAGAATTTCTTATAAT............................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aacttgaatacttgataagaatttcttataattttataggaatgttaagtgaaacaaagttgaatttgtaattaaaattttttgtattttacgaaaggagaatagtgattt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_1764:SSA_2385|SSA_1764:SSA_2385:hypothetical protein:hypothetical protein:->->:1752571..1752681 111 aacttgaatacttgataagaatttcttataattttataggaatgttaagtgaaacaaagttgaatttgtaattaaaattttttgtattttacgaaaggagaatagtgattt Intra-Species Hit: Count: 1 Min: 1 Max: 111 Len: 111 Subject: NC_009009_SSA_1764_SSA_2385|hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[1752571,1752681]|111 HSP 1 e-value: 7.0E-57 bit: 220.0 Len: 111 Query Start:1 Query End:111 Subject Strand: POSITIVE Subject Start: 1 Subject End: 111 aacttgaatacttgataagaatttcttataattttataggaatgttaagtgaaacaaagttgaatttgtaattaaaattttttgtattttacgaaaggagaatagtgattt aacttgaatacttgataagaatttcttataattttataggaatgttaagtgaaacaaagttgaatttgtaattaaaattttttgtattttacgaaaggagaatagtgattt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AACUUGAAUACUUGAUAAGAAUUUCUUAUAAUUUUAUAGGAAUGUUAAGUGAAACAAAGUUGAAUUUGUAAUUAAAAUUUUUUGUAUUUUACGAAAGGAGAAUAGUGAUUU ........(((((((((.....((((((((....)))))))))))))))))..(((((......)))))...............((((((.(....).))))))....... (-17.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAUCACUAUUCUCCUUUCGUAAAAUACAAAAAAUUUUAAUUACAAAUUCAACUUUGUUUCACUUAACAUUCCUAUAAAAUUAUAAGAAAUUCUUAUCAAGUAUUCAAGUU .......................(((((...........................((((......)))).............(((((.....)))))...)))))...... ( -5.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 197 69 25 190 150 NC_009009:SSA_1995|5end_hypothetical_protein_1993358..1993588_NEGATIVE 182 47 2 179 139 NC_009009:SSA_0108|5end_50S_ribosomal_protein_L4,_putative_108816..109046_POSITIVE 165 69 36 154 125 NC_009009:SSA_0465|5end_Precorrin-8X_methylmutase_/_precorrin_isomerase,_putative_469185..469415_POSITIVE 163 38 11 219 187 NC_009009:SSA_1106|5end_IgA-specific_metalloendopeptidase_1125974..1126204_POSITIVE 162 55 28 196 164 NC_009009:SSA_0915|5end_hypothetical_protein_927542..927772_POSITIVE 161 106 83 191 160 NC_009009:SSA_1420|5end_Homoserine_O-succinyltransferase,_putative_1430625..1430855_NEGATIVE 158 58 11 218 173 NC_009009:SSA_1866|5end_hypothetical_protein_1862182..1862412_NEGATIVE 158 70 22 217 169 NC_009009:SSA_1741|5end_ABC-type_Fe3+-siderophores_transporter,_ATPase_component,_putative_1728007..1728237_POSITIVE 157 69 23 157 111 NC_009009:SSA_1216|5end_AT-rich_DNA-binding_protein,_possible_redox-sensing_transcriptional_repressor,_putative_1238292..1238522_POSITIVE 157 47 4 125 82 NC_009009:SSA_1119|5end_Two-component_response_transcriptional_regulator_(CheY-like_receiver_and_AraC-type_DNA-binding_domains),_putative_1144491..1144721_POSITIVE 156 101 61 182 142 NC_009009:SSA_1915|5end_hypothetical_protein_1905440..1905670_NEGATIVE 152 56 18 90 59 NC_009009:SSA_0666|5end_hypothetical_protein_649788..650018_NEGATIVE 149 110 61 222 170 NC_009009:SSA_0755|5end_hypothetical_protein_736212..736442_POSITIVE 148 110 83 143 111 NC_009009:SSA_1367|5end_hypothetical_protein_1383593..1383823_POSITIVE 147 100 77 115 90 NC_009009:SSA_1208|5end_23S_rRNA_pseudouridine_synthase,_putative_1233185..1233415_NEGATIVE 145 70 25 182 133 NC_009009:SSA_0445|5end_hypothetical_protein_444487..444717_POSITIVE 143 102 66 159 124 NC_009009:SSA_1687|5end_NADH-binding_ferric-oxidoreductase,_putative_1680547..1680777_POSITIVE 142 101 64 153 109 NC_009009:SSA_2056|5end_Cinnamoyl_ester_hydrolase,_putative_2058587..2058817_POSITIVE 142 107 73 158 128 NC_009009:SSA_1624|5end_hypothetical_protein_1626070..1626300_POSITIVE 142 73 35 77 43 NC_009009:SSA_0872|5end_Zn-dependent_hydrolases,_including_glyoxylases,_putative_865305..865535_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 197 69 25 69 29 NC_009009:SSA_1996|3end_DNA-directed_RNA_polymerase_delta_subunit,_putative_1993479..1993629_NEGATIVE 182 50 1 81 30 NC_009009:SSA_1764|3end_hypothetical_protein_1752510..1752660_POSITIVE 169 110 61 51 6 NC_009009:SSA_1170|3end_hypothetical_protein_1196933..1197083_NEGATIVE 166 47 2 139 97 NC_009009:SSA_1186|3end_Acetyltransferase,_CysE/LacA/Lpx_A/NodL_family,_putative_1214656..1214806_NEGATIVE 165 69 36 144 115 NC_009009:SSA_0464|3end_Cobalamin_biosynthesis_protein_cobD,_putative_469255..469405_POSITIVE 161 106 83 43 12 NC_009009:SSA_1421|3end_Adenine_phosphoribosyltransferase,_putative_1430773..1430923_NEGATIVE 158 58 11 47 2 NC_009009:SSA_1867|3end_ABC-type_polar_amino_acid_transport_system,_ATPase_component,_putative_1862353..1862503_NEGATIVE 157 101 79 84 58 NC_009009:SSA_1350|3end_hypothetical_protein_1366945..1367095_NEGATIVE 157 47 4 65 22 NC_009009:SSA_1118|3end_Peptide_methionine_sulfoxide_reductase,_putative_1144511..1144661_POSITIVE 156 54 23 82 49 NC_009009:SSA_1242|3end_Dihydroorotate_dehydrogenase_B,_putative_1266448..1266598_NEGATIVE 156 61 22 112 67 NC_009009:SSA_0358|3end_hypothetical_protein_351288..351438_NEGATIVE 151 108 80 110 81 NC_009009:SSA_1624|3end_hypothetical_protein_1626497..1626647_POSITIVE 147 100 77 118 93 NC_009009:SSA_1209|3end_Inorganic_polyphosphate/ATP-NAD_kinase,_putative_1233182..1233332_NEGATIVE 146 44 2 151 114 NC_009009:SSA_0107|3end_50S_ribosomal_protein_L3,_putative_108871..109021_POSITIVE 141 51 11 114 67 NC_009009:SSA_2304|3end_Conserved_uncharacterized_protein_2305185..2305335_NEGATIVE 140 70 22 57 1 NC_009009:SSA_1968|3end_Ketol-acid_reductoisomerase,_putative_1963659..1963809_NEGATIVE 137 104 65 137 101 NC_009009:SSA_1508|3end_ABC-type_lipopolysaccharide_transport_system,_permease_component,_putative_1512444..1512594_NEGATIVE 136 27 4 149 127 NC_009009:SSA_0734|3end_Arsenical_resistance_operon_transcription_repressor_(ArsR),_putative_717196..717346_POSITIVE 135 60 33 40 12 NC_009009:SSA_1276|3end_Conserved_uncharacterized_protein_1298156..1298306_NEGATIVE 135 110 92 34 13 NC_009009:SSA_1150|3end_Tautomerase,_putative_1179894..1180044_NEGATIVE