Origin IGS: gatagactcctttcctgatgttagaaatatttaacactttttatgttataaatatatcacacagcgatttataaatcaagtatttatgtgctaaggtggcaattatttgaaaaaattctataataaaagcccttgccagataaataaccagcaaggtcctatgtttttattgattattcaagaatagcaaagtccc .........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 gggactttgctattcttgaataatcaataaaaacataggaccttgctggttatttatctggcaagggcttttattatagaattttttcaaataattgccaccttagcacataaatacttgatttataaatcgctgtgtgatatatttataacataaaaagtgttaaatatttctaacatcaggaaaggagtctatc Mask Tandem Repeat Region ================================================ gatagactcctttcctgatgttagaaatatttaacactttttatgttataaatatatcacacagcgatttataaatcaagtatttatgtgctaaggtggcaattatttgaaaaaattctataataaaagcccttgccagataaataaccagcaaggtcctatgtttttattgattattcaagaatagcaaagtccc Find is-nt database================================================ Query_seq: SSA_2297:SSA_2298|SSA_2297:SSA_2298:hypothetical protein:Serine protease containing a PDZ domain, putative:<-<-:2299463..2299658 196 gatagactcctttcctgatgttagaaatatttaacactttttatgttataaatatatcacacagcgatttataaatcaagtatttatgtgctaaggtggcaattatttgaaaaaattctataataaaagcccttgccagataaataaccagcaaggtcctatgtttttattgattattcaagaatagcaaagtccc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_2297:SSA_2298|SSA_2297:SSA_2298:hypothetical protein:Serine protease containing a PDZ domain, putative:<-<-:2299463..2299658 196 gatagactcctttcctgatgttagaaatatttaacactttttatgttataaatatatcacacagcgatttataaatcaagtatttatgtgctaaggtggcaattatttgaaaaaattctataataaaagcccttgccagataaataaccagcaaggtcctatgtttttattgattattcaagaatagcaaagtccc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_2297:SSA_2298|SSA_2297:SSA_2298:hypothetical protein:Serine protease containing a PDZ domain, putative:<-<-:2299463..2299658 196 gatagactcctttcctgatgttagaaatatttaacactttttatgttataaatatatcacacagcgatttataaatcaagtatttatgtgctaaggtggcaattatttgaaaaaattctataataaaagcccttgccagataaataaccagcaaggtcctatgtttttattgattattcaagaatagcaaagtccc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gatagactcctttcctgatgttagaaatatttaacactttttatgttataaatatatcacacagcgatttataaatcaagtatttatgtgctaaggtggcaattatttgaaaaaattctataataaaagcccttgccagataaataaccagcaaggtcctatgtttttattgattattcaagaatagcaaagtccc Predict ORF larger than 30AA ================================================ Protein_Len: 37 Strand: - Start: 44 End: 154 ........................................... T I F I D C L S K Y I L Y K H A L T A I I Q F F E I I F A R A L Y I V L M .......................................... gatagactcctttcctgatgttagaaatatttaacactttttatgttataaatatatcacacagcgatttataaatcaagtatttatgtgctaaggtggcaattatttgaaaaaattctataataaaagcccttgccagataaataaccagcaaggtcctatgtttttattgattattcaagaatagcaaagtccc 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: 83 Start: 51 End: 80 ..................................................CTTGATTTATAAATCGCTGTGTGATATATT.................................................................................................................... PromScan Matrix: RpoD-17 Strand: + Score: 83 Start: 95 End: 124 ..............................................................................................GGTGGCAATTATTTGAAAAAATTCTATAAT........................................................................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gatagactcctttcctgatgttagaaatatttaacactttttatgttataaatatatcacacagcgatttataaatcaagtatttatgtgctaaggtggcaattatttgaaaaaattctataataaaagcccttgccagataaataaccagcaaggtcctatgtttttattgattattcaagaatagcaaagtccc Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 70 HP_score: -4.9 Tail_Score: -4.78839 Start: 129 End: 158 Full_Region: tcaataaaaacatag gaccttgctggtt attt atctggcaagggc ttttattatagaatt ................................................................................................................................gaccttgctggttatttatctggcaagggc...................................... Find igs database================================================ Query_seq: SSA_2297:SSA_2298|SSA_2297:SSA_2298:hypothetical protein:Serine protease containing a PDZ domain, putative:<-<-:2299463..2299658 196 gatagactcctttcctgatgttagaaatatttaacactttttatgttataaatatatcacacagcgatttataaatcaagtatttatgtgctaaggtggcaattatttgaaaaaattctataataaaagcccttgccagataaataaccagcaaggtcctatgtttttattgattattcaagaatagcaaagtccc Intra-Species Hit: Count: 1 Min: 1 Max: 196 Len: 196 Subject: NC_009009_SSA_2297_SSA_2298|hypothetical protein:Serine protease containing a PDZ domain, putative|NEGATIVE:NEGATIVE|[2299463,2299658]|196 HSP 1 e-value: 1.0E-107 bit: 389.0 Len: 196 Query Start:1 Query End:196 Subject Strand: POSITIVE Subject Start: 1 Subject End: 196 gatagactcctttcctgatgttagaaatatttaacactttttatgttataaatatatcacacagcgatttataaatcaagtatttatgtgctaaggtggcaattatttgaaaaaattctataataaaagcccttgccagataaataaccagcaaggtcctatgtttttattgattattcaagaatagcaaagtccc gatagactcctttcctgatgttagaaatatttaacactttttatgttataaatatatcacacagcgatttataaatcaagtatttatgtgctaaggtggcaattatttgaaaaaattctataataaaagcccttgccagataaataaccagcaaggtcctatgtttttattgattattcaagaatagcaaagtccc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAUAGACUCCUUUCCUGAUGUUAGAAAUAUUUAACACUUUUUAUGUUAUAAAUAUAUCACACAGCGAUUUAUAAAUCAAGUAUUUAUGUGCUAAGGUGGCAAUUAUUUGAAAAAAUUCUAUAAUAAAAGCCCUUGCCAGAUAAAUAACCAGCAAGGUCCUAUGUUUUUAUUGAUUAUUCAAGAAUAGCAAAGUCCC ....((((((((..(((.(((..((.(((((((..((.......))..))))))).))..)))..((((....))))...(((((((.((...(((.(((..(((((.(((....)))...)))))..))))))..)).)))))))..))).)))).....((((....((((....))))....)))).)))).. (-32.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GGGACUUUGCUAUUCUUGAAUAAUCAAUAAAAACAUAGGACCUUGCUGGUUAUUUAUCUGGCAAGGGCUUUUAUUAUAGAAUUUUUUCAAAUAAUUGCCACCUUAGCACAUAAAUACUUGAUUUAUAAAUCGCUGUGUGAUAUAUUUAUAACAUAAAAAGUGUUAAAUAUUUCUAACAUCAGGAAAGGAGUCUAUC .(((((((....(((((((.................(((..(((((..(........)..)))))(((..(((((...(((....))).)))))..))).)))((((((..........((((....))))..(((((.(((....))).)))))....)))))).............))))))).)))))))... (-42.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 795 100 51 191 142 NC_009009:SSA_2297|5end_hypothetical_protein_2299372..2299602_NEGATIVE 336 166 123 76 24 NC_009009:SSA_0218|5end_Sugar-binding_periplasmic_protein,_putative_213863..214093_POSITIVE 282 163 128 179 143 NC_009009:SSA_0088|5end_V-type_sodium_ATPase,_subunit_C,_putative_88930..89160_POSITIVE 268 161 128 48 7 NC_009009:SSA_2353|5end_ABC-type_nitrate/sulfonate/bicarbonate_transport_system,_permease_component,_putative_2355302..2355532_NEGATIVE 267 165 128 38 5 NC_009009:SSA_0852|5end_ATP-dependent_DNA_helicase,_putative_839050..839280_POSITIVE 255 156 116 143 101 NC_009009:SSA_0172|5end_Transcriptional_regulator,_XRE_family,_putative_169140..169370_POSITIVE 252 159 126 55 14 NC_009009:SSA_0069|5end_Hypothetical_protein,_possibly_membrane-associated_73037..73267_POSITIVE 251 168 126 116 59 NC_009009:SSA_0977|5end_3-isopropylmalate_dehydrogenase,_putative_982771..983001_POSITIVE 248 166 128 68 30 NC_009009:SSA_0389|5end_hypothetical_protein_384172..384402_POSITIVE 247 156 116 143 100 NC_009009:SSA_1408|5end_hypothetical_protein_1421005..1421235_NEGATIVE 241 171 132 113 69 NC_009009:SSA_2138|5end_RNA-binding_protein,_Jag_family,_putative_2139487..2139717_NEGATIVE 240 174 135 230 175 NC_009009:SSA_0962|5end_Lactoylglutathione_lyase,_putative_970965..971195_POSITIVE 234 158 112 177 113 NC_009009:SSA_2334|5end_D-alanine--D-alanyl_carrier_protein_ligase,_putative_2338007..2338237_NEGATIVE 231 177 133 176 129 NC_009009:SSA_1648|5end_hypothetical_protein_1647909..1648139_NEGATIVE 229 163 131 57 28 NC_009009:SSA_1676|5end_Transcriptional_regulator,_LytTr_family,_putative_1671313..1671543_NEGATIVE 229 162 131 137 101 NC_009009:SSA_1017|5end_hypothetical_protein_1022072..1022302_POSITIVE 229 189 148 110 58 NC_009009:SSA_0554|5end_hypothetical_protein_549265..549495_POSITIVE 228 190 148 161 126 NC_009009:SSA_1891|5end_Oxidoreductase,_aldo/keto_reductase_family,_putative_1888991..1889221_NEGATIVE 228 168 123 159 113 NC_009009:SSA_0691|5end_D-ala,D-ala_ligase,_putative_675233..675463_POSITIVE 227 157 131 25 1 NC_009009:SSA_2083|5end_hypothetical_protein_2087969..2088199_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 336 166 123 79 27 NC_009009:SSA_0217|3end_Two-component_system_transcriptional_regulator_(CheY_domain_and_HTH-like_DNA-binding_domain),_putative_213946..214096_POSITIVE 260 176 135 118 61 NC_009009:SSA_0961|3end_Possible_ketopantoate_reductase_PanE/ApbA,_putative_970931..971081_POSITIVE 255 167 128 81 41 NC_009009:SSA_0921|3end_Zn-dependeant_threonine_dehydrogenase,_putative_932164..932314_POSITIVE 248 166 128 64 26 NC_009009:SSA_0388|3end_Mismatch_repair_ATPase_(MutS_family),_putative_384248..384398_POSITIVE 241 171 132 91 47 NC_009009:SSA_2139|3end_Membrane_protein_(preprotein_translocase)_oxaA_1_precursor,_putative_2139509..2139659_NEGATIVE 233 69 35 150 111 NC_009009:SSA_1821|3end_Acetyltransferase_(N-acetylase_of_ribosomal_proteins),_putative_1810047..1810197_NEGATIVE 232 180 132 93 45 NC_009009:SSA_0931|3end_hypothetical_protein_941335..941485_POSITIVE 229 163 131 34 5 NC_009009:SSA_1678|3end_ABC-type_multidrug_transport_system,_permease_component,_putative_1671336..1671486_NEGATIVE 229 188 146 108 61 NC_009009:SSA_1498|3end_50S_ribosomal_protein_L20,_putative_1503753..1503903_NEGATIVE 229 162 131 150 114 NC_009009:SSA_1016|3end_Phosphoenolpyruvate_synthase,_putative_1022165..1022315_POSITIVE 229 189 148 106 54 NC_009009:SSA_0553|3end_hypothetical_protein_549341..549491_POSITIVE 228 190 148 84 49 NC_009009:SSA_1892|3end_hypothetical_protein_1889068..1889218_NEGATIVE 226 161 126 148 118 NC_009009:SSA_0923|3end_Transcriptional_regulator,_TetR/AcrR_family,_putative_933698..933848_POSITIVE 223 171 131 102 59 NC_009009:SSA_1069|3end_Lipoprotein_signal_peptidase,_putative_1088838..1088988_POSITIVE 223 166 125 92 46 NC_009009:SSA_0690|3end_Recombinational_DNA_repair_protein_(RecF_pathway),_putative_675108..675258_POSITIVE 221 100 57 81 35 NC_009009:SSA_2287|3end_50S_ribosomal_protein_L32,_putative_2290083..2290233_POSITIVE 218 160 117 64 30 NC_009009:SSA_1256|3end_NAD-dependent_deacetylase,_putative_1282357..1282507_NEGATIVE 214 170 126 94 49 NC_009009:SSA_0385|3end_ABC_transporter,_glycine-betaine/proline_permease_protein,_putative_378526..378676_NEGATIVE 211 189 148 110 77 NC_009009:SSA_0319|3end_Branched-chain_amino_acid_permease_(L-methionine,_L-isoleucine,_leucine_and_valine),_putative_313496..313646_POSITIVE 210 187 148 96 49 NC_009009:SSA_0578|3end_Nicotinate-nucleotide_adenylyltransferase,_putative_572303..572453_POSITIVE