Origin IGS: tacgcaacctcttaactctgaaaacgttttataactaactacattataacatgattaaagcaaaaatagacttaatttgcctattttttagaaaacaaactgtttttcagtttcattttcagtgttttacaacagatgaaattttagggcgaaagcgggaacagacttgatcttagatgccggccaataaaaaatcagggcagaatctttattccaccctgatttcactttttaaaatgattttag .........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 ctaaaatcattttaaaaagtgaaatcagggtggaataaagattctgccctgattttttattggccggcatctaagatcaagtctgttcccgctttcgccctaaaatttcatctgttgtaaaacactgaaaatgaaactgaaaaacagtttgttttctaaaaaataggcaaattaagtctatttttgctttaatcatgttataatgtagttagttataaaacgttttcagagttaagaggttgcgta Mask Tandem Repeat Region ================================================ tacgcaacctcttaactctgaaaacgttttataactaactacattataacatgattaaagcaaaaatagacttaatttgcctattttttagaaaacaaactgtttttcagtttcattttcagtgttttacaacagatgaaattttagggcgaaagcgggaacagacttgatcttagatgccggccaataaaaaatcagggcagaatctttattccaccctgatttcactttttaaaatgattttag Find is-nt database================================================ Query_seq: SSA_1749:SSA_1750|SSA_1749:SSA_1750:Pyruvate formate-lyase-activating enzyme, putative:Extracellular nuclease, putative:<-<-:1735517..1735762 246 tacgcaacctcttaactctgaaaacgttttataactaactacattataacatgattaaagcaaaaatagacttaatttgcctattttttagaaaacaaactgtttttcagtttcattttcagtgttttacaacagatgaaattttagggcgaaagcgggaacagacttgatcttagatgccggccaataaaaaatcagggcagaatctttattccaccctgatttcactttttaaaatgattttag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1749:SSA_1750|SSA_1749:SSA_1750:Pyruvate formate-lyase-activating enzyme, putative:Extracellular nuclease, putative:<-<-:1735517..1735762 246 tacgcaacctcttaactctgaaaacgttttataactaactacattataacatgattaaagcaaaaatagacttaatttgcctattttttagaaaacaaactgtttttcagtttcattttcagtgttttacaacagatgaaattttagggcgaaagcgggaacagacttgatcttagatgccggccaataaaaaatcagggcagaatctttattccaccctgatttcactttttaaaatgattttag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1749:SSA_1750|SSA_1749:SSA_1750:Pyruvate formate-lyase-activating enzyme, putative:Extracellular nuclease, putative:<-<-:1735517..1735762 246 tacgcaacctcttaactctgaaaacgttttataactaactacattataacatgattaaagcaaaaatagacttaatttgcctattttttagaaaacaaactgtttttcagtttcattttcagtgttttacaacagatgaaattttagggcgaaagcgggaacagacttgatcttagatgccggccaataaaaaatcagggcagaatctttattccaccctgatttcactttttaaaatgattttag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tacgcaacctcttaactctgaaaacgttttataactaactacattataacatgattaaagcaaaaatagacttaatttgcctattttttagaaaacaaactgtttttcagtttcattttcagtgttttacaacagatgaaattttagggcgaaagcgggaacagacttgatcttagatgccggccaataaaaaatcagggcagaatctttattccaccctgatttcactttttaaaatgattttag Predict ORF larger than 30AA ================================================ Protein_Len: 39 Strand: + Start: 51 End: 167 .................................................. M I K A K I D L I C L F F R K Q T V F Q F H F Q C F T T D E I L G R K R E Q T ............................................................................... Protein_Len: 33 Strand: - Start: 130 End: 228 ................................................................................................................................. L L H F K L A F A P V S K I K S A P W Y F I L A S D K N W G S K M .................. tacgcaacctcttaactctgaaaacgttttataactaactacattataacatgattaaagcaaaaatagacttaatttgcctattttttagaaaacaaactgtttttcagtttcattttcagtgttttacaacagatgaaattttagggcgaaagcgggaacagacttgatcttagatgccggccaataaaaaatcagggcagaatctttattccaccctgatttcactttttaaaatgattttag 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================================================ tacgcaacctcttaactctgaaaacgttttataactaactacattataacatgattaaagcaaaaatagacttaatttgcctattttttagaaaacaaactgtttttcagtttcattttcagtgttttacaacagatgaaattttagggcgaaagcgggaacagacttgatcttagatgccggccaataaaaaatcagggcagaatctttattccaccctgatttcactttttaaaatgattttag Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 73 HP_score: -7.0 Tail_Score: -3.99805 Start: 195 End: 222 Full_Region: CCGGCCAATAAAAAA TCAGGGCAGAAT CTTT ATTCCACCCTGA TTTCACTTTTTAAAA ..................................................................................................................................................................................................TCAGGGCAGAATCTTTATTCCACCCTGA........................ Find igs database================================================ Query_seq: SSA_1749:SSA_1750|SSA_1749:SSA_1750:Pyruvate formate-lyase-activating enzyme, putative:Extracellular nuclease, putative:<-<-:1735517..1735762 246 tacgcaacctcttaactctgaaaacgttttataactaactacattataacatgattaaagcaaaaatagacttaatttgcctattttttagaaaacaaactgtttttcagtttcattttcagtgttttacaacagatgaaattttagggcgaaagcgggaacagacttgatcttagatgccggccaataaaaaatcagggcagaatctttattccaccctgatttcactttttaaaatgattttag Intra-Species Hit: Count: 1 Min: 1 Max: 246 Len: 246 Subject: NC_009009_SSA_1749_SSA_1750|Pyruvate formate-lyase-activating enzyme, putative:Extracellular nuclease, putative|NEGATIVE:NEGATIVE|[1735517,1735762]|246 HSP 1 e-value: 2.0E-50 bit: 200.0 Len: 101 Query Start:146 Query End:246 Subject Strand: POSITIVE Subject Start: 146 Subject End: 246 .................................................................................................................................................agggcgaaagcgggaacagacttgatcttagatgccggccaataaaaaatcagggcagaatctttattccaccctgatttcactttttaaaatgattttag .................................................................................................................................................agggcgaaagcgggaacagacttgatcttagatgccggccaataaaaaatcagggcagaatctttattccaccctgatttcactttttaaaatgattttag HSP 2 e-value: 9.0E-40 bit: 165.0 Len: 83 Query Start:1 Query End:83 Subject Strand: POSITIVE Subject Start: 1 Subject End: 83 tacgcaacctcttaactctgaaaacgttttataactaactacattataacatgattaaagcaaaaatagacttaatttgccta................................................................................................................................................................... tacgcaacctcttaactctgaaaacgttttataactaactacattataacatgattaaagcaaaaatagacttaatttgccta................................................................................................................................................................... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UACGCAACCUCUUAACUCUGAAAACGUUUUAUAACUAACUACAUUAUAACAUGAUUAAAGCAAAAAUAGACUUAAUUUGCCUAUUUUUUAGAAAACAAACUGUUUUUCAGUUUCAUUUUCAGUGUUUUACAACAGAUGAAAUUUUAGGGCGAAAGCGGGAACAGACUUGAUCUUAGAUGCCGGCCAAUAAAAAAUCAGGGCAGAAUCUUUAUUCCACCCUGAUUUCACUUUUUAAAAUGAUUUUAG .................((((((.(((((((.....................((((((...((((((((.(.......).))))))))...........(((((((..((((((((((....((.....))..)))))))))).....((....)).)))))))..))))))...................(((((((((..((((....))))..))))))))).......))))))).)))))) (-45.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUAAAAUCAUUUUAAAAAGUGAAAUCAGGGUGGAAUAAAGAUUCUGCCCUGAUUUUUUAUUGGCCGGCAUCUAAGAUCAAGUCUGUUCCCGCUUUCGCCCUAAAAUUUCAUCUGUUGUAAAACACUGAAAAUGAAACUGAAAAACAGUUUGUUUUCUAAAAAAUAGGCAAAUUAAGUCUAUUUUUGCUUUAAUCAUGUUAUAAUGUAGUUAGUUAUAAAACGUUUUCAGAGUUAAGAGGUUGCGUA ....................((((((((((..((((....))))..)))))))))).....(((.(((.....((((...))))......)))...)))....((((((....(((....))).(((((((((((((((.....))))))........((((((((((.......))))))))))............(((((((.......)))))))..)))))))))......))))))..... (-54.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 754 50 1 141 92 NC_009009:SSA_1749|5end_Pyruvate_formate-lyase-activating_enzyme,_putative_1735426..1735656_NEGATIVE 316 184 141 204 164 NC_009009:SSA_1558|5end_Hydrolase,_HAD_superfamily_1560862..1561092_NEGATIVE 312 186 148 45 8 NC_009009:SSA_2191|5end_Conserved_uncharacterized_protein_2192049..2192279_POSITIVE 300 203 162 43 2 NC_009009:SSA_0363|5end_D-alanine/glycine/Na_permease,_putative_353858..354088_POSITIVE 297 183 147 83 48 NC_009009:SSA_1304|5end_hypothetical_protein_1323449..1323679_NEGATIVE 294 185 142 63 18 NC_009009:SSA_0441|5end_hypothetical_protein_441481..441711_POSITIVE 291 200 154 63 3 NC_009009:SSA_1011|5end_hypothetical_protein_1014134..1014364_POSITIVE 282 224 198 197 171 NC_009009:SSA_2091|5end_Phosphotransferase_system_sugar-specific_EII_component,_putative_2095562..2095792_NEGATIVE 278 176 131 79 38 NC_009009:SSA_0218|5end_Sugar-binding_periplasmic_protein,_putative_213863..214093_POSITIVE 277 185 142 168 120 NC_009009:SSA_1012|5end_Phosphoenolpyruvate_synthase,_putative_1014739..1014969_POSITIVE 277 185 146 70 36 NC_009009:SSA_0801|5end_Mur_ligase_family_protein,_putative_784117..784347_NEGATIVE 275 186 154 68 35 NC_009009:SSA_0102|5end_Kinase,_putative_104035..104265_POSITIVE 274 220 177 184 142 NC_009009:SSA_0089|5end_V-type_sodium_ATPase,_subunit_F,_putative_89930..90160_POSITIVE 273 219 179 42 2 NC_009009:SSA_0793|5end_DNA-entry_nuclease,_putative_774859..775089_POSITIVE 272 216 177 71 17 NC_009009:SSA_1667|5end_hypothetical_protein_1667704..1667934_NEGATIVE 271 200 158 186 150 NC_009009:SSA_2324|5end_hypothetical_protein_2330109..2330339_NEGATIVE 271 185 147 209 166 NC_009009:SSA_1138|5end_Pyruvate_dehydrogenase,_TPP-dependent_E1_component_alpha-subunit,_putative_1165731..1165961_POSITIVE 267 187 142 171 128 NC_009009:SSA_0776|5end_Glucose-1-phosphate_adenylyltransferase,_putative_758298..758528_POSITIVE 267 210 163 156 110 NC_009009:SSA_0471|5end_CbiG_protein,_putative_473600..473830_POSITIVE 267 190 141 169 103 NC_009009:SSA_0217|5end_Two-component_system_transcriptional_regulator_(CheY_domain_and_HTH-like_DNA-binding_domain),_putative_213183..213413_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 282 224 198 62 36 NC_009009:SSA_2092|3end_Phosphotransferase_system_sugar-specific_EII_component,_putative_2095697..2095847_NEGATIVE 280 182 141 139 88 NC_009009:SSA_0052|3end_Transcriptional_regulator,_GntR_family,_putative_55942..56092_NEGATIVE 278 176 131 82 41 NC_009009:SSA_0217|3end_Two-component_system_transcriptional_regulator_(CheY_domain_and_HTH-like_DNA-binding_domain),_putative_213946..214096_POSITIVE 275 199 154 51 1 NC_009009:SSA_2119|3end_Pentose-5-phosphate-3-epimerase,_putative_2120439..2120589_NEGATIVE 275 186 154 66 33 NC_009009:SSA_0101|3end_Conserved_uncharacterized_protein_104113..104263_POSITIVE 274 190 141 42 4 NC_009009:SSA_1724|3end_CBS_domain_protein,_putative_1709897..1710047_NEGATIVE 265 184 146 106 59 NC_009009:SSA_1646|3end_hypothetical_protein_1646322..1646472_NEGATIVE 265 187 141 138 93 NC_009009:SSA_0318|3end_Secreted_metalloendopeptidase_Gcp_312791..312941_POSITIVE 263 184 144 84 38 NC_009009:SSA_0451|3end_Conserved_uncharacterized_protein_451636..451786_POSITIVE 262 229 181 109 67 NC_009009:SSA_0343|3end_DNA-damage-inducible_protein_P,_putative_338669..338819_POSITIVE 259 185 141 76 38 NC_009009:SSA_0045|3end_hypothetical_protein_50949..51099_POSITIVE 258 186 156 34 7 NC_009009:SSA_2190|3end_33_kDa_chaperonin,_putative_2192118..2192268_POSITIVE 258 189 142 58 16 NC_009009:SSA_1564|3end_Histidine_kinase,_putative_1567266..1567416_NEGATIVE 258 184 146 81 29 NC_009009:SSA_0319|3end_Branched-chain_amino_acid_permease_(L-methionine,_L-isoleucine,_leucine_and_valine),_putative_313496..313646_POSITIVE 256 97 52 76 27 NC_009009:SSA_2365|3end_Cobalt_transport_protein_cbiQ,_putative_2367243..2367393_NEGATIVE 250 185 152 112 73 NC_009009:SSA_1579|3end_ABC-type_Fe3+-siderophore_transport_system,_ATPase_component,_putative_1583686..1583836_POSITIVE 249 226 181 139 86 NC_009009:SSA_1484|3end_DNA_ligase,_putative_1490230..1490380_NEGATIVE 249 186 141 53 14 NC_009009:SSA_0884|3end_hypothetical_protein_878725..878875_NEGATIVE 248 188 146 46 15 NC_009009:SSA_1409|3end_DTDP-glucose-4,6-dehydratase,_putative_1421209..1421359_NEGATIVE 248 187 142 149 102 NC_009009:SSA_0956|3end_surface_protein_D_965418..965568_POSITIVE