Origin IGS: aggaattccgtttagctgaattgaataaagaatgctcacatttgagcgtcaaaaaaattgtactaaatgtaccaaaaaatgcagggttataacagaaaattttgtataaataaggtaaaaaaatctgtgcaaaacctttacgttcaaggtttcttaaaggtcagcggcacgcgtttgtcatatcatttcccttgctttagtcaaaacagggtgtaaactgaccgcactttatttgattgatgaaaaatt .........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 aatttttcatcaatcaaataaagtgcggtcagtttacaccctgttttgactaaagcaagggaaatgatatgacaaacgcgtgccgctgacctttaagaaaccttgaacgtaaaggttttgcacagatttttttaccttatttatacaaaattttctgttataaccctgcattttttggtacatttagtacaatttttttgacgctcaaatgtgagcattctttattcaattcagctaaacggaattcct Mask Tandem Repeat Region ================================================ aggaattccgtttagctgaattgaataaagaatgctcacatttgagcgtcaaaaaaattgtactaaatgtaccaaaaaatgcagggttataacagaaaattttgtataaataaggtaaaaaaatctgtgcaaaacctttacgttcaaggtttcttaaaggtcagcggcacgcgtttgtcatatcatttcccttgctttagtcaaaacagggtgtaaactgaccgcactttatttgattgatgaaaaatt Find is-nt database================================================ Query_seq: AA01371:AA01372|AA01371:AA01372:rod shape-determining protein:ribonuclease r, virulence associated protein:->->:927772..928020 249 aggaattccgtttagctgaattgaataaagaatgctcacatttgagcgtcaaaaaaattgtactaaatgtaccaaaaaatgcagggttataacagaaaattttgtataaataaggtaaaaaaatctgtgcaaaacctttacgttcaaggtttcttaaaggtcagcggcacgcgtttgtcatatcatttcccttgctttagtcaaaacagggtgtaaactgaccgcactttatttgattgatgaaaaatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: AA01371:AA01372|AA01371:AA01372:rod shape-determining protein:ribonuclease r, virulence associated protein:->->:927772..928020 249 aggaattccgtttagctgaattgaataaagaatgctcacatttgagcgtcaaaaaaattgtactaaatgtaccaaaaaatgcagggttataacagaaaattttgtataaataaggtaaaaaaatctgtgcaaaacctttacgttcaaggtttcttaaaggtcagcggcacgcgtttgtcatatcatttcccttgctttagtcaaaacagggtgtaaactgaccgcactttatttgattgatgaaaaatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: AA01371:AA01372|AA01371:AA01372:rod shape-determining protein:ribonuclease r, virulence associated protein:->->:927772..928020 249 aggaattccgtttagctgaattgaataaagaatgctcacatttgagcgtcaaaaaaattgtactaaatgtaccaaaaaatgcagggttataacagaaaattttgtataaataaggtaaaaaaatctgtgcaaaacctttacgttcaaggtttcttaaaggtcagcggcacgcgtttgtcatatcatttcccttgctttagtcaaaacagggtgtaaactgaccgcactttatttgattgatgaaaaatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aggaattccgtttagctgaattgaataaagaatgctcacatttgagcgtcaaaaaaattgtactaaatgtaccaaaaaatgcagggttataacagaaaattttgtataaataaggtaaaaaaatctgtgcaaaacctttacgttcaaggtttcttaaaggtcagcggcacgcgtttgtcatatcatttcccttgctttagtcaaaacagggtgtaaactgaccgcactttatttgattgatgaaaaatt Predict ORF larger than 30AA ================================================ Protein_Len: 49 Strand: + Start: 67 End: 213 .................................................................. M Y Q K M Q G Y N R K F C I N K V K K S V Q N L Y V Q G F L K V S G T R L S Y H F P C F S Q N R V .................................... Protein_Len: 32 Strand: - Start: 52 End: 147 ................................................... F F Q V L H V L F H L T I V S F K T Y I L Y F F R H L V K V N M ...................................................................................................... Protein_Len: 41 Strand: - Start: 2 End: 124 . S N R K A S N F L S H E C K L T L F I T S F T G F F A P N Y C F I K Y L Y P L F M ............................................................................................................................. aggaattccgtttagctgaattgaataaagaatgctcacatttgagcgtcaaaaaaattgtactaaatgtaccaaaaaatgcagggttataacagaaaattttgtataaataaggtaaaaaaatctgtgcaaaacctttacgttcaaggtttcttaaaggtcagcggcacgcgtttgtcatatcatttcccttgctttagtcaaaacagggtgtaaactgaccgcactttatttgattgatgaaaaatt 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================================================ aggaattccgtttagctgaattgaataaagaatgctcacatttgagcgtcaaaaaaattgtactaaatgtaccaaaaaatgcagggttataacagaaaattttgtataaataaggtaaaaaaatctgtgcaaaacctttacgttcaaggtttcttaaaggtcagcggcacgcgtttgtcatatcatttcccttgctttagtcaaaacagggtgtaaactgaccgcactttatttgattgatgaaaaatt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: AA01371:AA01372|AA01371:AA01372:rod shape-determining protein:ribonuclease r, virulence associated protein:->->:927772..928020 249 aggaattccgtttagctgaattgaataaagaatgctcacatttgagcgtcaaaaaaattgtactaaatgtaccaaaaaatgcagggttataacagaaaattttgtataaataaggtaaaaaaatctgtgcaaaacctttacgttcaaggtttcttaaaggtcagcggcacgcgtttgtcatatcatttcccttgctttagtcaaaacagggtgtaaactgaccgcactttatttgattgatgaaaaatt Intra-Species Hit: Count: 1 Min: 1 Max: 249 Len: 249 Subject: aact_AA01371_AA01372|rod shape-determining protein:ribonuclease r, virulence associated protein|POSITIVE:POSITIVE|[927772,928020]|249 HSP 1 e-value: 1.0E-114 bit: 410.0 Len: 249 Query Start:1 Query End:249 Subject Strand: POSITIVE Subject Start: 1 Subject End: 249 aggaattccgtttagctgaattgaataaagaatgctcacatttgagcgtcnnnnnnnttgtactaaatgtaccaaaaaatgcagggttataacagaaaattttgtataaataaggtnnnnnnntctgtgcaaaacctttacgttcaaggtttcttaaaggtcagcggcacgcgtttgtcatatcatttcccttgctttagtcaaaacagggtgtaaactgaccgcactttatttgattgatgaaaaatt aggaattccgtttagctgaattgaataaagaatgctcacatttgagcgtcaaaaaaattgtactaaatgtaccaaaaaatgcagggttataacagaaaattttgtataaataaggtaaaaaaatctgtgcaaaacctttacgttcaaggtttcttaaaggtcagcggcacgcgtttgtcatatcatttcccttgctttagtcaaaacagggtgtaaactgaccgcactttatttgattgatgaaaaatt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGGAAUUCCGUUUAGCUGAAUUGAAUAAAGAAUGCUCACAUUUGAGCGUCAAAAAAAUUGUACUAAAUGUACCAAAAAAUGCAGGGUUAUAACAGAAAAUUUUGUAUAAAUAAGGUAAAAAAAUCUGUGCAAAACCUUUACGUUCAAGGUUUCUUAAAGGUCAGCGGCACGCGUUUGUCAUAUCAUUUCCCUUGCUUUAGUCAAAACAGGGUGUAAACUGACCGCACUUUAUUUGAUUGAUGAAAAAUU .((....)).........(((..(((((((..(((.....(((((((((.(((....((((((......((((.....((((((((((.........))))))))))......)))).........))))))....))))))))))))..........((((((..((((.(.((((.(....((.......)).....).))))...).))))...))))))))))))))))..)))........... (-52.86) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUUUUUCAUCAAUCAAAUAAAGUGCGGUCAGUUUACACCCUGUUUUGACUAAAGCAAGGGAAAUGAUAUGACAAACGCGUGCCGCUGACCUUUAAGAAACCUUGAACGUAAAGGUUUUGCACAGAUUUUUUUACCUUAUUUAUACAAAAUUUUCUGUUAUAACCCUGCAUUUUUUGGUACAUUUAGUACAAUUUUUUUGACGCUCAAAUGUGAGCAUUCUUUAUUCAAUUCAGCUAAACGGAAUUCCU ....((((....((((((..(((((((((((((.....(((((((((....))))).))))......((((.(....)))))..))))))).....((((((((.......))))))))..(((((...((((.............))))...))))).........))))))))))))...((((((.(((.....)))..(((((....))))).................)))))).))))..... (-47.52) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 337 195 160 225 192 aact:AA01316|5end_hypothetical_protein_891262..891492_POSITIVE 332 240 193 160 114 aact:AA02084|5end_conserved_hypothetical_protein_1417843..1418073_POSITIVE 318 240 192 204 150 aact:AA02829|5end_peptidoglycan-associated_outer_membrane_1988247..1988477_POSITIVE 318 240 192 94 40 aact:AA02828|5end_hypothetical_protein_1988137..1988367_POSITIVE 316 184 148 55 13 aact:AA02436|5end_periplasmic_protein_1680497..1680727_POSITIVE 316 200 164 44 8 aact:AA01650|5end_maltose_transport_inner_membrane_protein_1118228..1118458_POSITIVE 315 239 192 66 11 aact:AA00170|5end_hypothetical_protein_121238..121468_POSITIVE 314 237 200 62 15 aact:AA02846|5end_crossover_junction_endodeoxyribonuclease_1998648..1998878_POSITIVE 307 227 190 178 140 aact:AA01792|5end_conserved_hypothetical_protein_1208058..1208288_POSITIVE 302 230 182 155 102 aact:AA01496|5end_glucose_inhibited_division_protein_A_1005125..1005355_POSITIVE 299 189 141 206 165 aact:AA02575|5end_transmembrane_protein_1793749..1793979_POSITIVE 299 220 171 88 31 aact:AA00839|5end_UDP-MurNAc-pentapeptide_phosphotransferase_578853..579083_POSITIVE 296 230 203 168 141 aact:AA02706|5end_2-oxoglutarate_dehydrogenase_E1_component_(decarboxylase_component)_1886843..1887073_POSITIVE 296 230 203 42 15 aact:AA02705|5end_hypothetical_protein_1886717..1886947_POSITIVE 296 230 189 200 156 aact:AA02365|5end_hflC_protein_1621997..1622227_POSITIVE 295 229 182 44 2 aact:AA02734|5end_leucine-responsive_regulatory_protein_1914956..1915186_POSITIVE 295 200 151 113 53 aact:AA01009|5end_universal_stress_protein_A_704443..704673_POSITIVE 295 230 184 81 33 aact:AA00908|5end_probable_sigma-E_factor_regulatory_protein_626076..626306_POSITIVE 294 178 135 66 30 aact:AA00823|5end_heat_shock_protein_565006..565236_POSITIVE 294 177 134 228 178 aact:AA00349|5end_hypothetical_protein_233274..233504_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 332 240 193 85 39 aact:AA02082|3end_glutaminyl-tRNA_synthetase_1417848..1417998_POSITIVE 310 239 193 93 50 aact:AA02280|3end_conserved_hypothetical_protein_1552767..1552917_POSITIVE 299 220 171 58 1 aact:AA00838|3end_UDP-N-acetylmuramoylalanine--D-glutamate_ligase_578903..579053_POSITIVE 296 230 203 40 13 aact:AA02704|3end_dihydrolipoamide_succinyltransferase_1886795..1886945_POSITIVE 295 230 184 68 20 aact:AA00906|3end_sigma-E_factor_regulatory_protein_626143..626293_POSITIVE 294 231 192 140 100 aact:AA00170|3end_hypothetical_protein_121407..121557_POSITIVE 292 232 202 71 33 aact:AA03012|3end_conserved_hypothetical_protein_2104556..2104706_POSITIVE 291 209 161 135 88 aact:AA02946|3end_virulence_factor_protein_2060870..2061020_POSITIVE 285 214 171 89 47 aact:AA01567|3end_conserved_hypothetical_protein_(possible_cell-wall-associated_hydrolase)_1055215..1055365_POSITIVE 281 203 164 127 75 aact:AA02543|3end_conserved_hypothetical_protein_1773434..1773584_POSITIVE 281 229 184 151 111 aact:AA00267|3end_hypothetical_protein_188143..188293_POSITIVE 275 226 185 126 90 aact:AA02140|3end_ABC_transporter_ATP-binding_protein_1464965..1465115_POSITIVE 275 230 190 149 110 aact:AA01025|3end_hypothetical_protein_717769..717919_POSITIVE 271 240 193 91 46 aact:AA02892|3end_oligopeptide_ABC_transporter,_periplasmic-binding_protein_2027177..2027327_POSITIVE 271 230 194 34 3 aact:AA01138|3end_anaerobic_dimethyl_sulfoxide_reductase,_chain_B_781685..781835_POSITIVE 268 175 136 147 96 aact:AA03003|3end_GTP-binding_membrane_protein_2098447..2098597_POSITIVE 263 239 203 133 97 aact:AA02731|3end_outer_membrane_lipoprotein_carrier_precursor_1912192..1912342_POSITIVE 263 196 151 83 36 aact:AA01575|3end_conserved_hypothetical_protein_1063147..1063297_POSITIVE 261 180 131 66 10 aact:AA01185|3end_conserved_hypothetical_protein_(possible_membrane_protein)_813401..813551_POSITIVE 260 177 142 57 14 aact:AA00623|3end_hypothetical_protein_430632..430782_POSITIVE