Origin IGS: attgcttgaatatgattttagccagattggatttgccaatctggtttttgctgttttaaaattgagggctttgttataattaaaaaggattatagaactgttaatgaatgaaactgaccgctttcgagctcgtctatcatgttattggaaagaaaataaaatgtattttggtttgaggctgcttttgtattttatacccatgtttatcttgtttttgttgctagtgtgttccctggtcttgatgattttctgcctgttttttcgaaaaaatttctttaaggaaaagcagggacgcaatttgctgctagctatcttttggctgggactcttcaatcttctgctgaacttgctagtatagaaatgatgagttcgtaaggagaacagtccaaatgaaatgatagggactagctttatccttgtttgttgaaactaaatattgattgagaattaaagaaagacgaaat .........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.........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 atttcgtctttctttaattctcaatcaatatttagtttcaacaaacaaggataaagctagtccctatcatttcatttggactgttctccttacgaactcatcatttctatactagcaagttcagcagaagattgaagagtcccagccaaaagatagctagcagcaaattgcgtccctgcttttccttaaagaaattttttcgaaaaaacaggcagaaaatcatcaagaccagggaacacactagcaacaaaaacaagataaacatgggtataaaatacaaaagcagcctcaaaccaaaatacattttattttctttccaataacatgatagacgagctcgaaagcggtcagtttcattcattaacagttctataatcctttttaattataacaaagccctcaattttaaaacagcaaaaaccagattggcaaatccaatctggctaaaatcatattcaagcaat Mask Tandem Repeat Region ================================================ attgcttgaatatgattttagccagattggatttgccaatctggtttttgctgttttaaaattgagggctttgttataattaaaaaggattatagaactgttaatgaatgaaactgaccgctttcgagctcgtctatcatgttattggaaagaaaataaaatgtattttggtttgaggctgcttttgtattttatacccatgtttatcttgtttttgttgctagtgtgttccctggtcttgatgattttctgcctgttttttcgaaaaaatttctttaaggaaaagcagggacgcaatttgctgctagctatcttttggctgggactcttcaatcttctgctgaacttgctagtatagaaatgatgagttcgtaaggagaacagtccaaatgaaatgatagggactagctttatccttgtttgttgaaactaaatattgattgagaattaaagaaagacgaaat Find is-nt database================================================ Query_seq: SSA_0380:SSA_0381|SSA_0380:SSA_0381:Enzyme of poly-gamma-glutamate biosynthesis (capsule formation), putative:hypothetical protein:->->:372439..372902 464 attgcttgaatatgattttagccagattggatttgccaatctggtttttgctgttttaaaattgagggctttgttataattaaaaaggattatagaactgttaatgaatgaaactgaccgctttcgagctcgtctatcatgttattggaaagaaaataaaatgtattttggtttgaggctgcttttgtattttatacccatgtttatcttgtttttgttgctagtgtgttccctggtcttgatgattttctgcctgttttttcgaaaaaatttctttaaggaaaagcagggacgcaatttgctgctagctatcttttggctgggactcttcaatcttctgctgaacttgctagtatagaaatgatgagttcgtaaggagaacagtccaaatgaaatgatagggactagctttatccttgtttgttgaaactaaatattgattgagaattaaagaaagacgaaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0380:SSA_0381|SSA_0380:SSA_0381:Enzyme of poly-gamma-glutamate biosynthesis (capsule formation), putative:hypothetical protein:->->:372439..372902 464 attgcttgaatatgattttagccagattggatttgccaatctggtttttgctgttttaaaattgagggctttgttataattaaaaaggattatagaactgttaatgaatgaaactgaccgctttcgagctcgtctatcatgttattggaaagaaaataaaatgtattttggtttgaggctgcttttgtattttatacccatgtttatcttgtttttgttgctagtgtgttccctggtcttgatgattttctgcctgttttttcgaaaaaatttctttaaggaaaagcagggacgcaatttgctgctagctatcttttggctgggactcttcaatcttctgctgaacttgctagtatagaaatgatgagttcgtaaggagaacagtccaaatgaaatgatagggactagctttatccttgtttgttgaaactaaatattgattgagaattaaagaaagacgaaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0380:SSA_0381|SSA_0380:SSA_0381:Enzyme of poly-gamma-glutamate biosynthesis (capsule formation), putative:hypothetical protein:->->:372439..372902 464 attgcttgaatatgattttagccagattggatttgccaatctggtttttgctgttttaaaattgagggctttgttataattaaaaaggattatagaactgttaatgaatgaaactgaccgctttcgagctcgtctatcatgttattggaaagaaaataaaatgtattttggtttgaggctgcttttgtattttatacccatgtttatcttgtttttgttgctagtgtgttccctggtcttgatgattttctgcctgttttttcgaaaaaatttctttaaggaaaagcagggacgcaatttgctgctagctatcttttggctgggactcttcaatcttctgctgaacttgctagtatagaaatgatgagttcgtaaggagaacagtccaaatgaaatgatagggactagctttatccttgtttgttgaaactaaatattgattgagaattaaagaaagacgaaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 attgcttgaatatgattttagccagattggatttgccaatctggtttttgctgttttaaaattgagggctttgttataattaaaaaggattatagaactgttaatgaatgaaactgaccgctttcgagctcgtctatcatgttattggaaagaaaataaaatgtattttggtttgaggctgcttttgtattttatacccatgtttatcttgtttttgttgctagtgtgttccctggtcttgatgattttctgcctgttttttcgaaaaaatttctttaaggaaaagcagggacgcaatttgctgctagctatcttttggctgggactcttcaatcttctgctgaacttgctagtatagaaatgatgagttcgtaaggagaacagtccaaatgaaatgatagggactagctttatccttgtttgttgaaactaaatattgattgagaattaaagaaagacgaaat Predict ORF larger than 30AA ================================================ Protein_Len: 60 Strand: + Start: 89 End: 355 ........................................................................................ M I E L L M N E T D R F R A R L S C Y W K E N K M Y F G L R L L L Y F I P M F I L F L L L V C S L V L M I F C L F F R K ............................................................................................................. Protein_Len: 32 Strand: - Start: 353 End: 448 ................................................................................................................................................................................................................................................................................................................................................................ Y L F S S N T L L V T W I F H Y P S A K D K N T S V L Y Q N L M ................ Protein_Len: 60 Strand: - Start: 145 End: 414 ................................................................................................................................................ T K I I K Q R N K R F F K K L S F C P R L K S S A I K Q S P S K L R R S F K S T Y F H H T R L S F L G F S I I P V L K M .................................................. Protein_Len: 35 Strand: - Start: 1 End: 105 N S S Y S K L W I P N A L R T K A T K F N L A K N Y N F L I I S S N M ....................................................................................................................................................................................................................................................................................................................................................................... attgcttgaatatgattttagccagattggatttgccaatctggtttttgctgttttaaaattgagggctttgttataattaaaaaggattatagaactgttaatgaatgaaactgaccgctttcgagctcgtctatcatgttattggaaagaaaataaaatgtattttggtttgaggctgcttttgtattttatacccatgtttatcttgtttttgttgctagtgtgttccctggtcttgatgattttctgcctgttttttcgaaaaaatttctttaaggaaaagcagggacgcaatttgctgctagctatcttttggctgggactcttcaatcttctgctgaacttgctagtatagaaatgatgagttcgtaaggagaacagtccaaatgaaatgatagggactagctttatccttgtttgttgaaactaaatattgattgagaattaaagaaagacgaaat 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================================================ PromScan Matrix: RpoN Strand: + Score: 81 Start: 287 End: 303 ..............................................................................................................................................................................................................................................................................................CAGGGACGCAATTTGCT................................................................................................................................................................. attgcttgaatatgattttagccagattggatttgccaatctggtttttgctgttttaaaattgagggctttgttataattaaaaaggattatagaactgttaatgaatgaaactgaccgctttcgagctcgtctatcatgttattggaaagaaaataaaatgtattttggtttgaggctgcttttgtattttatacccatgtttatcttgtttttgttgctagtgtgttccctggtcttgatgattttctgcctgttttttcgaaaaaatttctttaaggaaaagcagggacgcaatttgctgctagctatcttttggctgggactcttcaatcttctgctgaacttgctagtatagaaatgatgagttcgtaaggagaacagtccaaatgaaatgatagggactagctttatccttgtttgttgaaactaaatattgattgagaattaaagaaagacgaaat Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_0380:SSA_0381|SSA_0380:SSA_0381:Enzyme of poly-gamma-glutamate biosynthesis (capsule formation), putative:hypothetical protein:->->:372439..372902 464 attgcttgaatatgattttagccagattggatttgccaatctggtttttgctgttttaaaattgagggctttgttataattaaaaaggattatagaactgttaatgaatgaaactgaccgctttcgagctcgtctatcatgttattggaaagaaaataaaatgtattttggtttgaggctgcttttgtattttatacccatgtttatcttgtttttgttgctagtgtgttccctggtcttgatgattttctgcctgttttttcgaaaaaatttctttaaggaaaagcagggacgcaatttgctgctagctatcttttggctgggactcttcaatcttctgctgaacttgctagtatagaaatgatgagttcgtaaggagaacagtccaaatgaaatgatagggactagctttatccttgtttgttgaaactaaatattgattgagaattaaagaaagacgaaat Intra-Species Hit: Count: 1 Min: 1 Max: 464 Len: 464 Subject: NC_009009_SSA_0380_SSA_0381|Enzyme of poly-gamma-glutamate biosynthesis (capsule formation), putative:hypothetical protein|POSITIVE:POSITIVE|[372439,372902]|464 HSP 1 e-value: 0.0 bit: 920.0 Len: 464 Query Start:1 Query End:464 Subject Strand: POSITIVE Subject Start: 1 Subject End: 464 attgcttgaatatgattttagccagattggatttgccaatctggtttttgctgttttaaaattgagggctttgttataattaaaaaggattatagaactgttaatgaatgaaactgaccgctttcgagctcgtctatcatgttattggaaagaaaataaaatgtattttggtttgaggctgcttttgtattttatacccatgtttatcttgtttttgttgctagtgtgttccctggtcttgatgattttctgcctgttttttcgaaaaaatttctttaaggaaaagcagggacgcaatttgctgctagctatcttttggctgggactcttcaatcttctgctgaacttgctagtatagaaatgatgagttcgtaaggagaacagtccaaatgaaatgatagggactagctttatccttgtttgttgaaactaaatattgattgagaattaaagaaagacgaaat attgcttgaatatgattttagccagattggatttgccaatctggtttttgctgttttaaaattgagggctttgttataattaaaaaggattatagaactgttaatgaatgaaactgaccgctttcgagctcgtctatcatgttattggaaagaaaataaaatgtattttggtttgaggctgcttttgtattttatacccatgtttatcttgtttttgttgctagtgtgttccctggtcttgatgattttctgcctgttttttcgaaaaaatttctttaaggaaaagcagggacgcaatttgctgctagctatcttttggctgggactcttcaatcttctgctgaacttgctagtatagaaatgatgagttcgtaaggagaacagtccaaatgaaatgatagggactagctttatccttgtttgttgaaactaaatattgattgagaattaaagaaagacgaaat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUUGCUUGAAUAUGAUUUUAGCCAGAUUGGAUUUGCCAAUCUGGUUUUUGCUGUUUUAAAAUUGAGGGCUUUGUUAUAAUUAAAAAGGAUUAUAGAACUGUUAAUGAAUGAAACUGACCGCUUUCGAGCUCGUCUAUCAUGUUAUUGGAAAGAAAAUAAAAUGUAUUUUGGUUUGAGGCUGCUUUUGUAUUUUAUACCCAUGUUUAUCUUGUUUUUGUUGCUAGUGUGUUCCCUGGUCUUGAUGAUUUUCUGCCUGUUUUUUCGAAAAAAUUUCUUUAAGGAAAAGCAGGGACGCAAUUUGCUGCUAGCUAUCUUUUGGCUGGGACUCUUCAAUCUUCUGCUGAACUUGCUAGUAUAGAAAUGAUGAGUUCGUAAGGAGAACAGUCCAAAUGAAAUGAUAGGGACUAGCUUUAUCCUUGUUUGUUGAAACUAAAUAUUGAUUGAGAAUUAAAGAAAGACGAAAU ...(((((((..((.....(((((((((((.....)))))))))))......((((((..(((((.((.....((((((((......))))))))..)).)))))...))))))....))..)))))))((((((.((....((((((...((((((((.(((.((...(((.(((((.(((....)))))))).)))...)).))).))))))))....))))))......(((((((..((.(((((....((((((((((..(((......)))..))))))))))((((...........(((((((.....)))))))..........((((((..(((((((..((.........))..)))))))..))))))...))))....))))).))..)))))))(((.(((..((((((.......))))))..))).))).......)).))))))... (-114.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUUUCGUCUUUCUUUAAUUCUCAAUCAAUAUUUAGUUUCAACAAACAAGGAUAAAGCUAGUCCCUAUCAUUUCAUUUGGACUGUUCUCCUUACGAACUCAUCAUUUCUAUACUAGCAAGUUCAGCAGAAGAUUGAAGAGUCCCAGCCAAAAGAUAGCUAGCAGCAAAUUGCGUCCCUGCUUUUCCUUAAAGAAAUUUUUUCGAAAAAACAGGCAGAAAAUCAUCAAGACCAGGGAACACACUAGCAACAAAAACAAGAUAAACAUGGGUAUAAAAUACAAAAGCAGCCUCAAACCAAAAUACAUUUUAUUUUCUUUCCAAUAACAUGAUAGACGAGCUCGAAAGCGGUCAGUUUCAUUCAUUAACAGUUCUAUAAUCCUUUUUAAUUAUAACAAAGCCCUCAAUUUUAAAACAGCAAAAACCAGAUUGGCAAAUCCAAUCUGGCUAAAAUCAUAUUCAAGCAAU .........(((((((((..((........................(((((...(((.(((((..((......))..)))))))).)))))..(((((...................)))))....))..))))))))).....((.........(((((..((.....)).((((((.(((((...(((....)))....)))))........((......)).....)))))).....)))))...........(((......((((...........((((.................(((.(((((........))))).)))...(((..(((....))).))).))))................((((((........)))))).....)))).....................(((((((((.....))))))))).....)))........))... (-75.21) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 394 342 302 202 150 NC_009009:SSA_1933|5end_(3R)-hydroxymyristoyl-[acyl_carrier_protein]_dehydratase,_putative_1921315..1921545_NEGATIVE 377 343 301 196 152 NC_009009:SSA_0487|5end_Delta-aminolevulinic_acid_dehydratase,_putative_487349..487579_POSITIVE 345 350 301 148 101 NC_009009:SSA_1149|5end_Glycosyl_hydrolase,_family_1,_putative_1178399..1178629_POSITIVE 343 355 316 44 3 NC_009009:SSA_2131|5end_DNA-binding_protein,_putative_2133949..2134179_POSITIVE 332 350 302 64 4 NC_009009:SSA_0474|5end_Uroporphyrin-III_C-methyltransferase/uroporphyrinogen-III_synthase,_putative_476270..476500_POSITIVE 329 350 301 59 7 NC_009009:SSA_2053|5end_hypothetical_protein_2057747..2057977_NEGATIVE 328 339 293 117 51 NC_009009:SSA_1738|5end_Polysaccharide_biosynthesis_protein,_putative_1725503..1725733_NEGATIVE 320 343 301 203 150 NC_009009:SSA_1448|5end_ATP_phosphoribosyltransferase_regulatory_subunit,_putative_1450817..1451047_NEGATIVE 319 349 307 226 196 NC_009009:SSA_2119|5end_Pentose-5-phosphate-3-epimerase,_putative_2121098..2121328_NEGATIVE 318 70 21 153 115 NC_009009:SSA_0710|5end_Exopolysaccharide_biosynthesis_protein,_acetyltransferase,_putative_695639..695869_NEGATIVE 314 338 293 113 71 NC_009009:SSA_1501|5end_Cytidylate_kinase,_putative_1505772..1506002_NEGATIVE 314 349 301 76 25 NC_009009:SSA_2393|5end_Transcriptional_regulator,_XRE_family,_putative_204056..204286_POSITIVE 314 347 301 221 161 NC_009009:SSA_0140|5end_Copper-translocating_P-type_ATPase,_putative_134626..134856_POSITIVE 310 340 291 87 32 NC_009009:SSA_2356|5end_Replicative_DNA_helicase,_putative_2357958..2358188_NEGATIVE 310 420 371 104 52 NC_009009:SSA_0211|5end_hypothetical_protein_208041..208271_POSITIVE 308 320 272 181 135 NC_009009:SSA_1868|5end_ABC-type_arginine/histidine_transport_system,_permease_component,_putative_1863902..1864132_NEGATIVE 308 343 301 178 127 NC_009009:SSA_0893|5end_ATP-binding_cassette_transporter-like_protein,_putative_884527..884757_POSITIVE 308 70 23 220 161 NC_009009:SSA_0546|5end_Phospho-2-dehydro-3-deoxyheptonate_aldolase_(DAHP_synthatase),_possibly_tyr-sensitive,_putative_540852..541082_POSITIVE 307 350 302 219 177 NC_009009:SSA_2084|5end_Phosphotransferase_system_(PTS),_galactitol-specific_IIC_component,_putative_2089424..2089654_NEGATIVE 304 256 211 190 144 NC_009009:SSA_0826|5end_hypothetical_protein_805098..805328_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 345 350 301 142 95 NC_009009:SSA_1148|3end_Beta-glucosides_PTS,_EIIC,_putative_1178473..1178623_POSITIVE 338 340 299 122 80 NC_009009:SSA_2113|3end_hypothetical_protein_2116228..2116378_NEGATIVE 322 253 214 147 99 NC_009009:SSA_1869|3end_ATP-dependent_RNA_helicase,_putative_1864152..1864302_NEGATIVE 320 343 301 147 94 NC_009009:SSA_1449|3end_Histidinol-phosphate/aromatic_aminotransferase_and_cobyric_acid_decarboxylase,_putative_1450873..1451023_NEGATIVE 319 315 279 92 59 NC_009009:SSA_1309|3end_RNA-binding_protein_(KH_domain),_putative_1327079..1327229_NEGATIVE 317 372 334 138 87 NC_009009:SSA_1595|3end_Tellurite_resistance,_putative_1600951..1601101_NEGATIVE 314 338 293 103 61 NC_009009:SSA_1502|3end_Conserved_uncharacterized_protein_(contains_LysM,_Lysin_motif)_1505782..1505932_NEGATIVE 310 340 291 60 5 NC_009009:SSA_2357|3end_50S_ribosomal_protein_L9,_putative_2357985..2358135_NEGATIVE 310 420 371 107 55 NC_009009:SSA_0210|3end_hypothetical_protein_208124..208274_POSITIVE 308 343 301 149 98 NC_009009:SSA_0892|3end_ATP-binding_cassette_lipoprotein,_putative_884578..884728_POSITIVE 304 256 211 68 22 NC_009009:SSA_0825|3end_DNA-directed_RNA_polymerase,_sigma_subunit_(sigma70/sigma32),_putative_805056..805206_POSITIVE 303 330 285 110 73 NC_009009:SSA_0966|3end_Uridine_kinase,_putative_975790..975940_POSITIVE 301 330 284 111 47 NC_009009:SSA_0819|3end_hypothetical_protein_801181..801331_POSITIVE 301 253 212 151 113 NC_009009:SSA_0068|3end_Alcohol-acetaldehyde_dehydrogenase,_putative_72848..72998_POSITIVE 299 350 302 94 56 NC_009009:SSA_1779|3end_Segregation_and_condensation_protein_A,_putative_1765704..1765854_NEGATIVE 298 330 286 113 75 NC_009009:SSA_0508|3end_Conserved_uncharacterized_protein,_possible_phosphoserine_phosphatase_508064..508214_POSITIVE 296 325 283 104 62 NC_009009:SSA_2211|3end_Transmembrane_protein,_putative_2211499..2211649_NEGATIVE 296 54 20 39 1 NC_009009:SSA_0370|3end_Acetyltransferase,_GNAT_family,_putative_359897..360047_NEGATIVE 295 360 313 83 43 NC_009009:SSA_0897|3end_Two_component_system_histidine_kinase,_putative_889811..889961_POSITIVE 294 324 286 65 10 NC_009009:SSA_0996|3end_cGMP-specific_phosphodiesterase,_putative_996859..997009_POSITIVE