Origin IGS: gtgtaaaagcttaaaatggaagtgaggaacaagccttgcttccatttgtttttataaaatttgacaaattgttaagaaaacgcttgcaatttctctgacttctgatataatggacttatggattgttactggtcaagcaggcaaaacctaagcaaatacgagatataaagcagtttcttgctttctatttggtgtgtgtttaggtttttttcgtgccctattttccgggaataggaacagactgctaacctaaaaaatacaaggaggttccatt .........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 aatggaacctccttgtattttttaggttagcagtctgttcctattcccggaaaatagggcacgaaaaaaacctaaacacacaccaaatagaaagcaagaaactgctttatatctcgtatttgcttaggttttgcctgcttgaccagtaacaatccataagtccattatatcagaagtcagagaaattgcaagcgttttcttaacaatttgtcaaattttataaaaacaaatggaagcaaggcttgttcctcacttccattttaagcttttacac Mask Tandem Repeat Region ================================================ gtgtaaaagcttaaaatggaagtgaggaacaagccttgcttccatttgtttttataaaatttgacaaattgttaagaaaacgcttgcaatttctctgacttctgatataatggacttatggattgttactggtcaagcaggcaaaacctaagcaaatacgagatataaagcagtttcttgctttctatttggtgtgtgtttaggtttttttcgtgccctattttccgggaataggaacagactgctaacctaaaaaatacaaggaggttccatt Find is-nt database================================================ Query_seq: SSA_0378:SSA_0379|SSA_0378:SSA_0379:TRZ/ATZ family hydrolase, putative:PTS system, beta-glucoside-specific EII component, putative:->->:368688..368961 274 gtgtaaaagcttaaaatggaagtgaggaacaagccttgcttccatttgtttttataaaatttgacaaattgttaagaaaacgcttgcaatttctctgacttctgatataatggacttatggattgttactggtcaagcaggcaaaacctaagcaaatacgagatataaagcagtttcttgctttctatttggtgtgtgtttaggtttttttcgtgccctattttccgggaataggaacagactgctaacctaaaaaatacaaggaggttccatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0378:SSA_0379|SSA_0378:SSA_0379:TRZ/ATZ family hydrolase, putative:PTS system, beta-glucoside-specific EII component, putative:->->:368688..368961 274 gtgtaaaagcttaaaatggaagtgaggaacaagccttgcttccatttgtttttataaaatttgacaaattgttaagaaaacgcttgcaatttctctgacttctgatataatggacttatggattgttactggtcaagcaggcaaaacctaagcaaatacgagatataaagcagtttcttgctttctatttggtgtgtgtttaggtttttttcgtgccctattttccgggaataggaacagactgctaacctaaaaaatacaaggaggttccatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0378:SSA_0379|SSA_0378:SSA_0379:TRZ/ATZ family hydrolase, putative:PTS system, beta-glucoside-specific EII component, putative:->->:368688..368961 274 gtgtaaaagcttaaaatggaagtgaggaacaagccttgcttccatttgtttttataaaatttgacaaattgttaagaaaacgcttgcaatttctctgacttctgatataatggacttatggattgttactggtcaagcaggcaaaacctaagcaaatacgagatataaagcagtttcttgctttctatttggtgtgtgtttaggtttttttcgtgccctattttccgggaataggaacagactgctaacctaaaaaatacaaggaggttccatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gtgtaaaagcttaaaatggaagtgaggaacaagccttgcttccatttgtttttataaaatttgacaaattgttaagaaaacgcttgcaatttctctgacttctgatataatggacttatggattgttactggtcaagcaggcaaaacctaagcaaatacgagatataaagcagtttcttgctttctatttggtgtgtgtttaggtttttttcgtgccctattttccgggaataggaacagactgctaacctaaaaaatacaaggaggttccatt Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: - Start: 151 End: 240 ...................................................................................................................................................... A F V L Y L A T E Q K R N P T H K P K K R A R N E P F L F M .................................. Protein_Len: 31 Strand: - Start: 129 End: 221 ................................................................................................................................ Q D L L C F R L L Y S I Y L L K K S E I Q H T N L N K E H G M ..................................................... Protein_Len: 31 Strand: - Start: 14 End: 106 ............. F P L S S C A K S G N T K I F N S L N N L F R K C N R Q S R M ........................................................................................................................................................................ gtgtaaaagcttaaaatggaagtgaggaacaagccttgcttccatttgtttttataaaatttgacaaattgttaagaaaacgcttgcaatttctctgacttctgatataatggacttatggattgttactggtcaagcaggcaaaacctaagcaaatacgagatataaagcagtttcttgctttctatttggtgtgtgtttaggtttttttcgtgccctattttccgggaataggaacagactgctaacctaaaaaatacaaggaggttccatt 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: 81 Start: 82 End: 111 .................................................................................GCTTGCAATTTCTCTGACTTCTGATATAAT................................................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gtgtaaaagcttaaaatggaagtgaggaacaagccttgcttccatttgtttttataaaatttgacaaattgttaagaaaacgcttgcaatttctctgacttctgatataatggacttatggattgttactggtcaagcaggcaaaacctaagcaaatacgagatataaagcagtttcttgctttctatttggtgtgtgtttaggtttttttcgtgccctattttccgggaataggaacagactgctaacctaaaaaatacaaggaggttccatt Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 61 HP_score: -4.1 Tail_Score: -4.28049 Start: 17 End: 44 Full_Region: ttttataaaaacaaa tggaagcaagg cttgtt cctcacttcca ttttaagcttttaca ................tggaagcaaggcttgttcctcacttcca...................................................................................................................................................................................................................................... TransTerm Strand: + Conf: 100 HP_score: -8.7 Tail_Score: -5.52986 Start: 147 End: 204 Full_Region: GTCAAGCAGGCAAAA CCTAAGCAAATACGAGATATAAAGCAG TTTC TTGCTTTCTATTTGGTGTGTGTTTAGG TTTTTTTCGTGCCCT ..................................................................................................................................................CCTAAGCAAATACGAGATATAAAGCAGTTTCTTGCTTTCTATTTGGTGTGTGTTTAGG...................................................................... TransTerm Strand: - Conf: 43 HP_score: -2.5 Tail_Score: -2.9955 Start: 164 End: 187 Full_Region: taaacacacaccaaa tagaaagca agaaac tgctttata tctcgtatttgctta ...................................................................................................................................................................tagaaagcaagaaactgctttata....................................................................................... Find igs database================================================ Query_seq: SSA_0378:SSA_0379|SSA_0378:SSA_0379:TRZ/ATZ family hydrolase, putative:PTS system, beta-glucoside-specific EII component, putative:->->:368688..368961 274 gtgtaaaagcttaaaatggaagtgaggaacaagccttgcttccatttgtttttataaaatttgacaaattgttaagaaaacgcttgcaatttctctgacttctgatataatggacttatggattgttactggtcaagcaggcaaaacctaagcaaatacgagatataaagcagtttcttgctttctatttggtgtgtgtttaggtttttttcgtgccctattttccgggaataggaacagactgctaacctaaaaaatacaaggaggttccatt Intra-Species Hit: Count: 1 Min: 1 Max: 274 Len: 274 Subject: NC_009009_SSA_0378_SSA_0379|TRZ/ATZ family hydrolase, putative:PTS system, beta-glucoside-specific EII component, putative|POSITIVE:POSITIVE|[368688,368961]|274 HSP 1 e-value: 1.0E-141 bit: 502.0 Len: 274 Query Start:1 Query End:274 Subject Strand: POSITIVE Subject Start: 1 Subject End: 274 gtgtaaaagcttaaaatggaagtgaggaacaagccttgcttccatttgtttttataaaatttgacaaattgttaagaaaacgcttgcaatttctctgacttctgatataatggacttatggattgttactggtcaagcaggcaaaacctaagcaaatacgagatataaagcagtttcttgctttctatttggtgtgtgtttaggnnnnnnncgtgccctattttccgggaataggaacagactgctaacctaaaaaatacaaggaggttccatt gtgtaaaagcttaaaatggaagtgaggaacaagccttgcttccatttgtttttataaaatttgacaaattgttaagaaaacgcttgcaatttctctgacttctgatataatggacttatggattgttactggtcaagcaggcaaaacctaagcaaatacgagatataaagcagtttcttgctttctatttggtgtgtgtttaggtttttttcgtgccctattttccgggaataggaacagactgctaacctaaaaaatacaaggaggttccatt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUGUAAAAGCUUAAAAUGGAAGUGAGGAACAAGCCUUGCUUCCAUUUGUUUUUAUAAAAUUUGACAAAUUGUUAAGAAAACGCUUGCAAUUUCUCUGACUUCUGAUAUAAUGGACUUAUGGAUUGUUACUGGUCAAGCAGGCAAAACCUAAGCAAAUACGAGAUAUAAAGCAGUUUCUUGCUUUCUAUUUGGUGUGUGUUUAGGUUUUUUUCGUGCCCUAUUUUCCGGGAAUAGGAACAGACUGCUAACCUAAAAAAUACAAGGAGGUUCCAUU .(((((((((...(((((((((..(((......)))..))))))))))))))))))......((.(((((((.(((......)))))))))).)).............(((((((((.....((((....(((..(((((..((((((((((((.((((.(((((.(((((((....))))))).))))).)))).))))))))))))....((..(((((((.....))))))).))...))))).)))........))))..))).)))))) (-85.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUGGAACCUCCUUGUAUUUUUUAGGUUAGCAGUCUGUUCCUAUUCCCGGAAAAUAGGGCACGAAAAAAACCUAAACACACACCAAAUAGAAAGCAAGAAACUGCUUUAUAUCUCGUAUUUGCUUAGGUUUUGCCUGCUUGACCAGUAACAAUCCAUAAGUCCAUUAUAUCAGAAGUCAGAGAAAUUGCAAGCGUUUUCUUAACAAUUUGUCAAAUUUUAUAAAAACAAAUGGAAGCAAGGCUUGUUCCUCACUUCCAUUUUAAGCUUUUACAC ((((((.......((.(((.((..(((((((((..((((((((((.......))))))).)))...(((((((((.((.(.((...(((.((((((......)))))).)))...)).).)).)))))))))..)))).)))))...)).))).))....)))))).....((((((..((.((((((.(((......)))..)))))).))...............(((((((((..(((......)))..)))))))))...)))))).... (-59.00) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 304 250 203 187 125 NC_009009:SSA_1370|5end_CAAX_amino_terminal_protease_family,_putative_1386968..1387198_NEGATIVE 295 217 179 73 32 NC_009009:SSA_0176|5end_DNA-directed_RNA_polymerase_I,_beta_chain_(140_kDa_subunit),_putative_174981..175211_POSITIVE 291 218 172 101 43 NC_009009:SSA_1016|5end_Phosphoenolpyruvate_synthase,_putative_1019602..1019832_POSITIVE 289 245 206 132 97 NC_009009:SSA_0817|5end_Antirepressor_regulating_drug_resistance_(membrane-bound),_putative_797838..798068_POSITIVE 282 247 202 197 143 NC_009009:SSA_1237|5end_Uracil-DNA_glycosylase,_putative_1262366..1262596_NEGATIVE 282 51 14 97 54 NC_009009:SSA_0797|5end_Transcriptional_regulator,_putative_779521..779751_POSITIVE 279 216 174 47 5 NC_009009:SSA_1465|5end_Conserved_uncharacterized_protein_1471986..1472216_NEGATIVE 278 148 103 197 161 NC_009009:SSA_0763|5end_Transcription_repressor,_putative_744980..745210_POSITIVE 274 55 16 172 129 NC_009009:SSA_1099|5end_Calcium_binding_hemolysin-like_protein,_putative_1115361..1115591_POSITIVE 269 247 203 161 121 NC_009009:SSA_2301|5end_S-layer_protein/_peptidoglycan_endo-beta-N-acetylglucosaminidase,_putative_2303268..2303498_NEGATIVE 269 216 171 191 148 NC_009009:SSA_0256|5end_Metalloregulator_ScaR_(Fe/Mn-dependent_transcriptional_repressor),_putative_248699..248929_NEGATIVE 269 139 96 183 144 NC_009009:SSA_0137|5end_ABC_transporter_(permease),_Zn_porter,_putative_131717..131947_POSITIVE 268 218 171 217 155 NC_009009:SSA_1320|5end_hypothetical_protein_1337194..1337424_NEGATIVE 268 144 115 136 107 NC_009009:SSA_0272|5end_Oxidoreductase,_aldo/keto_reductase_family,_putative_266023..266253_POSITIVE 266 214 171 214 165 NC_009009:SSA_0694|5end_Mutator_protein,_putative_677730..677960_POSITIVE 262 253 211 231 187 NC_009009:SSA_1324|5end_Ceramide_glucosyltransferase,_putative_1341618..1341848_NEGATIVE 259 75 32 230 177 NC_009009:SSA_1119|5end_Two-component_response_transcriptional_regulator_(CheY-like_receiver_and_AraC-type_DNA-binding_domains),_putative_1144491..1144721_POSITIVE 259 250 203 102 34 NC_009009:SSA_0157|5end_hypothetical_protein_153513..153743_POSITIVE 256 239 191 124 64 NC_009009:SSA_1452|5end_Second_subunit_of_major_exonuclease,_putative_1459696..1459926_NEGATIVE 256 219 172 141 96 NC_009009:SSA_1442|5end_Imidazole_glycerol-phosphate_synthase_subunit_hisF,_putative_1445941..1446171_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 336 47 2 77 35 NC_009009:SSA_0378|3end_TRZ/ATZ_family_hydrolase,_putative_368627..368777_POSITIVE 304 250 203 104 42 NC_009009:SSA_1371|3end_FmtA-like_protein,_putative_1387051..1387201_NEGATIVE 291 218 172 101 43 NC_009009:SSA_1015|3end_4-hydroxybenzoate_octaprenyltransferase,_putative_1019682..1019832_POSITIVE 289 245 206 116 81 NC_009009:SSA_0816|3end_Copper_transport_operon_or_penicillinase_transcription_repressor,_putative_797902..798052_POSITIVE 287 184 141 57 8 NC_009009:SSA_0273|3end_hypothetical_protein_268566..268716_POSITIVE 270 244 205 139 97 NC_009009:SSA_0752|3end_hypothetical_protein_734934..735084_POSITIVE 269 247 203 125 85 NC_009009:SSA_2302|3end_Type_IV_fimbrial_biogenesis_protein,_prepilin_cysteine_protease_(C20)_PilD,_putative_2303304..2303454_NEGATIVE 268 144 115 126 97 NC_009009:SSA_0271|3end_Glycosylhydrolase,_family_35,_putative_266093..266243_POSITIVE 256 244 202 75 30 NC_009009:SSA_1537|3end_Conserved_uncharacterized_protein_1544229..1544379_NEGATIVE 256 219 172 138 93 NC_009009:SSA_1443|3end_1-(5-phosphoribosyl)-5-[(5-_phosphoribosylamino)methylideneamino]_imidazole-4-carboxamide_isomerase,_putative_1445944..1446094_NEGATIVE 256 197 151 50 6 NC_009009:SSA_1406|3end_Histone_acetyltransferase_HPA2,_putative_1419455..1419605_NEGATIVE 255 149 102 107 61 NC_009009:SSA_1547|3end_HPr_kinase/phosphorylase,_putative_1550045..1550195_NEGATIVE 254 244 207 137 94 NC_009009:SSA_1743|3end_ABC-type_Fe3+-siderophore_transport_system,_permease_component,_putative_1731005..1731155_POSITIVE 253 218 174 151 112 NC_009009:SSA_0907|3end_Fibronectin-binding_protein_A,_putative_917568..917718_NEGATIVE 252 153 119 141 104 NC_009009:SSA_0874|3end_hypothetical_protein_868995..869145_POSITIVE 252 44 9 130 88 NC_009009:SSA_0459|3end_hypothetical_protein_462513..462663_POSITIVE 252 210 163 83 33 NC_009009:SSA_0364|3end_Serine/threonine:Na+_symporter,_putative_355311..355461_NEGATIVE 251 235 191 55 15 NC_009009:SSA_0575|3end_Hydrolase,_HAD_superfamily,_putative_570116..570266_POSITIVE 249 188 141 79 32 NC_009009:SSA_1666|3end_Collagen-binding_surface_protein,_putative_1665375..1665525_NEGATIVE 249 251 222 46 15 NC_009009:SSA_1564|3end_Histidine_kinase,_putative_1567266..1567416_NEGATIVE