Origin IGS: tgattgacaactagggcctcagctggggctcttttttatgccataattgtattaaaagacttgcgcaattagattaggcttgttataatagctaaaatctcttgaaaccaagtgttgggaaagtgaggatatggcgg .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ccgccatatcctcactttcccaacacttggtttcaagagattttagctattataacaagcctaatctaattgcgcaagtcttttaatacaattatggcataaaaaagagccccagctgaggccctagttgtcaatca Mask Tandem Repeat Region ================================================ tgattgacaactagggcctcagctggggctcttttttatgccataattgtattaaaagacttgcgcaattagattaggcttgttataatagctaaaatctcttgaaaccaagtgttgggaaagtgaggatatggcgg Find is-nt database================================================ Query_seq: SSA_0377:SSA_0378|SSA_0377:SSA_0378:ABC-type methionine transporter, permease component, putative:TRZ/ATZ family hydrolase, putative:->->:367279..367415 137 tgattgacaactagggcctcagctggggctcttttttatgccataattgtattaaaagacttgcgcaattagattaggcttgttataatagctaaaatctcttgaaaccaagtgttgggaaagtgaggatatggcgg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0377:SSA_0378|SSA_0377:SSA_0378:ABC-type methionine transporter, permease component, putative:TRZ/ATZ family hydrolase, putative:->->:367279..367415 137 tgattgacaactagggcctcagctggggctcttttttatgccataattgtattaaaagacttgcgcaattagattaggcttgttataatagctaaaatctcttgaaaccaagtgttgggaaagtgaggatatggcgg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0377:SSA_0378|SSA_0377:SSA_0378:ABC-type methionine transporter, permease component, putative:TRZ/ATZ family hydrolase, putative:->->:367279..367415 137 tgattgacaactagggcctcagctggggctcttttttatgccataattgtattaaaagacttgcgcaattagattaggcttgttataatagctaaaatctcttgaaaccaagtgttgggaaagtgaggatatggcgg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgattgacaactagggcctcagctggggctcttttttatgccataattgtattaaaagacttgcgcaattagattaggcttgttataatagctaaaatctcttgaaaccaagtgttgggaaagtgaggatatggcgg Predict ORF larger than 30AA ================================================ tgattgacaactagggcctcagctggggctcttttttatgccataattgtattaaaagacttgcgcaattagattaggcttgttataatagctaaaatctcttgaaaccaagtgttgggaaagtgaggatatggcgg 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: 86 Start: 60 End: 89 ...........................................................CTTGCGCAATTAGATTAGGCTTGTTATAAT................................................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tgattgacaactagggcctcagctggggctcttttttatgccataattgtattaaaagacttgcgcaattagattaggcttgttataatagctaaaatctcttgaaaccaagtgttgggaaagtgaggatatggcgg Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_0377:SSA_0378|SSA_0377:SSA_0378:ABC-type methionine transporter, permease component, putative:TRZ/ATZ family hydrolase, putative:->->:367279..367415 137 tgattgacaactagggcctcagctggggctcttttttatgccataattgtattaaaagacttgcgcaattagattaggcttgttataatagctaaaatctcttgaaaccaagtgttgggaaagtgaggatatggcgg Intra-Species Hit: Count: 1 Min: 1 Max: 137 Len: 137 Subject: NC_009009_SSA_0377_SSA_0378|ABC-type methionine transporter, permease component, putative:TRZ/ATZ family hydrolase, putative|POSITIVE:POSITIVE|[367279,367415]|137 HSP 1 e-value: 3.0E-72 bit: 272.0 Len: 137 Query Start:1 Query End:137 Subject Strand: POSITIVE Subject Start: 1 Subject End: 137 tgattgacaactagggcctcagctggggctcttttttatgccataattgtattaaaagacttgcgcaattagattaggcttgttataatagctaaaatctcttgaaaccaagtgttgggaaagtgaggatatggcgg tgattgacaactagggcctcagctggggctcttttttatgccataattgtattaaaagacttgcgcaattagattaggcttgttataatagctaaaatctcttgaaaccaagtgttgggaaagtgaggatatggcgg Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGAUUGACAACUAGGGCCUCAGCUGGGGCUCUUUUUUAUGCCAUAAUUGUAUUAAAAGACUUGCGCAAUUAGAUUAGGCUUGUUAUAAUAGCUAAAAUCUCUUGAAACCAAGUGUUGGGAAAGUGAGGAUAUGGCGG ............((((((((....))))))))......(((((((.(..(.((..((.(((((..(((..(((((.((((.........))))..))))).)))....))))).))...)).)..)...))))))). (-33.00) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CCGCCAUAUCCUCACUUUCCCAACACUUGGUUUCAAGAGAUUUUAGCUAUUAUAACAAGCCUAAUCUAAUUGCGCAAGUCUUUUAAUACAAUUAUGGCAUAAAAAAGAGCCCCAGCUGAGGCCCUAGUUGUCAAUCA ..((((((...........(((.....)))....(((((((((..((.((((..............)))).))..)))))))))........))))))........((....((((((......))))))....)). (-23.44) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 333 46 13 93 60 NC_009009:SSA_2017|5end_Hypothetical_protein_(possibly_membrane-associated)_2017331..2017561_NEGATIVE 308 100 56 71 28 NC_009009:SSA_1934|5end_Biotin_carboxyl_carrier_protein_of_acetyl-CoA_carboxylase,_putative_1921800..1922030_NEGATIVE 301 29 2 166 131 NC_009009:SSA_0071|5end_N-acetylmannosamine-6-p_hosphate_2-epimerase_1,_putative_75210..75440_POSITIVE 280 53 11 98 52 NC_009009:SSA_2145|5end_Tributyrin_esterase,_putative_2146658..2146888_NEGATIVE 274 42 8 62 25 NC_009009:SSA_2102|5end_Conserved_uncharacterized_protein_2106410..2106640_NEGATIVE 274 44 6 46 5 NC_009009:SSA_1670|5end_Transcriptional_regulator,_TetR/AcrR_family,_putative_1669248..1669478_NEGATIVE 272 52 13 84 39 NC_009009:SSA_1865|5end_Thioredoxin_reductase,_putative_1861892..1862122_NEGATIVE 267 56 13 152 104 NC_009009:SSA_2267|5end_Lactose_operon_transcriptional_repressor,_LacI_family,_putative_2266127..2266357_POSITIVE 267 42 14 231 197 NC_009009:SSA_1167|5end_SRP54,_signal_recognition_particle_GTPase_protein,_putative_1192517..1192747_POSITIVE 262 29 7 63 37 NC_009009:SSA_1340|5end_Zn/Mn_ABC-type_porter_lipoprotein,_putative_1356372..1356602_NEGATIVE 261 54 13 156 115 NC_009009:SSA_2205|5end_Transcription_antitermination_factor_NusG,_putative_2206100..2206330_NEGATIVE 260 35 6 225 186 NC_009009:SSA_0625|5end_Phosphopantetheine_adenylyltransferase_615608..615838_POSITIVE 259 50 5 55 6 NC_009009:SSA_1077|5end_N-acetyl-glucosamine_matabolism,_putative_1094979..1095209_POSITIVE 259 43 19 35 9 NC_009009:SSA_1053|5end_Pyruvate_phosphate_dikinase,_putative_1070068..1070298_NEGATIVE 259 100 57 84 44 NC_009009:SSA_0217|5end_Two-component_system_transcriptional_regulator_(CheY_domain_and_HTH-like_DNA-binding_domain),_putative_213183..213413_POSITIVE 258 42 8 195 161 NC_009009:SSA_0087|5end_V-type_sodium_ATPase,_subunit_E,_putative_88329..88559_POSITIVE 254 41 3 149 113 NC_009009:SSA_2120|5end_GTPase,_putative_2121751..2121981_NEGATIVE 253 41 12 57 30 NC_009009:SSA_1440|5end_Phosphoribosyl-ATP_pyrophosphohydrolase,_putative_1444721..1444951_NEGATIVE 253 120 77 73 39 NC_009009:SSA_1417|5end_SAM-dependent_methyltransferase,_putative_1427993..1428223_NEGATIVE 253 45 1 81 33 NC_009009:SSA_1012|5end_Phosphoenolpyruvate_synthase,_putative_1014739..1014969_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 360 32 13 78 59 NC_009009:SSA_0377|3end_ABC-type_methionine_transporter,_permease_component,_putative_367218..367368_POSITIVE 308 100 56 64 21 NC_009009:SSA_1935|3end_Beta-ketoacyl-ACP_synthase_II_(3-oxoacyl-(Acyl-carrier-protein)_synthase_II),_putative_1921807..1921957_NEGATIVE 259 100 57 91 51 NC_009009:SSA_0216|3end_Histidine_kinase,_putative_213270..213420_POSITIVE 255 118 74 139 86 NC_009009:SSA_1457|3end_Neopullulanase,_putative_1462485..1462635_NEGATIVE 253 45 1 66 18 NC_009009:SSA_1011|3end_hypothetical_protein_1014804..1014954_POSITIVE 251 53 11 90 45 NC_009009:SSA_1393|3end_hypothetical_protein_1408414..1408564_NEGATIVE 249 64 21 51 16 NC_009009:SSA_0978|3end_hypothetical_protein_984082..984232_POSITIVE 249 67 24 142 101 NC_009009:SSA_0317|3end_Ribosomal_protein_alanine_acetyl_transferase,_putative_311791..311941_POSITIVE 248 48 10 86 38 NC_009009:SSA_2241|3end_Conserved_uncharacterized_protein_2237677..2237827_NEGATIVE 241 42 1 139 107 NC_009009:SSA_1879|3end_Glycyl-tRNA_synthetase_beta_chain,_putative_1872223..1872373_NEGATIVE 238 31 19 126 114 NC_009009:SSA_1874|3end_YorfE_protein,_putative_1870590..1870740_POSITIVE 238 30 4 90 69 NC_009009:SSA_0733|3end_hypothetical_protein_716937..717087_POSITIVE 237 129 100 41 10 NC_009009:SSA_2028|3end_Conserved_uncharacterized_protein_2035174..2035324_NEGATIVE 236 29 4 139 113 NC_009009:SSA_2325|3end_3-methyladenine_DNA_glycosylase,_putative_2330113..2330263_NEGATIVE 236 38 13 148 119 NC_009009:SSA_1980|3end_50S_ribosomal_protein_L28,_putative_1974444..1974594_NEGATIVE 236 41 11 90 62 NC_009009:SSA_1848|3end_Methionyl-tRNA_formyltransferase,_putative_1842243..1842393_NEGATIVE 233 90 46 108 60 NC_009009:SSA_2237|3end_Dihydrofolate:folylpolyglutamate_synthetase,_putative_2235508..2235658_NEGATIVE 233 50 2 52 15 NC_009009:SSA_2098|3end_ABC-type_arginine/histidine_transporter,_permease_protein,_putative_2102931..2103081_NEGATIVE 233 35 9 92 64 NC_009009:SSA_0332|3end_hypothetical_protein_326924..327074_POSITIVE 232 51 11 108 70 NC_009009:SSA_1590|3end_Transcriptional_regulator,_TetR/AcrR_family,_putative_1593342..1593492_POSITIVE