Origin IGS: taaaataaaaattaagtcaagttaatttttaacaaatttctaaaattaatataagaaatgtttgaaaaaacaagtagattttgataaggttatatcaaaagcatgaaagtgagaagaag .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 cttcttctcactttcatgcttttgatataaccttatcaaaatctacttgttttttcaaacatttcttatattaattttagaaatttgttaaaaattaacttgacttaatttttatttta Mask Tandem Repeat Region ================================================ taaaataaaaattaagtcaagttaatttttaacaaatttctaaaattaatataagaaatgtttgaaaaaacaagtagattttgataaggttatatcaaaagcatgaaagtgagaagaag Find is-nt database================================================ Query_seq: SSA_0262:SSA_0263|SSA_0262:SSA_0263:ABC-type Mn/Zn transporter, ATP-ase component, putative:Zinc metalloproteinase in scaA 5'region, putative:<-->:256295..256413 119 taaaataaaaattaagtcaagttaatttttaacaaatttctaaaattaatataagaaatgtttgaaaaaacaagtagattttgataaggttatatcaaaagcatgaaagtgagaagaag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0262:SSA_0263|SSA_0262:SSA_0263:ABC-type Mn/Zn transporter, ATP-ase component, putative:Zinc metalloproteinase in scaA 5'region, putative:<-->:256295..256413 119 taaaataaaaattaagtcaagttaatttttaacaaatttctaaaattaatataagaaatgtttgaaaaaacaagtagattttgataaggttatatcaaaagcatgaaagtgagaagaag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0262:SSA_0263|SSA_0262:SSA_0263:ABC-type Mn/Zn transporter, ATP-ase component, putative:Zinc metalloproteinase in scaA 5'region, putative:<-->:256295..256413 119 taaaataaaaattaagtcaagttaatttttaacaaatttctaaaattaatataagaaatgtttgaaaaaacaagtagattttgataaggttatatcaaaagcatgaaagtgagaagaag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taaaataaaaattaagtcaagttaatttttaacaaatttctaaaattaatataagaaatgtttgaaaaaacaagtagattttgataaggttatatcaaaagcatgaaagtgagaagaag Predict ORF larger than 30AA ================================================ taaaataaaaattaagtcaagttaatttttaacaaatttctaaaattaatataagaaatgtttgaaaaaacaagtagattttgataaggttatatcaaaagcatgaaagtgagaagaag 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: 82 Start: 61 End: 90 ............................................................TTTGAAAAAACAAGTAGATTTTGATAAGGT............................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ taaaataaaaattaagtcaagttaatttttaacaaatttctaaaattaatataagaaatgtttgaaaaaacaagtagattttgataaggttatatcaaaagcatgaaagtgagaagaag Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_0262:SSA_0263|SSA_0262:SSA_0263:ABC-type Mn/Zn transporter, ATP-ase component, putative:Zinc metalloproteinase in scaA 5'region, putative:<-->:256295..256413 119 taaaataaaaattaagtcaagttaatttttaacaaatttctaaaattaatataagaaatgtttgaaaaaacaagtagattttgataaggttatatcaaaagcatgaaagtgagaagaag Intra-Species Hit: Count: 1 Min: 1 Max: 119 Len: 119 Subject: NC_009009_SSA_0262_SSA_0263|ABC-type Mn/Zn transporter, ATP-ase component, putative:Zinc metalloproteinase in scaA 5'region, putative|NEGATIVE:POSITIVE|[256295,256413]|119 HSP 1 e-value: 1.0E-61 bit: 236.0 Len: 119 Query Start:1 Query End:119 Subject Strand: POSITIVE Subject Start: 1 Subject End: 119 taaaataaaaattaagtcaagttaatttttaacaaatttctaaaattaatataagaaatgtttgaaaaaacaagtagattttgataaggttatatcaaaagcatgaaagtgagaagaag taaaataaaaattaagtcaagttaatttttaacaaatttctaaaattaatataagaaatgtttgaaaaaacaagtagattttgataaggttatatcaaaagcatgaaagtgagaagaag Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAAAUAAAAAUUAAGUCAAGUUAAUUUUUAACAAAUUUCUAAAAUUAAUAUAAGAAAUGUUUGAAAAAACAAGUAGAUUUUGAUAAGGUUAUAUCAAAAGCAUGAAAGUGAGAAGAAG .....((((((((((......))))))))))......((((.................(((((....)))))......((((((((......)))))))).(((....)))...)))). (-16.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUUCUUCUCACUUUCAUGCUUUUGAUAUAACCUUAUCAAAAUCUACUUGUUUUUUCAAACAUUUCUUAUAUUAAUUUUAGAAAUUUGUUAAAAAUUAACUUGACUUAAUUUUUAUUUUA ...........((((....((((((((......))))))))......(((((....)))))..................)))).....((((((((((......))))))))))..... (-12.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 687 110 61 201 152 NC_009009:SSA_0262|5end_ABC-type_Mn/Zn_transporter,_ATP-ase_component,_putative_256204..256434_NEGATIVE 208 110 69 52 15 NC_009009:SSA_1019|5end_Collagen-binding_surface_protein,_putative_1032877..1033107_POSITIVE 194 49 6 220 176 NC_009009:SSA_0021|5end_hypothetical_protein_26842..27072_POSITIVE 181 109 72 151 106 NC_009009:SSA_0357|5end_Thioredoxin,_putative_350763..350993_POSITIVE 175 108 72 78 50 NC_009009:SSA_0714|5end_hypothetical_protein_700042..700272_POSITIVE 170 88 41 211 159 NC_009009:SSA_1525|5end_Lyzozyme_M1_(1,4-beta-N-acetylmuramidase),_putative_1532746..1532976_POSITIVE 163 110 73 168 130 NC_009009:SSA_1229|5end_hypothetical_protein_1252421..1252651_NEGATIVE 157 83 61 55 33 NC_009009:SSA_1001|5end_Arabinose_(multiple_sugar_metabolism)_operon_transcriptional_regulator,_putative_1001689..1001919_NEGATIVE 153 110 81 67 31 NC_009009:SSA_0880|5end_Lipoprotein,_putative_875451..875681_POSITIVE 153 106 79 65 46 NC_009009:SSA_0664|5end_Conserved_uncharacterized_protein_649086..649316_NEGATIVE 152 108 79 76 47 NC_009009:SSA_1405|5end_Copper_homeostasis_protein_CutC,_putative_1419393..1419623_NEGATIVE 149 107 86 171 149 NC_009009:SSA_1093|5end_ATP-dependent_Clp_protease_ATP-binding_subunit_clpX,_putative_1110336..1110566_POSITIVE 147 94 51 129 90 NC_009009:SSA_0801|5end_Mur_ligase_family_protein,_putative_784117..784347_NEGATIVE 146 90 59 160 130 NC_009009:SSA_0144|5end_Transcriptional_regulator,_TetR_family,_putative_138565..138795_NEGATIVE 145 108 79 142 108 NC_009009:SSA_1205|5end_Bta,_putative_1229630..1229860_POSITIVE 144 88 51 226 191 NC_009009:SSA_0135|5end_Multiple_antibiotic_resistance_operon_transcriptional_repressor_(MarR),_putative_130574..130804_POSITIVE 143 108 82 169 135 NC_009009:SSA_1147|5end_Beta-glucosides_PTS,_EIIB,_putative_1176782..1177012_POSITIVE 143 95 55 170 131 NC_009009:SSA_0824|5end_DNA_primase_(bacterial_type),_putative_802053..802283_POSITIVE 143 97 59 185 150 NC_009009:SSA_0123|5end_50S_ribosomal_protein_L18P,_putative_116048..116278_POSITIVE 142 91 55 96 55 NC_009009:SSA_0795|5end_hypothetical_protein_776620..776850_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 181 109 72 65 20 NC_009009:SSA_0356|3end_Dipeptidase,_putative_350757..350907_POSITIVE 155 93 53 77 31 NC_009009:SSA_0167|3end_Hypothetical_protein_(Asparagine/proline-rich)_166335..166485_POSITIVE 154 74 32 71 33 NC_009009:SSA_0245|3end_hypothetical_protein_239608..239758_POSITIVE 152 104 73 104 76 NC_009009:SSA_2329|3end_hypothetical_protein_2333169..2333319_POSITIVE 143 109 72 107 72 NC_009009:SSA_0253|3end_CAAX_amino_terminal_protease_family_protein,_putative_246983..247133_POSITIVE 143 97 59 100 65 NC_009009:SSA_0122|3end_50S_ribosomal_protein_L6,_putative_116043..116193_POSITIVE 142 91 55 91 50 NC_009009:SSA_0794|3end_Zn-dependent_protease,_putative_776695..776845_POSITIVE 142 107 75 70 47 NC_009009:SSA_0285|3end_Formate_acetyltransferase_3,_putative_278879..279029_POSITIVE 138 102 64 114 73 NC_009009:SSA_0891|3end_3-carboxymuconate_cyclase,_putative_883023..883173_NEGATIVE 138 105 72 136 103 NC_009009:SSA_0325|3end_Membrane-anchored_glycerophosphoryl_diester_phosphodiesterase,_putative_319437..319587_POSITIVE 137 110 83 144 118 NC_009009:SSA_0713|3end_1-acyl-sn-glycerol-3-phosphate_acyltransferase,_putative_700028..700178_POSITIVE 136 106 68 90 42 NC_009009:SSA_1436|3end_hypothetical_protein_1442199..1442349_NEGATIVE 134 91 52 60 12 NC_009009:SSA_1091|3end_Thymidylate_synthase,_putative_1109554..1109704_POSITIVE 134 91 51 78 44 NC_009009:SSA_1056|3end_Firmicute_fructose-1,6-bisphosphatase,_putative_1073750..1073900_POSITIVE 134 74 54 74 54 NC_009009:SSA_0888|3end_Magnesium/cobalt_transporter,_putative_882749..882899_POSITIVE 131 103 71 72 32 NC_009009:SSA_1214|3end_Conserved_uncharacterized_Lactobacillales_protein_1237909..1238059_POSITIVE 126 91 72 53 34 NC_009009:SSA_1432|3end_HflX_GTPase,_putative_1438663..1438813_NEGATIVE 126 90 73 20 2 NC_009009:SSA_1275|3end_hypothetical_protein_1297508..1297658_NEGATIVE 126 90 46 66 15 NC_009009:SSA_1105|3end_50S_ribosomal_protein_L7/_L12,_putative_1125765..1125915_POSITIVE 126 109 72 114 69 NC_009009:SSA_0573|3end_hypothetical_protein_568616..568766_NEGATIVE