Origin IGS: ggaaaacactccttattatttttacactgtttattttaccataacatttctctgtgcacaagttcgcctgctattaagctctctcttcagataaaatttaattacatcaagatgaatttgttcactctaccatacttttaacaagtcccagcaaaactcttgttcttgtgttagaataaaagggaattctaattaacagtaaaaacatatcaggaggaagata .........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 tatcttcctcctgatatgtttttactgttaattagaattcccttttattctaacacaagaacaagagttttgctgggacttgttaaaagtatggtagagtgaacaaattcatcttgatgtaattaaattttatctgaagagagagcttaatagcaggcgaacttgtgcacagagaaatgttatggtaaaataaacagtgtaaaaataataaggagtgttttcc Mask Tandem Repeat Region ================================================ ggaaaacactccttattatttttacactgtttattttaccataacatttctctgtgcacaagttcgcctgctattaagctctctcttcagataaaatttaattacatcaagatgaatttgttcactctaccatacttttaacaagtcccagcaaaactcttgttcttgtgttagaataaaagggaattctaattaacagtaaaaacatatcaggaggaagata Find is-nt database================================================ Query_seq: SSA_1627:SSA_1628|SSA_1627:SSA_1628:hypothetical protein:MutT/nudix family protein, putative:<-->:1629781..1630003 223 ggaaaacactccttattatttttacactgtttattttaccataacatttctctgtgcacaagttcgcctgctattaagctctctcttcagataaaatttaattacatcaagatgaatttgttcactctaccatacttttaacaagtcccagcaaaactcttgttcttgtgttagaataaaagggaattctaattaacagtaaaaacatatcaggaggaagata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1627:SSA_1628|SSA_1627:SSA_1628:hypothetical protein:MutT/nudix family protein, putative:<-->:1629781..1630003 223 ggaaaacactccttattatttttacactgtttattttaccataacatttctctgtgcacaagttcgcctgctattaagctctctcttcagataaaatttaattacatcaagatgaatttgttcactctaccatacttttaacaagtcccagcaaaactcttgttcttgtgttagaataaaagggaattctaattaacagtaaaaacatatcaggaggaagata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1627:SSA_1628|SSA_1627:SSA_1628:hypothetical protein:MutT/nudix family protein, putative:<-->:1629781..1630003 223 ggaaaacactccttattatttttacactgtttattttaccataacatttctctgtgcacaagttcgcctgctattaagctctctcttcagataaaatttaattacatcaagatgaatttgttcactctaccatacttttaacaagtcccagcaaaactcttgttcttgtgttagaataaaagggaattctaattaacagtaaaaacatatcaggaggaagata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ggaaaacactccttattatttttacactgtttattttaccataacatttctctgtgcacaagttcgcctgctattaagctctctcttcagataaaatttaattacatcaagatgaatttgttcactctaccatacttttaacaagtcccagcaaaactcttgttcttgtgttagaataaaagggaattctaattaacagtaaaaacatatcaggaggaagata Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: + Start: 46 End: 138 ............................................. M S L C T S S P A I K L S L Q I K F N Y I K M N L F T L P Y F ..................................................................................... ggaaaacactccttattatttttacactgtttattttaccataacatttctctgtgcacaagttcgcctgctattaagctctctcttcagataaaatttaattacatcaagatgaatttgttcactctaccatacttttaacaagtcccagcaaaactcttgttcttgtgttagaataaaagggaattctaattaacagtaaaaacatatcaggaggaagata 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: 33 End: 62 ................................CTTGTGCACAGAGAAATGTTATGGTAAAAT................................................................................................................................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ggaaaacactccttattatttttacactgtttattttaccataacatttctctgtgcacaagttcgcctgctattaagctctctcttcagataaaatttaattacatcaagatgaatttgttcactctaccatacttttaacaagtcccagcaaaactcttgttcttgtgttagaataaaagggaattctaattaacagtaaaaacatatcaggaggaagata Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_1627:SSA_1628|SSA_1627:SSA_1628:hypothetical protein:MutT/nudix family protein, putative:<-->:1629781..1630003 223 ggaaaacactccttattatttttacactgtttattttaccataacatttctctgtgcacaagttcgcctgctattaagctctctcttcagataaaatttaattacatcaagatgaatttgttcactctaccatacttttaacaagtcccagcaaaactcttgttcttgtgttagaataaaagggaattctaattaacagtaaaaacatatcaggaggaagata Intra-Species Hit: Count: 1 Min: 1 Max: 223 Len: 223 Subject: NC_009009_SSA_1627_SSA_1628|hypothetical protein:MutT/nudix family protein, putative|NEGATIVE:POSITIVE|[1629781,1630003]|223 HSP 1 e-value: 1.0E-123 bit: 442.0 Len: 223 Query Start:1 Query End:223 Subject Strand: POSITIVE Subject Start: 1 Subject End: 223 ggaaaacactccttattatttttacactgtttattttaccataacatttctctgtgcacaagttcgcctgctattaagctctctcttcagataaaatttaattacatcaagatgaatttgttcactctaccatacttttaacaagtcccagcaaaactcttgttcttgtgttagaataaaagggaattctaattaacagtaaaaacatatcaggaggaagata ggaaaacactccttattatttttacactgtttattttaccataacatttctctgtgcacaagttcgcctgctattaagctctctcttcagataaaatttaattacatcaagatgaatttgttcactctaccatacttttaacaagtcccagcaaaactcttgttcttgtgttagaataaaagggaattctaattaacagtaaaaacatatcaggaggaagata Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GGAAAACACUCCUUAUUAUUUUUACACUGUUUAUUUUACCAUAACAUUUCUCUGUGCACAAGUUCGCCUGCUAUUAAGCUCUCUCUUCAGAUAAAAUUUAAUUACAUCAAGAUGAAUUUGUUCACUCUACCAUACUUUUAACAAGUCCCAGCAAAACUCUUGUUCUUGUGUUAGAAUAAAAGGGAAUUCUAAUUAACAGUAAAAACAUAUCAGGAGGAAGAUA ........(((((.((..(((((((..((((...........)))).(((((((((.(((((((((.(((((....)))..(((....)))..................)).))))))))).)))..........((((((((......(((((.....)))))....))))))))....))))))............)))))))...)).)))))....... (-36.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAUCUUCCUCCUGAUAUGUUUUUACUGUUAAUUAGAAUUCCCUUUUAUUCUAACACAAGAACAAGAGUUUUGCUGGGACUUGUUAAAAGUAUGGUAGAGUGAACAAAUUCAUCUUGAUGUAAUUAAAUUUUAUCUGAAGAGAGAGCUUAAUAGCAGGCGAACUUGUGCACAGAGAAAUGUUAUGGUAAAAUAAACAGUGUAAAAAUAAUAAGGAGUGUUUUCC .......(((((....(((((((((((((..(((((((........))))))).((...((((.....(((((((..((((.....)))).)))))))(((.((((.(((.((((.(.((((.......)))).).))))....(((....)))....))).)))).))).......))))...))......)))))))..))))))...)))))........ (-43.70) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 909 90 41 181 132 NC_009009:SSA_1627|5end_hypothetical_protein_1629690..1629920_NEGATIVE 310 94 55 183 149 NC_009009:SSA_0377|5end_ABC-type_methionine_transporter,_permease_component,_putative_366446..366676_POSITIVE 303 99 66 51 15 NC_009009:SSA_1452|5end_Second_subunit_of_major_exonuclease,_putative_1459696..1459926_NEGATIVE 298 92 51 87 42 NC_009009:SSA_2317|5end_Tfp_pilus_assembly_protein,_pilus_retraction_ATPase_PilT,_putative_2319410..2319640_NEGATIVE 285 109 63 77 15 NC_009009:SSA_1459|5end_RNA_methyltransferase,_putative_1467481..1467711_NEGATIVE 284 80 32 139 91 NC_009009:SSA_0509|5end_Propanediol_utilization_protein,_putative_508024..508254_POSITIVE 281 157 113 64 10 NC_009009:SSA_2264|5end_hypothetical_protein_2261757..2261987_NEGATIVE 279 90 47 67 28 NC_009009:SSA_0487|5end_Delta-aminolevulinic_acid_dehydratase,_putative_487349..487579_POSITIVE 277 90 49 212 167 NC_009009:SSA_1693|5end_Phosphotransferase_system_lactose-specific_component_IIBC,_putative_1686811..1687041_NEGATIVE 277 80 39 75 24 NC_009009:SSA_1154|5end_hypothetical_protein_1182661..1182891_POSITIVE 276 168 124 68 11 NC_009009:SSA_1375|5end_Multidrug_ABC_transporter,_ATPase_and_permease_components,_putative_1394827..1395057_NEGATIVE 275 130 85 193 138 NC_009009:SSA_1345|5end_Bifunctional_pyrimidine_operon_transcriptional_attenuation_protein/uracil_phosphoribosyltransferase,_putative_1363879..1364109_NEGATIVE 274 97 51 54 5 NC_009009:SSA_0567|5end_Isochorismitase_family_protein,_putative_560805..561035_POSITIVE 266 183 141 208 160 NC_009009:SSA_2189|5end_hypothetical_protein_2191097..2191327_NEGATIVE 261 90 41 231 171 NC_009009:SSA_2239|5end_Conserved_uncharacterized_cytosolic_protein_2237233..2237463_NEGATIVE 257 84 45 71 41 NC_009009:SSA_1429|5end_hypothetical_protein_1437110..1437340_NEGATIVE 257 169 125 66 26 NC_009009:SSA_1280|5end_hypothetical_protein_1301596..1301826_NEGATIVE 256 87 45 102 49 NC_009009:SSA_0315|5end_Transcriptional_regulator,_MarR_family,_putative_310102..310332_POSITIVE 255 75 38 214 172 NC_009009:SSA_0870|5end_Cell_division_protein_FtsE,_putative_862936..863166_POSITIVE 255 92 53 107 61 NC_009009:SSA_0171|5end_Cro-like_transcriptional_repressor,_XRE_family,_putative_168956..169186_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 299 87 45 84 45 NC_009009:SSA_0567|3end_Isochorismitase_family_protein,_putative_561442..561592_POSITIVE 298 92 51 85 40 NC_009009:SSA_2318|3end_PilB-like_pili_biogenesis_ATPase,_putative_2319412..2319562_NEGATIVE 284 80 32 99 51 NC_009009:SSA_0508|3end_Conserved_uncharacterized_protein,_possible_phosphoserine_phosphatase_508064..508214_POSITIVE 279 90 47 80 41 NC_009009:SSA_0486|3end_Uroporphyrinogen-III_synthase,_putative_487442..487592_POSITIVE 277 80 39 82 31 NC_009009:SSA_1153|3end_HemK_protein,_putative_1182748..1182898_POSITIVE 274 97 51 54 5 NC_009009:SSA_0566|3end_GTP-sensing_transcriptional_pleiotropic_repressor,_putative_560885..561035_POSITIVE 257 84 45 74 44 NC_009009:SSA_1430|3end_Ribonuclease_Z,_putative_1437107..1437257_NEGATIVE 257 169 125 54 14 NC_009009:SSA_1281|3end_Uracil-DNA_glycosylase,_putative_1301608..1301758_NEGATIVE 250 168 123 123 72 NC_009009:SSA_0541|3end_Acetate_kinase,_putative_537082..537232_POSITIVE 248 69 24 54 4 NC_009009:SSA_0162|3end_hypothetical_protein_162139..162289_POSITIVE 245 88 43 63 4 NC_009009:SSA_2220|3end_Galactosyltransferase,_putative_2220834..2220984_NEGATIVE 244 97 60 46 6 NC_009009:SSA_1447|3end_ATP_phosphoribosyltransferase,_putative_1449187..1449337_NEGATIVE 243 88 60 123 96 NC_009009:SSA_0727|3end_Metal-dependent_membrane_protease,_putative_713639..713789_POSITIVE 243 80 47 30 5 NC_009009:SSA_0638|3end_Tryptophan_synthase_alpha_chain,_putative_627794..627944_POSITIVE 241 79 39 149 111 NC_009009:SSA_2121|3end_Cell_wall_surface_anchor_family_protein,_putative_2122222..2122372_NEGATIVE 241 153 122 113 83 NC_009009:SSA_0056|3end_Phosphotransferase_system_sugar-specific_EIID_component,_putative_60830..60980_POSITIVE 239 91 60 134 98 NC_009009:SSA_0491|3end_Alpha-ribazole-5'-phosphate_phosphatase,_putative_491613..491763_POSITIVE 238 91 55 105 64 NC_009009:SSA_1522|3end_Cell_division_protein_FtsW,_putative_1530730..1530880_NEGATIVE 236 92 51 130 90 NC_009009:SSA_1149|3end_Glycosyl_hydrolase,_family_1,_putative_1179876..1180026_POSITIVE 236 75 37 58 12 NC_009009:SSA_0832|3end_SecY-like_protein,_putative_818011..818161_POSITIVE