Origin IGS: accttttctccttcgaatgtcatatatgaactactatagcagatttcccttatttttacaagacgattctgacttttcaggcaaagtccgtctcaagtcggatgaagcatgactggcctaaccacattttttaaaaagtaaaaatcaggatgactaacaccctgattttatgtcttt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aaagacataaaatcagggtgttagtcatcctgatttttactttttaaaaaatgtggttaggccagtcatgcttcatccgacttgagacggactttgcctgaaaagtcagaatcgtcttgtaaaaataagggaaatctgctatagtagttcatatatgacattcgaaggagaaaaggt Mask Tandem Repeat Region ================================================ accttttctccttcgaatgtcatatatgaactactatagcagatttcccttatttttacaagacgattctgacttttcaggcaaagtccgtctcaagtcggatgaagcatgactggcctaaccacattttttaaaaagtaaaaatcaggatgactaacaccctgattttatgtcttt Find is-nt database================================================ Query_seq: SSA_2074:SSA_2075|SSA_2074:SSA_2075:Preprotein translocase subunit YajC, putative:Transketolase, putative:<-<-:2077026..2077202 177 accttttctccttcgaatgtcatatatgaactactatagcagatttcccttatttttacaagacgattctgacttttcaggcaaagtccgtctcaagtcggatgaagcatgactggcctaaccacattttttaaaaagtaaaaatcaggatgactaacaccctgattttatgtcttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_2074:SSA_2075|SSA_2074:SSA_2075:Preprotein translocase subunit YajC, putative:Transketolase, putative:<-<-:2077026..2077202 177 accttttctccttcgaatgtcatatatgaactactatagcagatttcccttatttttacaagacgattctgacttttcaggcaaagtccgtctcaagtcggatgaagcatgactggcctaaccacattttttaaaaagtaaaaatcaggatgactaacaccctgattttatgtcttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_2074:SSA_2075|SSA_2074:SSA_2075:Preprotein translocase subunit YajC, putative:Transketolase, putative:<-<-:2077026..2077202 177 accttttctccttcgaatgtcatatatgaactactatagcagatttcccttatttttacaagacgattctgacttttcaggcaaagtccgtctcaagtcggatgaagcatgactggcctaaccacattttttaaaaagtaaaaatcaggatgactaacaccctgattttatgtcttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 accttttctccttcgaatgtcatatatgaactactatagcagatttcccttatttttacaagacgattctgacttttcaggcaaagtccgtctcaagtcggatgaagcatgactggcctaaccacattttttaaaaagtaaaaatcaggatgactaacaccctgattttatgtcttt Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: + Start: 17 End: 109 ................ M S Y M N Y Y S R F P L F L Q D D S D F S G K V R L K S D E A .................................................................... Protein_Len: 32 Strand: + Start: 36 End: 131 ................................... M A D F P Y F Y K T I L T F Q A K S V S S R M K H D W P N H I F .............................................. accttttctccttcgaatgtcatatatgaactactatagcagatttcccttatttttacaagacgattctgacttttcaggcaaagtccgtctcaagtcggatgaagcatgactggcctaaccacattttttaaaaagtaaaaatcaggatgactaacaccctgattttatgtcttt 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: 33 End: 62 ................................CTTGTAAAAATAAGGGAAATCTGCTATAGT................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ accttttctccttcgaatgtcatatatgaactactatagcagatttcccttatttttacaagacgattctgacttttcaggcaaagtccgtctcaagtcggatgaagcatgactggcctaaccacattttttaaaaagtaaaaatcaggatgactaacaccctgattttatgtcttt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_2074:SSA_2075|SSA_2074:SSA_2075:Preprotein translocase subunit YajC, putative:Transketolase, putative:<-<-:2077026..2077202 177 accttttctccttcgaatgtcatatatgaactactatagcagatttcccttatttttacaagacgattctgacttttcaggcaaagtccgtctcaagtcggatgaagcatgactggcctaaccacattttttaaaaagtaaaaatcaggatgactaacaccctgattttatgtcttt Intra-Species Hit: Count: 1 Min: 1 Max: 177 Len: 177 Subject: NC_009009_SSA_2074_SSA_2075|Preprotein translocase subunit YajC, putative:Transketolase, putative|NEGATIVE:NEGATIVE|[2077026,2077202]|177 HSP 1 e-value: 5.0E-96 bit: 351.0 Len: 177 Query Start:1 Query End:177 Subject Strand: POSITIVE Subject Start: 1 Subject End: 177 accttttctccttcgaatgtcatatatgaactactatagcagatttcccttatttttacaagacgattctgacttttcaggcaaagtccgtctcaagtcggatgaagcatgactggcctaaccacattttttaaaaagtaaaaatcaggatgactaacaccctgattttatgtcttt accttttctccttcgaatgtcatatatgaactactatagcagatttcccttatttttacaagacgattctgacttttcaggcaaagtccgtctcaagtcggatgaagcatgactggcctaaccacattttttaaaaagtaaaaatcaggatgactaacaccctgattttatgtcttt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACCUUUUCUCCUUCGAAUGUCAUAUAUGAACUACUAUAGCAGAUUUCCCUUAUUUUUACAAGACGAUUCUGACUUUUCAGGCAAAGUCCGUCUCAAGUCGGAUGAAGCAUGACUGGCCUAACCACAUUUUUUAAAAAGUAAAAAUCAGGAUGACUAACACCCUGAUUUUAUGUCUUU ......(((.((.......(((....)))........)).)))................((((((......((((((((.((...(((((.(....).)))))...)).))).(((.....)))..........))))).(((((((((.((.....)).))))))))).)))))). (-31.26) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAGACAUAAAAUCAGGGUGUUAGUCAUCCUGAUUUUUACUUUUUAAAAAAUGUGGUUAGGCCAGUCAUGCUUCAUCCGACUUGAGACGGACUUUGCCUGAAAAGUCAGAAUCGUCUUGUAAAAAUAAGGGAAAUCUGCUAUAGUAGUUCAUAUAUGACAUUCGAAGGAGAAAAGGU ........((((((((((((.....)))))))))))).(((((((.....(((((.((((((.((((.((..(((.......)))..))))))..))))))..((.((((.((.((((((....))))))))..)))))).........))))).......((....)).))))))) (-43.00) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 988 120 71 211 162 NC_009009:SSA_2074|5end_Preprotein_translocase_subunit_YajC,_putative_2076935..2077165_NEGATIVE 392 130 83 147 95 NC_009009:SSA_1890|5end_Acetyltransferase,_putative_1888145..1888375_NEGATIVE 348 126 81 117 68 NC_009009:SSA_2347|5end_Coenzyme_F390_synthetase,_putative_2349939..2350169_NEGATIVE 341 110 61 195 143 NC_009009:SSA_1012|5end_Phosphoenolpyruvate_synthase,_putative_1014739..1014969_POSITIVE 330 118 72 142 81 NC_009009:SSA_1415|5end_Oxidoreductase,_putative_1426508..1426738_NEGATIVE 327 119 79 177 127 NC_009009:SSA_1017|5end_hypothetical_protein_1022072..1022302_POSITIVE 316 129 82 222 165 NC_009009:SSA_1452|5end_Second_subunit_of_major_exonuclease,_putative_1459696..1459926_NEGATIVE 316 127 82 158 97 NC_009009:SSA_1412|5end_hypothetical_protein_1424095..1424325_NEGATIVE 309 124 83 75 36 NC_009009:SSA_0984|5end_SlyA-like_protein,_putative_987054..987284_POSITIVE 306 124 81 59 11 NC_009009:SSA_0680|5end_Serine/threonine_protein_phosphatase,_putative_662425..662655_POSITIVE 306 120 80 48 11 NC_009009:SSA_0433|5end_Methenyl_tetrahydrofolate_cyclohydrolase,_putative_435654..435884_NEGATIVE 305 110 65 54 9 NC_009009:SSA_2156|5end_Conserved_uncharacterized_protein_2156932..2157162_NEGATIVE 300 119 77 75 28 NC_009009:SSA_1070|5end_Ribosomal_large_subunit_pseudouridine_synthase_D,_putative_1088742..1088972_POSITIVE 298 125 81 190 145 NC_009009:SSA_1217|5end_Conserved_uncharacterized_protein_1238964..1239194_POSITIVE 297 118 75 60 13 NC_009009:SSA_0788|5end_Proton-translocating_ATPase,_F1_sector,_beta_subunit,_putative_771037..771267_POSITIVE 296 130 82 80 14 NC_009009:SSA_2101|5end_Amino_acid_ABC_transporter,_periplasmic_amino_acid-binding_protein,_putative_2105393..2105623_NEGATIVE 295 106 63 197 145 NC_009009:SSA_1986|5end_Acetyltransferase,_GNAT_family,_putative_1982531..1982761_NEGATIVE 285 69 25 57 16 NC_009009:SSA_2140|5end_Ribonuclease_P_protein_component,_putative_2140574..2140804_NEGATIVE 282 119 74 187 136 NC_009009:SSA_0337|5end_Hydroxymethylglutaryl-CoA_reductase,_putative_332163..332393_NEGATIVE 282 118 74 56 15 NC_009009:SSA_0219|5end_PTS_system,_sugar-specific_enzyme_IIA_component,_putative_215367..215597_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 392 130 83 146 94 NC_009009:SSA_1891|3end_Oxidoreductase,_aldo/keto_reductase_family,_putative_1888146..1888296_NEGATIVE 336 116 79 140 109 NC_009009:SSA_0752|3end_hypothetical_protein_734934..735084_POSITIVE 330 118 72 130 69 NC_009009:SSA_1416|3end_hypothetical_protein_1426520..1426670_NEGATIVE 300 119 77 91 44 NC_009009:SSA_1069|3end_Lipoprotein_signal_peptidase,_putative_1088838..1088988_POSITIVE 295 106 63 145 93 NC_009009:SSA_1987|3end_hypothetical_protein_1982583..1982733_NEGATIVE 286 130 86 64 2 NC_009009:SSA_2102|3end_Conserved_uncharacterized_protein_2105409..2105559_NEGATIVE 281 102 61 150 107 NC_009009:SSA_0904|3end_CshA-like_fibrillar_surface_protein_A_902958..903108_POSITIVE 278 118 77 151 110 NC_009009:SSA_0062|3end_Aldose_1-epimerase,_putative_64858..65008_POSITIVE 276 130 81 88 43 NC_009009:SSA_0232|3end_hypothetical_protein_227277..227427_POSITIVE 273 102 66 124 78 NC_009009:SSA_1243|3end_Dihydroorotate_dehydrogenase_electron_transfer_subunit,_putative_1267398..1267548_NEGATIVE 270 105 62 44 1 NC_009009:SSA_2317|3end_Tfp_pilus_assembly_protein,_pilus_retraction_ATPase_PilT,_putative_2318346..2318496_NEGATIVE 269 118 74 80 38 NC_009009:SSA_1444|3end_Imidazole_glycerol-phosphate_synthase_subunit_hisH,_putative_1446644..1446794_NEGATIVE 269 117 79 73 17 NC_009009:SSA_0170|3end_hypothetical_protein_168130..168280_NEGATIVE 264 119 71 122 85 NC_009009:SSA_0418|3end_AraC-type_DNA-binding_domain-containing_protein,_putative_416184..416334_POSITIVE 263 118 80 78 31 NC_009009:SSA_0319|3end_Branched-chain_amino_acid_permease_(L-methionine,_L-isoleucine,_leucine_and_valine),_putative_313496..313646_POSITIVE 261 107 68 89 41 NC_009009:SSA_0485|3end_Porphobilinogen_deaminase,_putative_486732..486882_POSITIVE 259 115 71 151 97 NC_009009:SSA_1834|3end_30S_ribosomal_interface_protein_S30EA,_putative_1829652..1829802_NEGATIVE 259 118 80 132 101 NC_009009:SSA_1094|3end_GTP-binding_protein,_putative_1112243..1112393_POSITIVE 258 130 85 107 56 NC_009009:SSA_1448|3end_ATP_phosphoribosyltransferase_regulatory_subunit,_putative_1449828..1449978_NEGATIVE 257 118 73 137 97 NC_009009:SSA_0854|3end_hypothetical_protein_841813..841963_POSITIVE