Origin IGS: atctaaactacctctttccttccctacttcctcaatcagtcggatgtacacttcctagatttttttgtacttaatatgacatatgttctcaaagataatttatttacatctatcattatatcaattcctcctcattctataaagtatttatgcaaaaatccaatatttttttatcagcttccgccttcacattccctacccaatgtctattaaacaccaaaaatcccctagaatttacaattctaagggattatttt .........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 aaaataatcccttagaattgtaaattctaggggatttttggtgtttaatagacattgggtagggaatgtgaaggcggaagctgataaaaaaatattggatttttgcataaatactttatagaatgaggaggaattgatataatgatagatgtaaataaattatctttgagaacatatgtcatattaagtacaaaaaaatctaggaagtgtacatccgactgattgaggaagtagggaaggaaagaggtagtttagat Mask Tandem Repeat Region ================================================ atctaaactacctctttccttccctacttcctcaatcagtcggatgtacacttcctagatttttttgtacttaatatgacatatgttctcaaagataatttatttacatctatcattatatcaattcctcctcattctataaagtatttatgcaaaaatccaatatttttttatcagcttccgccttcacattccctacccaatgtctattaaacaccaaaaatcccctagaatttacaattctaagggattatttt Find is-nt database================================================ Query_seq: SSA_1888:SSA_1889|SSA_1888:SSA_1889:hypothetical protein:Conserved uncharacterized protein:<-<-:1886116..1886372 257 atctaaactacctctttccttccctacttcctcaatcagtcggatgtacacttcctagatttttttgtacttaatatgacatatgttctcaaagataatttatttacatctatcattatatcaattcctcctcattctataaagtatttatgcaaaaatccaatatttttttatcagcttccgccttcacattccctacccaatgtctattaaacaccaaaaatcccctagaatttacaattctaagggattatttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1888:SSA_1889|SSA_1888:SSA_1889:hypothetical protein:Conserved uncharacterized protein:<-<-:1886116..1886372 257 atctaaactacctctttccttccctacttcctcaatcagtcggatgtacacttcctagatttttttgtacttaatatgacatatgttctcaaagataatttatttacatctatcattatatcaattcctcctcattctataaagtatttatgcaaaaatccaatatttttttatcagcttccgccttcacattccctacccaatgtctattaaacaccaaaaatcccctagaatttacaattctaagggattatttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1888:SSA_1889|SSA_1888:SSA_1889:hypothetical protein:Conserved uncharacterized protein:<-<-:1886116..1886372 257 atctaaactacctctttccttccctacttcctcaatcagtcggatgtacacttcctagatttttttgtacttaatatgacatatgttctcaaagataatttatttacatctatcattatatcaattcctcctcattctataaagtatttatgcaaaaatccaatatttttttatcagcttccgccttcacattccctacccaatgtctattaaacaccaaaaatcccctagaatttacaattctaagggattatttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 atctaaactacctctttccttccctacttcctcaatcagtcggatgtacacttcctagatttttttgtacttaatatgacatatgttctcaaagataatttatttacatctatcattatatcaattcctcctcattctataaagtatttatgcaaaaatccaatatttttttatcagcttccgccttcacattccctacccaatgtctattaaacaccaaaaatcccctagaatttacaattctaagggattatttt Predict ORF larger than 30AA ================================================ Protein_Len: 45 Strand: + Start: 76 End: 210 ........................................................................... M T Y V L K D N L F T S I I I S I P P H S I K Y L C K N P I F F Y Q L P P S H S L P N V Y ............................................... Protein_Len: 37 Strand: + Start: 146 End: 256 ................................................................................................................................................. M Y A K I Q Y F F I S F R L H I P Y P M S I K H Q K S P R I Y N S K G L F . Protein_Len: 52 Strand: + Start: 102 End: 257 ..................................................................................................... M Y I Y H Y I N S S S F Y K V F M Q K S N I F L S A S A F T F P T Q C L L N T K N P L E F T I L R D Y F Protein_Len: 34 Strand: - Start: 140 End: 241 ........................................................................................................................................... L T N I C F D L I K K D A E A K V N G V W H R N F V L F G R S N V M ................ atctaaactacctctttccttccctacttcctcaatcagtcggatgtacacttcctagatttttttgtacttaatatgacatatgttctcaaagataatttatttacatctatcattatatcaattcctcctcattctataaagtatttatgcaaaaatccaatatttttttatcagcttccgccttcacattccctacccaatgtctattaaacaccaaaaatcccctagaatttacaattctaagggattatttt 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: 85 Start: 115 End: 144 ..................................................................................................................CTTTATAGAATGAGGAGGAATTGATATAAT................................................................................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ atctaaactacctctttccttccctacttcctcaatcagtcggatgtacacttcctagatttttttgtacttaatatgacatatgttctcaaagataatttatttacatctatcattatatcaattcctcctcattctataaagtatttatgcaaaaatccaatatttttttatcagcttccgccttcacattccctacccaatgtctattaaacaccaaaaatcccctagaatttacaattctaagggattatttt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_1888:SSA_1889|SSA_1888:SSA_1889:hypothetical protein:Conserved uncharacterized protein:<-<-:1886116..1886372 257 atctaaactacctctttccttccctacttcctcaatcagtcggatgtacacttcctagatttttttgtacttaatatgacatatgttctcaaagataatttatttacatctatcattatatcaattcctcctcattctataaagtatttatgcaaaaatccaatatttttttatcagcttccgccttcacattccctacccaatgtctattaaacaccaaaaatcccctagaatttacaattctaagggattatttt Intra-Species Hit: Count: 1 Min: 1 Max: 257 Len: 257 Subject: NC_009009_SSA_1888_SSA_1889|hypothetical protein:Conserved uncharacterized protein|NEGATIVE:NEGATIVE|[1886116,1886372]|257 HSP 1 e-value: 1.0E-118 bit: 426.0 Len: 257 Query Start:1 Query End:257 Subject Strand: POSITIVE Subject Start: 1 Subject End: 257 atctaaactacctctttccttccctacttcctcaatcagtcggatgtacacttcctagannnnnnngtacttaatatgacatatgttctcaaagataatttatttacatctatcattatatcaattcctcctcattctataaagtatttatgcaaaaatccaatannnnnnnatcagcttccgccttcacattccctacccaatgtctattaaacaccaaaaatcccctagaatttacaattctaagggattatttt atctaaactacctctttccttccctacttcctcaatcagtcggatgtacacttcctagatttttttgtacttaatatgacatatgttctcaaagataatttatttacatctatcattatatcaattcctcctcattctataaagtatttatgcaaaaatccaatatttttttatcagcttccgccttcacattccctacccaatgtctattaaacaccaaaaatcccctagaatttacaattctaagggattatttt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUCUAAACUACCUCUUUCCUUCCCUACUUCCUCAAUCAGUCGGAUGUACACUUCCUAGAUUUUUUUGUACUUAAUAUGACAUAUGUUCUCAAAGAUAAUUUAUUUACAUCUAUCAUUAUAUCAAUUCCUCCUCAUUCUAUAAAGUAUUUAUGCAAAAAUCCAAUAUUUUUUUAUCAGCUUCCGCCUUCACAUUCCCUACCCAAUGUCUAUUAAACACCAAAAAUCCCCUAGAAUUUACAAUUCUAAGGGAUUAUUUU ............(((.........(((.(((..........))).)))........)))......(((..((((((.(((((...........(((((.................(((((.................))))).(((....))).................))))).((....))..................)))))))))))))).....((((((.((((((.....)))))).))))))..... (-26.16) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAAUAAUCCCUUAGAAUUGUAAAUUCUAGGGGAUUUUUGGUGUUUAAUAGACAUUGGGUAGGGAAUGUGAAGGCGGAAGCUGAUAAAAAAAUAUUGGAUUUUUGCAUAAAUACUUUAUAGAAUGAGGAGGAAUUGAUAUAAUGAUAGAUGUAAAUAAAUUAUCUUUGAGAACAUAUGUCAUAUUAAGUACAAAAAAAUCUAGGAAGUGUACAUCCGACUGAUUGAGGAAGUAGGGAAGGAAAGAGGUAGUUUAGAU .....(((((((((((((.....)))))))))))))((..(((((.....)))))..))......((.((((.((((((((..(((......)))..).))))))).....((((((....(((.((..(((.........((((((.((((...((((.....))))...)))).)))))).....(((((...............))))).)))..)).)))...)))))).................)))).)) (-53.46) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 947 60 11 151 102 NC_009009:SSA_1888|5end_hypothetical_protein_1886025..1886255_NEGATIVE 311 217 173 55 6 NC_009009:SSA_1459|5end_RNA_methyltransferase,_putative_1467481..1467711_NEGATIVE 282 210 173 208 172 NC_009009:SSA_2037|5end_tRNA_(Guanosine-2'-O-)-methyltransferase,_TrmH_family,_putative_2041524..2041754_NEGATIVE 282 67 21 172 123 NC_009009:SSA_1847|5end_RRNA_methyltransferase_RsmB,_putative_1842004..1842234_NEGATIVE 279 56 11 145 98 NC_009009:SSA_0402|5end_Histidine_kinase,_putative_399144..399374_POSITIVE 278 207 169 70 25 NC_009009:SSA_0835|5end_Accessory_secretory_protein_Asp3,_putative_821036..821266_POSITIVE 277 67 22 75 21 NC_009009:SSA_1467|5end_Chorismate_synthase,_putative_1474293..1474523_NEGATIVE 276 196 172 83 58 NC_009009:SSA_2198|5end_hypothetical_protein_2198585..2198815_NEGATIVE 276 58 13 135 84 NC_009009:SSA_0422|5end_Phosphoglycerate_mutase_family_protein,_putative_420157..420387_POSITIVE 274 56 12 155 99 NC_009009:SSA_0601|5end_Phosphorylase,_Pnp/Udp_family,_putative_589147..589377_POSITIVE 272 47 8 134 98 NC_009009:SSA_0894|5end_ATP-binding_cassette_protein,_putative_885779..886009_POSITIVE 271 60 18 50 1 NC_009009:SSA_1901|5end_Conserved_uncharacterized_protein_1896599..1896829_NEGATIVE 269 48 1 168 107 NC_009009:SSA_2159|5end_hypothetical_protein_2159621..2159851_NEGATIVE 267 53 18 127 98 NC_009009:SSA_0620|5end_hypothetical_protein_612325..612555_NEGATIVE 265 218 175 186 147 NC_009009:SSA_0778|5end_Glycogen_synthase,_putative_760566..760796_POSITIVE 260 220 174 102 42 NC_009009:SSA_0241|5end_Ribosomal_protein_L11_methyltransferase,_putative_234021..234251_POSITIVE 259 191 152 92 42 NC_009009:SSA_0636|5end_N-(5'-phosphoribosyl)anthranilate_isomerase,_putative_625184..625414_POSITIVE 251 187 160 41 11 NC_009009:SSA_0629|5end_hypothetical_protein_618967..619197_POSITIVE 250 70 25 153 96 NC_009009:SSA_0377|5end_ABC-type_methionine_transporter,_permease_component,_putative_366446..366676_POSITIVE 248 197 165 60 19 NC_009009:SSA_0628|5end_Fe-S-cluster_redox_enzyme/radical_SAM_enzyme,_Cfr_family,_putative_617892..618122_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 293 219 176 139 97 NC_009009:SSA_1960|3end_hypothetical_protein_1956571..1956721_NEGATIVE 291 48 11 131 87 NC_009009:SSA_2213|3end_Nucleotide_sugar_dehydratase,_putative_2214047..2214197_NEGATIVE 291 205 166 142 97 NC_009009:SSA_1256|3end_NAD-dependent_deacetylase,_putative_1282357..1282507_NEGATIVE 289 64 23 62 15 NC_009009:SSA_1143|3end_Na+-driven_multidrug_efflux_pump,_putative_1172148..1172298_NEGATIVE 285 187 141 54 5 NC_009009:SSA_0628|3end_Fe-S-cluster_redox_enzyme/radical_SAM_enzyme,_Cfr_family,_putative_619060..619210_POSITIVE 279 56 11 143 96 NC_009009:SSA_0401|3end_Two-component_response_transcriptional_regulator_(CheY-like_receiver_and_winged-helix_DNA-binding_domains),_putative_399222..399372_POSITIVE 278 207 169 73 28 NC_009009:SSA_0834|3end_Accessory_secretory_protein_Asp2,_putative_821119..821269_POSITIVE 276 58 13 138 87 NC_009009:SSA_0421|3end_Phosphoglycerate_mutase_family_protein,_putative_420240..420390_POSITIVE 272 47 8 147 111 NC_009009:SSA_0893|3end_ATP-binding_cassette_transporter-like_protein,_putative_885872..886022_POSITIVE 267 53 18 130 101 NC_009009:SSA_0621|3end_SOS_responce_UmuC_protein,_putative_612322..612472_NEGATIVE 265 56 15 146 102 NC_009009:SSA_0716|3end_Competence_protein,_putative_703710..703860_POSITIVE 259 191 152 63 13 NC_009009:SSA_0635|3end_Indole-3-glycerol_phosphate_synthase,_putative_625235..625385_POSITIVE 259 46 8 138 99 NC_009009:SSA_0593|3end_Rhodanese-like_sulfurtransferase,_putative_585551..585701_POSITIVE 253 70 21 131 72 NC_009009:SSA_0303|3end_surface_protein_C_301051..301201_POSITIVE 250 206 165 122 84 NC_009009:SSA_0141|3end_Copper_chaperone,_putative_137191..137341_POSITIVE 248 145 102 63 20 NC_009009:SSA_1459|3end_RNA_methyltransferase,_putative_1466111..1466261_NEGATIVE 248 197 165 63 22 NC_009009:SSA_0627|3end_hypothetical_protein_617975..618125_POSITIVE 246 218 177 102 50 NC_009009:SSA_1343|3end_Aspartate_carbamoyltransferase,_putative_1361042..1361192_NEGATIVE 243 58 18 134 85 NC_009009:SSA_0980|3end_3-isopropylmalate_dehydratase_large_subunit,_putative_985466..985616_POSITIVE 242 65 21 77 33 NC_009009:SSA_1549|3end_hypothetical_protein_1551816..1551966_NEGATIVE