Origin IGS: gcgataacctctctgaattttcaaaaaatttttattgttagtattatactatttttagggaaaaatgcaaatatttctgaagaatataagtgcgatattttgataaactacactaactcaactttctcctgcagactcatttcatcaagagcaacagaaaaatccccaatccgtagactggggataagggcacttttgtgtgatcagcaggttcacacaactgatcaaggtccgctcctgcgttatgacctcccatgcttcaatttgcagaaaatctgcatatcgactcatcgcacgaaatatagtttaccttatctttttccgttttgtcaaggtgt .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9 acaccttgacaaaacggaaaaagataaggtaaactatatttcgtgcgatgagtcgatatgcagattttctgcaaattgaagcatgggaggtcataacgcaggagcggaccttgatcagttgtgtgaacctgctgatcacacaaaagtgcccttatccccagtctacggattggggatttttctgttgctcttgatgaaatgagtctgcaggagaaagttgagttagtgtagtttatcaaaatatcgcacttatattcttcagaaatatttgcatttttccctaaaaatagtataatactaacaataaaaattttttgaaaattcagagaggttatcgc Mask Tandem Repeat Region ================================================ gcgataacctctctgaattttcaaaaaatttttattgttagtattatactatttttagggaaaaatgcaaatatttctgaagaatataagtgcgatattttgataaactacactaactcaactttctcctgcagactcatttcatcaagagcaacagaaaaatccccaatccgtagactggggataagggcacttttgtgtgatcagcaggttcacacaactgatcaaggtccgctcctgcgttatgacctcccatgcttcaatttgcagaaaatctgcatatcgactcatcgcacgaaatatagtttaccttatctttttccgttttgtcaaggtgt Find is-nt database================================================ Query_seq: SSA_1194:SSA_1196|SSA_1194:SSA_1196:Aspartate-semialdehyde dehydrogenase, putative:Acetyltransferase, GNAT family, putative:<-<-:1221280..1221617 338 gcgataacctctctgaattttcaaaaaatttttattgttagtattatactatttttagggaaaaatgcaaatatttctgaagaatataagtgcgatattttgataaactacactaactcaactttctcctgcagactcatttcatcaagagcaacagaaaaatccccaatccgtagactggggataagggcacttttgtgtgatcagcaggttcacacaactgatcaaggtccgctcctgcgttatgacctcccatgcttcaatttgcagaaaatctgcatatcgactcatcgcacgaaatatagtttaccttatctttttccgttttgtcaaggtgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1194:SSA_1196|SSA_1194:SSA_1196:Aspartate-semialdehyde dehydrogenase, putative:Acetyltransferase, GNAT family, putative:<-<-:1221280..1221617 338 gcgataacctctctgaattttcaaaaaatttttattgttagtattatactatttttagggaaaaatgcaaatatttctgaagaatataagtgcgatattttgataaactacactaactcaactttctcctgcagactcatttcatcaagagcaacagaaaaatccccaatccgtagactggggataagggcacttttgtgtgatcagcaggttcacacaactgatcaaggtccgctcctgcgttatgacctcccatgcttcaatttgcagaaaatctgcatatcgactcatcgcacgaaatatagtttaccttatctttttccgttttgtcaaggtgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1194:SSA_1196|SSA_1194:SSA_1196:Aspartate-semialdehyde dehydrogenase, putative:Acetyltransferase, GNAT family, putative:<-<-:1221280..1221617 338 gcgataacctctctgaattttcaaaaaatttttattgttagtattatactatttttagggaaaaatgcaaatatttctgaagaatataagtgcgatattttgataaactacactaactcaactttctcctgcagactcatttcatcaagagcaacagaaaaatccccaatccgtagactggggataagggcacttttgtgtgatcagcaggttcacacaactgatcaaggtccgctcctgcgttatgacctcccatgcttcaatttgcagaaaatctgcatatcgactcatcgcacgaaatatagtttaccttatctttttccgttttgtcaaggtgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gcgataacctctctgaattttcaaaaaatttttattgttagtattatactatttttagggaaaaatgcaaatatttctgaagaatataagtgcgatattttgataaactacactaactcaactttctcctgcagactcatttcatcaagagcaacagaaaaatccccaatccgtagactggggataagggcacttttgtgtgatcagcaggttcacacaactgatcaaggtccgctcctgcgttatgacctcccatgcttcaatttgcagaaaatctgcatatcgactcatcgcacgaaatatagtttaccttatctttttccgttttgtcaaggtgt Predict ORF larger than 30AA ================================================ Protein_Len: 60 Strand: + Start: 4 End: 336 ... M T S L N F Q K I F I V S I I L F L G K N A N I S E E Y K C D I L I N Y T N S T F S C R L I S S R A T E K S P I R R L G .. Protein_Len: 46 Strand: + Start: 200 End: 337 ....................................................................................................................................................................................................... M I S R F T Q L I K V R S C V M T S H A S I C R K S A Y R L I A R N I V Y L I F F R F V K V . Protein_Len: 52 Strand: - Start: 148 End: 303 ................................................................................................................................................... S C C F F G W D T S Q P Y P C K Q T I L L N V C S I L T R E Q T I V E W A E I Q L F D A Y R S M A R F M ................................... Protein_Len: 39 Strand: - Start: 140 End: 256 ........................................................................................................................................... K M L L L L F I G L G Y V P S L P V K T H D A P E C L Q D L D A G A N H G G M .................................................................................. gcgataacctctctgaattttcaaaaaatttttattgttagtattatactatttttagggaaaaatgcaaatatttctgaagaatataagtgcgatattttgataaactacactaactcaactttctcctgcagactcatttcatcaagagcaacagaaaaatccccaatccgtagactggggataagggcacttttgtgtgatcagcaggttcacacaactgatcaaggtccgctcctgcgttatgacctcccatgcttcaatttgcagaaaatctgcatatcgactcatcgcacgaaatatagtttaccttatctttttccgttttgtcaaggtgt 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: 43 End: 72 ..........................................ATTTGCATTTTTCCCTAAAAATAGTATAAT.......................................................................................................................................................................................................................................................................... PromScan Matrix: RpoD-17 Strand: + Score: 82 Start: 18 End: 47 .................TTTTCAAAAAATTTTTATTGTTAGTATTAT................................................................................................................................................................................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gcgataacctctctgaattttcaaaaaatttttattgttagtattatactatttttagggaaaaatgcaaatatttctgaagaatataagtgcgatattttgataaactacactaactcaactttctcctgcagactcatttcatcaagagcaacagaaaaatccccaatccgtagactggggataagggcacttttgtgtgatcagcaggttcacacaactgatcaaggtccgctcctgcgttatgacctcccatgcttcaatttgcagaaaatctgcatatcgactcatcgcacgaaatatagtttaccttatctttttccgttttgtcaaggtgt Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 93 HP_score: -10.9 Tail_Score: -5.13344 Start: 163 End: 184 Full_Region: acaaaagtgccctta tccccagtc tacg gattgggga tttttctgttgctct ..................................................................................................................................................................tccccagtctacggattgggga.......................................................................................................................................................... Find igs database================================================ Query_seq: SSA_1194:SSA_1196|SSA_1194:SSA_1196:Aspartate-semialdehyde dehydrogenase, putative:Acetyltransferase, GNAT family, putative:<-<-:1221280..1221617 338 gcgataacctctctgaattttcaaaaaatttttattgttagtattatactatttttagggaaaaatgcaaatatttctgaagaatataagtgcgatattttgataaactacactaactcaactttctcctgcagactcatttcatcaagagcaacagaaaaatccccaatccgtagactggggataagggcacttttgtgtgatcagcaggttcacacaactgatcaaggtccgctcctgcgttatgacctcccatgcttcaatttgcagaaaatctgcatatcgactcatcgcacgaaatatagtttaccttatctttttccgttttgtcaaggtgt Intra-Species Hit: Count: 1 Min: 1 Max: 338 Len: 338 Subject: NC_009009_SSA_1194_SSA_1196|Aspartate-semialdehyde dehydrogenase, putative:Acetyltransferase, GNAT family, putative|NEGATIVE:NEGATIVE|[1221280,1221617]|338 HSP 1 e-value: 0.0 bit: 670.0 Len: 338 Query Start:1 Query End:338 Subject Strand: POSITIVE Subject Start: 1 Subject End: 338 gcgataacctctctgaattttcaaaaaatttttattgttagtattatactatttttagggaaaaatgcaaatatttctgaagaatataagtgcgatattttgataaactacactaactcaactttctcctgcagactcatttcatcaagagcaacagaaaaatccccaatccgtagactggggataagggcacttttgtgtgatcagcaggttcacacaactgatcaaggtccgctcctgcgttatgacctcccatgcttcaatttgcagaaaatctgcatatcgactcatcgcacgaaatatagtttaccttatctttttccgttttgtcaaggtgt gcgataacctctctgaattttcaaaaaatttttattgttagtattatactatttttagggaaaaatgcaaatatttctgaagaatataagtgcgatattttgataaactacactaactcaactttctcctgcagactcatttcatcaagagcaacagaaaaatccccaatccgtagactggggataagggcacttttgtgtgatcagcaggttcacacaactgatcaaggtccgctcctgcgttatgacctcccatgcttcaatttgcagaaaatctgcatatcgactcatcgcacgaaatatagtttaccttatctttttccgttttgtcaaggtgt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GCGAUAACCUCUCUGAAUUUUCAAAAAAUUUUUAUUGUUAGUAUUAUACUAUUUUUAGGGAAAAAUGCAAAUAUUUCUGAAGAAUAUAAGUGCGAUAUUUUGAUAAACUACACUAACUCAACUUUCUCCUGCAGACUCAUUUCAUCAAGAGCAACAGAAAAAUCCCCAAUCCGUAGACUGGGGAUAAGGGCACUUUUGUGUGAUCAGCAGGUUCACACAACUGAUCAAGGUCCGCUCCUGCGUUAUGACCUCCCAUGCUUCAAUUUGCAGAAAAUCUGCAUAUCGACUCAUCGCACGAAAUAUAGUUUACCUUAUCUUUUUCCGUUUUGUCAAGGUGU (((((((.......((((((.....)))))))))))))..(((((....(((((((..(((((.((....)).))))).)))))))...(((((((...((((((...........................................(((((........(((((((.((....)).)))))))..(((..(..((((((((((....)).))))))))..)....((((((((....)))....)))))))).))))).....(((((.....)))))))))))...)))))))..)))))....((((((..(............)..)))))). (-73.11) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACACCUUGACAAAACGGAAAAAGAUAAGGUAAACUAUAUUUCGUGCGAUGAGUCGAUAUGCAGAUUUUCUGCAAAUUGAAGCAUGGGAGGUCAUAACGCAGGAGCGGACCUUGAUCAGUUGUGUGAACCUGCUGAUCACACAAAAGUGCCCUUAUCCCCAGUCUACGGAUUGGGGAUUUUUCUGUUGCUCUUGAUGAAAUGAGUCUGCAGGAGAAAGUUGAGUUAGUGUAGUUUAUCAAAAUAUCGCACUUAUAUUCUUCAGAAAUAUUUGCAUUUUUCCCUAAAAAUAGUAUAAUACUAACAAUAAAAAUUUUUUGAAAAUUCAGAGAGGUUAUCGC ......((((.....(((((((.....(((((((((((((.(..((.(((..(((((.(((((.....))))).)))))..)))(((.((((....(((....))))))).((((((((.(.(....)).))))))))..........)))..((((((((((....))))))))))((((((((.((((..........))))..))))))))..))...)..)))))))))))))........(((..(((.(((....))))))..))).))))))).......(((((...)))))...........(((((((....))))))).)))).... (-97.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 839 140 91 231 182 NC_009009:SSA_1194|5end_Aspartate-semialdehyde_dehydrogenase,_putative_1221189..1221419_NEGATIVE 384 259 223 201 158 NC_009009:SSA_0251|5end_D-tyrosyl-tRNA(Tyr)_deacylase,_putative_244455..244685_POSITIVE 375 190 148 64 21 NC_009009:SSA_1562|5end_hypothetical_protein_1566364..1566594_NEGATIVE 371 167 123 104 58 NC_009009:SSA_0734|5end_Arsenical_resistance_operon_transcription_repressor_(ArsR),_putative_716895..717125_POSITIVE 369 238 192 70 29 NC_009009:SSA_0470|5end_Precorrin-4_methylase,_putative_472879..473109_POSITIVE 366 210 161 143 95 NC_009009:SSA_1078|5end_hypothetical_protein_1095742..1095972_POSITIVE 361 268 221 48 3 NC_009009:SSA_2296|5end_Transcriptional_regulator,_XRE_family,_putative_2298773..2299003_NEGATIVE 352 210 164 58 4 NC_009009:SSA_0704|5end_Isocitrate_dehydrogenase_[NADP],_putative_689274..689504_POSITIVE 333 270 221 64 15 NC_009009:SSA_0405|5end_Transcriptional_regulator,_XRE_family,_putative_401418..401648_POSITIVE 331 241 208 216 175 NC_009009:SSA_1770|5end_hypothetical_protein_1758431..1758661_NEGATIVE 328 268 223 171 110 NC_009009:SSA_1209|5end_Inorganic_polyphosphate/ATP-NAD_kinase,_putative_1234030..1234260_NEGATIVE 328 289 241 211 156 NC_009009:SSA_1010|5end_UDP-glucose_4-epimerase,_putative_1012739..1012969_POSITIVE 328 269 221 220 163 NC_009009:SSA_0978|5end_hypothetical_protein_983736..983966_POSITIVE 322 239 196 197 152 NC_009009:SSA_0051|5end_Dihydroxyacetone_kinase_phosphotransfer_protein,_putative_55190..55420_POSITIVE 316 157 123 135 95 NC_009009:SSA_1545|5end_Conserved_uncharacterized_protein_1549210..1549440_NEGATIVE 314 261 221 229 195 NC_009009:SSA_1438|5end_Acetyltransferase,_putative_1443612..1443842_NEGATIVE 314 250 201 228 179 NC_009009:SSA_1087|5end_ABC-type_transporter_(antibiotic_resistance_protein),_ATPase_component,_putative_1104524..1104754_POSITIVE 314 207 164 70 25 NC_009009:SSA_0551|5end_L-asparaginase,_putative_547293..547523_NEGATIVE 313 218 171 214 151 NC_009009:SSA_1594|5end_Metalloendopeptidase,_putative_1600526..1600756_NEGATIVE 313 267 221 82 23 NC_009009:SSA_1367|5end_hypothetical_protein_1383593..1383823_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 384 259 223 132 89 NC_009009:SSA_0250|3end_GTP_pyrophosphokinase,_putative_244466..244616_POSITIVE 371 167 123 66 20 NC_009009:SSA_0733|3end_hypothetical_protein_716937..717087_POSITIVE 369 238 192 70 29 NC_009009:SSA_0469|3end_Precorrin-6B_methylase_2,putative_472959..473109_POSITIVE 366 210 161 150 102 NC_009009:SSA_1077|3end_N-acetyl-glucosamine_matabolism,_putative_1095829..1095979_POSITIVE 352 210 164 56 2 NC_009009:SSA_0703|3end_Citrate_synthase,_putative_689352..689502_POSITIVE 344 189 159 86 57 NC_009009:SSA_0914|3end_Phenylalanyl-tRNA_synthetase_beta_chain,_putative_927437..927587_POSITIVE 323 268 229 45 7 NC_009009:SSA_2297|3end_hypothetical_protein_2298776..2298926_NEGATIVE 323 239 208 151 115 NC_009009:SSA_1771|3end_Conserved_DNA_methyltransferase_protein,_putative_1758491..1758641_NEGATIVE 322 260 211 148 97 NC_009009:SSA_1124|3end_Oxidoreductase,_putative_1148547..1148697_NEGATIVE 316 157 123 78 38 NC_009009:SSA_1546|3end_Prolipoprotein_diacylglyceryl_transferase,_putative_1549267..1549417_NEGATIVE 309 214 171 85 43 NC_009009:SSA_2140|3end_Ribonuclease_P_protein_component,_putative_2140308..2140458_NEGATIVE 308 195 154 67 21 NC_009009:SSA_1621|3end_Amino_acid_transporter,_putative_1623172..1623322_NEGATIVE 306 268 231 131 86 NC_009009:SSA_1617|3end_hypothetical_protein_1620436..1620586_NEGATIVE 300 250 201 71 25 NC_009009:SSA_1938|3end_Enoyl-acyl_carrier_protein(ACP)_reductase,_putative_1924764..1924914_NEGATIVE 299 277 232 130 70 NC_009009:SSA_0553|3end_hypothetical_protein_549341..549491_POSITIVE 299 269 221 146 86 NC_009009:SSA_0263|3end_Zinc_metalloproteinase_in_scaA_5'region,_putative_258246..258396_POSITIVE 295 245 204 140 91 NC_009009:SSA_2126|3end_hypothetical_protein_2129985..2130135_NEGATIVE 295 279 231 53 9 NC_009009:SSA_1189|3end_GTP-binding_protein,_putative_1216806..1216956_NEGATIVE 294 250 209 68 31 NC_009009:SSA_0451|3end_Conserved_uncharacterized_protein_451636..451786_POSITIVE 293 217 171 67 8 NC_009009:SSA_0319|3end_Branched-chain_amino_acid_permease_(L-methionine,_L-isoleucine,_leucine_and_valine),_putative_313496..313646_POSITIVE