Origin IGS: gcatttgcgtacctgctttcatttatcgaaccaaaagcaattaacagattgattatttgctacctttgcagagttgctgaatgaaacacatttgcaattatcatcttaatcataaacaatcttattctaattaggatt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aatcctaattagaataagattgtttatgattaagatgataattgcaaatgtgtttcattcagcaactctgcaaaggtagcaaataatcaatctgttaattgcttttggttcgataaatgaaagcaggtacgcaaatgc Mask Tandem Repeat Region ================================================ gcatttgcgtacctgctttcatttatcgaaccaaaagcaattaacagattgattatttgctacctttgcagagttgctgaatgaaacacatttgcaattatcatcttaatcataaacaatcttattctaattaggatt Find is-nt database================================================ Query_seq: PG1289:PG1290|PG1289:PG1290:GDP-fucose synthetase:branched-chain amino acid aminotransferase:->->:1368255..1368392 138 gcatttgcgtacctgctttcatttatcgaaccaaaagcaattaacagattgattatttgctacctttgcagagttgctgaatgaaacacatttgcaattatcatcttaatcataaacaatcttattctaattaggatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG1289:PG1290|PG1289:PG1290:GDP-fucose synthetase:branched-chain amino acid aminotransferase:->->:1368255..1368392 138 gcatttgcgtacctgctttcatttatcgaaccaaaagcaattaacagattgattatttgctacctttgcagagttgctgaatgaaacacatttgcaattatcatcttaatcataaacaatcttattctaattaggatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG1289:PG1290|PG1289:PG1290:GDP-fucose synthetase:branched-chain amino acid aminotransferase:->->:1368255..1368392 138 gcatttgcgtacctgctttcatttatcgaaccaaaagcaattaacagattgattatttgctacctttgcagagttgctgaatgaaacacatttgcaattatcatcttaatcataaacaatcttattctaattaggatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gcatttgcgtacctgctttcatttatcgaaccaaaagcaattaacagattgattatttgctacctttgcagagttgctgaatgaaacacatttgcaattatcatcttaatcataaacaatcttattctaattaggatt Predict ORF larger than 30AA ================================================ gcatttgcgtacctgctttcatttatcgaaccaaaagcaattaacagattgattatttgctacctttgcagagttgctgaatgaaacacatttgcaattatcatcttaatcataaacaatcttattctaattaggatt Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gcatttgcgtacctgctttcatttatcgaaccaaaagcaattaacagattgattatttgctacctttgcagagttgctgaatgaaacacatttgcaattatcatcttaatcataaacaatcttattctaattaggatt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PG1289:PG1290|PG1289:PG1290:GDP-fucose synthetase:branched-chain amino acid aminotransferase:->->:1368255..1368392 138 gcatttgcgtacctgctttcatttatcgaaccaaaagcaattaacagattgattatttgctacctttgcagagttgctgaatgaaacacatttgcaattatcatcttaatcataaacaatcttattctaattaggatt Intra-Species Hit: Count: 1 Min: 1 Max: 138 Len: 138 Subject: NC_002950_PG1289_PG1290|GDP-fucose synthetase:branched-chain amino acid aminotransferase|POSITIVE:POSITIVE|[1368255,1368392]|138 HSP 1 e-value: 7.0E-73 bit: 274.0 Len: 138 Query Start:1 Query End:138 Subject Strand: POSITIVE Subject Start: 1 Subject End: 138 gcatttgcgtacctgctttcatttatcgaaccaaaagcaattaacagattgattatttgctacctttgcagagttgctgaatgaaacacatttgcaattatcatcttaatcataaacaatcttattctaattaggatt gcatttgcgtacctgctttcatttatcgaaccaaaagcaattaacagattgattatttgctacctttgcagagttgctgaatgaaacacatttgcaattatcatcttaatcataaacaatcttattctaattaggatt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GCAUUUGCGUACCUGCUUUCAUUUAUCGAACCAAAAGCAAUUAACAGAUUGAUUAUUUGCUACCUUUGCAGAGUUGCUGAAUGAAACACAUUUGCAAUUAUCAUCUUAAUCAUAAACAAUCUUAUUCUAAUUAGGAUU ....(((((....((.(((((((((.(((........(((((....)))))....(((((.......))))).))).)))))))))))....)))))....................(((((((.......))))))) (-22.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUCCUAAUUAGAAUAAGAUUGUUUAUGAUUAAGAUGAUAAUUGCAAAUGUGUUUCAUUCAGCAACUCUGCAAAGGUAGCAAAUAAUCAAUCUGUUAAUUGCUUUUGGUUCGAUAAAUGAAAGCAGGUACGCAAAUGC .(((.(((((((((((....))))).)))))).))).....((((..((.(((((((((...(((((..((((...(((((.((.....)).))))).))))....)))).)...)))).))))).))..)))).... (-22.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 278 44 1 52 12 NC_002950:PG0906|5end_lipoprotein,_putative_970616..970846_POSITIVE 266 95 58 68 26 NC_002950:PG0678|5end_pyrazinamidase/nicotinamidase,_putative_728879..729109_POSITIVE 260 91 59 145 107 NC_002950:PG0021|5end_TIM-barrel_protein,_putative,_NifR3_family_25123..25353_NEGATIVE 256 80 45 157 123 NC_002950:PG1672|5end_hypothetical_protein_1757637..1757867_POSITIVE 256 80 45 157 123 NC_002950:PG0100|5end_hypothetical_protein_119219..119449_NEGATIVE 254 96 53 187 126 NC_002950:PG0171|5end_5'-nucleotidase_family_protein_191724..191954_POSITIVE 247 72 37 131 101 NC_002950:PG1722|5end_hypothetical_protein_1812938..1813168_NEGATIVE 246 96 58 49 7 NC_002950:PG1421|5end_ferredoxin,_4Fe-4S_1507044..1507274_NEGATIVE 246 60 13 144 106 NC_002950:PG1162|5end_ATP:cob(I)alamin_adenosyltransferase,_putative_1242039..1242269_NEGATIVE 245 41 1 164 122 NC_002950:PG0715|5end_transporter_769596..769826_NEGATIVE 243 47 6 40 8 NC_002950:PG2134|5end_lipoprotein,_putative_2239927..2240157_POSITIVE 242 40 14 75 55 NC_002950:PG1799|5end_hypothetical_protein_1894499..1894729_POSITIVE 241 78 31 145 104 NC_002950:PG1351|5end_hypothetical_protein_1432744..1432974_NEGATIVE 239 47 1 196 148 NC_002950:PG1975|5end_hemagglutinin_protein_HagC_2063218..2063448_POSITIVE 237 93 56 84 51 NC_002950:PG1068|5end_hypothetical_protein_1134636..1134866_POSITIVE 236 104 62 177 130 NC_002950:PG1101|5end_sodium:solute_symporter_family_protein_1170469..1170699_NEGATIVE 235 79 36 41 8 NC_002950:PG1091|5end_DHH_subfamily_1_protein_1157017..1157247_POSITIVE 235 70 22 169 129 NC_002950:PG0479|5end_hypothetical_protein_519686..519916_POSITIVE 234 95 56 212 181 NC_002950:PG0205|5end_peptide_chain_release_factor_3_242093..242323_NEGATIVE 233 98 59 40 14 NC_002950:PG1697|5end_type_II_restriction_endonuclease,_putative_1781020..1781250_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 260 91 59 148 110 NC_002950:PG0022|3end_sulfate_permease_family_protein_25120..25270_NEGATIVE 253 85 56 145 115 NC_002950:PG1625|3end_hypothetical_protein_1708718..1708868_POSITIVE 246 60 13 121 83 NC_002950:PG1163|3end_cobyrinic_acid_a,c-diamide_synthase_1242062..1242212_NEGATIVE 243 79 37 120 76 NC_002950:PG1030|3end_hypothetical_protein_1092820..1092970_POSITIVE 239 60 12 58 3 NC_002950:PG2161|3end_transcriptional_regulator,_AraC_family_2266717..2266867_NEGATIVE 237 79 36 122 73 NC_002950:PG1846|3end_hypothetical_protein_1946254..1946404_POSITIVE 237 93 56 56 23 NC_002950:PG1067|3end_hypothetical_protein_1134688..1134838_POSITIVE 233 98 59 30 4 NC_002950:PG1696|3end_type_II_DNA_modification_methyltransferase,_putative_1781090..1781240_POSITIVE 229 84 50 39 8 NC_002950:PG0200|3end_hypothetical_protein_238121..238271_NEGATIVE 226 60 12 105 65 NC_002950:PG0063|3end_outer_membrane_efflux_protein_75878..76028_NEGATIVE 224 79 56 146 119 NC_002950:PG0377|3end_30S_ribosomal_protein_S2_407845..407995_POSITIVE 223 94 56 142 97 NC_002950:PG0997|3end_transcriptional_regulator,_putative_1057012..1057162_POSITIVE 222 77 31 151 111 NC_002950:PG1352|3end_hypothetical_protein_1432737..1432887_NEGATIVE 220 98 59 135 90 NC_002950:PG2091|3end_dihydroneopterin_aldolase_2191610..2191760_POSITIVE 217 38 2 145 106 NC_002950:PG0429|3end_pyruvate_synthase_468039..468189_POSITIVE 214 95 55 35 4 NC_002950:PG0664|3end_oxidoreductase,_Gfo/Idh/MocA_family_711860..712010_POSITIVE 212 79 44 130 93 NC_002950:PG0443|3end_hemagglutinin-related_protein_483147..483297_POSITIVE 212 84 53 137 96 NC_002950:PG0170|3end_methionyl-tRNA_synthetase_191774..191924_POSITIVE 209 83 51 47 17 NC_002950:PG1041|3end_K+-dependent_Na+/Ca+_exchanger_related-protein_1107970..1108120_NEGATIVE 209 97 55 96 53 NC_002950:PG0114|3end_hypothetical_protein_137998..138148_POSITIVE