Origin IGS: aatactaattgtttttgattggcagcggcaccggttttaacaaacctacgctcttgatatagcatgcctctctgttaaaaaaatcgttgttagtttgctttgaaagagtttg .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 caaactctttcaaagcaaactaacaacgatttttttaacagagaggcatgctatatcaagagcgtaggtttgttaaaaccggtgccgctgccaatcaaaaacaattagtatt Mask Tandem Repeat Region ================================================ aatactaattgtttttgattggcagcggcaccggttttaacaaacctacgctcttgatatagcatgcctctctgttaaaaaaatcgttgttagtttgctttgaaagagtttg Find is-nt database================================================ Query_seq: PG0989:PG0990|PG0989:PG0990:50S ribosomal protein L20:ribosomal protein L35:<-<-:1051137..1051248 112 aatactaattgtttttgattggcagcggcaccggttttaacaaacctacgctcttgatatagcatgcctctctgttaaaaaaatcgttgttagtttgctttgaaagagtttg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG0989:PG0990|PG0989:PG0990:50S ribosomal protein L20:ribosomal protein L35:<-<-:1051137..1051248 112 aatactaattgtttttgattggcagcggcaccggttttaacaaacctacgctcttgatatagcatgcctctctgttaaaaaaatcgttgttagtttgctttgaaagagtttg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG0989:PG0990|PG0989:PG0990:50S ribosomal protein L20:ribosomal protein L35:<-<-:1051137..1051248 112 aatactaattgtttttgattggcagcggcaccggttttaacaaacctacgctcttgatatagcatgcctctctgttaaaaaaatcgttgttagtttgctttgaaagagtttg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aatactaattgtttttgattggcagcggcaccggttttaacaaacctacgctcttgatatagcatgcctctctgttaaaaaaatcgttgttagtttgctttgaaagagtttg Predict ORF larger than 30AA ================================================ aatactaattgtttttgattggcagcggcaccggttttaacaaacctacgctcttgatatagcatgcctctctgttaaaaaaatcgttgttagtttgctttgaaagagtttg 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================================================ aatactaattgtttttgattggcagcggcaccggttttaacaaacctacgctcttgatatagcatgcctctctgttaaaaaaatcgttgttagtttgctttgaaagagtttg Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PG0989:PG0990|PG0989:PG0990:50S ribosomal protein L20:ribosomal protein L35:<-<-:1051137..1051248 112 aatactaattgtttttgattggcagcggcaccggttttaacaaacctacgctcttgatatagcatgcctctctgttaaaaaaatcgttgttagtttgctttgaaagagtttg Intra-Species Hit: Count: 1 Min: 1 Max: 112 Len: 112 Subject: NC_002950_PG0989_PG0990|50S ribosomal protein L20:ribosomal protein L35|NEGATIVE:NEGATIVE|[1051137,1051248]|112 HSP 1 e-value: 6.0E-45 bit: 180.0 Len: 112 Query Start:1 Query End:112 Subject Strand: POSITIVE Subject Start: 1 Subject End: 112 aatactaattgtttttgattggcagcggcaccggttttaacaaacctacgctcttgatatagcatgcctctctgttnnnnnnntcgttgttagtttgctttgaaagagtttg aatactaattgtttttgattggcagcggcaccggttttaacaaacctacgctcttgatatagcatgcctctctgttaaaaaaatcgttgttagtttgctttgaaagagtttg Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUACUAAUUGUUUUUGAUUGGCAGCGGCACCGGUUUUAACAAACCUACGCUCUUGAUAUAGCAUGCCUCUCUGUUAAAAAAAUCGUUGUUAGUUUGCUUUGAAAGAGUUUG ...((((((.((((((..(((((((.((((..(((((....)))))...(((........))).))))...)))))))))))))....))))))..((((.....))))... (-21.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CAAACUCUUUCAAAGCAAACUAACAACGAUUUUUUUAACAGAGAGGCAUGCUAUAUCAAGAGCGUAGGUUUGUUAAAACCGGUGCCGCUGCCAAUCAAAAACAAUUAGUAUU ..................(((((...............(((...((((((((........)))...(((((....))))).))))).)))..............)))))... (-18.15) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 1012 70 21 161 112 NC_002950:PG0989|5end_50S_ribosomal_protein_L20_1051046..1051276_NEGATIVE 389 69 21 62 1 NC_002950:PG1819|5end_hypothetical_protein_1914322..1914552_NEGATIVE 338 70 21 193 143 NC_002950:PG0538|5end_outer_membrane_efflux_protein_589142..589372_POSITIVE 337 56 16 44 4 NC_002950:PG1398|5end_hypothetical_protein_1480694..1480924_POSITIVE 329 70 21 231 178 NC_002950:PG1709|5end_ISPg5,_transposase_Orf1_1794914..1795144_POSITIVE 327 52 17 206 173 NC_002950:PG1601|5end_biotin--acetyl-CoA-carboxylase_ligase_1681792..1682022_NEGATIVE 325 58 20 192 147 NC_002950:PG0660|5end_nitroreductase_family_protein_709695..709925_NEGATIVE 306 65 21 54 2 NC_002950:PG0444|5end_oligopeptide_transporter,_OPT_family_483256..483486_POSITIVE 305 70 21 61 14 NC_002950:PG1297|5end_ribosomal_protein_S1_1375831..1376061_POSITIVE 305 66 21 224 176 NC_002950:PG0219|5end_hypothetical_protein_255558..255788_NEGATIVE 303 58 11 112 62 NC_002950:PG1926|5end_50S_ribosomal_protein_L5_2019237..2019467_NEGATIVE 296 70 24 89 36 NC_002950:PG0524|5end_hypothetical_protein_568599..568829_POSITIVE 294 48 21 57 32 NC_002950:PG0401|5end_hypothetical_protein_439306..439536_NEGATIVE 291 70 21 58 4 NC_002950:PG0090|5end_Dps_family_protein_105524..105754_POSITIVE 289 66 22 80 34 NC_002950:PG0308|5end_electron_transport_complex,_RnfABCDGE_type,_A_subunit_343175..343405_POSITIVE 289 67 21 47 5 NC_002950:PG0070|5end_UDP-N-acetylglucosamine_acyltransferase_84734..84964_NEGATIVE 286 68 21 134 72 NC_002950:PG1311|5end_hypothetical_protein_1389709..1389939_POSITIVE 282 68 30 43 7 NC_002950:PG2091|5end_dihydroneopterin_aldolase_2191177..2191407_POSITIVE 282 70 23 42 1 NC_002950:PG1416|5end_enoyl-(acyl-carrier-protein)_reductase_II_1500057..1500287_POSITIVE 281 56 15 223 171 NC_002950:PG1959|5end_ribosomal_protein_L33_2048405..2048635_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 342 52 11 104 61 NC_002950:PG0086|3end_ATP-dependent_RNA_helicase,_DEAD/DEAH_box_family_100545..100695_NEGATIVE 305 69 21 131 68 NC_002950:PG0320|3end_hypothetical_protein_354577..354727_POSITIVE 303 58 11 112 62 NC_002950:PG1927|3end_50S_ribosomal_protein_L24_2019237..2019387_NEGATIVE 296 55 17 103 57 NC_002950:PG2094|3end_hypothetical_protein_2193321..2193471_NEGATIVE 289 66 22 55 9 NC_002950:PG0307|3end_NADH-ubiquinone_oxidoreductase_343230..343380_POSITIVE 289 67 21 50 8 NC_002950:PG0071|3end_UDP-3-O-acyl-GlcNAc_deacetylase/beta-hydroxyacyl-[acyl_carrier_protein]_dehydratase_FabZ_84731..84881_NEGATIVE 288 60 11 77 22 NC_002950:PG2091|3end_dihydroneopterin_aldolase_2191610..2191760_POSITIVE 280 70 22 58 5 NC_002950:PG0429|3end_pyruvate_synthase_468039..468189_POSITIVE 275 69 21 78 23 NC_002950:PG0439|3end_hypothetical_protein_478810..478960_POSITIVE 273 76 31 140 98 NC_002950:PG0603|3end_cytidylate_kinase_660345..660495_POSITIVE 272 56 11 135 87 NC_002950:PG0090|3end_Dps_family_protein_106083..106233_POSITIVE 270 50 18 115 80 NC_002950:PG2041|3end_hypothetical_protein_2139235..2139385_NEGATIVE 269 55 16 62 18 NC_002950:PG2210|3end_excinuclease_ABC,_A_subunit_2320952..2321102_NEGATIVE 269 69 21 55 17 NC_002950:PG1866|3end_hypothetical_protein_1964736..1964886_POSITIVE 263 64 21 77 31 NC_002950:PG1110|3end_hypothetical_protein_1183237..1183387_POSITIVE 261 68 21 118 77 NC_002950:PG0604|3end_4-hydroxy-3-methylbut-2-enyl_diphosphate_reductase_661211..661361_POSITIVE 259 70 21 101 38 NC_002950:PG1522|3end_mandelate_racemase/muconate_lactonizing_enzyme_family_protein_1599100..1599250_NEGATIVE 259 51 17 48 2 NC_002950:PG0735|3end_aminotransferase,_class_V_785677..785827_POSITIVE 258 61 22 47 12 NC_002950:PG2217|3end_1-deoxy-D-xylulose-5-phosphate_synthase_2331607..2331757_POSITIVE 258 70 26 84 43 NC_002950:PG1112|3end_hypothetical_protein_1185571..1185721_POSITIVE