Origin IGS: gaaacttggagaaatccaggtttctttgtgattttcgcacaatctcctcagatttttttaaaatttaaaaaaagttgataaaaaagaaagcgttttattttatatactagttactgtagaggaaacatcctcaagatttttactaggaggacagttc .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gaactgtcctcctagtaaaaatcttgaggatgtttcctctacagtaactagtatataaaataaaacgctttcttttttatcaactttttttaaattttaaaaaaatctgaggagattgtgcgaaaatcacaaagaaacctggatttctccaagtttc Mask Tandem Repeat Region ================================================ gaaacttggagaaatccaggtttctttgtgattttcgcacaatctcctcagatttttttaaaatttaaaaaaagttgataaaaaagaaagcgttttattttatatactagttactgtagaggaaacatcctcaagatttttactaggaggacagttc Find is-nt database================================================ Query_seq: SSA_1825:SSA_1826|SSA_1825:SSA_1826:hypothetical protein:Glycerol kinase, putative:->->:1814519..1814675 157 gaaacttggagaaatccaggtttctttgtgattttcgcacaatctcctcagatttttttaaaatttaaaaaaagttgataaaaaagaaagcgttttattttatatactagttactgtagaggaaacatcctcaagatttttactaggaggacagttc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1825:SSA_1826|SSA_1825:SSA_1826:hypothetical protein:Glycerol kinase, putative:->->:1814519..1814675 157 gaaacttggagaaatccaggtttctttgtgattttcgcacaatctcctcagatttttttaaaatttaaaaaaagttgataaaaaagaaagcgttttattttatatactagttactgtagaggaaacatcctcaagatttttactaggaggacagttc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1825:SSA_1826|SSA_1825:SSA_1826:hypothetical protein:Glycerol kinase, putative:->->:1814519..1814675 157 gaaacttggagaaatccaggtttctttgtgattttcgcacaatctcctcagatttttttaaaatttaaaaaaagttgataaaaaagaaagcgttttattttatatactagttactgtagaggaaacatcctcaagatttttactaggaggacagttc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gaaacttggagaaatccaggtttctttgtgattttcgcacaatctcctcagatttttttaaaatttaaaaaaagttgataaaaaagaaagcgttttattttatatactagttactgtagaggaaacatcctcaagatttttactaggaggacagttc Predict ORF larger than 30AA ================================================ gaaacttggagaaatccaggtttctttgtgattttcgcacaatctcctcagatttttttaaaatttaaaaaaagttgataaaaaagaaagcgttttattttatatactagttactgtagaggaaacatcctcaagatttttactaggaggacagttc 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================================================ gaaacttggagaaatccaggtttctttgtgattttcgcacaatctcctcagatttttttaaaatttaaaaaaagttgataaaaaagaaagcgttttattttatatactagttactgtagaggaaacatcctcaagatttttactaggaggacagttc Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_1825:SSA_1826|SSA_1825:SSA_1826:hypothetical protein:Glycerol kinase, putative:->->:1814519..1814675 157 gaaacttggagaaatccaggtttctttgtgattttcgcacaatctcctcagatttttttaaaatttaaaaaaagttgataaaaaagaaagcgttttattttatatactagttactgtagaggaaacatcctcaagatttttactaggaggacagttc Intra-Species Hit: Count: 1 Min: 1 Max: 157 Len: 157 Subject: NC_009009_SSA_1825_SSA_1826|hypothetical protein:Glycerol kinase, putative|POSITIVE:POSITIVE|[1814519,1814675]|157 HSP 1 e-value: 3.0E-23 bit: 109.0 Len: 55 Query Start:103 Query End:157 Subject Strand: POSITIVE Subject Start: 103 Subject End: 157 ......................................................................................................tatactagttactgtagaggaaacatcctcaagatttttactaggaggacagttc ......................................................................................................tatactagttactgtagaggaaacatcctcaagatttttactaggaggacagttc HSP 2 e-value: 2.0E-21 bit: 103.0 Len: 52 Query Start:1 Query End:52 Subject Strand: POSITIVE Subject Start: 1 Subject End: 52 gaaacttggagaaatccaggtttctttgtgattttcgcacaatctcctcaga......................................................................................................... gaaacttggagaaatccaggtttctttgtgattttcgcacaatctcctcaga......................................................................................................... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAAACUUGGAGAAAUCCAGGUUUCUUUGUGAUUUUCGCACAAUCUCCUCAGAUUUUUUUAAAAUUUAAAAAAAGUUGAUAAAAAAGAAAGCGUUUUAUUUUAUAUACUAGUUACUGUAGAGGAAACAUCCUCAAGAUUUUUACUAGGAGGACAGUUC ((((((((((....)))))))))).(((((.......)))))..(((((.(((((((((........))))))))).((((((.((((....)))).))))))...(((((....((.(((((....)))))...))....))))))))))...... (-39.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAACUGUCCUCCUAGUAAAAAUCUUGAGGAUGUUUCCUCUACAGUAACUAGUAUAUAAAAUAAAACGCUUUCUUUUUUAUCAACUUUUUUUAAAUUUUAAAAAAAUCUGAGGAGAUUGUGCGAAAAUCACAAAGAAACCUGGAUUUCUCCAAGUUUC ((.........(((((.........(((((....))))).......)))))..............(((...(..((((.(((..((((((((.....))))))))..))).))))..).)))....)).....(((((.((((....)))).))))) (-29.49) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 306 53 16 106 70 NC_009009:SSA_1261|5end_Ribose-5-phosphate_isomerase_A,_putative_1287654..1287884_NEGATIVE 281 50 5 224 172 NC_009009:SSA_0242|5end_hypothetical_protein_234978..235208_POSITIVE 258 50 1 103 52 NC_009009:SSA_0832|5end_SecY-like_protein,_putative_816708..816938_POSITIVE 253 45 3 208 159 NC_009009:SSA_2010|5end_ABC-type_multidrug_transport_system,_permease_component,_putative_2012024..2012254_NEGATIVE 244 69 23 71 9 NC_009009:SSA_1475|5end_hypothetical_protein_1480121..1480351_NEGATIVE 244 49 5 213 162 NC_009009:SSA_0676|5end_Farnesyl_diphosphate_synthase,_putative_658598..658828_POSITIVE 243 59 17 218 178 NC_009009:SSA_1023|5end_Von_Willebrand_factor-binding_protein_precursor,_putative_1038411..1038641_POSITIVE 239 59 18 117 62 NC_009009:SSA_0749|5end_Competence_protein,_putative_730668..730898_POSITIVE 237 50 6 125 79 NC_009009:SSA_0690|5end_Recombinational_DNA_repair_protein_(RecF_pathway),_putative_674432..674662_POSITIVE 235 58 15 141 100 NC_009009:SSA_0119|5end_50S_ribosomal_protein_L5,_putative_113692..113922_POSITIVE 228 48 5 125 71 NC_009009:SSA_1809|5end_PTS_system_glucose-specific_EIIC_BA_component_(EIICBA-Glc)_(EII-_Glc/EIII-Glc),_putative_1794419..1794649_NEGATIVE 228 52 18 111 63 NC_009009:SSA_0748|5end_Sugar:H+_symporter,_permease_of_the_major_facilitator_superfamily,_putative_729386..729616_POSITIVE 227 49 8 170 127 NC_009009:SSA_1728|5end_ABC_transporter_membrane-spanning_permease-branched_chain_amino_acid_transport,_putative_1714293..1714523_NEGATIVE 227 56 18 202 166 NC_009009:SSA_1478|5end_Transposase_ORF1,_putative_1482889..1483119_POSITIVE 227 49 7 145 107 NC_009009:SSA_0245|5end_hypothetical_protein_239136..239366_POSITIVE 226 47 7 44 11 NC_009009:SSA_0913|5end_Acetyltransferase,_putative_924195..924425_POSITIVE 226 148 107 120 79 NC_009009:SSA_0171|5end_Cro-like_transcriptional_repressor,_XRE_family,_putative_168956..169186_NEGATIVE 225 48 4 159 122 NC_009009:SSA_0967|5end_hypothetical_protein_975872..976102_POSITIVE 221 49 5 84 35 NC_009009:SSA_2175|5end_hypothetical_protein_2174042..2174272_NEGATIVE 221 50 6 207 164 NC_009009:SSA_1878|5end_Conserved_uncharacterized_protein_1872200..1872430_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 267 60 17 117 74 NC_009009:SSA_0796|3end_ABC-NBD_transporters_with_duplicated_ATPase_domains,_putative_779060..779210_POSITIVE 258 50 1 70 19 NC_009009:SSA_0831|3end_Nucleotide_sugar_synthetase-like_protein,_putative_816755..816905_POSITIVE 239 31 1 97 67 NC_009009:SSA_1825|3end_hypothetical_protein_1814458..1814608_POSITIVE 235 58 15 117 76 NC_009009:SSA_0118|3end_50S_ribosomal_protein_L24,_putative_113748..113898_POSITIVE 227 56 18 147 111 NC_009009:SSA_1477|3end_Truncated_transposase,_putative_1482914..1483064_POSITIVE 227 49 7 99 61 NC_009009:SSA_0244|3end_hypothetical_protein_239170..239320_POSITIVE 225 49 5 102 54 NC_009009:SSA_0686|3end_Fe2+/Zn2+_uptake_regulation_protein,_putative_670079..670229_POSITIVE 222 149 118 77 49 NC_009009:SSA_1302|3end_tRNA_(Guanine-N(1)-)-methyltransferase,_putative_1321762..1321912_NEGATIVE 217 51 11 120 81 NC_009009:SSA_1821|3end_Acetyltransferase_(N-acetylase_of_ribosomal_proteins),_putative_1810047..1810197_NEGATIVE 216 59 16 49 11 NC_009009:SSA_0028|3end_Phosphoribosylaminoimidazole-succinocarboxamide_synthase,_putative_32670..32820_POSITIVE 213 47 4 150 103 NC_009009:SSA_1124|3end_Oxidoreductase,_putative_1148547..1148697_NEGATIVE 212 58 14 102 66 NC_009009:SSA_0852|3end_ATP-dependent_DNA_helicase,_putative_841418..841568_POSITIVE 211 59 14 120 66 NC_009009:SSA_0837|3end_Glucosyltransferase,_putative_825502..825652_POSITIVE 209 48 6 115 68 NC_009009:SSA_0126|3end_50S_ribosomal_protein_L15,_putative_117787..117937_POSITIVE 207 60 13 110 65 NC_009009:SSA_2217|3end_Cps9H,_putative_2218086..2218236_NEGATIVE 207 38 6 72 36 NC_009009:SSA_1447|3end_ATP_phosphoribosyltransferase,_putative_1449187..1449337_NEGATIVE 207 62 21 47 8 NC_009009:SSA_0820|3end_Ribosomal_protein_S21,_putative_801505..801655_POSITIVE 205 47 4 112 64 NC_009009:SSA_1013|3end_Phosphatidylserine_synthase,_putative_1017933..1018083_POSITIVE 205 55 13 140 93 NC_009009:SSA_0694|3end_Mutator_protein,_putative_678421..678571_POSITIVE 204 47 5 48 5 NC_009009:SSA_1307|3end_Trk_transporter_membrane-spanning_protein-K+_transport,_putative_1324921..1325071_NEGATIVE