Origin IGS: agagtataaaacatcaggagcaacgataaggttgcccctgatgttttattgtctagtaataaattgaaatgaaccatgatacagcttcggaagtctacctaattcggaaaaatcttctccaaggaatcaggaacaatttcaatagctgatg .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 catcagctattgaaattgttcctgattccttggagaagatttttccgaattaggtagacttccgaagctgtatcatggttcatttcaatttattactagacaataaaacatcaggggcaaccttatcgttgctcctgatgttttatactct Mask Tandem Repeat Region ================================================ agagtataaaacatcaggagcaacgataaggttgcccctgatgttttattgtctagtaataaattgaaatgaaccatgatacagcttcggaagtctacctaattcggaaaaatcttctccaaggaatcaggaacaatttcaatagctgatg Find is-nt database================================================ Query_seq: SSA_1687:SSA_1689|SSA_1687:SSA_1689:NADH-binding ferric-oxidoreductase, putative:hypothetical protein:-><-:1681884..1682034 151 agagtataaaacatcaggagcaacgataaggttgcccctgatgttttattgtctagtaataaattgaaatgaaccatgatacagcttcggaagtctacctaattcggaaaaatcttctccaaggaatcaggaacaatttcaatagctgatg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1687:SSA_1689|SSA_1687:SSA_1689:NADH-binding ferric-oxidoreductase, putative:hypothetical protein:-><-:1681884..1682034 151 agagtataaaacatcaggagcaacgataaggttgcccctgatgttttattgtctagtaataaattgaaatgaaccatgatacagcttcggaagtctacctaattcggaaaaatcttctccaaggaatcaggaacaatttcaatagctgatg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1687:SSA_1689|SSA_1687:SSA_1689:NADH-binding ferric-oxidoreductase, putative:hypothetical protein:-><-:1681884..1682034 151 agagtataaaacatcaggagcaacgataaggttgcccctgatgttttattgtctagtaataaattgaaatgaaccatgatacagcttcggaagtctacctaattcggaaaaatcttctccaaggaatcaggaacaatttcaatagctgatg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 agagtataaaacatcaggagcaacgataaggttgcccctgatgttttattgtctagtaataaattgaaatgaaccatgatacagcttcggaagtctacctaattcggaaaaatcttctccaaggaatcaggaacaatttcaatagctgatg Predict ORF larger than 30AA ================================================ agagtataaaacatcaggagcaacgataaggttgcccctgatgttttattgtctagtaataaattgaaatgaaccatgatacagcttcggaagtctacctaattcggaaaaatcttctccaaggaatcaggaacaatttcaatagctgatg 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================================================ agagtataaaacatcaggagcaacgataaggttgcccctgatgttttattgtctagtaataaattgaaatgaaccatgatacagcttcggaagtctacctaattcggaaaaatcttctccaaggaatcaggaacaatttcaatagctgatg Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 65 HP_score: -8.0 Tail_Score: -2.99458 Start: 17 End: 38 Full_Region: gacaataaaacatca ggggcaac cttatc gttgctcc tgatgttttatactc ................ggggcaaccttatcgttgctcc................................................................................................................. Find igs database================================================ Query_seq: SSA_1687:SSA_1689|SSA_1687:SSA_1689:NADH-binding ferric-oxidoreductase, putative:hypothetical protein:-><-:1681884..1682034 151 agagtataaaacatcaggagcaacgataaggttgcccctgatgttttattgtctagtaataaattgaaatgaaccatgatacagcttcggaagtctacctaattcggaaaaatcttctccaaggaatcaggaacaatttcaatagctgatg Intra-Species Hit: Count: 1 Min: 1 Max: 151 Len: 151 Subject: NC_009009_SSA_1687_SSA_1689|NADH-binding ferric-oxidoreductase, putative:hypothetical protein|POSITIVE:NEGATIVE|[1681884,1682034]|151 HSP 1 e-value: 1.0E-80 bit: 299.0 Len: 151 Query Start:1 Query End:151 Subject Strand: POSITIVE Subject Start: 1 Subject End: 151 agagtataaaacatcaggagcaacgataaggttgcccctgatgttttattgtctagtaataaattgaaatgaaccatgatacagcttcggaagtctacctaattcggaaaaatcttctccaaggaatcaggaacaatttcaatagctgatg agagtataaaacatcaggagcaacgataaggttgcccctgatgttttattgtctagtaataaattgaaatgaaccatgatacagcttcggaagtctacctaattcggaaaaatcttctccaaggaatcaggaacaatttcaatagctgatg Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGAGUAUAAAACAUCAGGAGCAACGAUAAGGUUGCCCCUGAUGUUUUAUUGUCUAGUAAUAAAUUGAAAUGAACCAUGAUACAGCUUCGGAAGUCUACCUAAUUCGGAAAAAUCUUCUCCAAGGAAUCAGGAACAAUUUCAAUAGCUGAUG (((..(((((((((((((.(((((......))))).)))))))))))))..)))...........................(((((...(((((...(((.(((((((.........)))...)))).)))....)))))...)))))... (-44.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CAUCAGCUAUUGAAAUUGUUCCUGAUUCCUUGGAGAAGAUUUUUCCGAAUUAGGUAGACUUCCGAAGCUGUAUCAUGGUUCAUUUCAAUUUAUUACUAGACAAUAAAACAUCAGGGGCAACCUUAUCGUUGCUCCUGAUGUUUUAUACUCU ...(((((...(((.((...((((((((...(((((.....)))))))))))))..)).)))...)))))...........................(((..(((((((((((((((((((......)))))))))))))))))))..))) (-49.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 345 132 92 51 1 NC_009009:SSA_0213|5end_hypothetical_protein_210135..210365_NEGATIVE 300 48 13 78 30 NC_009009:SSA_0792|5end_hypothetical_protein_774618..774848_POSITIVE 283 118 74 168 125 NC_009009:SSA_0789|5end_Proton-translocating_ATPase,_F1_sector,_epsilon_subunit,_putative_772451..772681_POSITIVE 270 56 12 72 28 NC_009009:SSA_0515|5end_Propanediol_utilization_protein_PduU,_putative_514134..514364_POSITIVE 266 56 12 71 20 NC_009009:SSA_2166|5end_ABC-type_multidrug_transporter,_ATPase_and_permease_components,_putative_2165642..2165872_NEGATIVE 265 42 1 68 19 NC_009009:SSA_0735|5end_Integral_membrane_protein,_putative_717103..717333_POSITIVE 259 52 13 94 57 NC_009009:SSA_0641|5end_hypothetical_protein_628898..629128_POSITIVE 255 130 84 144 85 NC_009009:SSA_1764|5end_hypothetical_protein_1750868..1751098_POSITIVE 254 47 13 223 177 NC_009009:SSA_2110|5end_30S_ribosomal_protein_S7,_putative_2115579..2115809_NEGATIVE 252 120 76 61 18 NC_009009:SSA_0551|5end_L-asparaginase,_putative_547293..547523_NEGATIVE 251 129 82 188 136 NC_009009:SSA_1726|5end_ABC_transporter_ATP-binding_protein-branched_chain_amino_acid_transport,_putative_1712467..1712697_NEGATIVE 247 50 17 171 139 NC_009009:SSA_0903|5end_NAD(P)H_dehydrogenase_(quinone),_putative_893242..893472_POSITIVE 246 57 15 95 32 NC_009009:SSA_1133|5end_TatA,_sec-independent_protein_secretion_pathway_component,_putative_1159397..1159627_POSITIVE 246 54 13 84 30 NC_009009:SSA_0498|5end_ABC-type_dipeptide/oligopeptide/nickel_transport_systems,_permease_components,_putative_497910..498140_POSITIVE 245 55 17 229 189 NC_009009:SSA_0631|5end_Tryptophan_synthase_beta_chain,_putative_619872..620102_POSITIVE 245 60 16 58 11 NC_009009:SSA_0118|5end_50S_ribosomal_protein_L24,_putative_113363..113593_POSITIVE 244 146 115 73 46 NC_009009:SSA_2168|5end_Glycerol-3-phosphate_dehydrogenase_[NAD(P)+],_putative_2167461..2167691_POSITIVE 244 51 14 229 182 NC_009009:SSA_2088|5end_Carbohydrate_isomerase,_AraD/FucA_family,_putative_2093476..2093706_NEGATIVE 244 130 83 57 2 NC_009009:SSA_1248|5end_hypothetical_protein_1273263..1273493_NEGATIVE 242 54 12 68 28 NC_009009:SSA_1840|5end_RNA_binding_protein,_putative_1834422..1834652_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 441 49 1 85 37 NC_009009:SSA_1687|3end_NADH-binding_ferric-oxidoreductase,_putative_1681823..1681973_POSITIVE 300 48 13 85 37 NC_009009:SSA_0791|3end_UDP-N-acetylglucosamine-like_protein,_putative_774705..774855_POSITIVE 295 50 8 84 48 NC_009009:SSA_0462|3end_ABC-type_multidrug_transport_system_(phospholipid,_LPS,_lipid_A_and_drug_exporter),_ATPase_and_permease_components,_putative_466652..466802_POSITIVE 266 56 12 69 18 NC_009009:SSA_2167|3end_ABC-type_multidrug_transporter,_ATPase_and_permease_components,_putative_2165644..2165794_NEGATIVE 265 42 1 81 32 NC_009009:SSA_0734|3end_Arsenical_resistance_operon_transcription_repressor_(ArsR),_putative_717196..717346_POSITIVE 264 126 85 143 97 NC_009009:SSA_1335|3end_Ankyrin_repeat_protein,_putative_1349055..1349205_NEGATIVE 258 53 20 39 7 NC_009009:SSA_0248|3end_hypothetical_protein_241844..241994_POSITIVE 255 130 84 147 88 NC_009009:SSA_1763|3end_ABC-type_molybdenum_transport_system,_ATPase_component,_putative_1750951..1751101_POSITIVE 247 50 17 95 63 NC_009009:SSA_0901|3end_Alpha-acetolactate_decarboxylase,_putative_893246..893396_POSITIVE 246 57 15 95 32 NC_009009:SSA_1132|3end_TatC,_sec-independent_protein_translocase,_putative_1159477..1159627_POSITIVE 246 54 13 91 37 NC_009009:SSA_0497|3end_Nickel_ABC_transporter,_putative_497997..498147_POSITIVE 242 54 12 68 28 NC_009009:SSA_1841|3end_Cof_family_protein/peptidyl-prolyl_cis-trans_isomerase,_cyclophilin_type,_putative_1834422..1834572_NEGATIVE 242 79 35 121 83 NC_009009:SSA_0124|3end_30S_ribosomal_protein_S5,_putative_116996..117146_POSITIVE 239 129 85 44 2 NC_009009:SSA_1864|3end_Nicotinate_phosphoribosyltransferase_(NAPRTase),_subgroup_A,_putative_1859410..1859560_NEGATIVE 237 54 11 112 56 NC_009009:SSA_1690|3end_hypothetical_protein_1683348..1683498_POSITIVE 237 52 14 63 21 NC_009009:SSA_0924|3end_ABC-type_antimicrobial_peptide_transport_system,_permease_component,_putative_934828..934978_POSITIVE 235 57 12 127 89 NC_009009:SSA_2105|3end_hypothetical_protein_2106756..2106906_NEGATIVE 233 130 82 55 10 NC_009009:SSA_2101|3end_Amino_acid_ABC_transporter,_periplasmic_amino_acid-binding_protein,_putative_2104509..2104659_NEGATIVE 232 54 13 85 51 NC_009009:SSA_0217|3end_Two-component_system_transcriptional_regulator_(CheY_domain_and_HTH-like_DNA-binding_domain),_putative_213946..214096_POSITIVE 228 59 12 63 16 NC_009009:SSA_0531|3end_Ethanolamine_utilization_protein_eutQ_(cobalamin-dependent_degradation_of_ethanolamine),_putative_527884..528034_POSITIVE