Origin IGS: aaagttatttttcaatccttttttagaaaatttaaaaaggttctagaaaacgctatcaaaagaaagaactttgtgatatactatacatagtttaaattaataggagaatttttt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aaaaaattctcctattaatttaaactatgtatagtatatcacaaagttctttcttttgatagcgttttctagaacctttttaaattttctaaaaaaggattgaaaaataacttt Mask Tandem Repeat Region ================================================ aaagttatttttcaatccttttttagaaaatttaaaaaggttctagaaaacgctatcaaaagaaagaactttgtgatatactatacatagtttaaattaataggagaatttttt Find is-nt database================================================ Query_seq: SSA_1096:SSA_1098|SSA_1096:SSA_1098:Methyltransferase, putative:Formate-nitrate transporter, putative:->->:1114160..1114273 114 aaagttatttttcaatccttttttagaaaatttaaaaaggttctagaaaacgctatcaaaagaaagaactttgtgatatactatacatagtttaaattaataggagaatttttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1096:SSA_1098|SSA_1096:SSA_1098:Methyltransferase, putative:Formate-nitrate transporter, putative:->->:1114160..1114273 114 aaagttatttttcaatccttttttagaaaatttaaaaaggttctagaaaacgctatcaaaagaaagaactttgtgatatactatacatagtttaaattaataggagaatttttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1096:SSA_1098|SSA_1096:SSA_1098:Methyltransferase, putative:Formate-nitrate transporter, putative:->->:1114160..1114273 114 aaagttatttttcaatccttttttagaaaatttaaaaaggttctagaaaacgctatcaaaagaaagaactttgtgatatactatacatagtttaaattaataggagaatttttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aaagttatttttcaatccttttttagaaaatttaaaaaggttctagaaaacgctatcaaaagaaagaactttgtgatatactatacatagtttaaattaataggagaatttttt Predict ORF larger than 30AA ================================================ aaagttatttttcaatccttttttagaaaatttaaaaaggttctagaaaacgctatcaaaagaaagaactttgtgatatactatacatagtttaaattaataggagaatttttt 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================================================ aaagttatttttcaatccttttttagaaaatttaaaaaggttctagaaaacgctatcaaaagaaagaactttgtgatatactatacatagtttaaattaataggagaatttttt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_1096:SSA_1098|SSA_1096:SSA_1098:Methyltransferase, putative:Formate-nitrate transporter, putative:->->:1114160..1114273 114 aaagttatttttcaatccttttttagaaaatttaaaaaggttctagaaaacgctatcaaaagaaagaactttgtgatatactatacatagtttaaattaataggagaatttttt Intra-Species Hit: Count: 1 Min: 1 Max: 114 Len: 114 Subject: NC_009009_SSA_1096_SSA_1098|Methyltransferase, putative:Formate-nitrate transporter, putative|POSITIVE:POSITIVE|[1114160,1114273]|114 HSP 1 e-value: 1.0E-58 bit: 226.0 Len: 114 Query Start:1 Query End:114 Subject Strand: POSITIVE Subject Start: 1 Subject End: 114 aaagttatttttcaatccttttttagaaaatttaaaaaggttctagaaaacgctatcaaaagaaagaactttgtgatatactatacatagtttaaattaataggagaatttttt aaagttatttttcaatccttttttagaaaatttaaaaaggttctagaaaacgctatcaaaagaaagaactttgtgatatactatacatagtttaaattaataggagaatttttt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAGUUAUUUUUCAAUCCUUUUUUAGAAAAUUUAAAAAGGUUCUAGAAAACGCUAUCAAAAGAAAGAACUUUGUGAUAUACUAUACAUAGUUUAAAUUAAUAGGAGAAUUUUUU .(((..(((((((.....((((((((((..((....))..))))))))))...............(((((.((((........)))).))))).........)))))))..))) (-16.20) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAAAAUUCUCCUAUUAAUUUAAACUAUGUAUAGUAUAUCACAAAGUUCUUUCUUUUGAUAGCGUUUUCUAGAACCUUUUUAAAUUUUCUAAAAAAGGAUUGAAAAAUAACUUU ...........(((((((....((((.(((..........))).)))).......)))))))..(((((.....(((((((..........)))))))...)))))........ (-11.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 247 84 45 96 53 NC_009009:SSA_1638|5end_hypothetical_protein_1641325..1641555_NEGATIVE 195 80 38 185 142 NC_009009:SSA_1001|5end_Arabinose_(multiple_sugar_metabolism)_operon_transcriptional_regulator,_putative_1001689..1001919_NEGATIVE 184 45 2 180 128 NC_009009:SSA_2351|5end_ABC-type_nitrate/sulfonate/bicarbonate_transport_system,_ATPase_component,_putative_2353507..2353737_NEGATIVE 183 43 6 121 76 NC_009009:SSA_2065|5end_hypothetical_protein_2065743..2065973_NEGATIVE 179 89 42 142 91 NC_009009:SSA_1759|5end_hypothetical_protein_1746969..1747199_NEGATIVE 178 47 1 183 127 NC_009009:SSA_2358|5end_hypothetical_protein_2360497..2360727_NEGATIVE 173 70 38 150 106 NC_009009:SSA_0796|5end_ABC-NBD_transporters_with_duplicated_ATPase_domains,_putative_777085..777315_POSITIVE 172 108 69 146 101 NC_009009:SSA_2286|5end_Dihydroxy-acid_dehydratase,_putative_2289596..2289826_NEGATIVE 171 80 40 146 115 NC_009009:SSA_1814|5end_hypothetical_protein_1799979..1800209_NEGATIVE 171 83 56 128 99 NC_009009:SSA_1635|5end_hypothetical_protein_1639221..1639451_NEGATIVE 171 54 16 150 99 NC_009009:SSA_0913|5end_Acetyltransferase,_putative_924195..924425_POSITIVE 169 43 8 157 111 NC_009009:SSA_1079|5end_hypothetical_protein_1096385..1096615_POSITIVE 168 85 41 68 31 NC_009009:SSA_0708|5end_hypothetical_protein_694144..694374_POSITIVE 165 50 1 152 105 NC_009009:SSA_0151|5end_hypothetical_protein_145354..145584_POSITIVE 164 72 39 189 149 NC_009009:SSA_0479|5end_CbiQ_protein,_putative_480425..480655_POSITIVE 163 57 16 121 71 NC_009009:SSA_1134|5end_Xanthine_phosphoribosyltransferase,_putative_1159628..1159858_POSITIVE 163 77 42 78 45 NC_009009:SSA_0116|5end_30S_ribosomal_protein_S17,_putative_112632..112862_POSITIVE 162 25 1 108 84 NC_009009:SSA_1174|5end_Dihydrolipoamide_dehydrogenase,_putative_1202854..1203084_NEGATIVE 162 64 42 151 129 NC_009009:SSA_0767|5end_Diacylglycerol_kinase_catalytic_domain_protein,_putative_747087..747317_POSITIVE 161 99 52 185 133 NC_009009:SSA_2052|5end_Thioredoxin,_putative_2057507..2057737_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 247 84 45 82 39 NC_009009:SSA_1639|3end_5'-methylthioadenosine/S-adenosylhomocysteine_nucleosidase,_putative_1641339..1641489_NEGATIVE 183 43 6 115 70 NC_009009:SSA_2066|3end_DNA_polymerase_III_polC-type,_putative_2065749..2065899_NEGATIVE 178 47 1 67 11 NC_009009:SSA_2359|3end_Glucose_inhibited_division_protein_A,_putative_2360613..2360763_NEGATIVE 173 70 38 50 6 NC_009009:SSA_0795|3end_hypothetical_protein_777065..777215_POSITIVE 172 43 1 75 28 NC_009009:SSA_1585|3end_hypothetical_protein_1586975..1587125_NEGATIVE 172 74 43 62 38 NC_009009:SSA_1131|3end_High-affinity_Fe_2+/Pb2+_permease,_putative_1158768..1158918_POSITIVE 171 80 40 142 111 NC_009009:SSA_1815|3end_hypothetical_protein_1799983..1800133_NEGATIVE 171 54 16 104 53 NC_009009:SSA_0912|3end_Phenylalanyl-tRNA_synthetase_alpha_chain,_putative_924229..924379_POSITIVE 169 44 1 149 106 NC_009009:SSA_1793|3end_Histidine_kinase_(sensor_protein),_putative_1775126..1775276_NEGATIVE 169 43 8 143 97 NC_009009:SSA_1078|3end_hypothetical_protein_1096451..1096601_POSITIVE 169 75 34 89 45 NC_009009:SSA_0690|3end_Recombinational_DNA_repair_protein_(RecF_pathway),_putative_675108..675258_POSITIVE 165 46 8 116 81 NC_009009:SSA_1921|3end_hypothetical_protein_1911317..1911467_POSITIVE 164 72 39 71 31 NC_009009:SSA_0478|3end_Cobalt_transport_protein_cbiN,_putative_480387..480537_POSITIVE 163 57 16 78 28 NC_009009:SSA_1133|3end_TatA,_sec-independent_protein_secretion_pathway_component,_putative_1159665..1159815_POSITIVE 163 77 42 54 21 NC_009009:SSA_0115|3end_50S_ribosomal_protein_L29,_putative_112688..112838_POSITIVE 162 25 1 29 5 NC_009009:SSA_1175|3end_Acetoin_dehydrogenase_complex,_E2_component,_dihydrolipoamide_acetyltransferase,_putative_1202933..1203083_NEGATIVE 159 29 3 107 83 NC_009009:SSA_1644|3end_hypothetical_protein_1645471..1645621_NEGATIVE 157 56 16 94 44 NC_009009:SSA_0051|3end_Dihydroxyacetone_kinase_phosphotransfer_protein,_putative_55644..55794_POSITIVE 153 59 11 104 69 NC_009009:SSA_1980|3end_50S_ribosomal_protein_L28,_putative_1974444..1974594_NEGATIVE 151 84 42 54 19 NC_009009:SSA_0445|3end_hypothetical_protein_444776..444926_POSITIVE