Origin IGS: tctagtataaagaatttagggtaggatgctttccttgcccttttcgtatcataatcatcatccctctcataaacaaaaaaactagagcagatgtgtactacacatctgctctagttt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aaactagagcagatgtgtagtacacatctgctctagtttttttgtttatgagagggatgatgattatgatacgaaaagggcaaggaaagcatcctaccctaaattctttatactaga Mask Tandem Repeat Region ================================================ tctagtataaagaatttagggtaggatgctttccttgcccttttcgtatcataatcatcatccctctcataaacaaaaaaactagagcagatgtgtactacacatctgctctagttt Find is-nt database================================================ Query_seq: SSA_0562:SSA_0563|SSA_0562:SSA_0563:hypothetical protein:Universal stress protein family, putative:-><-:554920..555036 117 tctagtataaagaatttagggtaggatgctttccttgcccttttcgtatcataatcatcatccctctcataaacaaaaaaactagagcagatgtgtactacacatctgctctagttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0562:SSA_0563|SSA_0562:SSA_0563:hypothetical protein:Universal stress protein family, putative:-><-:554920..555036 117 tctagtataaagaatttagggtaggatgctttccttgcccttttcgtatcataatcatcatccctctcataaacaaaaaaactagagcagatgtgtactacacatctgctctagttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0562:SSA_0563|SSA_0562:SSA_0563:hypothetical protein:Universal stress protein family, putative:-><-:554920..555036 117 tctagtataaagaatttagggtaggatgctttccttgcccttttcgtatcataatcatcatccctctcataaacaaaaaaactagagcagatgtgtactacacatctgctctagttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tctagtataaagaatttagggtaggatgctttccttgcccttttcgtatcataatcatcatccctctcataaacaaaaaaactagagcagatgtgtactacacatctgctctagttt Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: - Start: 3 End: 92 .. L I F F K P Y S A K R A R K T D Y D D D R E Y V F F S S C M ......................... tctagtataaagaatttagggtaggatgctttccttgcccttttcgtatcataatcatcatccctctcataaacaaaaaaactagagcagatgtgtactacacatctgctctagttt 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================================================ tctagtataaagaatttagggtaggatgctttccttgcccttttcgtatcataatcatcatccctctcataaacaaaaaaactagagcagatgtgtactacacatctgctctagttt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_0562:SSA_0563|SSA_0562:SSA_0563:hypothetical protein:Universal stress protein family, putative:-><-:554920..555036 117 tctagtataaagaatttagggtaggatgctttccttgcccttttcgtatcataatcatcatccctctcataaacaaaaaaactagagcagatgtgtactacacatctgctctagttt Intra-Species Hit: Count: 1 Min: 1 Max: 117 Len: 117 Subject: NC_009009_SSA_0562_SSA_0563|hypothetical protein:Universal stress protein family, putative|POSITIVE:NEGATIVE|[554920,555036]|117 HSP 1 e-value: 7.0E-48 bit: 190.0 Len: 117 Query Start:1 Query End:117 Subject Strand: POSITIVE Subject Start: 1 Subject End: 117 tctagtataaagaatttagggtaggatgctttccttgcccttttcgtatcataatcatcatccctctcataaacnnnnnnnctagagcagatgtgtactacacatctgctctagttt tctagtataaagaatttagggtaggatgctttccttgcccttttcgtatcataatcatcatccctctcataaacaaaaaaactagagcagatgtgtactacacatctgctctagttt HSP 2 e-value: 1.0E-9 bit: 63.9 Len: 36 Query Start:82 Query End:117 Subject Strand: NEGATIVE Subject Start: 79 Subject End: 114 .................................................................................ctagagcagatgtgtactacacatctgctctagttt .................................................................................ctagagcagatgtgtagtacacatctgctctagttt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCUAGUAUAAAGAAUUUAGGGUAGGAUGCUUUCCUUGCCCUUUUCGUAUCAUAAUCAUCAUCCCUCUCAUAAACAAAAAAACUAGAGCAGAUGUGUACUACACAUCUGCUCUAGUUU ...........(((...(((((((((.....))).)))))).))).................................(((((((((((((((((.....))))))))))))))))) (-41.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAACUAGAGCAGAUGUGUAGUACACAUCUGCUCUAGUUUUUUUGUUUAUGAGAGGGAUGAUGAUUAUGAUACGAAAAGGGCAAGGAAAGCAUCCUACCCUAAAUUCUUUAUACUAGA (((((((((((((((((.....))))))))))))))))).(((((((((((..(......)..)))))).))))).((((..((((.....)))).))))................. (-39.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 296 49 18 154 118 NC_009009:SSA_0589|5end_Acetylornithine_deacetylase/succinyl-diaminopimelate_desuccinylase_(M20/M25/M40_family_peptidase),_putative_580745..580975_POSITIVE 293 65 21 180 120 NC_009009:SSA_1601|5end_VacB-like_protein,_putative_1607059..1607289_NEGATIVE 290 69 28 224 185 NC_009009:SSA_1540|5end_hypothetical_protein_1545268..1545498_NEGATIVE 289 67 22 231 182 NC_009009:SSA_1035|5end_Pyrimidine_nucleoside_phosphorylase,_putative_1050174..1050404_POSITIVE 279 68 29 101 59 NC_009009:SSA_0467|5end_Cobalt-precorrin-6A_synthase_[deacetylating],_putative_470588..470818_POSITIVE 273 56 20 156 120 NC_009009:SSA_0955|5end_Aminopeptidase_N,_putative_958519..958749_POSITIVE 272 69 32 102 58 NC_009009:SSA_0422|5end_Phosphoglycerate_mutase_family_protein,_putative_420157..420387_POSITIVE 269 107 61 155 107 NC_009009:SSA_0601|5end_Phosphorylase,_Pnp/Udp_family,_putative_589147..589377_POSITIVE 268 60 27 222 184 NC_009009:SSA_0826|5end_hypothetical_protein_805098..805328_POSITIVE 267 60 12 161 111 NC_009009:SSA_0679|5end_DNA_repair_and_genetic_recombination,_putative_660714..660944_POSITIVE 267 48 18 223 183 NC_009009:SSA_0661|5end_Isoleucyl-tRNA_synthetase,_putative_644876..645106_POSITIVE 264 52 11 91 47 NC_009009:SSA_1901|5end_Conserved_uncharacterized_protein_1896599..1896829_NEGATIVE 264 60 19 223 179 NC_009009:SSA_1402|5end_ABC-type_multidrug_transport_system,_ATPase_and_permease_components,_putative_1416220..1416450_NEGATIVE 259 54 25 32 2 NC_009009:SSA_0352|5end_Ribonuclease_HIII,_putative_345879..346109_NEGATIVE 256 65 31 105 68 NC_009009:SSA_1789|5end_Metal-dependent_phosphohydrolase,_HD_superfamily,_putative_1772856..1773086_NEGATIVE 254 88 46 163 122 NC_009009:SSA_1436|5end_hypothetical_protein_1443125..1443355_NEGATIVE 250 71 33 92 43 NC_009009:SSA_0558|5end_Conserved_hypothetical_cytosolic_protein,_putative_552335..552565_POSITIVE 246 55 18 64 16 NC_009009:SSA_0810|5end_P-loop_ATPase,_putative_791582..791812_POSITIVE 243 48 19 181 143 NC_009009:SSA_0496|5end_Succinylglutamate_desuccinylase_/_Aspartoacylase_family,_putative_495946..496176_POSITIVE 242 59 11 180 132 NC_009009:SSA_1459|5end_RNA_methyltransferase,_putative_1467481..1467711_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 290 67 22 65 7 NC_009009:SSA_1949|3end_AliA_protein,_putative_1942403..1942553_NEGATIVE 279 68 29 101 59 NC_009009:SSA_0466|3end_Precorrin-8X_methylmutase_/_precorrin_isomerase,_putative_470668..470818_POSITIVE 277 49 19 36 1 NC_009009:SSA_0588|3end_L-cystine_ABC_transporter,_substrate-binding_component,_putative_580707..580857_POSITIVE 275 68 27 110 62 NC_009009:SSA_0825|3end_DNA-directed_RNA_polymerase,_sigma_subunit_(sigma70/sigma32),_putative_805056..805206_POSITIVE 272 69 32 105 61 NC_009009:SSA_0421|3end_Phosphoglycerate_mutase_family_protein,_putative_420240..420390_POSITIVE 256 65 31 60 23 NC_009009:SSA_1790|3end_SpoU_rRNA_Methylase_family_protein,_putative_1772901..1773051_NEGATIVE 254 88 46 146 105 NC_009009:SSA_1438|3end_Acetyltransferase,_putative_1443142..1443292_NEGATIVE 250 59 12 151 102 NC_009009:SSA_0678|3end_Transcriptional_regulator,_ArgR_family,_putative_660785..660935_POSITIVE 250 71 33 70 21 NC_009009:SSA_0557|3end_hypothetical_protein_552393..552543_POSITIVE 246 45 2 70 28 NC_009009:SSA_1750|3end_Extracellular_nuclease,_putative_1735673..1735823_NEGATIVE 245 58 18 56 15 NC_009009:SSA_0375|3end_D-methionine-binding_lipoprotein_(ABC-type_transporter),_putative_365209..365359_POSITIVE 242 59 11 95 47 NC_009009:SSA_1460|3end_Transcriptional_attenuator_LytR,_putative_1467566..1467716_NEGATIVE 235 49 1 87 32 NC_009009:SSA_1827|3end_Alpha-glycerophosphate_oxidase,_putative_1818018..1818168_POSITIVE 231 69 23 93 41 NC_009009:SSA_1255|3end_hypothetical_protein_1281456..1281606_NEGATIVE 230 47 24 147 121 NC_009009:SSA_1985|3end_hypothetical_protein_1979623..1979773_NEGATIVE 229 47 1 80 29 NC_009009:SSA_1207|3end_Phosphate_acetyltransferase,_putative_1231297..1231447_NEGATIVE 228 64 23 128 80 NC_009009:SSA_1836|3end_Superfamily_II_ATP-dependent_DNA/RNA_helicase_required_for_DNA_uptake_(late_competence_protein),_putative_1830938..1831088_NEGATIVE 226 60 11 136 88 NC_009009:SSA_0272|3end_Oxidoreductase,_aldo/keto_reductase_family,_putative_267032..267182_POSITIVE 225 63 21 97 62 NC_009009:SSA_2186|3end_Glutathione_biosynthesis_bifunctional_protein_gshAB_(Gamma-GCS-GS)_(GCS-GS),_putative_2187870..2188020_POSITIVE 225 47 21 141 110 NC_009009:SSA_1084|3end_Conserved_uncharacterized_protein_1102603..1102753_POSITIVE