Origin IGS: atttactttattctaccatatttcatgagaaaacaatcgggccaaaggctgattataccttgaaagttcattctttaaaaaagagagttcattgaagaactctcttactaatcta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tagattagtaagagagttcttcaatgaactctcttttttaaagaatgaactttcaaggtataatcagcctttggcccgattgttttctcatgaaatatggtagaataaagtaaat Mask Tandem Repeat Region ================================================ atttactttattctaccatatttcatgagaaaacaatcgggccaaaggctgattataccttgaaagttcattctttaaaaaagagagttcattgaagaactctcttactaatcta Find is-nt database================================================ Query_seq: SSA_1549:SSA_1550|SSA_1549:SSA_1550:hypothetical protein:hypothetical protein:<-<-:1552203..1552317 115 atttactttattctaccatatttcatgagaaaacaatcgggccaaaggctgattataccttgaaagttcattctttaaaaaagagagttcattgaagaactctcttactaatcta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1549:SSA_1550|SSA_1549:SSA_1550:hypothetical protein:hypothetical protein:<-<-:1552203..1552317 115 atttactttattctaccatatttcatgagaaaacaatcgggccaaaggctgattataccttgaaagttcattctttaaaaaagagagttcattgaagaactctcttactaatcta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1549:SSA_1550|SSA_1549:SSA_1550:hypothetical protein:hypothetical protein:<-<-:1552203..1552317 115 atttactttattctaccatatttcatgagaaaacaatcgggccaaaggctgattataccttgaaagttcattctttaaaaaagagagttcattgaagaactctcttactaatcta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 atttactttattctaccatatttcatgagaaaacaatcgggccaaaggctgattataccttgaaagttcattctttaaaaaagagagttcattgaagaactctcttactaatcta Predict ORF larger than 30AA ================================================ atttactttattctaccatatttcatgagaaaacaatcgggccaaaggctgattataccttgaaagttcattctttaaaaaagagagttcattgaagaactctcttactaatcta Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ PromScan Matrix: RpoD-17 Strand: - Score: 82 Start: 52 End: 81 ...................................................TTTTTAAAGAATGAACTTTCAAGGTATAAT.................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ atttactttattctaccatatttcatgagaaaacaatcgggccaaaggctgattataccttgaaagttcattctttaaaaaagagagttcattgaagaactctcttactaatcta Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_1549:SSA_1550|SSA_1549:SSA_1550:hypothetical protein:hypothetical protein:<-<-:1552203..1552317 115 atttactttattctaccatatttcatgagaaaacaatcgggccaaaggctgattataccttgaaagttcattctttaaaaaagagagttcattgaagaactctcttactaatcta Intra-Species Hit: Count: 1 Min: 1 Max: 115 Len: 115 Subject: NC_009009_SSA_1549_SSA_1550|hypothetical protein:hypothetical protein|NEGATIVE:NEGATIVE|[1552203,1552317]|115 HSP 1 e-value: 3.0E-59 bit: 228.0 Len: 115 Query Start:1 Query End:115 Subject Strand: POSITIVE Subject Start: 1 Subject End: 115 atttactttattctaccatatttcatgagaaaacaatcgggccaaaggctgattataccttgaaagttcattctttaaaaaagagagttcattgaagaactctcttactaatcta atttactttattctaccatatttcatgagaaaacaatcgggccaaaggctgattataccttgaaagttcattctttaaaaaagagagttcattgaagaactctcttactaatcta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUUUACUUUAUUCUACCAUAUUUCAUGAGAAAACAAUCGGGCCAAAGGCUGAUUAUACCUUGAAAGUUCAUUCUUUAAAAAAGAGAGUUCAUUGAAGAACUCUCUUACUAAUCUA ....(((((...........((((....))))..((((((.(....).))))))........))))).............((((((((((......))))))))))......... (-22.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAGAUUAGUAAGAGAGUUCUUCAAUGAACUCUCUUUUUUAAAGAAUGAACUUUCAAGGUAUAAUCAGCCUUUGGCCCGAUUGUUUUCUCAUGAAAUAUGGUAGAAUAAAGUAAAU ..(((((..((((((((((......)))))))))).......(((......)))......))))).(((...)))....(((((((..((((...))))..)))))))....... (-24.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 861 60 11 151 102 NC_009009:SSA_1549|5end_hypothetical_protein_1552112..1552342_NEGATIVE 257 90 41 225 166 NC_009009:SSA_0337|5end_Hydroxymethylglutaryl-CoA_reductase,_putative_332163..332393_NEGATIVE 252 76 32 45 1 NC_009009:SSA_1418|5end_Conserved_uncharacterized_protein_1428927..1429157_NEGATIVE 251 70 35 48 8 NC_009009:SSA_1259|5end_Purine_nucleoside_phosphorylase,_putative_1285722..1285952_NEGATIVE 246 70 25 84 39 NC_009009:SSA_0425|5end_Glycosyltransferase,_putative_423279..423509_NEGATIVE 246 59 11 204 162 NC_009009:SSA_0098|5end_Hydrolase,_haloacid_dehalogenase-like_family,_putative_99422..99652_POSITIVE 239 72 42 52 16 NC_009009:SSA_0476|5end_Precorrin-2_C20-methyltransferase,_putative_478500..478730_POSITIVE 238 67 24 64 19 NC_009009:SSA_1912|5end_hypothetical_protein_1903220..1903450_NEGATIVE 238 67 24 179 134 NC_009009:SSA_1911|5end_Conserved_uncharacterized_protein_1903105..1903335_NEGATIVE 238 86 41 63 17 NC_009009:SSA_1526|5end_hypothetical_protein_1533722..1533952_POSITIVE 237 67 34 230 190 NC_009009:SSA_1405|5end_Copper_homeostasis_protein_CutC,_putative_1419393..1419623_NEGATIVE 237 61 21 169 141 NC_009009:SSA_0519|5end_Ethanolamine_ammonia-lyase_large_subunit,_putative_518075..518305_POSITIVE 236 75 40 159 132 NC_009009:SSA_2370|5end_Zn-dependemt_peptidase_(insulinase),_M16_family,_putative_2372422..2372652_NEGATIVE 229 66 25 205 158 NC_009009:SSA_2350|5end_30S_ribosomal_protein_S4,_putative_2352648..2352878_NEGATIVE 229 51 14 178 133 NC_009009:SSA_0931|5end_hypothetical_protein_940281..940511_POSITIVE 227 63 21 177 128 NC_009009:SSA_0462|5end_ABC-type_multidrug_transport_system_(phospholipid,_LPS,_lipid_A_and_drug_exporter),_ATPase_and_permease_components,_putative_464815..465045_POSITIVE 225 62 26 173 145 NC_009009:SSA_1443|5end_1-(5-phosphoribosyl)-5-[(5-_phosphoribosylamino)methylideneamino]_imidazole-4-carboxamide_isomerase,_putative_1446672..1446902_NEGATIVE 223 50 2 167 118 NC_009009:SSA_0457|5end_Fructokinase,_putative_460663..460893_POSITIVE 222 68 27 215 171 NC_009009:SSA_2256|5end_hypothetical_protein_2250604..2250834_POSITIVE 221 50 2 156 95 NC_009009:SSA_0596|5end_hypothetical_protein_586913..587143_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 251 50 23 141 117 NC_009009:SSA_0841|3end_hypothetical_protein_827236..827386_POSITIVE 245 54 17 43 5 NC_009009:SSA_0573|3end_hypothetical_protein_568616..568766_NEGATIVE 239 72 42 42 6 NC_009009:SSA_0475|3end_CbiK_protein,_putative_478570..478720_POSITIVE 237 61 21 137 109 NC_009009:SSA_0518|3end_Ethanolamine_utilization_protein_EutA,_putative_518123..518273_POSITIVE 229 66 25 68 21 NC_009009:SSA_2351|3end_ABC-type_nitrate/sulfonate/bicarbonate_transport_system,_ATPase_component,_putative_2352785..2352935_NEGATIVE 229 51 14 80 35 NC_009009:SSA_0929|3end_ABC-type_multidrug_transporter,_ATPase_and_permease_components,_putative_940263..940413_POSITIVE 224 47 1 148 93 NC_009009:SSA_2106|3end_Flavin_monoxygenase,_putative_2108015..2108165_NEGATIVE 224 54 11 89 44 NC_009009:SSA_0931|3end_hypothetical_protein_941335..941485_POSITIVE 221 50 2 146 85 NC_009009:SSA_0595|3end_hypothetical_protein_586983..587133_POSITIVE 220 106 69 42 7 NC_009009:SSA_0937|3end_Arsenate_reductase,_glutaredoxin_family,_putative_946664..946814_POSITIVE 219 59 16 60 13 NC_009009:SSA_0581|3end_Conserved_uncharacterized_protein_573774..573924_POSITIVE 218 49 5 142 102 NC_009009:SSA_1970|3end_Acetolactate_synthase,_large_subunit,_biosynthetic_type,_putative_1965215..1965365_NEGATIVE 218 77 36 71 19 NC_009009:SSA_0590|3end_hypothetical_protein_582817..582967_POSITIVE 217 51 28 146 123 NC_009009:SSA_1964|3end_conserved_uncharacterized_protein_1960996..1961146_NEGATIVE 216 67 35 39 3 NC_009009:SSA_1913|3end_Xanthine/uracil_permease_family_protein,_putative_1903245..1903395_NEGATIVE 216 50 1 84 27 NC_009009:SSA_1576|3end_Catabolite_control_protein_A,_putative_1579177..1579327_NEGATIVE 215 69 25 100 57 NC_009009:SSA_0410|3end_hypothetical_protein_405750..405900_NEGATIVE 215 49 1 67 23 NC_009009:SSA_0008|3end_Transcription-repair_coupling_factor,_putative_9154..9304_POSITIVE 214 54 25 121 84 NC_009009:SSA_0454|3end_Lactose_operon_transcriptional_repressor,_LacI_family,_putative_456050..456200_NEGATIVE 213 60 11 100 57 NC_009009:SSA_0880|3end_Lipoprotein,_putative_876208..876358_POSITIVE