Origin IGS: taatttaaaaacatttgataatttttacgctgatttagcgcgctcagtcaatttctaatttaacgagaatacttttcaaaagtatttttttaatgcattcatgatataataatagtaacttctattcttaaggaggacaa .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ttgtcctccttaagaatagaagttactattattatatcatgaatgcattaaaaaaatacttttgaaaagtattctcgttaaattagaaattgactgagcgcgctaaatcagcgtaaaaattatcaaatgtttttaaatta Mask Tandem Repeat Region ================================================ taatttaaaaacatttgataatttttacgctgatttagcgcgctcagtcaatttctaatttaacgagaatacttttcaaaagtatttttttaatgcattcatgatataataatagtaacttctattcttaaggaggacaa Find is-nt database================================================ Query_seq: SSA_0969:SSA_0970|SSA_0969:SSA_0970:hypothetical protein:hypothetical protein:->->:977790..977929 140 taatttaaaaacatttgataatttttacgctgatttagcgcgctcagtcaatttctaatttaacgagaatacttttcaaaagtatttttttaatgcattcatgatataataatagtaacttctattcttaaggaggacaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0969:SSA_0970|SSA_0969:SSA_0970:hypothetical protein:hypothetical protein:->->:977790..977929 140 taatttaaaaacatttgataatttttacgctgatttagcgcgctcagtcaatttctaatttaacgagaatacttttcaaaagtatttttttaatgcattcatgatataataatagtaacttctattcttaaggaggacaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0969:SSA_0970|SSA_0969:SSA_0970:hypothetical protein:hypothetical protein:->->:977790..977929 140 taatttaaaaacatttgataatttttacgctgatttagcgcgctcagtcaatttctaatttaacgagaatacttttcaaaagtatttttttaatgcattcatgatataataatagtaacttctattcttaaggaggacaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taatttaaaaacatttgataatttttacgctgatttagcgcgctcagtcaatttctaatttaacgagaatacttttcaaaagtatttttttaatgcattcatgatataataatagtaacttctattcttaaggaggacaa Predict ORF larger than 30AA ================================================ taatttaaaaacatttgataatttttacgctgatttagcgcgctcagtcaatttctaatttaacgagaatacttttcaaaagtatttttttaatgcattcatgatataataatagtaacttctattcttaaggaggacaa 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================================================ taatttaaaaacatttgataatttttacgctgatttagcgcgctcagtcaatttctaatttaacgagaatacttttcaaaagtatttttttaatgcattcatgatataataatagtaacttctattcttaaggaggacaa Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 82 HP_score: -5.8 Tail_Score: -5.54894 Start: 70 End: 84 Full_Region: CTAATTTAACGAGAA TACTTT TCA AAAGTA TTTTTTTAATGCATT .....................................................................TACTTTTCAAAAGTA........................................................ Find igs database================================================ Query_seq: SSA_0969:SSA_0970|SSA_0969:SSA_0970:hypothetical protein:hypothetical protein:->->:977790..977929 140 taatttaaaaacatttgataatttttacgctgatttagcgcgctcagtcaatttctaatttaacgagaatacttttcaaaagtatttttttaatgcattcatgatataataatagtaacttctattcttaaggaggacaa Intra-Species Hit: Count: 2 Min: 1 Max: 140 Len: 140 Subject: NC_009009_SSA_0969_SSA_0970|hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[977790,977929]|140 HSP 1 e-value: 2.0E-61 bit: 236.0 Len: 140 Query Start:1 Query End:140 Subject Strand: POSITIVE Subject Start: 1 Subject End: 140 taatttaaaaacatttgataatttttacgctgatttagcgcgctcagtcaatttctaatttaacgagaatacttttcaaaagtannnnnnnaatgcattcatgatataataatagtaacttctattcttaaggaggacaa taatttaaaaacatttgataatttttacgctgatttagcgcgctcagtcaatttctaatttaacgagaatacttttcaaaagtatttttttaatgcattcatgatataataatagtaacttctattcttaaggaggacaa Subject: NC_009009_SSA_0968_SSA_0969|hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[977202,977351]|150 HSP 1 e-value: 4.0E-31 bit: 135.0 Len: 121 Query Start:1 Query End:121 Subject Strand: POSITIVE Subject Start: 4 Subject End: 124 taatttaaaaacatttgataatttttacgctgatttagcgcgctcagtcaatttctaatttaacgagaatacttttcaaaagtannnnnnnaatgcattcatgatataataatagtaactt................... taatttaaaaacttttgataatttttatgcagatttagcgcagtcagccaatttctaatttaacgagaatacttttcaaaagtatttttttactgtattcatgatataataatagtaactt................... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAUUUAAAAACAUUUGAUAAUUUUUACGCUGAUUUAGCGCGCUCAGUCAAUUUCUAAUUUAACGAGAAUACUUUUCAAAAGUAUUUUUUUAAUGCAUUCAUGAUAUAAUAAUAGUAACUUCUAUUCUUAAGGAGGACAA ...........................(((((...)))))..(((.((((.........((((.((((((((((.....))))))))))))))........)))).(((.(((((......))))).)))..)))..... (-17.13) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUGUCCUCCUUAAGAAUAGAAGUUACUAUUAUUAUAUCAUGAAUGCAUUAAAAAAAUACUUUUGAAAAGUAUUCUCGUUAAAUUAGAAAUUGACUGAGCGCGCUAAAUCAGCGUAAAAAUUAUCAAAUGUUUUUAAAUUA ..........(((.(((((......))))).))).....((((.(((((.....(((((((.....)))))))((((((((........))))).))).(((((.....)))))...........))))).))))..... (-18.00) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 292 57 12 67 13 NC_009009:SSA_2216|5end_LPS_biosynthesis_protein,_putative_2218080..2218310_NEGATIVE 275 56 22 96 66 NC_009009:SSA_2014|5end_D-alanyl-D-alanine_carboxypeptidase,_putative_2014807..2015037_NEGATIVE 256 57 29 33 6 NC_009009:SSA_2008|5end_Molecular_chaperone_GrpE_(HSP-70_cofactor),_putative_2010062..2010292_NEGATIVE 256 52 13 161 110 NC_009009:SSA_0743|5end_Transcriptional_repressor_(arginine_synthesis),_putative_725759..725989_NEGATIVE 241 60 14 163 116 NC_009009:SSA_0512|5end_Nicotinate-nucleotide--dimethylbenzimidazole_phosphoribosyltransferase,_putative_510439..510669_POSITIVE 238 67 27 51 9 NC_009009:SSA_1936|5end_3-oxoacyl-[acyl-carrier_protein]_reductase,_putative_1923838..1924068_NEGATIVE 237 56 12 98 40 NC_009009:SSA_1175|5end_Acetoin_dehydrogenase_complex,_E2_component,_dihydrolipoamide_acetyltransferase,_putative_1203976..1204206_NEGATIVE 231 51 14 43 2 NC_009009:SSA_1198|5end_ATPase_(PilT_family),_putative_1223314..1223544_NEGATIVE 231 56 16 189 136 NC_009009:SSA_0127|5end_Multispanning_membrane_protein,_translocator_of_proteins,_putative_117720..117950_POSITIVE 230 60 14 163 118 NC_009009:SSA_0199|5end_GTP_cyclohydrolase_I,_putative_198276..198506_POSITIVE 228 67 27 66 26 NC_009009:SSA_1614|5end_Acetyltransferase,_GNAT_family,_putative_1618045..1618275_NEGATIVE 228 58 23 70 38 NC_009009:SSA_0837|5end_Glucosyltransferase,_putative_823902..824132_POSITIVE 226 80 38 106 62 NC_009009:SSA_0171|5end_Cro-like_transcriptional_repressor,_XRE_family,_putative_168956..169186_NEGATIVE 221 140 94 194 145 NC_009009:SSA_2009|5end_Heat_shock_transcription_repressor_HrcA,_putative_2011132..2011362_NEGATIVE 221 61 25 228 180 NC_009009:SSA_1695|5end_Transcriptional_antiterminator,_BglG/SacY_family_(induction_of_sugar_metabolism),_putative_1688010..1688240_NEGATIVE 218 56 29 152 124 NC_009009:SSA_1856|5end_hypothetical_protein_1852208..1852438_NEGATIVE 218 56 11 98 57 NC_009009:SSA_0331|5end_C3-degrading_proteinase,_putative_325178..325408_POSITIVE 217 49 31 206 185 NC_009009:SSA_1343|5end_Aspartate_carbamoyltransferase,_putative_1361959..1362189_NEGATIVE 214 70 22 214 171 NC_009009:SSA_1226|5end_ParC,_putative_1251233..1251463_NEGATIVE 214 69 29 160 124 NC_009009:SSA_0817|5end_Antirepressor_regulating_drug_resistance_(membrane-bound),_putative_797838..798068_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 292 57 12 61 7 NC_009009:SSA_2217|3end_Cps9H,_putative_2218086..2218236_NEGATIVE 282 65 30 150 118 NC_009009:SSA_1182|3end_Gid-like_protein,_putative_1209532..1209682_NEGATIVE 275 56 22 109 79 NC_009009:SSA_2015|3end_Phosphoglycerate_mutase,_putative_2014794..2014944_NEGATIVE 256 52 13 144 93 NC_009009:SSA_0744|3end_S-adenosylmethio_nine:tRNA-ribosyltransferase-isomerase_(queuine_synthetase),_putative_725776..725926_NEGATIVE 233 45 14 141 109 NC_009009:SSA_2184|3end_hypothetical_protein_2183284..2183434_NEGATIVE 231 51 14 46 5 NC_009009:SSA_1199|3end_Phosphinothricin_acetyltransferase,_putative_1223311..1223461_NEGATIVE 231 69 27 71 23 NC_009009:SSA_0327|3end_Glycosyltransferase,_putative_320436..320586_POSITIVE 228 58 23 57 25 NC_009009:SSA_0836|3end_SecA-like_protein,_putative_823969..824119_POSITIVE 217 49 31 96 75 NC_009009:SSA_1344|3end_Xanthine/uracil_permeases,_putative_1362069..1362219_NEGATIVE 214 69 29 144 108 NC_009009:SSA_0816|3end_Copper_transport_operon_or_penicillinase_transcription_repressor,_putative_797902..798052_POSITIVE 213 66 28 119 77 NC_009009:SSA_0702|3end_Aconitase_A,_putative_688231..688381_POSITIVE 213 67 26 52 14 NC_009009:SSA_0185|3end_Competence_protein_ComYB,_putative_190141..190291_POSITIVE 213 44 28 62 45 NC_009009:SSA_0110|3end_50S_ribosomal_protein_L2,_putative_110666..110816_POSITIVE 212 49 14 134 101 NC_009009:SSA_1063|3end_Peptidoglycan-binding_domain-containing_protein,_putative_1080260..1080410_POSITIVE 211 56 28 76 54 NC_009009:SSA_1057|3end_Aminotransferase,_class-V,_putative_1074993..1075143_POSITIVE 211 58 29 39 15 NC_009009:SSA_0870|3end_Cell_division_protein_FtsE,_putative_863708..863858_POSITIVE 209 56 12 57 11 NC_009009:SSA_1093|3end_ATP-dependent_Clp_protease_ATP-binding_subunit_clpX,_putative_1111645..1111795_POSITIVE 208 57 12 143 98 NC_009009:SSA_2353|3end_ABC-type_nitrate/sulfonate/bicarbonate_transport_system,_permease_component,_putative_2354550..2354700_NEGATIVE 208 50 27 30 6 NC_009009:SSA_1258|3end_Purine_nucleoside_phosphorylase,_family_1,_putative_1283858..1284008_NEGATIVE 206 56 23 89 52 NC_009009:SSA_1446|3end_Histidinol_dehydrogenase,_putative_1447898..1448048_NEGATIVE