Origin IGS: attaaaacactttctttttatttaatattttaatatacctattttaagttgtcaataaaaacccttgcaaaatctacaagagtcctttctttcttatttttaacaatagatt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aatctattgttaaaaataagaaagaaaggactcttgtagattttgcaagggtttttattgacaacttaaaataggtatattaaaatattaaataaaaagaaagtgttttaat Mask Tandem Repeat Region ================================================ attaaaacactttctttttatttaatattttaatatacctattttaagttgtcaataaaaacccttgcaaaatctacaagagtcctttctttcttatttttaacaatagatt Find is-nt database================================================ Query_seq: SSA_1255:SSA_1256|SSA_1255:SSA_1256:hypothetical protein:NAD-dependent deacetylase, putative:<-<-:1282335..1282446 112 attaaaacactttctttttatttaatattttaatatacctattttaagttgtcaataaaaacccttgcaaaatctacaagagtcctttctttcttatttttaacaatagatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1255:SSA_1256|SSA_1255:SSA_1256:hypothetical protein:NAD-dependent deacetylase, putative:<-<-:1282335..1282446 112 attaaaacactttctttttatttaatattttaatatacctattttaagttgtcaataaaaacccttgcaaaatctacaagagtcctttctttcttatttttaacaatagatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1255:SSA_1256|SSA_1255:SSA_1256:hypothetical protein:NAD-dependent deacetylase, putative:<-<-:1282335..1282446 112 attaaaacactttctttttatttaatattttaatatacctattttaagttgtcaataaaaacccttgcaaaatctacaagagtcctttctttcttatttttaacaatagatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 attaaaacactttctttttatttaatattttaatatacctattttaagttgtcaataaaaacccttgcaaaatctacaagagtcctttctttcttatttttaacaatagatt Predict ORF larger than 30AA ================================================ attaaaacactttctttttatttaatattttaatatacctattttaagttgtcaataaaaacccttgcaaaatctacaagagtcctttctttcttatttttaacaatagatt 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: 89 Start: 27 End: 56 ..........................ATTGACAACTTAAAATAGGTATATTAAAAT........................................................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ attaaaacactttctttttatttaatattttaatatacctattttaagttgtcaataaaaacccttgcaaaatctacaagagtcctttctttcttatttttaacaatagatt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_1255:SSA_1256|SSA_1255:SSA_1256:hypothetical protein:NAD-dependent deacetylase, putative:<-<-:1282335..1282446 112 attaaaacactttctttttatttaatattttaatatacctattttaagttgtcaataaaaacccttgcaaaatctacaagagtcctttctttcttatttttaacaatagatt Intra-Species Hit: Count: 1 Min: 1 Max: 112 Len: 112 Subject: NC_009009_SSA_1255_SSA_1256|hypothetical protein:NAD-dependent deacetylase, putative|NEGATIVE:NEGATIVE|[1282335,1282446]|112 HSP 1 e-value: 2.0E-57 bit: 222.0 Len: 112 Query Start:1 Query End:112 Subject Strand: POSITIVE Subject Start: 1 Subject End: 112 attaaaacactttctttttatttaatattttaatatacctattttaagttgtcaataaaaacccttgcaaaatctacaagagtcctttctttcttatttttaacaatagatt attaaaacactttctttttatttaatattttaatatacctattttaagttgtcaataaaaacccttgcaaaatctacaagagtcctttctttcttatttttaacaatagatt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUUAAAACACUUUCUUUUUAUUUAAUAUUUUAAUAUACCUAUUUUAAGUUGUCAAUAAAAACCCUUGCAAAAUCUACAAGAGUCCUUUCUUUCUUAUUUUUAACAAUAGAUU .((((((.......((((((((....((((.((((....))))..))))....))))))))................(((((........)))))..))))))......... ( -5.00) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUCUAUUGUUAAAAAUAAGAAAGAAAGGACUCUUGUAGAUUUUGCAAGGGUUUUUAUUGACAACUUAAAAUAGGUAUAUUAAAAUAUUAAAUAAAAAGAAAGUGUUUUAAU .(((((((.((((........((..((((((((((((((...)))))))))))))).))......)))))))))))..(((((((((((............))))))))))) (-19.24) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 758 110 61 201 152 NC_009009:SSA_1255|5end_hypothetical_protein_1282244..1282474_NEGATIVE 276 99 52 114 63 NC_009009:SSA_2138|5end_RNA-binding_protein,_Jag_family,_putative_2139487..2139717_NEGATIVE 244 85 41 182 139 NC_009009:SSA_0255|5end_Multiple_antibiotic_resistance_operon_transcription_repressor_(MarR),_putative_247946..248176_NEGATIVE 229 106 64 125 85 NC_009009:SSA_0022|5end_Surface_protein_cell_wall_anchor,_sortase_B_family,_putative_27506..27736_POSITIVE 227 98 52 108 57 NC_009009:SSA_1835|5end_Late_competence_protein,_putative_1830941..1831171_NEGATIVE 225 93 52 194 161 NC_009009:SSA_0849|5end_Signal_peptidase_I,_putative_836127..836357_POSITIVE 217 101 65 155 107 NC_009009:SSA_1545|5end_Conserved_uncharacterized_protein_1549210..1549440_NEGATIVE 204 110 64 120 75 NC_009009:SSA_0287|5end_Glycerol_dehydrogenase,_NAD+_dependent,_putative_279528..279758_POSITIVE 203 90 41 76 24 NC_009009:SSA_0835|5end_Accessory_secretory_protein_Asp3,_putative_821036..821266_POSITIVE 198 94 59 111 55 NC_009009:SSA_1724|5end_CBS_domain_protein,_putative_1710553..1710783_NEGATIVE 197 100 53 192 150 NC_009009:SSA_0201|5end_ABC_multidrug_transporter_(3-component_subtilin_immunity_exporter),_putative_199825..200055_POSITIVE 195 88 46 181 141 NC_009009:SSA_0674|5end_Exodeoxyribonuclease_VII_large_subunit,_putative_657071..657301_POSITIVE 195 105 73 132 101 NC_009009:SSA_0305|5end_hypothetical_protein_301985..302215_POSITIVE 193 106 61 140 100 NC_009009:SSA_0783|5end_Proton-translocating_ATPase,_F0_sector,_subunit_a,_putative_766815..767045_POSITIVE 192 108 79 35 11 NC_009009:SSA_0158|5end_hypothetical_protein_153801..154031_POSITIVE 191 105 73 171 137 NC_009009:SSA_1650|5end_3-Ketoacyl-ACP_reductase,_putative_1649594..1649824_NEGATIVE 190 91 65 224 195 NC_009009:SSA_0669|5end_ATP_dependent_protease,_putative_653720..653950_NEGATIVE 189 102 63 225 181 NC_009009:SSA_2010|5end_ABC-type_multidrug_transport_system,_permease_component,_putative_2012024..2012254_NEGATIVE 187 75 32 146 93 NC_009009:SSA_0572|5end_Dehydrogenase,_putative_567426..567656_POSITIVE 184 110 73 117 87 NC_009009:SSA_1881|5end_hypothetical_protein_1875964..1876194_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 276 99 52 92 41 NC_009009:SSA_2139|3end_Membrane_protein_(preprotein_translocase)_oxaA_1_precursor,_putative_2139509..2139659_NEGATIVE 244 85 41 76 33 NC_009009:SSA_0256|3end_Metalloregulator_ScaR_(Fe/Mn-dependent_transcriptional_repressor),_putative_248052..248202_NEGATIVE 227 98 52 111 60 NC_009009:SSA_1836|3end_Superfamily_II_ATP-dependent_DNA/RNA_helicase_required_for_DNA_uptake_(late_competence_protein),_putative_1830938..1831088_NEGATIVE 217 101 65 98 50 NC_009009:SSA_1546|3end_Prolipoprotein_diacylglyceryl_transferase,_putative_1549267..1549417_NEGATIVE 204 110 64 74 29 NC_009009:SSA_0286|3end_Transaldolase-like_protein,_putative_279562..279712_POSITIVE 203 99 60 86 37 NC_009009:SSA_1030|3end_Transcriptional_regulator,_TetR_family,_putative_1047749..1047899_POSITIVE 203 90 41 79 27 NC_009009:SSA_0834|3end_Accessory_secretory_protein_Asp2,_putative_821119..821269_POSITIVE 199 86 54 54 16 NC_009009:SSA_2298|3end_Serine_protease_containing_a_PDZ_domain,_putative_2299569..2299719_NEGATIVE 197 100 53 97 55 NC_009009:SSA_0200|3end_Bifunctional_folate_synthesis_protein,_putative_199810..199960_POSITIVE 193 106 61 104 64 NC_009009:SSA_0782|3end_Proton-translocating_ATPase,_F0_sector,_subunit_c,_putative_766859..767009_POSITIVE 192 108 79 31 7 NC_009009:SSA_0157|3end_hypothetical_protein_153877..154027_POSITIVE 190 85 49 124 88 NC_009009:SSA_0923|3end_Transcriptional_regulator,_TetR/AcrR_family,_putative_933698..933848_POSITIVE 188 95 63 68 33 NC_009009:SSA_2242|3end_hypothetical_protein_2238121..2238271_NEGATIVE 184 97 62 94 64 NC_009009:SSA_1153|3end_HemK_protein,_putative_1182748..1182898_POSITIVE 180 68 37 56 20 NC_009009:SSA_1877|3end_hypothetical_protein_1871915..1872065_POSITIVE 178 79 39 104 63 NC_009009:SSA_0697|3end_hypothetical_protein_680276..680426_POSITIVE 177 105 61 120 56 NC_009009:SSA_0469|3end_Precorrin-6B_methylase_2,putative_472959..473109_POSITIVE 176 110 62 59 10 NC_009009:SSA_1578|3end_ABC-type_Fe3+-siderophore_transport_system,_permease_component,_putative_1582929..1583079_POSITIVE 176 107 79 106 79 NC_009009:SSA_1545|3end_Conserved_uncharacterized_protein_1548812..1548962_NEGATIVE 176 96 60 74 30 NC_009009:SSA_1412|3end_hypothetical_protein_1423994..1424144_NEGATIVE