Origin IGS: gttaccattataccacaaatcatagtaggaaaaaaatcaaagctgcaactgaaagaagagcaattttatcctttttttgataaaatagggaaagaaaaagagaaacgag .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ctcgtttctctttttctttccctattttatcaaaaaaaggataaaattgctcttctttcagttgcagctttgatttttttcctactatgatttgtggtataatggtaac Mask Tandem Repeat Region ================================================ gttaccattataccacaaatcatagtaggaaaaaaatcaaagctgcaactgaaagaagagcaattttatcctttttttgataaaatagggaaagaaaaagagaaacgag Find is-nt database================================================ Query_seq: SSA_0864:SSA_0865|SSA_0864:SSA_0865:hypothetical protein:hypothetical protein:<-->:856409..856517 109 gttaccattataccacaaatcatagtaggaaaaaaatcaaagctgcaactgaaagaagagcaattttatcctttttttgataaaatagggaaagaaaaagagaaacgag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0864:SSA_0865|SSA_0864:SSA_0865:hypothetical protein:hypothetical protein:<-->:856409..856517 109 gttaccattataccacaaatcatagtaggaaaaaaatcaaagctgcaactgaaagaagagcaattttatcctttttttgataaaatagggaaagaaaaagagaaacgag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0864:SSA_0865|SSA_0864:SSA_0865:hypothetical protein:hypothetical protein:<-->:856409..856517 109 gttaccattataccacaaatcatagtaggaaaaaaatcaaagctgcaactgaaagaagagcaattttatcctttttttgataaaatagggaaagaaaaagagaaacgag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gttaccattataccacaaatcatagtaggaaaaaaatcaaagctgcaactgaaagaagagcaattttatcctttttttgataaaatagggaaagaaaaagagaaacgag Predict ORF larger than 30AA ================================================ Protein_Len: 34 Strand: + Start: 7 End: 108 ...... M I P Q I I V G K K S K L Q L K E E Q F Y P F F D K I G K E K E K R . gttaccattataccacaaatcatagtaggaaaaaaatcaaagctgcaactgaaagaagagcaattttatcctttttttgataaaatagggaaagaaaaagagaaacgag 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: 83 Start: 7 End: 36 ......TTTTTTTCCTACTATGATTTGTGGTATAAT......................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gttaccattataccacaaatcatagtaggaaaaaaatcaaagctgcaactgaaagaagagcaattttatcctttttttgataaaatagggaaagaaaaagagaaacgag Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_0864:SSA_0865|SSA_0864:SSA_0865:hypothetical protein:hypothetical protein:<-->:856409..856517 109 gttaccattataccacaaatcatagtaggaaaaaaatcaaagctgcaactgaaagaagagcaattttatcctttttttgataaaatagggaaagaaaaagagaaacgag Intra-Species Hit: Count: 1 Min: 1 Max: 109 Len: 109 Subject: NC_009009_SSA_0864_SSA_0865|hypothetical protein:hypothetical protein|NEGATIVE:POSITIVE|[856409,856517]|109 HSP 1 e-value: 1.0E-30 bit: 133.0 Len: 109 Query Start:1 Query End:109 Subject Strand: POSITIVE Subject Start: 1 Subject End: 109 gttaccattataccacaaatcatagtaggnnnnnnntcaaagctgcaactgaaagaagagcaattttatccnnnnnnngataaaatagggaaagaaaaagagaaacgag gttaccattataccacaaatcatagtaggaaaaaaatcaaagctgcaactgaaagaagagcaattttatcctttttttgataaaatagggaaagaaaaagagaaacgag Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUUACCAUUAUACCACAAAUCAUAGUAGGAAAAAAAUCAAAGCUGCAACUGAAAGAAGAGCAAUUUUAUCCUUUUUUUGAUAAAAUAGGGAAAGAAAAAGAGAAACGAG (((.........((((........)).)).......((...(((.(..(.....)..))))..((((.(((((((((....)))).))))).))))...))..)))... ( -9.00) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUCGUUUCUCUUUUUCUUUCCCUAUUUUAUCAAAAAAAGGAUAAAAUUGCUCUUCUUUCAGUUGCAGCUUUGAUUUUUUUCCUACUAUGAUUUGUGGUAUAAUGGUAAC ..........................((((((..((((((((.(((((((.((......))..)))).))).))))))))..((((((.....))))))...)))))). (-12.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 801 60 11 151 102 NC_009009:SSA_0864|5end_hypothetical_protein_856318..856548_NEGATIVE 341 50 5 142 100 NC_009009:SSA_0213|5end_hypothetical_protein_210135..210365_NEGATIVE 250 45 6 129 89 NC_009009:SSA_1068|5end_Transcriptional_regulator,_LysR_family_(capsular_polysaccharide_biosynthesis_regulation),_putative_1087355..1087585_POSITIVE 237 80 36 220 172 NC_009009:SSA_0703|5end_Citrate_synthase,_putative_688154..688384_POSITIVE 222 81 41 86 54 NC_009009:SSA_1682|5end_hypothetical_protein_1676885..1677115_NEGATIVE 218 99 58 135 86 NC_009009:SSA_1728|5end_ABC_transporter_membrane-spanning_permease-branched_chain_amino_acid_transport,_putative_1714293..1714523_NEGATIVE 215 76 35 109 50 NC_009009:SSA_2155|5end_hypothetical_protein_2156102..2156332_NEGATIVE 214 62 21 57 17 NC_009009:SSA_2122|5end_hypothetical_protein_2127607..2127837_NEGATIVE 211 61 21 67 32 NC_009009:SSA_1434|5end_Conserved_uncharacterized_Firmicutes_protein_1440850..1441080_POSITIVE 211 90 41 49 8 NC_009009:SSA_0279|5end_Sugar-binding_transcriptional_repressor_(DeoR),_putative_272319..272549_POSITIVE 211 60 24 175 141 NC_009009:SSA_0209|5end_Glutamyl_aminopeptidase,_putative_207636..207866_NEGATIVE 209 82 41 222 178 NC_009009:SSA_0469|5end_Precorrin-6B_methylase_2,putative_472310..472540_POSITIVE 208 78 36 110 59 NC_009009:SSA_1665|5end_hypothetical_protein_1665353..1665583_NEGATIVE 207 70 36 59 29 NC_009009:SSA_0879|5end_Cell_division_regulator,_negative_regulator_of_FtsZ_septation_ring_formation,_putative_873632..873862_POSITIVE 207 69 22 216 175 NC_009009:SSA_0225|5end_10_kDa_chaperonin_218642..218872_POSITIVE 202 75 37 229 192 NC_009009:SSA_0916|5end_2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate_hydrolase,_putative_928085..928315_POSITIVE 199 77 39 61 29 NC_009009:SSA_0153|5end_hypothetical_protein_148677..148907_POSITIVE 198 79 44 84 48 NC_009009:SSA_0258|5end_hypothetical_protein_251845..252075_POSITIVE 197 90 41 78 44 NC_009009:SSA_0243|5end_Cyclo-nucleotide_phosphodiesterase,_putative_238235..238465_NEGATIVE 196 61 23 143 102 NC_009009:SSA_2002|5end_tRNA_pseudouridine_synthase_A,_putative_1998959..1999189_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 239 96 53 62 25 NC_009009:SSA_0394|3end_hypothetical_protein_390931..391081_POSITIVE 210 45 8 39 1 NC_009009:SSA_1067|3end_hypothetical_protein_1087345..1087495_POSITIVE 208 78 36 88 37 NC_009009:SSA_1666|3end_Collagen-binding_surface_protein,_putative_1665375..1665525_NEGATIVE 208 52 11 64 22 NC_009009:SSA_0572|3end_Dehydrogenase,_putative_568552..568702_POSITIVE 205 89 41 83 17 NC_009009:SSA_0387|3end_Transcriptional_regulator,_GntR_family,_putative_381702..381852_NEGATIVE 202 75 37 78 41 NC_009009:SSA_0915|3end_hypothetical_protein_928014..928164_POSITIVE 200 61 24 128 97 NC_009009:SSA_1126|3end_Thiamine_biosynthesis_lipoprotein,_putative_1150587..1150737_NEGATIVE 200 90 41 70 17 NC_009009:SSA_0599|3end_hypothetical_protein_589007..589157_POSITIVE 199 77 39 35 3 NC_009009:SSA_0152|3end_hypothetical_protein_148731..148881_POSITIVE 195 61 40 143 121 NC_009009:SSA_1135|3end_Na+-driven_multidrug_efflux_pump,_putative_1161775..1161925_POSITIVE 194 80 39 67 10 NC_009009:SSA_1923|3end_NADPH-q_uinone_reductase_(modulator_of_drug_activity_B),_putative_1912120..1912270_NEGATIVE 194 66 22 119 70 NC_009009:SSA_1134|3end_Xanthine_phosphoribosyltransferase,_putative_1160316..1160466_POSITIVE 193 71 37 51 10 NC_009009:SSA_1840|3end_RNA_binding_protein,_putative_1834060..1834210_NEGATIVE 191 90 41 56 5 NC_009009:SSA_0575|3end_Hydrolase,_HAD_superfamily,_putative_570116..570266_POSITIVE 190 88 46 67 11 NC_009009:SSA_0459|3end_hypothetical_protein_462513..462663_POSITIVE 188 95 55 53 12 NC_009009:SSA_2226|3end_Organic_radical_activating_chaperone,_putative_2227151..2227301_NEGATIVE 187 89 41 138 101 NC_009009:SSA_1741|3end_ABC-type_Fe3+-siderophores_transporter,_ATPase_component,_putative_1728872..1729022_POSITIVE 187 100 64 146 97 NC_009009:SSA_0911|3end_hypothetical_protein_922898..923048_POSITIVE 187 51 13 148 116 NC_009009:SSA_0165|3end_hypothetical_protein_164623..164773_POSITIVE 185 80 35 76 24 NC_009009:SSA_0767|3end_Diacylglycerol_kinase_catalytic_domain_protein,_putative_748054..748204_POSITIVE