Origin IGS: actaaccctccacgtattccattataccacacaagaaattataagcggaatgaagtatacaataaactaaaaaagaagacaaatgtctcctctgtgcactgatc .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gatcagtgcacagaggagacatttgtcttcttttttagtttattgtatacttcattccgcttataatttcttgtgtggtataatggaatacgtggagggttagt Mask Tandem Repeat Region ================================================ actaaccctccacgtattccattataccacacaagaaattataagcggaatgaagtatacaataaactaaaaaagaagacaaatgtctcctctgtgcactgatc Find is-nt database================================================ Query_seq: SSA_1330:SSA_1331|SSA_1330:SSA_1331:hypothetical protein:Conserved uncharacterized protein:<-<-:1346459..1346562 104 actaaccctccacgtattccattataccacacaagaaattataagcggaatgaagtatacaataaactaaaaaagaagacaaatgtctcctctgtgcactgatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1330:SSA_1331|SSA_1330:SSA_1331:hypothetical protein:Conserved uncharacterized protein:<-<-:1346459..1346562 104 actaaccctccacgtattccattataccacacaagaaattataagcggaatgaagtatacaataaactaaaaaagaagacaaatgtctcctctgtgcactgatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1330:SSA_1331|SSA_1330:SSA_1331:hypothetical protein:Conserved uncharacterized protein:<-<-:1346459..1346562 104 actaaccctccacgtattccattataccacacaagaaattataagcggaatgaagtatacaataaactaaaaaagaagacaaatgtctcctctgtgcactgatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 actaaccctccacgtattccattataccacacaagaaattataagcggaatgaagtatacaataaactaaaaaagaagacaaatgtctcctctgtgcactgatc Predict ORF larger than 30AA ================================================ Protein_Len: 34 Strand: - Start: 5 End: 103 .... * G E V Y E M I G C L F N Y A S H L I C Y V L F S S L H R R Q A S M . actaaccctccacgtattccattataccacacaagaaattataagcggaatgaagtatacaataaactaaaaaagaagacaaatgtctcctctgtgcactgatc 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: 86 Start: 54 End: 83 .....................................................TTTGTCTTCTTTTTTAGTTTATTGTATACT..................... PromScan Matrix: RpoD-17 Strand: - Score: 85 Start: 38 End: 67 .....................................GTTTATTGTATACTTCATTCCGCTTATAAT..................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ actaaccctccacgtattccattataccacacaagaaattataagcggaatgaagtatacaataaactaaaaaagaagacaaatgtctcctctgtgcactgatc Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_1330:SSA_1331|SSA_1330:SSA_1331:hypothetical protein:Conserved uncharacterized protein:<-<-:1346459..1346562 104 actaaccctccacgtattccattataccacacaagaaattataagcggaatgaagtatacaataaactaaaaaagaagacaaatgtctcctctgtgcactgatc Intra-Species Hit: Count: 1 Min: 1 Max: 104 Len: 104 Subject: NC_009009_SSA_1330_SSA_1331|hypothetical protein:Conserved uncharacterized protein|NEGATIVE:NEGATIVE|[1346459,1346562]|104 HSP 1 e-value: 1.0E-52 bit: 206.0 Len: 104 Query Start:1 Query End:104 Subject Strand: POSITIVE Subject Start: 1 Subject End: 104 actaaccctccacgtattccattataccacacaagaaattataagcggaatgaagtatacaataaactaaaaaagaagacaaatgtctcctctgtgcactgatc actaaccctccacgtattccattataccacacaagaaattataagcggaatgaagtatacaataaactaaaaaagaagacaaatgtctcctctgtgcactgatc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACUAACCCUCCACGUAUUCCAUUAUACCACACAAGAAAUUAUAAGCGGAAUGAAGUAUACAAUAAACUAAAAAAGAAGACAAAUGUCUCCUCUGUGCACUGAUC ..........(((.((((((.(((((.............)))))..)))))).....................((.((((....)))).))..)))........ (-11.52) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAUCAGUGCACAGAGGAGACAUUUGUCUUCUUUUUUAGUUUAUUGUAUACUUCAUUCCGCUUAUAAUUUCUUGUGUGGUAUAAUGGAAUACGUGGAGGGUUAGU ...(((((.(((((((((((....)))))))))....)).)))))....((((((((((.(((((....(....)...)))))))))....))))))....... (-21.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 857 50 1 141 92 NC_009009:SSA_1330|5end_hypothetical_protein_1346368..1346598_NEGATIVE 324 49 2 146 95 NC_009009:SSA_0365|5end_Small-conductance_mechanosensitive_efflux_channel,_putative_356621..356851_POSITIVE 234 48 2 146 96 NC_009009:SSA_0596|5end_hypothetical_protein_586913..587143_POSITIVE 233 50 7 199 149 NC_009009:SSA_0924|5end_ABC-type_antimicrobial_peptide_transport_system,_permease_component,_putative_933738..933968_POSITIVE 218 98 77 225 202 NC_009009:SSA_1592|5end_hypothetical_protein_1596397..1596627_NEGATIVE 214 98 56 192 145 NC_009009:SSA_0557|5end_hypothetical_protein_551900..552130_POSITIVE 209 49 5 146 100 NC_009009:SSA_0076|5end_ABC_sugar_transporter,_permease_protein,_putative_79847..80077_POSITIVE 205 31 13 132 112 NC_009009:SSA_2184|5end_hypothetical_protein_2183754..2183984_NEGATIVE 204 49 15 119 85 NC_009009:SSA_2114|5end_Transcriptional_repressor_of_purine_operon,_putative_2117559..2117789_NEGATIVE 199 40 1 144 115 NC_009009:SSA_1697|5end_Tagatose-6-phosphate_kinase,_putative_1690120..1690350_NEGATIVE 196 100 70 171 144 NC_009009:SSA_2052|5end_Thioredoxin,_putative_2057507..2057737_NEGATIVE 195 48 1 134 97 NC_009009:SSA_0604|5end_hypothetical_protein_592451..592681_POSITIVE 193 50 19 122 96 NC_009009:SSA_0864|5end_hypothetical_protein_856318..856548_NEGATIVE 191 94 51 222 181 NC_009009:SSA_1011|5end_hypothetical_protein_1014134..1014364_POSITIVE 190 56 13 76 44 NC_009009:SSA_0395|5end_6-phospho-beta-glucosidase,_putative_391061..391291_POSITIVE 190 78 31 177 136 NC_009009:SSA_0331|5end_C3-degrading_proteinase,_putative_325178..325408_POSITIVE 189 32 9 148 125 NC_009009:SSA_0829|5end_Platelet-binding_glycoprotein_807208..807438_POSITIVE 189 48 8 211 154 NC_009009:SSA_0483|5end_Siroheme_synthase,_putative_484045..484275_POSITIVE 189 38 6 132 97 NC_009009:SSA_0258|5end_hypothetical_protein_251845..252075_POSITIVE 187 55 37 197 177 NC_009009:SSA_2119|5end_Pentose-5-phosphate-3-epimerase,_putative_2121098..2121328_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 234 48 2 136 86 NC_009009:SSA_0595|3end_hypothetical_protein_586983..587133_POSITIVE 233 50 7 79 29 NC_009009:SSA_0923|3end_Transcriptional_regulator,_TetR/AcrR_family,_putative_933698..933848_POSITIVE 214 98 56 134 87 NC_009009:SSA_0556|3end_hypothetical_protein_551922..552072_POSITIVE 211 98 67 134 99 NC_009009:SSA_0559|3end_hypothetical_protein_553119..553269_POSITIVE 209 49 5 146 100 NC_009009:SSA_0075|3end_ABC_sugar_transporter,_permease_protein,_putative_79927..80077_POSITIVE 205 95 63 85 48 NC_009009:SSA_0394|3end_hypothetical_protein_390931..391081_POSITIVE 204 49 15 56 22 NC_009009:SSA_2116|3end_Cmp-binding-factor_1,_putative_2117622..2117772_NEGATIVE 199 40 1 131 102 NC_009009:SSA_1698|3end_Galactose-6-phosphate_isomerase,_LacB_subunit,_putative_1690133..1690283_NEGATIVE 198 89 47 85 49 NC_009009:SSA_2268|3end_Type_II_secretory_pathway,_pullulanase_PulA_glycosidase,_putative_2269386..2269536_POSITIVE 197 49 6 109 77 NC_009009:SSA_0325|3end_Membrane-anchored_glycerophosphoryl_diester_phosphodiesterase,_putative_319437..319587_POSITIVE 195 48 1 115 78 NC_009009:SSA_0603|3end_Cobalt_transporter,_putative_592512..592662_POSITIVE 190 97 70 149 125 NC_009009:SSA_2053|3end_hypothetical_protein_2057526..2057676_NEGATIVE 190 78 31 81 40 NC_009009:SSA_0330|3end_hypothetical_protein_325162..325312_POSITIVE 189 38 6 47 12 NC_009009:SSA_0257|3end_N-acetylmuramidase/lysin,_putative_251840..251990_POSITIVE 188 98 86 134 122 NC_009009:SSA_0562|3end_hypothetical_protein_554859..555009_POSITIVE 186 50 8 55 3 NC_009009:SSA_1476|3end_Phosphoglycerol_transferase,_alkaline_phosphatase_superfamily,_putative_1482448..1482598_POSITIVE 185 56 12 41 6 NC_009009:SSA_1315|3end_hypothetical_protein_1331408..1331558_NEGATIVE 183 49 6 64 11 NC_009009:SSA_0563|3end_Universal_stress_protein_family,_putative_554947..555097_NEGATIVE 182 92 70 46 24 NC_009009:SSA_0210|3end_hypothetical_protein_208124..208274_POSITIVE 179 100 61 88 52 NC_009009:SSA_0596|3end_hypothetical_protein_587352..587502_POSITIVE