Origin IGS: aaagtcacatttggataaataatactagaaagaaaggcttaccaaaaggggtggccttttttataatgaaagtggaagtttgattgcagactgtgaaaggagaagacc .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ggtcttctcctttcacagtctgcaatcaaacttccactttcattataaaaaaggccaccccttttggtaagcctttctttctagtattatttatccaaatgtgacttt Mask Tandem Repeat Region ================================================ aaagtcacatttggataaataatactagaaagaaaggcttaccaaaaggggtggccttttttataatgaaagtggaagtttgattgcagactgtgaaaggagaagacc Find is-nt database================================================ Query_seq: SSA_0418:SSA_0419|SSA_0418:SSA_0419:AraC-type DNA-binding domain-containing protein, putative:Alpha-galactosidase, putative:->->:416245..416352 108 aaagtcacatttggataaataatactagaaagaaaggcttaccaaaaggggtggccttttttataatgaaagtggaagtttgattgcagactgtgaaaggagaagacc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0418:SSA_0419|SSA_0418:SSA_0419:AraC-type DNA-binding domain-containing protein, putative:Alpha-galactosidase, putative:->->:416245..416352 108 aaagtcacatttggataaataatactagaaagaaaggcttaccaaaaggggtggccttttttataatgaaagtggaagtttgattgcagactgtgaaaggagaagacc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0418:SSA_0419|SSA_0418:SSA_0419:AraC-type DNA-binding domain-containing protein, putative:Alpha-galactosidase, putative:->->:416245..416352 108 aaagtcacatttggataaataatactagaaagaaaggcttaccaaaaggggtggccttttttataatgaaagtggaagtttgattgcagactgtgaaaggagaagacc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aaagtcacatttggataaataatactagaaagaaaggcttaccaaaaggggtggccttttttataatgaaagtggaagtttgattgcagactgtgaaaggagaagacc Predict ORF larger than 30AA ================================================ aaagtcacatttggataaataatactagaaagaaaggcttaccaaaaggggtggccttttttataatgaaagtggaagtttgattgcagactgtgaaaggagaagacc 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: 38 End: 67 .....................................CTTACCAAAAGGGGTGGCCTTTTTTATAAT......................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aaagtcacatttggataaataatactagaaagaaaggcttaccaaaaggggtggccttttttataatgaaagtggaagtttgattgcagactgtgaaaggagaagacc Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_0418:SSA_0419|SSA_0418:SSA_0419:AraC-type DNA-binding domain-containing protein, putative:Alpha-galactosidase, putative:->->:416245..416352 108 aaagtcacatttggataaataatactagaaagaaaggcttaccaaaaggggtggccttttttataatgaaagtggaagtttgattgcagactgtgaaaggagaagacc Intra-Species Hit: Count: 1 Min: 1 Max: 108 Len: 108 Subject: NC_009009_SSA_0418_SSA_0419|AraC-type DNA-binding domain-containing protein, putative:Alpha-galactosidase, putative|POSITIVE:POSITIVE|[416245,416352]|108 HSP 1 e-value: 4.0E-55 bit: 214.0 Len: 108 Query Start:1 Query End:108 Subject Strand: POSITIVE Subject Start: 1 Subject End: 108 aaagtcacatttggataaataatactagaaagaaaggcttaccaaaaggggtggccttttttataatgaaagtggaagtttgattgcagactgtgaaaggagaagacc aaagtcacatttggataaataatactagaaagaaaggcttaccaaaaggggtggccttttttataatgaaagtggaagtttgattgcagactgtgaaaggagaagacc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAGUCACAUUUGGAUAAAUAAUACUAGAAAGAAAGGCUUACCAAAAGGGGUGGCCUUUUUUAUAAUGAAAGUGGAAGUUUGAUUGCAGACUGUGAAAGGAGAAGACC ....((((.....................((((((((((.(((......)))))))))))))..............((((((....))))))))))............ (-22.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GGUCUUCUCCUUUCACAGUCUGCAAUCAAACUUCCACUUUCAUUAUAAAAAAGGCCACCCCUUUUGGUAAGCCUUUCUUUCUAGUAUUAUUUAUCCAAAUGUGACUUU ((......))..(((((((.((....)).))..........((((.(((((((((.(((......)))..)))))).))).))))..............))))).... (-12.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 286 59 21 179 145 NC_009009:SSA_0063|5end_Holliday_junction_DNA_helicase_ruvB,_putative_65335..65565_POSITIVE 278 90 48 164 112 NC_009009:SSA_0452|5end_Nitrogen_utilization_substance_protein_B,_putative_451534..451764_POSITIVE 274 97 52 158 116 NC_009009:SSA_0778|5end_Glycogen_synthase,_putative_760566..760796_POSITIVE 265 61 29 37 7 NC_009009:SSA_0164|5end_hypothetical_protein_162478..162708_POSITIVE 264 100 51 74 32 NC_009009:SSA_2159|5end_hypothetical_protein_2159621..2159851_NEGATIVE 263 82 49 37 3 NC_009009:SSA_2391|5end_30S_ribosomal_protein_S14,_putative_114252..114482_POSITIVE 257 80 35 217 176 NC_009009:SSA_0032|5end_Phosphoribosylformylglycinamidine_cyclo-ligase,_putative_37938..38168_POSITIVE 253 61 31 180 148 NC_009009:SSA_1861|5end_Aminopeptidase_C,_putative_1857902..1858132_NEGATIVE 252 92 51 217 180 NC_009009:SSA_1737|5end_Cystathionine_gamma-synthase,_putative_1723778..1724008_NEGATIVE 252 89 43 58 7 NC_009009:SSA_1553|5end_Permease,_putative_1555047..1555277_POSITIVE 249 55 11 189 149 NC_009009:SSA_1906|5end_Diadenosine_tetraphosphate_(Ap4A)_hydrolase_(histidine_triad_protein,_cell-cycle_regulation),_putative_1900026..1900256_POSITIVE 248 59 12 164 109 NC_009009:SSA_0770|5end_Ribonucleoside-diphosphate_reductase,_putative_751411..751641_NEGATIVE 247 94 51 227 175 NC_009009:SSA_1119|5end_Two-component_response_transcriptional_regulator_(CheY-like_receiver_and_AraC-type_DNA-binding_domains),_putative_1144491..1144721_POSITIVE 245 100 66 154 125 NC_009009:SSA_0604|5end_hypothetical_protein_592451..592681_POSITIVE 244 89 47 172 134 NC_009009:SSA_0369|5end_NADP-specific_glutamate_dehydrogenase,_putative_359896..360126_NEGATIVE 240 95 53 230 192 NC_009009:SSA_2223|5end_Capsular_polysaccharide_biosynthesis_protein_Wzd_(chain_length_regulator),_putative_2224703..2224933_NEGATIVE 235 56 24 148 116 NC_009009:SSA_1616|5end_PhoH-like_protein,_putative_1620258..1620488_NEGATIVE 235 60 24 187 154 NC_009009:SSA_1365|5end_FmtA-like_protein,_putative_1382299..1382529_NEGATIVE 235 59 25 207 162 NC_009009:SSA_0398|5end_hypothetical_protein_396452..396682_NEGATIVE 233 96 52 195 148 NC_009009:SSA_2016|5end_Phosphoglycerate_mutase,_putative_2016293..2016523_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 265 56 22 52 13 NC_009009:SSA_0068|3end_Alcohol-acetaldehyde_dehydrogenase,_putative_72848..72998_POSITIVE 264 100 51 72 30 NC_009009:SSA_2160|3end_Deoxyuridinetriphosphatase,_putative_2159623..2159773_NEGATIVE 256 75 31 89 42 NC_009009:SSA_2039|3end_Aminoacid_specific_permease,_putative_2042707..2042857_NEGATIVE 253 61 31 101 69 NC_009009:SSA_1862|3end_hypothetical_protein_1857981..1858131_NEGATIVE 253 64 25 89 48 NC_009009:SSA_0661|3end_Isoleucyl-tRNA_synthetase,_putative_647748..647898_POSITIVE 252 92 51 120 83 NC_009009:SSA_1738|3end_Polysaccharide_biosynthesis_protein,_putative_1723875..1724025_NEGATIVE 252 89 43 61 10 NC_009009:SSA_1552|3end_hypothetical_protein_1555130..1555280_POSITIVE 246 55 25 85 56 NC_009009:SSA_0070|3end_Acetylxylan_esterase,_putative_74914..75064_POSITIVE 245 100 66 135 106 NC_009009:SSA_0603|3end_Cobalt_transporter,_putative_592512..592662_POSITIVE 233 96 52 53 6 NC_009009:SSA_2017|3end_Hypothetical_protein_(possibly_membrane-associated)_2016435..2016585_NEGATIVE 231 57 25 151 114 NC_009009:SSA_2170|3end_hypothetical_protein_2169557..2169707_NEGATIVE 230 72 36 66 34 NC_009009:SSA_1761|3end_Hemolysin_(containing_CBS_domains),_putative_1747437..1747587_NEGATIVE 228 61 25 84 41 NC_009009:SSA_1485|3end_Citrulline_cluster-linked_gene,_putative_1492294..1492444_NEGATIVE 222 63 23 86 40 NC_009009:SSA_1306|3end_Trk_transporter_NAD+_binding_protein-K+_transport,_putative_1324245..1324395_NEGATIVE 220 90 41 59 9 NC_009009:SSA_0992|3end_hypothetical_protein_994147..994297_POSITIVE 218 90 43 62 18 NC_009009:SSA_0087|3end_V-type_sodium_ATPase,_subunit_E,_putative_88999..89149_POSITIVE 218 76 37 146 100 NC_009009:SSA_0020|3end_Ribose-phosphate_pyrophosphokinase_1,_putative_26609..26759_POSITIVE 213 80 31 137 81 NC_009009:SSA_1952|3end_ABC-type_Fe-S_cluster_assembly_transporter,_permease_component,_putative_1948212..1948362_NEGATIVE 212 61 26 86 52 NC_009009:SSA_1042|3end_Xylanase/chitin_deacetylase,_putative_1057509..1057659_NEGATIVE 208 100 52 146 84 NC_009009:SSA_2018|3end_hypothetical_protein_2017464..2017614_NEGATIVE