Origin IGS: aatcttccttctttttgtatcattttgcctatctagtatatcatattttctgcctggaaactgcaaatagaagtgcaaccggtggttgacaaaatgtacaggaagctgtattctcaagataactaaaagctgttaggatagagttagcaaagaaaaggaggctgcgaac .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gttcgcagcctccttttctttgctaactctatcctaacagcttttagttatcttgagaatacagcttcctgtacattttgtcaaccaccggttgcacttctatttgcagtttccaggcagaaaatatgatatactagataggcaaaatgatacaaaaagaaggaagatt Mask Tandem Repeat Region ================================================ aatcttccttctttttgtatcattttgcctatctagtatatcatattttctgcctggaaactgcaaatagaagtgcaaccggtggttgacaaaatgtacaggaagctgtattctcaagataactaaaagctgttaggatagagttagcaaagaaaaggaggctgcgaac Find is-nt database================================================ Query_seq: SSA_2254:SSA_2255|SSA_2254:SSA_2255:Holliday junction DNA helicase ruvA, putative:Transcriptional regulator, XRE family, putative:<-->:2250115..2250283 169 aatcttccttctttttgtatcattttgcctatctagtatatcatattttctgcctggaaactgcaaatagaagtgcaaccggtggttgacaaaatgtacaggaagctgtattctcaagataactaaaagctgttaggatagagttagcaaagaaaaggaggctgcgaac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_2254:SSA_2255|SSA_2254:SSA_2255:Holliday junction DNA helicase ruvA, putative:Transcriptional regulator, XRE family, putative:<-->:2250115..2250283 169 aatcttccttctttttgtatcattttgcctatctagtatatcatattttctgcctggaaactgcaaatagaagtgcaaccggtggttgacaaaatgtacaggaagctgtattctcaagataactaaaagctgttaggatagagttagcaaagaaaaggaggctgcgaac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_2254:SSA_2255|SSA_2254:SSA_2255:Holliday junction DNA helicase ruvA, putative:Transcriptional regulator, XRE family, putative:<-->:2250115..2250283 169 aatcttccttctttttgtatcattttgcctatctagtatatcatattttctgcctggaaactgcaaatagaagtgcaaccggtggttgacaaaatgtacaggaagctgtattctcaagataactaaaagctgttaggatagagttagcaaagaaaaggaggctgcgaac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aatcttccttctttttgtatcattttgcctatctagtatatcatattttctgcctggaaactgcaaatagaagtgcaaccggtggttgacaaaatgtacaggaagctgtattctcaagataactaaaagctgttaggatagagttagcaaagaaaaggaggctgcgaac Predict ORF larger than 30AA ================================================ Protein_Len: 32 Strand: - Start: 44 End: 139 ........................................... I K Q R S V A F L L A V P P Q C F T C S A T N E L Y S F A T L M .............................. Protein_Len: 40 Strand: - Start: 1 End: 120 I K R R K T D N Q R D L I D Y K R G P F Q L Y F H L R H N V F H V P L Q I R L M ................................................. aatcttccttctttttgtatcattttgcctatctagtatatcatattttctgcctggaaactgcaaatagaagtgcaaccggtggttgacaaaatgtacaggaagctgtattctcaagataactaaaagctgttaggatagagttagcaaagaaaaggaggctgcgaac 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: 85 End: 114 ....................................................................................GTTGACAAAATGTACAGGAAGCTGTATTCT....................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aatcttccttctttttgtatcattttgcctatctagtatatcatattttctgcctggaaactgcaaatagaagtgcaaccggtggttgacaaaatgtacaggaagctgtattctcaagataactaaaagctgttaggatagagttagcaaagaaaaggaggctgcgaac Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_2254:SSA_2255|SSA_2254:SSA_2255:Holliday junction DNA helicase ruvA, putative:Transcriptional regulator, XRE family, putative:<-->:2250115..2250283 169 aatcttccttctttttgtatcattttgcctatctagtatatcatattttctgcctggaaactgcaaatagaagtgcaaccggtggttgacaaaatgtacaggaagctgtattctcaagataactaaaagctgttaggatagagttagcaaagaaaaggaggctgcgaac Intra-Species Hit: Count: 1 Min: 1 Max: 169 Len: 169 Subject: NC_009009_SSA_2254_SSA_2255|Holliday junction DNA helicase ruvA, putative:Transcriptional regulator, XRE family, putative|NEGATIVE:POSITIVE|[2250115,2250283]|169 HSP 1 e-value: 3.0E-91 bit: 335.0 Len: 169 Query Start:1 Query End:169 Subject Strand: POSITIVE Subject Start: 1 Subject End: 169 aatcttccttctttttgtatcattttgcctatctagtatatcatattttctgcctggaaactgcaaatagaagtgcaaccggtggttgacaaaatgtacaggaagctgtattctcaagataactaaaagctgttaggatagagttagcaaagaaaaggaggctgcgaac aatcttccttctttttgtatcattttgcctatctagtatatcatattttctgcctggaaactgcaaatagaagtgcaaccggtggttgacaaaatgtacaggaagctgtattctcaagataactaaaagctgttaggatagagttagcaaagaaaaggaggctgcgaac Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUCUUCCUUCUUUUUGUAUCAUUUUGCCUAUCUAGUAUAUCAUAUUUUCUGCCUGGAAACUGCAAAUAGAAGUGCAACCGGUGGUUGACAAAAUGUACAGGAAGCUGUAUUCUCAAGAUAACUAAAAGCUGUUAGGAUAGAGUUAGCAAAGAAAAGGAGGCUGCGAAC ...(((((((.(((((((...((((((((((..((((.............(((..(....).)))..(((..((.(((((...))))))).....((((((....))))))...........)))...)))).)))).))))))..))))))).)))))))........ (-40.50) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUUCGCAGCCUCCUUUUCUUUGCUAACUCUAUCCUAACAGCUUUUAGUUAUCUUGAGAAUACAGCUUCCUGUACAUUUUGUCAACCACCGGUUGCACUUCUAUUUGCAGUUUCCAGGCAGAAAAUAUGAUAUACUAGAUAGGCAAAAUGAUACAAAAAGAAGGAAGAUU ..........(((((((.((((.......((((......(((((((((((((.......(((((....)))))..(((((((.(((...)))((((........)))).......))))))).....)))).))))))..))).....)))))))).)))))))..... (-29.21) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 916 100 51 191 142 NC_009009:SSA_2254|5end_Holliday_junction_DNA_helicase_ruvA,_putative_2250024..2250254_NEGATIVE 379 66 23 194 150 NC_009009:SSA_0284|5end_Phosphotransferase_system_(PTS),_cellobiose-specific_IIC_component,_putative_274888..275118_POSITIVE 350 56 11 148 102 NC_009009:SSA_2231|5end_Heme/copper-type_cytochrome/quinol_oxidases,_subunit_1,_putative_2232928..2233158_NEGATIVE 301 117 72 225 179 NC_009009:SSA_1061|5end_50S_ribosomal_protein_L21,_putative_1077592..1077822_POSITIVE 292 49 6 137 96 NC_009009:SSA_0747|5end_DD-carboxypeptidase,_putative_727936..728166_POSITIVE 272 90 46 54 21 NC_009009:SSA_1911|5end_Conserved_uncharacterized_protein_1903105..1903335_NEGATIVE 271 108 70 50 8 NC_009009:SSA_0092|5end_V-type_sodium_ATPase,_subunit_B,_putative_92895..93125_POSITIVE 268 108 61 227 188 NC_009009:SSA_1419|5end_hypothetical_protein_1429675..1429905_NEGATIVE 268 138 105 159 128 NC_009009:SSA_0971|5end_Conserved_uncharacterized_protein_978241..978471_POSITIVE 268 101 61 70 29 NC_009009:SSA_0320|5end_hypothetical_protein_313406..313636_POSITIVE 266 97 51 96 32 NC_009009:SSA_0243|5end_Cyclo-nucleotide_phosphodiesterase,_putative_238235..238465_NEGATIVE 264 147 101 194 145 NC_009009:SSA_1860|5end_Penicillin-binding_protein_1A,_putative_1854299..1854529_POSITIVE 263 88 41 145 110 NC_009009:SSA_1306|5end_Trk_transporter_NAD+_binding_protein-K+_transport,_putative_1324910..1325140_NEGATIVE 263 110 72 204 163 NC_009009:SSA_0106|5end_30S_ribosomal_protein_S10,_putative_107772..108002_POSITIVE 261 93 56 231 191 NC_009009:SSA_0980|5end_3-isopropylmalate_dehydratase_large_subunit,_putative_984004..984234_POSITIVE 260 86 50 74 44 NC_009009:SSA_0937|5end_Arsenate_reductase,_glutaredoxin_family,_putative_946183..946413_POSITIVE 259 110 61 60 8 NC_009009:SSA_2271|5end_hypothetical_protein_2272450..2272680_NEGATIVE 257 116 75 90 54 NC_009009:SSA_1194|5end_Aspartate-semialdehyde_dehydrogenase,_putative_1221189..1221419_NEGATIVE 257 139 96 73 29 NC_009009:SSA_0815|5end_hypothetical_protein_796975..797205_POSITIVE 256 93 52 53 3 NC_009009:SSA_0883|5end_Glycerate_kinase,_putative_877560..877790_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 350 56 11 109 63 NC_009009:SSA_2233|3end_hypothetical_protein_2232967..2233117_NEGATIVE 272 90 46 46 13 NC_009009:SSA_1912|3end_hypothetical_protein_1903113..1903263_NEGATIVE 271 108 70 63 21 NC_009009:SSA_0091|3end_V-type_sodium_ATPase,_subunit_A,_putative_92988..93138_POSITIVE 268 101 61 80 39 NC_009009:SSA_0319|3end_Branched-chain_amino_acid_permease_(L-methionine,_L-isoleucine,_leucine_and_valine),_putative_313496..313646_POSITIVE 263 88 41 134 99 NC_009009:SSA_1307|3end_Trk_transporter_membrane-spanning_protein-K+_transport,_putative_1324921..1325071_NEGATIVE 263 130 81 58 3 NC_009009:SSA_0407|3end_ABC-type_multidrug_transport_system_(3-component_subtilin_immunity_exporter),_ATPase_component,_putative_402911..403061_NEGATIVE 255 148 102 68 19 NC_009009:SSA_1248|3end_hypothetical_protein_1272355..1272505_NEGATIVE 248 88 42 128 80 NC_009009:SSA_0678|3end_Transcriptional_regulator,_ArgR_family,_putative_660785..660935_POSITIVE 247 90 46 64 22 NC_009009:SSA_0089|3end_V-type_sodium_ATPase,_subunit_F,_putative_90330..90480_POSITIVE 245 88 49 145 113 NC_009009:SSA_1104|3end_50S_ribosomal_protein_L10,_putative_1125323..1125473_POSITIVE 244 150 105 68 21 NC_009009:SSA_1130|3end_Iron-dependent_peroxidase,_putative_1157090..1157240_POSITIVE 240 88 44 124 80 NC_009009:SSA_2073|3end_Undecaprenyl_pyrophosphate_synthetase,_putative_2075622..2075772_NEGATIVE 240 122 81 129 96 NC_009009:SSA_0781|3end_Mannose-6-phosphate_isomerase,_putative_766394..766544_POSITIVE 237 83 41 128 71 NC_009009:SSA_0655|3end_Cell_division_protein_FtsA,_putative_640222..640372_POSITIVE 236 87 46 62 11 NC_009009:SSA_1354|3end_hypothetical_protein_1368555..1368705_NEGATIVE 236 76 43 68 27 NC_009009:SSA_0766|3end_hypothetical_protein_746975..747125_POSITIVE 236 87 48 135 94 NC_009009:SSA_0087|3end_V-type_sodium_ATPase,_subunit_E,_putative_88999..89149_POSITIVE 235 70 21 144 98 NC_009009:SSA_2121|3end_Cell_wall_surface_anchor_family_protein,_putative_2122222..2122372_NEGATIVE 234 90 41 124 68 NC_009009:SSA_0142|3end_hypothetical_protein_137489..137639_POSITIVE 232 89 52 138 104 NC_009009:SSA_0299|3end_hypothetical_protein_293342..293492_POSITIVE