Origin IGS: aggaaaaggattcagtttgagctggattcttttttgtacatgataatagaaaatttgacaatgattattatttttttgacaaatatacttgtcaaaaagaaaagaatctgttacaatgattttatccaagggagaataataaataaggagttt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aaactccttatttattattctcccttggataaaatcattgtaacagattcttttctttttgacaagtatatttgtcaaaaaaataataatcattgtcaaattttctattatcatgtacaaaaaagaatccagctcaaactgaatccttttcct Mask Tandem Repeat Region ================================================ aggaaaaggattcagtttgagctggattcttttttgtacatgataatagaaaatttgacaatgattattatttttttgacaaatatacttgtcaaaaagaaaagaatctgttacaatgattttatccaagggagaataataaataaggagttt Find is-nt database================================================ Query_seq: SSA_0760:SSA_0761|SSA_0760:SSA_0761:Acetylornithine aminotransferase, putative:Transcriptional regulator, XRE family, putative:->->:743864..744016 153 aggaaaaggattcagtttgagctggattcttttttgtacatgataatagaaaatttgacaatgattattatttttttgacaaatatacttgtcaaaaagaaaagaatctgttacaatgattttatccaagggagaataataaataaggagttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0760:SSA_0761|SSA_0760:SSA_0761:Acetylornithine aminotransferase, putative:Transcriptional regulator, XRE family, putative:->->:743864..744016 153 aggaaaaggattcagtttgagctggattcttttttgtacatgataatagaaaatttgacaatgattattatttttttgacaaatatacttgtcaaaaagaaaagaatctgttacaatgattttatccaagggagaataataaataaggagttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0760:SSA_0761|SSA_0760:SSA_0761:Acetylornithine aminotransferase, putative:Transcriptional regulator, XRE family, putative:->->:743864..744016 153 aggaaaaggattcagtttgagctggattcttttttgtacatgataatagaaaatttgacaatgattattatttttttgacaaatatacttgtcaaaaagaaaagaatctgttacaatgattttatccaagggagaataataaataaggagttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aggaaaaggattcagtttgagctggattcttttttgtacatgataatagaaaatttgacaatgattattatttttttgacaaatatacttgtcaaaaagaaaagaatctgttacaatgattttatccaagggagaataataaataaggagttt Predict ORF larger than 30AA ================================================ Protein_Len: 48 Strand: + Start: 10 End: 153 ......... M Q F E L D S F L Y M I I E N L T M I I I F L T N I L V K K K R I C Y N D F I Q G R I I N K E F Protein_Len: 31 Strand: - Start: 15 End: 107 .............. N S S S E K K Y M I I S F K V I I I I K K V F I S T L F F L M .............................................. Protein_Len: 48 Strand: - Start: 1 End: 144 P F P N L K L Q I R K Q V H Y Y F I Q C H N N N K Q C I Y K D F L F S D T V I I K D L P S Y Y M ......... aggaaaaggattcagtttgagctggattcttttttgtacatgataatagaaaatttgacaatgattattatttttttgacaaatatacttgtcaaaaagaaaagaatctgttacaatgattttatccaagggagaataataaataaggagttt 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: 88 Start: 88 End: 117 .......................................................................................CTTGTCAAAAAGAAAAGAATCTGTTACAAT.................................... PromScan Matrix: RpoD-17 Strand: - Score: 85 Start: 67 End: 96 ..................................................................TTTGACAAGTATATTTGTCAAAAAAATAAT......................................................... PromScan Matrix: RpoD-17 Strand: - Score: 82 Start: 33 End: 62 ................................ATTGTCAAATTTTCTATTATCATGTACAAA........................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aggaaaaggattcagtttgagctggattcttttttgtacatgataatagaaaatttgacaatgattattatttttttgacaaatatacttgtcaaaaagaaaagaatctgttacaatgattttatccaagggagaataataaataaggagttt Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 65 HP_score: -7.2 Tail_Score: -3.09131 Start: 63 End: 108 Full_Region: AGAAAATTTGACAAT GATTATTATTTTTTTGACAA ATATAC TTGTCAAAAAGAAAAGAATC TGTTACAATGATTTT ..............................................................GATTATTATTTTTTTGACAAATATACTTGTCAAAAAGAAAAGAATC............................................. TransTerm Strand: + Conf: 46 HP_score: -4.0 Tail_Score: -3.09557 Start: 65 End: 106 Full_Region: AAAATTTGACAATGA TTATTATTTTTTTGACAA ATATAC TTGTCAAAAAGAAAAGAA TCTGTTACAATGATT ................................................................TTATTATTTTTTTGACAAATATACTTGTCAAAAAGAAAAGAA............................................... Find igs database================================================ Query_seq: SSA_0760:SSA_0761|SSA_0760:SSA_0761:Acetylornithine aminotransferase, putative:Transcriptional regulator, XRE family, putative:->->:743864..744016 153 aggaaaaggattcagtttgagctggattcttttttgtacatgataatagaaaatttgacaatgattattatttttttgacaaatatacttgtcaaaaagaaaagaatctgttacaatgattttatccaagggagaataataaataaggagttt Intra-Species Hit: Count: 1 Min: 1 Max: 153 Len: 153 Subject: NC_009009_SSA_0760_SSA_0761|Acetylornithine aminotransferase, putative:Transcriptional regulator, XRE family, putative|POSITIVE:POSITIVE|[743864,744016]|153 HSP 1 e-value: 3.0E-69 bit: 262.0 Len: 153 Query Start:1 Query End:153 Subject Strand: POSITIVE Subject Start: 1 Subject End: 153 aggaaaaggattcagtttgagctggattcttttttgtacatgataatagaaaatttgacaatgattattannnnnnngacaaatatacttgtcaaaaagaaaagaatctgttacaatgattttatccaagggagaataataaataaggagttt aggaaaaggattcagtttgagctggattcttttttgtacatgataatagaaaatttgacaatgattattatttttttgacaaatatacttgtcaaaaagaaaagaatctgttacaatgattttatccaagggagaataataaataaggagttt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGGAAAAGGAUUCAGUUUGAGCUGGAUUCUUUUUUGUACAUGAUAAUAGAAAAUUUGACAAUGAUUAUUAUUUUUUUGACAAAUAUACUUGUCAAAAAGAAAAGAAUCUGUUACAAUGAUUUUAUCCAAGGGAGAAUAAUAAAUAAGGAGUUU .(((((((((((((((....)))))))))))))))...(((..(((((((.((((.......))))....((((((((((((......))))))))))))......)))))))..)))......(((...................))).... (-33.81) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAACUCCUUAUUUAUUAUUCUCCCUUGGAUAAAAUCAUUGUAACAGAUUCUUUUCUUUUUGACAAGUAUAUUUGUCAAAAAAAUAAUAAUCAUUGUCAAAUUUUCUAUUAUCAUGUACAAAAAAGAAUCCAGCUCAAACUGAAUCCUUUUCCU ..............((((((......))))))..((((((.....(((((((((.(((((((((((....))))))))))).((((((...(((....)))....)))))).........))))))))).....)))..)))........... (-20.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 246 41 1 154 106 NC_009009:SSA_0294|5end_hypothetical_protein_287876..288106_NEGATIVE 213 34 6 221 190 NC_009009:SSA_1923|5end_NADPH-q_uinone_reductase_(modulator_of_drug_activity_B),_putative_1912698..1912928_NEGATIVE 213 134 103 207 176 NC_009009:SSA_0278|5end_Transcriptional_repressor_of_sugar_metabolism,_GlpR/DeoR_family,_putative_271559..271789_POSITIVE 212 60 11 84 29 NC_009009:SSA_1907|5end_hypothetical_protein_1900446..1900676_POSITIVE 212 26 2 198 172 NC_009009:SSA_0001|5end_Chromosomal_replication_initiator_protein_dnaA,_putative_74..304_POSITIVE 211 46 8 226 186 NC_009009:SSA_0694|5end_Mutator_protein,_putative_677730..677960_POSITIVE 210 36 6 50 15 NC_009009:SSA_1715|5end_Phosphoserine_aminotransferase,_putative_1702488..1702718_NEGATIVE 209 43 6 93 59 NC_009009:SSA_2017|5end_Hypothetical_protein_(possibly_membrane-associated)_2017331..2017561_NEGATIVE 209 43 6 48 8 NC_009009:SSA_1478|5end_Transposase_ORF1,_putative_1482889..1483119_POSITIVE 209 48 11 53 17 NC_009009:SSA_1468|5end_3-dehydroquinate_synthase,_putative_1475452..1475682_NEGATIVE 208 44 1 216 166 NC_009009:SSA_1636|5end_ABC-type_antibiotic_exporter,_ATPase_component,_putative_1640905..1641135_NEGATIVE 206 138 98 60 23 NC_009009:SSA_0965|5end_Oxidoreductase,_putative_975045..975275_NEGATIVE 205 60 11 90 32 NC_009009:SSA_2148|5end_Alkaline_shock_stress_response_protein,_putative_2150039..2150269_NEGATIVE 205 39 1 164 126 NC_009009:SSA_0017|5end_Cell_shape_determining_protein_MreC,_putative_22811..23041_POSITIVE 201 37 2 120 75 NC_009009:SSA_0432|5end_Formate--tetrahydrofolate_ligase,_putative_434991..435221_NEGATIVE 200 43 1 161 106 NC_009009:SSA_1068|5end_Transcriptional_regulator,_LysR_family_(capsular_polysaccharide_biosynthesis_regulation),_putative_1087355..1087585_POSITIVE 198 32 2 231 207 NC_009009:SSA_0220|5end_PTS_system,_mannose-specific_IIB_component,_putative_215848..216078_POSITIVE 197 26 1 231 207 NC_009009:SSA_0252|5end_hypothetical_protein_245839..246069_NEGATIVE 195 57 13 80 35 NC_009009:SSA_0907|5end_Fibronectin-binding_protein_A,_putative_919217..919447_NEGATIVE 191 29 4 214 184 NC_009009:SSA_1565|5end_Two-component_response_transcriptional_regulator_(CheY-like_receiver_and_winged-helix_DNA-binding_domains),_putative_1569309..1569539_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 274 41 1 98 56 NC_009009:SSA_0760|3end_Acetylornithine_aminotransferase,_putative_743803..743953_POSITIVE 248 50 1 84 38 NC_009009:SSA_1962|3end_Amino_acid_ABC_transporter,_ATP-binding_protein,_putative_1960930..1961080_POSITIVE 212 60 11 74 19 NC_009009:SSA_1906|3end_Diadenosine_tetraphosphate_(Ap4A)_hydrolase_(histidine_triad_protein,_cell-cycle_regulation),_putative_1900516..1900666_POSITIVE 212 25 7 151 130 NC_009009:SSA_1223|3end_30S_ribosomal_protein_S1,_putative_1245667..1245817_NEGATIVE 211 40 1 44 6 NC_009009:SSA_0302|3end_Phosphoglycerate_kinase,_putative_296166..296316_POSITIVE 209 48 11 42 6 NC_009009:SSA_1469|3end_Shikimate_dehydrogenase,_putative_1475463..1475613_NEGATIVE 208 44 1 104 54 NC_009009:SSA_1638|3end_hypothetical_protein_1641017..1641167_NEGATIVE 205 60 11 71 13 NC_009009:SSA_2386|3end_hypothetical_protein_2150058..2150208_NEGATIVE 201 29 11 150 130 NC_009009:SSA_0753|3end_Foldase_protein_prsA_precursor,_putative_736055..736205_POSITIVE 201 37 2 83 38 NC_009009:SSA_0433|3end_Methenyl_tetrahydrofolate_cyclohydrolase,_putative_435028..435178_NEGATIVE 200 43 1 71 16 NC_009009:SSA_1067|3end_hypothetical_protein_1087345..1087495_POSITIVE 191 44 1 104 63 NC_009009:SSA_1098|3end_Formate-nitrate_transporter,_putative_1115011..1115161_POSITIVE 190 36 7 120 82 NC_009009:SSA_1621|3end_Amino_acid_transporter,_putative_1623172..1623322_NEGATIVE 190 58 20 66 26 NC_009009:SSA_0174|3end_Tyrosyl-tRNA_synthetase_1,_putative_170629..170779_NEGATIVE 189 41 1 80 37 NC_009009:SSA_1752|3end_Phosphotransferase_system,_trehalose-specific_IIBC_component,_putative_1739812..1739962_NEGATIVE 189 60 14 53 15 NC_009009:SSA_0191|3end_Adenine-specific_DNA_methylase,_putative_192952..193102_POSITIVE 188 50 1 97 46 NC_009009:SSA_2005|3end_Chaperone_protein_dnaJ,_putative_2005251..2005401_NEGATIVE 188 44 2 83 40 NC_009009:SSA_1363|3end_FmtA-like_protein,_putative_1378639..1378789_NEGATIVE 188 130 89 81 43 NC_009009:SSA_0511|3end_Propanediol_utilization_kinase,_putative_510556..510706_POSITIVE 187 33 1 81 49 NC_009009:SSA_2108|3end_Glyceraldehyde_3-phosphate_dehydrogenase,_putative_2111457..2111607_NEGATIVE