Origin IGS: tatccgcagtagaattgtcaaaagattgttactcttttgtaatatgaaatgtgcgcttgcatgttataataatctcattaaacctcacaaaaggacagcaactgcacaactgctgtccttttgttttgcttatttttcgattttgacaaaaaccctgactagagcagtaaaatctttttgaatattttgcagtttagcccggaacggatattgtaaaaatagcaaatgcgtagtaaaatagagga .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tcctctattttactacgcatttgctatttttacaatatccgttccgggctaaactgcaaaatattcaaaaagattttactgctctagtcagggtttttgtcaaaatcgaaaaataagcaaaacaaaaggacagcagttgtgcagttgctgtccttttgtgaggtttaatgagattattataacatgcaagcgcacatttcatattacaaaagagtaacaatcttttgacaattctactgcggata Mask Tandem Repeat Region ================================================ tatccgcagtagaattgtcaaaagattgttactcttttgtaatatgaaatgtgcgcttgcatgttataataatctcattaaacctcacaaaaggacagcaactgcacaactgctgtccttttgttttgcttatttttcgattttgacaaaaaccctgactagagcagtaaaatctttttgaatattttgcagtttagcccggaacggatattgtaaaaatagcaaatgcgtagtaaaatagagga Find is-nt database================================================ Query_seq: SSA_0935:SSA_0936|SSA_0935:SSA_0936:tRNA pseudouridine synthase B, putative:FAD synthase, putative:->->:945034..945278 245 tatccgcagtagaattgtcaaaagattgttactcttttgtaatatgaaatgtgcgcttgcatgttataataatctcattaaacctcacaaaaggacagcaactgcacaactgctgtccttttgttttgcttatttttcgattttgacaaaaaccctgactagagcagtaaaatctttttgaatattttgcagtttagcccggaacggatattgtaaaaatagcaaatgcgtagtaaaatagagga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0935:SSA_0936|SSA_0935:SSA_0936:tRNA pseudouridine synthase B, putative:FAD synthase, putative:->->:945034..945278 245 tatccgcagtagaattgtcaaaagattgttactcttttgtaatatgaaatgtgcgcttgcatgttataataatctcattaaacctcacaaaaggacagcaactgcacaactgctgtccttttgttttgcttatttttcgattttgacaaaaaccctgactagagcagtaaaatctttttgaatattttgcagtttagcccggaacggatattgtaaaaatagcaaatgcgtagtaaaatagagga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0935:SSA_0936|SSA_0935:SSA_0936:tRNA pseudouridine synthase B, putative:FAD synthase, putative:->->:945034..945278 245 tatccgcagtagaattgtcaaaagattgttactcttttgtaatatgaaatgtgcgcttgcatgttataataatctcattaaacctcacaaaaggacagcaactgcacaactgctgtccttttgttttgcttatttttcgattttgacaaaaaccctgactagagcagtaaaatctttttgaatattttgcagtttagcccggaacggatattgtaaaaatagcaaatgcgtagtaaaatagagga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tatccgcagtagaattgtcaaaagattgttactcttttgtaatatgaaatgtgcgcttgcatgttataataatctcattaaacctcacaaaaggacagcaactgcacaactgctgtccttttgttttgcttatttttcgattttgacaaaaaccctgactagagcagtaaaatctttttgaatattttgcagtttagcccggaacggatattgtaaaaatagcaaatgcgtagtaaaatagagga Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: + Start: 51 End: 143 .................................................. M R L H V I I I S L N L T K G Q Q L H N C C P F V L L I F R F ...................................................................................................... Protein_Len: 59 Strand: + Start: 2 End: 178 . M R S R I V K R L L L F C N M K C A L A C Y N N L I K P H K R T A T A Q L L S F C F A Y F S I L T K T L T R A V K S F ................................................................... Protein_Len: 31 Strand: - Start: 133 End: 225 .................................................................................................................................... K E I K V F V R V L A T F D K Q I N Q L K A R F P Y Q L F L M .................... Protein_Len: 34 Strand: - Start: 32 End: 133 ............................... E K T I H F T R K C T I I I E N F R V F P C C S C L Q Q G K T K S M ................................................................................................................ tatccgcagtagaattgtcaaaagattgttactcttttgtaatatgaaatgtgcgcttgcatgttataataatctcattaaacctcacaaaaggacagcaactgcacaactgctgtccttttgttttgcttatttttcgattttgacaaaaaccctgactagagcagtaaaatctttttgaatattttgcagtttagcccggaacggatattgtaaaaatagcaaatgcgtagtaaaatagagga 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: 210 End: 239 .................................................................................................................................................................................................................ATTGTAAAAATAGCAAATGCGTAGTAAAAT...... PromScan Matrix: RpoD-17 Strand: + Score: 83 Start: 14 End: 43 .............ATTGTCAAAAGATTGTTACTCTTTTGTAAT.......................................................................................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tatccgcagtagaattgtcaaaagattgttactcttttgtaatatgaaatgtgcgcttgcatgttataataatctcattaaacctcacaaaaggacagcaactgcacaactgctgtccttttgttttgcttatttttcgattttgacaaaaaccctgactagagcagtaaaatctttttgaatattttgcagtttagcccggaacggatattgtaaaaatagcaaatgcgtagtaaaatagagga Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 100 HP_score: -12.1 Tail_Score: -4.70739 Start: 88 End: 123 Full_Region: TCTCATTAAACCTCA CAAAAGGACAGCA ACTGCACAAC TGCTGTCCTTTTG TTTTGCTTATTTTTC .......................................................................................CAAAAGGACAGCAACTGCACAACTGCTGTCCTTTTG.......................................................................................................................... TransTerm Strand: + Conf: 83 HP_score: -6.2 Tail_Score: -5.19998 Start: 93 End: 118 Full_Region: TTAAACCTCACAAAA GGACAGCA ACTGCACAAC TGCTGTCC TTTTGTTTTGCTTAT ............................................................................................GGACAGCAACTGCACAACTGCTGTCC............................................................................................................................... TransTerm Strand: - Conf: 100 HP_score: -10.5 Tail_Score: -4.44974 Start: 93 End: 118 Full_Region: ataagcaaaacaaaa ggacagcagtt gtgc agttgctgtcc ttttgtgaggtttaa ............................................................................................ggacagcagttgtgcagttgctgtcc............................................................................................................................... Find igs database================================================ Query_seq: SSA_0935:SSA_0936|SSA_0935:SSA_0936:tRNA pseudouridine synthase B, putative:FAD synthase, putative:->->:945034..945278 245 tatccgcagtagaattgtcaaaagattgttactcttttgtaatatgaaatgtgcgcttgcatgttataataatctcattaaacctcacaaaaggacagcaactgcacaactgctgtccttttgttttgcttatttttcgattttgacaaaaaccctgactagagcagtaaaatctttttgaatattttgcagtttagcccggaacggatattgtaaaaatagcaaatgcgtagtaaaatagagga Intra-Species Hit: Count: 1 Min: 1 Max: 245 Len: 245 Subject: NC_009009_SSA_0935_SSA_0936|tRNA pseudouridine synthase B, putative:FAD synthase, putative|POSITIVE:POSITIVE|[945034,945278]|245 HSP 1 e-value: 1.0E-136 bit: 486.0 Len: 245 Query Start:1 Query End:245 Subject Strand: POSITIVE Subject Start: 1 Subject End: 245 tatccgcagtagaattgtcaaaagattgttactcttttgtaatatgaaatgtgcgcttgcatgttataataatctcattaaacctcacaaaaggacagcaactgcacaactgctgtccttttgttttgcttatttttcgattttgacaaaaaccctgactagagcagtaaaatctttttgaatattttgcagtttagcccggaacggatattgtaaaaatagcaaatgcgtagtaaaatagagga tatccgcagtagaattgtcaaaagattgttactcttttgtaatatgaaatgtgcgcttgcatgttataataatctcattaaacctcacaaaaggacagcaactgcacaactgctgtccttttgttttgcttatttttcgattttgacaaaaaccctgactagagcagtaaaatctttttgaatattttgcagtttagcccggaacggatattgtaaaaatagcaaatgcgtagtaaaatagagga Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAUCCGCAGUAGAAUUGUCAAAAGAUUGUUACUCUUUUGUAAUAUGAAAUGUGCGCUUGCAUGUUAUAAUAAUCUCAUUAAACCUCACAAAAGGACAGCAACUGCACAACUGCUGUCCUUUUGUUUUGCUUAUUUUUCGAUUUUGACAAAAACCCUGACUAGAGCAGUAAAAUCUUUUUGAAUAUUUUGCAGUUUAGCCCGGAACGGAUAUUGUAAAAAUAGCAAAUGCGUAGUAAAAUAGAGGA ((((((........(((((((((...((((((......)))))).((((.(((.((......(((.((((......)))))))...((((((((((((((..........))))))))))))))...)).))).))))..)))))))))....((.(.(((((.(.(((((((.((....)).))))))).)))))).).))..))))))...........((....))................ (-54.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCCUCUAUUUUACUACGCAUUUGCUAUUUUUACAAUAUCCGUUCCGGGCUAAACUGCAAAAUAUUCAAAAAGAUUUUACUGCUCUAGUCAGGGUUUUUGUCAAAAUCGAAAAAUAAGCAAAACAAAAGGACAGCAGUUGUGCAGUUGCUGUCCUUUUGUGAGGUUUAAUGAGAUUAUUAUAACAUGCAAGCGCACAUUUCAUAUUACAAAAGAGUAACAAUCUUUUGACAAUUCUACUGCGGAUA ................((....))...........(((((((...(.(((....((((.............((((((((.(((((....)))))....)).))))))......(((((...((((((((((((((..(....)..))))))))))))))...))))).................))))))).).............(((((((.......)))))))...........))))))) (-59.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 359 129 84 162 119 NC_009009:SSA_2063|5end_Aminopeptidase_PepS,_putative_2064857..2065087_NEGATIVE 296 208 161 173 122 NC_009009:SSA_1659|5end_ABC-type_antimicrobial_peptide_transport_system,_permease_component,_putative_1656819..1657049_NEGATIVE 287 200 154 206 164 NC_009009:SSA_1972|5end_Two-component_system_transcriptional_regulator_(CheY_domain_and_HTH-like_DNA-binding_domain),_putative_1968410..1968640_NEGATIVE 287 126 83 150 100 NC_009009:SSA_0955|5end_Aminopeptidase_N,_putative_958519..958749_POSITIVE 287 130 89 217 163 NC_009009:SSA_0350|5end_Helicase,_putative_344218..344448_NEGATIVE 285 130 84 74 17 NC_009009:SSA_1922|5end_hypothetical_protein_1912106..1912336_NEGATIVE 278 139 96 76 32 NC_009009:SSA_0923|5end_Transcriptional_regulator,_TetR/AcrR_family,_putative_933010..933240_POSITIVE 275 167 127 205 174 NC_009009:SSA_1489|5end_hypothetical_protein_1495788..1496018_NEGATIVE 273 140 92 51 8 NC_009009:SSA_0791|5end_UDP-N-acetylglucosamine-like_protein,_putative_773345..773575_POSITIVE 268 130 83 144 106 NC_009009:SSA_0509|5end_Propanediol_utilization_protein,_putative_508024..508254_POSITIVE 266 124 92 228 193 NC_009009:SSA_2245|5end_RecA_protein,_putative_2241109..2241339_NEGATIVE 266 140 92 161 118 NC_009009:SSA_1606|5end_Dephospho-CoA_kinase,_putative_1612425..1612655_NEGATIVE 265 214 177 94 51 NC_009009:SSA_1431|5end_hypothetical_protein_1438730..1438960_NEGATIVE 263 122 83 171 138 NC_009009:SSA_1481|5end_FmtA-like_protein,_putative_1486622..1486852_NEGATIVE 262 137 91 192 142 NC_009009:SSA_0154|5end_hypothetical_protein_149836..150066_POSITIVE 259 147 104 166 114 NC_009009:SSA_2140|5end_Ribonuclease_P_protein_component,_putative_2140574..2140804_NEGATIVE 259 158 111 140 91 NC_009009:SSA_1982|5end_Transcriptional_regulator,_LytR/AlgR_family,_putative_1975873..1976103_NEGATIVE 258 140 92 130 69 NC_009009:SSA_0157|5end_hypothetical_protein_153513..153743_POSITIVE 255 142 101 83 33 NC_009009:SSA_1986|5end_Acetyltransferase,_GNAT_family,_putative_1982531..1982761_NEGATIVE 255 128 87 204 164 NC_009009:SSA_1484|5end_DNA_ligase,_putative_1492188..1492418_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 359 129 84 140 97 NC_009009:SSA_2064|3end_hypothetical_protein_2064879..2065029_NEGATIVE 293 230 183 129 92 NC_009009:SSA_1569|3end_ABC_transporter_membrane-spanning_permease,_arginine/histidine_transport,_putative_1572630..1572780_POSITIVE 285 130 84 60 3 NC_009009:SSA_1923|3end_NADPH-q_uinone_reductase_(modulator_of_drug_activity_B),_putative_1912120..1912270_NEGATIVE 285 140 92 86 30 NC_009009:SSA_0531|3end_Ethanolamine_utilization_protein_eutQ_(cobalamin-dependent_degradation_of_ethanolamine),_putative_527884..528034_POSITIVE 279 114 75 83 28 NC_009009:SSA_0563|3end_Universal_stress_protein_family,_putative_554947..555097_NEGATIVE 269 148 101 145 104 NC_009009:SSA_1372|3end_hypothetical_protein_1388946..1389096_NEGATIVE 269 138 91 83 37 NC_009009:SSA_0419|3end_Alpha-galactosidase,_putative_418530..418680_POSITIVE 268 140 98 101 67 NC_009009:SSA_1848|3end_Methionyl-tRNA_formyltransferase,_putative_1842243..1842393_NEGATIVE 268 130 83 104 66 NC_009009:SSA_0508|3end_Conserved_uncharacterized_protein,_possible_phosphoserine_phosphatase_508064..508214_POSITIVE 261 230 189 51 8 NC_009009:SSA_1397|3end_hypothetical_protein_1410995..1411145_POSITIVE 261 140 91 101 42 NC_009009:SSA_1245|3end_Transcriptional_regulator,_LysR_family,_putative_1269710..1269860_POSITIVE 258 118 74 66 15 NC_009009:SSA_1069|3end_Lipoprotein_signal_peptidase,_putative_1088838..1088988_POSITIVE 258 130 87 91 49 NC_009009:SSA_0819|3end_hypothetical_protein_801181..801331_POSITIVE 255 128 87 98 58 NC_009009:SSA_1485|3end_Citrulline_cluster-linked_gene,_putative_1492294..1492444_NEGATIVE 253 169 122 107 66 NC_009009:SSA_1368|3end_hypothetical_protein_1383748..1383898_NEGATIVE 251 140 91 101 63 NC_009009:SSA_2074|3end_Preprotein_translocase_subunit_YajC,_putative_2076600..2076750_NEGATIVE 250 64 24 128 95 NC_009009:SSA_0048|3end_Transcriptional_regulator,_TetR/AcrR_family,_putative_52847..52997_NEGATIVE 247 116 87 82 53 NC_009009:SSA_0440|3end_30S_ribosomal_protein_S18,_putative_441465..441615_POSITIVE 245 129 85 139 96 NC_009009:SSA_1084|3end_Conserved_uncharacterized_protein_1102603..1102753_POSITIVE 242 140 97 101 50 NC_009009:SSA_2217|3end_Cps9H,_putative_2218086..2218236_NEGATIVE