Origin IGS: aagtaccttccttcttttttattaagttcttgctggtttgtctaaaaacagagcaaattccaacaaaatagtttaccgattgtcaactaaaatgataacactttatagaggaaatgtccaattatttttaaaatttaatataaaaatattaaaaaaccagtcttcccttacaaggaccggttctgtcatttctctgtttttcttctagttgg .........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 ccaactagaagaaaaacagagaaatgacagaaccggtccttgtaagggaagactggttttttaatatttttatattaaattttaaaaataattggacatttcctctataaagtgttatcattttagttgacaatcggtaaactattttgttggaatttgctctgtttttagacaaaccagcaagaacttaataaaaaagaaggaaggtactt Mask Tandem Repeat Region ================================================ aagtaccttccttcttttttattaagttcttgctggtttgtctaaaaacagagcaaattccaacaaaatagtttaccgattgtcaactaaaatgataacactttatagaggaaatgtccaattatttttaaaatttaatataaaaatattaaaaaaccagtcttcccttacaaggaccggttctgtcatttctctgtttttcttctagttgg Find is-nt database================================================ Query_seq: SSA_0144:SSA_0145|SSA_0144:SSA_0145:Transcriptional regulator, TetR family, putative:Transcriptional regulator, TetR family, putative:<-<-:138656..138867 212 aagtaccttccttcttttttattaagttcttgctggtttgtctaaaaacagagcaaattccaacaaaatagtttaccgattgtcaactaaaatgataacactttatagaggaaatgtccaattatttttaaaatttaatataaaaatattaaaaaaccagtcttcccttacaaggaccggttctgtcatttctctgtttttcttctagttgg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0144:SSA_0145|SSA_0144:SSA_0145:Transcriptional regulator, TetR family, putative:Transcriptional regulator, TetR family, putative:<-<-:138656..138867 212 aagtaccttccttcttttttattaagttcttgctggtttgtctaaaaacagagcaaattccaacaaaatagtttaccgattgtcaactaaaatgataacactttatagaggaaatgtccaattatttttaaaatttaatataaaaatattaaaaaaccagtcttcccttacaaggaccggttctgtcatttctctgtttttcttctagttgg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0144:SSA_0145|SSA_0144:SSA_0145:Transcriptional regulator, TetR family, putative:Transcriptional regulator, TetR family, putative:<-<-:138656..138867 212 aagtaccttccttcttttttattaagttcttgctggtttgtctaaaaacagagcaaattccaacaaaatagtttaccgattgtcaactaaaatgataacactttatagaggaaatgtccaattatttttaaaatttaatataaaaatattaaaaaaccagtcttcccttacaaggaccggttctgtcatttctctgtttttcttctagttgg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aagtaccttccttcttttttattaagttcttgctggtttgtctaaaaacagagcaaattccaacaaaatagtttaccgattgtcaactaaaatgataacactttatagaggaaatgtccaattatttttaaaatttaatataaaaatattaaaaaaccagtcttcccttacaaggaccggttctgtcatttctctgtttttcttctagttgg Predict ORF larger than 30AA ================================================ Protein_Len: 56 Strand: + Start: 38 End: 205 ..................................... M S K N R A N S N K I V Y R L S T K M I T L Y R G N V Q L F L K F N I K I L K N Q S S L T R T G S V I S L F F F ....... aagtaccttccttcttttttattaagttcttgctggtttgtctaaaaacagagcaaattccaacaaaatagtttaccgattgtcaactaaaatgataacactttatagaggaaatgtccaattatttttaaaatttaatataaaaatattaaaaaaccagtcttcccttacaaggaccggttctgtcatttctctgtttttcttctagttgg 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: 92 End: 121 ...........................................................................................TTGGACATTTCCTCTATAAAGTGTTATCAT........................................................................................... PromScan Matrix: RpoD-17 Strand: + Score: 81 Start: 105 End: 134 ........................................................................................................ATAGAGGAAATGTCCAATTATTTTTAAAAT.............................................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aagtaccttccttcttttttattaagttcttgctggtttgtctaaaaacagagcaaattccaacaaaatagtttaccgattgtcaactaaaatgataacactttatagaggaaatgtccaattatttttaaaatttaatataaaaatattaaaaaaccagtcttcccttacaaggaccggttctgtcatttctctgtttttcttctagttgg Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 60 HP_score: -2.6 Tail_Score: -4.6971 Start: 69 End: 89 Full_Region: aaagtgttatcattt tagttgac aatcg gtaaacta ttttgttggaatttg ....................................................................tagttgacaatcggtaaacta........................................................................................................................... Find igs database================================================ Query_seq: SSA_0144:SSA_0145|SSA_0144:SSA_0145:Transcriptional regulator, TetR family, putative:Transcriptional regulator, TetR family, putative:<-<-:138656..138867 212 aagtaccttccttcttttttattaagttcttgctggtttgtctaaaaacagagcaaattccaacaaaatagtttaccgattgtcaactaaaatgataacactttatagaggaaatgtccaattatttttaaaatttaatataaaaatattaaaaaaccagtcttcccttacaaggaccggttctgtcatttctctgtttttcttctagttgg Intra-Species Hit: Count: 1 Min: 1 Max: 212 Len: 212 Subject: NC_009009_SSA_0144_SSA_0145|Transcriptional regulator, TetR family, putative:Transcriptional regulator, TetR family, putative|NEGATIVE:NEGATIVE|[138656,138867]|212 HSP 1 e-value: 2.0E-61 bit: 236.0 Len: 119 Query Start:1 Query End:119 Subject Strand: POSITIVE Subject Start: 1 Subject End: 119 aagtaccttccttcttttttattaagttcttgctggtttgtctaaaaacagagcaaattccaacaaaatagtttaccgattgtcaactaaaatgataacactttatagaggaaatgtcc............................................................................................. aagtaccttccttcttttttattaagttcttgctggtttgtctaaaaacagagcaaattccaacaaaatagtttaccgattgtcaactaaaatgataacactttatagaggaaatgtcc............................................................................................. HSP 2 e-value: 1.0E-23 bit: 111.0 Len: 56 Query Start:157 Query End:212 Subject Strand: POSITIVE Subject Start: 157 Subject End: 212 ............................................................................................................................................................ccagtcttcccttacaaggaccggttctgtcatttctctgtttttcttctagttgg ............................................................................................................................................................ccagtcttcccttacaaggaccggttctgtcatttctctgtttttcttctagttgg Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAGUACCUUCCUUCUUUUUUAUUAAGUUCUUGCUGGUUUGUCUAAAAACAGAGCAAAUUCCAACAAAAUAGUUUACCGAUUGUCAACUAAAAUGAUAACACUUUAUAGAGGAAAUGUCCAAUUAUUUUUAAAAUUUAAUAUAAAAAUAUUAAAAAACCAGUCUUCCCUUACAAGGACCGGUUCUGUCAUUUCUCUGUUUUUCUUCUAGUUGG .............................(((((.((((......))))..)))))...(((((....(((((.((.....)).)))))...............((((((.(((((.(...............((((((((....)))))))).((((.(((((........))))).))))..).)))))))))))..........))))) (-35.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CCAACUAGAAGAAAAACAGAGAAAUGACAGAACCGGUCCUUGUAAGGGAAGACUGGUUUUUUAAUAUUUUUAUAUUAAAUUUUAAAAAUAAUUGGACAUUUCCUCUAUAAAGUGUUAUCAUUUUAGUUGACAAUCGGUAAACUAUUUUGUUGGAAUUUGCUCUGUUUUUAGACAAACCAGCAAGAACUUAAUAAAAAAGAAGGAAGGUACUU .(((((((((....((((((((((((..((((((((((.((......)).))))))))))....((((((((..........))))))))......))))).))).......))))....)))))))))......((((.....(((((((((..((((.((((....))))))))))))))))).(((.......)))........)))). (-43.41) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 800 80 31 171 122 NC_009009:SSA_0144|5end_Transcriptional_regulator,_TetR_family,_putative_138565..138795_NEGATIVE 342 209 161 112 66 NC_009009:SSA_0341|5end_hypothetical_protein_334731..334961_NEGATIVE 295 205 166 107 67 NC_009009:SSA_1410|5end_DTDP-4-keto-6-deoxyglucose-3,5-epimerase,_putative_1423086..1423316_NEGATIVE 295 80 31 186 135 NC_009009:SSA_0079|5end_ROK_family_protein,_putative_82855..83085_POSITIVE 292 44 2 112 66 NC_009009:SSA_2256|5end_hypothetical_protein_2250604..2250834_POSITIVE 280 210 163 111 67 NC_009009:SSA_0515|5end_Propanediol_utilization_protein_PduU,_putative_514134..514364_POSITIVE 274 207 166 69 21 NC_009009:SSA_0936|5end_FAD_synthase,_putative_945139..945369_POSITIVE 271 193 154 87 51 NC_009009:SSA_0512|5end_Nicotinate-nucleotide--dimethylbenzimidazole_phosphoribosyltransferase,_putative_510439..510669_POSITIVE 268 44 6 133 94 NC_009009:SSA_2298|5end_Serine_protease_containing_a_PDZ_domain,_putative_2300603..2300833_NEGATIVE 266 196 155 102 53 NC_009009:SSA_0547|5end_Acyl_carrier_protein_synthase,_putative_541991..542221_POSITIVE 263 192 156 213 166 NC_009009:SSA_1870|5end_Phospho-N-acetylmuramoyl-pentapeptide-_transferase,_putative_1866583..1866813_NEGATIVE 260 200 161 145 98 NC_009009:SSA_0392|5end_hypothetical_protein_387876..388106_POSITIVE 257 208 164 124 69 NC_009009:SSA_0869|5end_Peptide_chain_release_factor_2,_putative_861914..862144_POSITIVE 256 210 182 164 137 NC_009009:SSA_1795|5end_Guanosine_3',5'-bis-pyrophosphate_(ppGpp)_synthetase,_putative_1777671..1777901_NEGATIVE 255 210 161 114 56 NC_009009:SSA_0551|5end_L-asparaginase,_putative_547293..547523_NEGATIVE 253 210 161 174 112 NC_009009:SSA_1448|5end_ATP_phosphoribosyltransferase_regulatory_subunit,_putative_1450817..1451047_NEGATIVE 253 201 162 86 41 NC_009009:SSA_1432|5end_HflX_GTPase,_putative_1439901..1440131_NEGATIVE 253 198 157 50 11 NC_009009:SSA_0629|5end_hypothetical_protein_618967..619197_POSITIVE 249 204 173 153 121 NC_009009:SSA_2260|5end_DNA_mismatch_repair_protein_hexA,_putative_2258150..2258380_NEGATIVE 248 207 163 104 55 NC_009009:SSA_1306|5end_Trk_transporter_NAD+_binding_protein-K+_transport,_putative_1324910..1325140_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 295 205 166 102 62 NC_009009:SSA_1411|3end_Glucose-1-phosphate_thymidylytransferase,_putative_1423091..1423241_NEGATIVE 282 79 31 151 101 NC_009009:SSA_0078|3end_N-acetylneuraminate_lyase,_putative_82901..83051_POSITIVE 274 208 161 138 72 NC_009009:SSA_0963|3end_Peptidoglycan_N-acetylglucosamine_deacetylase_A,_putative_972890..973040_POSITIVE 271 193 154 124 88 NC_009009:SSA_0511|3end_Propanediol_utilization_kinase,_putative_510556..510706_POSITIVE 268 44 6 81 42 NC_009009:SSA_2299|3end_hypothetical_protein_2300655..2300805_NEGATIVE 258 196 151 80 40 NC_009009:SSA_1379|3end_hypothetical_protein_1398178..1398328_NEGATIVE 254 204 169 87 49 NC_009009:SSA_2346|3end_3-oxoacyl-[acyl-carrier-protein]_synthase_III,_putative_2347602..2347752_NEGATIVE 253 210 161 118 56 NC_009009:SSA_1449|3end_Histidinol-phosphate/aromatic_aminotransferase_and_cobyric_acid_decarboxylase,_putative_1450873..1451023_NEGATIVE 253 201 162 54 9 NC_009009:SSA_1433|3end_tRNA_delta(2)-isopentenylpyrophosphate_transferase,_putative_1439933..1440083_NEGATIVE 253 198 157 63 24 NC_009009:SSA_0628|3end_Fe-S-cluster_redox_enzyme/radical_SAM_enzyme,_Cfr_family,_putative_619060..619210_POSITIVE 250 194 157 44 4 NC_009009:SSA_0023|3end_Aspartate_aminotransferase,_putative_29781..29931_POSITIVE 249 204 173 74 42 NC_009009:SSA_2261|3end_Transcriptional_repressor_(arginine_synthesis),_putative_2258229..2258379_NEGATIVE 248 207 163 93 44 NC_009009:SSA_1307|3end_Trk_transporter_membrane-spanning_protein-K+_transport,_putative_1324921..1325071_NEGATIVE 247 194 157 143 100 NC_009009:SSA_2063|3end_Aminopeptidase_PepS,_putative_2063616..2063766_NEGATIVE 247 46 7 127 87 NC_009009:SSA_1076|3end_hypothetical_protein_1095047..1095197_POSITIVE 247 209 176 66 32 NC_009009:SSA_0834|3end_Accessory_secretory_protein_Asp2,_putative_821119..821269_POSITIVE 245 197 157 144 99 NC_009009:SSA_2091|3end_Phosphotransferase_system_sugar-specific_EII_component,_putative_2095062..2095212_NEGATIVE 244 64 34 69 41 NC_009009:SSA_1324|3end_Ceramide_glucosyltransferase,_putative_1340428..1340578_NEGATIVE 244 210 161 125 58 NC_009009:SSA_0480|3end_Cobalt_ABC_transporter,_ATP-binding_protein,_putative_482057..482207_POSITIVE 242 40 8 132 98 NC_009009:SSA_2184|3end_hypothetical_protein_2183284..2183434_NEGATIVE