Origin IGS: aacttcctcctaaaaactctgtgacgttttttgattttacagtcatagcttatcatataaactaaaaaatgtcaaaagtcttatatcttctttgtaagaaaatataagactttaaatttacacacatcataattctcttcttttggacctatttatttgagtttcacaatttaaaaaataaggatacagtactgaaagctcctattgtctggcttttctctctgtatccttattgtatc .........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 gatacaataaggatacagagagaaaagccagacaataggagctttcagtactgtatccttattttttaaattgtgaaactcaaataaataggtccaaaagaagagaattatgatgtgtgtaaatttaaagtcttatattttcttacaaagaagatataagacttttgacattttttagtttatatgataagctatgactgtaaaatcaaaaaacgtcacagagtttttaggaggaagtt Mask Tandem Repeat Region ================================================ aacttcctcctaaaaactctgtgacgttttttgattttacagtcatagcttatcatataaactaaaaaatgtcaaaagtcttatatcttctttgtaagaaaatataagactttaaatttacacacatcataattctcttcttttggacctatttatttgagtttcacaatttaaaaaataaggatacagtactgaaagctcctattgtctggcttttctctctgtatccttattgtatc Find is-nt database================================================ Query_seq: SSA_1768:SSA_1769|SSA_1768:SSA_1769:Transcriptional regulator, TetR/AcrR family, putative:hypothetical protein:<-<-:1756790..1757028 239 aacttcctcctaaaaactctgtgacgttttttgattttacagtcatagcttatcatataaactaaaaaatgtcaaaagtcttatatcttctttgtaagaaaatataagactttaaatttacacacatcataattctcttcttttggacctatttatttgagtttcacaatttaaaaaataaggatacagtactgaaagctcctattgtctggcttttctctctgtatccttattgtatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1768:SSA_1769|SSA_1768:SSA_1769:Transcriptional regulator, TetR/AcrR family, putative:hypothetical protein:<-<-:1756790..1757028 239 aacttcctcctaaaaactctgtgacgttttttgattttacagtcatagcttatcatataaactaaaaaatgtcaaaagtcttatatcttctttgtaagaaaatataagactttaaatttacacacatcataattctcttcttttggacctatttatttgagtttcacaatttaaaaaataaggatacagtactgaaagctcctattgtctggcttttctctctgtatccttattgtatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1768:SSA_1769|SSA_1768:SSA_1769:Transcriptional regulator, TetR/AcrR family, putative:hypothetical protein:<-<-:1756790..1757028 239 aacttcctcctaaaaactctgtgacgttttttgattttacagtcatagcttatcatataaactaaaaaatgtcaaaagtcttatatcttctttgtaagaaaatataagactttaaatttacacacatcataattctcttcttttggacctatttatttgagtttcacaatttaaaaaataaggatacagtactgaaagctcctattgtctggcttttctctctgtatccttattgtatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aacttcctcctaaaaactctgtgacgttttttgattttacagtcatagcttatcatataaactaaaaaatgtcaaaagtcttatatcttctttgtaagaaaatataagactttaaatttacacacatcataattctcttcttttggacctatttatttgagtttcacaatttaaaaaataaggatacagtactgaaagctcctattgtctggcttttctctctgtatccttattgtatc Predict ORF larger than 30AA ================================================ Protein_Len: 38 Strand: + Start: 126 End: 239 ............................................................................................................................. M I I L F F W T Y L F E F H N L K N K D T V L K A P I V W L F S L Y P Y C I aacttcctcctaaaaactctgtgacgttttttgattttacagtcatagcttatcatataaactaaaaaatgtcaaaagtcttatatcttctttgtaagaaaatataagactttaaatttacacacatcataattctcttcttttggacctatttatttgagtttcacaatttaaaaaataaggatacagtactgaaagctcctattgtctggcttttctctctgtatccttattgtatc 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: 84 Start: 47 End: 76 ..............................................TTTGACATTTTTTAGTTTATATGATAAGCT................................................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aacttcctcctaaaaactctgtgacgttttttgattttacagtcatagcttatcatataaactaaaaaatgtcaaaagtcttatatcttctttgtaagaaaatataagactttaaatttacacacatcataattctcttcttttggacctatttatttgagtttcacaatttaaaaaataaggatacagtactgaaagctcctattgtctggcttttctctctgtatccttattgtatc Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 89 HP_score: -6.3 Tail_Score: -5.4387 Start: 70 End: 118 Full_Region: attatgatgtgtgta aatttaaagtcttatattttctt aca aagaagatataagacttttgaca ttttttagtttatat .....................................................................aatttaaagtcttatattttcttacaaagaagatataagacttttgaca......................................................................................................................... TransTerm Strand: - Conf: 100 HP_score: -14.5 Tail_Score: -4.33739 Start: 78 End: 110 Full_Region: gtgtgtaaatttaaa gtcttatattttctt aca aagaagatataagac ttttgacatttttta .............................................................................gtcttatattttcttacaaagaagatataagac................................................................................................................................. Find igs database================================================ Query_seq: SSA_1768:SSA_1769|SSA_1768:SSA_1769:Transcriptional regulator, TetR/AcrR family, putative:hypothetical protein:<-<-:1756790..1757028 239 aacttcctcctaaaaactctgtgacgttttttgattttacagtcatagcttatcatataaactaaaaaatgtcaaaagtcttatatcttctttgtaagaaaatataagactttaaatttacacacatcataattctcttcttttggacctatttatttgagtttcacaatttaaaaaataaggatacagtactgaaagctcctattgtctggcttttctctctgtatccttattgtatc Intra-Species Hit: Count: 1 Min: 1 Max: 239 Len: 239 Subject: NC_009009_SSA_1768_SSA_1769|Transcriptional regulator, TetR/AcrR family, putative:hypothetical protein|NEGATIVE:NEGATIVE|[1756790,1757028]|239 HSP 1 e-value: 1.0E-133 bit: 474.0 Len: 239 Query Start:1 Query End:239 Subject Strand: POSITIVE Subject Start: 1 Subject End: 239 aacttcctcctaaaaactctgtgacgttttttgattttacagtcatagcttatcatataaactaaaaaatgtcaaaagtcttatatcttctttgtaagaaaatataagactttaaatttacacacatcataattctcttcttttggacctatttatttgagtttcacaatttaaaaaataaggatacagtactgaaagctcctattgtctggcttttctctctgtatccttattgtatc aacttcctcctaaaaactctgtgacgttttttgattttacagtcatagcttatcatataaactaaaaaatgtcaaaagtcttatatcttctttgtaagaaaatataagactttaaatttacacacatcataattctcttcttttggacctatttatttgagtttcacaatttaaaaaataaggatacagtactgaaagctcctattgtctggcttttctctctgtatccttattgtatc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AACUUCCUCCUAAAAACUCUGUGACGUUUUUUGAUUUUACAGUCAUAGCUUAUCAUAUAAACUAAAAAAUGUCAAAAGUCUUAUAUCUUCUUUGUAAGAAAAUAUAAGACUUUAAAUUUACACACAUCAUAAUUCUCUUCUUUUGGACCUAUUUAUUUGAGUUUCACAAUUUAAAAAAUAAGGAUACAGUACUGAAAGCUCCUAUUGUCUGGCUUUUCUCUCUGUAUCCUUAUUGUAUC .............((((((..((((((((((((.(((.....................))).))))))))))))((((((((((((.((((.....)))).)))))))))))).............................................))))))............(((((((((((((....(((((((..........)))))))....)))))))))))))..... (-51.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAUACAAUAAGGAUACAGAGAGAAAAGCCAGACAAUAGGAGCUUUCAGUACUGUAUCCUUAUUUUUUAAAUUGUGAAACUCAAAUAAAUAGGUCCAAAAGAAGAGAAUUAUGAUGUGUGUAAAUUUAAAGUCUUAUAUUUUCUUACAAAGAAGAUAUAAGACUUUUGACAUUUUUUAGUUUAUAUGAUAAGCUAUGACUGUAAAAUCAAAAAACGUCACAGAGUUUUUAGGAGGAAGUU .....((((((((((((((..((((..((........))...))))..).)))))))))))))((((.......(((((((...........((.....)).........((((((..........(((((((((((((((((.....)))))))))))))))))..(((.((..((((((((...)))))))).)).)))...........))))))..)))))))......)))).. (-54.02) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 802 50 1 141 92 NC_009009:SSA_1768|5end_Transcriptional_regulator,_TetR/AcrR_family,_putative_1756699..1756929_NEGATIVE 268 147 104 113 64 NC_009009:SSA_2352|5end_ABC-type_nitrate/sulfonate/bicarbonate_transporter,_periplasmic_component,_putative_2354508..2354738_NEGATIVE 268 226 187 220 172 NC_009009:SSA_1796|5end_Transcription_elongation_factor_GreA,_putative_1778307..1778537_NEGATIVE 266 230 181 131 72 NC_009009:SSA_0354|5end_Uncharacterized_membrane_protein_346241..346471_POSITIVE 257 224 199 68 40 NC_009009:SSA_0483|5end_Siroheme_synthase,_putative_484045..484275_POSITIVE 252 54 15 219 167 NC_009009:SSA_1617|5end_hypothetical_protein_1620651..1620881_NEGATIVE 252 88 42 131 87 NC_009009:SSA_1349|5end_Transcriptional_regulator,_biotin_repressor_family,_putative_1365918..1366148_POSITIVE 247 227 197 208 177 NC_009009:SSA_1492|5end_hypothetical_protein_1498954..1499184_NEGATIVE 247 230 187 66 31 NC_009009:SSA_1453|5end_hypothetical_protein_1460208..1460438_NEGATIVE 247 218 171 181 127 NC_009009:SSA_0903|5end_NAD(P)H_dehydrogenase_(quinone),_putative_893242..893472_POSITIVE 245 228 182 230 175 NC_009009:SSA_0656|5end_Cell_division_protein_FtsZ,_putative_640159..640389_POSITIVE 244 230 192 54 10 NC_009009:SSA_0299|5end_hypothetical_protein_292759..292989_POSITIVE 242 224 181 164 113 NC_009009:SSA_2322|5end_Transcriptional_regulator,_TetR/AcrR_family,_putative_2327044..2327274_POSITIVE 242 217 192 37 11 NC_009009:SSA_1685|5end_Two-component_response_transcriptional_regulator_(CheY-like_receiver_and_winged-helix_DNA-binding_domains),_putative_1679076..1679306_NEGATIVE 242 225 182 61 16 NC_009009:SSA_0488|5end_Glutamate-1-semialdehyde_2,1-aminotransferase,_putative_488364..488594_POSITIVE 239 224 181 189 146 NC_009009:SSA_2323|5end_Transporter,_putative_2327604..2327834_POSITIVE 238 226 184 127 90 NC_009009:SSA_1795|5end_Guanosine_3',5'-bis-pyrophosphate_(ppGpp)_synthetase,_putative_1777671..1777901_NEGATIVE 237 211 176 161 125 NC_009009:SSA_2063|5end_Aminopeptidase_PepS,_putative_2064857..2065087_NEGATIVE 236 50 1 202 152 NC_009009:SSA_1758|5end_hypothetical_protein_1746619..1746849_NEGATIVE 235 51 16 81 47 NC_009009:SSA_2286|5end_Dihydroxy-acid_dehydratase,_putative_2289596..2289826_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 298 224 181 69 10 NC_009009:SSA_1397|3end_hypothetical_protein_1410995..1411145_POSITIVE 278 230 187 58 11 NC_009009:SSA_0345|3end_hypothetical_protein_339209..339359_POSITIVE 269 230 183 110 68 NC_009009:SSA_0966|3end_Uridine_kinase,_putative_975790..975940_POSITIVE 268 147 104 71 22 NC_009009:SSA_2353|3end_ABC-type_nitrate/sulfonate/bicarbonate_transport_system,_permease_component,_putative_2354550..2354700_NEGATIVE 268 226 187 79 31 NC_009009:SSA_1797|3end_Aminodeoxychorismate_lyase,_putative_1778448..1778598_NEGATIVE 266 230 181 120 61 NC_009009:SSA_0353|3end_Conserved_uncharacterized_protein_346310..346460_POSITIVE 257 224 199 56 28 NC_009009:SSA_0482|3end_ATP:cobalamin_adenosyl_transferase,_putative_484113..484263_POSITIVE 252 54 15 150 98 NC_009009:SSA_1618|3end_hypothetical_protein_1620720..1620870_NEGATIVE 252 88 42 92 48 NC_009009:SSA_1348|3end_hypothetical_protein_1365959..1366109_POSITIVE 247 218 171 105 51 NC_009009:SSA_0901|3end_Alpha-acetolactate_decarboxylase,_putative_893246..893396_POSITIVE 244 223 192 143 106 NC_009009:SSA_1361|3end_ORFA,_transposon_ISSsa2_1377784..1377934_POSITIVE 244 223 192 143 106 NC_009009:SSA_0265|3end_ORFA,_transposon_ISSsa1_260007..260157_POSITIVE 239 224 181 150 107 NC_009009:SSA_2322|3end_Transcriptional_regulator,_TetR/AcrR_family,_putative_2327645..2327795_POSITIVE 237 211 176 139 103 NC_009009:SSA_2064|3end_hypothetical_protein_2064879..2065029_NEGATIVE 230 230 181 127 73 NC_009009:SSA_1249|3end_hypothetical_protein_1273275..1273425_NEGATIVE 230 230 181 85 42 NC_009009:SSA_0212|3end_Phenylalanyl-tRNA_synthetase,_beta_subunit,_putative_209079..209229_POSITIVE 228 230 187 75 34 NC_009009:SSA_0834|3end_Accessory_secretory_protein_Asp2,_putative_821119..821269_POSITIVE 226 229 184 120 77 NC_009009:SSA_0894|3end_ATP-binding_cassette_protein,_putative_886533..886683_POSITIVE 226 229 181 82 38 NC_009009:SSA_0767|3end_Diacylglycerol_kinase_catalytic_domain_protein,_putative_748054..748204_POSITIVE 225 229 181 56 3 NC_009009:SSA_2197|3end_hypothetical_protein_2197314..2197464_NEGATIVE