Origin IGS: ggattgatatcctttgttaattttttcacaagtttattataacgcattatttcaactttgtaaacagtttcataaacatttcacaaagaattttttattgtttgtgaattttttatcattttctttacttatcaagtttttccgttagagtttgtgaaatcaatttcaaatattttttatttcacaagcttgattggaagaggagcttggaaagagatagattttctagtaagcgcttacttttagatgctaacaatacctcctttgataaggaggct .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9 agcctccttatcaaaggaggtattgttagcatctaaaagtaagcgcttactagaaaatctatctctttccaagctcctcttccaatcaagcttgtgaaataaaaaatatttgaaattgatttcacaaactctaacggaaaaacttgataagtaaagaaaatgataaaaaattcacaaacaataaaaaattctttgtgaaatgtttatgaaactgtttacaaagttgaaataatgcgttataataaacttgtgaaaaaattaacaaaggatatcaatcc Mask Tandem Repeat Region ================================================ ggattgatatcctttgttaattttttcacaagtttattataacgcattatttcaactttgtaaacagtttcataaacatttcacaaagaattttttattgtttgtgaattttttatcattttctttacttatcaagtttttccgttagagtttgtgaaatcaatttcaaatattttttatttcacaagcttgattggaagaggagcttggaaagagatagattttctagtaagcgcttacttttagatgctaacaatacctcctttgataaggaggct Find is-nt database================================================ Query_seq: SMT_1097:SMT_1098|SMT_1097:SMT_1098:alcohol dehydrogenase / acetaldehyde dehydrogenase:hypothetical protein:<-<-:1041460..1041737 278 ggattgatatcctttgttaattttttcacaagtttattataacgcattatttcaactttgtaaacagtttcataaacatttcacaaagaattttttattgtttgtgaattttttatcattttctttacttatcaagtttttccgttagagtttgtgaaatcaatttcaaatattttttatttcacaagcttgattggaagaggagcttggaaagagatagattttctagtaagcgcttacttttagatgctaacaatacctcctttgataaggaggct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_1097:SMT_1098|SMT_1097:SMT_1098:alcohol dehydrogenase / acetaldehyde dehydrogenase:hypothetical protein:<-<-:1041460..1041737 278 ggattgatatcctttgttaattttttcacaagtttattataacgcattatttcaactttgtaaacagtttcataaacatttcacaaagaattttttattgtttgtgaattttttatcattttctttacttatcaagtttttccgttagagtttgtgaaatcaatttcaaatattttttatttcacaagcttgattggaagaggagcttggaaagagatagattttctagtaagcgcttacttttagatgctaacaatacctcctttgataaggaggct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_1097:SMT_1098|SMT_1097:SMT_1098:alcohol dehydrogenase / acetaldehyde dehydrogenase:hypothetical protein:<-<-:1041460..1041737 278 ggattgatatcctttgttaattttttcacaagtttattataacgcattatttcaactttgtaaacagtttcataaacatttcacaaagaattttttattgtttgtgaattttttatcattttctttacttatcaagtttttccgttagagtttgtgaaatcaatttcaaatattttttatttcacaagcttgattggaagaggagcttggaaagagatagattttctagtaagcgcttacttttagatgctaacaatacctcctttgataaggaggct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ggattgatatcctttgttaattttttcacaagtttattataacgcattatttcaactttgtaaacagtttcataaacatttcacaaagaattttttattgtttgtgaattttttatcattttctttacttatcaagtttttccgttagagtttgtgaaatcaatttcaaatattttttatttcacaagcttgattggaagaggagcttggaaagagatagattttctagtaagcgcttacttttagatgctaacaatacctcctttgataaggaggct Predict ORF larger than 30AA ================================================ Protein_Len: 44 Strand: + Start: 14 End: 145 ............. M L I F S Q V Y Y N A L F Q L C K Q F H K H F T K N F L L F V N F L S F S L L I K F F R ..................................................................................................................................... Protein_Len: 49 Strand: + Start: 97 End: 243 ................................................................................................ M V C E F F I I F F T Y Q V F P L E F V K S I S N I F Y F T S L I G R G A W K E I D F L V S A Y F ................................... Protein_Len: 57 Strand: + Start: 108 End: 278 ........................................................................................................... M F Y H F L Y L S S F S V R V C E I N F K Y F L F H K L D W K R S L E R D R F S S K R L L L D A N N T S F D K E A ggattgatatcctttgttaattttttcacaagtttattataacgcattatttcaactttgtaaacagtttcataaacatttcacaaagaattttttattgtttgtgaattttttatcattttctttacttatcaagtttttccgttagagtttgtgaaatcaatttcaaatattttttatttcacaagcttgattggaagaggagcttggaaagagatagattttctagtaagcgcttacttttagatgctaacaatacctcctttgataaggaggct 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: 89 Start: 36 End: 65 ...................................GTTTACAAAGTTGAAATAATGCGTTATAAT..................................................................................................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ggattgatatcctttgttaattttttcacaagtttattataacgcattatttcaactttgtaaacagtttcataaacatttcacaaagaattttttattgtttgtgaattttttatcattttctttacttatcaagtttttccgttagagtttgtgaaatcaatttcaaatattttttatttcacaagcttgattggaagaggagcttggaaagagatagattttctagtaagcgcttacttttagatgctaacaatacctcctttgataaggaggct Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 46 HP_score: -2.7 Tail_Score: -3.53174 Start: 79 End: 109 Full_Region: agaaaatgataaaaa attcacaaacaat aaaaa attctttgtgaaa tgtttatgaaactgt ..............................................................................attcacaaacaataaaaaattctttgtgaaa......................................................................................................................................................................... TransTerm Strand: + Conf: 100 HP_score: -6.2 Tail_Score: -5.4588 Start: 80 End: 108 Full_Region: CAGTTTCATAAACAT TTCACAAAGAAT TTTTT ATTGTTTGTGAA TTTTTTATCATTTTC ...............................................................................TTCACAAAGAATTTTTTATTGTTTGTGAA.......................................................................................................................................................................... TransTerm Strand: - Conf: 58 HP_score: -6.2 Tail_Score: -2.71422 Start: 80 End: 108 Full_Region: gaaaatgataaaaaa ttcacaaacaat aaaaa attctttgtgaa atgtttatgaaactg ...............................................................................ttcacaaacaataaaaaattctttgtgaa.......................................................................................................................................................................... Find igs database================================================ Query_seq: SMT_1097:SMT_1098|SMT_1097:SMT_1098:alcohol dehydrogenase / acetaldehyde dehydrogenase:hypothetical protein:<-<-:1041460..1041737 278 ggattgatatcctttgttaattttttcacaagtttattataacgcattatttcaactttgtaaacagtttcataaacatttcacaaagaattttttattgtttgtgaattttttatcattttctttacttatcaagtttttccgttagagtttgtgaaatcaatttcaaatattttttatttcacaagcttgattggaagaggagcttggaaagagatagattttctagtaagcgcttacttttagatgctaacaatacctcctttgataaggaggct Intra-Species Hit: Count: 1 Min: 1 Max: 278 Len: 278 Subject: smit_SMT_1097_SMT_1098|alcohol dehydrogenase / acetaldehyde dehydrogenase:hypothetical protein|NEGATIVE:NEGATIVE|[1041460,1041737]|278 HSP 1 e-value: 6.0E-72 bit: 272.0 Len: 137 Query Start:142 Query End:278 Subject Strand: POSITIVE Subject Start: 142 Subject End: 278 .............................................................................................................................................ccgttagagtttgtgaaatcaatttcaaatattttttatttcacaagcttgattggaagaggagcttggaaagagatagattttctagtaagcgcttacttttagatgctaacaatacctcctttgataaggaggct .............................................................................................................................................ccgttagagtttgtgaaatcaatttcaaatattttttatttcacaagcttgattggaagaggagcttggaaagagatagattttctagtaagcgcttacttttagatgctaacaatacctcctttgataaggaggct HSP 2 e-value: 3.0E-43 bit: 176.0 Len: 89 Query Start:1 Query End:89 Subject Strand: POSITIVE Subject Start: 1 Subject End: 89 ggattgatatcctttgttaattttttcacaagtttattataacgcattatttcaactttgtaaacagtttcataaacatttcacaaaga............................................................................................................................................................................................. ggattgatatcctttgttaattttttcacaagtttattataacgcattatttcaactttgtaaacagtttcataaacatttcacaaaga............................................................................................................................................................................................. Inter-species Hit: Count: 2 Min: 6 Max: 278 Len: 273 Subject: NC_003098_spr1837_spr1838|Alcohol-acetaldehyde dehydrogenase:hypothetical protein|NEGATIVE:NEGATIVE|[1814370,1814647]|278 HSP 1 e-value: 3.0E-40 bit: 167.0 Len: 84 Query Start:6 Query End:89 Subject Strand: POSITIVE Subject Start: 6 Subject End: 89 .....gatatcctttgttaattttttcacaagtttattataacgcattatttcaactttgtaaacagtttcataaacatttcacaaaga............................................................................................................................................................................................. .....gatatcctttgttaattttttcacaagtttattataacgcattatttcaactttgtaaacagtttcataaacatttcacaaaga............................................................................................................................................................................................. HSP 2 e-value: 2.0E-22 bit: 107.0 Len: 130 Query Start:149 Query End:278 Subject Strand: POSITIVE Subject Start: 149 Subject End: 278 ....................................................................................................................................................agtttgtgaaatcaatttcaaatattttttatttcacaagcttgattggaagaggagcttggaaagagatagattttctagtaagcgcttacttttagatgctaacaatacctcctttgataaggaggct ....................................................................................................................................................agtttgtgaaatttatttcaaatattttttatttcacaaacttgcttggaagagggatttggaaagaaagggatttacaggtaagcgcttaccttgtaattctaataatacctcctttgataaggaggct Subject: NC_003028_SP_2026_SP_2027|alcohol dehydrogenase, iron-containing:hypothetical protein|NEGATIVE:NEGATIVE|[1933427,1933725]|299 HSP 1 e-value: 3.0E-40 bit: 167.0 Len: 84 Query Start:6 Query End:89 Subject Strand: POSITIVE Subject Start: 27 Subject End: 110 .....gatatcctttgttaattttttcacaagtttattataacgcattatttcaactttgtaaacagtttcataaacatttcacaaaga............................................................................................................................................................................................. .....gatatcctttgttaattttttcacaagtttattataacgcattatttcaactttgtaaacagtttcataaacatttcacaaaga............................................................................................................................................................................................. HSP 2 e-value: 8.0E-25 bit: 115.0 Len: 130 Query Start:149 Query End:278 Subject Strand: POSITIVE Subject Start: 170 Subject End: 299 ....................................................................................................................................................agtttgtgaaatcaatttcaaatattttttatttcacaagcttgattggaagaggagcttggaaagagatagattttctagtaagcgcttacttttagatgctaacaatacctcctttgataaggaggct ....................................................................................................................................................agtttgtgaaatttatttcaaatattttttatttcacaaacttgcttggaagagggatttggaaagaaagggatttgcaggtaagcgcttaccttgcgattctaataatacctcctttgataaggaggct Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAUAUCCUUUGUUAAUUUUUUCACAAGUUUAUUAUAACGCAUUAUUUCAACUUUGUAAACAGUUUCAUAAACAUUUCACAAAGAAUUUUUUAUUGUUUGUGAAUUUUUUAUCAUUUUCUUUACUUAUCAAGUUUUUCCGUUAGAGUUUGUGAAAUCAAUUUCAAAUAUUUUUUAUUUCACAAGCUUGAUUGGAAGAGGAGCUUGGAAAGAGAUAGAUUUUCUAGUAAGCGCUUACUUUUAGAUGCUAACAAUACCUCCUUUGAUAAGGAGGCU ........((((((.(((((((.(((((((........................(((((.((..(.(((((...((((((((.(((.....))).))))))))...))))).)..)).))))).........(((((((...(((((((((((((.((............)).)))))))))))))...))))))).))))))))))))))....((((...(((((....)))))...))))..))))))..(((((((....))))))).. (-64.20) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGCCUCCUUAUCAAAGGAGGUAUUGUUAGCAUCUAAAAGUAAGCGCUUACUAGAAAAUCUAUCUCUUUCCAAGCUCCUCUUCCAAUCAAGCUUGUGAAAUAAAAAAUAUUUGAAAUUGAUUUCACAAACUCUAACGGAAAAACUUGAUAAGUAAAGAAAAUGAUAAAAAAUUCACAAACAAUAAAAAAUUCUUUGUGAAAUGUUUAUGAAACUGUUUACAAAGUUGAAAUAAUGCGUUAUAAUAAACUUGUGAAAAAAUUAACAAAGGAUAUC .((((((((....)))))))).(((((((.........((((((...............((((..((((...(((..((((((.....((.(((((((((....(((.......))).))))))))).)).....))))......))..)))...))))..)))).....((((((((.(((.....))).))))))))..)))))).......(((((((.(((...((((....))))....))))))))))....)))))))........ (-50.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 687 70 21 166 117 smit:SMT_1097|5end_alcohol_dehydrogenase_/_acetaldehyde_dehydrogenase_1041369..1041599_NEGATIVE 308 222 184 99 46 smit:SMT_107|5end_ribose-phosphate_pyrophosphokinase_52402..52632_POSITIVE 283 229 183 193 153 smit:SMT_1397|5end_mutator_MutT_protein_1372727..1372957_POSITIVE 281 269 227 228 178 smit:SMT_1673|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1659831..1660061_POSITIVE 267 268 223 175 127 smit:SMT_954|5end_cation-transporting_ATPase,_E1-E2_family_904025..904255_NEGATIVE 265 269 227 81 40 smit:SMT_1622|5end_K03499_trk_system_potassium_uptake_protein_TrkA_1608243..1608473_POSITIVE 260 269 221 115 50 smit:SMT_1350|5end_multidrug_resistance_efflux_pump_1329225..1329455_NEGATIVE 256 138 92 100 55 smit:SMT_747|5end_transcriptional_regulator,_LytR_family_652653..652883_NEGATIVE 256 212 179 127 98 smit:SMT_146|5end_sugar_transport_system_permease_protein_96664..96894_POSITIVE 248 269 221 63 3 smit:SMT_2018|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1936760..1936990_POSITIVE 248 247 201 56 5 smit:SMT_154|5end_K03647_protein_involved_in_ribonucleotide_reduction_101930..102160_POSITIVE 244 210 166 80 31 smit:SMT_112|5end_hypothetical_protein_predicted_by_Glimmer/Critica_61473..61703_NEGATIVE 242 140 94 119 65 smit:SMT_1109|5end_hypothetical_protein_1050315..1050545_NEGATIVE 240 158 131 87 55 smit:SMT_1973|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1905438..1905668_NEGATIVE 238 216 171 65 23 smit:SMT_1242|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1203383..1203613_NEGATIVE 235 260 227 208 166 smit:SMT_1292|5end_K02050_sulfonate/nitrate/taurine_transport_system_permease_protein_1254179..1254409_POSITIVE 232 138 93 114 64 smit:SMT_1070|5end_hypothetical_protein_1009946..1010176_NEGATIVE 231 230 183 79 27 smit:SMT_1358|5end_dihydroorotate_dehydrogenase_B_1337192..1337422_NEGATIVE 229 225 181 96 56 smit:SMT_1430|5end_hypothetical_protein_1414857..1415087_POSITIVE 229 226 183 60 22 smit:SMT_691|5end_endonuclease_III_603008..603238_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 295 227 182 51 5 smit:SMT_668|3end_hypothetical_protein_predicted_by_Glimmer/Critica_578057..578207_NEGATIVE 280 157 111 149 95 smit:SMT_168|3end_anaerobic_ribonucleoside-triphosphate_reductase_activating_protein_114340..114490_POSITIVE 260 269 221 128 63 smit:SMT_1351|3end_dephospho-CoA_kinase_1329212..1329362_NEGATIVE 256 138 92 103 58 smit:SMT_748|3end_prephenate_dehydratase_652650..652800_NEGATIVE 253 229 181 84 34 smit:SMT_455|3end_cation_transport_ATPase_393993..394143_POSITIVE 242 140 94 58 4 smit:SMT_1110|3end_hypothetical_protein_1050376..1050526_NEGATIVE 241 247 201 40 6 smit:SMT_1866|3end_extramembranal_protein_1827939..1828089_POSITIVE 232 239 192 127 82 smit:SMT_1090|3end_K07485_transposase_1026425..1026575_POSITIVE 231 230 183 68 16 smit:SMT_1359|3end_dihydroorotate_dehydrogenase_electron_transfer_subunit_1337203..1337353_NEGATIVE 229 225 181 95 55 smit:SMT_1429|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1414936..1415086_POSITIVE 229 226 183 60 22 smit:SMT_692|3end_hypothetical_protein_603008..603158_NEGATIVE 227 230 193 151 103 smit:SMT_1775|3end_K07478_putative_ATPase_1751315..1751465_NEGATIVE 226 230 183 63 7 smit:SMT_1871|3end_modification_methylase,_HemK_family_1829803..1829953_NEGATIVE 226 270 221 58 1 smit:SMT_1573|3end_MutT/NUDIX_family_protein_1566960..1567110_POSITIVE 226 270 224 132 78 smit:SMT_125|3end_hypothetical_protein_76717..76867_NEGATIVE 225 201 166 136 105 smit:SMT_1265|3end_hypothetical_protein_1230872..1231022_NEGATIVE 222 209 166 145 85 smit:SMT_2168|3end_threonyl-tRNA_synthetase_2041262..2041412_POSITIVE 222 209 166 145 85 smit:SMT_2150|3end_threonyl-tRNA_synthetase_2024905..2025055_POSITIVE 222 209 166 145 85 smit:SMT_2146|3end_threonyl-tRNA_synthetase_2022280..2022430_POSITIVE 222 225 188 95 57 smit:SMT_1581|3end_transcriptional_regulator,_biotin_repressor_family_1573120..1573270_NEGATIVE