Origin IGS: aagtcaggaaattcctgatttttctttttcattaaagaagtgataggagtagaattaccgtttagattagcagattaagaataattcacaaaaactttgtaaaacacttgcaatttagctgaaatttgataaaatagtaaggaaagttagactgtattgcctactgtctatctataaaatatattttattggaggcttttactcaa .........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 ttgagtaaaagcctccaataaaatatattttatagatagacagtaggcaatacagtctaactttccttactattttatcaaatttcagctaaattgcaagtgttttacaaagtttttgtgaattattcttaatctgctaatctaaacggtaattctactcctatcacttctttaatgaaaaagaaaaatcaggaatttcctgactt Mask Tandem Repeat Region ================================================ aagtcaggaaattcctgatttttctttttcattaaagaagtgataggagtagaattaccgtttagattagcagattaagaataattcacaaaaactttgtaaaacacttgcaatttagctgaaatttgataaaatagtaaggaaagttagactgtattgcctactgtctatctataaaatatattttattggaggcttttactcaa Find is-nt database================================================ Query_seq: SMT_560:SMT_561|SMT_560:SMT_561:predicted permease:putative translation elongation factor EF-Tu:->->:479345..479550 206 aagtcaggaaattcctgatttttctttttcattaaagaagtgataggagtagaattaccgtttagattagcagattaagaataattcacaaaaactttgtaaaacacttgcaatttagctgaaatttgataaaatagtaaggaaagttagactgtattgcctactgtctatctataaaatatattttattggaggcttttactcaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_560:SMT_561|SMT_560:SMT_561:predicted permease:putative translation elongation factor EF-Tu:->->:479345..479550 206 aagtcaggaaattcctgatttttctttttcattaaagaagtgataggagtagaattaccgtttagattagcagattaagaataattcacaaaaactttgtaaaacacttgcaatttagctgaaatttgataaaatagtaaggaaagttagactgtattgcctactgtctatctataaaatatattttattggaggcttttactcaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_560:SMT_561|SMT_560:SMT_561:predicted permease:putative translation elongation factor EF-Tu:->->:479345..479550 206 aagtcaggaaattcctgatttttctttttcattaaagaagtgataggagtagaattaccgtttagattagcagattaagaataattcacaaaaactttgtaaaacacttgcaatttagctgaaatttgataaaatagtaaggaaagttagactgtattgcctactgtctatctataaaatatattttattggaggcttttactcaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aagtcaggaaattcctgatttttctttttcattaaagaagtgataggagtagaattaccgtttagattagcagattaagaataattcacaaaaactttgtaaaacacttgcaatttagctgaaatttgataaaatagtaaggaaagttagactgtattgcctactgtctatctataaaatatattttattggaggcttttactcaa Predict ORF larger than 30AA ================================================ aagtcaggaaattcctgatttttctttttcattaaagaagtgataggagtagaattaccgtttagattagcagattaagaataattcacaaaaactttgtaaaacacttgcaatttagctgaaatttgataaaatagtaaggaaagttagactgtattgcctactgtctatctataaaatatattttattggaggcttttactcaa 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: 81 Start: 156 End: 185 ...........................................................................................................................................................ATTGCCTACTGTCTATCTATAAAATATATT..................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aagtcaggaaattcctgatttttctttttcattaaagaagtgataggagtagaattaccgtttagattagcagattaagaataattcacaaaaactttgtaaaacacttgcaatttagctgaaatttgataaaatagtaaggaaagttagactgtattgcctactgtctatctataaaatatattttattggaggcttttactcaa Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 55 HP_score: -3.7 Tail_Score: -4.02979 Start: 146 End: 172 Full_Region: aaaatatattttata gatagacagta ggcaa tacagtctaac tttccttactatttt .................................................................................................................................................gatagacagtaggcaatacagtctaac.................................. TransTerm Strand: + Conf: 51 HP_score: -4.9 Tail_Score: -2.91507 Start: 148 End: 170 Full_Region: AATAGTAAGGAAAGT TAGACTGTA TTGCC TACTGTCTA TCTATAAAATATATT ...................................................................................................................................................TAGACTGTATTGCCTACTGTCTA.................................... TransTerm Strand: + Conf: 44 HP_score: -3.1 Tail_Score: -3.00498 Start: 150 End: 168 Full_Region: TAGTAAGGAAAGTTA GACTGTA TTGCC TACTGTC TATCTATAAAATATA .....................................................................................................................................................GACTGTATTGCCTACTGTC...................................... Find igs database================================================ Query_seq: SMT_560:SMT_561|SMT_560:SMT_561:predicted permease:putative translation elongation factor EF-Tu:->->:479345..479550 206 aagtcaggaaattcctgatttttctttttcattaaagaagtgataggagtagaattaccgtttagattagcagattaagaataattcacaaaaactttgtaaaacacttgcaatttagctgaaatttgataaaatagtaaggaaagttagactgtattgcctactgtctatctataaaatatattttattggaggcttttactcaa Intra-Species Hit: Count: 1 Min: 1 Max: 206 Len: 206 Subject: smit_SMT_560_SMT_561|predicted permease:putative translation elongation factor EF-Tu|POSITIVE:POSITIVE|[479345,479550]|206 HSP 1 e-value: 1.0E-113 bit: 408.0 Len: 206 Query Start:1 Query End:206 Subject Strand: POSITIVE Subject Start: 1 Subject End: 206 aagtcaggaaattcctgatttttctttttcattaaagaagtgataggagtagaattaccgtttagattagcagattaagaataattcacaaaaactttgtaaaacacttgcaatttagctgaaatttgataaaatagtaaggaaagttagactgtattgcctactgtctatctataaaatatattttattggaggcttttactcaa aagtcaggaaattcctgatttttctttttcattaaagaagtgataggagtagaattaccgtttagattagcagattaagaataattcacaaaaactttgtaaaacacttgcaatttagctgaaatttgataaaatagtaaggaaagttagactgtattgcctactgtctatctataaaatatattttattggaggcttttactcaa Inter-species Hit: Count: 4 Min: 77 Max: 206 Len: 130 Subject: NC_008533_SPD_1318_SPD_1319|translation elongation factor Tu:hypothetical protein|NEGATIVE:NEGATIVE|[1335692,1336033]|342 HSP 1 e-value: 2.0E-65 bit: 250.0 Len: 130 Query Start:77 Query End:206 Subject Strand: NEGATIVE Subject Start: 1 Subject End: 130 ............................................................................aagaataattcacaaaaactttgtaaaacacttgcaatttagctgaaatttgataaaatagtaaggaaagttagactgtattgcctactgtctatctataaaatatattttattggaggcttttactcaa ............................................................................aagaataattcacaaaaacgttgtaaaacacttgcaatttagctgaaatttgataaaatagtaaggaaagttagactgtattgcctactgtctatctataaaatatattttattggaggcttttactcaa Subject: NC_003098_spr1343_spr1344|elongation factor Tu:Glycerol uptake facilitator protein paralog|NEGATIVE:NEGATIVE|[1328161,1329081]|921 HSP 1 e-value: 2.0E-65 bit: 250.0 Len: 130 Query Start:77 Query End:206 Subject Strand: NEGATIVE Subject Start: 1 Subject End: 130 ............................................................................aagaataattcacaaaaactttgtaaaacacttgcaatttagctgaaatttgataaaatagtaaggaaagttagactgtattgcctactgtctatctataaaatatattttattggaggcttttactcaa ............................................................................aagaataattcacaaaaacgttgtaaaacacttgcaatttagctgaaatttgataaaatagtaaggaaagttagactgtattgcctactgtctatctataaaatatattttattggaggcttttactcaa Subject: NC_003028_SP_1489_SP_1490|elongation factor Tu:hypothetical protein|NEGATIVE:NEGATIVE|[1400533,1400738]|206 HSP 1 e-value: 2.0E-65 bit: 250.0 Len: 130 Query Start:77 Query End:206 Subject Strand: NEGATIVE Subject Start: 1 Subject End: 130 ............................................................................aagaataattcacaaaaactttgtaaaacacttgcaatttagctgaaatttgataaaatagtaaggaaagttagactgtattgcctactgtctatctataaaatatattttattggaggcttttactcaa ............................................................................aagaataattcacaaaaacgttgtaaaacacttgcaatttagctgaaatttgataaaatagtaaggaaagttagactgtattgcctactgtctatctataaaatatattttattggaggcttttactcaa Subject: NC_009009_SSA_1520_SSA_1521|Elongation factor Tu, putative:Phosphoenolpyruvate carboxylase, putative|NEGATIVE:NEGATIVE|[1527672,1527926]|255 HSP 1 e-value: 7.0E-43 bit: 174.0 Len: 128 Query Start:79 Query End:206 Subject Strand: NEGATIVE Subject Start: 1 Subject End: 128 ..............................................................................gaataattcacaaaaactttgtaaaacacttgcaatttagctgaaatttgataaaatagtaaggaaagttagactgtattgcctactgtctatctataaaatatattttattggaggcttttactcaa ..............................................................................gaataattcacaaaaaaatgctaaaagacttgcattttcatttaaatttgataaaatagtaaggaaagttagactgtattgcctactgtctatctataaaatatattttattggaggcttttactcaa Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAGAAUAAUUCACAAAAACUUUGUAAAACACUUGCAAUUUAGCUGAAAUUUGAUAAAAUAGUAAGGAAAGUUAGACUGUAUUGCCUACUGUCUAUCUAUAAAAUAUAUUUUAUUGGAGGCUUUUACUCAA ..((.(((............((((((.....))))))...((((....((..((((((((........((.(((((.(((.....))).))))).))........))))))))..)))))).))).)).. (-21.09) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUGAGUAAAAGCCUCCAAUAAAAUAUAUUUUAUAGAUAGACAGUAGGCAAUACAGUCUAACUUUCCUUACUAUUUUAUCAAAUUUCAGCUAAAUUGCAAGUGUUUUACAAAGUUUUUGUGAAUUAUUCUU ..((((((.........((((((((........((.(((((.(((.....))).))))).))........)))))))).........((......))......(((((((.....))))))))))))).. (-18.39) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 224 121 86 118 83 smit:SMT_585|5end_ATP_synthase_gamma_chain_501569..501799_POSITIVE 217 97 63 177 136 smit:SMT_643|5end_hypothetical_protein_548495..548725_NEGATIVE 210 95 58 97 62 smit:SMT_1529|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1512880..1513110_NEGATIVE 209 103 63 72 29 smit:SMT_1704|5end_D-alanine-D-alanine_ligase_1687431..1687661_POSITIVE 201 120 75 70 21 smit:SMT_1193|5end_phosphoribosylglycinamide_formyltransferase_1152152..1152382_NEGATIVE 196 76 34 145 104 smit:SMT_703|5end_hypothetical_protein_612345..612575_POSITIVE 195 127 81 205 165 smit:SMT_574|5end_PTS_system,_fructose_specific_IIABC_components_491884..492114_POSITIVE 193 93 54 148 106 smit:SMT_1307|5end_glycerol_uptake_facilitator_protein_1271664..1271894_POSITIVE 193 98 63 146 100 smit:SMT_1291|5end_hypothetical_protein_1253875..1254105_POSITIVE 193 98 54 197 150 smit:SMT_991|5end_hypothetical_protein_934425..934655_NEGATIVE 192 129 84 53 5 smit:SMT_2066|5end_K02074_zinc/manganese_transport_system_ATP-binding_protein_1973105..1973335_POSITIVE 192 129 84 53 5 smit:SMT_1321|5end_K02074_zinc/manganese_transport_system_ATP-binding_protein_1290674..1290904_POSITIVE 186 112 71 160 114 smit:SMT_1758|5end_hypothetical_protein_1735601..1735831_NEGATIVE 186 62 28 161 125 smit:SMT_403|5end_two-component_sensor_kinase_YesM_331580..331810_POSITIVE 184 67 31 197 149 smit:SMT_709|5end_hypothetical_protein_618919..619149_NEGATIVE 184 85 42 194 154 smit:SMT_590|5end_tetratricopeptide_repeat_family_protein_506737..506967_POSITIVE 184 105 67 68 35 smit:SMT_288|5end_hypothetical_protein_231184..231414_POSITIVE 184 77 52 70 50 smit:SMT_156|5end_hypothetical_protein_102869..103099_POSITIVE 183 97 60 51 7 smit:SMT_1959|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1892585..1892815_POSITIVE 183 130 85 133 73 smit:SMT_806|5end_hypothetical_protein_716166..716396_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 264 119 71 58 8 smit:SMT_484|3end_hypothetical_protein_419659..419809_NEGATIVE 224 121 86 102 67 smit:SMT_584|3end_ATP_synthase_alpha_chain_501633..501783_POSITIVE 218 89 41 105 56 smit:SMT_398|3end_hypothetical_protein_328279..328429_POSITIVE 217 97 63 81 40 smit:SMT_644|3end_O-acetylhomoserine_(thiol)-lyase_548591..548741_NEGATIVE 210 124 83 80 40 smit:SMT_605|3end_DNA-binding_protein_HU_519257..519407_POSITIVE 201 120 75 73 24 smit:SMT_1194|3end_phosphoribosylformylglycinamidine_cyclo-ligase_1152149..1152299_NEGATIVE 198 55 12 78 29 smit:SMT_1226|3end_ribosomal_protein_S9_1189209..1189359_POSITIVE 193 93 54 77 35 smit:SMT_1306|3end_alpha-glycerophosphate_oxidase_1271673..1271823_POSITIVE 193 98 54 93 46 smit:SMT_992|3end_hypothetical_protein_934529..934679_NEGATIVE 192 129 84 53 5 smit:SMT_2065|3end_transcriptional_regulator,_MarR_family_1973185..1973335_POSITIVE 192 129 84 53 5 smit:SMT_1320|3end_transcriptional_regulator,_MarR_family_1290754..1290904_POSITIVE 188 98 64 83 44 smit:SMT_651|3end_DNA_ligase_559986..560136_NEGATIVE 188 87 48 93 53 smit:SMT_163|3end_cardiolipin_synthetase_108936..109086_POSITIVE 186 112 71 83 37 smit:SMT_1759|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1735678..1735828_NEGATIVE 184 105 67 84 51 smit:SMT_1960|3end_UDP-galactopyranose_mutase_1894094..1894244_POSITIVE 184 105 67 78 45 smit:SMT_287|3end_UDP-galactopyranose_mutase_231274..231424_POSITIVE 179 97 69 127 102 smit:SMT_1898|3end_aminotransferase_(class_V),_putative_1848877..1849027_NEGATIVE 177 66 21 47 4 smit:SMT_1095|3end_ribosomal_large_subunit_pseudouridine_synthase,_RluD_subfamily_1037328..1037478_POSITIVE 177 119 80 121 83 smit:SMT_879|3end_hypothetical_protein_826288..826438_NEGATIVE 177 43 1 80 35 smit:SMT_562|3end_ATP-dependent_RNA_helicase,_DEAD/DEAH_box_family_480809..480959_NEGATIVE