Origin IGS: taaggaatgatgctcggtcaatcatattccgtgccatagtaaatccgcataaaagcattacaagcggtttgtacatatgcccgatatgttatatatttgcagtgaatcatccgtaacatatcaaggaaataaacaaataac .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gttatttgtttatttccttgatatgttacggatgattcactgcaaatatataacatatcgggcatatgtacaaaccgcttgtaatgcttttatgcggatttactatggcacggaatatgattgaccgagcatcattcctta Mask Tandem Repeat Region ================================================ taaggaatgatgctcggtcaatcatattccgtgccatagtaaatccgcataaaagcattacaagcggtttgtacatatgcccgatatgttatatatttgcagtgaatcatccgtaacatatcaaggaaataaacaaataac Find is-nt database================================================ Query_seq: TF0671:TF0672|TF0671:TF0672:histidine kinase sensor protein:RNA polymerase sigma-70 factor, ECF subfamily:->->:716404..716544 141 taaggaatgatgctcggtcaatcatattccgtgccatagtaaatccgcataaaagcattacaagcggtttgtacatatgcccgatatgttatatatttgcagtgaatcatccgtaacatatcaaggaaataaacaaataac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF0671:TF0672|TF0671:TF0672:histidine kinase sensor protein:RNA polymerase sigma-70 factor, ECF subfamily:->->:716404..716544 141 taaggaatgatgctcggtcaatcatattccgtgccatagtaaatccgcataaaagcattacaagcggtttgtacatatgcccgatatgttatatatttgcagtgaatcatccgtaacatatcaaggaaataaacaaataac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF0671:TF0672|TF0671:TF0672:histidine kinase sensor protein:RNA polymerase sigma-70 factor, ECF subfamily:->->:716404..716544 141 taaggaatgatgctcggtcaatcatattccgtgccatagtaaatccgcataaaagcattacaagcggtttgtacatatgcccgatatgttatatatttgcagtgaatcatccgtaacatatcaaggaaataaacaaataac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taaggaatgatgctcggtcaatcatattccgtgccatagtaaatccgcataaaagcattacaagcggtttgtacatatgcccgatatgttatatatttgcagtgaatcatccgtaacatatcaaggaaataaacaaataac Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: + Start: 21 End: 113 .................... M I F R A I V N P H K S I T S G L Y I C P I C Y I F A V N H P ............................ Protein_Len: 33 Strand: - Start: 21 End: 119 .................... D Y E T G Y Y I R M F A N C A T Q V Y A R Y T I Y K C H I M R L M ...................... taaggaatgatgctcggtcaatcatattccgtgccatagtaaatccgcataaaagcattacaagcggtttgtacatatgcccgatatgttatatatttgcagtgaatcatccgtaacatatcaaggaaataaacaaataac Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ PromScan Matrix: RpoN Strand: - Score: 81 Start: 21 End: 37 ....................ATGGCACGGAATATGAT........................................................................................................ taaggaatgatgctcggtcaatcatattccgtgccatagtaaatccgcataaaagcattacaagcggtttgtacatatgcccgatatgttatatatttgcagtgaatcatccgtaacatatcaaggaaataaacaaataac Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 41 HP_score: -2.9 Tail_Score: -2.50077 Start: 59 End: 73 Full_Region: catatcgggcatatg tacaa accgc ttgta atgcttttatgcgga ..........................................................tacaaaccgcttgta.................................................................... TransTerm Strand: + Conf: 51 HP_score: -2.9 Tail_Score: -3.76634 Start: 74 End: 88 Full_Region: TACAAGCGGTTTGTA CATAT GCCCG ATATG TTATATATTTGCAGT .........................................................................CATATGCCCGATATG..................................................... Find igs database================================================ Query_seq: TF0671:TF0672|TF0671:TF0672:histidine kinase sensor protein:RNA polymerase sigma-70 factor, ECF subfamily:->->:716404..716544 141 taaggaatgatgctcggtcaatcatattccgtgccatagtaaatccgcataaaagcattacaagcggtttgtacatatgcccgatatgttatatatttgcagtgaatcatccgtaacatatcaaggaaataaacaaataac Intra-Species Hit: Count: 1 Min: 1 Max: 141 Len: 141 Subject: tfor_TF0671_TF0672|histidine kinase sensor protein:RNA polymerase sigma-70 factor, ECF subfamily|POSITIVE:POSITIVE|[716404,716544]|141 HSP 1 e-value: 1.0E-74 bit: 280.0 Len: 141 Query Start:1 Query End:141 Subject Strand: POSITIVE Subject Start: 1 Subject End: 141 taaggaatgatgctcggtcaatcatattccgtgccatagtaaatccgcataaaagcattacaagcggtttgtacatatgcccgatatgttatatatttgcagtgaatcatccgtaacatatcaaggaaataaacaaataac taaggaatgatgctcggtcaatcatattccgtgccatagtaaatccgcataaaagcattacaagcggtttgtacatatgcccgatatgttatatatttgcagtgaatcatccgtaacatatcaaggaaataaacaaataac Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAGGAAUGAUGCUCGGUCAAUCAUAUUCCGUGCCAUAGUAAAUCCGCAUAAAAGCAUUACAAGCGGUUUGUACAUAUGCCCGAUAUGUUAUAUAUUUGCAGUGAAUCAUCCGUAACAUAUCAAGGAAAUAAACAAAUAAC ....((.((((.....)))).))...((((....(((((((...((((...............))))....))).))))...((((((((((..((((.....)))).....))))))))))..))))............. (-25.66) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUUAUUUGUUUAUUUCCUUGAUAUGUUACGGAUGAUUCACUGCAAAUAUAUAACAUAUCGGGCAUAUGUACAAACCGCUUGUAAUGCUUUUAUGCGGAUUUACUAUGGCACGGAAUAUGAUUGACCGAGCAUCAUUCCUUA ....(((((.(((...(((((((((((((((........)))........))))))))))))...))).)))))..(((.(((((((......)))...))))...)))..((((((((.((....)).))).)))))... (-27.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 356 90 43 70 18 tfor:TF1258|5end_hypothetical_protein_1338321..1338551_POSITIVE 306 89 42 103 54 tfor:TF0604|5end_hypothetical_protein_635385..635615_POSITIVE 301 48 10 143 109 tfor:TF1720|5end_conserved_hypothetical_protein_1843679..1843909_POSITIVE 295 70 27 65 25 tfor:TF2449|5end_undecaprenyl_diphosphate_synthase_2625718..2625948_POSITIVE 295 48 1 226 174 tfor:TF0251|5end_conserved_hypothetical_protein;_possible_exporter_279955..280185_POSITIVE 281 48 8 66 24 tfor:TF2833|5end_lipid_A_disaccharide_synthase_3023973..3024203_POSITIVE 280 48 4 200 160 tfor:TF0984|5end_possible_mucin-desulfating_sulfatase_(MdsC_protein)_1040259..1040489_POSITIVE 276 88 55 119 81 tfor:TF1253|5end_hypothetical_protein_1335982..1336212_POSITIVE 273 80 31 150 96 tfor:TF1721|5end_2,3-bisphosphoglycerate-independent_phosphoglycerate_mutase_1844374..1844604_POSITIVE 271 109 61 72 26 tfor:TF1160|5end_MutT/nudix_family_protein_1240305..1240535_POSITIVE 267 56 15 51 14 tfor:TF2297|5end_hypothetical_protein_2449234..2449464_POSITIVE 267 49 4 70 27 tfor:TF0861|5end_HAD-superfamily_hydrolase,_subfamily_IA,_variant_1_family_protein_913377..913607_POSITIVE 265 66 22 107 58 tfor:TF0826|5end_primosomal_protein_N'_883751..883981_POSITIVE 262 57 12 45 1 tfor:TF0610|5end_conserved_hypothetical_protein;_possible_phosphatidylglycerophosphate_synthase_643460..643690_POSITIVE 261 87 43 87 41 tfor:TF2831|5end_ABC_transporter,_permease_component_3021317..3021547_POSITIVE 261 49 7 53 10 tfor:TF0228|5end_probable_integral_outer_membrane_protein_253851..254081_POSITIVE 260 48 3 212 168 tfor:TF0903|5end_conserved_hypothetical_protein_947866..948096_POSITIVE 258 107 63 137 86 tfor:TF1030|5end_3-oxoacyl-[acyl-carrier-protein]_synthase_1088229..1088459_POSITIVE 257 56 11 204 153 tfor:TF3022|5end_chorismate_synthase_3246136..3246366_POSITIVE 257 66 22 63 18 tfor:TF2342|5end_glutathione_peroxidase_2505963..2506193_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 301 48 10 52 18 tfor:TF1719|3end_ribonuclease_R_1843668..1843818_POSITIVE 295 70 27 46 6 tfor:TF2448|3end_conserved_hypothetical_protein_2625779..2625929_POSITIVE 291 88 44 70 39 tfor:TF0145|3end_glutamine_synthetase_154718..154868_POSITIVE 276 88 55 141 103 tfor:TF1252|3end_phosphofructokinase;_pyrophosphate-fructose_6-phosphate_1-phosphotransferase_(probable_beta_subunit)_1336084..1336234_POSITIVE 273 80 31 72 18 tfor:TF1720|3end_conserved_hypothetical_protein_1844376..1844526_POSITIVE 267 47 9 151 109 tfor:TF2804|3end_conserved_hypothetical_protein_2994449..2994599_POSITIVE 265 66 22 126 77 tfor:TF0825|3end_hypothetical_protein_883850..884000_POSITIVE 261 87 43 109 63 tfor:TF2830|3end_ABC_transporter,_ATP-binding_protein_3021419..3021569_POSITIVE 258 107 63 96 45 tfor:TF1029|3end_conserved_hypothetical_protein;_possible_phytoene_dehydrogenase_1088268..1088418_POSITIVE 257 66 22 47 2 tfor:TF2341|3end_hypothetical_protein_2506027..2506177_POSITIVE 251 110 63 91 50 tfor:TF0531|3end_hypothetical_protein_557469..557619_POSITIVE 250 82 44 63 21 tfor:TF0193|3end_conserved_hypothetical_protein;_possible_internalin-like_protein_(LPXTG_motif)_215240..215390_POSITIVE 249 57 16 149 112 tfor:TF1668|3end_possible_glycosylhydrolase_1783615..1783765_POSITIVE 248 100 56 65 11 tfor:TF2533|3end_adenylosuccinate_synthetase_2717014..2717164_POSITIVE 248 129 97 56 26 tfor:TF1567|3end_V-type_ATP_synthase,_subunit_I_1676421..1676571_POSITIVE 248 49 8 42 5 tfor:TF1120|3end_conserved_hypothetical_protein_1195256..1195406_POSITIVE 247 47 4 144 99 tfor:TF1461|3end_DNA-damage-inducible_protein_F_1552253..1552403_POSITIVE 246 88 42 66 21 tfor:TF0795|3end_hypothetical_protein_853199..853349_POSITIVE 245 47 2 63 18 tfor:TF2655|3end_DNA_topoisomerase_I_2826962..2827112_POSITIVE 245 85 47 141 98 tfor:TF2600|3end_ribose-phosphate_pyrophosphokinase_2774709..2774859_POSITIVE