Origin IGS: aatgatgtcaagactttatcaacttgaaacataaaactgaaagcctttaccatatttaaatttgcattataaacatttatatgatataattcttcttacatttattaaatgtccggaggtttat .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ataaacctccggacatttaataaatgtaagaagaattatatcatataaatgtttataatgcaaatttaaatatggtaaaggctttcagttttatgtttcaagttgataaagtcttgacatcatt Mask Tandem Repeat Region ================================================ aatgatgtcaagactttatcaacttgaaacataaaactgaaagcctttaccatatttaaatttgcattataaacatttatatgatataattcttcttacatttattaaatgtccggaggtttat Find is-nt database================================================ Query_seq: TDE0206:TDE0207|TDE0206:TDE0207:surface antigen, putative:permease, GntP family:<-->:241618..241741 124 aatgatgtcaagactttatcaacttgaaacataaaactgaaagcctttaccatatttaaatttgcattataaacatttatatgatataattcttcttacatttattaaatgtccggaggtttat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0206:TDE0207|TDE0206:TDE0207:surface antigen, putative:permease, GntP family:<-->:241618..241741 124 aatgatgtcaagactttatcaacttgaaacataaaactgaaagcctttaccatatttaaatttgcattataaacatttatatgatataattcttcttacatttattaaatgtccggaggtttat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0206:TDE0207|TDE0206:TDE0207:surface antigen, putative:permease, GntP family:<-->:241618..241741 124 aatgatgtcaagactttatcaacttgaaacataaaactgaaagcctttaccatatttaaatttgcattataaacatttatatgatataattcttcttacatttattaaatgtccggaggtttat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aatgatgtcaagactttatcaacttgaaacataaaactgaaagcctttaccatatttaaatttgcattataaacatttatatgatataattcttcttacatttattaaatgtccggaggtttat Predict ORF larger than 30AA ================================================ aatgatgtcaagactttatcaacttgaaacataaaactgaaagcctttaccatatttaaatttgcattataaacatttatatgatataattcttcttacatttattaaatgtccggaggtttat 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: 61 End: 90 ............................................................TTTGCATTATAAACATTTATATGATATAAT.................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aatgatgtcaagactttatcaacttgaaacataaaactgaaagcctttaccatatttaaatttgcattataaacatttatatgatataattcttcttacatttattaaatgtccggaggtttat Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE0206:TDE0207|TDE0206:TDE0207:surface antigen, putative:permease, GntP family:<-->:241618..241741 124 aatgatgtcaagactttatcaacttgaaacataaaactgaaagcctttaccatatttaaatttgcattataaacatttatatgatataattcttcttacatttattaaatgtccggaggtttat Intra-Species Hit: Count: 1 Min: 1 Max: 124 Len: 124 Subject: NC_002967_TDE0206_TDE0207|surface antigen, putative:permease, GntP family|NEGATIVE:POSITIVE|[241618,241741]|124 HSP 1 e-value: 1.0E-64 bit: 246.0 Len: 124 Query Start:1 Query End:124 Subject Strand: POSITIVE Subject Start: 1 Subject End: 124 aatgatgtcaagactttatcaacttgaaacataaaactgaaagcctttaccatatttaaatttgcattataaacatttatatgatataattcttcttacatttattaaatgtccggaggtttat aatgatgtcaagactttatcaacttgaaacataaaactgaaagcctttaccatatttaaatttgcattataaacatttatatgatataattcttcttacatttattaaatgtccggaggtttat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUGAUGUCAAGACUUUAUCAACUUGAAACAUAAAACUGAAAGCCUUUACCAUAUUUAAAUUUGCAUUAUAAACAUUUAUAUGAUAUAAUUCUUCUUACAUUUAUUAAAUGUCCGGAGGUUUAU .(((...(((((..........)))))..)))........((((((((...((((((((........(((((....))))).((......))............))))))))..)))))))).. (-14.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUAAACCUCCGGACAUUUAAUAAAUGUAAGAAGAAUUAUAUCAUAUAAAUGUUUAUAAUGCAAAUUUAAAUAUGGUAAAGGCUUUCAGUUUUAUGUUUCAAGUUGAUAAAGUCUUGACAUCAUU ..........(((((((((....((((((......))))))....))))))))).................(((((.((((((((((..((........))..)))..)))))))...))))). (-17.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 750 50 1 141 92 NC_002967:TDE0206|5end_surface_antigen,_putative_241527..241757_NEGATIVE 207 119 71 130 82 NC_002967:TDE0781|5end_30S_ribosomal_protein_S8_812561..812791_POSITIVE 204 48 17 83 50 NC_002967:TDE2679|5end_hypothetical_protein_2719518..2719748_POSITIVE 198 42 1 66 26 NC_002967:TDE0333|5end_MATE_efflux_family_protein_371648..371878_POSITIVE 196 47 10 70 21 NC_002967:TDE2617|5end_cyclic_nucleotide-binding_protein_2659344..2659574_NEGATIVE 192 50 5 167 126 NC_002967:TDE0582|5end_hypothetical_protein_620383..620613_POSITIVE 188 120 105 52 37 NC_002967:TDE1375|5end_pantetheine-phosphate_adenylyltransferase_1418081..1418311_POSITIVE 186 45 3 225 181 NC_002967:TDE1216|5end_flagellar_motor_protein_1248441..1248671_POSITIVE 184 90 41 212 178 NC_002967:TDE1726|5end_polyA_polymerase_family_protein_1779546..1779776_POSITIVE 179 65 23 152 106 NC_002967:TDE2717|5end_phosphatidate_cytidylyltransferase,_putative_2774547..2774777_NEGATIVE 179 66 24 71 31 NC_002967:TDE1214|5end_flagellar_basal_body_protein_1246307..1246537_POSITIVE 179 68 22 184 134 NC_002967:TDE1213|5end_flagellar_basal_body_rod_protein_1245817..1246047_POSITIVE 178 118 76 182 120 NC_002967:TDE0502|5end_ankyrin_repeat_protein_556558..556788_NEGATIVE 177 73 32 118 68 NC_002967:TDE2309|5end_sigma-54_dependent_transcriptional_regulator,_putative_2348099..2348329_NEGATIVE 177 120 72 124 74 NC_002967:TDE0451|5end_arginine_deiminase_508653..508883_POSITIVE 173 70 39 172 142 NC_002967:TDE0084|5end_phosphoenolpyruvate-protein_phosphotransferase_97455..97685_NEGATIVE 169 65 23 120 81 NC_002967:TDE2545|5end_hypothetical_protein_2571814..2572044_NEGATIVE 168 66 42 197 176 NC_002967:TDE1895|5end_GTP-binding_protein_Era_1914963..1915193_POSITIVE 168 115 75 230 185 NC_002967:TDE1792|5end_hypothetical_protein_1829795..1830025_NEGATIVE 168 46 4 204 151 NC_002967:TDE1678|5end_ribosomal_protein_S6_1730483..1730713_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 207 119 71 118 70 NC_002967:TDE0780|3end_ribosomal_protein_S14_812629..812779_POSITIVE 198 50 7 59 1 NC_002967:TDE1629|3end_dihydrolipoamide_dehydrogenase_1677153..1677303_NEGATIVE 192 119 90 109 82 NC_002967:TDE2330|3end_hypothetical_protein_2366698..2366848_POSITIVE 192 50 5 120 79 NC_002967:TDE0581|3end_transglutaminase-like_domain_protein_620416..620566_POSITIVE 187 120 75 79 23 NC_002967:TDE1793|3end_hydrolase,_carbon-nitrogen_family_1829957..1830107_NEGATIVE 186 119 85 64 22 NC_002967:TDE1669|3end_hemolysin_1723878..1724028_POSITIVE 179 65 23 147 101 NC_002967:TDE2718|3end_magnesium_transporter_2774552..2774702_NEGATIVE 178 120 80 59 24 NC_002967:TDE2014|3end_ankyrin_repeat_protein_2035435..2035585_NEGATIVE 178 81 41 45 9 NC_002967:TDE1213|3end_flagellar_basal_body_rod_protein_1246352..1246502_POSITIVE 176 50 6 63 18 NC_002967:TDE0759|3end_hypothetical_protein_799128..799278_NEGATIVE 176 53 23 37 2 NC_002967:TDE0645|3end_hypothetical_protein_680569..680719_NEGATIVE 175 47 6 69 25 NC_002967:TDE0900|3end_ABC_transporter,_ATP-binding_protein_918692..918842_POSITIVE 173 70 39 31 1 NC_002967:TDE0085|3end_ATP-dependent_DNA_helicase,_UvrD/Rep_family_97596..97746_NEGATIVE 169 65 23 57 18 NC_002967:TDE2546|3end_hypothetical_protein_2571877..2572027_NEGATIVE 168 48 2 121 77 NC_002967:TDE1929|3end_hypothetical_protein_1946574..1946724_NEGATIVE 168 46 4 60 7 NC_002967:TDE1679|3end_ATP_synthase_subunit_K_1730627..1730777_NEGATIVE 168 60 22 145 110 NC_002967:TDE1212|3end_flagellar_basal-body_rod_protein_FlgB_1245873..1246023_POSITIVE 165 118 76 137 90 NC_002967:TDE2531|3end_hypothetical_protein_2558545..2558695_POSITIVE 161 51 14 139 109 NC_002967:TDE2627|3end_transcriptional_regulator,_TetR_family_2668532..2668682_NEGATIVE 159 48 8 40 7 NC_002967:TDE0434|3end_rubrerythrin_489564..489714_POSITIVE