Origin IGS: attgcctcttttgaagttattataagaataatatacaccctttagggtataatgtcaagcaattagcactaaaatacaccctaacaggtataattatttaatcagaggcgattatatacccgatagggtgtatcttgaaatggttaatgattttatactctatctacattatgtacacggcttt .........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 aaagccgtgtacataatgtagatagagtataaaatcattaaccatttcaagatacaccctatcgggtatataatcgcctctgattaaataattatacctgttagggtgtattttagtgctaattgcttgacattataccctaaagggtgtatattattcttataataacttcaaaagaggcaat Mask Tandem Repeat Region ================================================ attgcctcttttgaagttattataagaataatatacaccctttagggtataatgtcaagcaattagcactaaaatacaccctaacaggtataattatttaatcagaggcgattatatacccgatagggtgtatcttgaaatggttaatgattttatactctatctacattatgtacacggcttt Find is-nt database================================================ Query_seq: TDE0496:TDE0497|TDE0496:TDE0497:DNA-binding protein, putative:hypothetical protein:<-<-:551280..551463 184 attgcctcttttgaagttattataagaataatatacaccctttagggtataatgtcaagcaattagcactaaaatacaccctaacaggtataattatttaatcagaggcgattatatacccgatagggtgtatcttgaaatggttaatgattttatactctatctacattatgtacacggcttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0496:TDE0497|TDE0496:TDE0497:DNA-binding protein, putative:hypothetical protein:<-<-:551280..551463 184 attgcctcttttgaagttattataagaataatatacaccctttagggtataatgtcaagcaattagcactaaaatacaccctaacaggtataattatttaatcagaggcgattatatacccgatagggtgtatcttgaaatggttaatgattttatactctatctacattatgtacacggcttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0496:TDE0497|TDE0496:TDE0497:DNA-binding protein, putative:hypothetical protein:<-<-:551280..551463 184 attgcctcttttgaagttattataagaataatatacaccctttagggtataatgtcaagcaattagcactaaaatacaccctaacaggtataattatttaatcagaggcgattatatacccgatagggtgtatcttgaaatggttaatgattttatactctatctacattatgtacacggcttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 attgcctcttttgaagttattataagaataatatacaccctttagggtataatgtcaagcaattagcactaaaatacaccctaacaggtataattatttaatcagaggcgattatatacccgatagggtgtatcttgaaatggttaatgattttatactctatctacattatgtacacggcttt Predict ORF larger than 30AA ================================================ Protein_Len: 41 Strand: + Start: 62 End: 184 ............................................................. M S T K I H P N R Y N Y L I R G D Y I P D R V Y L E M V N D F I L Y L H Y V H G F attgcctcttttgaagttattataagaataatatacaccctttagggtataatgtcaagcaattagcactaaaatacaccctaacaggtataattatttaatcagaggcgattatatacccgatagggtgtatcttgaaatggttaatgattttatactctatctacattatgtacacggcttt 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: 87 Start: 30 End: 59 .............................CTTGACATTATACCCTAAAGGGTGTATATT............................................................................................................................. PromScan Matrix: RpoD-17 Strand: - Score: 82 Start: 111 End: 140 ..............................................................................................................TTTCAAGATACACCCTATCGGGTATATAAT............................................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ attgcctcttttgaagttattataagaataatatacaccctttagggtataatgtcaagcaattagcactaaaatacaccctaacaggtataattatttaatcagaggcgattatatacccgatagggtgtatcttgaaatggttaatgattttatactctatctacattatgtacacggcttt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE0496:TDE0497|TDE0496:TDE0497:DNA-binding protein, putative:hypothetical protein:<-<-:551280..551463 184 attgcctcttttgaagttattataagaataatatacaccctttagggtataatgtcaagcaattagcactaaaatacaccctaacaggtataattatttaatcagaggcgattatatacccgatagggtgtatcttgaaatggttaatgattttatactctatctacattatgtacacggcttt Intra-Species Hit: Count: 1 Min: 1 Max: 184 Len: 184 Subject: NC_002967_TDE0496_TDE0497|DNA-binding protein, putative:hypothetical protein|NEGATIVE:NEGATIVE|[551280,551463]|184 HSP 1 e-value: 1.0E-100 bit: 365.0 Len: 184 Query Start:1 Query End:184 Subject Strand: POSITIVE Subject Start: 1 Subject End: 184 attgcctcttttgaagttattataagaataatatacaccctttagggtataatgtcaagcaattagcactaaaatacaccctaacaggtataattatttaatcagaggcgattatatacccgatagggtgtatcttgaaatggttaatgattttatactctatctacattatgtacacggcttt attgcctcttttgaagttattataagaataatatacaccctttagggtataatgtcaagcaattagcactaaaatacaccctaacaggtataattatttaatcagaggcgattatatacccgatagggtgtatcttgaaatggttaatgattttatactctatctacattatgtacacggcttt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUUGCCUCUUUUGAAGUUAUUAUAAGAAUAAUAUACACCCUUUAGGGUAUAAUGUCAAGCAAUUAGCACUAAAAUACACCCUAACAGGUAUAAUUAUUUAAUCAGAGGCGAUUAUAUACCCGAUAGGGUGUAUCUUGAAAUGGUUAAUGAUUUUAUACUCUAUCUACAUUAUGUACACGGCUUU ...(((.........((((((((....)))))).))......((((((((((.((((.((.....))..(((.((((((((((.(.((((((......(((((......))))))))))).).)))))))))).)))..........)))).))))))))))................)))... (-45.50) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAGCCGUGUACAUAAUGUAGAUAGAGUAUAAAAUCAUUAACCAUUUCAAGAUACACCCUAUCGGGUAUAUAAUCGCCUCUGAUUAAAUAAUUAUACCUGUUAGGGUGUAUUUUAGUGCUAAUUGCUUGACAUUAUACCCUAAAGGGUGUAUAUUAUUCUUAUAAUAACUUCAAAAGAGGCAAU ...(((..((((.(((((....((.....))....)))))........(((((((((((((.((((((((((((((....))))))......)))))))).))))))))))))).)))).......((((...(((((((....)))))))((((((....))))))...))))....)))... (-51.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 838 130 81 221 172 NC_002967:TDE0496|5end_DNA-binding_protein,_putative_551189..551419_NEGATIVE 256 145 103 214 165 NC_002967:TDE0768|5end_50S_ribosomal_protein_L4_806996..807226_POSITIVE 245 88 42 67 24 NC_002967:TDE0523|5end_hypothetical_protein_569831..570061_NEGATIVE 240 143 106 203 157 NC_002967:TDE0756|5end_iron_compound_ABC_transporter,_ATP-binding_protein,_putative_796859..797089_NEGATIVE 232 88 43 117 60 NC_002967:TDE2426|5end_transcription_antitermination_protein_NusG_2455799..2456029_NEGATIVE 232 166 121 90 55 NC_002967:TDE1048|5end_30S_ribosomal_protein_S7_1074482..1074712_POSITIVE 229 135 94 147 106 NC_002967:TDE0447|5end_TPR_domain_protein_502758..502988_POSITIVE 224 50 5 131 76 NC_002967:TDE1035|5end_transcriptional_regulator,_PadR_family_1063454..1063684_POSITIVE 219 80 37 80 41 NC_002967:TDE1413|5end_cytidylyltransferase/phosphoenolpyruvate_phosphomutase,_putative_1455510..1455740_POSITIVE 217 48 5 148 98 NC_002967:TDE1271|5end_oligopeptide/dipeptide_ABC_transporter,_ATP-binding_protein_1306000..1306230_NEGATIVE 217 143 102 168 133 NC_002967:TDE0899|5end_ABC_transporter,_permease_protein,_putative_916481..916711_POSITIVE 217 149 120 32 4 NC_002967:TDE0765|5end_translation_elongation_factor_Tu_804732..804962_POSITIVE 217 138 107 204 162 NC_002967:TDE0350|5end_MATE_efflux_family_protein_393572..393802_POSITIVE 215 131 100 99 67 NC_002967:TDE2493|5end_hypothetical_protein_2518364..2518594_NEGATIVE 213 66 29 42 1 NC_002967:TDE2440|5end_ABC_transporter,_ATP-binding/permease_protein,_putative_2472043..2472273_NEGATIVE 213 90 45 77 26 NC_002967:TDE1505|5end_hypothetical_protein_1553614..1553844_POSITIVE 213 51 17 214 177 NC_002967:TDE0836|5end_Na(+)-translocating_NADH-quinone_reductase,_C_subunit_856096..856326_NEGATIVE 211 68 21 128 77 NC_002967:TDE1318|5end_hypothetical_protein_1355447..1355677_POSITIVE 210 129 84 202 150 NC_002967:TDE2258|5end_surface_antigen_BspA,_putative_2296401..2296631_NEGATIVE 210 159 120 153 116 NC_002967:TDE0354|5end_general_stress_protein_14_398367..398597_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 237 146 101 146 109 NC_002967:TDE2646|3end_ABC_transporter,_ATP-binding_protein,_putative_2686030..2686180_POSITIVE 232 88 43 113 56 NC_002967:TDE2427|3end_preprotein_translocase,_SecE_subunit_2455803..2455953_NEGATIVE 232 166 121 79 44 NC_002967:TDE1047|3end_30S_ribosomal_protein_S12_1074551..1074701_POSITIVE 224 50 5 63 8 NC_002967:TDE1034|3end_magnesium_and_cobalt_transporter,_putative_1063466..1063616_POSITIVE 220 145 105 44 2 NC_002967:TDE2038|3end_UVR_domain_protein_2067704..2067854_NEGATIVE 216 100 59 79 41 NC_002967:TDE0501|3end_hypothetical_protein_554185..554335_NEGATIVE 215 139 100 40 2 NC_002967:TDE2135|3end_hypothetical_protein_2165418..2165568_POSITIVE 210 150 106 64 18 NC_002967:TDE2308|3end_hypothetical_protein_2346313..2346463_POSITIVE 210 129 84 76 24 NC_002967:TDE2259|3end_hypothetical_protein_2296527..2296677_NEGATIVE 207 160 112 72 3 NC_002967:TDE0868|3end_oxidoreductase,_FAD/FMN-binding_891472..891622_POSITIVE 205 145 109 84 53 NC_002967:TDE1934|3end_hypothetical_protein_1952804..1952954_POSITIVE 202 71 36 139 112 NC_002967:TDE1736|3end_ferredoxin,_2(4Fe-4S)_1790158..1790308_POSITIVE 201 144 104 65 21 NC_002967:TDE0214|3end_hypothetical_protein_249505..249655_NEGATIVE 199 153 125 92 64 NC_002967:TDE2610|3end_hypothetical_protein_2651854..2652004_NEGATIVE 199 70 34 117 80 NC_002967:TDE0455|3end_kinase,_GHMP_family_512477..512627_POSITIVE 194 144 104 76 40 NC_002967:TDE1964|3end_Na/Pi_cotransporter_family_protein_1977131..1977281_NEGATIVE 194 140 119 90 69 NC_002967:TDE0984|3end_oligopeptide/dipeptide_ABC_transporter,_permease_protein,_putative_1011053..1011203_POSITIVE 194 61 24 72 36 NC_002967:TDE0462|3end_metallo-beta-lactamase_family_protein_516178..516328_NEGATIVE 190 49 2 141 91 NC_002967:TDE1402|3end_hypothetical_protein_1444515..1444665_POSITIVE 189 76 37 54 11 NC_002967:TDE2577|3end_hypothetical_protein_2602490..2602640_NEGATIVE