Origin IGS: ttttttcctccaaattatcagaattgaatgtttacaagcttgtaatttcaatttatggtattataaaacaaaagtcaagttgaattttaaaatatttaataaaatatttgaaaattcttatatttttagctaaaattattatattttttaatttttactgcatatattttaatatttttgatgaatcctcttgacaccagaaagaatttttattatcatagaattaaagtttttatgggggatagc .........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 gctatcccccataaaaactttaattctatgataataaaaattctttctggtgtcaagaggattcatcaaaaatattaaaatatatgcagtaaaaattaaaaaatataataattttagctaaaaatataagaattttcaaatattttattaaatattttaaaattcaacttgacttttgttttataataccataaattgaaattacaagcttgtaaacattcaattctgataatttggaggaaaaaa Mask Tandem Repeat Region ================================================ ttttttcctccaaattatcagaattgaatgtttacaagcttgtaatttcaatttatggtattataaaacaaaagtcaagttgaattttaaaatatttaataaaatatttgaaaattcttatatttttagctaaaattattatattttttaatttttactgcatatattttaatatttttgatgaatcctcttgacaccagaaagaatttttattatcatagaattaaagtttttatgggggatagc Find is-nt database================================================ Query_seq: TDE0316:TDE0317|TDE0316:TDE0317:ABC transporter, ATP-binding/permease protein:hypothetical protein:<-->:350550..350795 246 ttttttcctccaaattatcagaattgaatgtttacaagcttgtaatttcaatttatggtattataaaacaaaagtcaagttgaattttaaaatatttaataaaatatttgaaaattcttatatttttagctaaaattattatattttttaatttttactgcatatattttaatatttttgatgaatcctcttgacaccagaaagaatttttattatcatagaattaaagtttttatgggggatagc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0316:TDE0317|TDE0316:TDE0317:ABC transporter, ATP-binding/permease protein:hypothetical protein:<-->:350550..350795 246 ttttttcctccaaattatcagaattgaatgtttacaagcttgtaatttcaatttatggtattataaaacaaaagtcaagttgaattttaaaatatttaataaaatatttgaaaattcttatatttttagctaaaattattatattttttaatttttactgcatatattttaatatttttgatgaatcctcttgacaccagaaagaatttttattatcatagaattaaagtttttatgggggatagc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0316:TDE0317|TDE0316:TDE0317:ABC transporter, ATP-binding/permease protein:hypothetical protein:<-->:350550..350795 246 ttttttcctccaaattatcagaattgaatgtttacaagcttgtaatttcaatttatggtattataaaacaaaagtcaagttgaattttaaaatatttaataaaatatttgaaaattcttatatttttagctaaaattattatattttttaatttttactgcatatattttaatatttttgatgaatcctcttgacaccagaaagaatttttattatcatagaattaaagtttttatgggggatagc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttttttcctccaaattatcagaattgaatgtttacaagcttgtaatttcaatttatggtattataaaacaaaagtcaagttgaattttaaaatatttaataaaatatttgaaaattcttatatttttagctaaaattattatattttttaatttttactgcatatattttaatatttttgatgaatcctcttgacaccagaaagaatttttattatcatagaattaaagtttttatgggggatagc Predict ORF larger than 30AA ================================================ Protein_Len: 39 Strand: + Start: 14 End: 130 ............. M I R I E C L Q A C N F N L W Y Y K T K V K L N F K I F N K I F E N S Y I F S .................................................................................................................... Protein_Len: 36 Strand: + Start: 84 End: 191 ................................................................................... M L K Y L I K Y L K I L I F L A K I I I F F N F Y C I Y F N I F D E S S ....................................................... Protein_Len: 32 Strand: + Start: 151 End: 246 ...................................................................................................................................................... M F T A Y I L I F L M N P L D T R K N F Y Y H R I K V F M G D S ttttttcctccaaattatcagaattgaatgtttacaagcttgtaatttcaatttatggtattataaaacaaaagtcaagttgaattttaaaatatttaataaaatatttgaaaattcttatatttttagctaaaattattatattttttaatttttactgcatatattttaatatttttgatgaatcctcttgacaccagaaagaatttttattatcatagaattaaagtttttatgggggatagc 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: 91 Start: 190 End: 219 .............................................................................................................................................................................................CTTGACACCAGAAAGAATTTTTATTATCAT........................... PromScan Matrix: RpoD-17 Strand: + Score: 89 Start: 107 End: 136 ..........................................................................................................TTTGAAAATTCTTATATTTTTAGCTAAAAT.............................................................................................................. PromScan Matrix: RpoD-17 Strand: - Score: 82 Start: 50 End: 79 .................................................CTTGACTTTTGTTTTATAATACCATAAATT....................................................................................................................................................................... PromScan Matrix: RpoD-17 Strand: - Score: 82 Start: 84 End: 113 ...................................................................................TTTCAAATATTTTATTAAATATTTTAAAAT..................................................................................................................................... PromScan Matrix: RpoD-17 Strand: + Score: 81 Start: 30 End: 59 .............................GTTTACAAGCTTGTAATTTCAATTTATGGT........................................................................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ttttttcctccaaattatcagaattgaatgtttacaagcttgtaatttcaatttatggtattataaaacaaaagtcaagttgaattttaaaatatttaataaaatatttgaaaattcttatatttttagctaaaattattatattttttaatttttactgcatatattttaatatttttgatgaatcctcttgacaccagaaagaatttttattatcatagaattaaagtttttatgggggatagc Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 86 HP_score: -9.4 Tail_Score: -4.09353 Start: 82 End: 117 Full_Region: AACAAAAGTCAAGTT GAATTTTAAAATATTT AATA AAATATTTGAAAATTC TTATATTTTTAGCTA .................................................................................GAATTTTAAAATATTTAATAAAATATTTGAAAATTC................................................................................................................................. Find igs database================================================ Query_seq: TDE0316:TDE0317|TDE0316:TDE0317:ABC transporter, ATP-binding/permease protein:hypothetical protein:<-->:350550..350795 246 ttttttcctccaaattatcagaattgaatgtttacaagcttgtaatttcaatttatggtattataaaacaaaagtcaagttgaattttaaaatatttaataaaatatttgaaaattcttatatttttagctaaaattattatattttttaatttttactgcatatattttaatatttttgatgaatcctcttgacaccagaaagaatttttattatcatagaattaaagtttttatgggggatagc Intra-Species Hit: Count: 1 Min: 1 Max: 246 Len: 246 Subject: NC_002967_TDE0316_TDE0317|ABC transporter, ATP-binding/permease protein:hypothetical protein|NEGATIVE:POSITIVE|[350550,350795]|246 HSP 1 e-value: 3.0E-39 bit: 163.0 Len: 82 Query Start:1 Query End:82 Subject Strand: POSITIVE Subject Start: 1 Subject End: 82 ttttttcctccaaattatcagaattgaatgtttacaagcttgtaatttcaatttatggtattataaaacaaaagtcaagttg.................................................................................................................................................................... ttttttcctccaaattatcagaattgaatgtttacaagcttgtaatttcaatttatggtattataaaacaaaagtcaagttg.................................................................................................................................................................... HSP 2 e-value: 3.0E-30 bit: 133.0 Len: 67 Query Start:180 Query End:246 Subject Strand: POSITIVE Subject Start: 180 Subject End: 246 ...................................................................................................................................................................................gatgaatcctcttgacaccagaaagaatttttattatcatagaattaaagtttttatgggggatagc ...................................................................................................................................................................................gatgaatcctcttgacaccagaaagaatttttattatcatagaattaaagtttttatgggggatagc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUUUUCCUCCAAAUUAUCAGAAUUGAAUGUUUACAAGCUUGUAAUUUCAAUUUAUGGUAUUAUAAAACAAAAGUCAAGUUGAAUUUUAAAAUAUUUAAUAAAAUAUUUGAAAAUUCUUAUAUUUUUAGCUAAAAUUAUUAUAUUUUUUAAUUUUUACUGCAUAUAUUUUAAUAUUUUUGAUGAAUCCUCUUGACACCAGAAAGAAUUUUUAUUAUCAUAGAAUUAAAGUUUUUAUGGGGGAUAGC .....(((((((...(((((((((((((...(((((....))))).)))))))).))))).............((((((..(((((((.((((((((....)))))))).))))))).(((((...(((..(((((((..(....)..)))))))..))).))))).......................))))))......(((((((((.(((.......))).))))))))).))))))).... (-44.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GCUAUCCCCCAUAAAAACUUUAAUUCUAUGAUAAUAAAAAUUCUUUCUGGUGUCAAGAGGAUUCAUCAAAAAUAUUAAAAUAUAUGCAGUAAAAAUUAAAAAAUAUAAUAAUUUUAGCUAAAAAUAUAAGAAUUUUCAAAUAUUUUAUUAAAUAUUUUAAAAUUCAACUUGACUUUUGUUUUAUAAUACCAUAAAUUGAAAUUACAAGCUUGUAAACAUUCAAUUCUGAUAAUUUGGAGGAAAAAA ....(((.(((....................................((((((((((((.....................(((((..(((.(((((((..........))))))).)))....))))).(((((((.((((((((....)))))))).))))))).......)))))).......))))))..(((((((.(((((....)))))...))))))).........))).)))..... (-35.91) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 707 50 1 141 92 NC_002967:TDE0316|5end_ABC_transporter,_ATP-binding/permease_protein_350459..350689_NEGATIVE 271 67 28 181 144 NC_002967:TDE2140|5end_protease_II_2175140..2175370_NEGATIVE 227 228 186 67 29 NC_002967:TDE2648|5end_hypothetical_protein_2687777..2688007_NEGATIVE 214 223 181 99 50 NC_002967:TDE2569|5end_3-deoxy-7-phosphoheptulonate_synthase_2596308..2596538_POSITIVE 212 205 171 197 167 NC_002967:TDE1294|5end_phosphocarrier_protein_HPr_1332321..1332551_NEGATIVE 211 224 183 67 24 NC_002967:TDE2335|5end_ATP-dependent_DNA_helicase,_UvrD/Rep_family_2369641..2369871_POSITIVE 209 199 151 94 44 NC_002967:TDE2421|5end_DNA-directed_RNA_polymerase_beta_subunit_2452762..2452992_NEGATIVE 207 49 7 165 106 NC_002967:TDE1885|5end_hypothetical_protein_1906857..1907087_POSITIVE 201 47 20 37 12 NC_002967:TDE0683|5end_hypothetical_protein_721303..721533_NEGATIVE 199 199 158 56 10 NC_002967:TDE0745|5end_glycine_reductase_complex_selenoprotein_GrdA_780287..780517_POSITIVE 199 136 115 70 49 NC_002967:TDE0127|5end_DNA-binding_protein_145750..145980_POSITIVE 194 198 152 100 50 NC_002967:TDE0819|5end_ABC_transporter,_ATP-binding/permease_protein_843385..843615_NEGATIVE 193 42 2 138 93 NC_002967:TDE1679|5end_ATP_synthase_subunit_K_1731049..1731279_NEGATIVE 188 43 6 45 3 NC_002967:TDE1739|5end_femAB_family_protein_1791513..1791743_POSITIVE 187 58 15 230 188 NC_002967:TDE2183|5end_hypothetical_protein_2215199..2215429_POSITIVE 187 59 28 94 60 NC_002967:TDE1650|5end_ABC_transporter,_ATP-binding_protein_1698117..1698347_NEGATIVE 186 218 188 41 12 NC_002967:TDE2176|5end_site-specific_recombinase,_putative_2206239..2206469_NEGATIVE 181 42 19 178 151 NC_002967:TDE0575|5end_aspartyl/glutamyl-tRNA_amidotransferase_subunit_B_607733..607963_NEGATIVE 180 200 153 132 77 NC_002967:TDE0485|5end_hypothetical_protein_542791..543021_NEGATIVE 177 78 36 118 73 NC_002967:TDE0232|5end_appr-1-p_processing_enzyme_domain_protein_265214..265444_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 227 228 186 65 27 NC_002967:TDE2649|3end_ABC_transporter,_ATP-binding_protein_2687779..2687929_NEGATIVE 214 223 181 96 47 NC_002967:TDE2568|3end_thiamine_biosynthesis_protein_ThiI_2596385..2596535_POSITIVE 200 218 176 86 43 NC_002967:TDE1963|3end_selenocysteine-specific_translation_elongation_factor_1977141..1977291_POSITIVE 199 87 49 54 4 NC_002967:TDE0407|3end_glutamate_synthase_(NADPH),_homotetrameric_459011..459161_NEGATIVE 198 60 19 79 33 NC_002967:TDE0948|3end_hypothetical_protein_970959..971109_NEGATIVE 187 59 28 90 56 NC_002967:TDE1651|3end_BioY_family_protein_1698121..1698271_NEGATIVE 180 200 153 111 56 NC_002967:TDE0486|3end_hypothetical_protein_542812..542962_NEGATIVE 179 50 7 134 96 NC_002967:TDE1573|3end_DNA-damage-inducible_protein_J,_putative_1621541..1621691_NEGATIVE 179 45 20 151 128 NC_002967:TDE0683|3end_hypothetical_protein_721187..721337_NEGATIVE 175 198 158 104 60 NC_002967:TDE2262|3end_peptidase,_U32_family_2298033..2298183_NEGATIVE 175 58 19 100 51 NC_002967:TDE2234|3end_iron_compound_ABC_transporter,_periplasmic_iron_compound-binding_protein,_putative_2272310..2272460_NEGATIVE 175 218 173 96 47 NC_002967:TDE0956|3end_hypothetical_protein_980330..980480_POSITIVE 170 49 8 38 4 NC_002967:TDE2669|3end_CDP-alcohol_phosphatidyltransferase_family_protein_2706161..2706311_NEGATIVE 170 199 159 105 62 NC_002967:TDE2127|3end_vapC_protein,_putative_2160244..2160394_POSITIVE 170 49 20 126 87 NC_002967:TDE0118|3end_hypothetical_protein_136574..136724_NEGATIVE 168 227 183 65 17 NC_002967:TDE1599|3end_ABC_transporter,_ATP-binding/permease_protein_1648920..1649070_NEGATIVE 167 50 5 111 54 NC_002967:TDE1760|3end_HD_domain_protein_1809203..1809353_NEGATIVE 165 47 19 92 57 NC_002967:TDE2457|3end_hypothetical_protein_2484698..2484848_NEGATIVE 162 209 173 36 4 NC_002967:TDE2761|3end_hypothetical_protein_2815878..2816028_NEGATIVE 162 200 152 127 71 NC_002967:TDE0523|3end_hypothetical_protein_569238..569388_NEGATIVE