Origin IGS: gtgcaaatacctatcactgccatttactttataaatgggtagcggtatggagatgcgaaaaaaataaactcatagtggaggtcgaatatgttggcagtcgtgaaaatgccccatactagttttaccgtatcgggcgatattcctgaaaatattttaagtatattaaaaacttactataagaaacatcttatacttgaagacgataaaactgaatatgttgaagcttcaacg .........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 cgttgaagcttcaacatattcagttttatcgtcttcaagtataagatgtttcttatagtaagtttttaatatacttaaaatattttcaggaatatcgcccgatacggtaaaactagtatggggcattttcacgactgccaacatattcgacctccactatgagtttatttttttcgcatctccataccgctacccatttataaagtaaatggcagtgataggtatttgcac Mask Tandem Repeat Region ================================================ gtgcaaatacctatcactgccatttactttataaatgggtagcggtatggagatgcgaaaaaaataaactcatagtggaggtcgaatatgttggcagtcgtgaaaatgccccatactagttttaccgtatcgggcgatattcctgaaaatattttaagtatattaaaaacttactataagaaacatcttatacttgaagacgataaaactgaatatgttgaagcttcaacg Find is-nt database================================================ Query_seq: TDE1304:TDE1305|TDE1304:TDE1305:hypothetical protein:DNA-binding protein:->->:1340009..1340239 231 gtgcaaatacctatcactgccatttactttataaatgggtagcggtatggagatgcgaaaaaaataaactcatagtggaggtcgaatatgttggcagtcgtgaaaatgccccatactagttttaccgtatcgggcgatattcctgaaaatattttaagtatattaaaaacttactataagaaacatcttatacttgaagacgataaaactgaatatgttgaagcttcaacg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE1304:TDE1305|TDE1304:TDE1305:hypothetical protein:DNA-binding protein:->->:1340009..1340239 231 gtgcaaatacctatcactgccatttactttataaatgggtagcggtatggagatgcgaaaaaaataaactcatagtggaggtcgaatatgttggcagtcgtgaaaatgccccatactagttttaccgtatcgggcgatattcctgaaaatattttaagtatattaaaaacttactataagaaacatcttatacttgaagacgataaaactgaatatgttgaagcttcaacg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE1304:TDE1305|TDE1304:TDE1305:hypothetical protein:DNA-binding protein:->->:1340009..1340239 231 gtgcaaatacctatcactgccatttactttataaatgggtagcggtatggagatgcgaaaaaaataaactcatagtggaggtcgaatatgttggcagtcgtgaaaatgccccatactagttttaccgtatcgggcgatattcctgaaaatattttaagtatattaaaaacttactataagaaacatcttatacttgaagacgataaaactgaatatgttgaagcttcaacg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 1 Min: 12 Max: 116 Len: 105 Subject: UniRef90_Q2YZZ4 Cluster: Hypothetical protein; n=1; uncultured candidate division OP8 bacterium|Rep: Hypothetical protein - uncultured candidate division OP8 bacterium HSP 1 e-value: 3.0E-7 bit: 56.2 Len: 105 Query Start:12 Query End:116 Subject Strand: null Subject Start: 54 Subject End: 88 ........... Y H C H L L Y K W V A V W R C E K N K L I V E V E Y V G S R E N A P Y ................................................................................................................... ........... Y H C H L I Y R Y V A C W T H R K G E I I I E V Y Y V G S R E K A P Y ................................................................................................................... gtgcaaataccnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnntagttttaccgtatcgggcgatattcctgaaaatattttaagtatattaaaaacttactataagaaacatcttatacttgaagacgataaaactgaatatgttgaagcttcaacg Predict ORF larger than 30AA ================================================ Protein_Len: 48 Strand: + Start: 88 End: 231 ....................................................................................... M L A V V K M P H T S F T V S G D I P E N I L S I L K T Y Y K K H L I L E D D K T E Y V E A S T Protein_Len: 45 Strand: - Start: 27 End: 161 .......................... K I F P Y R Y P S A F F I F E Y H L D F I N A T T F I G W V L K V T D P S I G S F I K L M ...................................................................... gtgcaaataccnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnntagttttaccgtatcgggcgatattcctgaaaatattttaagtatattaaaaacttactataagaaacatcttatacttgaagacgataaaactgaatatgttgaagcttcaacg 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================================================ gtgcaaataccnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnntagttttaccgtatcgggcgatattcctgaaaatattttaagtatattaaaaacttactataagaaacatcttatacttgaagacgataaaactgaatatgttgaagcttcaacg Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 47 HP_score: -2.4 Tail_Score: -3.64984 Start: 152 End: 168 Full_Region: tttcttatagtaagt ttttaa tatac ttaaaa tattttcaggaatat .......................................................................................................................................................ttttaatatacttaaaa............................................................... TransTerm Strand: - Conf: 70 HP_score: -4.0 Tail_Score: -4.84274 Start: 170 End: 180 Full_Region: aagtataagatgttt ctta tag taag tttttaatatactta .........................................................................................................................................................................cttatagtaag................................................... Find igs database================================================ Query_seq: TDE1304:TDE1305|TDE1304:TDE1305:hypothetical protein:DNA-binding protein:->->:1340009..1340239 231 gtgcaaataccnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnntagttttaccgtatcgggcgatattcctgaaaatattttaagtatattaaaaacttactataagaaacatcttatacttgaagacgataaaactgaatatgttgaagcttcaacg Intra-Species Hit: Count: 1 Min: 117 Max: 231 Len: 115 Subject: NC_002967_TDE1304_TDE1305|hypothetical protein:DNA-binding protein|POSITIVE:POSITIVE|[1340009,1340239]|231 HSP 1 e-value: 7.0E-59 bit: 228.0 Len: 115 Query Start:117 Query End:231 Subject Strand: POSITIVE Subject Start: 117 Subject End: 231 ....................................................................................................................tagttttaccgtatcgggcgatattcctgaaaatattttaagtatattaaaaacttactataagaaacatcttatacttgaagacgataaaactgaatatgttgaagcttcaacg ....................................................................................................................tagttttaccgtatcgggcgatattcctgaaaatattttaagtatattaaaaacttactataagaaacatcttatacttgaagacgataaaactgaatatgttgaagcttcaacg Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAGUUUUACCGUAUCGGGCGAUAUUCCUGAAAAUAUUUUAAGUAUAUUAAAAACUUACUAUAAGAAACAUCUUAUACUUGAAGACGAUAAAACUGAAUAUGUUGAAGCUUCAACG ((((((((.(((.(((((.......)))))......((((((((((.......((((...))))........)))))))))).))).)))))))).....(((((....))))). (-24.06) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CGUUGAAGCUUCAACAUAUUCAGUUUUAUCGUCUUCAAGUAUAAGAUGUUUCUUAUAGUAAGUUUUUAAUAUACUUAAAAUAUUUUCAGGAAUAUCGCCCGAUACGGUAAAACUA .(((((....)))))......(((((((((((..((..((....(((((((((.(((.(((((.........)))))...)))....)))))))))))..)).))))))))))). (-26.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 251 43 3 87 48 NC_002967:TDE0476|5end_hypothetical_protein_532914..533144_NEGATIVE 214 49 4 128 80 NC_002967:TDE2718|5end_magnesium_transporter_2775910..2776140_NEGATIVE 209 46 9 98 61 NC_002967:TDE1716|5end_glyoxalase_family_protein_1771228..1771458_NEGATIVE 206 40 10 35 7 NC_002967:TDE0874|5end_transcriptional_regulator,_putative_896939..897169_POSITIVE 205 18 4 34 20 NC_002967:TDE0401|5end_adenylate/guanylate_cyclase_catalytic_domain_protein_454230..454460_NEGATIVE 203 60 16 113 71 NC_002967:TDE0054|5end_flagellar_biosynthesis_protein_62384..62614_POSITIVE 202 28 9 228 210 NC_002967:TDE0104|5end_3-dehydroquinate_synthase_124714..124944_NEGATIVE 199 30 3 137 116 NC_002967:TDE0736|5end_hypothetical_protein_775230..775460_NEGATIVE 197 49 10 101 50 NC_002967:TDE1035|5end_transcriptional_regulator,_PadR_family_1063454..1063684_POSITIVE 193 29 2 180 147 NC_002967:TDE1850|5end_ABC_transporter,_permease_protein,_putative_1879561..1879791_NEGATIVE 193 29 2 57 32 NC_002967:TDE1294|5end_phosphocarrier_protein_HPr_1332321..1332551_NEGATIVE 193 35 1 61 17 NC_002967:TDE1096|5end_hydroxymethylbutenyl_pyrophosphate_reductase_1130989..1131219_POSITIVE 191 35 14 224 206 NC_002967:TDE0836|5end_Na(+)-translocating_NADH-quinone_reductase,_C_subunit_856096..856326_NEGATIVE 190 29 11 174 156 NC_002967:TDE1430|5end_beta-1,4-galactosyltransferase,_putative_1473430..1473660_POSITIVE 188 32 9 123 97 NC_002967:TDE2526|5end_hypothetical_protein_2555034..2555264_NEGATIVE 188 45 8 82 51 NC_002967:TDE0408|5end_oxidoreductase,_NAD-binding_461372..461602_NEGATIVE 184 28 5 200 178 NC_002967:TDE2570|5end_ribonuclease_HI_2597375..2597605_POSITIVE 181 29 7 158 136 NC_002967:TDE2251|5end_uracil_permease_2289440..2289670_POSITIVE 181 36 8 105 74 NC_002967:TDE1726|5end_polyA_polymerase_family_protein_1779546..1779776_POSITIVE 179 39 2 186 151 NC_002967:TDE2410|5end_hemolysin_2437247..2437477_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 257 29 3 50 23 NC_002967:TDE2269|3end_hypothetical_protein_2304931..2305081_NEGATIVE 253 50 1 131 86 NC_002967:TDE1409|3end_flagellar_filament_outer_layer_protein_FlaA,_putative_1452381..1452531_POSITIVE 228 20 3 149 132 NC_002967:TDE2268|3end_hypothetical_protein_2304822..2304972_NEGATIVE 205 18 4 16 2 NC_002967:TDE0402|3end_hypothetical_protein_454248..454398_NEGATIVE 204 109 67 60 8 NC_002967:TDE0862|3end_hypothetical_protein_884126..884276_POSITIVE 203 60 16 116 74 NC_002967:TDE0053|3end_flagellar_biosynthetic_protein_FliR_62467..62617_POSITIVE 201 23 5 147 130 NC_002967:TDE1961|3end_PIN_domain_protein_1974550..1974700_NEGATIVE 200 43 15 31 3 NC_002967:TDE0477|3end_hypothetical_protein_532970..533120_NEGATIVE 189 27 1 145 123 NC_002967:TDE0156|3end_adenylate/guanylate_cyclase_catalytic_domain_protein_180344..180494_NEGATIVE 188 32 4 30 2 NC_002967:TDE1225|3end_zinc_ABC_transporter,_ATP-binding_protein_1258751..1258901_NEGATIVE 185 23 1 115 97 NC_002967:TDE1856|3end_radical_SAM_domain_protein_1883956..1884106_POSITIVE 183 28 9 118 100 NC_002967:TDE1232|3end_hypothetical_protein_1265353..1265503_NEGATIVE 182 49 3 113 59 NC_002967:TDE2714|3end_hypothetical_protein_2770627..2770777_NEGATIVE 181 29 7 47 25 NC_002967:TDE2250|3end_hypothetical_protein_2289409..2289559_POSITIVE 180 28 8 138 118 NC_002967:TDE2609|3end_MiaB-like_tRNA_modifying_enzyme_YliG,_TIGR01125_2651904..2652054_POSITIVE 180 46 13 141 107 NC_002967:TDE2389|3end_cobalamin_biosynthesis_protein_CobD_2418348..2418498_NEGATIVE 180 29 5 31 2 NC_002967:TDE0353|3end_lipase/acylhydrolase,_GDSL_family_396743..396893_NEGATIVE 179 28 2 79 52 NC_002967:TDE2343|3end_phosphatidate_cytidylyltransferase_2380383..2380533_NEGATIVE 179 54 13 98 49 NC_002967:TDE1887|3end_TPR_domain_protein_1908492..1908642_NEGATIVE 178 76 36 53 13 NC_002967:TDE1742|3end_AMP-binding_enzyme_family_protein_1795653..1795803_NEGATIVE