Origin IGS: aaaatatcctcttataaattgaccataaaaatgcaatggaaaccatttataatagaatttaacaattgagtaaagaaaataaaattctacctcagagaaaatagcagaataaaactctgatta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taatcagagttttattctgctattttctctgaggtagaattttattttctttactcaattgttaaattctattataaatggtttccattgcatttttatggtcaatttataagaggatatttt Mask Tandem Repeat Region ================================================ aaaatatcctcttataaattgaccataaaaatgcaatggaaaccatttataatagaatttaacaattgagtaaagaaaataaaattctacctcagagaaaatagcagaataaaactctgatta Find is-nt database================================================ Query_seq: AA02853:AA02854|AA02853:AA02854:conserved hypothetical protein:hypothetical protein:->->:2002430..2002552 123 aaaatatcctcttataaattgaccataaaaatgcaatggaaaccatttataatagaatttaacaattgagtaaagaaaataaaattctacctcagagaaaatagcagaataaaactctgatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: AA02853:AA02854|AA02853:AA02854:conserved hypothetical protein:hypothetical protein:->->:2002430..2002552 123 aaaatatcctcttataaattgaccataaaaatgcaatggaaaccatttataatagaatttaacaattgagtaaagaaaataaaattctacctcagagaaaatagcagaataaaactctgatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: AA02853:AA02854|AA02853:AA02854:conserved hypothetical protein:hypothetical protein:->->:2002430..2002552 123 aaaatatcctcttataaattgaccataaaaatgcaatggaaaccatttataatagaatttaacaattgagtaaagaaaataaaattctacctcagagaaaatagcagaataaaactctgatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aaaatatcctcttataaattgaccataaaaatgcaatggaaaccatttataatagaatttaacaattgagtaaagaaaataaaattctacctcagagaaaatagcagaataaaactctgatta Predict ORF larger than 30AA ================================================ Protein_Len: 34 Strand: - Start: 1 End: 102 F Y G R I F Q G Y F H L P F W K Y Y F K V I S Y L F Y F E V E S F M ..................... aaaatatcctcttataaattgaccataaaaatgcaatggaaaccatttataatagaatttaacaattgagtaaagaaaataaaattctacctcagagaaaatagcagaataaaactctgatta 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: 81 Start: 46 End: 75 .............................................CTTTACTCAATTGTTAAATTCTATTATAAA................................................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aaaatatcctcttataaattgaccataaaaatgcaatggaaaccatttataatagaatttaacaattgagtaaagaaaataaaattctacctcagagaaaatagcagaataaaactctgatta Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: AA02853:AA02854|AA02853:AA02854:conserved hypothetical protein:hypothetical protein:->->:2002430..2002552 123 aaaatatcctcttataaattgaccataaaaatgcaatggaaaccatttataatagaatttaacaattgagtaaagaaaataaaattctacctcagagaaaatagcagaataaaactctgatta Intra-Species Hit: Count: 1 Min: 1 Max: 123 Len: 123 Subject: aact_AA02853_AA02854|conserved hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[2002430,2002552]|123 HSP 1 e-value: 6.0E-64 bit: 244.0 Len: 123 Query Start:1 Query End:123 Subject Strand: POSITIVE Subject Start: 1 Subject End: 123 aaaatatcctcttataaattgaccataaaaatgcaatggaaaccatttataatagaatttaacaattgagtaaagaaaataaaattctacctcagagaaaatagcagaataaaactctgatta aaaatatcctcttataaattgaccataaaaatgcaatggaaaccatttataatagaatttaacaattgagtaaagaaaataaaattctacctcagagaaaatagcagaataaaactctgatta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAAUAUCCUCUUAUAAAUUGACCAUAAAAAUGCAAUGGAAACCAUUUAUAAUAGAAUUUAACAAUUGAGUAAAGAAAAUAAAAUUCUACCUCAGAGAAAAUAGCAGAAUAAAACUCUGAUUA ........((.((((((((.(.((((.........))))...).)))))))).))..........(((((...((((.......))))..))))).........((((.......)))).... (-13.20) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAUCAGAGUUUUAUUCUGCUAUUUUCUCUGAGGUAGAAUUUUAUUUUCUUUACUCAAUUGUUAAAUUCUAUUAUAAAUGGUUUCCAUUGCAUUUUUAUGGUCAAUUUAUAAGAGGAUAUUUU ....((((((...))))))..........((((..((((.......))))...))))........(((((.((((((((.....((((.........))))...)))))))).)))))..... (-20.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 193 54 19 107 73 aact:AA00606|5end_membrane-associated_zinc_metalloprotease_411808..412038_POSITIVE 184 74 35 73 30 aact:AA00263|5end_ATP-dependent_RNA_helicase_183690..183920_POSITIVE 182 120 90 71 41 aact:AA02080|5end_ABC_transporter,_ATP-binding/permease_1412744..1412974_POSITIVE 182 46 7 146 100 aact:AA01577|5end_conserved_hypothetical_transmembrane_protein_1063084..1063314_POSITIVE 174 108 67 56 13 aact:AA02193|5end_oxaloacetate_decarboxylase_gamma_chain_1494219..1494449_POSITIVE 172 28 6 93 73 aact:AA01072|5end_GTP_pyrophosphokinase_(ppGpp_synthetase_I)_/_ATP:GTP3'-pyrophosphotransferase_742934..743164_POSITIVE 169 74 33 205 156 aact:AA03012|5end_conserved_hypothetical_protein_2104216..2104446_POSITIVE 169 120 86 103 74 aact:AA00218|5end_argininosuccinate_lyase_150758..150988_POSITIVE 165 45 8 124 98 aact:AA02686|5end_hydrogenase_4_component_C_1871546..1871776_POSITIVE 163 44 17 71 47 aact:AA00872|5end_rough_colony_protein_B_603940..604170_POSITIVE 163 46 1 228 186 aact:AA00093|5end_L-serine_dehydratase_(L-serine_deaminase)_69732..69962_POSITIVE 162 106 66 100 61 aact:AA02919|5end_CagE_protein_(tranport-associated)_2044202..2044432_POSITIVE 161 99 52 137 93 aact:AA01017|5end_conserved_hypothetical_protein_710915..711145_POSITIVE 161 109 86 102 78 aact:AA00592|5end_conserved_hypothetical_protein_(membrane/transport_protein)_405536..405766_POSITIVE 159 119 92 181 158 aact:AA02629|5end_hypothetical_protein_1830072..1830302_POSITIVE 159 45 11 128 88 aact:AA01174|5end_hypothetical_protein_804700..804930_POSITIVE 159 70 23 83 27 aact:AA00057|5end_cytochrome_c-type_biogenesis_protein_44440..44670_POSITIVE 157 58 11 142 101 aact:AA01600|5end_phosphotransferase_system_enzyme_I_1080481..1080711_POSITIVE 155 106 69 90 47 aact:AA02895|5end_oligopeptide_transport_system_permease_protein,_C-terminal_2027484..2027714_POSITIVE 153 45 5 231 190 aact:AA00869|5end_tight_adherence_protein_V;_prepilin_peptidase_601255..601485_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 193 54 19 95 61 aact:AA00605|3end_CDP-diglyceride_pyrophosphorylase_411876..412026_POSITIVE 182 120 90 40 10 aact:AA02078|3end_hypothetical_protein_1412793..1412943_POSITIVE 182 46 7 129 83 aact:AA01575|3end_conserved_hypothetical_protein_1063147..1063297_POSITIVE 172 28 6 80 60 aact:AA01071|3end_RNA_methyltransferase_743001..743151_POSITIVE 170 49 8 138 97 aact:AA01729|3end_hypothetical_protein_1169027..1169177_POSITIVE 169 120 86 90 61 aact:AA00217|3end_hypothetical_protein_150825..150975_POSITIVE 165 45 8 110 84 aact:AA02684|3end_hydrogenase_4_membrane_subunit_1871612..1871762_POSITIVE 164 24 1 60 40 aact:AA01224|3end_CTP_synthase_837899..838049_POSITIVE 163 44 17 71 47 aact:AA00871|3end_rough_colony_protein_A_604020..604170_POSITIVE 163 46 1 132 90 aact:AA00092|3end_serine_transporter_69716..69866_POSITIVE 161 99 52 47 3 aact:AA01015|3end_met_repressor_710905..711055_POSITIVE 159 119 92 34 11 aact:AA02628|3end_exodeoxyribonuclease_III_1830005..1830155_POSITIVE 159 44 1 117 73 aact:AA00993|3end_possible_D-tyrosyl-tRNA(Tyr)_deacylase_694999..695149_POSITIVE 159 70 23 83 27 aact:AA00056|3end_cytochrome_c-type_biogenesis_protein_44520..44670_POSITIVE 155 106 69 70 27 aact:AA02893|3end_oligopeptide_transport_system_permease_protein,_N-terminal_2027544..2027694_POSITIVE 155 109 74 117 83 aact:AA02003|3end_purine_nucleotide_synthesis_repressor_protein_1361708..1361858_POSITIVE 151 43 2 151 103 aact:AA00876|3end_tight_adherence_protein_C_608704..608854_POSITIVE 149 47 23 119 93 aact:AA01901|3end_hypothetical_protein_1282870..1283020_POSITIVE 149 47 7 82 41 aact:AA00636|3end_MrsA_protein_(phosphoglucomutase/phosphomannomutase)_438194..438344_POSITIVE 147 119 85 48 16 aact:AA02964|3end_opacity_associated_protein_A_2074128..2074278_POSITIVE