Origin IGS: taaaacagaacatataaagataaatgcaaaaatattcgattgctacaagttgtgacaacgaattgcagaataatcattagccgctgctacaacaatctatcattacagaatttattttttaatatcataatatagtaaatcaatc .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gattgatttactatattatgatattaaaaaataaattctgtaatgatagattgttgtagcagcggctaatgattattctgcaattcgttgtcacaacttgtagcaatcgaatatttttgcatttatctttatatgttctgtttta Mask Tandem Repeat Region ================================================ taaaacagaacatataaagataaatgcaaaaatattcgattgctacaagttgtgacaacgaattgcagaataatcattagccgctgctacaacaatctatcattacagaatttattttttaatatcataatatagtaaatcaatc Find is-nt database================================================ Query_seq: TF1779:TF1780|TF1779:TF1780:conserved hypothetical protein:formiminotransferase-cyclodeaminases:->->:1921109..1921253 145 taaaacagaacatataaagataaatgcaaaaatattcgattgctacaagttgtgacaacgaattgcagaataatcattagccgctgctacaacaatctatcattacagaatttattttttaatatcataatatagtaaatcaatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF1779:TF1780|TF1779:TF1780:conserved hypothetical protein:formiminotransferase-cyclodeaminases:->->:1921109..1921253 145 taaaacagaacatataaagataaatgcaaaaatattcgattgctacaagttgtgacaacgaattgcagaataatcattagccgctgctacaacaatctatcattacagaatttattttttaatatcataatatagtaaatcaatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF1779:TF1780|TF1779:TF1780:conserved hypothetical protein:formiminotransferase-cyclodeaminases:->->:1921109..1921253 145 taaaacagaacatataaagataaatgcaaaaatattcgattgctacaagttgtgacaacgaattgcagaataatcattagccgctgctacaacaatctatcattacagaatttattttttaatatcataatatagtaaatcaatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taaaacagaacatataaagataaatgcaaaaatattcgattgctacaagttgtgacaacgaattgcagaataatcattagccgctgctacaacaatctatcattacagaatttattttttaatatcataatatagtaaatcaatc Predict ORF larger than 30AA ================================================ Protein_Len: 33 Strand: + Start: 34 End: 132 ................................. M R L L Q V V T T N C R I I I S R C Y N N L S L Q N L F F N I I I ............. taaaacagaacatataaagataaatgcaaaaatattcgattgctacaagttgtgacaacgaattgcagaataatcattagccgctgctacaacaatctatcattacagaatttattttttaatatcataatatagtaaatcaatc 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================================================ taaaacagaacatataaagataaatgcaaaaatattcgattgctacaagttgtgacaacgaattgcagaataatcattagccgctgctacaacaatctatcattacagaatttattttttaatatcataatatagtaaatcaatc Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF1779:TF1780|TF1779:TF1780:conserved hypothetical protein:formiminotransferase-cyclodeaminases:->->:1921109..1921253 145 taaaacagaacatataaagataaatgcaaaaatattcgattgctacaagttgtgacaacgaattgcagaataatcattagccgctgctacaacaatctatcattacagaatttattttttaatatcataatatagtaaatcaatc Intra-Species Hit: Count: 1 Min: 1 Max: 145 Len: 145 Subject: tfor_TF1779_TF1780|conserved hypothetical protein:formiminotransferase- cyclodeaminases|POSITIVE:POSITIVE|[1921109,1921253]|145 HSP 1 e-value: 5.0E-77 bit: 287.0 Len: 145 Query Start:1 Query End:145 Subject Strand: POSITIVE Subject Start: 1 Subject End: 145 taaaacagaacatataaagataaatgcaaaaatattcgattgctacaagttgtgacaacgaattgcagaataatcattagccgctgctacaacaatctatcattacagaatttattttttaatatcataatatagtaaatcaatc taaaacagaacatataaagataaatgcaaaaatattcgattgctacaagttgtgacaacgaattgcagaataatcattagccgctgctacaacaatctatcattacagaatttattttttaatatcataatatagtaaatcaatc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAAACAGAACAUAUAAAGAUAAAUGCAAAAAUAUUCGAUUGCUACAAGUUGUGACAACGAAUUGCAGAAUAAUCAUUAGCCGCUGCUACAACAAUCUAUCAUUACAGAAUUUAUUUUUUAAUAUCAUAAUAUAGUAAAUCAAUC ..................((((..((((.....(((((.(((.(((.....))).))))))))))))..........((((....))))........))))......((.((((((..(((......)))...)))))))).... (-15.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAUUGAUUUACUAUAUUAUGAUAUUAAAAAAUAAAUUCUGUAAUGAUAGAUUGUUGUAGCAGCGGCUAAUGAUUAUUCUGCAAUUCGUUGUCACAACUUGUAGCAAUCGAAUAUUUUUGCAUUUAUCUUUAUAUGUUCUGUUUUA ...........................(((((((((..(((((.((((((..(((((..((((((.....((....))......))))))..))))).....((((..........)))).)))))).))))).))).)))))). (-23.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 328 90 54 50 2 tfor:TF1240|5end_conserved_hypothetical_protein_1324304..1324534_POSITIVE 319 90 46 45 10 tfor:TF2276|5end_conserved_hypothetical_protein_2438226..2438456_POSITIVE 252 87 41 111 57 tfor:TF2818|5end_acetylornithine_aminotransferase_3007739..3007969_POSITIVE 247 88 47 184 151 tfor:TF2159|5end_conserved_hypothetical_protein_2334446..2334676_POSITIVE 246 86 42 153 108 tfor:TF2217|5end_hypothetical_protein_2389891..2390121_POSITIVE 241 87 42 137 95 tfor:TF1623|5end_5-formyltetrahydrofolate_cyclo-ligase_1736698..1736928_POSITIVE 239 97 51 81 26 tfor:TF1179|5end_two-component_sensor_histidine_kinase_1266057..1266287_POSITIVE 239 87 41 178 114 tfor:TF0568|5end_indolepyruvate_ferredoxin_oxidoreductase,_alpha_subunit_600129..600359_POSITIVE 236 88 41 179 135 tfor:TF0544|5end_metallo-beta_lactamase_family_protein_575121..575351_POSITIVE 234 86 41 68 13 tfor:TF0284|5end_alanine_racemase_311988..312218_POSITIVE 234 87 43 168 132 tfor:TF0098|5end_permease_108103..108333_POSITIVE 233 100 59 74 31 tfor:TF0537|5end_conserved_hypothetical_protein_563145..563375_POSITIVE 231 90 48 51 5 tfor:TF2206|5end_conserved_hypothetical_protein;_possible_sugar_phosphate_isomerase/epimerase_2379969..2380199_POSITIVE 229 86 41 55 15 tfor:TF2771|5end_undecaprenol_kinase,_bacitracin_resistance_protein_2956559..2956789_POSITIVE 229 88 46 116 70 tfor:TF2126|5end_S-adenosylhomocysteine_hydrolase_2302501..2302731_POSITIVE 229 87 44 164 128 tfor:TF1359|5end_hypothetical_protein_1438977..1439207_POSITIVE 227 84 42 231 185 tfor:TF2848|5end_cobalamin_biosynthesis_protein_3036368..3036598_POSITIVE 227 94 51 57 14 tfor:TF1979|5end_conserved_hypothetical_protein_2127957..2128187_POSITIVE 227 87 53 167 113 tfor:TF1681|5end_dTDP-4-keto-L-rhamnose_reductase_1794904..1795134_POSITIVE 226 66 29 67 27 tfor:TF0989|5end_conserved_hypothetical_protein_1044806..1045036_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 319 90 46 39 4 tfor:TF2275|3end_conserved_hypothetical_protein_2438300..2438450_POSITIVE 283 87 51 81 50 tfor:TF0242|3end_conserved_hypothetical_protein_274069..274219_POSITIVE 246 86 42 126 81 tfor:TF2216|3end_fumarate_hydratase,_class_I_2389944..2390094_POSITIVE 246 88 51 146 110 tfor:TF1782|3end_conserved_hypothetical_protein_1923333..1923483_POSITIVE 241 87 42 122 80 tfor:TF1622|3end_conserved_hypothetical_protein_1736763..1736913_POSITIVE 239 97 51 72 17 tfor:TF1178|3end_sigma-54_dependent_DNA-binding_response_regulator_1266128..1266278_POSITIVE 239 87 41 103 39 tfor:TF0567|3end_conserved_hypothetical_protein;_possible_periplasmic_solute-binding_protein_600134..600284_POSITIVE 234 86 41 74 19 tfor:TF0283|3end_possible_nicotinamide_mononucleotide_transporter_312074..312224_POSITIVE 229 86 41 55 15 tfor:TF2770|3end_conserved_hypothetical_protein_2956639..2956789_POSITIVE 226 66 29 80 40 tfor:TF0988|3end_conserved_hypothetical_protein;_possible_nucleotidyltransferase_1044899..1045049_POSITIVE 224 87 42 93 41 tfor:TF0478|3end_conserved_hypothetical_protein_498627..498777_POSITIVE 222 87 44 123 83 tfor:TF1924|3end_prenyltransferase,_UbiA_family_2073827..2073977_POSITIVE 222 88 49 150 107 tfor:TF1184|3end_hypothetical_protein_1269311..1269461_POSITIVE 222 88 49 150 107 tfor:TF1183|3end_hypothetical_protein_1268728..1268878_POSITIVE 220 90 51 110 71 tfor:TF2442|3end_heat_shock_protein_60_2620271..2620421_POSITIVE 219 67 34 145 106 tfor:TF0284|3end_alanine_racemase_314542..314692_POSITIVE 218 109 78 63 32 tfor:TF1758|3end_conserved_hypothetical_protein_1895544..1895694_POSITIVE 218 90 43 126 74 tfor:TF0200|3end_2-nitropropane_dioxygenase_226082..226232_POSITIVE 216 94 59 48 6 tfor:TF0172|3end_transposase_element_185151..185301_POSITIVE 215 87 42 117 46 tfor:TF0174|3end_hypothetical_protein_185600..185750_POSITIVE