Origin IGS: ttttctttccttctattttctacaaatttttattaaaaaacaatacagccaagctgtacggcctccgagattcaatataacaacaattgtttagaaagtcactaggcgcaatagggtttta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taaaaccctattgcgcctagtgactttctaaacaattgttgttatattgaatctcggaggccgtacagcttggctgtattgttttttaataaaaatttgtagaaaatagaaggaaagaaaa Mask Tandem Repeat Region ================================================ ttttctttccttctattttctacaaatttttattaaaaaacaatacagccaagctgtacggcctccgagattcaatataacaacaattgtttagaaagtcactaggcgcaatagggtttta Find is-nt database================================================ Query_seq: AA01584:AA01585|AA01584:AA01585:host factor-I protein:tRNA delta(2)-isopentenylpyrophosphate:->->:1066026..1066146 121 ttttctttccttctattttctacaaatttttattaaaaaacaatacagccaagctgtacggcctccgagattcaatataacaacaattgtttagaaagtcactaggcgcaatagggtttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: AA01584:AA01585|AA01584:AA01585:host factor-I protein:tRNA delta(2)-isopentenylpyrophosphate:->->:1066026..1066146 121 ttttctttccttctattttctacaaatttttattaaaaaacaatacagccaagctgtacggcctccgagattcaatataacaacaattgtttagaaagtcactaggcgcaatagggtttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: AA01584:AA01585|AA01584:AA01585:host factor-I protein:tRNA delta(2)-isopentenylpyrophosphate:->->:1066026..1066146 121 ttttctttccttctattttctacaaatttttattaaaaaacaatacagccaagctgtacggcctccgagattcaatataacaacaattgtttagaaagtcactaggcgcaatagggtttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttttctttccttctattttctacaaatttttattaaaaaacaatacagccaagctgtacggcctccgagattcaatataacaacaattgtttagaaagtcactaggcgcaatagggtttta Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: - Start: 23 End: 112 ...................... L N K N F F L V A L S Y P R R S E I Y C C N N L F D S P A M ......... ttttctttccttctattttctacaaatttttattaaaaaacaatacagccaagctgtacggcctccgagattcaatataacaacaattgtttagaaagtcactaggcgcaatagggtttta 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: 74 End: 103 .........................................................................AGTGACTTTCTAAACAATTGTTGTTATATT.................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ttttctttccttctattttctacaaatttttattaaaaaacaatacagccaagctgtacggcctccgagattcaatataacaacaattgtttagaaagtcactaggcgcaatagggtttta Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 81 HP_score: -6.1 Tail_Score: -5.14965 Start: 41 End: 61 Full_Region: attgaatctcggagg ccgtacagc ttg gctgtattg ttttttaataaaaat ........................................ccgtacagcttggctgtattg............................................................ TransTerm Strand: - Conf: 89 HP_score: -8.6 Tail_Score: -4.67552 Start: 44 End: 58 Full_Region: gaatctcggaggccg tacagc ttg gctgta ttgttttttaataaa ...........................................tacagcttggctgta............................................................... Find igs database================================================ Query_seq: AA01584:AA01585|AA01584:AA01585:host factor-I protein:tRNA delta(2)-isopentenylpyrophosphate:->->:1066026..1066146 121 ttttctttccttctattttctacaaatttttattaaaaaacaatacagccaagctgtacggcctccgagattcaatataacaacaattgtttagaaagtcactaggcgcaatagggtttta Intra-Species Hit: Count: 1 Min: 1 Max: 121 Len: 121 Subject: aact_AA01584_AA01585|host factor-I protein:tRNA delta(2)- isopentenylpyrophosphate|POSITIVE:POSITIVE|[1066026, 1066146]|121 HSP 1 e-value: 8.0E-63 bit: 240.0 Len: 121 Query Start:1 Query End:121 Subject Strand: POSITIVE Subject Start: 1 Subject End: 121 ttttctttccttctattttctacaaatttttattaaaaaacaatacagccaagctgtacggcctccgagattcaatataacaacaattgtttagaaagtcactaggcgcaatagggtttta ttttctttccttctattttctacaaatttttattaaaaaacaatacagccaagctgtacggcctccgagattcaatataacaacaattgtttagaaagtcactaggcgcaatagggtttta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUUCUUUCCUUCUAUUUUCUACAAAUUUUUAUUAAAAAACAAUACAGCCAAGCUGUACGGCCUCCGAGAUUCAAUAUAACAACAAUUGUUUAGAAAGUCACUAGGCGCAAUAGGGUUUUA ..........(((((((..........................((((((...))))))..((((..(.((((......((((.....)))).....)))).).))))..)))))))..... (-16.20) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAAACCCUAUUGCGCCUAGUGACUUUCUAAACAAUUGUUGUUAUAUUGAAUCUCGGAGGCCGUACAGCUUGGCUGUAUUGUUUUUUAAUAAAAAUUUGUAGAAAAUAGAAGGAAAGAAAA ......(((.....((((..(((..(((..((((.....)))).....)))..))).)))).(((((((...)))))))(((((((((.(((....))))))))))))..)))........ (-20.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 311 75 40 64 30 aact:AA02046|5end_PTS_system_galactitol-specific_enzyme_IIC_1392246..1392476_POSITIVE 289 69 47 161 133 aact:AA01340|5end_possible_lipoprotein;_possible_HlyD_family_secretion_domain_protein;_possible_membrane_fusion_protein_905746..905976_POSITIVE 287 75 35 146 102 aact:AA01543|5end_hypothetical_protein_1034175..1034405_POSITIVE 282 66 26 187 148 aact:AA01069|5end_translation_elongation_factor_(EF-Ts)_739775..740005_POSITIVE 282 66 26 81 42 aact:AA01068|5end_hypothetical_protein_739669..739899_POSITIVE 276 90 44 86 43 aact:AA01138|5end_anaerobic_dimethyl_sulfoxide_reductase,_chain_B_780991..781221_POSITIVE 275 78 46 183 151 aact:AA01922|5end_translation_initiation_factor_IF2_1294710..1294940_POSITIVE 263 64 27 225 183 aact:AA01544|5end_conserved_hypothetical_protein_1034265..1034495_POSITIVE 252 74 40 163 131 aact:AA02807|5end_leukotoxin_activator_(leukotoxin_C)_1977102..1977332_POSITIVE 251 84 43 178 128 aact:AA00163|5end_type_IV_prepilin_peptidase;_type_II_secretion_pathway_related_protein_116006..116236_POSITIVE 245 75 51 206 180 aact:AA01871|5end_conserved_hypothetical_protein_1258223..1258453_POSITIVE 242 70 48 224 198 aact:AA00292|5end_dihydrofolate_reductase_201800..202030_POSITIVE 242 70 48 139 113 aact:AA00291|5end_hypothetical_protein_201715..201945_POSITIVE 241 78 48 71 44 aact:AA01834|5end_hypothetical_protein_1234640..1234870_POSITIVE 240 73 44 80 38 aact:AA02351|5end_conserved_hypothetical_protein_1609233..1609463_POSITIVE 238 77 47 193 154 aact:AA01957|5end_conserved_hypothetical_protein_1323211..1323441_POSITIVE 232 68 43 148 125 aact:AA02132|5end_dihydroorotate_dehydrogenase_1455089..1455319_POSITIVE 231 68 46 158 132 aact:AA01067|5end_30S_ribosomal_protein_S2_738898..739128_POSITIVE 230 70 48 104 79 aact:AA00732|5end_citrate_lyase_ligase_501343..501573_POSITIVE 228 68 39 224 195 aact:AA03012|5end_conserved_hypothetical_protein_2104216..2104446_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 311 75 40 55 21 aact:AA02045|3end_PTS_system,_galactitol-specific_IIB_component_1392317..1392467_POSITIVE 289 69 47 132 104 aact:AA01339|3end_transcriptional_regulator,_AcrR/TetR_family_905797..905947_POSITIVE 287 75 35 78 34 aact:AA01539|3end_UDP-N-acetylglucosamine_pyrophosphorylase_(bifunctional_enzyme)_1034187..1034337_POSITIVE 276 90 44 72 29 aact:AA01137|3end_anaerobic_dimethyl_sulfoxide_reductase,_chain_A_781057..781207_POSITIVE 252 74 40 147 115 aact:AA02806|3end_leukotoxin_A;_hemolysin_A_1977166..1977316_POSITIVE 247 66 42 29 5 aact:AA01067|3end_30S_ribosomal_protein_S2_739697..739847_POSITIVE 232 68 43 131 108 aact:AA02131|3end_conserved_hypothetical_protein_(possible_TrpH_protein)_1455152..1455302_POSITIVE 231 68 46 80 54 aact:AA01066|3end_conserved_hypothetical_protein_738900..739050_POSITIVE 231 67 30 147 109 aact:AA00671|3end_virulence_plasmid_protein_460610..460760_POSITIVE 230 64 45 70 55 aact:AA01342|3end_conserved_hypotheticl_protein_(possible_ribosomal_RNA_adenine_dimethylase)_911085..911235_POSITIVE 230 70 48 63 38 aact:AA00730|3end_hypothetical_protein_501382..501532_POSITIVE 228 74 46 72 52 aact:AA01359|3end_conserved_hypothetical_protein_921109..921259_POSITIVE 227 67 38 126 98 aact:AA03010|3end_thiophene_and_furan_oxidation_protein_2102534..2102684_POSITIVE 226 66 33 142 101 aact:AA01476|3end_hypothetical_protein_992261..992411_POSITIVE 226 72 38 115 86 aact:AA00044|3end_formate_dependent_nitrite_reductase,_Fe-S_protein/_anaerobic_DMSO_reductase_B_36094..36244_POSITIVE 223 77 47 128 100 aact:AA01263|3end_hypothetical_protein_861086..861236_POSITIVE 221 72 51 54 34 aact:AA01705|3end_beta-galactosidase_1157980..1158130_POSITIVE 218 68 36 146 109 aact:AA01651|3end_hypothetical_protein_1120004..1120154_POSITIVE 218 86 48 50 9 aact:AA01407|3end_outer_membrane_antigenic_lipoprotein_b_precursor_950251..950401_POSITIVE 215 67 45 25 1 aact:AA01181|3end_conserved_hypothetical_protein_809294..809444_POSITIVE