Origin IGS: attatgaagacggtttacatgtcaaatatcctaaacttggtcgttcgttgggagggatatttttagggaagctaagatttatcttcgtctttttatcgtatttttgtgaaagaaataagaac .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gttcttatttctttcacaaaaatacgataaaaagacgaagataaatcttagcttccctaaaaatatccctcccaacgaacgaccaagtttaggatatttgacatgtaaaccgtcttcataat Mask Tandem Repeat Region ================================================ attatgaagacggtttacatgtcaaatatcctaaacttggtcgttcgttgggagggatatttttagggaagctaagatttatcttcgtctttttatcgtatttttgtgaaagaaataagaac Find is-nt database================================================ Query_seq: TF2528:TF2527|TF2528:TF2527:anti-sigma factor:RNA polymerase ECF-type sigma factor:->->:2710115..2710236 122 attatgaagacggtttacatgtcaaatatcctaaacttggtcgttcgttgggagggatatttttagggaagctaagatttatcttcgtctttttatcgtatttttgtgaaagaaataagaac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF2528:TF2527|TF2528:TF2527:anti-sigma factor:RNA polymerase ECF-type sigma factor:->->:2710115..2710236 122 attatgaagacggtttacatgtcaaatatcctaaacttggtcgttcgttgggagggatatttttagggaagctaagatttatcttcgtctttttatcgtatttttgtgaaagaaataagaac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF2528:TF2527|TF2528:TF2527:anti-sigma factor:RNA polymerase ECF-type sigma factor:->->:2710115..2710236 122 attatgaagacggtttacatgtcaaatatcctaaacttggtcgttcgttgggagggatatttttagggaagctaagatttatcttcgtctttttatcgtatttttgtgaaagaaataagaac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 attatgaagacggtttacatgtcaaatatcctaaacttggtcgttcgttgggagggatatttttagggaagctaagatttatcttcgtctttttatcgtatttttgtgaaagaaataagaac Predict ORF larger than 30AA ================================================ attatgaagacggtttacatgtcaaatatcctaaacttggtcgttcgttgggagggatatttttagggaagctaagatttatcttcgtctttttatcgtatttttgtgaaagaaataagaac 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================================================ attatgaagacggtttacatgtcaaatatcctaaacttggtcgttcgttgggagggatatttttagggaagctaagatttatcttcgtctttttatcgtatttttgtgaaagaaataagaac Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF2528:TF2527|TF2528:TF2527:anti-sigma factor:RNA polymerase ECF-type sigma factor:->->:2710115..2710236 122 attatgaagacggtttacatgtcaaatatcctaaacttggtcgttcgttgggagggatatttttagggaagctaagatttatcttcgtctttttatcgtatttttgtgaaagaaataagaac Intra-Species Hit: Count: 1 Min: 1 Max: 122 Len: 122 Subject: tfor_TF2528_TF2527|anti-sigma factor:RNA polymerase ECF-type sigma factor|POSITIVE:POSITIVE|[2710115,2710236]|122 HSP 1 e-value: 2.0E-63 bit: 242.0 Len: 122 Query Start:1 Query End:122 Subject Strand: POSITIVE Subject Start: 1 Subject End: 122 attatgaagacggtttacatgtcaaatatcctaaacttggtcgttcgttgggagggatatttttagggaagctaagatttatcttcgtctttttatcgtatttttgtgaaagaaataagaac attatgaagacggtttacatgtcaaatatcctaaacttggtcgttcgttgggagggatatttttagggaagctaagatttatcttcgtctttttatcgtatttttgtgaaagaaataagaac Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUUAUGAAGACGGUUUACAUGUCAAAUAUCCUAAACUUGGUCGUUCGUUGGGAGGGAUAUUUUUAGGGAAGCUAAGAUUUAUCUUCGUCUUUUUAUCGUAUUUUUGUGAAAGAAAUAAGAAC .....((((((((.......(((.....(((((((....(((.(((.....))).)))...))))))).......)))......))))))))...((.(((((((.....))))))).)).. (-23.32) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUUCUUAUUUCUUUCACAAAAAUACGAUAAAAAGACGAAGAUAAAUCUUAGCUUCCCUAAAAAUAUCCCUCCCAACGAACGACCAAGUUUAGGAUAUUUGACAUGUAAACCGUCUUCAUAAU ...............................((((((((((....))))...........((((((((........((((......)))).))))))))...........))))))...... (-12.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 323 56 18 229 199 tfor:TF2443|5end_amidophosphoribosyl-transferase_2620287..2620517_POSITIVE 318 58 11 200 151 tfor:TF1609|5end_hypothetical_protein_1728340..1728570_POSITIVE 309 90 41 169 128 tfor:TF1585|5end_hypothetical_protein_1690369..1690599_POSITIVE 309 90 41 45 4 tfor:TF1584|5end_hypothetical_protein_1690245..1690475_POSITIVE 309 90 41 45 4 tfor:TF1582|5end_hypothetical_protein_1690121..1690351_POSITIVE 301 59 12 89 35 tfor:TF0044|5end_conserved_hypothetical_protein_48334..48564_POSITIVE 292 54 11 197 144 tfor:TF1294|5end_conserved_hypothetical_protein_1377142..1377372_POSITIVE 286 70 27 192 142 tfor:TF2763|5end_pyridine_nucleotide-disulphide_oxidoreductase_family_protein_2946073..2946303_POSITIVE 285 90 42 93 30 tfor:TF1342|5end_possible_lipoprotein_1423125..1423355_POSITIVE 284 74 37 148 107 tfor:TF0301|5end_outer_membrane_protein,_TonB_dependent_receptor_325457..325687_POSITIVE 283 57 11 177 136 tfor:TF2835|5end_stationary-phase_survival_protein_SurE_3025113..3025343_POSITIVE 280 90 41 164 104 tfor:TF1590|5end_hypothetical_protein_1705811..1706041_POSITIVE 276 90 44 65 20 tfor:TF1930|5end_two-component_response_regulator_2076582..2076812_POSITIVE 274 87 41 143 88 tfor:TF1665|5end_conserved_hypothetical_protein_1779148..1779378_POSITIVE 274 73 31 225 175 tfor:TF0949|5end_conserved_hypothetical_protein_993863..994093_POSITIVE 270 90 41 229 185 tfor:TF1732|5end_conserved_hypothetical_protein_1854619..1854849_POSITIVE 269 58 13 215 177 tfor:TF2837|5end_conserved_hypothetical_protein_3027939..3028169_POSITIVE 268 75 34 185 145 tfor:TF1962|5end_TatD-related_deoxyribonuclease,_Mg-dependent_DNase_2112417..2112647_POSITIVE 264 90 41 208 147 tfor:TF2791|5end_GTP-binding_protein_TypA_2975298..2975528_POSITIVE 264 46 1 59 3 tfor:TF2533|5end_adenylosuccinate_synthetase_2715666..2715896_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 323 56 18 133 103 tfor:TF2442|3end_heat_shock_protein_60_2620271..2620421_POSITIVE 309 90 41 67 26 tfor:TF1583|3end_conserved_hypothetical_protein;_possible_endonuclease_1690223..1690373_POSITIVE 301 59 12 72 18 tfor:TF0043|3end_conserved_hypothetical_protein_48397..48547_POSITIVE 285 90 42 88 25 tfor:TF1341|3end_glycogen_synthase_1423200..1423350_POSITIVE 277 55 27 149 123 tfor:TF2762|3end_conserved_hypothetical_protein_2946134..2946284_POSITIVE 277 90 50 121 73 tfor:TF1985|3end_surface_antigen_BspA_2136905..2137055_POSITIVE 274 87 41 121 66 tfor:TF1664|3end_conserved_hypothetical_protein_1779206..1779356_POSITIVE 263 57 11 82 25 tfor:TF0504|3end_Fe-S_oxidoreductase,_family_2_530303..530453_POSITIVE 261 59 19 138 91 tfor:TF3147|3end_adenylate_kinase_3383704..3383854_POSITIVE 261 69 35 103 71 tfor:TF1002|3end_replicative_DNA_helicase_1058232..1058382_POSITIVE 260 56 27 124 89 tfor:TF0710|3end_two_component_system_histidine_kinase_761385..761535_POSITIVE 260 72 37 150 111 tfor:TF0300|3end_hypothetical_protein_325541..325691_POSITIVE 259 69 24 59 6 tfor:TF0556|3end_Bacteroides_aerotolerance_protein,_BatA_589149..589299_POSITIVE 256 80 42 103 64 tfor:TF1181|3end_methylated-DNA--[protein]-cysteine_S-methyltransferase_1267991..1268141_POSITIVE 252 54 11 134 98 tfor:TF1358|3end_hypothetical_protein_1438879..1439029_POSITIVE 251 80 37 151 98 tfor:TF3145|3end_conserved_hypothetical_protein;_possible_GTP_cyclohydrolase_I_family_3381822..3381972_POSITIVE 251 58 11 150 102 tfor:TF2975|3end_endonuclease_IV_3183304..3183454_POSITIVE 250 54 11 117 81 tfor:TF2300|3end_conserved_hypothetical_protein_2453328..2453478_POSITIVE 250 52 11 147 97 tfor:TF1109|3end_lipoprotein_1179997..1180147_POSITIVE 247 90 45 58 5 tfor:TF2406|3end_anti-sigma_factor_2581659..2581809_POSITIVE