Origin IGS: taaaacgaccaccctgttattttataaattatgtataccatctataatatatcataattacacgctcaatatttgcttttgcgatttattttcgattattttgcgatcggaataccaattctttgaaatagtcatacaatttgacttttttcttaacaggtttttaagaattgaatattcatgggtggccatactgctttttgcggtgtatttctaataatcatttttgaatgaagtatatttgacttatttctttatctaaaattgacgttacaacattgttgtgtactaatttattcattaaaatctaattatt .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9 aataattagattttaatgaataaattagtacacaacaatgttgtaacgtcaattttagataaagaaataagtcaaatatacttcattcaaaaatgattattagaaatacaccgcaaaaagcagtatggccacccatgaatattcaattcttaaaaacctgttaagaaaaaagtcaaattgtatgactatttcaaagaattggtattccgatcgcaaaataatcgaaaataaatcgcaaaagcaaatattgagcgtgtaattatgatatattatagatggtatacataatttataaaataacagggtggtcgtttta Mask Tandem Repeat Region ================================================ taaaacgaccaccctgttattttataaattatgtataccatctataatatatcataattacacgctcaatatttgcttttgcgatttattttcgattattttgcgatcggaataccaattctttgaaatagtcatacaatttgacttttttcttaacaggtttttaagaattgaatattcatgggtggccatactgctttttgcggtgtatttctaataatcatttttgaatgaagtatatttgacttatttctttatctaaaattgacgttacaacattgttgtgtactaatttattcattaaaatctaattatt Find is-nt database================================================ Query_seq: TF1149:TF1150|TF1149:TF1150:conserved hypothetical protein; possible branched-chain amino acid aminotransferase:pyruvate-formate lyase:->->:1229988..1230303 316 taaaacgaccaccctgttattttataaattatgtataccatctataatatatcataattacacgctcaatatttgcttttgcgatttattttcgattattttgcgatcggaataccaattctttgaaatagtcatacaatttgacttttttcttaacaggtttttaagaattgaatattcatgggtggccatactgctttttgcggtgtatttctaataatcatttttgaatgaagtatatttgacttatttctttatctaaaattgacgttacaacattgttgtgtactaatttattcattaaaatctaattatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF1149:TF1150|TF1149:TF1150:conserved hypothetical protein; possible branched-chain amino acid aminotransferase:pyruvate-formate lyase:->->:1229988..1230303 316 taaaacgaccaccctgttattttataaattatgtataccatctataatatatcataattacacgctcaatatttgcttttgcgatttattttcgattattttgcgatcggaataccaattctttgaaatagtcatacaatttgacttttttcttaacaggtttttaagaattgaatattcatgggtggccatactgctttttgcggtgtatttctaataatcatttttgaatgaagtatatttgacttatttctttatctaaaattgacgttacaacattgttgtgtactaatttattcattaaaatctaattatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF1149:TF1150|TF1149:TF1150:conserved hypothetical protein; possible branched-chain amino acid aminotransferase:pyruvate-formate lyase:->->:1229988..1230303 316 taaaacgaccaccctgttattttataaattatgtataccatctataatatatcataattacacgctcaatatttgcttttgcgatttattttcgattattttgcgatcggaataccaattctttgaaatagtcatacaatttgacttttttcttaacaggtttttaagaattgaatattcatgggtggccatactgctttttgcggtgtatttctaataatcatttttgaatgaagtatatttgacttatttctttatctaaaattgacgttacaacattgttgtgtactaatttattcattaaaatctaattatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taaaacgaccaccctgttattttataaattatgtataccatctataatatatcataattacacgctcaatatttgcttttgcgatttattttcgattattttgcgatcggaataccaattctttgaaatagtcatacaatttgacttttttcttaacaggtttttaagaattgaatattcatgggtggccatactgctttttgcggtgtatttctaataatcatttttgaatgaagtatatttgacttatttctttatctaaaattgacgttacaacattgttgtgtactaatttattcattaaaatctaattatt Predict ORF larger than 30AA ================================================ Protein_Len: 60 Strand: + Start: 14 End: 214 ............. M L F Y K L C I P S I I Y H N Y T L N I C F C D L F S I I L R S E Y Q F F E I V I Q F D F F L N R F L R I E Y S W V A I ...................................................................................................... Protein_Len: 44 Strand: - Start: 61 End: 192 ............................................................ V S L I Q K Q S K N E I I K R D S Y W N K S I T M C N S K K R L L N K L I S Y E H T A M ............................................................................................................................ taaaacgaccaccctgttattttataaattatgtataccatctataatatatcataattacacgctcaatatttgcttttgcgatttattttcgattattttgcgatcggaataccaattctttgaaatagtcatacaatttgacttttttcttaacaggtttttaagaattgaatattcatgggtggccatactgctttttgcggtgtatttctaataatcatttttgaatgaagtatatttgacttatttctttatctaaaattgacgttacaacattgttgtgtactaatttattcattaaaatctaattatt 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: 278 End: 307 .....................................................................................................................................................................................................................................................................................ATTGTTGTGTACTAATTTATTCATTAAAAT......... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ taaaacgaccaccctgttattttataaattatgtataccatctataatatatcataattacacgctcaatatttgcttttgcgatttattttcgattattttgcgatcggaataccaattctttgaaatagtcatacaatttgacttttttcttaacaggtttttaagaattgaatattcatgggtggccatactgctttttgcggtgtatttctaataatcatttttgaatgaagtatatttgacttatttctttatctaaaattgacgttacaacattgttgtgtactaatttattcattaaaatctaattatt Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 71 HP_score: -2.8 Tail_Score: -5.4505 Start: 131 End: 145 Full_Region: CAATTCTTTGAAATA GTCATA CAA TTTGAC TTTTTTCTTAACAGG ..................................................................................................................................GTCATACAATTTGAC........................................................................................................................................................................... Find igs database================================================ Query_seq: TF1149:TF1150|TF1149:TF1150:conserved hypothetical protein; possible branched-chain amino acid aminotransferase:pyruvate-formate lyase:->->:1229988..1230303 316 taaaacgaccaccctgttattttataaattatgtataccatctataatatatcataattacacgctcaatatttgcttttgcgatttattttcgattattttgcgatcggaataccaattctttgaaatagtcatacaatttgacttttttcttaacaggtttttaagaattgaatattcatgggtggccatactgctttttgcggtgtatttctaataatcatttttgaatgaagtatatttgacttatttctttatctaaaattgacgttacaacattgttgtgtactaatttattcattaaaatctaattatt Intra-Species Hit: Count: 1 Min: 1 Max: 316 Len: 316 Subject: tfor_TF1149_TF1150|conserved hypothetical protein; possible branched-chain amino acid aminotransferase:pyruvate-formate lyase|POSITIVE:POSITIVE|[1229988,1230303]|316 HSP 1 e-value: 1.0E-178 bit: 626.0 Len: 316 Query Start:1 Query End:316 Subject Strand: POSITIVE Subject Start: 1 Subject End: 316 taaaacgaccaccctgttattttataaattatgtataccatctataatatatcataattacacgctcaatatttgcttttgcgatttattttcgattattttgcgatcggaataccaattctttgaaatagtcatacaatttgacttttttcttaacaggtttttaagaattgaatattcatgggtggccatactgctttttgcggtgtatttctaataatcatttttgaatgaagtatatttgacttatttctttatctaaaattgacgttacaacattgttgtgtactaatttattcattaaaatctaattatt taaaacgaccaccctgttattttataaattatgtataccatctataatatatcataattacacgctcaatatttgcttttgcgatttattttcgattattttgcgatcggaataccaattctttgaaatagtcatacaatttgacttttttcttaacaggtttttaagaattgaatattcatgggtggccatactgctttttgcggtgtatttctaataatcatttttgaatgaagtatatttgacttatttctttatctaaaattgacgttacaacattgttgtgtactaatttattcattaaaatctaattatt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAAACGACCACCCUGUUAUUUUAUAAAUUAUGUAUACCAUCUAUAAUAUAUCAUAAUUACACGCUCAAUAUUUGCUUUUGCGAUUUAUUUUCGAUUAUUUUGCGAUCGGAAUACCAAUUCUUUGAAAUAGUCAUACAAUUUGACUUUUUUCUUAACAGGUUUUUAAGAAUUGAAUAUUCAUGGGUGGCCAUACUGCUUUUUGCGGUGUAUUUCUAAUAAUCAUUUUUGAAUGAAGUAUAUUUGACUUAUUUCUUUAUCUAAAAUUGACGUUACAACAUUGUUGUGUACUAAUUUAUUCAUUAAAAUCUAAUUAUU ........((((((............(((((((((((..........)))).)))))))...(((..((((.((((....))))............))))..)))....(((((.((((((((.((((((((((.......))))).............))))).))))))))..)))))..))))))..(((((((.....)))))))...........(((.(((((.((((((.(((.......)))..)))))).))))).))).((((((((...)))))).))........................... (-56.03) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUAAUUAGAUUUUAAUGAAUAAAUUAGUACACAACAAUGUUGUAACGUCAAUUUUAGAUAAAGAAAUAAGUCAAAUAUACUUCAUUCAAAAAUGAUUAUUAGAAAUACACCGCAAAAAGCAGUAUGGCCACCCAUGAAUAUUCAAUUCUUAAAAACCUGUUAAGAAAAAAGUCAAAUUGUAUGACUAUUUCAAAGAAUUGGUAUUCCGAUCGCAAAAUAAUCGAAAAUAAAUCGCAAAAGCAAAUAUUGAGCGUGUAAUUAUGAUAUAUUAUAGAUGGUAUACAUAAUUUAUAAAAUAACAGGGUGGUCGUUUUA ((((((((..(((.((((((...........(((((...))))).............(((..(....)..)))........)))))).)))..))))))))...........((.....))...((((((((((..((((((.((((((((......((....)).....(((((.......)))))......))))))))))))))....(((..((((...((.......))((....))...))))..)))...(((((((.(((((((....))))))))))))))............)))))))))).... (-55.70) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 292 146 102 166 118 tfor:TF1899|5end_anti-sigma_factor_2052767..2052997_POSITIVE 286 210 175 156 123 tfor:TF0555|5end_Bacteroides_aerotolerance_protein,_BatB_587048..587278_POSITIVE 284 119 74 52 6 tfor:TF1001|5end_penicillin-binding_protein_1A_1054097..1054327_POSITIVE 282 211 177 221 185 tfor:TF1500|5end_conserved_hypothetical_protein_1599693..1599923_POSITIVE 280 107 61 231 186 tfor:TF2240|5end__tetracycline_resistance_element_mobilization_regulatory_protein_2414723..2414953_POSITIVE 279 116 71 175 130 tfor:TF2570|5end_50S_ribosomal_protein_L18_2742198..2742428_POSITIVE 275 210 180 157 123 tfor:TF2229.1|5end_rteR_regulatory_ortholog_(with_internal_stop)_2399454..2399684_POSITIVE 268 208 180 29 10 tfor:TF1909|5end_cobalamin_(5`-phosphate)_synthase_2063207..2063437_POSITIVE 265 210 172 172 134 tfor:TF2420|5end_hypothetical_protein_2599235..2599465_POSITIVE 265 216 172 134 92 tfor:TF2001|5end_conserved_hypothetical_protein_2155384..2155614_POSITIVE 264 214 171 185 135 tfor:TF2947|5end_isochorismate_synthase_3153633..3153863_POSITIVE 264 208 175 204 166 tfor:TF0745|5end_conserved_hypothetical_protein_790653..790883_POSITIVE 262 209 181 65 39 tfor:TF1346|5end_hypothetical_protein_1425880..1426110_POSITIVE 261 214 187 89 56 tfor:TF2542|5end_DNA_topoisomerase_III_2725544..2725774_POSITIVE 260 116 76 226 189 tfor:TF2380|5end_hemagglutinin_2545012..2545242_POSITIVE 260 212 173 36 1 tfor:TF0062|5end_conserved_hypothetical_protein_64916..65146_POSITIVE 259 229 181 212 166 tfor:TF2951|5end_O-succinylbenzoic_acid--CoA_ligase_3158496..3158726_POSITIVE 259 216 171 202 154 tfor:TF2160|5end_magnesium_chelatase,_subunit_I_2335974..2336204_POSITIVE 256 209 180 223 182 tfor:TF2301|5end_outer_membrane_protein,_TonB_dependent_receptor_2453288..2453518_POSITIVE 256 215 172 225 174 tfor:TF1863|5end_Fe-S_oxidoreductase_2018820..2019050_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 292 224 181 64 20 tfor:TF1993|3end_hypothetical_protein_2144522..2144672_POSITIVE 292 224 181 91 47 tfor:TF1992|3end_hypothetical_protein_2144549..2144699_POSITIVE 292 146 102 89 41 tfor:TF1898|3end_RNA_polymerase_ECF-type_sigma_factor_2052770..2052920_POSITIVE 286 210 175 142 109 tfor:TF0554|3end_Bacteroides_aerotolerance_protein,_BatC_587114..587264_POSITIVE 279 116 71 147 102 tfor:TF2569|3end_50S_ribosomal_protein_L6_2742250..2742400_POSITIVE 269 116 71 62 17 tfor:TF2823|3end_TPR-containing_protein_3014337..3014487_POSITIVE 268 208 180 41 22 tfor:TF1908|3end_possible_phosphoglycerate_mutase_2063299..2063449_POSITIVE 262 209 181 38 12 tfor:TF1344|3end_conserved_hypothetical_protein_1425933..1426083_POSITIVE 262 125 81 51 6 tfor:TF1000|3end_sec-independent_protein_translocase_1054169..1054319_POSITIVE 260 212 173 46 11 tfor:TF0061|3end_hypothetical_protein_65006..65156_POSITIVE 256 215 172 109 58 tfor:TF1862|3end_hypothetical_protein_2018784..2018934_POSITIVE 255 214 177 151 121 tfor:TF2607|3end_conserved_hypothetical_protein_2784645..2784795_POSITIVE 252 207 184 139 115 tfor:TF2347|3end_outer_membrane_protein,_TonB_dependent_receptor_2511092..2511242_POSITIVE 251 118 80 129 84 tfor:TF0442|3end_Na+-transporting_NADH:ubiquinone_oxidoreductase,_subunit_4_465928..466078_POSITIVE 250 110 64 149 96 tfor:TF2943|3end_50S_ribosomal_protein_L7/L12_3143567..3143717_POSITIVE 249 116 78 37 3 tfor:TF2816|3end_hypothetical_protein_3007184..3007334_POSITIVE 248 108 63 103 50 tfor:TF2850|3end_endoribonuclease_L-PSP_3038871..3039021_POSITIVE 248 200 155 102 54 tfor:TF0505|3end_4-diphosphocytidyl-2-C-methyl-D-erythritol_kinase_531103..531253_POSITIVE 247 215 184 140 111 tfor:TF2238|3end_conserved_hypothetical_protein_2414588..2414738_POSITIVE 245 215 180 143 111 tfor:TF2549|3end_30S_ribosomal_protein_S7_2732345..2732495_POSITIVE