Origin IGS: ttttaagcctccattattattttttaataaagcctaatttcagtataatactctattaagaataaatcaatagcaaaaataatattttcttattttttgataagaattataaaaaatagtagaatatattgataaattattataatatatataaatgacaacatcatattaaatattgcattaaaaagacatttagaatatagaaaaaaatgtaagttttagaaaaaagggagggaaattta .........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 taaatttccctcccttttttctaaaacttacatttttttctatattctaaatgtctttttaatgcaatatttaatatgatgttgtcatttatatatattataataatttatcaatatattctactattttttataattcttatcaaaaaataagaaaatattatttttgctattgatttattcttaatagagtattatactgaaattaggctttattaaaaaataataatggaggcttaaaa Mask Tandem Repeat Region ================================================ ttttaagcctccattattattttttaataaagcctaatttcagtataatactctattaagaataaatcaatagcaaaaataatattttcttattttttgataagaattataaaaaatagtagaatatattgataaattattataatatatataaatgacaacatcatattaaatattgcattaaaaagacatttagaatatagaaaaaaatgtaagttttagaaaaaagggagggaaattta Find is-nt database================================================ Query_seq: FN1055:FN1056|FN1055:FN1056:Cysteine synthase:hypothetical protein:<-->:1703591..1703832 242 ttttaagcctccattattattttttaataaagcctaatttcagtataatactctattaagaataaatcaatagcaaaaataatattttcttattttttgataagaattataaaaaatagtagaatatattgataaattattataatatatataaatgacaacatcatattaaatattgcattaaaaagacatttagaatatagaaaaaaatgtaagttttagaaaaaagggagggaaattta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN1055:FN1056|FN1055:FN1056:Cysteine synthase:hypothetical protein:<-->:1703591..1703832 242 ttttaagcctccattattattttttaataaagcctaatttcagtataatactctattaagaataaatcaatagcaaaaataatattttcttattttttgataagaattataaaaaatagtagaatatattgataaattattataatatatataaatgacaacatcatattaaatattgcattaaaaagacatttagaatatagaaaaaaatgtaagttttagaaaaaagggagggaaattta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN1055:FN1056|FN1055:FN1056:Cysteine synthase:hypothetical protein:<-->:1703591..1703832 242 ttttaagcctccattattattttttaataaagcctaatttcagtataatactctattaagaataaatcaatagcaaaaataatattttcttattttttgataagaattataaaaaatagtagaatatattgataaattattataatatatataaatgacaacatcatattaaatattgcattaaaaagacatttagaatatagaaaaaaatgtaagttttagaaaaaagggagggaaattta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttttaagcctccattattattttttaataaagcctaatttcagtataatactctattaagaataaatcaatagcaaaaataatattttcttattttttgataagaattataaaaaatagtagaatatattgataaattattataatatatataaatgacaacatcatattaaatattgcattaaaaagacatttagaatatagaaaaaaatgtaagttttagaaaaaagggagggaaattta Predict ORF larger than 30AA ================================================ ttttaagcctccattattattttttaataaagcctaatttcagtataatactctattaagaataaatcaatagcaaaaataatattttcttattttttgataagaattataaaaaatagtagaatatattgataaattattataatatatataaatgacaacatcatattaaatattgcattaaaaagacatttagaatatagaaaaaaatgtaagttttagaaaaaagggagggaaattta 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: 83 Start: 20 End: 49 ...................TTTTTTAATAAAGCCTAATTTCAGTATAAT................................................................................................................................................................................................. PromScan Matrix: RpoD-17 Strand: - Score: 83 Start: 42 End: 71 .........................................ATTGATTTATTCTTAATAGAGTATTATACT........................................................................................................................................................................... PromScan Matrix: RpoD-17 Strand: + Score: 83 Start: 96 End: 125 ...............................................................................................TTTGATAAGAATTATAAAAAATAGTAGAAT..................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ttttaagcctccattattattttttaataaagcctaatttcagtataatactctattaagaataaatcaatagcaaaaataatattttcttattttttgataagaattataaaaaatagtagaatatattgataaattattataatatatataaatgacaacatcatattaaatattgcattaaaaagacatttagaatatagaaaaaaatgtaagttttagaaaaaagggagggaaattta Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: FN1055:FN1056|FN1055:FN1056:Cysteine synthase:hypothetical protein:<-->:1703591..1703832 242 ttttaagcctccattattattttttaataaagcctaatttcagtataatactctattaagaataaatcaatagcaaaaataatattttcttattttttgataagaattataaaaaatagtagaatatattgataaattattataatatatataaatgacaacatcatattaaatattgcattaaaaagacatttagaatatagaaaaaaatgtaagttttagaaaaaagggagggaaattta Intra-Species Hit: Count: 1 Min: 1 Max: 242 Len: 242 Subject: NC_003454_FN1055_FN1056|Cysteine synthase:hypothetical protein|NEGATIVE:POSITIVE|[1703591,1703832]|242 HSP 1 e-value: 2.0E-43 bit: 176.0 Len: 89 Query Start:1 Query End:89 Subject Strand: POSITIVE Subject Start: 1 Subject End: 89 ttttaagcctccattattattttttaataaagcctaatttcagtataatactctattaagaataaatcaatagcaaaaataatattttc......................................................................................................................................................... ttttaagcctccattattattttttaataaagcctaatttcagtataatactctattaagaataaatcaatagcaaaaataatattttc......................................................................................................................................................... HSP 2 e-value: 1.0E-10 bit: 67.9 Len: 55 Query Start:188 Query End:242 Subject Strand: POSITIVE Subject Start: 188 Subject End: 242 ...........................................................................................................................................................................................gacatttagaatatagnnnnnnntgtaagttttagaaaaaagggagggaaattta ...........................................................................................................................................................................................gacatttagaatatagaaaaaaatgtaagttttagaaaaaagggagggaaattta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUUAAGCCUCCAUUAUUAUUUUUUAAUAAAGCCUAAUUUCAGUAUAAUACUCUAUUAAGAAUAAAUCAAUAGCAAAAAUAAUAUUUUCUUAUUUUUUGAUAAGAAUUAUAAAAAAUAGUAGAAUAUAUUGAUAAAUUAUUAUAAUAUAUAUAAAUGACAACAUCAUAUUAAAUAUUGCAUUAAAAAGACAUUUAGAAUAUAGAAAAAAAUGUAAGUUUUAGAAAAAAGGGAGGGAAAUUUA .......(((((.......(((((((((......(((((((((((((....(((((((.((.....))..................((((((((....))))))))..........))))))).))))))))..)))))...((((((.((...((((.....))))..)).)))))).)))))))))...((((((((.((.(......).)).))))))))......)))))........ (-34.20) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAAUUUCCCUCCCUUUUUUCUAAAACUUACAUUUUUUUCUAUAUUCUAAAUGUCUUUUUAAUGCAAUAUUUAAUAUGAUGUUGUCAUUUAUAUAUAUUAUAAUAAUUUAUCAAUAUAUUCUACUAUUUUUUAUAAUUCUUAUCAAAAAAUAAGAAAAUAUUAUUUUUGCUAUUGAUUUAUUCUUAAUAGAGUAUUAUACUGAAAUUAGGCUUUAUUAAAAAAUAAUAAUGGAGGCUUAAAA ........(((((......(((((................(((((..((((((..........((((((((......)))))))))))))).))))).............(((.((((..((.(((((....((((.((......((((((((.......))))))))......)).))))....)))))))...)))).)))..)))))..((((((.....)))))).)))))....... (-33.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 687 80 31 171 122 NC_003454:FN1055|5end_Cysteine_synthase_1703500..1703730_NEGATIVE 234 130 84 151 95 NC_003454:FN0773|5end_hypothetical_protein_1429274..1429504_POSITIVE 216 47 8 196 154 NC_003454:FN1939|5end_hypothetical_protein_439465..439695_NEGATIVE 216 44 1 189 148 NC_003454:FN1911|5end_Outer_membrane_protein_405285..405515_NEGATIVE 213 33 4 176 144 NC_003454:FN1047|5end_Hypothetical_membrane-spanning_protein_1697175..1697405_POSITIVE 203 23 1 118 93 NC_003454:FN0854|5end_Glucose-1-phosphate_adenylyltransferase_1513487..1513717_NEGATIVE 199 234 194 193 158 NC_003454:FN0122|5end_hypothetical_protein_753401..753631_POSITIVE 196 45 1 74 28 NC_003454:FN1366|5end_Triosephosphate_isomerase_2017518..2017748_NEGATIVE 196 239 194 193 146 NC_003454:FN0407|5end_hypothetical_protein_1045178..1045408_NEGATIVE 195 238 208 220 191 NC_003454:FN1796|5end_hypothetical_protein_278476..278706_POSITIVE 189 41 6 132 87 NC_003454:FN2115|5end_hypothetical_protein_624843..625073_NEGATIVE 186 220 178 160 120 NC_003454:FN0790|5end_Xylose_repressor_1446457..1446687_NEGATIVE 184 58 16 160 120 NC_003454:FN0766|5end_Large-conductance_mechanosensitive_channel_1421910..1422140_POSITIVE 183 46 6 130 83 NC_003454:FN0777|5end_GTP-binding_protein_LepA_1434832..1435062_NEGATIVE 181 35 9 125 97 NC_003454:FN1367|5end_Methyl-accepting_chemotaxis_protein_2018143..2018373_NEGATIVE 177 35 8 54 24 NC_003454:FN1092|5end_hypothetical_protein_1737267..1737497_POSITIVE 176 45 2 74 33 NC_003454:FN0087|5end_Ethanolamine_utilization_protein_eutN_724626..724856_POSITIVE 176 225 188 216 174 NC_003454:FN0008|5end_quinolinate_synthetase_648010..648240_POSITIVE 175 43 12 209 175 NC_003454:FN0039|5end_DNA_primase_(bacterial_type)_and_small_primase-like_proteins_679212..679442_NEGATIVE 173 58 23 81 45 NC_003454:FN1519|5end_23S_rRNA_methyltransferase_24792..25022_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 234 130 84 80 24 NC_003454:FN0772|3end_Flavodoxin_1429283..1429433_POSITIVE 216 47 8 76 34 NC_003454:FN1940|3end_Na+_driven_multidrug_efflux_pump_439585..439735_NEGATIVE 216 44 1 56 15 NC_003454:FN1912|3end_hypothetical_protein_405418..405568_NEGATIVE 213 33 4 109 77 NC_003454:FN1046|3end_hypothetical_protein_1697188..1697338_POSITIVE 203 23 1 97 72 NC_003454:FN0855|3end_glucose-1-phosphate_adenylyltransferase_1513508..1513658_NEGATIVE 200 234 195 59 21 NC_003454:FN1655|3end_Hypothetical_cytosolic_protein_152516..152666_POSITIVE 199 54 28 145 112 NC_003454:FN0766|3end_Large-conductance_mechanosensitive_channel_1422418..1422568_POSITIVE 196 45 1 54 8 NC_003454:FN1367|3end_Methyl-accepting_chemotaxis_protein_2017538..2017688_NEGATIVE 193 127 86 118 78 NC_003454:FN1668|3end_Cholinephosphate_cytidylyltransferase_164691..164841_NEGATIVE 188 233 195 67 33 NC_003454:FN0620|3end_hypothetical_protein_1279819..1279969_POSITIVE 186 47 5 126 81 NC_003454:FN1009|3end_hypothetical_protein_1663606..1663756_NEGATIVE 184 58 16 130 90 NC_003454:FN0765|3end_tRNA_(5-methylaminomethyl-2-thiouridylate)_-methyltransferase_1421960..1422110_POSITIVE 183 236 191 65 17 NC_003454:FN1175|3end_hypothetical_protein_1836557..1836707_NEGATIVE 183 46 6 113 66 NC_003454:FN0778|3end_Methyltransferase_1434849..1434999_NEGATIVE 182 46 4 91 36 NC_003454:FN0031|3end_hypothetical_protein_667899..668049_NEGATIVE 181 35 9 111 83 NC_003454:FN1368|3end_COMF_operon_protein_3_2018157..2018307_NEGATIVE 178 236 210 101 79 NC_003454:FN1705|3end_hypothetical_protein_201464..201614_NEGATIVE 177 35 8 45 15 NC_003454:FN1091|3end_Sigma_factor_sigB_regulation_protein_rsbU_1737338..1737488_POSITIVE 176 45 2 72 31 NC_003454:FN0086|3end_hypothetical_protein_724704..724854_POSITIVE 173 40 6 123 75 NC_003454:FN1880|3end_Dihydropteridine_reductase_368211..368361_POSITIVE