Origin IGS: cttactctccttgaaaaatttgctcaaaaaaattataacatattaagtctattattacaatttttagattaattatttaccttagacttcaaaaattaattgaaagtttgtttaatttttttacaaaaaataagaaatagaagatgtgttcttgttggaaactttttagtaatgaaagtgttaattaagattaagtagttttatataattacaattttttctaattagctctctttattatattaaaaaatgtgttataatatatttatacaggtagtattaa .........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 ttaatactacctgtataaatatattataacacattttttaatataataaagagagctaattagaaaaaattgtaattatataaaactacttaatcttaattaacactttcattactaaaaagtttccaacaagaacacatcttctatttcttattttttgtaaaaaaattaaacaaactttcaattaatttttgaagtctaaggtaaataattaatctaaaaattgtaataatagacttaatatgttataatttttttgagcaaatttttcaaggagagtaag Mask Tandem Repeat Region ================================================ cttactctccttgaaaaatttgctcaaaaaaattataacatattaagtctattattacaatttttagattaattatttaccttagacttcaaaaattaattgaaagtttgtttaatttttttacaaaaaataagaaatagaagatgtgttcttgttggaaactttttagtaatgaaagtgttaattaagattaagtagttttatataattacaattttttctaattagctctctttattatattaaaaaatgtgttataatatatttatacaggtagtattaa Find is-nt database================================================ Query_seq: FN1837:FN1838|FN1837:FN1838:putative nucleotide-binding protein:Glycerol uptake facilitator protein:<-->:327346..327628 283 cttactctccttgaaaaatttgctcaaaaaaattataacatattaagtctattattacaatttttagattaattatttaccttagacttcaaaaattaattgaaagtttgtttaatttttttacaaaaaataagaaatagaagatgtgttcttgttggaaactttttagtaatgaaagtgttaattaagattaagtagttttatataattacaattttttctaattagctctctttattatattaaaaaatgtgttataatatatttatacaggtagtattaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN1837:FN1838|FN1837:FN1838:putative nucleotide-binding protein:Glycerol uptake facilitator protein:<-->:327346..327628 283 cttactctccttgaaaaatttgctcaaaaaaattataacatattaagtctattattacaatttttagattaattatttaccttagacttcaaaaattaattgaaagtttgtttaatttttttacaaaaaataagaaatagaagatgtgttcttgttggaaactttttagtaatgaaagtgttaattaagattaagtagttttatataattacaattttttctaattagctctctttattatattaaaaaatgtgttataatatatttatacaggtagtattaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN1837:FN1838|FN1837:FN1838:putative nucleotide-binding protein:Glycerol uptake facilitator protein:<-->:327346..327628 283 cttactctccttgaaaaatttgctcaaaaaaattataacatattaagtctattattacaatttttagattaattatttaccttagacttcaaaaattaattgaaagtttgtttaatttttttacaaaaaataagaaatagaagatgtgttcttgttggaaactttttagtaatgaaagtgttaattaagattaagtagttttatataattacaattttttctaattagctctctttattatattaaaaaatgtgttataatatatttatacaggtagtattaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 cttactctccttgaaaaatttgctcaaaaaaattataacatattaagtctattattacaatttttagattaattatttaccttagacttcaaaaattaattgaaagtttgtttaatttttttacaaaaaataagaaatagaagatgtgttcttgttggaaactttttagtaatgaaagtgttaattaagattaagtagttttatataattacaattttttctaattagctctctttattatattaaaaaatgtgttataatatatttatacaggtagtattaa Predict ORF larger than 30AA ================================================ Protein_Len: 32 Strand: + Start: 42 End: 137 ......................................... M K S I I T I F R L I I Y L R L Q K L I E S L F N F F T K N K K .................................................................................................................................................. Protein_Len: 32 Strand: + Start: 100 End: 195 ................................................................................................... M K V C L I F L Q K I R N R R C V L V G N F L V M K V L I K I K ........................................................................................ Protein_Len: 31 Strand: - Start: 99 End: 191 .................................................................................................. N F T Q K I K K C F I L F L L H T R T P F K K T I F T N I L M ............................................................................................ cttactctccttgaaaaatttgctcaaaaaaattataacatattaagtctattattacaatttttagattaattatttaccttagacttcaaaaattaattgaaagtttgtttaatttttttacaaaaaataagaaatagaagatgtgttcttgttggaaactttttagtaatgaaagtgttaattaagattaagtagttttatataattacaattttttctaattagctctctttattatattaaaaaatgtgttataatatatttatacaggtagtattaa 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: 87 Start: 32 End: 61 ...............................ATTGTAATAATAGACTTAATATGTTATAAT.............................................................................................................................................................................................................................. PromScan Matrix: RpoD-17 Strand: + Score: 83 Start: 10 End: 39 .........CTTGAAAAATTTGCTCAAAAAAATTATAAC.................................................................................................................................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ cttactctccttgaaaaatttgctcaaaaaaattataacatattaagtctattattacaatttttagattaattatttaccttagacttcaaaaattaattgaaagtttgtttaatttttttacaaaaaataagaaatagaagatgtgttcttgttggaaactttttagtaatgaaagtgttaattaagattaagtagttttatataattacaattttttctaattagctctctttattatattaaaaaatgtgttataatatatttatacaggtagtattaa Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: FN1837:FN1838|FN1837:FN1838:putative nucleotide-binding protein:Glycerol uptake facilitator protein:<-->:327346..327628 283 cttactctccttgaaaaatttgctcaaaaaaattataacatattaagtctattattacaatttttagattaattatttaccttagacttcaaaaattaattgaaagtttgtttaatttttttacaaaaaataagaaatagaagatgtgttcttgttggaaactttttagtaatgaaagtgttaattaagattaagtagttttatataattacaattttttctaattagctctctttattatattaaaaaatgtgttataatatatttatacaggtagtattaa Intra-Species Hit: Count: 1 Min: 1 Max: 283 Len: 283 Subject: NC_003454_FN1837_FN1838|putative nucleotide-binding protein:Glycerol uptake facilitator protein|NEGATIVE:POSITIVE|[327346,327628]|283 HSP 1 e-value: 1.0E-134 bit: 478.0 Len: 283 Query Start:1 Query End:283 Subject Strand: POSITIVE Subject Start: 1 Subject End: 283 cttactctccttgaaaaatttgctcnnnnnnnttataacatattaagtctattattacaatttttagattaattatttaccttagacttcaaaaattaattgaaagtttgtttaannnnnnnacaaaaaataagaaatagaagatgtgttcttgttggaaactttttagtaatgaaagtgttaattaagattaagtagttttatataattacaattttttctaattagctctctttattatattaaaaaatgtgttataatatatttatacaggtagtattaa cttactctccttgaaaaatttgctcaaaaaaattataacatattaagtctattattacaatttttagattaattatttaccttagacttcaaaaattaattgaaagtttgtttaatttttttacaaaaaataagaaatagaagatgtgttcttgttggaaactttttagtaatgaaagtgttaattaagattaagtagttttatataattacaattttttctaattagctctctttattatattaaaaaatgtgttataatatatttatacaggtagtattaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUUACUCUCCUUGAAAAAUUUGCUCAAAAAAAUUAUAACAUAUUAAGUCUAUUAUUACAAUUUUUAGAUUAAUUAUUUACCUUAGACUUCAAAAAUUAAUUGAAAGUUUGUUUAAUUUUUUUACAAAAAAUAAGAAAUAGAAGAUGUGUUCUUGUUGGAAACUUUUUAGUAAUGAAAGUGUUAAUUAAGAUUAAGUAGUUUUAUAUAAUUACAAUUUUUUCUAAUUAGCUCUCUUUAUUAUAUUAAAAAAUGUGUUAUAAUAUAUUUAUACAGGUAGUAUUAA ..((((..((((((.........))).....(((((((((((((.((((((..(.......)..)))))).........((.((((((((((.......))).)))))))..................(((((((((((.....))).))))))))))..........((((((((((.((((((((.((..((((((((......))))))...))..)))))))))).)).)))))))).......)))))))))))))..........))).)))).... (-42.50) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUAAUACUACCUGUAUAAAUAUAUUAUAACACAUUUUUUAAUAUAAUAAAGAGAGCUAAUUAGAAAAAAUUGUAAUUAUAUAAAACUACUUAAUCUUAAUUAACACUUUCAUUACUAAAAAGUUUCCAACAAGAACACAUCUUCUAUUUCUUAUUUUUUGUAAAAAAAUUAAACAAACUUUCAAUUAAUUUUUGAAGUCUAAGGUAAAUAAUUAAUCUAAAAAUUGUAAUAAUAGACUUAAUAUGUUAUAAUUUUUUUGAGCAAAUUUUUCAAGGAGAGUAAG ....((((.(((.......(((((((............))))))).........(((.....((((((((((((((.((((..............................((((.(((((((........((((......)))).......)))))))))))(((((((((............))))))))).(((((((..((..((((((........)))))).))..))))))).)))))))))))))))))).)))..........)))..)))).. (-33.96) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 686 50 1 141 92 NC_003454:FN1837|5end_putative_nucleotide-binding_protein_327255..327485_NEGATIVE 218 200 152 105 55 NC_003454:FN0666|5end_hypothetical_protein_1321599..1321829_POSITIVE 218 48 3 138 97 NC_003454:FN1972|5end_hypothetical_protein_472071..472301_NEGATIVE 206 253 214 119 78 NC_003454:FN1408|5end_Aminoacyl-histidine_dipeptidase_2067395..2067625_POSITIVE 206 236 197 106 69 NC_003454:FN0708|5end_Hypothetical_cytosolic_protein_1366668..1366898_POSITIVE 206 24 1 149 121 NC_003454:FN0573|5end_hypothetical_protein_1222518..1222748_POSITIVE 206 241 212 88 55 NC_003454:FN0044|5end_Shikimate_5-dehydrogenase_682701..682931_POSITIVE 203 84 43 104 58 NC_003454:FN1045|5end_hypothetical_protein_1695987..1696217_NEGATIVE 197 248 205 119 68 NC_003454:FN1711|5end_Methyltransferase_206325..206555_POSITIVE 195 236 214 155 131 NC_003454:FN0940|5end_hypothetical_protein_1593508..1593738_NEGATIVE 194 168 147 205 184 NC_003454:FN2034|5end_Protein_yicC_538795..539025_NEGATIVE 190 173 150 176 152 NC_003454:FN1137|5end_Phosphonates_transport_system_permease_protein_phnE_1783769..1783999_POSITIVE 183 90 41 103 65 NC_003454:FN0732|5end_hypothetical_protein_1388270..1388500_POSITIVE 180 246 228 54 36 NC_003454:FN0989|5end_phosphoribosylaminoimidazole_carboxylase_catalytic_subunit_1641667..1641897_NEGATIVE 179 34 5 98 68 NC_003454:FN0840|5end_Transposase_1501361..1501591_POSITIVE 179 182 142 59 26 NC_003454:FN0658|5end_ABC_transporter_substrate-binding_protein_1315675..1315905_NEGATIVE 179 34 5 98 68 NC_003454:FN0485|5end_Transposase_1130267..1130497_POSITIVE 178 49 1 143 93 NC_003454:FN0710|5end_hypothetical_protein_1368875..1369105_POSITIVE 177 54 15 116 80 NC_003454:FN0962|5end_Hypothetical_cytosolic_protein_1616887..1617117_NEGATIVE 176 240 194 226 181 NC_003454:FN1289|5end_hypothetical_protein_1946447..1946677_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 218 200 152 52 2 NC_003454:FN0665|3end_N-acetylmuramoyl-L-alanine_amidase_1321626..1321776_POSITIVE 206 236 197 134 97 NC_003454:FN0707|3end_FMN_adenylyltransferase_1366776..1366926_POSITIVE 206 241 212 125 92 NC_003454:FN0043|3end_Hypothetical_exported_24-amino_acid_repeat_protein_682818..682968_POSITIVE 197 248 205 61 10 NC_003454:FN1710|3end_Integral_membrane_protein,_YGGT_family_206347..206497_POSITIVE 195 236 214 136 112 NC_003454:FN0941|3end_Gamma-glutamyltranspeptidase_1593527..1593677_NEGATIVE 183 90 41 86 48 NC_003454:FN0731|3end_hypothetical_protein_1388333..1388483_POSITIVE 180 246 228 42 24 NC_003454:FN0990|3end_Phosphoribosylformylglycinamidine_synthase_1641679..1641829_NEGATIVE 180 230 186 112 66 NC_003454:FN0216|3end_3-oxoacyl-[acyl-carrier_protein]_reductase_840112..840262_NEGATIVE 179 182 142 44 11 NC_003454:FN0659|3end_ABC_transporter_permease_protein_1315690..1315840_NEGATIVE 178 167 130 110 60 NC_003454:FN1060|3end_Molybdate_metabolism_regulator_1707032..1707182_NEGATIVE 178 49 1 76 26 NC_003454:FN0709|3end_Virulence_factor_mviN_1368888..1369038_POSITIVE 178 240 196 77 36 NC_003454:FN0415|3end_hypothetical_protein_1053996..1054146_POSITIVE 176 48 4 113 74 NC_003454:FN0100|3end_Flavodoxins/hemoproteins_735119..735269_NEGATIVE 176 155 128 47 17 NC_003454:FN1550|3end_hypothetical_protein_64887..65037_NEGATIVE 175 233 191 115 69 NC_003454:FN1713|3end_tRNA_(Uracil-5-)_-methyltransferase_208968..209118_POSITIVE 174 267 222 132 88 NC_003454:FN1847|3end_DTDP-4-dehydrorhamnose_3,5-epimerase_337208..337358_POSITIVE 173 257 215 112 66 NC_003454:FN0591|3end_Putative_efflux_pump_component_MtrF_1244053..1244203_NEGATIVE 172 236 215 151 132 NC_003454:FN2065|3end_Transcriptional_repressor_576397..576547_POSITIVE 171 236 209 119 91 NC_003454:FN1443|3end_Transposase_2111009..2111159_NEGATIVE 171 200 154 81 40 NC_003454:FN1064|3end_hypothetical_protein_1711369..1711519_POSITIVE