Origin IGS: aaaaaaatttagctacaaagtattaattttaggtttgtagcttttttttatacattttttttaaattctcttgcaaaaataatttttttattatataatagatatataaataaatttaatttgcaaaacaaaataaatttataaaagttttttaagatgttatcataccaaccttataataaaaagggctgctacattctaattttgtggcagcccttttacttttattttata .........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 tataaaataaaagtaaaagggctgccacaaaattagaatgtagcagccctttttattataaggttggtatgataacatcttaaaaaacttttataaatttattttgttttgcaaattaaatttatttatatatctattatataataaaaaaattatttttgcaagagaatttaaaaaaaatgtataaaaaaaagctacaaacctaaaattaatactttgtagctaaattttttt Mask Tandem Repeat Region ================================================ aaaaaaatttagctacaaagtattaattttaggtttgtagcttttttttatacattttttttaaattctcttgcaaaaataatttttttattatataatagatatataaataaatttaatttgcaaaacaaaataaatttataaaagttttttaagatgttatcataccaaccttataataaaaagggctgctacattctaattttgtggcagcccttttacttttattttata Find is-nt database================================================ Query_seq: FN1783:FN1784|FN1783:FN1784:Ethanolamine utilization protein eutJ:hypothetical protein:-><-:265591..265824 234 aaaaaaatttagctacaaagtattaattttaggtttgtagcttttttttatacattttttttaaattctcttgcaaaaataatttttttattatataatagatatataaataaatttaatttgcaaaacaaaataaatttataaaagttttttaagatgttatcataccaaccttataataaaaagggctgctacattctaattttgtggcagcccttttacttttattttata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN1783:FN1784|FN1783:FN1784:Ethanolamine utilization protein eutJ:hypothetical protein:-><-:265591..265824 234 aaaaaaatttagctacaaagtattaattttaggtttgtagcttttttttatacattttttttaaattctcttgcaaaaataatttttttattatataatagatatataaataaatttaatttgcaaaacaaaataaatttataaaagttttttaagatgttatcataccaaccttataataaaaagggctgctacattctaattttgtggcagcccttttacttttattttata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN1783:FN1784|FN1783:FN1784:Ethanolamine utilization protein eutJ:hypothetical protein:-><-:265591..265824 234 aaaaaaatttagctacaaagtattaattttaggtttgtagcttttttttatacattttttttaaattctcttgcaaaaataatttttttattatataatagatatataaataaatttaatttgcaaaacaaaataaatttataaaagttttttaagatgttatcataccaaccttataataaaaagggctgctacattctaattttgtggcagcccttttacttttattttata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aaaaaaatttagctacaaagtattaattttaggtttgtagcttttttttatacattttttttaaattctcttgcaaaaataatttttttattatataatagatatataaataaatttaatttgcaaaacaaaataaatttataaaagttttttaagatgttatcataccaaccttataataaaaagggctgctacattctaattttgtggcagcccttttacttttattttata Predict ORF larger than 30AA ================================================ Protein_Len: 40 Strand: + Start: 22 End: 141 ..................... M N F R F V A F F Y T F F L N S L A K I I F L L Y N R Y I N K F N L Q N K I N L ............................................................................................. Protein_Len: 36 Strand: - Start: 51 End: 158 .................................................. V N K K F E R A F I I K K N Y L L Y I F L N L K C F L I F K Y F N K L M ............................................................................ aaaaaaatttagctacaaagtattaattttaggtttgtagcttttttttatacattttttttaaattctcttgcaaaaataatttttttattatataatagatatataaataaatttaatttgcaaaacaaaataaatttataaaagttttttaagatgttatcataccaaccttataataaaaagggctgctacattctaattttgtggcagcccttttacttttattttata 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: 88 Start: 70 End: 99 .....................................................................CTTGCAAAAATAATTTTTTTATTATATAAT....................................................................................................................................... PromScan Matrix: RpoD-17 Strand: + Score: 83 Start: 151 End: 180 ......................................................................................................................................................TTTAAGATGTTATCATACCAACCTTATAAT...................................................... PromScan Matrix: RpoD-17 Strand: + Score: 82 Start: 137 End: 166 ........................................................................................................................................ATTTATAAAAGTTTTTTAAGATGTTATCAT.................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aaaaaaatttagctacaaagtattaattttaggtttgtagcttttttttatacattttttttaaattctcttgcaaaaataatttttttattatataatagatatataaataaatttaatttgcaaaacaaaataaatttataaaagttttttaagatgttatcataccaaccttataataaaaagggctgctacattctaattttgtggcagcccttttacttttattttata Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 95 HP_score: -10.5 Tail_Score: -4.83677 Start: 186 End: 216 Full_Region: ACCTTATAATAAAAA GGGCTGCTACA TTCTAATTT TGTGGCAGCCC TTTTACTTTTATTTT .........................................................................................................................................................................................GGGCTGCTACATTCTAATTTTGTGGCAGCCC.................. Find igs database================================================ Query_seq: FN1783:FN1784|FN1783:FN1784:Ethanolamine utilization protein eutJ:hypothetical protein:-><-:265591..265824 234 aaaaaaatttagctacaaagtattaattttaggtttgtagcttttttttatacattttttttaaattctcttgcaaaaataatttttttattatataatagatatataaataaatttaatttgcaaaacaaaataaatttataaaagttttttaagatgttatcataccaaccttataataaaaagggctgctacattctaattttgtggcagcccttttacttttattttata Intra-Species Hit: Count: 1 Min: 8 Max: 234 Len: 227 Subject: NC_003454_FN1783_FN1784|Ethanolamine utilization protein eutJ:hypothetical protein|POSITIVE:NEGATIVE|[265591,265824]|234 HSP 1 e-value: 2.0E-37 bit: 157.0 Len: 79 Query Start:156 Query End:234 Subject Strand: POSITIVE Subject Start: 156 Subject End: 234 ...........................................................................................................................................................gatgttatcataccaaccttataataaaaagggctgctacattctaattttgtggcagcccttttacttttattttata ...........................................................................................................................................................gatgttatcataccaaccttataataaaaagggctgctacattctaattttgtggcagcccttttacttttattttata HSP 2 e-value: 1.0E-10 bit: 67.9 Len: 34 Query Start:8 Query End:41 Subject Strand: POSITIVE Subject Start: 8 Subject End: 41 .......tttagctacaaagtattaattttaggtttgtagc................................................................................................................................................................................................. .......tttagctacaaagtattaattttaggtttgtagc................................................................................................................................................................................................. Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUAGCUACAAAGUAUUAAUUUUAGGUUUGUAGCUUUUUUUUAUACAUUUUUUUUAAAUUCUCUUGCAAAAAUAAUUUUUUUAUUAUAUAAUAGAUAUAUAAAUAAAUUUAAUUUGCAAAACAAAAUAAAUUUAUAAAAGUUUUUUAAGAUGUUAUCAUACCAACCUUAUAAUAAAAAGGGCUGCUACAUUCUAAUUUUGUGGCAGCCCUUUUACUUUUAUUUUAUA ...(((((((((.(..........).)))))))))............................(((((((...(((((.(((((.((((.....))))))))).)))))...)))))))......(((((...((((((((........(((....)))...............(((((((((((((((.........)))))))))))))))))))))))))))). (-48.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAUAAAAUAAAAGUAAAAGGGCUGCCACAAAAUUAGAAUGUAGCAGCCCUUUUUAUUAUAAGGUUGGUAUGAUAACAUCUUAAAAAACUUUUAUAAAUUUAUUUUGUUUUGCAAAUUAAAUUUAUUUAUAUAUCUAUUAUAUAAUAAAAAAAUUAUUUUUGCAAGAGAAUUUAAAAAAAAUGUAUAAAAAAAAGCUACAAACCUAAAAUUAAUACUUUGUAGCUAAA ......((((((((.((((((((((.(((.........))).))))))))))((((((((.......))))))))...........))))))))...((((..((.(((((((((...(((((..(((((((.....))))))).....)))))...))))))))).))..)))).................(((((((((..............)))))))))... (-50.94) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 362 217 173 143 96 NC_003454:FN1269|5end_Hypothetical_lipoprotein_1926242..1926472_NEGATIVE 270 210 166 56 5 NC_003454:FN1192|5end_hypothetical_protein_1854679..1854909_POSITIVE 267 216 179 92 52 NC_003454:FN1003|5end_Outer_membrane_protein_P1_precursor_1658822..1659052_POSITIVE 265 207 174 187 146 NC_003454:FN0851|5end_Biotin_synthesis_protein_bioC_1509520..1509750_POSITIVE 249 68 21 169 121 NC_003454:FN2109|5end_UDP-glucose_4-epimerase_620848..621078_POSITIVE 245 213 178 62 33 NC_003454:FN1723|5end_glucose-inhibited_division_protein_A_222645..222875_NEGATIVE 224 214 177 156 119 NC_003454:FN0740|5end_imidazolonepropionase_1398914..1399144_NEGATIVE 224 210 176 169 127 NC_003454:FN2104|5end_hypothetical_protein_614237..614467_POSITIVE 215 207 175 231 200 NC_003454:FN0512|5end_Flavoprotein_1162597..1162827_NEGATIVE 215 62 21 108 65 NC_003454:FN0092|5end_NADPH-dependent_butanol_dehydrogenase_727908..728138_POSITIVE 213 209 178 189 150 NC_003454:FN1941|5end_ClpB_protein_441279..441509_POSITIVE 212 84 47 40 8 NC_003454:FN0288|5end_Hypoxanthine-guanine_phosphoribosyltransferase_915765..915995_NEGATIVE 211 216 181 68 33 NC_003454:FN0007|5end_glucose-inhibited_division_protein_A_645938..646168_POSITIVE 209 187 148 113 77 NC_003454:FN0626|5end_Hypothetical_cytosolic_protein_1286092..1286322_NEGATIVE 209 210 178 71 36 NC_003454:FN0310|5end_Iron(III)-transport_ATP-binding_protein_sfuC_945796..946026_POSITIVE 208 45 4 185 144 NC_003454:FN0317|5end_tryptophan_synthase_subunit_beta_955006..955236_NEGATIVE 207 204 182 43 19 NC_003454:FN0706|5end_Hypothetical_cytosolic_protein_1364823..1365053_POSITIVE 204 208 181 57 33 NC_003454:FN1927|5end_DEGV_protein_427952..428182_NEGATIVE 202 210 165 203 146 NC_003454:FN1678|5end_hypothetical_protein_174287..174517_POSITIVE 201 44 4 63 23 NC_003454:FN0342|5end_Peptidyl-prolyl_cis-trans_isomerase_975925..976155_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 362 217 173 59 12 NC_003454:FN1270|3end_Hypothetical_cytosolic_protein_1926326..1926476_NEGATIVE 278 219 173 106 44 NC_003454:FN1140|3end_Activator_of_(R)-2-hydroxyglutaryl-CoA_dehydratase_1790473..1790623_POSITIVE 277 214 171 68 12 NC_003454:FN1908|3end_Glycerophosphoryl_diester_phosphodiesterase_400596..400746_NEGATIVE 272 220 171 69 21 NC_003454:FN1881|3end_Esterase_368250..368400_NEGATIVE 264 218 177 92 40 NC_003454:FN1141|3end_Formate_transporter_1790493..1790643_NEGATIVE 258 220 174 76 32 NC_003454:FN1170|3end_Pyruvate-flavodoxin_oxidoreductase_1828707..1828857_NEGATIVE 257 202 168 60 27 NC_003454:FN1464|3end_1-deoxy-D-xylulose-5-phosphate_synthase_2145954..2146104_NEGATIVE 253 212 175 85 42 NC_003454:FN0637|3end_Hypothetical_exported_24-amino_acid_repeat_protein_1295636..1295786_NEGATIVE 245 213 178 53 24 NC_003454:FN1724|3end_Potassium_uptake_protein_KtrA_222654..222804_NEGATIVE 234 220 171 101 41 NC_003454:FN0853|3end_Glycogen_synthase_1510922..1511072_NEGATIVE 231 215 175 80 42 NC_003454:FN1381|3end_hypothetical_protein_2028904..2029054_NEGATIVE 229 210 177 84 43 NC_003454:FN0590|3end_N-acyl-L-amino_acid_amidohydrolase_1242856..1243006_NEGATIVE 228 211 178 86 45 NC_003454:FN0589|3end_Transcriptional_regulator,_MarR_family_1242833..1242983_POSITIVE 227 219 173 106 47 NC_003454:FN1380|3end_Citrate_lyase_beta_chain_2028878..2029028_POSITIVE 225 213 172 83 31 NC_003454:FN0636|3end_hypothetical_protein_1295609..1295759_POSITIVE 224 214 177 79 42 NC_003454:FN0741|3end_Glutamate_formiminotransferase_1398991..1399141_NEGATIVE 224 210 176 61 19 NC_003454:FN2103|3end_RecA_protein_614209..614359_POSITIVE 224 213 179 61 29 NC_003454:FN1508|3end_3,4-dihydroxy-2-butanone-4-phosphate_synthase_14117..14267_POSITIVE 219 212 179 85 54 NC_003454:FN0532|3end_Hypothetical_membrane-spanning_protein_1186524..1186674_NEGATIVE 219 207 172 80 45 NC_003454:FN0212|3end_hypothetical_protein_837583..837733_NEGATIVE