Origin IGS: aatattttaaagaggataagttatgaaaatagaaaagtagtaaataaatagaggaattctattcctctattttacttgttattaaggtgtaattgtataaaataaaaaaaatatttaataatttttaccaaattttaatgataaattcatataattaagatataattttataagcaatctattttttgtaagaaagattatagaaattgtactaaagaatttatataataaagtaggtaaatatataaaaatttcatatcaaatttataatagttattataaaaacaaataaaatgttttaggaggaataaatgaaaaagttgttagcagggttattattagtaagctca .........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 tgagcttactaataataaccctgctaacaactttttcatttattcctcctaaaacattttatttgtttttataataactattataaatttgatatgaaatttttatatatttacctactttattatataaattctttagtacaatttctataatctttcttacaaaaaatagattgcttataaaattatatcttaattatatgaatttatcattaaaatttggtaaaaattattaaatattttttttattttatacaattacaccttaataacaagtaaaatagaggaatagaattcctctatttatttactacttttctattttcataacttatcctctttaaaatatt Mask Tandem Repeat Region ================================================ aatattttaaagaggataagttatgaaaatagaaaagtagtaaataaatagaggaattctattcctctattttacttgttattaaggtgtaattgtataaaataaaaaaaatatttaataatttttaccaaattttaatgataaattcatataattaagatataattttataagcaatctattttttgtaagaaagattatagaaattgtactaaagaatttatataataaagtaggtaaatatataaaaatttcatatcaaatttataatagttattataaaaacaaataaaatgttttaggaggaataaatgaaaaagttgttagcagggttattattagtaagctca Find is-nt database================================================ Query_seq: FN0023:FN0024|FN0023:FN0024:Short-chain fatty acids transporter:Hypothetical exported 24-amino acid repeat protein:->->:662841..663190 350 aatattttaaagaggataagttatgaaaatagaaaagtagtaaataaatagaggaattctattcctctattttacttgttattaaggtgtaattgtataaaataaaaaaaatatttaataatttttaccaaattttaatgataaattcatataattaagatataattttataagcaatctattttttgtaagaaagattatagaaattgtactaaagaatttatataataaagtaggtaaatatataaaaatttcatatcaaatttataatagttattataaaaacaaataaaatgttttaggaggaataaatgaaaaagttgttagcagggttattattagtaagctca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN0023:FN0024|FN0023:FN0024:Short-chain fatty acids transporter:Hypothetical exported 24-amino acid repeat protein:->->:662841..663190 350 aatattttaaagaggataagttatgaaaatagaaaagtagtaaataaatagaggaattctattcctctattttacttgttattaaggtgtaattgtataaaataaaaaaaatatttaataatttttaccaaattttaatgataaattcatataattaagatataattttataagcaatctattttttgtaagaaagattatagaaattgtactaaagaatttatataataaagtaggtaaatatataaaaatttcatatcaaatttataatagttattataaaaacaaataaaatgttttaggaggaataaatgaaaaagttgttagcagggttattattagtaagctca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN0023:FN0024|FN0023:FN0024:Short-chain fatty acids transporter:Hypothetical exported 24-amino acid repeat protein:->->:662841..663190 350 aatattttaaagaggataagttatgaaaatagaaaagtagtaaataaatagaggaattctattcctctattttacttgttattaaggtgtaattgtataaaataaaaaaaatatttaataatttttaccaaattttaatgataaattcatataattaagatataattttataagcaatctattttttgtaagaaagattatagaaattgtactaaagaatttatataataaagtaggtaaatatataaaaatttcatatcaaatttataatagttattataaaaacaaataaaatgttttaggaggaataaatgaaaaagttgttagcagggttattattagtaagctca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aatattttaaagaggataagttatgaaaatagaaaagtagtaaataaatagaggaattctattcctctattttacttgttattaaggtgtaattgtataaaataaaaaaaatatttaataatttttaccaaattttaatgataaattcatataattaagatataattttataagcaatctattttttgtaagaaagattatagaaattgtactaaagaatttatataataaagtaggtaaatatataaaaatttcatatcaaatttataatagttattataaaaacaaataaaatgttttaggaggaataaatgaaaaagttgttagcagggttattattagtaagctca Predict ORF larger than 30AA ================================================ Protein_Len: 40 Strand: + Start: 170 End: 289 ......................................................................................................................................................................... M S N L F F V R K I I E I V L K N L Y N K V G K Y I K I S Y Q I Y N S Y Y K N K ............................................................. Protein_Len: 30 Strand: - Start: 201 End: 290 ........................................................................................................................................................................................................ L F Q V L S N I Y Y L L Y I Y L F K M D F K Y Y N N Y F C M ............................................................ Protein_Len: 45 Strand: - Start: 118 End: 252 ..................................................................................................................... Y N K G F K L S L N M Y N L Y L K I L L R N K T L F I I S I T S F F K Y L L T P L Y I F M .................................................................................................. aatattttaaagaggataagttatgaaaatagaaaagtagtaaataaatagaggaattctattcctctattttacttgttattaaggtgtaattgtataaaataaaaaaaatatttaataatttttaccaaattttaatgataaattcatataattaagatataattttataagcaatctattttttgtaagaaagattatagaaattgtactaaagaatttatataataaagtaggtaaatatataaaaatttcatatcaaatttataatagttattataaaaacaaataaaatgttttaggaggaataaatgaaaaagttgttagcagggttattattagtaagctca 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: 137 End: 166 ........................................................................................................................................AATGATAAATTCATATAATTAAGATATAAT........................................................................................................................................................................................ PromScan Matrix: RpoD-17 Strand: + Score: 81 Start: 200 End: 229 .......................................................................................................................................................................................................ATAGAAATTGTACTAAAGAATTTATATAAT......................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aatattttaaagaggataagttatgaaaatagaaaagtagtaaataaatagaggaattctattcctctattttacttgttattaaggtgtaattgtataaaataaaaaaaatatttaataatttttaccaaattttaatgataaattcatataattaagatataattttataagcaatctattttttgtaagaaagattatagaaattgtactaaagaatttatataataaagtaggtaaatatataaaaatttcatatcaaatttataatagttattataaaaacaaataaaatgttttaggaggaataaatgaaaaagttgttagcagggttattattagtaagctca Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 100 HP_score: -11.3 Tail_Score: -4.61824 Start: 49 End: 69 Full_Region: AAAGTAGTAAATAAA TAGAGGAAT TCT ATTCCTCTA TTTTACTTGTTATTA ................................................TAGAGGAATTCTATTCCTCTA......................................................................................................................................................................................................................................................................................... TransTerm Strand: - Conf: 100 HP_score: -11.3 Tail_Score: -4.54253 Start: 49 End: 69 Full_Region: taataacaagtaaaa tagaggaat aga attcctcta tttatttactacttt ................................................tagaggaatagaattcctcta......................................................................................................................................................................................................................................................................................... Find igs database================================================ Query_seq: FN0023:FN0024|FN0023:FN0024:Short-chain fatty acids transporter:Hypothetical exported 24-amino acid repeat protein:->->:662841..663190 350 aatattttaaagaggataagttatgaaaatagaaaagtagtaaataaatagaggaattctattcctctattttacttgttattaaggtgtaattgtataaaataaaaaaaatatttaataatttttaccaaattttaatgataaattcatataattaagatataattttataagcaatctattttttgtaagaaagattatagaaattgtactaaagaatttatataataaagtaggtaaatatataaaaatttcatatcaaatttataatagttattataaaaacaaataaaatgttttaggaggaataaatgaaaaagttgttagcagggttattattagtaagctca Intra-Species Hit: Count: 1 Min: 1 Max: 350 Len: 350 Subject: NC_003454_FN0023_FN0024|Short-chain fatty acids transporter:Hypothetical exported 24-amino acid repeat protein|POSITIVE:POSITIVE|[662841,663190]|350 HSP 1 e-value: 1.0E-51 bit: 204.0 Len: 103 Query Start:1 Query End:103 Subject Strand: POSITIVE Subject Start: 1 Subject End: 103 aatattttaaagaggataagttatgaaaatagaaaagtagtaaataaatagaggaattctattcctctattttacttgttattaaggtgtaattgtataaaat....................................................................................................................................................................................................................................................... aatattttaaagaggataagttatgaaaatagaaaagtagtaaataaatagaggaattctattcctctattttacttgttattaaggtgtaattgtataaaat....................................................................................................................................................................................................................................................... HSP 2 e-value: 7.0E-23 bit: 109.0 Len: 55 Query Start:296 Query End:350 Subject Strand: POSITIVE Subject Start: 296 Subject End: 350 .......................................................................................................................................................................................................................................................................................................gttttaggaggaataaatgaaaaagttgttagcagggttattattagtaagctca .......................................................................................................................................................................................................................................................................................................gttttaggaggaataaatgaaaaagttgttagcagggttattattagtaagctca HSP 3 e-value: 2.0E-16 bit: 87.7 Len: 44 Query Start:174 Query End:217 Subject Strand: POSITIVE Subject Start: 174 Subject End: 217 .............................................................................................................................................................................gcaatctattttttgtaagaaagattatagaaattgtactaaag..................................................................................................................................... .............................................................................................................................................................................gcaatctattttttgtaagaaagattatagaaattgtactaaag..................................................................................................................................... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUAUUUUAAAGAGGAUAAGUUAUGAAAAUAGAAAAGUAGUAAAUAAAUAGAGGAAUUCUAUUCCUCUAUUUUACUUGUUAUUAAGGUGUAAUUGUAUAAAAUAAAAAAAAUAUUUAAUAAUUUUUACCAAAUUUUAAUGAUAAAUUCAUAUAAUUAAGAUAUAAUUUUAUAAGCAAUCUAUUUUUUGUAAGAAAGAUUAUAGAAAUUGUACUAAAGAAUUUAUAUAAUAAAGUAGGUAAAUAUAUAAAAAUUUCAUAUCAAAUUUAUAAUAGUUAUUAUAAAAACAAAUAAAAUGUUUUAGGAGGAAUAAAUGAAAAAGUUGUUAGCAGGGUUAUUAUUAGUAAGCUCA ...........(((......((((....))))...((((((((..((((((((((((...))))))))))))..(((((((.(((.......(((((((...((((.......))))......((((((..((((((...((((((((.(((((((....(((((((((....((((........))))....)))))))))..))))))).....))))))))....)))))).)))))))))))))...((((((......((((((((....))))))))...........((((((....)))))).))))))...))).))))))).))))))))......))). (-55.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGAGCUUACUAAUAAUAACCCUGCUAACAACUUUUUCAUUUAUUCCUCCUAAAACAUUUUAUUUGUUUUUAUAAUAACUAUUAUAAAUUUGAUAUGAAAUUUUUAUAUAUUUACCUACUUUAUUAUAUAAAUUCUUUAGUACAAUUUCUAUAAUCUUUCUUACAAAAAAUAGAUUGCUUAUAAAAUUAUAUCUUAAUUAUAUGAAUUUAUCAUUAAAAUUUGGUAAAAAUUAUUAAAUAUUUUUUUUAUUUUAUACAAUUACACCUUAAUAACAAGUAAAAUAGAGGAAUAGAAUUCCUCUAUUUAUUUACUACUUUUCUAUUUUCAUAACUUAUCCUCUUUAAAAUAUU ..(((.................))).............((((((((((.......((((((((((((((((((((....)))))))).(((.((((((((......(((((((.........((((((((........(((.(((((.(((((.(..(((..........)))..).)))))))))).))).....)))))))).(((((((........)))))))......))))))).......)))))))))))............)))))))))))).))))))))))......................................................... (-40.77) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 255 343 302 43 3 NC_003454:FN0246|5end_hypothetical_protein_870797..871027_NEGATIVE 244 318 272 159 115 NC_003454:FN0349|5end_D-tyrosyl-tRNA_deacylase_981792..982022_POSITIVE 234 348 318 44 14 NC_003454:FN1120|5end_phosphoenolpyruvate_carboxykinase_1761438..1761668_POSITIVE 233 96 56 228 196 NC_003454:FN0940|5end_hypothetical_protein_1593508..1593738_NEGATIVE 230 61 24 164 127 NC_003454:FN0590|5end_N-acyl-L-amino_acid_amidohydrolase_1244037..1244267_NEGATIVE 224 142 106 174 139 NC_003454:FN0238|5end_hypothetical_protein_863314..863544_NEGATIVE 209 71 31 67 33 NC_003454:FN1920|5end_tRNA_(5-methylaminomethyl-2-thiouridylate)_-methyltransferase_416910..417140_NEGATIVE 205 44 1 71 25 NC_003454:FN0978|5end_NA+/H+_antiporter_NHAC_1631965..1632195_NEGATIVE 204 90 49 214 174 NC_003454:FN0801|5end_Amino_acid_transport_ATP-binding_protein_1461433..1461663_NEGATIVE 202 89 57 228 191 NC_003454:FN0437|5end_Allophanate_hydrolase_1079642..1079872_NEGATIVE 200 83 52 227 197 NC_003454:FN0698|5end_DNA_integration/recombination/invertion_protein_1356611..1356841_POSITIVE 198 73 33 102 59 NC_003454:FN0477|5end_Cell_wall_endopeptidase_family_M23/M37_1124872..1125102_POSITIVE 196 350 304 229 185 NC_003454:FN0735|5end_Cell_surface_protein_1392666..1392896_POSITIVE 194 73 31 155 114 NC_003454:FN1347|5end_Hypothetical_cytosolic_protein_2000300..2000530_NEGATIVE 194 220 173 226 170 NC_003454:FN0232|5end_hypothetical_protein_858018..858248_NEGATIVE 193 343 301 117 71 NC_003454:FN1955|5end_hypothetical_protein_459936..460166_POSITIVE 191 65 24 89 41 NC_003454:FN1058|5end_hypothetical_protein_1704802..1705032_POSITIVE 190 90 56 129 90 NC_003454:FN0084|5end_Acetaldehyde_dehydrogenase_[acetylating]_721572..721802_POSITIVE 188 60 11 137 80 NC_003454:FN0144|5end_hypothetical_protein_774353..774583_NEGATIVE 186 98 52 164 122 NC_003454:FN0665|5end_N-acetylmuramoyl-L-alanine_amidase_1321085..1321315_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 283 76 36 52 8 NC_003454:FN0023|3end_Short-chain_fatty_acids_transporter_662780..662930_POSITIVE 230 61 24 148 111 NC_003454:FN0591|3end_Putative_efflux_pump_component_MtrF_1244053..1244203_NEGATIVE 209 71 31 67 33 NC_003454:FN1921|3end_Biotin_operon_repressor_416910..417060_NEGATIVE 197 329 294 31 1 NC_003454:FN0340|3end_Hypothetical_membrane-spanning_Protein_972638..972788_NEGATIVE 196 350 304 78 34 NC_003454:FN0734|3end_Fe-S_oxidoreductase_1392595..1392745_POSITIVE 192 343 301 135 85 NC_003454:FN0115|3end_hypothetical_protein_748215..748365_NEGATIVE 191 65 24 53 5 NC_003454:FN1057|3end_Diamine_acetyltransferase_1704846..1704996_POSITIVE 187 96 52 84 45 NC_003454:FN0793|3end_Sodium/glutamate_symport_carrier_protein_1451791..1451941_POSITIVE 185 350 302 59 17 NC_003454:FN0636|3end_hypothetical_protein_1295609..1295759_POSITIVE 185 334 292 82 42 NC_003454:FN2006|3end_Cobalt_transport_protein_cbiQ_506959..507109_POSITIVE 185 68 27 83 36 NC_003454:FN1791|3end_Mutator_MutT_protein_272879..273029_POSITIVE 185 336 293 116 63 NC_003454:FN1674|3end_hypothetical_protein_172225..172375_POSITIVE 179 84 45 104 62 NC_003454:FN1828|3end_LSU_ribosomal_protein_L9P_317251..317401_NEGATIVE 178 75 50 140 113 NC_003454:FN0495|3end_Acetyl-CoA_acetyltransferase_1140855..1141005_POSITIVE 177 56 11 75 29 NC_003454:FN0552|3end_Serine_racemase_1203606..1203756_NEGATIVE 174 222 195 70 40 NC_003454:FN1313|3end_Oligopeptide-binding_protein_oppA_1968557..1968707_POSITIVE 174 96 51 70 25 NC_003454:FN0708|3end_Hypothetical_cytosolic_protein_1367425..1367575_POSITIVE 174 77 36 103 60 NC_003454:FN1616|3end_transcription_antitermination_protein_NusB_125976..126126_NEGATIVE 173 349 301 75 26 NC_003454:FN0047|3end_Exodeoxyribonuclease_III_685268..685418_POSITIVE 171 97 58 36 5 NC_003454:FN0970|3end_Precorrin-8X_methylmutase_1622607..1622757_NEGATIVE