Origin IGS: aacatttccccttttaaattaaaatatacaattcctccttttattttaactcgtttataaattaaagtcaactaaatccttacttttttagtacaatattttagtaaatgaaatatatgttttaaaacataacttatacaatttatttataaaatatatatttaaaaatttaaaacttttatagcttttatagaaataaaaaaccgtgagactactcacggttttcatattattaattaataattttttattaattttaaccttagctaagctaga .........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 tctagcttagctaaggttaaaattaataaaaaattattaattaataatatgaaaaccgtgagtagtctcacggttttttatttctataaaagctataaaagttttaaatttttaaatatatattttataaataaattgtataagttatgttttaaaacatatatttcatttactaaaatattgtactaaaaaagtaaggatttagttgactttaatttataaacgagttaaaataaaaggaggaattgtatattttaatttaaaaggggaaatgtt Mask Tandem Repeat Region ================================================ aacatttccccttttaaattaaaatatacaattcctccttttattttaactcgtttataaattaaagtcaactaaatccttacttttttagtacaatattttagtaaatgaaatatatgttttaaaacataacttatacaatttatttataaaatatatatttaaaaatttaaaacttttatagcttttatagaaataaaaaaccgtgagactactcacggttttcatattattaattaataattttttattaattttaaccttagctaagctaga Find is-nt database================================================ Query_seq: FN1858:FN1859|FN1858:FN1859:Short-chain fatty acids transporter:Major outer membrane protein:<-<-:348363..348638 276 aacatttccccttttaaattaaaatatacaattcctccttttattttaactcgtttataaattaaagtcaactaaatccttacttttttagtacaatattttagtaaatgaaatatatgttttaaaacataacttatacaatttatttataaaatatatatttaaaaatttaaaacttttatagcttttatagaaataaaaaaccgtgagactactcacggttttcatattattaattaataattttttattaattttaaccttagctaagctaga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN1858:FN1859|FN1858:FN1859:Short-chain fatty acids transporter:Major outer membrane protein:<-<-:348363..348638 276 aacatttccccttttaaattaaaatatacaattcctccttttattttaactcgtttataaattaaagtcaactaaatccttacttttttagtacaatattttagtaaatgaaatatatgttttaaaacataacttatacaatttatttataaaatatatatttaaaaatttaaaacttttatagcttttatagaaataaaaaaccgtgagactactcacggttttcatattattaattaataattttttattaattttaaccttagctaagctaga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN1858:FN1859|FN1858:FN1859:Short-chain fatty acids transporter:Major outer membrane protein:<-<-:348363..348638 276 aacatttccccttttaaattaaaatatacaattcctccttttattttaactcgtttataaattaaagtcaactaaatccttacttttttagtacaatattttagtaaatgaaatatatgttttaaaacataacttatacaatttatttataaaatatatatttaaaaatttaaaacttttatagcttttatagaaataaaaaaccgtgagactactcacggttttcatattattaattaataattttttattaattttaaccttagctaagctaga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aacatttccccttttaaattaaaatatacaattcctccttttattttaactcgtttataaattaaagtcaactaaatccttacttttttagtacaatattttagtaaatgaaatatatgttttaaaacataacttatacaatttatttataaaatatatatttaaaaatttaaaacttttatagcttttatagaaataaaaaaccgtgagactactcacggttttcatattattaattaataattttttattaattttaaccttagctaagctaga Predict ORF larger than 30AA ================================================ Protein_Len: 55 Strand: - Start: 91 End: 255 .......................................................................................... Y L I K T F S I Y T K F C L K Y L K N I F Y I N L F K F S K Y S K Y F Y F V T L S S V T K M N N I L L K K N M ..................... aacatttccccttttaaattaaaatatacaattcctccttttattttaactcgtttataaattaaagtcaactaaatccttacttttttagtacaatattttagtaaatgaaatatatgttttaaaacataacttatacaatttatttataaaatatatatttaaaaatttaaaacttttatagcttttatagaaataaaaaaccgtgagactactcacggttttcatattattaattaataattttttattaattttaaccttagctaagctaga 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: 43 End: 72 ..........................................GTTGACTTTAATTTATAAACGAGTTAAAAT............................................................................................................................................................................................................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aacatttccccttttaaattaaaatatacaattcctccttttattttaactcgtttataaattaaagtcaactaaatccttacttttttagtacaatattttagtaaatgaaatatatgttttaaaacataacttatacaatttatttataaaatatatatttaaaaatttaaaacttttatagcttttatagaaataaaaaaccgtgagactactcacggttttcatattattaattaataattttttattaattttaaccttagctaagctaga Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 93 HP_score: -11.4 Tail_Score: -2.69348 Start: 199 End: 226 Full_Region: GCTTTTATAGAAATA AAAAACCGTGAG ACTA CTCACGGTTTTC ATATTATTAATTAAT ......................................................................................................................................................................................................AAAAACCGTGAGACTACTCACGGTTTTC.................................................. TransTerm Strand: + Conf: 95 HP_score: -11.3 Tail_Score: -4.49937 Start: 204 End: 221 Full_Region: TATAGAAATAAAAAA CCGTGAG ACTA CTCACGG TTTTCATATTATTAA ...........................................................................................................................................................................................................CCGTGAGACTACTCACGG....................................................... TransTerm Strand: - Conf: 100 HP_score: -11.3 Tail_Score: -5.76237 Start: 204 End: 221 Full_Region: ttaataatatgaaaa ccgtgag tagt ctcacgg ttttttatttctata ...........................................................................................................................................................................................................ccgtgagtagtctcacgg....................................................... Find igs database================================================ Query_seq: FN1858:FN1859|FN1858:FN1859:Short-chain fatty acids transporter:Major outer membrane protein:<-<-:348363..348638 276 aacatttccccttttaaattaaaatatacaattcctccttttattttaactcgtttataaattaaagtcaactaaatccttacttttttagtacaatattttagtaaatgaaatatatgttttaaaacataacttatacaatttatttataaaatatatatttaaaaatttaaaacttttatagcttttatagaaataaaaaaccgtgagactactcacggttttcatattattaattaataattttttattaattttaaccttagctaagctaga Intra-Species Hit: Count: 1 Min: 1 Max: 104 Len: 104 Subject: NC_003454_FN1858_FN1859|Short-chain fatty acids transporter:Major outer membrane protein|NEGATIVE:NEGATIVE|[348363,348638]|276 HSP 1 e-value: 3.0E-52 bit: 206.0 Len: 104 Query Start:1 Query End:104 Subject Strand: POSITIVE Subject Start: 1 Subject End: 104 aacatttccccttttaaattaaaatatacaattcctccttttattttaactcgtttataaattaaagtcaactaaatccttacttttttagtacaatattttag............................................................................................................................................................................ aacatttccccttttaaattaaaatatacaattcctccttttattttaactcgtttataaattaaagtcaactaaatccttacttttttagtacaatattttag............................................................................................................................................................................ Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AACAUUUCCCCUUUUAAAUUAAAAUAUACAAUUCCUCCUUUUAUUUUAACUCGUUUAUAAAUUAAAGUCAACUAAAUCCUUACUUUUUUAGUACAAUAUUUUAG ...................((((((((..........((((.((((............)))).))))...((((((..........))))))...)))))))). ( -6.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUAAAAUAUUGUACUAAAAAAGUAAGGAUUUAGUUGACUUUAAUUUAUAAACGAGUUAAAAUAAAAGGAGGAAUUGUAUAUUUUAAUUUAAAAGGGGAAAUGUU ....((((((...((......(((((.....((....))....)))))....(((((((((((..((......))...)))))))))))....))...)))))) ( -7.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 689 80 31 171 122 NC_003454:FN1858|5end_Short-chain_fatty_acids_transporter_348272..348502_NEGATIVE 244 42 4 107 57 NC_003454:FN1537|5end_Arsenical_pump-driving_ATPase_51112..51342_NEGATIVE 238 61 24 226 186 NC_003454:FN1894|5end_BAX_protein_382342..382572_NEGATIVE 217 58 29 91 64 NC_003454:FN2029|5end_O-antigen_acetylase_533863..534093_NEGATIVE 206 49 4 152 97 NC_003454:FN1585|5end_hypothetical_protein_97394..97624_NEGATIVE 202 43 22 143 121 NC_003454:FN0663|5end_hypothetical_protein_1319286..1319516_POSITIVE 202 49 4 113 66 NC_003454:FN0019|5end_Transcription-repair_coupling_factor_656549..656779_POSITIVE 197 68 22 113 71 NC_003454:FN0989|5end_phosphoribosylaminoimidazole_carboxylase_catalytic_subunit_1641667..1641897_NEGATIVE 197 73 32 146 98 NC_003454:FN1527|5end_hypothetical_protein_42572..42802_NEGATIVE 189 42 3 127 89 NC_003454:FN0755|5end_Glutamyl-tRNA(Gln)_amidotransferase_subunit_C_1414953..1415183_NEGATIVE 189 64 27 74 32 NC_003454:FN0299|5end_Aspartyl-tRNA_synthetase_932393..932623_POSITIVE 189 70 24 157 90 NC_003454:FN1550|5end_hypothetical_protein_65630..65860_NEGATIVE 187 40 2 187 149 NC_003454:FN0766|5end_Large-conductance_mechanosensitive_channel_1421910..1422140_POSITIVE 185 80 33 138 97 NC_003454:FN0980|5end_hypothetical_protein_1632478..1632708_POSITIVE 185 73 31 152 97 NC_003454:FN0903|5end_Polysialic_acid_capsule_expression_protein_kpsF_1561116..1561346_POSITIVE 180 45 3 142 101 NC_003454:FN0592|5end_ATP-dependent_DNA_helicase_pcrA_1245712..1245942_POSITIVE 179 80 34 218 177 NC_003454:FN0226|5end_4-hydroxythreonine-4-phosphate_dehydrogenase_854089..854319_NEGATIVE 177 69 24 140 84 NC_003454:FN1050|5end_Lactoylglutathione_lyase_1699377..1699607_POSITIVE 177 56 11 165 123 NC_003454:FN2067|5end_Thiol:disulfide_interchange_protein_tlpA_577378..577608_NEGATIVE 176 71 34 137 97 NC_003454:FN0652|5end_Glyceraldehyde_3-phosphate_dehydrogenase_1310362..1310592_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 244 42 4 110 60 NC_003454:FN1538|3end_Arsenical_pump-driving_ATPase_51109..51259_NEGATIVE 206 49 4 131 76 NC_003454:FN1586|3end_O-succinylbenzoate-CoA_synthase_97415..97565_NEGATIVE 197 68 22 101 59 NC_003454:FN0990|3end_Phosphoribosylformylglycinamidine_synthase_1641679..1641829_NEGATIVE 197 73 32 130 82 NC_003454:FN1528|3end_hypothetical_protein_42588..42738_NEGATIVE 189 42 3 118 80 NC_003454:FN0756|3end_Ribosomal_large_subunit_pseudouridine_synthase_B_1414962..1415112_NEGATIVE 189 64 27 55 13 NC_003454:FN0298|3end_Histidyl-tRNA_synthetase_932454..932604_POSITIVE 189 70 24 133 66 NC_003454:FN1551|3end_hypothetical_protein_65654..65804_NEGATIVE 185 80 33 124 83 NC_003454:FN0979|3end_hypothetical_protein_1632544..1632694_POSITIVE 185 73 31 130 75 NC_003454:FN0902|3end_5-formyltetrahydrofolate_cyclo-ligase_1561174..1561324_POSITIVE 178 52 31 83 64 NC_003454:FN1294|3end_Ribosomal-protein-alanine_acetyltransferase_1952517..1952667_NEGATIVE 177 69 24 124 68 NC_003454:FN1049|3end_hypothetical_protein_1699441..1699591_POSITIVE 177 56 11 98 56 NC_003454:FN2068|3end_dGTP_triphosphohydrolase_577445..577595_NEGATIVE 174 54 36 115 97 NC_003454:FN1033|3end_Methyltransferase_1686364..1686514_NEGATIVE 173 77 31 113 74 NC_003454:FN0100|3end_Flavodoxins/hemoproteins_735119..735269_NEGATIVE 169 45 5 151 104 NC_003454:FN0195|3end_Dipeptide_transport_ATP-binding_protein_dppD_822407..822557_POSITIVE 169 80 32 142 85 NC_003454:FN0024|3end_Hypothetical_exported_24-amino_acid_repeat_protein_663817..663967_POSITIVE 167 50 6 123 75 NC_003454:FN0717|3end_Ribosomal_small_subunit_pseudouridine_synthase_A_1375673..1375823_POSITIVE 167 28 3 36 8 NC_003454:FN0349|3end_D-tyrosyl-tRNA_deacylase_982336..982486_POSITIVE 166 80 32 136 77 NC_003454:FN1063|3end_N-acyl-L-amino_acid_amidohydrolase_1710589..1710739_POSITIVE 165 64 32 125 97 NC_003454:FN1864|3end_DNA_mismatch_repair_protein_mutS_354678..354828_NEGATIVE