Origin IGS: cttatttccctccaaattaatttttttgatatttaaggcatactataccaaaaaaaaagaaaaaagtaaagtatttttttaatatttttgtatcaataaaaaagacagtttatttagactgcctttttattctttatttgcttaactttttaatctt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aagattaaaaagttaagcaaataaagaataaaaaggcagtctaaataaactgtcttttttattgatacaaaaatattaaaaaaatactttacttttttctttttttttggtatagtatgccttaaatatcaaaaaaattaatttggagggaaataag Mask Tandem Repeat Region ================================================ cttatttccctccaaattaatttttttgatatttaaggcatactataccaaaaaaaaagaaaaaagtaaagtatttttttaatatttttgtatcaataaaaaagacagtttatttagactgcctttttattctttatttgcttaactttttaatctt Find is-nt database================================================ Query_seq: FN1432:FN1433|FN1432:FN1433:Leucine-, isoleucine-, valine-, threonine-, and alanine-binding protein:Short chain dehydrogenase:<-<-:2101671..2101827 157 cttatttccctccaaattaatttttttgatatttaaggcatactataccaaaaaaaaagaaaaaagtaaagtatttttttaatatttttgtatcaataaaaaagacagtttatttagactgcctttttattctttatttgcttaactttttaatctt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN1432:FN1433|FN1432:FN1433:Leucine-, isoleucine-, valine-, threonine-, and alanine-binding protein:Short chain dehydrogenase:<-<-:2101671..2101827 157 cttatttccctccaaattaatttttttgatatttaaggcatactataccaaaaaaaaagaaaaaagtaaagtatttttttaatatttttgtatcaataaaaaagacagtttatttagactgcctttttattctttatttgcttaactttttaatctt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN1432:FN1433|FN1432:FN1433:Leucine-, isoleucine-, valine-, threonine-, and alanine-binding protein:Short chain dehydrogenase:<-<-:2101671..2101827 157 cttatttccctccaaattaatttttttgatatttaaggcatactataccaaaaaaaaagaaaaaagtaaagtatttttttaatatttttgtatcaataaaaaagacagtttatttagactgcctttttattctttatttgcttaactttttaatctt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 cttatttccctccaaattaatttttttgatatttaaggcatactataccaaaaaaaaagaaaaaagtaaagtatttttttaatatttttgtatcaataaaaaagacagtttatttagactgcctttttattctttatttgcttaactttttaatctt Predict ORF larger than 30AA ================================================ Protein_Len: 37 Strand: + Start: 45 End: 155 ............................................ M P K K K K K V K Y F F N I F V S I K K T V Y L D C L F I L Y L L N F L I .. cttatttccctccaaattaatttttttgatatttaaggcatactataccaaaaaaaaagaaaaaagtaaagtatttttttaatatttttgtatcaataaaaaagacagtttatttagactgcctttttattctttatttgcttaactttttaatctt 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: 85 Start: 42 End: 71 .........................................CTTTACTTTTTTCTTTTTTTTTGGTATAGT...................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ cttatttccctccaaattaatttttttgatatttaaggcatactataccaaaaaaaaagaaaaaagtaaagtatttttttaatatttttgtatcaataaaaaagacagtttatttagactgcctttttattctttatttgcttaactttttaatctt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: FN1432:FN1433|FN1432:FN1433:Leucine-, isoleucine-, valine-, threonine-, and alanine-binding protein:Short chain dehydrogenase:<-<-:2101671..2101827 157 cttatttccctccaaattaatttttttgatatttaaggcatactataccaaaaaaaaagaaaaaagtaaagtatttttttaatatttttgtatcaataaaaaagacagtttatttagactgcctttttattctttatttgcttaactttttaatctt Intra-Species Hit: Count: 1 Min: 1 Max: 157 Len: 157 Subject: NC_003454_FN1432_FN1433|Leucine-, isoleucine-, valine-, threonine-, and alanine-binding protein:Short chain dehydrogenase|NEGATIVE:NEGATIVE|[2101671,2101827]|157 HSP 1 e-value: 2.0E-36 bit: 153.0 Len: 77 Query Start:81 Query End:157 Subject Strand: POSITIVE Subject Start: 81 Subject End: 157 ................................................................................aatatttttgtatcaataaaaaagacagtttatttagactgcctttttattctttatttgcttaactttttaatctt ................................................................................aatatttttgtatcaataaaaaagacagtttatttagactgcctttttattctttatttgcttaactttttaatctt HSP 2 e-value: 4.0E-7 bit: 56.0 Len: 49 Query Start:1 Query End:49 Subject Strand: POSITIVE Subject Start: 1 Subject End: 49 cttatttccctccaaattaannnnnnngatatttaaggcatactatacc............................................................................................................ cttatttccctccaaattaatttttttgatatttaaggcatactatacc............................................................................................................ Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUUAUUUCCCUCCAAAUUAAUUUUUUUGAUAUUUAAGGCAUACUAUACCAAAAAAAAAGAAAAAAGUAAAGUAUUUUUUUAAUAUUUUUGUAUCAAUAAAAAAGACAGUUUAUUUAGACUGCCUUUUUAUUCUUUAUUUGCUUAACUUUUUAAUCUU ....................((((((((.(((...((.....))))).))))))))....(((((((.(((((........((((....)))).....((((((.((((((....)))))).))))))..........))))).)))))))...... (-20.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAGAUUAAAAAGUUAAGCAAAUAAAGAAUAAAAAGGCAGUCUAAAUAAACUGUCUUUUUUAUUGAUACAAAAAUAUUAAAAAAAUACUUUACUUUUUUCUUUUUUUUUGGUAUAGUAUGCCUUAAAUAUCAAAAAAAUUAAUUUGGAGGGAAAUAAG ((((..(((((((.(((............(((((((((((........)))))))))))..((((((......)))))).......))).)))))))))))((((((((((((............)))))))))))).................... (-24.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 713 50 1 141 92 NC_003454:FN1432|5end_Leucine-,_isoleucine-,_valine-,_threonine-,_and_alanine-binding_protein_2101580..2101810_NEGATIVE 265 44 2 119 78 NC_003454:FN0882|5end_Hemin_transport_system_ATP-binding_protein_hmuV_1543717..1543947_NEGATIVE 254 41 1 149 110 NC_003454:FN1323|5end_Thymidylate_kinase_1979152..1979382_NEGATIVE 232 150 106 205 165 NC_003454:FN1044|5end_hypothetical_protein_1695181..1695411_NEGATIVE 227 50 1 86 43 NC_003454:FN0384|5end_hypothetical_protein_1015571..1015801_POSITIVE 227 149 109 124 87 NC_003454:FN1914|5end_Anti-sigma_F_factor_antagonist_411990..412220_NEGATIVE 203 148 107 182 136 NC_003454:FN1311|5end_Biopolymer_transport_exbD_protein_1966250..1966480_NEGATIVE 202 149 108 131 86 NC_003454:FN0358|5end_ATP_synthase_subunit_B_989674..989904_NEGATIVE 189 50 1 164 108 NC_003454:FN1144|5end_hypothetical_protein_1794152..1794382_NEGATIVE 189 150 119 39 10 NC_003454:FN0445|5end_hypothetical_protein_1084816..1085046_POSITIVE 188 39 5 136 96 NC_003454:FN1527|5end_hypothetical_protein_42572..42802_NEGATIVE 185 36 1 129 87 NC_003454:FN1658|5end_prolyl-tRNA_synthetase_154891..155121_NEGATIVE 182 42 4 206 170 NC_003454:FN0616|5end_hypothetical_protein_1276511..1276741_NEGATIVE 181 49 20 116 90 NC_003454:FN0627|5end_Glucosamine--fructose-6-phosphate_aminotransferase_[isomerizing]_1287165..1287395_NEGATIVE 180 143 106 78 40 NC_003454:FN1023|5end_5-Nitroimidazole_antibiotic_resistance_protein_1678030..1678260_NEGATIVE 180 146 107 169 131 NC_003454:FN1557|5end_30S_ribosomal_protein_S7_80122..80352_NEGATIVE 179 79 34 74 22 NC_003454:FN1262|5end_Integral_membrane_protein_1918043..1918273_POSITIVE 179 143 103 75 37 NC_003454:FN1088|5end_NADH_oxidase_1731708..1731938_POSITIVE 179 50 2 225 183 NC_003454:FN0937|5end_Gamma-polyglutamic_acid_synthetase_1590245..1590475_NEGATIVE 178 45 4 133 100 NC_003454:FN1631|5end_SSU_ribosomal_protein_S14P_135247..135477_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 265 44 2 132 91 NC_003454:FN0884|3end_Hemin_transport_system_permease_protein_hmuU_1543704..1543854_NEGATIVE 227 50 1 84 41 NC_003454:FN0383|3end_Lipopolysaccharide_N-acetylglucosaminyltransferase_1015649..1015799_POSITIVE 227 149 109 123 86 NC_003454:FN1915|3end_Anti-sigma_B_factor_411991..412141_NEGATIVE 203 148 107 92 46 NC_003454:FN1312|3end_Biopolymer_transport_exbB_protein_1966340..1966490_NEGATIVE 189 50 1 64 8 NC_003454:FN1145|3end_Oligoendopeptidase_F_1794252..1794402_NEGATIVE 188 39 5 120 80 NC_003454:FN1528|3end_hypothetical_protein_42588..42738_NEGATIVE 182 42 4 115 79 NC_003454:FN0617|3end_DNA_polymerase_III,_beta_chain_1276602..1276752_NEGATIVE 181 49 20 82 56 NC_003454:FN0628|3end_Glucosamine--fructose-6-phosphate_aminotransferase_[isomerizing]_1287199..1287349_NEGATIVE 180 146 107 141 103 NC_003454:FN1558|3end_30S_ribosomal_protein_S12_80150..80300_NEGATIVE 179 50 2 133 91 NC_003454:FN0938|3end_hypothetical_protein_1590337..1590487_NEGATIVE 178 127 81 63 20 NC_003454:FN0793|3end_Sodium/glutamate_symport_carrier_protein_1451791..1451941_POSITIVE 178 45 4 112 79 NC_003454:FN1632|3end_LSU_ribosomal_protein_L5P_135268..135418_NEGATIVE 177 150 105 136 86 NC_003454:FN1472|3end_N-acetylneuraminate-binding_protein_2155088..2155238_POSITIVE 177 136 99 100 63 NC_003454:FN0011|3end_Transcriptional_regulator_651620..651770_POSITIVE 176 150 105 134 87 NC_003454:FN0991|3end_CDP-diacylglycerol--serine_O-phosphatidyltransferase_1646675..1646825_POSITIVE 176 142 107 106 70 NC_003454:FN1734|3end_V-type_ATP_synthase_subunit_B_232882..233032_NEGATIVE 173 142 115 133 95 NC_003454:FN0455|3end_Rubrerythrin_1101813..1101963_POSITIVE 173 135 116 91 66 NC_003454:FN1987|3end_Transcriptional_regulator,_GntR_family_490018..490168_NEGATIVE 171 142 109 121 90 NC_003454:FN1456|3end_UDP-N-acetylmuramate--alanine_ligase_2136516..2136666_NEGATIVE 170 36 4 75 45 NC_003454:FN0117|3end_O6-methylguanine-DNA_methyltransferase_750930..751080_POSITIVE