Origin IGS: cctctactaaattttatgattacttatctaactcaaaagctttatagttttaataaaaatattgcatattctataatgtgagtgttttttagcaataaattgtaactttaaactcaaaatttagtaagctattcatattataaagcagaagttgtttttatccttttattttaatt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aattaaaataaaaggataaaaacaacttctgctttataatatgaatagcttactaaattttgagtttaaagttacaatttattgctaaaaaacactcacattatagaatatgcaatatttttattaaaactataaagcttttgagttagataagtaatcataaaatttagtagagg Mask Tandem Repeat Region ================================================ cctctactaaattttatgattacttatctaactcaaaagctttatagttttaataaaaatattgcatattctataatgtgagtgttttttagcaataaattgtaactttaaactcaaaatttagtaagctattcatattataaagcagaagttgtttttatccttttattttaatt Find is-nt database================================================ Query_seq: FN1431:FN1432|FN1431:FN1432:Branched-chain amino acid transport system permease protein livH:Leucine-, isoleucine-, valine-, threonine-, and alanine-binding protein:<-<-:2100343..2100518 176 cctctactaaattttatgattacttatctaactcaaaagctttatagttttaataaaaatattgcatattctataatgtgagtgttttttagcaataaattgtaactttaaactcaaaatttagtaagctattcatattataaagcagaagttgtttttatccttttattttaatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN1431:FN1432|FN1431:FN1432:Branched-chain amino acid transport system permease protein livH:Leucine-, isoleucine-, valine-, threonine-, and alanine-binding protein:<-<-:2100343..2100518 176 cctctactaaattttatgattacttatctaactcaaaagctttatagttttaataaaaatattgcatattctataatgtgagtgttttttagcaataaattgtaactttaaactcaaaatttagtaagctattcatattataaagcagaagttgtttttatccttttattttaatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN1431:FN1432|FN1431:FN1432:Branched-chain amino acid transport system permease protein livH:Leucine-, isoleucine-, valine-, threonine-, and alanine-binding protein:<-<-:2100343..2100518 176 cctctactaaattttatgattacttatctaactcaaaagctttatagttttaataaaaatattgcatattctataatgtgagtgttttttagcaataaattgtaactttaaactcaaaatttagtaagctattcatattataaagcagaagttgtttttatccttttattttaatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 cctctactaaattttatgattacttatctaactcaaaagctttatagttttaataaaaatattgcatattctataatgtgagtgttttttagcaataaattgtaactttaaactcaaaatttagtaagctattcatattataaagcagaagttgtttttatccttttattttaatt Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: - Start: 31 End: 120 .............................. S L L K I T K I F I N C I R Y H S H K K A I F Q L K L S L M ........................................................ cctctactaaattttatgattacttatctaactcaaaagctttatagttttaataaaaatattgcatattctataatgtgagtgttttttagcaataaattgtaactttaaactcaaaatttagtaagctattcatattataaagcagaagttgtttttatccttttattttaatt 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: 48 End: 77 ...............................................TTTTAATAAAAATATTGCATATTCTATAAT................................................................................................... PromScan Matrix: RpoD-17 Strand: - Score: 81 Start: 99 End: 128 ..................................................................................................CTTACTAAATTTTGAGTTTAAAGTTACAAT................................................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ cctctactaaattttatgattacttatctaactcaaaagctttatagttttaataaaaatattgcatattctataatgtgagtgttttttagcaataaattgtaactttaaactcaaaatttagtaagctattcatattataaagcagaagttgtttttatccttttattttaatt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: FN1431:FN1432|FN1431:FN1432:Branched-chain amino acid transport system permease protein livH:Leucine-, isoleucine-, valine-, threonine-, and alanine-binding protein:<-<-:2100343..2100518 176 cctctactaaattttatgattacttatctaactcaaaagctttatagttttaataaaaatattgcatattctataatgtgagtgttttttagcaataaattgtaactttaaactcaaaatttagtaagctattcatattataaagcagaagttgtttttatccttttattttaatt Intra-Species Hit: Count: 1 Min: 1 Max: 176 Len: 176 Subject: NC_003454_FN1431_FN1432|Branched-chain amino acid transport system permease protein livH:Leucine-, isoleucine-, valine-, threonine-, and alanine-binding protein|NEGATIVE:NEGATIVE|[2100343,2100518]|176 HSP 1 e-value: 2.0E-95 bit: 349.0 Len: 176 Query Start:1 Query End:176 Subject Strand: POSITIVE Subject Start: 1 Subject End: 176 cctctactaaattttatgattacttatctaactcaaaagctttatagttttaataaaaatattgcatattctataatgtgagtgttttttagcaataaattgtaactttaaactcaaaatttagtaagctattcatattataaagcagaagttgtttttatccttttattttaatt cctctactaaattttatgattacttatctaactcaaaagctttatagttttaataaaaatattgcatattctataatgtgagtgttttttagcaataaattgtaactttaaactcaaaatttagtaagctattcatattataaagcagaagttgtttttatccttttattttaatt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CCUCUACUAAAUUUUAUGAUUACUUAUCUAACUCAAAAGCUUUAUAGUUUUAAUAAAAAUAUUGCAUAUUCUAUAAUGUGAGUGUUUUUUAGCAAUAAAUUGUAACUUUAAACUCAAAAUUUAGUAAGCUAUUCAUAUUAUAAAGCAGAAGUUGUUUUUAUCCUUUUAUUUUAAUU ....(((((((((((..(((.....))).......((((..(((((((((....(((((((((.((((((....))))))))))))))).......)))))))))))))......)))))))))))..............(((((.(((((...........))))).)))))... (-23.50) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUUAAAAUAAAAGGAUAAAAACAACUUCUGCUUUAUAAUAUGAAUAGCUUACUAAAUUUUGAGUUUAAAGUUACAAUUUAUUGCUAAAAAACACUCACAUUAUAGAAUAUGCAAUAUUUUUAUUAAAACUAUAAAGCUUUUGAGUUAGAUAAGUAAUCAUAAAAUUUAGUAGAGG .........................((((((((..((..(((((...(((((((((.((..((((((..((((..(((.((((((..........................)))))).....)))..))))...))))))..)).)))).)))))..)))))..))..)))))))) (-29.07) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 696 50 1 141 92 NC_003454:FN1431|5end_Branched-chain_amino_acid_transport_system_permease_protein_livH_2100252..2100482_NEGATIVE 223 51 25 212 185 NC_003454:FN1606|5end_3-deoxy-D-manno-octulosonic-acid_transferase_117208..117438_NEGATIVE 205 38 1 124 83 NC_003454:FN0882|5end_Hemin_transport_system_ATP-binding_protein_hmuV_1543717..1543947_NEGATIVE 202 170 129 204 151 NC_003454:FN1594|5end_Nitrogen_fixation_protein_RNFG_104893..105123_NEGATIVE 199 109 64 108 59 NC_003454:FN1458|5end_UDP-N-acetylmuramoylalanine--D-glutamate_ligase_2140341..2140571_NEGATIVE 199 88 59 163 134 NC_003454:FN1556|5end_Protein_Translation_Elongation_Factor_G_(EF-G)_79606..79836_NEGATIVE 198 74 32 64 27 NC_003454:FN0071|5end_GTP_cyclohydrolase_I_710962..711192_POSITIVE 194 104 67 44 8 NC_003454:FN1850|5end_3-oxoacyl-[acyl-carrier-protein]_synthase_III_339205..339435_POSITIVE 193 170 121 227 181 NC_003454:FN1027|5end_Rod_shape-determining_protein_rodA_1681923..1682153_NEGATIVE 191 107 81 193 164 NC_003454:FN2068|5end_dGTP_triphosphohydrolase_578986..579216_NEGATIVE 190 50 3 127 78 NC_003454:FN2129|5end_Hypothetical_cytosolic_protein_639815..640045_NEGATIVE 186 166 128 104 60 NC_003454:FN0383|5end_Lipopolysaccharide_N-acetylglucosaminyltransferase_1014148..1014378_POSITIVE 183 88 44 179 128 NC_003454:FN1439|5end_Transcriptional_regulator,_DeoR_family_2106428..2106658_POSITIVE 183 88 44 75 24 NC_003454:FN1438|5end_hypothetical_protein_2106324..2106554_POSITIVE 183 51 11 54 7 NC_003454:FN0439|5end_hypothetical_protein_1081610..1081840_NEGATIVE 183 97 69 229 198 NC_003454:FN1545|5end_Ferredoxin_like_protein_59133..59363_POSITIVE 182 110 61 167 109 NC_003454:FN0972|5end_Cobyrinic_acid_a,c-diamide_synthase_1625607..1625837_NEGATIVE 181 54 14 205 175 NC_003454:FN0446|5end_hypothetical_protein_1085719..1085949_POSITIVE 178 167 123 159 114 NC_003454:FN0447|5end_NIFS_protein_1089343..1089573_POSITIVE 177 109 62 190 136 NC_003454:FN0594|5end_(3R)-hydroxymyristoyl-[acyl_carrier_protein]_dehydratase_1248785..1249015_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 250 166 124 52 3 NC_003454:FN1550|3end_hypothetical_protein_64887..65037_NEGATIVE 224 170 121 87 34 NC_003454:FN1196|3end_hypothetical_protein_1856512..1856662_NEGATIVE 212 90 43 88 33 NC_003454:FN0853|3end_Glycogen_synthase_1510922..1511072_NEGATIVE 206 111 77 128 92 NC_003454:FN0030|3end_5-nitroimidazole_antibiotic_resistance_protein_667676..667826_POSITIVE 205 38 1 137 96 NC_003454:FN0884|3end_Hemin_transport_system_permease_protein_hmuU_1543704..1543854_NEGATIVE 199 88 59 117 88 NC_003454:FN1557|3end_30S_ribosomal_protein_S7_79652..79802_NEGATIVE 198 74 32 64 27 NC_003454:FN0070|3end_Glycyl-tRNA_synthetase_beta_chain_711042..711192_POSITIVE 194 104 67 47 11 NC_003454:FN1849|3end_Coenzyme_F390_synthetase_339288..339438_POSITIVE 193 52 20 119 91 NC_003454:FN2086|3end_General_secretion_pathway_protein_D_597507..597657_NEGATIVE 190 50 3 77 28 NC_003454:FN0001|3end_Chromosomal_replication_initiator_protein_dnaA_639865..640015_NEGATIVE 186 166 128 100 56 NC_003454:FN0382|3end_hypothetical_protein_1014224..1014374_POSITIVE 186 164 121 151 104 NC_003454:FN1590|3end_Hypothetical_lipoprotein_100560..100710_NEGATIVE 182 110 61 148 90 NC_003454:FN0973|3end_Histidinol-phosphate_aminotransferase_1625626..1625776_NEGATIVE 182 170 129 115 85 NC_003454:FN0359|3end_ATP_synthase_gamma_chain,_sodium_ion_specific_989995..990145_NEGATIVE 178 167 123 140 95 NC_003454:FN0446|3end_hypothetical_protein_1089404..1089554_POSITIVE 177 162 123 89 45 NC_003454:FN1927|3end_DEGV_protein_425415..425565_NEGATIVE 175 79 41 91 59 NC_003454:FN0839|3end_hypothetical_protein_1501244..1501394_NEGATIVE 174 90 46 87 46 NC_003454:FN1281|3end_Cysteine_protease_1941242..1941392_POSITIVE 174 64 35 51 20 NC_003454:FN0550|3end_Mannose-1-phosphate_guanylyl_transferase_(GDP)_1203166..1203316_POSITIVE 171 48 1 124 67 NC_003454:FN1632|3end_LSU_ribosomal_protein_L5P_135268..135418_NEGATIVE