Origin IGS: gtttcacttcctttcatataaaatatattttaatattacaaaatgaagcatttaaaaatatacaagtatttttctaattttctgacattatggtacattataattttagatataaaaaatgtcaataagtttatagtaagatgagatttttttgttaatatataaaaaatataacagttttttatatattttaattttta .........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 taaaaattaaaatatataaaaaactgttatattttttatatattaacaaaaaaatctcatcttactataaacttattgacattttttatatctaaaattataatgtaccataatgtcagaaaattagaaaaatacttgtatatttttaaatgcttcattttgtaatattaaaatatattttatatgaaaggaagtgaaac Mask Tandem Repeat Region ================================================ gtttcacttcctttcatataaaatatattttaatattacaaaatgaagcatttaaaaatatacaagtatttttctaattttctgacattatggtacattataattttagatataaaaaatgtcaataagtttatagtaagatgagatttttttgttaatatataaaaaatataacagttttttatatattttaattttta Find is-nt database================================================ Query_seq: FN1743:FN1744|FN1743:FN1744:Multidrug-efflux transporter 2 regulator:Transporter:<-<-:241929..242128 200 gtttcacttcctttcatataaaatatattttaatattacaaaatgaagcatttaaaaatatacaagtatttttctaattttctgacattatggtacattataattttagatataaaaaatgtcaataagtttatagtaagatgagatttttttgttaatatataaaaaatataacagttttttatatattttaattttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN1743:FN1744|FN1743:FN1744:Multidrug-efflux transporter 2 regulator:Transporter:<-<-:241929..242128 200 gtttcacttcctttcatataaaatatattttaatattacaaaatgaagcatttaaaaatatacaagtatttttctaattttctgacattatggtacattataattttagatataaaaaatgtcaataagtttatagtaagatgagatttttttgttaatatataaaaaatataacagttttttatatattttaattttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN1743:FN1744|FN1743:FN1744:Multidrug-efflux transporter 2 regulator:Transporter:<-<-:241929..242128 200 gtttcacttcctttcatataaaatatattttaatattacaaaatgaagcatttaaaaatatacaagtatttttctaattttctgacattatggtacattataattttagatataaaaaatgtcaataagtttatagtaagatgagatttttttgttaatatataaaaaatataacagttttttatatattttaattttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gtttcacttcctttcatataaaatatattttaatattacaaaatgaagcatttaaaaatatacaagtatttttctaattttctgacattatggtacattataattttagatataaaaaatgtcaataagtttatagtaagatgagatttttttgttaatatataaaaaatataacagttttttatatattttaattttta Predict ORF larger than 30AA ================================================ Protein_Len: 33 Strand: + Start: 43 End: 141 .......................................... M K H L K I Y K Y F S N F L T L W Y I I I L D I K N V N K F I V R ........................................................... Protein_Len: 49 Strand: - Start: 39 End: 185 ...................................... L I F C K F I Y L Y K E L K R V N H Y M I I K S I F F T L L N I T L H S K K T L I Y F I Y C N K M ............... gtttcacttcctttcatataaaatatattttaatattacaaaatgaagcatttaaaaatatacaagtatttttctaattttctgacattatggtacattataattttagatataaaaaatgtcaataagtttatagtaagatgagatttttttgttaatatataaaaaatataacagttttttatatattttaattttta 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: 92 Start: 97 End: 126 ................................................................................................ATTGACATTTTTTATATCTAAAATTATAAT.......................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gtttcacttcctttcatataaaatatattttaatattacaaaatgaagcatttaaaaatatacaagtatttttctaattttctgacattatggtacattataattttagatataaaaaatgtcaataagtttatagtaagatgagatttttttgttaatatataaaaaatataacagttttttatatattttaattttta Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: FN1743:FN1744|FN1743:FN1744:Multidrug-efflux transporter 2 regulator:Transporter:<-<-:241929..242128 200 gtttcacttcctttcatataaaatatattttaatattacaaaatgaagcatttaaaaatatacaagtatttttctaattttctgacattatggtacattataattttagatataaaaaatgtcaataagtttatagtaagatgagatttttttgttaatatataaaaaatataacagttttttatatattttaattttta Intra-Species Hit: Count: 1 Min: 1 Max: 146 Len: 146 Subject: NC_003454_FN1743_FN1744|Multidrug-efflux transporter 2 regulator:Transporter|NEGATIVE:NEGATIVE|[241929, 242128]|200 HSP 1 e-value: 2.0E-77 bit: 289.0 Len: 146 Query Start:1 Query End:146 Subject Strand: POSITIVE Subject Start: 1 Subject End: 146 gtttcacttcctttcatataaaatatattttaatattacaaaatgaagcatttaaaaatatacaagtatttttctaattttctgacattatggtacattataattttagatataaaaaatgtcaataagtttatagtaagatgaga...................................................... gtttcacttcctttcatataaaatatattttaatattacaaaatgaagcatttaaaaatatacaagtatttttctaattttctgacattatggtacattataattttagatataaaaaatgtcaataagtttatagtaagatgaga...................................................... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUUUCACUUCCUUUCAUAUAAAAUAUAUUUUAAUAUUACAAAAUGAAGCAUUUAAAAAUAUACAAGUAUUUUUCUAAUUUUCUGACAUUAUGGUACAUUAUAAUUUUAGAUAUAAAAAAUGUCAAUAAGUUUAUAGUAAGAUGAGA .(((((....(((...((((((...((((((........))))))..((((((((((((((....)))))))).......(((((.(((((((....))))))).)))))......)))))).......))))))..))).))))) (-15.20) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCUCAUCUUACUAUAAACUUAUUGACAUUUUUUAUAUCUAAAAUUAUAAUGUACCAUAAUGUCAGAAAAUUAGAAAAAUACUUGUAUAUUUUUAAAUGCUUCAUUUUGUAAUAUUAAAAUAUAUUUUAUAUGAAAGGAAGUGAAAC .....................((((((((...(((((...........)))))....))))))))....(((((((.(((....))).)))))))..(((((.(((..((((((......))))....))..))).)))))..... (-17.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 656 130 81 221 172 NC_003454:FN1743|5end_Multidrug-efflux_transporter_2_regulator_241838..242068_NEGATIVE 207 140 96 134 86 NC_003454:FN0727|5end_hypothetical_protein_1385507..1385737_NEGATIVE 207 128 85 224 185 NC_003454:FN1647|5end_hypothetical_protein_141983..142213_POSITIVE 201 108 69 159 117 NC_003454:FN1011|5end_MGPA_protein_1665660..1665890_NEGATIVE 183 83 48 162 124 NC_003454:FN0682|5end_Fibronectin-binding_protein-like_protein_A_1336794..1337024_POSITIVE 183 108 63 129 89 NC_003454:FN1870|5end_hypothetical_protein_362182..362412_NEGATIVE 182 101 64 189 147 NC_003454:FN2103|5end_RecA_protein_613203..613433_POSITIVE 181 39 6 101 64 NC_003454:FN1838|5end_Glycerol_uptake_facilitator_protein_327489..327719_POSITIVE 175 47 1 174 123 NC_003454:FN1679|5end_LPS_biosynthesis_protein_WbpG_175711..175941_NEGATIVE 172 47 1 134 93 NC_003454:FN0633|5end_Replication_protein_1290928..1291158_POSITIVE 171 115 77 93 50 NC_003454:FN0771|5end_Oxygen-independent_coproporphyrinogen_III_oxidase_1427462..1427692_POSITIVE 167 50 7 106 75 NC_003454:FN1177|5end_hypothetical_protein_1838805..1839035_NEGATIVE 165 102 62 144 102 NC_003454:FN0074|5end_Ethanolamine_utilization_protein_eutS_713328..713558_POSITIVE 164 50 10 98 47 NC_003454:FN0764|5end_Transporter,_LysE_family_1420327..1420557_POSITIVE 164 44 5 129 89 NC_003454:FN0449|5end_hypothetical_protein_1092683..1092913_POSITIVE 163 36 1 152 113 NC_003454:FN0375|5end_Iron(III)-binding_protein_1005293..1005523_POSITIVE 162 33 2 156 125 NC_003454:FN2121|5end_Hypothetical_exported_24-amino_acid_repeat_protein_629728..629958_NEGATIVE 159 35 2 137 100 NC_003454:FN1030|5end_Hypothetical_membrane-spanning_protein_1684721..1684951_NEGATIVE 159 110 63 218 181 NC_003454:FN1674|5end_hypothetical_protein_172041..172271_POSITIVE 158 31 2 182 149 NC_003454:FN0825|5end_Hypothetical_cytosolic_protein_1485124..1485354_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 201 108 69 139 97 NC_003454:FN1012|3end_HPr_kinase/phosphorylase_1665680..1665830_NEGATIVE 182 101 64 58 16 NC_003454:FN2102|3end_ABC_transporter_ATP-binding_protein_613152..613302_POSITIVE 171 115 77 79 36 NC_003454:FN0770|3end_Hemin_transport_system_ATP-binding_protein_hmuV_1427528..1427678_POSITIVE 171 130 81 145 82 NC_003454:FN0728|3end_hypothetical_protein_1385485..1385635_NEGATIVE 167 50 7 118 87 NC_003454:FN1178|3end_Hypothetical_cytosolic_protein_1838793..1838943_NEGATIVE 167 109 65 128 87 NC_003454:FN0031|3end_hypothetical_protein_667899..668049_NEGATIVE 164 50 10 131 80 NC_003454:FN0763|3end_Transporter,_LysE_family_1420440..1420590_POSITIVE 164 44 5 113 73 NC_003454:FN0448|3end_DNA-repair_protein_1092747..1092897_POSITIVE 163 36 1 47 8 NC_003454:FN0374|3end_Single-stranded-DNA-specific_exonuclease_recJ_1005268..1005418_POSITIVE 162 33 2 86 55 NC_003454:FN2122|3end_Phenylalanyl-tRNA_synthetase_beta_chain_629798..629948_NEGATIVE 159 35 2 137 100 NC_003454:FN1031|3end_Hypothetical_membrane-spanning_protein_1684721..1684871_NEGATIVE 158 31 2 97 64 NC_003454:FN0824|3end_Transcriptional_regulator,_DeoR_family_1485119..1485269_POSITIVE 156 88 49 114 71 NC_003454:FN0829|3end_hypothetical_protein_1489580..1489730_NEGATIVE 155 97 56 50 5 NC_003454:FN0886|3end_Hemin_receptor_1547830..1547980_POSITIVE 155 32 2 104 74 NC_003454:FN0464|3end_hypothetical_protein_1110087..1110237_POSITIVE 155 138 94 52 12 NC_003454:FN0328|3end_Na(+)-linked_D-alanine_glycine_permease_962335..962485_NEGATIVE 147 122 85 60 21 NC_003454:FN0603|3end_Transcriptional_regulatory_protein,_LYSR_family_1257501..1257651_NEGATIVE 147 49 2 119 75 NC_003454:FN0594|3end_(3R)-hydroxymyristoyl-[acyl_carrier_protein]_dehydratase_1249290..1249440_POSITIVE 146 88 42 113 74 NC_003454:FN2036|3end_DNA-directed_RNA_polymerase_beta_chain_542817..542967_NEGATIVE 146 91 64 126 99 NC_003454:FN1757|3end_thiamine_biosynthesis_protein_ThiC_251948..252098_NEGATIVE