Origin IGS: gtaagtaaaatattgaaaggtattttatgaaaatagaattaatgaaaataactttaaaagatacaaaagaaatttgggaaatgcaagtaaaagcattcaaggaattacttgataaatatcaagattttgaaactaatcctgcaagtgaacctatttcaaatattgaa .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ttcaatatttgaaataggttcacttgcaggattagtttcaaaatcttgatatttatcaagtaattccttgaatgcttttacttgcatttcccaaatttcttttgtatcttttaaagttattttcattaattctattttcataaaatacctttcaatattttacttac Mask Tandem Repeat Region ================================================ gtaagtaaaatattgaaaggtattttatgaaaatagaattaatgaaaataactttaaaagatacaaaagaaatttgggaaatgcaagtaaaagcattcaaggaattacttgataaatatcaagattttgaaactaatcctgcaagtgaacctatttcaaatattgaa Find is-nt database================================================ Query_seq: FN1106:FN1107|FN1106:FN1107:L-serine dehydratase:Acetyltransferase:->->:1751934..1752100 167 gtaagtaaaatattgaaaggtattttatgaaaatagaattaatgaaaataactttaaaagatacaaaagaaatttgggaaatgcaagtaaaagcattcaaggaattacttgataaatatcaagattttgaaactaatcctgcaagtgaacctatttcaaatattgaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN1106:FN1107|FN1106:FN1107:L-serine dehydratase:Acetyltransferase:->->:1751934..1752100 167 gtaagtaaaatattgaaaggtattttatgaaaatagaattaatgaaaataactttaaaagatacaaaagaaatttgggaaatgcaagtaaaagcattcaaggaattacttgataaatatcaagattttgaaactaatcctgcaagtgaacctatttcaaatattgaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN1106:FN1107|FN1106:FN1107:L-serine dehydratase:Acetyltransferase:->->:1751934..1752100 167 gtaagtaaaatattgaaaggtattttatgaaaatagaattaatgaaaataactttaaaagatacaaaagaaatttgggaaatgcaagtaaaagcattcaaggaattacttgataaatatcaagattttgaaactaatcctgcaagtgaacctatttcaaatattgaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gtaagtaaaatattgaaaggtattttatgaaaatagaattaatgaaaataactttaaaagatacaaaagaaatttgggaaatgcaagtaaaagcattcaaggaattacttgataaatatcaagattttgaaactaatcctgcaagtgaacctatttcaaatattgaa Predict ORF larger than 30AA ================================================ Protein_Len: 52 Strand: + Start: 12 End: 167 ........... M E R Y F M K I E L M K I T L K D T K E I W E M Q V K A F K E L L D K Y Q D F E T N P A S E P I S N I E Protein_Len: 33 Strand: - Start: 2 End: 100 . L Y F I S L Y K I F I S N I F I V K F S V F S I Q S I C T F A N M ................................................................... gtaagtaaaatattgaaaggtattttatgaaaatagaattaatgaaaataactttaaaagatacaaaagaaatttgggaaatgcaagtaaaagcattcaaggaattacttgataaatatcaagattttgaaactaatcctgcaagtgaacctatttcaaatattgaa Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gtaagtaaaatattgaaaggtattttatgaaaatagaattaatgaaaataactttaaaagatacaaaagaaatttgggaaatgcaagtaaaagcattcaaggaattacttgataaatatcaagattttgaaactaatcctgcaagtgaacctatttcaaatattgaa Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 42 HP_score: -3.3 Tail_Score: -2.50479 Start: 97 End: 112 Full_Region: aaatcttgatattta tcaag taattc cttga atgcttttacttgca ................................................................................................tcaagtaattccttga....................................................... Find igs database================================================ Query_seq: FN1106:FN1107|FN1106:FN1107:L-serine dehydratase:Acetyltransferase:->->:1751934..1752100 167 gtaagtaaaatattgaaaggtattttatgaaaatagaattaatgaaaataactttaaaagatacaaaagaaatttgggaaatgcaagtaaaagcattcaaggaattacttgataaatatcaagattttgaaactaatcctgcaagtgaacctatttcaaatattgaa Intra-Species Hit: Count: 1 Min: 1 Max: 167 Len: 167 Subject: NC_003454_FN1106_FN1107|L-serine dehydratase:Acetyltransferase|POSITIVE:POSITIVE|[1751934 ,1752100]|167 HSP 1 e-value: 4.0E-90 bit: 331.0 Len: 167 Query Start:1 Query End:167 Subject Strand: POSITIVE Subject Start: 1 Subject End: 167 gtaagtaaaatattgaaaggtattttatgaaaatagaattaatgaaaataactttaaaagatacaaaagaaatttgggaaatgcaagtaaaagcattcaaggaattacttgataaatatcaagattttgaaactaatcctgcaagtgaacctatttcaaatattgaa gtaagtaaaatattgaaaggtattttatgaaaatagaattaatgaaaataactttaaaagatacaaaagaaatttgggaaatgcaagtaaaagcattcaaggaattacttgataaatatcaagattttgaaactaatcctgcaagtgaacctatttcaaatattgaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUAAGUAAAAUAUUGAAAGGUAUUUUAUGAAAAUAGAAUUAAUGAAAAUAACUUUAAAAGAUACAAAAGAAAUUUGGGAAAUGCAAGUAAAAGCAUUCAAGGAAUUACUUGAUAAAUAUCAAGAUUUUGAAACUAAUCCUGCAAGUGAACCUAUUUCAAAUAUUGAA ....((((((((((....))))))))))..........((((((.......((.....))........(((((..((..(((((........)))))..((((.(((((((((....))))))..........))))))).........)).)))))...)))))). (-22.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUCAAUAUUUGAAAUAGGUUCACUUGCAGGAUUAGUUUCAAAAUCUUGAUAUUUAUCAAGUAAUUCCUUGAAUGCUUUUACUUGCAUUUCCCAAAUUUCUUUUGUAUCUUUUAAAGUUAUUUUCAUUAAUUCUAUUUUCAUAAAAUACCUUUCAAUAUUUUACUUAC ...((((((.(((..((((.....(((((((..((((((((...((((((....)))))).......))))).)))..).))))))......((((..((((..........))))..))))........................)))))))))))))........ (-21.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 221 155 119 47 1 NC_003454:FN0671|5end_High-affinity_zinc_uptake_system_membrane_protein_znuB_1326616..1326846_POSITIVE 213 142 112 231 203 NC_003454:FN0363|5end_ATP_synthase_C_chain,_sodium_ion_specific_993703..993933_NEGATIVE 212 110 82 135 107 NC_003454:FN1384|5end_IAA_acetyltransferase_2038256..2038486_NEGATIVE 212 159 136 45 24 NC_003454:FN1040|5end_Branched-chain_amino_acid_transport_protein_azlD_1691746..1691976_POSITIVE 207 153 126 158 131 NC_003454:FN0887|5end_Oligoendopeptidase_F_1549711..1549941_NEGATIVE 193 117 76 64 22 NC_003454:FN0367|5end_Integral_membrane_protein_996901..997131_NEGATIVE 187 89 59 117 86 NC_003454:FN0601|5end_Hypothetical_exported_24-amino_acid_repeat_protein_1256527..1256757_NEGATIVE 186 153 111 226 190 NC_003454:FN0362|5end_ATP_synthase_B_chain,_sodium_ion_specific_993393..993623_NEGATIVE 186 158 130 62 24 NC_003454:FN0216|5end_3-oxoacyl-[acyl-carrier_protein]_reductase_840864..841094_NEGATIVE 185 99 66 90 59 NC_003454:FN0569|5end_Hypothetical_membrane-spanning_protein_1220732..1220962_NEGATIVE 184 148 101 211 165 NC_003454:FN1398|5end_Amino_acid_carrier_protein_alsT_2052808..2053038_POSITIVE 184 120 80 53 12 NC_003454:FN1312|5end_Biopolymer_transport_exbB_protein_1966948..1967178_NEGATIVE 182 148 101 226 171 NC_003454:FN1284|5end_30S_ribosomal_protein_S4_1943243..1943473_NEGATIVE 180 157 132 75 50 NC_003454:FN0332|5end_Magnesium_and_cobalt_transport_protein_corA_967230..967460_NEGATIVE 179 41 3 174 138 NC_003454:FN2087|5end_hypothetical_protein_599719..599949_NEGATIVE 178 151 111 153 115 NC_003454:FN2073|5end_adenine_phosphoribosyltransferase_583585..583815_POSITIVE 176 114 82 44 11 NC_003454:FN1533|5end_Electron_transfer_flavoprotein_alpha-subunit_46321..46551_NEGATIVE 175 107 65 63 29 NC_003454:FN0131|5end_Hemolysin_activator_protein_precursor_759547..759777_POSITIVE 175 107 65 186 152 NC_003454:FN1818|5end_Hemolysin_activator_protein_precursor_306955..307185_NEGATIVE 172 140 94 76 28 NC_003454:FN0119|5end_Flavodoxin_752073..752303_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 221 155 119 50 4 NC_003454:FN0670|3end_High-affinity_zinc_uptake_system_membrane_protein_znuB_1326699..1326849_POSITIVE 212 159 136 48 27 NC_003454:FN1039|3end_Branched-chain_amino_acid_transport_protein_azlC_1691829..1691979_POSITIVE 207 153 126 143 116 NC_003454:FN0888|3end_Uracil_permease_1549726..1549876_NEGATIVE 187 159 116 37 1 NC_003454:FN0010|3end_nicotinate-nucleotide_pyrophosphorylase_651118..651268_POSITIVE 181 145 101 150 107 NC_003454:FN1397|3end_glutaminase_2052830..2052980_POSITIVE 181 35 8 136 109 NC_003454:FN0256|3end_Hypothetical_cytosolic_protein_882467..882617_POSITIVE 180 157 132 58 33 NC_003454:FN0333|3end_Glycerol_uptake_operon_antiterminator_regulatory_protein_967247..967397_NEGATIVE 180 154 113 147 105 NC_003454:FN0201|3end_Glutaconyl-COA_decarboxylase_beta_subunit_827749..827899_POSITIVE 179 41 3 45 9 NC_003454:FN2088|3end_hypothetical_protein_599848..599998_NEGATIVE 178 151 111 141 103 NC_003454:FN2072|3end_Guanine-hypoxanthine_permease_583653..583803_POSITIVE 174 79 32 58 11 NC_003454:FN1509|3end_hypothetical_protein_14099..14249_NEGATIVE 173 40 6 42 1 NC_003454:FN1499|3end_Cell_surface_protein_5166..5316_POSITIVE 172 140 94 79 31 NC_003454:FN0118|3end_Chaperone_protein_dnaJ_752156..752306_POSITIVE 172 147 120 99 76 NC_003454:FN2006|3end_Cobalt_transport_protein_cbiQ_506959..507109_POSITIVE 171 51 18 150 119 NC_003454:FN0744|3end_metal_dependent_phosphohydrolase_1403358..1403508_POSITIVE 166 144 122 134 115 NC_003454:FN2040|3end_LSU_ribosomal_protein_L11P_548618..548768_NEGATIVE 165 118 71 143 104 NC_003454:FN0014|3end_Transporter_652839..652989_POSITIVE 164 158 115 72 29 NC_003454:FN0743|3end_ATP-dependent_helicase,_DinG_family_1403155..1403305_POSITIVE 161 120 73 59 11 NC_003454:FN0907|3end_Ribosomal_RNA_small_subunit_methyltransferase_C_1565324..1565474_NEGATIVE 160 130 81 70 16 NC_003454:FN1884|3end_hypothetical_protein_370328..370478_NEGATIVE