Origin IGS: gcaggttacaatagtaactattatagttattttaaaaagctttttaatttcctccatctgatacctttccttcttagtttttataagctataaaactgaatgttccttatattagcacaaatagaaaaaaaataaaacttaaaaattt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aaatttttaagttttattttttttctatttgtgctaatataaggaacattcagttttatagcttataaaaactaagaaggaaaggtatcagatggaggaaattaaaaagctttttaaaataactataatagttactattgtaacctgc Mask Tandem Repeat Region ================================================ gcaggttacaatagtaactattatagttattttaaaaagctttttaatttcctccatctgatacctttccttcttagtttttataagctataaaactgaatgttccttatattagcacaaatagaaaaaaaataaaacttaaaaattt Find is-nt database================================================ Query_seq: FN0365:FN0366|FN0365:FN0366:ATP synthase protein I, sodium ion specific:Phosphoacetylglucosamine mutase:<-<-:994950..995097 148 gcaggttacaatagtaactattatagttattttaaaaagctttttaatttcctccatctgatacctttccttcttagtttttataagctataaaactgaatgttccttatattagcacaaatagaaaaaaaataaaacttaaaaattt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN0365:FN0366|FN0365:FN0366:ATP synthase protein I, sodium ion specific:Phosphoacetylglucosamine mutase:<-<-:994950..995097 148 gcaggttacaatagtaactattatagttattttaaaaagctttttaatttcctccatctgatacctttccttcttagtttttataagctataaaactgaatgttccttatattagcacaaatagaaaaaaaataaaacttaaaaattt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN0365:FN0366|FN0365:FN0366:ATP synthase protein I, sodium ion specific:Phosphoacetylglucosamine mutase:<-<-:994950..995097 148 gcaggttacaatagtaactattatagttattttaaaaagctttttaatttcctccatctgatacctttccttcttagtttttataagctataaaactgaatgttccttatattagcacaaatagaaaaaaaataaaacttaaaaattt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gcaggttacaatagtaactattatagttattttaaaaagctttttaatttcctccatctgatacctttccttcttagtttttataagctataaaactgaatgttccttatattagcacaaatagaaaaaaaataaaacttaaaaattt Predict ORF larger than 30AA ================================================ gcaggttacaatagtaactattatagttattttaaaaagctttttaatttcctccatctgatacctttccttcttagtttttataagctataaaactgaatgttccttatattagcacaaatagaaaaaaaataaaacttaaaaattt 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================================================ gcaggttacaatagtaactattatagttattttaaaaagctttttaatttcctccatctgatacctttccttcttagtttttataagctataaaactgaatgttccttatattagcacaaatagaaaaaaaataaaacttaaaaattt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: FN0365:FN0366|FN0365:FN0366:ATP synthase protein I, sodium ion specific:Phosphoacetylglucosamine mutase:<-<-:994950..995097 148 gcaggttacaatagtaactattatagttattttaaaaagctttttaatttcctccatctgatacctttccttcttagtttttataagctataaaactgaatgttccttatattagcacaaatagaaaaaaaataaaacttaaaaattt Intra-Species Hit: Count: 1 Min: 1 Max: 124 Len: 124 Subject: NC_003454_FN0365_FN0366|ATP synthase protein I, sodium ion specific:Phosphoacetylglucosamine mutase|NEGATIVE:NEGATIVE|[994950,995097]|148 HSP 1 e-value: 2.0E-64 bit: 246.0 Len: 124 Query Start:1 Query End:124 Subject Strand: POSITIVE Subject Start: 1 Subject End: 124 gcaggttacaatagtaactattatagttattttaaaaagctttttaatttcctccatctgatacctttccttcttagtttttataagctataaaactgaatgttccttatattagcacaaatag........................ gcaggttacaatagtaactattatagttattttaaaaagctttttaatttcctccatctgatacctttccttcttagtttttataagctataaaactgaatgttccttatattagcacaaatag........................ Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GCAGGUUACAAUAGUAACUAUUAUAGUUAUUUUAAAAAGCUUUUUAAUUUCCUCCAUCUGAUACCUUUCCUUCUUAGUUUUUAUAAGCUAUAAAACUGAAUGUUCCUUAUAUUAGCACAAAUAG .(((((......((((((((...))))))))((((((....))))))........)))))................(((..((((((..(((........)))..))))))..)))........ (-13.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUAUUUGUGCUAAUAUAAGGAACAUUCAGUUUUAUAGCUUAUAAAAACUAAGAAGGAAAGGUAUCAGAUGGAGGAAAUUAAAAAGCUUUUUAAAAUAACUAUAAUAGUUACUAUUGUAACCUGC (((((((((((..((((((((((.....)))).....))))))....((....))....)))).))))))).((...((((((....))))))......((((((((...)))))))).))... (-16.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 785 100 51 191 142 NC_003454:FN0365|5end_ATP_synthase_protein_I,_sodium_ion_specific_994859..995089_NEGATIVE 282 97 53 135 87 NC_003454:FN1035|5end_Iron-sulfur_flavoprotein_1688280..1688510_POSITIVE 261 110 66 143 99 NC_003454:FN1167|5end_beta-methylgalactoside_transporter_inner_membrane_component_1825538..1825768_POSITIVE 258 83 46 218 190 NC_003454:FN1426|5end_Serine_protease_2095462..2095692_NEGATIVE 247 45 9 215 182 NC_003454:FN1048|5end_Hypothetical_membrane-spanning_protein_1697911..1698141_POSITIVE 245 90 48 80 40 NC_003454:FN0847|5end_TPR-repeat-containing_proteins_1505253..1505483_POSITIVE 236 66 41 119 94 NC_003454:FN2123|5end_Phenylalanyl-tRNA_synthetase_alpha_chain_633224..633454_NEGATIVE 235 81 41 114 75 NC_003454:FN0208|5end_(R)-2-hydroxyglutaryl-CoA_dehydratase_beta-subunit_834968..835198_POSITIVE 233 61 27 142 113 NC_003454:FN1784|5end_hypothetical_protein_266190..266420_NEGATIVE 231 83 48 113 78 NC_003454:FN0988|5end_phosphoribosylaminoimidazole-succinocarboxamide_synthase_1640968..1641198_NEGATIVE 229 100 52 227 187 NC_003454:FN0460|5end_delta-aminolevulinic_acid_dehydratase_1105482..1105712_POSITIVE 225 90 54 118 88 NC_003454:FN1733|5end_ATP_synthase_subunit_D_232871..233101_NEGATIVE 221 89 42 143 91 NC_003454:FN1626|5end_LSU_ribosomal_protein_L30P_133049..133279_NEGATIVE 218 63 24 187 143 NC_003454:FN0009|5end_L-aspartate_oxidase_648908..649138_POSITIVE 218 107 64 148 100 NC_003454:FN1968|5end_Hemin_transport_system_ATP-binding_protein_hmuV_467189..467419_NEGATIVE 218 97 51 97 49 NC_003454:FN1787|5end_Tetratricopeptide_repeat_family_protein_267762..267992_POSITIVE 217 80 38 166 128 NC_003454:FN1270|5end_Hypothetical_cytosolic_protein_1926592..1926822_NEGATIVE 216 80 38 133 84 NC_003454:FN1317|5end_RNA_polymerase_sigma_factor_1971085..1971315_NEGATIVE 216 70 39 209 178 NC_003454:FN1229|5end_hypothetical_protein_1886700..1886930_NEGATIVE 215 110 68 134 94 NC_003454:FN1977|5end_Cell_cycle_protein_MesJ_478136..478366_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 282 97 53 120 72 NC_003454:FN1034|3end_Transcriptional_regulator,_TetR_family_1688345..1688495_POSITIVE 261 110 66 120 76 NC_003454:FN1166|3end_Galactoside_transport_ATP-binding_protein_mglA_1825595..1825745_POSITIVE 236 66 41 92 67 NC_003454:FN2124|3end_Hypothetical_protein_with_Metallo-phosphoesterase_motif_633251..633401_NEGATIVE 235 81 41 92 53 NC_003454:FN0207|3end_(R)-2-hydroxyglutaryl-CoA_dehydratase_alpha-subunit_835026..835176_POSITIVE 233 61 27 120 91 NC_003454:FN1785|3end_hypothetical_protein_266212..266362_NEGATIVE 225 90 54 107 77 NC_003454:FN1734|3end_V-type_ATP_synthase_subunit_B_232882..233032_NEGATIVE 221 89 42 130 78 NC_003454:FN1627|3end_SSU_ribosomal_protein_S5P_133062..133212_NEGATIVE 218 107 64 151 103 NC_003454:FN1969|3end_Hemin_transport_system_permease_protein_hmuU_467186..467336_NEGATIVE 218 97 51 76 28 NC_003454:FN1786|3end_ADP-heptose_synthase_267821..267971_POSITIVE 216 80 38 117 68 NC_003454:FN1318|3end_RNA_polymerase_sigma_factor_rpoD_1971101..1971251_NEGATIVE 215 110 68 125 85 NC_003454:FN1976|3end_4-amino-4-deoxychorismate_lyase_478207..478357_POSITIVE 207 99 52 114 72 NC_003454:FN0200|3end_Biotin_carboxyl_carrier_protein_of_glutaconyl-COA_decarboxylase_826607..826757_POSITIVE 206 87 47 45 2 NC_003454:FN1308|3end_Phosphatidate_cytidylyltransferase_1964861..1965011_POSITIVE 206 70 48 107 82 NC_003454:FN0286|3end_hypothetical_protein_914183..914333_NEGATIVE 204 80 34 97 49 NC_003454:FN0070|3end_Glycyl-tRNA_synthetase_beta_chain_711042..711192_POSITIVE 203 106 64 131 99 NC_003454:FN0272|3end_Acetoacetate:butyrate/acetate_coenzyme_A_transferase_899503..899653_POSITIVE 200 89 48 55 11 NC_003454:FN0950|3end_Precorrin-6X_reductase_1606975..1607125_NEGATIVE 199 89 48 139 101 NC_003454:FN1348|3end_ABC_transporter_ATP-binding_protein_2000470..2000620_NEGATIVE 197 80 38 66 26 NC_003454:FN0297|3end_ATPase_associated_with_chromosome_architecture/replication_931201..931351_POSITIVE 194 70 23 72 16 NC_003454:FN0367|3end_Integral_membrane_protein_996383..996533_NEGATIVE