Origin IGS: tattataaataaattaaaaaaacttaacttactaaattatatattaattactaacctgctgaaaacttataagtccatgaggtgagaaacaggcttgcttctactttacattattttttaaatttaataccatataagtatatagtattttttagaacttgtcaagaaaaatattattgtatgat .........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 atcatacaataatatttttcttgacaagttctaaaaaatactatatacttatatggtattaaatttaaaaaataatgtaaagtagaagcaagcctgtttctcacctcatggacttataagttttcagcaggttagtaattaatatataatttagtaagttaagtttttttaatttatttataata Mask Tandem Repeat Region ================================================ tattataaataaattaaaaaaacttaacttactaaattatatattaattactaacctgctgaaaacttataagtccatgaggtgagaaacaggcttgcttctactttacattattttttaaatttaataccatataagtatatagtattttttagaacttgtcaagaaaaatattattgtatgat Find is-nt database================================================ Query_seq: FN0327:FN0328|FN0327:FN0328:Bacterial Protein Translation Initiation Factor 3 (IF-3):Na(+)-linked D-alanine glycine permease:<-<-:962240..962424 185 tattataaataaattaaaaaaacttaacttactaaattatatattaattactaacctgctgaaaacttataagtccatgaggtgagaaacaggcttgcttctactttacattattttttaaatttaataccatataagtatatagtattttttagaacttgtcaagaaaaatattattgtatgat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN0327:FN0328|FN0327:FN0328:Bacterial Protein Translation Initiation Factor 3 (IF-3):Na(+)-linked D-alanine glycine permease:<-<-:962240..962424 185 tattataaataaattaaaaaaacttaacttactaaattatatattaattactaacctgctgaaaacttataagtccatgaggtgagaaacaggcttgcttctactttacattattttttaaatttaataccatataagtatatagtattttttagaacttgtcaagaaaaatattattgtatgat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN0327:FN0328|FN0327:FN0328:Bacterial Protein Translation Initiation Factor 3 (IF-3):Na(+)-linked D-alanine glycine permease:<-<-:962240..962424 185 tattataaataaattaaaaaaacttaacttactaaattatatattaattactaacctgctgaaaacttataagtccatgaggtgagaaacaggcttgcttctactttacattattttttaaatttaataccatataagtatatagtattttttagaacttgtcaagaaaaatattattgtatgat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tattataaataaattaaaaaaacttaacttactaaattatatattaattactaacctgctgaaaacttataagtccatgaggtgagaaacaggcttgcttctactttacattattttttaaatttaataccatataagtatatagtattttttagaacttgtcaagaaaaatattattgtatgat Predict ORF larger than 30AA ================================================ Protein_Len: 34 Strand: + Start: 82 End: 183 ................................................................................. M R N R L A S T L H Y F L N L I P Y K Y I V F F R T C Q E K Y Y C M .. tattataaataaattaaaaaaacttaacttactaaattatatattaattactaacctgctgaaaacttataagtccatgaggtgagaaacaggcttgcttctactttacattattttttaaatttaataccatataagtatatagtattttttagaacttgtcaagaaaaatattattgtatgat 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: 87 Start: 137 End: 166 ........................................................................................................................................CTTGACAAGTTCTAAAAAATACTATATACT................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tattataaataaattaaaaaaacttaacttactaaattatatattaattactaacctgctgaaaacttataagtccatgaggtgagaaacaggcttgcttctactttacattattttttaaatttaataccatataagtatatagtattttttagaacttgtcaagaaaaatattattgtatgat Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: FN0327:FN0328|FN0327:FN0328:Bacterial Protein Translation Initiation Factor 3 (IF-3):Na(+)-linked D-alanine glycine permease:<-<-:962240..962424 185 tattataaataaattaaaaaaacttaacttactaaattatatattaattactaacctgctgaaaacttataagtccatgaggtgagaaacaggcttgcttctactttacattattttttaaatttaataccatataagtatatagtattttttagaacttgtcaagaaaaatattattgtatgat Intra-Species Hit: Count: 1 Min: 1 Max: 185 Len: 185 Subject: NC_003454_FN0327_FN0328|Bacterial Protein Translation Initiation Factor 3 (IF-3):Na(+)-linked D-alanine glycine permease|NEGATIVE:NEGATIVE|[962240,962424]|185 HSP 1 e-value: 3.0E-88 bit: 325.0 Len: 185 Query Start:1 Query End:185 Subject Strand: POSITIVE Subject Start: 1 Subject End: 185 tattataaataaattnnnnnnncttaacttactaaattatatattaattactaacctgctgaaaacttataagtccatgaggtgagaaacaggcttgcttctactttacattattttttaaatttaataccatataagtatatagtattttttagaacttgtcaagaaaaatattattgtatgat tattataaataaattaaaaaaacttaacttactaaattatatattaattactaacctgctgaaaacttataagtccatgaggtgagaaacaggcttgcttctactttacattattttttaaatttaataccatataagtatatagtattttttagaacttgtcaagaaaaatattattgtatgat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAUUAUAAAUAAAUUAAAAAAACUUAACUUACUAAAUUAUAUAUUAAUUACUAACCUGCUGAAAACUUAUAAGUCCAUGAGGUGAGAAACAGGCUUGCUUCUACUUUACAUUAUUUUUUAAAUUUAAUACCAUAUAAGUAUAUAGUAUUUUUUAGAACUUGUCAAGAAAAAUAUUAUUGUAUGAU ...................................((((((((.((((..............................((((..((.......))..))))..(((.(((.....(((((((...(((((.((((....)))).))))).)))))))..))).)))......)))).)))))))) (-21.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUCAUACAAUAAUAUUUUUCUUGACAAGUUCUAAAAAAUACUAUAUACUUAUAUGGUAUUAAAUUUAAAAAAUAAUGUAAAGUAGAAGCAAGCCUGUUUCUCACCUCAUGGACUUAUAAGUUUUCAGCAGGUUAGUAAUUAAUAUAUAAUUUAGUAAGUUAAGUUUUUUUAAUUUAUUUAUAAUA ....((((((.........((((..((((((.....((((((((((....)))))))))).....................(((((((((....))))))).)).....)))))).))))..........))).))).......(((((....((((((((((....)))))))))))))))... (-26.11) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 900 100 51 191 142 NC_003454:FN0327|5end_Bacterial_Protein_Translation_Initiation_Factor_3_(IF-3)_962149..962379_NEGATIVE 251 113 74 183 147 NC_003454:FN1126|5end_Acetyltransferase_1770287..1770517_NEGATIVE 229 99 51 113 73 NC_003454:FN1805|5end_hypothetical_protein_286453..286683_POSITIVE 222 132 94 145 99 NC_003454:FN1454|5end_D-alanine--D-alanine_ligase_2135659..2135889_NEGATIVE 220 82 48 95 55 NC_003454:FN0514|5end_hypothetical_protein_1163431..1163661_POSITIVE 213 109 66 158 100 NC_003454:FN1753|5end_thiamine_biosynthesis_protein_ThiH_250344..250574_NEGATIVE 212 106 73 47 16 NC_003454:FN2040|5end_LSU_ribosomal_protein_L11P_549043..549273_NEGATIVE 209 96 56 219 180 NC_003454:FN0578|5end_ATP-dependent_DNA_helicase_recQ_1227941..1228171_POSITIVE 209 110 70 43 2 NC_003454:FN0296|5end_Hypothetical_cytosolic_protein_929789..930019_NEGATIVE 205 178 133 203 158 NC_003454:FN1983|5end_Alkyl_hydroperoxide_reductase_C22_protein_484619..484849_POSITIVE 202 105 65 191 155 NC_003454:FN1904|5end_Transcriptional_regulator,_MarR_family_393107..393337_POSITIVE 199 102 73 227 197 NC_003454:FN1360|5end_Dipeptide_transport_system_permease_protein_dppB_2012134..2012364_POSITIVE 199 107 71 69 29 NC_003454:FN0508|5end_Serine_protease_1158652..1158882_NEGATIVE 196 98 56 46 7 NC_003454:FN0238|5end_hypothetical_protein_863314..863544_NEGATIVE 194 98 60 183 145 NC_003454:FN1362|5end_Dipeptide_transport_ATP-binding_protein_dppD_2013818..2014048_POSITIVE 194 107 74 213 176 NC_003454:FN0698|5end_DNA_integration/recombination/invertion_protein_1356611..1356841_POSITIVE 194 120 74 108 59 NC_003454:FN0176|5end_Cell_division_inhibitor_MinD_801157..801387_POSITIVE 193 116 73 202 149 NC_003454:FN0312|5end_Anaerobic_ribonucleoside-triphosphate_reductase_activating_protein_949316..949546_POSITIVE 190 108 64 192 147 NC_003454:FN0463|5end_Hypothetical_cytosolic_protein_1109126..1109356_POSITIVE 190 77 45 230 189 NC_003454:FN0452|5end_Glucosamine--fructose-6-phosphate_aminotransferase_[isomerizing]_1095699..1095929_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 229 99 51 45 5 NC_003454:FN1804|3end_Aminoacyl-histidine_dipeptidase_286465..286615_POSITIVE 224 118 77 114 60 NC_003454:FN2110|3end_Hypothetical_exported_24-amino_acid_repeat_protein_621908..622058_NEGATIVE 222 132 94 130 84 NC_003454:FN1455|3end_UDP-N-acetylenolpyruvoylglucosamine_reductase_2135674..2135824_NEGATIVE 217 94 57 36 3 NC_003454:FN0807|3end_3-deoxy-manno-octulosonate_cytidylyltransferase_1467157..1467307_NEGATIVE 214 112 77 68 23 NC_003454:FN0453|3end_Xaa-Pro_aminopeptidase_1099381..1099531_POSITIVE 206 102 68 85 57 NC_003454:FN2109|3end_UDP-glucose_4-epimerase_621917..622067_POSITIVE 205 106 79 71 33 NC_003454:FN0861|3end_hypothetical_protein_1521738..1521888_NEGATIVE 205 178 133 76 31 NC_003454:FN1982|3end_hypothetical_protein_484572..484722_POSITIVE 203 107 66 135 90 NC_003454:FN1302|3end_hypothetical_protein_1959667..1959817_POSITIVE 200 116 75 49 1 NC_003454:FN1376|3end_oxaloacetate_decarboxylase_2025305..2025455_POSITIVE 194 120 74 106 57 NC_003454:FN0175|3end_Cell_division_inhibitor_MinC_801235..801385_POSITIVE 190 106 65 66 20 NC_003454:FN0643|3end_hypothetical_protein_1299434..1299584_NEGATIVE 183 99 54 46 1 NC_003454:FN2122|3end_Phenylalanyl-tRNA_synthetase_beta_chain_629798..629948_NEGATIVE 181 110 72 68 21 NC_003454:FN0559|3end_Phosphoglucomutase_1213138..1213288_POSITIVE 181 62 25 144 108 NC_003454:FN2082|3end_Formate--tetrahydrofolate_ligase_593257..593407_NEGATIVE 180 93 53 117 85 NC_003454:FN2006|3end_Cobalt_transport_protein_cbiQ_506959..507109_POSITIVE 178 89 52 142 108 NC_003454:FN0978|3end_NA+/H+_antiporter_NHAC_1630670..1630820_NEGATIVE 176 119 80 43 1 NC_003454:FN1495|3end_hypothetical_protein_-89..61_NEGATIVE 169 139 91 64 17 NC_003454:FN0180|3end_Tetratricopeptide_repeat_family_protein_804846..804996_NEGATIVE 168 70 22 140 93 NC_003454:FN0903|3end_Polysialic_acid_capsule_expression_protein_kpsF_1562167..1562317_POSITIVE