Origin IGS: gattaaatattttttgtaattcatttgtcctccaatttttatttgtcctaaaaaataatttatcataaattggaattaatatcaaattttattatgatagtattttaatatattaaaattaaggtttgattaaaaatttttagtaaaagaaaaagagtagcaagttttagaatttttactacccttatataattttatagttaatcctattaaaaacaacca .........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 tggttgtttttaataggattaactataaaattatataagggtagtaaaaattctaaaacttgctactctttttcttttactaaaaatttttaatcaaaccttaattttaatatattaaaatactatcataataaaatttgatattaattccaatttatgataaattattttttaggacaaataaaaattggaggacaaatgaattacaaaaaatatttaatc Mask Tandem Repeat Region ================================================ gattaaatattttttgtaattcatttgtcctccaatttttatttgtcctaaaaaataatttatcataaattggaattaatatcaaattttattatgatagtattttaatatattaaaattaaggtttgattaaaaatttttagtaaaagaaaaagagtagcaagttttagaatttttactacccttatataattttatagttaatcctattaaaaacaacca Find is-nt database================================================ Query_seq: FN1933:FN1934|FN1933:FN1934:hypothetical protein:hypothetical protein:<-<-:434134..434355 222 gattaaatattttttgtaattcatttgtcctccaatttttatttgtcctaaaaaataatttatcataaattggaattaatatcaaattttattatgatagtattttaatatattaaaattaaggtttgattaaaaatttttagtaaaagaaaaagagtagcaagttttagaatttttactacccttatataattttatagttaatcctattaaaaacaacca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN1933:FN1934|FN1933:FN1934:hypothetical protein:hypothetical protein:<-<-:434134..434355 222 gattaaatattttttgtaattcatttgtcctccaatttttatttgtcctaaaaaataatttatcataaattggaattaatatcaaattttattatgatagtattttaatatattaaaattaaggtttgattaaaaatttttagtaaaagaaaaagagtagcaagttttagaatttttactacccttatataattttatagttaatcctattaaaaacaacca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN1933:FN1934|FN1933:FN1934:hypothetical protein:hypothetical protein:<-<-:434134..434355 222 gattaaatattttttgtaattcatttgtcctccaatttttatttgtcctaaaaaataatttatcataaattggaattaatatcaaattttattatgatagtattttaatatattaaaattaaggtttgattaaaaatttttagtaaaagaaaaagagtagcaagttttagaatttttactacccttatataattttatagttaatcctattaaaaacaacca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gattaaatattttttgtaattcatttgtcctccaatttttatttgtcctaaaaaataatttatcataaattggaattaatatcaaattttattatgatagtattttaatatattaaaattaaggtttgattaaaaatttttagtaaaagaaaaagagtagcaagttttagaatttttactacccttatataattttatagttaatcctattaaaaacaacca Predict ORF larger than 30AA ================================================ gattaaatattttttgtaattcatttgtcctccaatttttatttgtcctaaaaaataatttatcataaattggaattaatatcaaattttattatgatagtattttaatatattaaaattaaggtttgattaaaaatttttagtaaaagaaaaagagtagcaagttttagaatttttactacccttatataattttatagttaatcctattaaaaacaacca 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: 85 Start: 57 End: 86 ........................................................TTTGATATTAATTCCAATTTATGATAAATT........................................................................................................................................ PromScan Matrix: RpoD-17 Strand: + Score: 83 Start: 69 End: 98 ....................................................................ATTGGAATTAATATCAAATTTTATTATGAT............................................................................................................................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gattaaatattttttgtaattcatttgtcctccaatttttatttgtcctaaaaaataatttatcataaattggaattaatatcaaattttattatgatagtattttaatatattaaaattaaggtttgattaaaaatttttagtaaaagaaaaagagtagcaagttttagaatttttactacccttatataattttatagttaatcctattaaaaacaacca Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: FN1933:FN1934|FN1933:FN1934:hypothetical protein:hypothetical protein:<-<-:434134..434355 222 gattaaatattttttgtaattcatttgtcctccaatttttatttgtcctaaaaaataatttatcataaattggaattaatatcaaattttattatgatagtattttaatatattaaaattaaggtttgattaaaaatttttagtaaaagaaaaagagtagcaagttttagaatttttactacccttatataattttatagttaatcctattaaaaacaacca Intra-Species Hit: Count: 1 Min: 1 Max: 222 Len: 222 Subject: NC_003454_FN1933_FN1934|hypothetical protein:hypothetical protein|NEGATIVE:NEGATIVE|[434134,434355]|222 HSP 1 e-value: 8.0E-40 bit: 165.0 Len: 83 Query Start:1 Query End:83 Subject Strand: POSITIVE Subject Start: 1 Subject End: 83 gattaaatattttttgtaattcatttgtcctccaatttttatttgtcctaaaaaataatttatcataaattggaattaatatc........................................................................................................................................... gattaaatattttttgtaattcatttgtcctccaatttttatttgtcctaaaaaataatttatcataaattggaattaatatc........................................................................................................................................... HSP 2 e-value: 2.0E-34 bit: 147.0 Len: 74 Query Start:149 Query End:222 Subject Strand: POSITIVE Subject Start: 149 Subject End: 222 ....................................................................................................................................................gaaaaagagtagcaagttttagaatttttactacccttatataattttatagttaatcctattaaaaacaacca ....................................................................................................................................................gaaaaagagtagcaagttttagaatttttactacccttatataattttatagttaatcctattaaaaacaacca Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAUUAAAUAUUUUUUGUAAUUCAUUUGUCCUCCAAUUUUUAUUUGUCCUAAAAAAUAAUUUAUCAUAAAUUGGAAUUAAUAUCAAAUUUUAUUAUGAUAGUAUUUUAAUAUAUUAAAAUUAAGGUUUGAUUAAAAAUUUUUAGUAAAAGAAAAAGAGUAGCAAGUUUUAGAAUUUUUACUACCCUUAUAUAAUUUUAUAGUUAAUCCUAUUAAAAACAACCA ((((((.(((...(((((.(((.((((...((((((((((((((........))))))........))))))))......(((((((((((......((((((......))))))....))))))))))).............)))).))).(((.((((.(((((....)))))...)))).))).)))))....))).))))))................ (-26.50) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGGUUGUUUUUAAUAGGAUUAACUAUAAAAUUAUAUAAGGGUAGUAAAAAUUCUAAAACUUGCUACUCUUUUUCUUUUACUAAAAAUUUUUAAUCAAACCUUAAUUUUAAUAUAUUAAAAUACUAUCAUAAUAAAAUUUGAUAUUAAUUCCAAUUUAUGAUAAAUUAUUUUUUAGGACAAAUAAAAAUUGGAGGACAAAUGAAUUACAAAAAAUAUUUAAUC ...((((((((.((((......))))....((((..(((((((((((............))))))))))).........(((((((.................(((((((....)))))))..((((((((....(((.((.......)).)))))))))))......))))))).....))))......))))))))........................ (-27.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 655 50 1 141 92 NC_003454:FN1933|5end_hypothetical_protein_434043..434273_NEGATIVE 253 70 21 136 88 NC_003454:FN0853|5end_Glycogen_synthase_1512307..1512537_NEGATIVE 248 66 21 135 88 NC_003454:FN1322|5end_Membrane_metalloprotease_1978474..1978704_NEGATIVE 240 46 8 114 77 NC_003454:FN2017|5end_Trigger_factor,_ppiase_520241..520471_NEGATIVE 240 46 9 162 123 NC_003454:FN1692|5end_Glycosyl_transferase_188589..188819_NEGATIVE 232 49 7 111 57 NC_003454:FN2126|5end_DNA_gyrase_subunit_B_638225..638455_NEGATIVE 212 55 20 120 87 NC_003454:FN1070|5end_glucose-inhibited_division_protein_A_1717121..1717351_POSITIVE 209 42 10 98 67 NC_003454:FN0777|5end_GTP-binding_protein_LepA_1434832..1435062_NEGATIVE 208 47 6 145 105 NC_003454:FN0749|5end_hypothetical_protein_1408929..1409159_NEGATIVE 207 46 7 117 75 NC_003454:FN1309|5end_hypothetical_protein_1964856..1965086_POSITIVE 205 50 2 106 65 NC_003454:FN0996|5end_Hypothetical_membrane-spanning_protein_1651371..1651601_NEGATIVE 204 57 13 118 75 NC_003454:FN0633|5end_Replication_protein_1290928..1291158_POSITIVE 197 46 8 108 73 NC_003454:FN0398|5end_Dipeptide_transport_system_permease_protein_dppC_1036758..1036988_POSITIVE 195 99 53 229 182 NC_003454:FN1939|5end_hypothetical_protein_439465..439695_NEGATIVE 194 51 13 125 74 NC_003454:FN1236|5end_Choline_transport_protein_1893480..1893710_NEGATIVE 193 180 134 170 107 NC_003454:FN0467|5end_murein_hydrolase_exporter_1112864..1113094_POSITIVE 191 47 8 116 80 NC_003454:FN0116|5end_Chaperone_protein_dnaK_748253..748483_POSITIVE 189 53 11 229 176 NC_003454:FN1167|5end_beta-methylgalactoside_transporter_inner_membrane_component_1825538..1825768_POSITIVE 187 44 5 112 66 NC_003454:FN0204|5end_Glutaconyl-CoA_decarboxylase_A_subunit_829572..829802_POSITIVE 186 50 13 44 9 NC_003454:FN1452|5end_Cell_division_protein_ftsA_2134076..2134306_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 253 70 21 119 71 NC_003454:FN0854|3end_Glucose-1-phosphate_adenylyltransferase_1512324..1512474_NEGATIVE 248 66 21 134 87 NC_003454:FN1323|3end_Thymidylate_kinase_1978475..1978625_NEGATIVE 240 46 8 98 61 NC_003454:FN2018|3end_Single-stranded-DNA-specific_exonuclease_recJ_520257..520407_NEGATIVE 232 49 7 110 56 NC_003454:FN2127|3end_hypothetical_protein_638226..638376_NEGATIVE 215 48 8 130 86 NC_003454:FN0589|3end_Transcriptional_regulator,_MarR_family_1242833..1242983_POSITIVE 209 42 10 81 50 NC_003454:FN0778|3end_Methyltransferase_1434849..1434999_NEGATIVE 208 47 6 100 60 NC_003454:FN0750|3end_hypothetical_protein_1408974..1409124_NEGATIVE 205 50 2 93 52 NC_003454:FN0997|3end_hypothetical_protein_1651384..1651534_NEGATIVE 197 178 142 50 15 NC_003454:FN0907|3end_Ribosomal_RNA_small_subunit_methyltransferase_C_1565324..1565474_NEGATIVE 197 46 8 98 63 NC_003454:FN0397|3end_Dipeptide_transport_system_permease_protein_dppB_1036828..1036978_POSITIVE 195 99 53 109 62 NC_003454:FN1940|3end_Na+_driven_multidrug_efflux_pump_439585..439735_NEGATIVE 194 46 8 42 1 NC_003454:FN1308|3end_Phosphatidate_cytidylyltransferase_1964861..1965011_POSITIVE 193 180 134 88 25 NC_003454:FN0466|3end_Lysyl-tRNA_synthetase_1112862..1113012_POSITIVE 191 45 13 144 101 NC_003454:FN1237|3end_Choline_kinase_1893453..1893603_NEGATIVE 191 47 8 85 49 NC_003454:FN0114|3end_GrpE_protein_748302..748452_POSITIVE 189 200 154 77 36 NC_003454:FN0794|3end_hypothetical_protein_1451840..1451990_NEGATIVE 187 44 5 91 45 NC_003454:FN0203|3end_Glutaconate_CoA-transferase_subunit_B_829631..829781_POSITIVE 186 51 16 67 34 NC_003454:FN1459|3end_Phospho-N-acetylmuramoyl-pentapeptide-_transferase_2140275..2140425_NEGATIVE 186 50 13 47 12 NC_003454:FN1453|3end_hypothetical_protein_2134073..2134223_NEGATIVE 185 57 13 106 60 NC_003454:FN0850|3end_Hypothetical_cytosolic_protein_1509583..1509733_POSITIVE