Origin IGS: ctgcttgagggcttcctttcttgcttcggctgaattatgttttcttgcacccattgttcttaatacttttaattgttcagattcctgaagtgtttgtattcaaccgaa .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ttcggttgaatacaaacacttcaggaatctgaacaattaaaagtattaagaacaatgggtgcaagaaaacataattcagccgaagcaagaaaggaagccctcaagcag Mask Tandem Repeat Region ================================================ ctgcttgagggcttcctttcttgcttcggctgaattatgttttcttgcacccattgttcttaatacttttaattgttcagattcctgaagtgtttgtattcaaccgaa Find is-nt database================================================ Query_seq: PG1933:PG1934|PG1933:PG1934:ribosomal protein L22:30S ribosomal protein S19:<-<-:2022058..2022165 108 ctgcttgagggcttcctttcttgcttcggctgaattatgttttcttgcacccattgttcttaatacttttaattgttcagattcctgaagtgtttgtattcaaccgaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG1933:PG1934|PG1933:PG1934:ribosomal protein L22:30S ribosomal protein S19:<-<-:2022058..2022165 108 ctgcttgagggcttcctttcttgcttcggctgaattatgttttcttgcacccattgttcttaatacttttaattgttcagattcctgaagtgtttgtattcaaccgaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG1933:PG1934|PG1933:PG1934:ribosomal protein L22:30S ribosomal protein S19:<-<-:2022058..2022165 108 ctgcttgagggcttcctttcttgcttcggctgaattatgttttcttgcacccattgttcttaatacttttaattgttcagattcctgaagtgtttgtattcaaccgaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ctgcttgagggcttcctttcttgcttcggctgaattatgttttcttgcacccattgttcttaatacttttaattgttcagattcctgaagtgtttgtattcaaccgaa Predict ORF larger than 30AA ================================================ Protein_Len: 33 Strand: - Start: 1 End: 99 Q K L A E K R A E A S N H K R A G M T R L V K L Q E S E Q L T Q M ......... ctgcttgagggcttcctttcttgcttcggctgaattatgttttcttgcacccattgttcttaatacttttaattgttcagattcctgaagtgtttgtattcaaccgaa 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================================================ ctgcttgagggcttcctttcttgcttcggctgaattatgttttcttgcacccattgttcttaatacttttaattgttcagattcctgaagtgtttgtattcaaccgaa Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PG1933:PG1934|PG1933:PG1934:ribosomal protein L22:30S ribosomal protein S19:<-<-:2022058..2022165 108 ctgcttgagggcttcctttcttgcttcggctgaattatgttttcttgcacccattgttcttaatacttttaattgttcagattcctgaagtgtttgtattcaaccgaa Intra-Species Hit: Count: 1 Min: 1 Max: 108 Len: 108 Subject: NC_002950_PG1933_PG1934|ribosomal protein L22:30S ribosomal protein S19|NEGATIVE:NEGATIVE|[2022058,2022165]|108 HSP 1 e-value: 4.0E-55 bit: 214.0 Len: 108 Query Start:1 Query End:108 Subject Strand: POSITIVE Subject Start: 1 Subject End: 108 ctgcttgagggcttcctttcttgcttcggctgaattatgttttcttgcacccattgttcttaatacttttaattgttcagattcctgaagtgtttgtattcaaccgaa ctgcttgagggcttcctttcttgcttcggctgaattatgttttcttgcacccattgttcttaatacttttaattgttcagattcctgaagtgtttgtattcaaccgaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUGCUUGAGGGCUUCCUUUCUUGCUUCGGCUGAAUUAUGUUUUCUUGCACCCAUUGUUCUUAAUACUUUUAAUUGUUCAGAUUCCUGAAGUGUUUGUAUUCAACCGAA .(((..((((((.....(((..((....)).)))....))))))..)))............(((((....(((..(((((....)))))..))).)))))........ (-21.20) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUCGGUUGAAUACAAACACUUCAGGAAUCUGAACAAUUAAAAGUAUUAAGAACAAUGGGUGCAAGAAAACAUAAUUCAGCCGAAGCAAGAAAGGAAGCCCUCAAGCAG .((((((((((........(((((....))))).........((((..(......)..))))...........)))))))))).((.....(((....)))...)).. (-21.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 937 50 1 141 92 NC_002950:PG1933|5end_ribosomal_protein_L22_2021967..2022197_NEGATIVE 362 48 2 109 54 NC_002950:PG1027|5end_hypothetical_protein_1089439..1089669_NEGATIVE 340 33 1 158 124 NC_002950:PG0888|5end_hypothetical_protein_949910..950140_POSITIVE 307 47 1 86 32 NC_002950:PG1195|5end_8-amino-7-oxononanoate_synthase_1273979..1274209_POSITIVE 305 47 4 170 123 NC_002950:PG0191|5end_outer_membrane_protein,_putative_226858..227088_POSITIVE 302 48 10 139 97 NC_002950:PG0604|5end_4-hydroxy-3-methylbut-2-enyl_diphosphate_reductase_660262..660492_POSITIVE 301 49 7 143 102 NC_002950:PG2076|5end_hypothetical_protein_2176445..2176675_POSITIVE 301 49 7 143 102 NC_002950:PG1267|5end_hypothetical_protein_1346966..1347196_POSITIVE 299 33 1 43 18 NC_002950:PG1861|5end_hypothetical_protein_1960057..1960287_NEGATIVE 299 50 2 213 158 NC_002950:PG1253|5end_DNA_ligase,_NAD-dependent_1331606..1331836_NEGATIVE 295 49 4 90 32 NC_002950:PG0629|5end_inorganic_polyphosphate/ATP-NAD_kinase_683364..683594_NEGATIVE 293 49 7 143 102 NC_002950:PG1672|5end_hypothetical_protein_1757637..1757867_POSITIVE 293 49 7 143 102 NC_002950:PG0100|5end_hypothetical_protein_119219..119449_NEGATIVE 292 57 11 86 39 NC_002950:PG1391|5end_hypothetical_protein_1471670..1471900_POSITIVE 292 32 1 163 134 NC_002950:PG1089|5end_DNA-binding_response_regulator_RprY_1156260..1156490_NEGATIVE 290 48 1 96 34 NC_002950:PG1848|5end_RNA_methyltransferase,_TrmH_family_1947382..1947612_NEGATIVE 287 41 1 70 22 NC_002950:PG0278|5end_hypothetical_protein_310047..310277_POSITIVE 286 49 1 90 45 NC_002950:PG1677|5end_phosphoglycerate_kinase_1762342..1762572_POSITIVE 284 54 11 176 134 NC_002950:PG0339|5end_hypothetical_protein_375062..375292_POSITIVE 283 47 2 59 15 NC_002950:PG0790|5end_GTP-binding_protein_Obg_842583..842813_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 316 49 2 145 101 NC_002950:PG2047|3end_helicase,_putative_2145758..2145908_NEGATIVE 302 48 10 142 100 NC_002950:PG0603|3end_cytidylate_kinase_660345..660495_POSITIVE 299 33 1 30 5 NC_002950:PG1862|3end_hypothetical_protein_1960070..1960220_NEGATIVE 294 48 1 148 101 NC_002950:PG1975|3end_hemagglutinin_protein_HagC_2064350..2064500_POSITIVE 294 48 1 148 101 NC_002950:PG1972|3end_hemagglutinin_protein_HagB_2061203..2061353_POSITIVE 292 31 1 147 116 NC_002950:PG2101|3end_hypothetical_protein_2210278..2210428_NEGATIVE 290 48 1 99 37 NC_002950:PG1849|3end_DNA_repair_protein_RecN_1947379..1947529_NEGATIVE 286 30 1 147 114 NC_002950:PG0393|3end_ribosomal_protein_L7/L12_425017..425167_POSITIVE 283 47 2 49 5 NC_002950:PG0791|3end_adenylate_kinase_842593..842743_NEGATIVE 281 68 21 132 72 NC_002950:PG2037|3end_hypothetical_protein_2137591..2137741_NEGATIVE 274 59 13 139 83 NC_002950:PG1676|3end_phosphoenolpyruvate_carboxykinase_1760489..1760639_NEGATIVE 273 48 7 63 22 NC_002950:PG0573|3end_S-adenosyl-methyltransferase_MraW_629098..629248_POSITIVE 272 59 11 99 37 NC_002950:PG1477|3end_hypothetical_protein_1553209..1553359_NEGATIVE 272 57 11 143 100 NC_002950:PG0997|3end_transcriptional_regulator,_putative_1057012..1057162_POSITIVE 271 57 11 70 17 NC_002950:PG0647|3end_iron_compound_ABC_transporter,_permease_protein_699079..699229_NEGATIVE 270 58 12 149 85 NC_002950:PG1162|3end_ATP:cob(I)alamin_adenosyltransferase,_putative_1241473..1241623_NEGATIVE 269 58 11 81 20 NC_002950:PG0577|3end_phospho-N-acetylmuramoyl-pentapeptide-_transferase_634536..634686_POSITIVE 269 45 4 150 105 NC_002950:PG0190|3end_undecaprenyl_diphosphate_synthase_226920..227070_POSITIVE 268 28 2 83 57 NC_002950:PG1543|3end_thioesterase_family_protein_1622587..1622737_POSITIVE 264 29 1 65 41 NC_002950:PG0332|3end_transcription_termination_factor_Rho_367675..367825_POSITIVE