Origin IGS: cattttctgtgagccatcaaattcttttatcatataacaacctctctccttttttatacttttgacaagaattaatccaataaacagtattgaaaaatccaacaactcttttcta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tagaaaagagttgttggatttttcaatactgtttattggattaattcttgtcaaaagtataaaaaaggagagaggttgttatatgataaaagaatttgatggctcacagaaaatg Mask Tandem Repeat Region ================================================ cattttctgtgagccatcaaattcttttatcatataacaacctctctccttttttatacttttgacaagaattaatccaataaacagtattgaaaaatccaacaactcttttcta Find is-nt database================================================ Query_seq: FN1278:FN1279|FN1278:FN1279:Acetyltransferase:Zinc metallohydrolase, glyoxalase II family:<-<-:1937265..1937379 115 cattttctgtgagccatcaaattcttttatcatataacaacctctctccttttttatacttttgacaagaattaatccaataaacagtattgaaaaatccaacaactcttttcta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN1278:FN1279|FN1278:FN1279:Acetyltransferase:Zinc metallohydrolase, glyoxalase II family:<-<-:1937265..1937379 115 cattttctgtgagccatcaaattcttttatcatataacaacctctctccttttttatacttttgacaagaattaatccaataaacagtattgaaaaatccaacaactcttttcta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN1278:FN1279|FN1278:FN1279:Acetyltransferase:Zinc metallohydrolase, glyoxalase II family:<-<-:1937265..1937379 115 cattttctgtgagccatcaaattcttttatcatataacaacctctctccttttttatacttttgacaagaattaatccaataaacagtattgaaaaatccaacaactcttttcta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 cattttctgtgagccatcaaattcttttatcatataacaacctctctccttttttatacttttgacaagaattaatccaataaacagtattgaaaaatccaacaactcttttcta Predict ORF larger than 30AA ================================================ Protein_Len: 35 Strand: - Start: 1 End: 105 M K Q S G D F E K I M Y C G R E K K I S K V L I L G I F L I S F D L M .......... cattttctgtgagccatcaaattcttttatcatataacaacctctctccttttttatacttttgacaagaattaatccaataaacagtattgaaaaatccaacaactcttttcta 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================================================ cattttctgtgagccatcaaattcttttatcatataacaacctctctccttttttatacttttgacaagaattaatccaataaacagtattgaaaaatccaacaactcttttcta Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: FN1278:FN1279|FN1278:FN1279:Acetyltransferase:Zinc metallohydrolase, glyoxalase II family:<-<-:1937265..1937379 115 cattttctgtgagccatcaaattcttttatcatataacaacctctctccttttttatacttttgacaagaattaatccaataaacagtattgaaaaatccaacaactcttttcta Intra-Species Hit: Count: 1 Min: 1 Max: 115 Len: 115 Subject: NC_003454_FN1278_FN1279|Acetyltransferase:Zinc metallohydrolase, glyoxalase II family|NEGATIVE:NEGATIVE|[1937265,1937379]|115 HSP 1 e-value: 3.0E-59 bit: 228.0 Len: 115 Query Start:1 Query End:115 Subject Strand: POSITIVE Subject Start: 1 Subject End: 115 cattttctgtgagccatcaaattcttttatcatataacaacctctctccttttttatacttttgacaagaattaatccaataaacagtattgaaaaatccaacaactcttttcta cattttctgtgagccatcaaattcttttatcatataacaacctctctccttttttatacttttgacaagaattaatccaataaacagtattgaaaaatccaacaactcttttcta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CAUUUUCUGUGAGCCAUCAAAUUCUUUUAUCAUAUAACAACCUCUCUCCUUUUUUAUACUUUUGACAAGAAUUAAUCCAAUAAACAGUAUUGAAAAAUCCAACAACUCUUUUCUA ..........(((......(((((((...(((..............................))).)))))))....(((((.....))))).............)))....... ( -6.11) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAGAAAAGAGUUGUUGGAUUUUUCAAUACUGUUUAUUGGAUUAAUUCUUGUCAAAAGUAUAAAAAAGGAGAGAGGUUGUUAUAUGAUAAAAGAAUUUGAUGGCUCACAGAAAAUG .......((((..(..(((((((..(((((.......(((.....))).......)))))...............(((((....))))))))))))..)..)))).......... (-19.34) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 809 50 1 141 92 NC_003454:FN1278|5end_Acetyltransferase_1937174..1937404_NEGATIVE 260 60 17 108 66 NC_003454:FN0449|5end_hypothetical_protein_1092683..1092913_POSITIVE 258 45 2 104 64 NC_003454:FN1954|5end_Glycerophosphoryl_diester_phosphodiesterase_459992..460222_NEGATIVE 251 60 21 102 56 NC_003454:FN0614|5end_Export_ABC_transporter_1271447..1271677_POSITIVE 248 90 42 140 96 NC_003454:FN1897|5end_ABC_transporter_integral_membrane_protein_384984..385214_NEGATIVE 242 50 1 109 57 NC_003454:FN0906|5end_Glycerol-3-phosphate_dehydrogenase_[NAD(P)+]_1565131..1565361_NEGATIVE 230 60 20 116 72 NC_003454:FN1401|5end_urocanate_hydratase_2058592..2058822_POSITIVE 229 70 25 192 142 NC_003454:FN1293|5end_hypothetical_protein_1952147..1952377_NEGATIVE 225 49 14 172 138 NC_003454:FN1750|5end_Pyruvate-flavodoxin_oxidoreductase_247811..248041_POSITIVE 221 50 2 101 38 NC_003454:FN1367|5end_Methyl-accepting_chemotaxis_protein_2018143..2018373_NEGATIVE 217 60 22 102 50 NC_003454:FN0054|5end_tyrosyl-tRNA_synthetase_690836..691066_POSITIVE 217 58 24 115 82 NC_003454:FN1529|5end_hypothetical_protein_43364..43594_NEGATIVE 215 49 1 108 46 NC_003454:FN1475|5end_N-acetylneuraminate_lyase_2157785..2158015_POSITIVE 214 57 19 184 142 NC_003454:FN0043|5end_Hypothetical_exported_24-amino_acid_repeat_protein_682262..682492_POSITIVE 212 50 1 222 170 NC_003454:FN1214|5end_Fe-S_oxidoreductase_1875473..1875703_NEGATIVE 212 38 3 124 93 NC_003454:FN1634|5end_LSU_ribosomal_protein_L24P_136179..136409_NEGATIVE 211 79 45 123 94 NC_003454:FN1150|5end_hypothetical_protein_1805151..1805381_NEGATIVE 207 50 3 212 167 NC_003454:FN1264|5end_hypothetical_protein_1920766..1920996_POSITIVE 206 86 41 150 88 NC_003454:FN1518|5end_RNA_polymerase_sigma-70_factor_24077..24307_NEGATIVE 204 50 4 99 54 NC_003454:FN1421|5end_Pyruvate-flavodoxin_oxidoreductase_2083305..2083535_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 260 60 17 92 50 NC_003454:FN0448|3end_DNA-repair_protein_1092747..1092897_POSITIVE 248 90 42 138 94 NC_003454:FN1898|3end_Sugar_transport_ATP-binding_protein_384986..385136_NEGATIVE 221 50 2 87 24 NC_003454:FN1368|3end_COMF_operon_protein_3_2018157..2018307_NEGATIVE 215 49 1 86 24 NC_003454:FN1474|3end_N-acetylmannosamine_kinase_2157843..2157993_POSITIVE 212 38 3 99 68 NC_003454:FN1635|3end_LSU_ribosomal_protein_L14P_136204..136354_NEGATIVE 211 79 45 111 82 NC_003454:FN1151|3end_Na+_driven_multidrug_efflux_pump_1805163..1805313_NEGATIVE 206 86 41 139 77 NC_003454:FN1519|3end_23S_rRNA_methyltransferase_24088..24238_NEGATIVE 201 79 44 123 83 NC_003454:FN1789|3end_Na+_driven_multidrug_efflux_pump_271579..271729_POSITIVE 199 47 13 41 10 NC_003454:FN1038|3end_Transporter_1691066..1691216_POSITIVE 197 70 25 57 7 NC_003454:FN1637|3end_LSU_ribosomal_protein_L29P_136888..137038_NEGATIVE 196 68 25 123 83 NC_003454:FN1031|3end_Hypothetical_membrane-spanning_protein_1684721..1684871_NEGATIVE 194 77 44 122 90 NC_003454:FN1916|3end_hypothetical_protein_412406..412556_NEGATIVE 191 44 2 138 93 NC_003454:FN0084|3end_Acetaldehyde_dehydrogenase_[acetylating]_723094..723244_POSITIVE 191 50 1 78 28 NC_003454:FN2021|3end_ABC1_family_protein_524549..524699_NEGATIVE 188 67 39 103 68 NC_003454:FN1088|3end_NADH_oxidase_1733095..1733245_POSITIVE 188 31 2 95 69 NC_003454:FN1739|3end_V-type_sodium_ATP_synthase_subunit_E_237351..237501_NEGATIVE 183 54 12 119 72 NC_003454:FN0937|3end_Gamma-polyglutamic_acid_synthetase_1589097..1589247_NEGATIVE 183 48 13 89 51 NC_003454:FN0855|3end_glucose-1-phosphate_adenylyltransferase_1513508..1513658_NEGATIVE 181 32 2 148 114 NC_003454:FN0361|3end_ATP_synthase_delta_chain,_sodium_ion_specific_992381..992531_NEGATIVE 175 90 42 134 94 NC_003454:FN0583|3end_hypothetical_protein_1239518..1239668_POSITIVE