Origin IGS: ataatcttcaacaagctcatttaaattaaaaactactgttttaactccttttaaagaaactttatctttatttttcaactttcctaatataaaaaaaataggaataagaagaacaattataataactattgaaataataactgcttgtaacaatgcagataaaacaaacatataaacctccaac .........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 gttggaggtttatatgtttgttttatctgcattgttacaagcagttattatttcaatagttattataattgttcttcttattcctattttttttatattaggaaagttgaaaaataaagataaagtttctttaaaaggagttaaaacagtagtttttaatttaaatgagcttgttgaagattat Mask Tandem Repeat Region ================================================ ataatcttcaacaagctcatttaaattaaaaactactgttttaactccttttaaagaaactttatctttatttttcaactttcctaatataaaaaaaataggaataagaagaacaattataataactattgaaataataactgcttgtaacaatgcagataaaacaaacatataaacctccaac Find is-nt database================================================ Query_seq: FN0873:FN0874|FN0873:FN0874:Protease IV:Phosphohydrolase (MUTT/NUDIX family protein):<-<-:1534278..1534461 184 ataatcttcaacaagctcatttaaattaaaaactactgttttaactccttttaaagaaactttatctttatttttcaactttcctaatataaaaaaaataggaataagaagaacaattataataactattgaaataataactgcttgtaacaatgcagataaaacaaacatataaacctccaac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN0873:FN0874|FN0873:FN0874:Protease IV:Phosphohydrolase (MUTT/NUDIX family protein):<-<-:1534278..1534461 184 ataatcttcaacaagctcatttaaattaaaaactactgttttaactccttttaaagaaactttatctttatttttcaactttcctaatataaaaaaaataggaataagaagaacaattataataactattgaaataataactgcttgtaacaatgcagataaaacaaacatataaacctccaac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN0873:FN0874|FN0873:FN0874:Protease IV:Phosphohydrolase (MUTT/NUDIX family protein):<-<-:1534278..1534461 184 ataatcttcaacaagctcatttaaattaaaaactactgttttaactccttttaaagaaactttatctttatttttcaactttcctaatataaaaaaaataggaataagaagaacaattataataactattgaaataataactgcttgtaacaatgcagataaaacaaacatataaacctccaac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ataatcttcaacaagctcatttaaattaaaaactactgttttaactccttttaaagaaactttatctttatttttcaactttcctaatataaaaaaaataggaataagaagaacaattataataactattgaaataataactgcttgtaacaatgcagataaaacaaacatataaacctccaac Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: - Start: 71 End: 160 ...................................................................... K E V K R I Y F F Y S Y S S C N Y Y S N F Y Y S S T V I C M ........................ Protein_Len: 60 Strand: - Start: 1 End: 183 D E V L E N L N F V V T K V G K L S V K D K N K L K G L I F F I P I L L V I I I V I S I I V A Q L L A S L V F M Y V E M . ataatcttcaacaagctcatttaaattaaaaactactgttttaactccttttaaagaaactttatctttatttttcaactttcctaatataaaaaaaataggaataagaagaacaattataataactattgaaataataactgcttgtaacaatgcagataaaacaaacatataaacctccaac 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================================================ ataatcttcaacaagctcatttaaattaaaaactactgttttaactccttttaaagaaactttatctttatttttcaactttcctaatataaaaaaaataggaataagaagaacaattataataactattgaaataataactgcttgtaacaatgcagataaaacaaacatataaacctccaac Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: FN0873:FN0874|FN0873:FN0874:Protease IV:Phosphohydrolase (MUTT/NUDIX family protein):<-<-:1534278..1534461 184 ataatcttcaacaagctcatttaaattaaaaactactgttttaactccttttaaagaaactttatctttatttttcaactttcctaatataaaaaaaataggaataagaagaacaattataataactattgaaataataactgcttgtaacaatgcagataaaacaaacatataaacctccaac Intra-Species Hit: Count: 1 Min: 1 Max: 184 Len: 184 Subject: NC_003454_FN0873_FN0874|Protease IV:Phosphohydrolase (MUTT/NUDIX family protein)|NEGATIVE:NEGATIVE|[1534278,1534461]|184 HSP 1 e-value: 7.0E-86 bit: 317.0 Len: 184 Query Start:1 Query End:184 Subject Strand: POSITIVE Subject Start: 1 Subject End: 184 ataatcttcaacaagctcatttaaattaaaaactactgttttaactccttttaaagaaactttatctttatttttcaactttcctaatatnnnnnnnntaggaataagaagaacaattataataactattgaaataataactgcttgtaacaatgcagataaaacaaacatataaacctccaac ataatcttcaacaagctcatttaaattaaaaactactgttttaactccttttaaagaaactttatctttatttttcaactttcctaatataaaaaaaataggaataagaagaacaattataataactattgaaataataactgcttgtaacaatgcagataaaacaaacatataaacctccaac Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUAAUCUUCAACAAGCUCAUUUAAAUUAAAAACUACUGUUUUAACUCCUUUUAAAGAAACUUUAUCUUUAUUUUUCAACUUUCCUAAUAUAAAAAAAAUAGGAAUAAGAAGAACAAUUAUAAUAACUAUUGAAAUAAUAACUGCUUGUAACAAUGCAGAUAAAACAAACAUAUAAACCUCCAAC ...((((.((((((((............(((((....)))))......((((((.......((((..((.((((((....((((((............))))))...)))))).))..))))......))))))........)))))).....)).))))........................ (-20.52) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUUGGAGGUUUAUAUGUUUGUUUUAUCUGCAUUGUUACAAGCAGUUAUUAUUUCAAUAGUUAUUAUAAUUGUUCUUCUUAUUCCUAUUUUUUUUAUAUUAGGAAAGUUGAAAAAUAAAGAUAAAGUUUCUUUAAAAGGAGUUAAAACAGUAGUUUUUAAUUUAAAUGAGCUUGUUGAAGAUUAU (((((((.......(((((((..((.......))..))))))).......)))))))................((((((.((((((............))))))..........((((((.......)))))).))))))........((((((((((((............)))))))))))) (-30.04) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 689 50 1 141 92 NC_003454:FN0873|5end_Protease_IV_1534187..1534417_NEGATIVE 268 49 8 209 168 NC_003454:FN1482|5end_Guanosine-3',5'-bis(Diphosphate)_3'-pyrophosphohydrolase_2165992..2166222_NEGATIVE 244 143 110 75 42 NC_003454:FN0341|5end_transport_protein_975381..975611_NEGATIVE 244 86 41 231 184 NC_003454:FN1928|5end_Transcriptional_regulator,_MerR_family_428518..428748_NEGATIVE 212 50 4 201 152 NC_003454:FN1318|5end_RNA_polymerase_sigma_factor_rpoD_1972096..1972326_NEGATIVE 211 50 2 156 104 NC_003454:FN0179|5end_Ankyrin_repeat_proteins_804790..805020_NEGATIVE 205 122 85 196 157 NC_003454:FN0487|5end_D-lactate_dehydrogenase_1132772..1133002_NEGATIVE 202 78 40 36 2 NC_003454:FN0259|5end_Zinc-transporting_ATPase_886258..886488_NEGATIVE 202 97 58 115 75 NC_003454:FN0192|5end_Dipeptide-binding_protein_817342..817572_POSITIVE 202 56 16 81 44 NC_003454:FN1901|5end_Transcription_regulator,_CRP_family_390017..390247_NEGATIVE 194 73 37 99 62 NC_003454:FN0021|5end_4-diphosphocytidyl-2-C-methyl-D-erythritol_kinase_659890..660120_POSITIVE 194 90 48 96 54 NC_003454:FN1858|5end_Short-chain_fatty_acids_transporter_348272..348502_NEGATIVE 191 131 94 167 127 NC_003454:FN0302|5end_Iron(III)_dicitrate_transport_ATP-binding_protein_fecE_936734..936964_POSITIVE 187 114 71 118 68 NC_003454:FN1833|5end_Biopolymer_transport_exbD_protein_322566..322796_NEGATIVE 186 132 94 67 24 NC_003454:FN1829|5end_hypothetical_protein_318556..318786_NEGATIVE 184 67 34 56 20 NC_003454:FN1454|5end_D-alanine--D-alanine_ligase_2135659..2135889_NEGATIVE 183 76 31 143 87 NC_003454:FN1628|5end_LSU_ribosomal_protein_L18P_133948..134178_NEGATIVE 180 47 3 199 160 NC_003454:FN1009|5end_hypothetical_protein_1663950..1664180_NEGATIVE 180 128 95 40 9 NC_003454:FN1798|5end_Spermidine/putrescine_transport_system_permease_protein_potB_279938..280168_POSITIVE 178 37 2 157 119 NC_003454:FN1269|5end_Hypothetical_lipoprotein_1926242..1926472_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 244 143 110 34 1 NC_003454:FN0342|3end_Peptidyl-prolyl_cis-trans_isomerase_975422..975572_NEGATIVE 211 50 2 100 48 NC_003454:FN0180|3end_Tetratricopeptide_repeat_family_protein_804846..804996_NEGATIVE 202 56 16 71 34 NC_003454:FN1902|3end_Deoxycytidylate_deaminase_390027..390177_NEGATIVE 197 156 125 133 97 NC_003454:FN0599|3end_Transposase_1255199..1255349_POSITIVE 197 156 125 133 97 NC_003454:FN0274|3end_Transposase_900285..900435_NEGATIVE 194 73 37 118 81 NC_003454:FN0020|3end_Heat_shock_protein_15_659989..660139_POSITIVE 188 49 2 151 92 NC_003454:FN0461|3end_Probable_sigma(54)_modulation_protein_1107147..1107297_POSITIVE 186 132 94 52 9 NC_003454:FN1830|3end_DNA_polymerase_III_subunits_gamma_and_tau_318571..318721_NEGATIVE 184 67 34 41 5 NC_003454:FN1455|3end_UDP-N-acetylenolpyruvoylglucosamine_reductase_2135674..2135824_NEGATIVE 184 78 42 33 1 NC_003454:FN0260|3end_Transcriptional_repressor_smtB_886261..886411_NEGATIVE 183 76 31 116 60 NC_003454:FN1629|3end_50S_ribosomal_protein_L6_133975..134125_NEGATIVE 180 128 95 53 22 NC_003454:FN1797|3end_Spermidine/putrescine_transport_ATP-binding_protein_potA_280031..280181_POSITIVE 178 37 2 73 35 NC_003454:FN1270|3end_Hypothetical_cytosolic_protein_1926326..1926476_NEGATIVE 178 90 45 125 84 NC_003454:FN0251|3end_Hypothetical_membrane-spanning_Protein_874256..874406_POSITIVE 178 90 45 125 84 NC_003454:FN2061|3end_Hypothetical_membrane-spanning_protein_573666..573816_NEGATIVE 178 90 45 125 84 NC_003454:FN2050|3end_Hypothetical_membrane-spanning_protein_559590..559740_NEGATIVE 177 151 117 147 117 NC_003454:FN1290|3end_hypothetical_protein_1946444..1946594_NEGATIVE 177 85 45 69 17 NC_003454:FN0958|3end_hypothetical_protein_1613617..1613767_NEGATIVE 175 83 45 109 68 NC_003454:FN2036|3end_DNA-directed_RNA_polymerase_beta_chain_542817..542967_NEGATIVE 173 85 47 140 109 NC_003454:FN1452|3end_Cell_division_protein_ftsA_2132733..2132883_NEGATIVE