Origin IGS: aattgactgtcaataaatatccatatattaaaaggtaagatgaatagaaattaatatttgtcttatcttttttgttgattttagtagactttttatataaaaatgatataataccttaataattaataaaatttaaaggagagttcttatgagaaaattattattagttatactattc .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gaatagtataactaataataattttctcataagaactctcctttaaattttattaattattaaggtattatatcatttttatataaaaagtctactaaaatcaacaaaaaagataagacaaatattaatttctattcatcttaccttttaatatatggatatttattgacagtcaatt Mask Tandem Repeat Region ================================================ aattgactgtcaataaatatccatatattaaaaggtaagatgaatagaaattaatatttgtcttatcttttttgttgattttagtagactttttatataaaaatgatataataccttaataattaataaaatttaaaggagagttcttatgagaaaattattattagttatactattc Find is-nt database================================================ Query_seq: FN0664:FN0665|FN0664:FN0665:2-nitropropane dioxygenase:N-acetylmuramoyl-L-alanine amidase:->->:1321047..1321224 178 aattgactgtcaataaatatccatatattaaaaggtaagatgaatagaaattaatatttgtcttatcttttttgttgattttagtagactttttatataaaaatgatataataccttaataattaataaaatttaaaggagagttcttatgagaaaattattattagttatactattc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN0664:FN0665|FN0664:FN0665:2-nitropropane dioxygenase:N-acetylmuramoyl-L-alanine amidase:->->:1321047..1321224 178 aattgactgtcaataaatatccatatattaaaaggtaagatgaatagaaattaatatttgtcttatcttttttgttgattttagtagactttttatataaaaatgatataataccttaataattaataaaatttaaaggagagttcttatgagaaaattattattagttatactattc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN0664:FN0665|FN0664:FN0665:2-nitropropane dioxygenase:N-acetylmuramoyl-L-alanine amidase:->->:1321047..1321224 178 aattgactgtcaataaatatccatatattaaaaggtaagatgaatagaaattaatatttgtcttatcttttttgttgattttagtagactttttatataaaaatgatataataccttaataattaataaaatttaaaggagagttcttatgagaaaattattattagttatactattc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aattgactgtcaataaatatccatatattaaaaggtaagatgaatagaaattaatatttgtcttatcttttttgttgattttagtagactttttatataaaaatgatataataccttaataattaataaaatttaaaggagagttcttatgagaaaattattattagttatactattc Predict ORF larger than 30AA ================================================ Protein_Len: 34 Strand: - Start: 31 End: 132 .............................. F T L H I S I L I Q R I K K T S K L L S K I Y F H Y L V K I I L L M .............................................. Protein_Len: 37 Strand: - Start: 2 End: 112 . N V T L L Y G Y I L L Y S S Y F N I N T K D K K N I K T S K K Y L F S I M .................................................................. aattgactgtcaataaatatccatatattaaaaggtaagatgaatagaaattaatatttgtcttatcttttttgttgattttagtagactttttatataaaaatgatataataccttaataattaataaaatttaaaggagagttcttatgagaaaattattattagttatactattc 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================================================ aattgactgtcaataaatatccatatattaaaaggtaagatgaatagaaattaatatttgtcttatcttttttgttgattttagtagactttttatataaaaatgatataataccttaataattaataaaatttaaaggagagttcttatgagaaaattattattagttatactattc Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: FN0664:FN0665|FN0664:FN0665:2-nitropropane dioxygenase:N-acetylmuramoyl-L-alanine amidase:->->:1321047..1321224 178 aattgactgtcaataaatatccatatattaaaaggtaagatgaatagaaattaatatttgtcttatcttttttgttgattttagtagactttttatataaaaatgatataataccttaataattaataaaatttaaaggagagttcttatgagaaaattattattagttatactattc Intra-Species Hit: Count: 1 Min: 1 Max: 178 Len: 178 Subject: NC_003454_FN0664_FN0665|2-nitropropane dioxygenase:N-acetylmuramoyl-L-alanine amidase|POSITIVE:POSITIVE|[1321047,1321224]|178 HSP 1 e-value: 1.0E-96 bit: 353.0 Len: 178 Query Start:1 Query End:178 Subject Strand: POSITIVE Subject Start: 1 Subject End: 178 aattgactgtcaataaatatccatatattaaaaggtaagatgaatagaaattaatatttgtcttatcttttttgttgattttagtagactttttatataaaaatgatataataccttaataattaataaaatttaaaggagagttcttatgagaaaattattattagttatactattc aattgactgtcaataaatatccatatattaaaaggtaagatgaatagaaattaatatttgtcttatcttttttgttgattttagtagactttttatataaaaatgatataataccttaataattaataaaatttaaaggagagttcttatgagaaaattattattagttatactattc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUUGACUGUCAAUAAAUAUCCAUAUAUUAAAAGGUAAGAUGAAUAGAAAUUAAUAUUUGUCUUAUCUUUUUUGUUGAUUUUAGUAGACUUUUUAUAUAAAAAUGAUAUAAUACCUUAAUAAUUAAUAAAAUUUAAAGGAGAGUUCUUAUGAGAAAAUUAUUAUUAGUUAUACUAUUC ...((((((..(((((...(((........((((((((((..((((........))))..))))))))))((((((((((.....((.....((((((.......))))))...))....)))))))))).......)))...((((....))))..)))))..))))))........ (-31.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAAUAGUAUAACUAAUAAUAAUUUUCUCAUAAGAACUCUCCUUUAAAUUUUAUUAAUUAUUAAGGUAUUAUAUCAUUUUUAUAUAAAAAGUCUACUAAAAUCAACAAAAAAGAUAAGACAAAUAUUAAUUUCUAUUCAUCUUACCUUUUAAUAUAUGGAUAUUUAUUGACAGUCAAUU (((((((((...((((((((((........(((.......)))........))).)))))))..))))))).))...............(((...(((((((.....(((((.(((((..((((........))))..))))).)))))........))).))))..)))........ (-17.71) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 228 95 53 130 87 NC_003454:FN1628|5end_LSU_ribosomal_protein_L18P_133948..134178_NEGATIVE 205 154 121 208 175 NC_003454:FN1678|5end_hypothetical_protein_174287..174517_POSITIVE 190 89 44 175 125 NC_003454:FN1972|5end_hypothetical_protein_472071..472301_NEGATIVE 186 93 62 79 42 NC_003454:FN1526|5end_Fusobacterium_outer_membrane_protein_family_38183..38413_NEGATIVE 183 50 5 130 74 NC_003454:FN1999|5end_HIPA_protein_500262..500492_POSITIVE 181 159 111 210 162 NC_003454:FN0122|5end_hypothetical_protein_753401..753631_POSITIVE 180 88 62 46 20 NC_003454:FN1199|5end_DNA_polymerase_IV_1859061..1859291_POSITIVE 178 45 11 146 115 NC_003454:FN0803|5end_trifunctional_thioredoxin/methionine_sulfoxide_reductase_A/B_protein_1463871..1464101_NEGATIVE 178 94 60 69 30 NC_003454:FN0676|5end_10_kDa_chaperonin_GROES_1332380..1332610_NEGATIVE 177 87 50 149 109 NC_003454:FN0709|5end_Virulence_factor_mviN_1367339..1367569_POSITIVE 177 116 72 211 162 NC_003454:FN0338|5end_hypothetical_protein_971673..971903_POSITIVE 176 89 59 65 30 NC_003454:FN0050|5end_Fumarate_reductase_flavoprotein_subunit_687043..687273_POSITIVE 175 148 102 75 24 NC_003454:FN0944|5end_Na+_driven_multidrug_efflux_pump_1598855..1599085_NEGATIVE 173 92 56 225 196 NC_003454:FN1914|5end_Anti-sigma_F_factor_antagonist_411990..412220_NEGATIVE 171 82 46 71 37 NC_003454:FN0464|5end_hypothetical_protein_1109675..1109905_POSITIVE 168 60 32 209 180 NC_003454:FN1955|5end_hypothetical_protein_459936..460166_POSITIVE 167 115 76 97 55 NC_003454:FN1415|5end_NADH-dependent_butanol_dehydrogenase_A_2076765..2076995_NEGATIVE 167 85 54 230 198 NC_003454:FN1893|5end_Fusobacterium_outer_membrane_protein_family_378497..378727_NEGATIVE 165 96 57 163 119 NC_003454:FN0159|5end_hypothetical_protein_787332..787562_POSITIVE 165 50 2 213 175 NC_003454:FN1590|5end_Hypothetical_lipoprotein_101804..102034_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 228 70 30 60 20 NC_003454:FN0664|3end_2-nitropropane_dioxygenase_1320986..1321136_POSITIVE 228 95 53 103 60 NC_003454:FN1629|3end_50S_ribosomal_protein_L6_133975..134125_NEGATIVE 187 78 33 59 17 NC_003454:FN1550|3end_hypothetical_protein_64887..65037_NEGATIVE 178 45 11 64 33 NC_003454:FN0804|3end_Cytochrome_C-type_biogenesis_protein_ccdA_1463953..1464103_NEGATIVE 177 148 111 39 1 NC_003454:FN0023|3end_Short-chain_fatty_acids_transporter_662780..662930_POSITIVE 165 96 57 129 85 NC_003454:FN0158|3end_DNA-binding_protein_787378..787528_POSITIVE 165 50 2 39 1 NC_003454:FN1591|3end_RNFB-related_protein_101978..102128_NEGATIVE 163 94 58 74 29 NC_003454:FN1553|3end_Transporter_67150..67300_NEGATIVE 159 83 50 149 115 NC_003454:FN0708|3end_Hypothetical_cytosolic_protein_1367425..1367575_POSITIVE 158 94 61 140 108 NC_003454:FN1379|3end_Citrate_lyase_beta_chain_2027325..2027475_POSITIVE 158 88 66 38 16 NC_003454:FN0802|3end_Amino_acid_transport_system_permease_protein_1461426..1461576_NEGATIVE 157 83 50 119 90 NC_003454:FN0065|3end_Transcription_accessory_protein_(S1_RNA_binding_domain)_702184..702334_POSITIVE 156 75 31 101 51 NC_003454:FN1017|3end_hypothetical_protein_1672164..1672314_POSITIVE 156 95 57 116 77 NC_003454:FN0035|3end_hypothetical_protein_676240..676390_NEGATIVE 156 95 51 112 71 NC_003454:FN1665|3end_Virulence-associated_protein_I_162894..163044_POSITIVE 155 52 14 88 47 NC_003454:FN1418|3end_AMINOTRANSFERASE_CLASS-I_2079073..2079223_NEGATIVE 155 98 51 85 34 NC_003454:FN0079|3end_Ethanolamine_ammonia-lyase_heavy_chain_719109..719259_POSITIVE 155 81 45 144 108 NC_003454:FN1562|3end_3-deoxy-7-phosphoheptulonate_synthase_83760..83910_NEGATIVE 154 168 130 135 93 NC_003454:FN0847|3end_TPR-repeat-containing_proteins_1507132..1507282_POSITIVE 153 155 115 66 31 NC_003454:FN0812|3end_Hypothetical_cytosolic_protein_1471397..1471547_POSITIVE