Origin IGS: ttaattacattgattagctattataaatgaatacattatttataatagctaattttatttaaaaaaaatttttttaaatataaaaataaaaacggaatattaacgataataaaatataatcatcttataagagtaaaaaacttatcccacatattaagttaaaattagattagttaaaaaaggagagtgaagtttt .........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 aaaacttcactctccttttttaactaatctaattttaacttaatatgtgggataagttttttactcttataagatgattatattttattatcgttaatattccgtttttatttttatatttaaaaaaattttttttaaataaaattagctattataaataatgtattcatttataatagctaatcaatgtaattaa Mask Tandem Repeat Region ================================================ ttaattacattgattagctattataaatgaatacattatttataatagctaattttatttaaaaaaaatttttttaaatataaaaataaaaacggaatattaacgataataaaatataatcatcttataagagtaaaaaacttatcccacatattaagttaaaattagattagttaaaaaaggagagtgaagtttt Find is-nt database================================================ Query_seq: FN1400:FN1401|FN1400:FN1401:serine/threonine kinase:urocanate hydratase:->->:2058536..2058731 196 ttaattacattgattagctattataaatgaatacattatttataatagctaattttatttaaaaaaaatttttttaaatataaaaataaaaacggaatattaacgataataaaatataatcatcttataagagtaaaaaacttatcccacatattaagttaaaattagattagttaaaaaaggagagtgaagtttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN1400:FN1401|FN1400:FN1401:serine/threonine kinase:urocanate hydratase:->->:2058536..2058731 196 ttaattacattgattagctattataaatgaatacattatttataatagctaattttatttaaaaaaaatttttttaaatataaaaataaaaacggaatattaacgataataaaatataatcatcttataagagtaaaaaacttatcccacatattaagttaaaattagattagttaaaaaaggagagtgaagtttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN1400:FN1401|FN1400:FN1401:serine/threonine kinase:urocanate hydratase:->->:2058536..2058731 196 ttaattacattgattagctattataaatgaatacattatttataatagctaattttatttaaaaaaaatttttttaaatataaaaataaaaacggaatattaacgataataaaatataatcatcttataagagtaaaaaacttatcccacatattaagttaaaattagattagttaaaaaaggagagtgaagtttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttaattacattgattagctattataaatgaatacattatttataatagctaattttatttaaaaaaaatttttttaaatataaaaataaaaacggaatattaacgataataaaatataatcatcttataagagtaaaaaacttatcccacatattaagttaaaattagattagttaaaaaaggagagtgaagtttt Predict ORF larger than 30AA ================================================ Protein_Len: 36 Strand: + Start: 52 End: 159 ................................................... M L F K K N F F K Y K N K N G I L T I I K Y N H L I R V K N L S H I L S ..................................... ttaattacattgattagctattataaatgaatacattatttataatagctaattttatttaaaaaaaatttttttaaatataaaaataaaaacggaatattaacgataataaaatataatcatcttataagagtaaaaaacttatcccacatattaagttaaaattagattagttaaaaaaggagagtgaagtttt 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================================================ ttaattacattgattagctattataaatgaatacattatttataatagctaattttatttaaaaaaaatttttttaaatataaaaataaaaacggaatattaacgataataaaatataatcatcttataagagtaaaaaacttatcccacatattaagttaaaattagattagttaaaaaaggagagtgaagtttt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: FN1400:FN1401|FN1400:FN1401:serine/threonine kinase:urocanate hydratase:->->:2058536..2058731 196 ttaattacattgattagctattataaatgaatacattatttataatagctaattttatttaaaaaaaatttttttaaatataaaaataaaaacggaatattaacgataataaaatataatcatcttataagagtaaaaaacttatcccacatattaagttaaaattagattagttaaaaaaggagagtgaagtttt Intra-Species Hit: Count: 1 Min: 1 Max: 196 Len: 196 Subject: NC_003454_FN1400_FN1401|serine/threonine kinase:urocanate hydratase|POSITIVE:POSITIVE|[2058536,2058731]|196 HSP 1 e-value: 9.0E-24 bit: 111.0 Len: 56 Query Start:141 Query End:196 Subject Strand: POSITIVE Subject Start: 141 Subject End: 196 ............................................................................................................................................cttatcccacatattaagttaaaattagattagttaaaaaaggagagtgaagtttt ............................................................................................................................................cttatcccacatattaagttaaaattagattagttaaaaaaggagagtgaagtttt HSP 2 e-value: 2.0E-21 bit: 103.0 Len: 52 Query Start:1 Query End:52 Subject Strand: POSITIVE Subject Start: 1 Subject End: 52 ttaattacattgattagctattataaatgaatacattatttataatagctaa................................................................................................................................................ ttaattacattgattagctattataaatgaatacattatttataatagctaa................................................................................................................................................ Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUAAUUACAUUGAUUAGCUAUUAUAAAUGAAUACAUUAUUUAUAAUAGCUAAUUUUAUUUAAAAAAAAUUUUUUUAAAUAUAAAAAUAAAAACGGAAUAUUAACGAUAAUAAAAUAUAAUCAUCUUAUAAGAGUAAAAAACUUAUCCCACAUAUUAAGUUAAAAUUAGAUUAGUUAAAAAAGGAGAGUGAAGUUUU ....((((...(((((((((((((((((((.....))))))))))))))))))).((((((((((.....))))))))))..........(((..(((.(((((..(((((...(((((.....))))).((((.....))))........))))).))))).)))......)))...........))))...... (-30.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAACUUCACUCUCCUUUUUUAACUAAUCUAAUUUUAACUUAAUAUGUGGGAUAAGUUUUUUACUCUUAUAAGAUGAUUAUAUUUUAUUAUCGUUAAUAUUCCGUUUUUAUUUUUAUAUUUAAAAAAAUUUUUUUUAAAUAAAAUUAGCUAUUAUAAAUAAUGUAUUCAUUUAUAAUAGCUAAUCAAUGUAAUUAA ......................................((((....((((((......)))))).....)))).((((((((((................................((((((((((.....))))))))))..((((((((((((((((.........)))))))))))))))).)))))))))). (-28.70) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 205 134 92 82 42 NC_003454:FN0940|5end_hypothetical_protein_1593508..1593738_NEGATIVE 205 147 103 39 2 NC_003454:FN0312|5end_Anaerobic_ribonucleoside-triphosphate_reductase_activating_protein_949316..949546_POSITIVE 203 49 11 148 113 NC_003454:FN0528|5end_Cold_shock_protein_1184451..1184681_POSITIVE 193 60 11 169 117 NC_003454:FN0389|5end_hypothetical_protein_1027561..1027791_POSITIVE 186 189 151 185 152 NC_003454:FN1233|5end_Putative_NAD(P)H_oxidoreductase_1889389..1889619_POSITIVE 183 50 1 69 21 NC_003454:FN0766|5end_Large-conductance_mechanosensitive_channel_1421910..1422140_POSITIVE 179 180 132 166 121 NC_003454:FN2082|5end_Formate--tetrahydrofolate_ligase_594891..595121_NEGATIVE 179 190 145 175 131 NC_003454:FN1793|5end_Phosphoenolpyruvate-protein_phosphotransferase_275273..275503_NEGATIVE 176 135 95 180 145 NC_003454:FN1536|5end_(S)-2-hydroxy-acid_oxidase_chain_D_49718..49948_NEGATIVE 174 70 26 183 135 NC_003454:FN0318|5end_CITX_protein_955800..956030_NEGATIVE 167 155 119 82 44 NC_003454:FN0209|5end_Hypothetical_cytosolic_protein_836127..836357_POSITIVE 164 176 141 78 42 NC_003454:FN0046|5end_3-dehydroquinate_dehydratase_683742..683972_POSITIVE 161 60 36 60 33 NC_003454:FN0268|5end_DNA_repair_protein_recN_894330..894560_POSITIVE 160 190 155 52 16 NC_003454:FN0570|5end_hypothetical_protein_1220912..1221142_POSITIVE 158 160 121 162 122 NC_003454:FN1798|5end_Spermidine/putrescine_transport_system_permease_protein_potB_279938..280168_POSITIVE 157 160 128 154 117 NC_003454:FN0248|5end_hypothetical_protein_871562..871792_POSITIVE 152 160 120 41 10 NC_003454:FN1351|5end_15_kDa_lipoprotein_precursor_2003372..2003602_NEGATIVE 152 106 78 146 123 NC_003454:FN0302|5end_Iron(III)_dicitrate_transport_ATP-binding_protein_fecE_936734..936964_POSITIVE 152 172 137 131 92 NC_003454:FN0099|5end_Inorganic_pyrophosphatase_734682..734912_POSITIVE 151 148 109 168 131 NC_003454:FN1968|5end_Hemin_transport_system_ATP-binding_protein_hmuV_467189..467419_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 300 53 11 78 34 NC_003454:FN1400|3end_serine/threonine_kinase_2058475..2058625_POSITIVE 205 134 92 63 23 NC_003454:FN0941|3end_Gamma-glutamyltranspeptidase_1593527..1593677_NEGATIVE 202 60 16 90 37 NC_003454:FN1364|3end_LSU_ribosomal_protein_L32P_2015382..2015532_NEGATIVE 181 190 163 60 28 NC_003454:FN1344|3end_hypothetical_protein_1998034..1998184_POSITIVE 179 190 145 120 76 NC_003454:FN1794|3end_Phosphocarrier_protein_HPr_275328..275478_NEGATIVE 169 50 16 66 23 NC_003454:FN1363|3end_Dipeptide_transport_ATP-binding_protein_dppF_2015333..2015483_POSITIVE 168 50 3 139 100 NC_003454:FN0319|3end_Citrate_(pro-3S)-lyase_ligase_955818..955968_NEGATIVE 167 155 119 71 33 NC_003454:FN0208|3end_(R)-2-hydroxyglutaryl-CoA_dehydratase_beta-subunit_836196..836346_POSITIVE 164 176 141 97 61 NC_003454:FN0045|3end_Shikimate_5-dehydrogenase_683841..683991_POSITIVE 161 60 36 81 54 NC_003454:FN0267|3end_ATP-NAD_kinase_894431..894581_POSITIVE 157 160 128 90 53 NC_003454:FN0247|3end_Hypothetical_cytosolic_protein_871578..871728_POSITIVE 156 147 115 34 8 NC_003454:FN0311|3end_anaerobic_ribonucleoside_triphosphate_reductase_949391..949541_POSITIVE 153 60 12 100 46 NC_003454:FN1423|3end_Flavoprotein_2088853..2089003_NEGATIVE 153 60 16 92 51 NC_003454:FN0691|3end_hypothetical_protein_1345827..1345977_NEGATIVE 152 106 78 143 120 NC_003454:FN0301|3end_Iron(III)_dicitrate_transport_system_permease_protein_fecD_936811..936961_POSITIVE 148 60 14 87 38 NC_003454:FN0950|3end_Precorrin-6X_reductase_1606975..1607125_NEGATIVE 147 181 141 51 3 NC_003454:FN0520|3end_hypothetical_protein_1171678..1171828_NEGATIVE 147 189 152 63 25 NC_003454:FN1515|3end_Phophatidylinositol-4-phosphate_5-kinase_20652..20802_POSITIVE 146 189 143 59 9 NC_003454:FN0466|3end_Lysyl-tRNA_synthetase_1112862..1113012_POSITIVE 144 50 5 127 86 NC_003454:FN1780|3end_hypothetical_protein_260921..261071_NEGATIVE