Origin IGS: taaaaaagtaatgagggataaaaaattctctcattttttaattaattttaacttgcattattaatgcaaatatgctaaaattattttttgatatcagaaaattttaggaaggtgaaaaa .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tttttcaccttcctaaaattttctgatatcaaaaaataattttagcatatttgcattaataatgcaagttaaaattaattaaaaaatgagagaattttttatccctcattactttttta Mask Tandem Repeat Region ================================================ taaaaaagtaatgagggataaaaaattctctcattttttaattaattttaacttgcattattaatgcaaatatgctaaaattattttttgatatcagaaaattttaggaaggtgaaaaa Find is-nt database================================================ Query_seq: FN0481:FN0482|FN0481:FN0482:hypothetical protein:LSU ribosomal protein L31P:->->:1128316..1128434 119 taaaaaagtaatgagggataaaaaattctctcattttttaattaattttaacttgcattattaatgcaaatatgctaaaattattttttgatatcagaaaattttaggaaggtgaaaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN0481:FN0482|FN0481:FN0482:hypothetical protein:LSU ribosomal protein L31P:->->:1128316..1128434 119 taaaaaagtaatgagggataaaaaattctctcattttttaattaattttaacttgcattattaatgcaaatatgctaaaattattttttgatatcagaaaattttaggaaggtgaaaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN0481:FN0482|FN0481:FN0482:hypothetical protein:LSU ribosomal protein L31P:->->:1128316..1128434 119 taaaaaagtaatgagggataaaaaattctctcattttttaattaattttaacttgcattattaatgcaaatatgctaaaattattttttgatatcagaaaattttaggaaggtgaaaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taaaaaagtaatgagggataaaaaattctctcattttttaattaattttaacttgcattattaatgcaaatatgctaaaattattttttgatatcagaaaattttaggaaggtgaaaaa Predict ORF larger than 30AA ================================================ taaaaaagtaatgagggataaaaaattctctcattttttaattaattttaacttgcattattaatgcaaatatgctaaaattattttttgatatcagaaaattttaggaaggtgaaaaa Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ PromScan Matrix: RpoD-17 Strand: + Score: 84 Start: 52 End: 81 ...................................................CTTGCATTATTAATGCAAATATGCTAAAAT...................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ taaaaaagtaatgagggataaaaaattctctcattttttaattaattttaacttgcattattaatgcaaatatgctaaaattattttttgatatcagaaaattttaggaaggtgaaaaa Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: FN0481:FN0482|FN0481:FN0482:hypothetical protein:LSU ribosomal protein L31P:->->:1128316..1128434 119 taaaaaagtaatgagggataaaaaattctctcattttttaattaattttaacttgcattattaatgcaaatatgctaaaattattttttgatatcagaaaattttaggaaggtgaaaaa Intra-Species Hit: Count: 1 Min: 1 Max: 119 Len: 119 Subject: NC_003454_FN0481_FN0482|hypothetical protein:LSU ribosomal protein L31P|POSITIVE:POSITIVE|[1128316,1128434]|119 HSP 1 e-value: 1.0E-9 bit: 63.9 Len: 32 Query Start:1 Query End:32 Subject Strand: POSITIVE Subject Start: 1 Subject End: 32 taaaaaagtaatgagggataaaaaattctctc....................................................................................... taaaaaagtaatgagggataaaaaattctctc....................................................................................... HSP 2 e-value: 2.0E-8 bit: 60.0 Len: 30 Query Start:90 Query End:119 Subject Strand: POSITIVE Subject Start: 90 Subject End: 119 .........................................................................................gatatcagaaaattttaggaaggtgaaaaa .........................................................................................gatatcagaaaattttaggaaggtgaaaaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAAAAAGUAAUGAGGGAUAAAAAAUUCUCUCAUUUUUUAAUUAAUUUUAACUUGCAUUAUUAAUGCAAAUAUGCUAAAAUUAUUUUUUGAUAUCAGAAAAUUUUAGGAAGGUGAAAAA ....((((.(((((((((........)))))))))))))......(((((..((((((.....))))))...(.((((((((...(((((....))))))))))))).)...))))).. (-22.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUUUCACCUUCCUAAAAUUUUCUGAUAUCAAAAAAUAAUUUUAGCAUAUUUGCAUUAAUAAUGCAAGUUAAAAUUAAUUAAAAAAUGAGAGAAUUUUUUAUCCCUCAUUACUUUUUUA ..............((((((((((.((.........((((((((((....((((((.....))))))))))))))))........)).))))))))))..................... (-18.03) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 209 59 25 191 158 NC_003454:FN0662|5end_Formiminoglutamase_1318152..1318382_POSITIVE 204 32 1 146 116 NC_003454:FN1980|5end_Transporter_482063..482293_POSITIVE 188 57 12 71 23 NC_003454:FN0715|5end_hypothetical_protein_1373104..1373334_POSITIVE 188 56 27 172 144 NC_003454:FN0132|5end_Hemolysin_761715..761945_POSITIVE 178 77 34 41 3 NC_003454:FN0785|5end_Electron_transfer_flavoprotein_alpha-subunit_1441146..1441376_POSITIVE 171 107 78 229 201 NC_003454:FN1385|5end_hypothetical_protein_2040130..2040360_NEGATIVE 170 67 28 207 163 NC_003454:FN1035|5end_Iron-sulfur_flavoprotein_1688280..1688510_POSITIVE 168 67 29 224 186 NC_003454:FN0209|5end_Hypothetical_cytosolic_protein_836127..836357_POSITIVE 164 89 45 88 45 NC_003454:FN0698|5end_DNA_integration/recombination/invertion_protein_1356611..1356841_POSITIVE 163 56 14 97 59 NC_003454:FN1950|5end_Serine_protease_457855..458085_NEGATIVE 162 59 11 163 120 NC_003454:FN0261|5end_Pyruvate_formate-lyase_activating_enzyme_887510..887740_NEGATIVE 162 61 32 132 100 NC_003454:FN0089|5end_Ethanolamine_permease_725222..725452_POSITIVE 161 54 22 132 92 NC_003454:FN1401|5end_urocanate_hydratase_2058592..2058822_POSITIVE 161 100 54 175 128 NC_003454:FN1175|5end_hypothetical_protein_1836748..1836978_NEGATIVE 161 42 24 99 81 NC_003454:FN1105|5end_hypothetical_protein_1750041..1750271_POSITIVE 159 67 24 223 186 NC_003454:FN1202|5end_NAD(+)_synthetase_1862298..1862528_NEGATIVE 159 68 24 150 100 NC_003454:FN0754|5end_Glutamyl-tRNA(Gln)_amidotransferase_subunit_A_1414646..1414876_NEGATIVE 159 76 46 38 10 NC_003454:FN0007|5end_glucose-inhibited_division_protein_A_645938..646168_POSITIVE 156 77 31 74 28 NC_003454:FN0683|5end_hypothetical_protein_1338759..1338989_NEGATIVE 156 90 46 125 74 NC_003454:FN1641|5end_SSU_ribosomal_protein_S19P_138827..139057_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 238 67 22 52 4 NC_003454:FN1935|3end_Adenine-specific_methyltransferase_436060..436210_NEGATIVE 213 80 51 143 115 NC_003454:FN1944|3end_Sodium-dependent_tryptophan_transporter_448026..448176_POSITIVE 204 32 1 76 46 NC_003454:FN1979|3end_SSU_ribosomal_protein_S15P_482073..482223_POSITIVE 182 48 2 101 53 NC_003454:FN2001|3end_hypothetical_protein_501298..501448_NEGATIVE 180 70 30 80 40 NC_003454:FN0830|3end_hypothetical_protein_1491902..1492052_POSITIVE 164 89 45 72 29 NC_003454:FN0697|3end_Alanyl-tRNA_synthetase_1356675..1356825_POSITIVE 162 59 11 97 54 NC_003454:FN0262|3end_Formate_acetyltransferase_887576..887726_NEGATIVE 162 61 32 132 100 NC_003454:FN0088|3end_hypothetical_protein_725302..725452_POSITIVE 161 42 24 95 77 NC_003454:FN1104|3end_Holliday_junction_DNA_helicase_ruvA_1750117..1750267_POSITIVE 161 63 25 93 58 NC_003454:FN0401|3end_hypothetical_protein_1039905..1040055_NEGATIVE 159 68 24 133 83 NC_003454:FN0755|3end_Glutamyl-tRNA(Gln)_amidotransferase_subunit_C_1414663..1414813_NEGATIVE 156 90 46 100 49 NC_003454:FN1642|3end_50S_ribosomal_protein_L2_138852..139002_NEGATIVE 155 70 25 41 5 NC_003454:FN1139|3end_Activator_of_(R)-2-hydroxyglutaryl-CoA_dehydratase_1789248..1789398_POSITIVE 155 48 4 85 42 NC_003454:FN1059|3end_Branched_chain_amino_acid_transport_system_II_carrier_protein_1707020..1707170_POSITIVE 154 34 14 147 125 NC_003454:FN1181|3end_hypothetical_protein_1842970..1843120_NEGATIVE 149 95 52 41 1 NC_003454:FN1604|3end_hypothetical_protein_113658..113808_NEGATIVE 148 51 20 87 57 NC_003454:FN1610|3end_33_kDa_chaperonin_119740..119890_NEGATIVE 147 63 24 78 37 NC_003454:FN1212|3end_hypothetical_protein_1872746..1872896_NEGATIVE 147 83 43 48 8 NC_003454:FN0481|3end_hypothetical_protein_1128255..1128405_POSITIVE 147 92 53 151 114 NC_003454:FN0376|3end_Iron(III)-transport_ATP-binding_protein_sfuC_1007560..1007710_POSITIVE