Origin IGS: aaacacctttttacggcattgacttttttttaaaatttatgttatactgtactttctgatattccgtagtgctggcggataaattaaggagataaggctt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aagccttatctccttaatttatccgccagcactacggaatatcagaaagtacagtataacataaattttaaaaaaaagtcaatgccgtaaaaaggtgttt Mask Tandem Repeat Region ================================================ aaacacctttttacggcattgacttttttttaaaatttatgttatactgtactttctgatattccgtagtgctggcggataaattaaggagataaggctt Find is-nt database================================================ Query_seq: TDE1046:TDE1047|TDE1046:TDE1047:hypothetical protein:30S ribosomal protein S12:->->:1074137..1074236 100 aaacacctttttacggcattgacttttttttaaaatttatgttatactgtactttctgatattccgtagtgctggcggataaattaaggagataaggctt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE1046:TDE1047|TDE1046:TDE1047:hypothetical protein:30S ribosomal protein S12:->->:1074137..1074236 100 aaacacctttttacggcattgacttttttttaaaatttatgttatactgtactttctgatattccgtagtgctggcggataaattaaggagataaggctt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE1046:TDE1047|TDE1046:TDE1047:hypothetical protein:30S ribosomal protein S12:->->:1074137..1074236 100 aaacacctttttacggcattgacttttttttaaaatttatgttatactgtactttctgatattccgtagtgctggcggataaattaaggagataaggctt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aaacacctttttacggcattgacttttttttaaaatttatgttatactgtactttctgatattccgtagtgctggcggataaattaaggagataaggctt Predict ORF larger than 30AA ================================================ aaacacctttttacggcattgacttttttttaaaatttatgttatactgtactttctgatattccgtagtgctggcggataaattaaggagataaggctt 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================================================ aaacacctttttacggcattgacttttttttaaaatttatgttatactgtactttctgatattccgtagtgctggcggataaattaaggagataaggctt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE1046:TDE1047|TDE1046:TDE1047:hypothetical protein:30S ribosomal protein S12:->->:1074137..1074236 100 aaacacctttttacggcattgacttttttttaaaatttatgttatactgtactttctgatattccgtagtgctggcggataaattaaggagataaggctt Intra-Species Hit: Count: 1 Min: 1 Max: 100 Len: 100 Subject: NC_002967_TDE1046_TDE1047|hypothetical protein:30S ribosomal protein S12|POSITIVE:POSITIVE|[1074137,1074236]|100 HSP 1 e-value: 5.0E-36 bit: 151.0 Len: 100 Query Start:1 Query End:100 Subject Strand: POSITIVE Subject Start: 1 Subject End: 100 aaacacctttttacggcattgacnnnnnnnnaaaatttatgttatactgtactttctgatattccgtagtgctggcggataaattaaggagataaggctt aaacacctttttacggcattgacttttttttaaaatttatgttatactgtactttctgatattccgtagtgctggcggataaattaaggagataaggctt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAACACCUUUUUACGGCAUUGACUUUUUUUUAAAAUUUAUGUUAUACUGUACUUUCUGAUAUUCCGUAGUGCUGGCGGAUAAAUUAAGGAGAUAAGGCUU .....((((..(((((...((((.................))))..)))))(((..((((..(((((.......)))))...))))..)))..))))... (-16.63) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAGCCUUAUCUCCUUAAUUUAUCCGCCAGCACUACGGAAUAUCAGAAAGUACAGUAUAACAUAAAUUUUAAAAAAAAGUCAAUGCCGUAAAAAGGUGUUU ..(((((..............((((.........))))...........(((.((((........................)))).)))..))))).... ( -9.86) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 304 86 47 114 73 NC_002967:TDE2586|5end_DNA_polymerase_III_subunits_gamma_and_tau_2622089..2622319_NEGATIVE 302 98 51 64 17 NC_002967:TDE0882|5end_hypothetical_protein_901449..901679_POSITIVE 277 79 47 71 42 NC_002967:TDE0142|5end_hypothetical_protein_164074..164304_NEGATIVE 270 79 42 205 169 NC_002967:TDE0294|5end_TrkA_domain_protein_324210..324440_NEGATIVE 264 97 52 68 18 NC_002967:TDE2234|5end_iron_compound_ABC_transporter,_periplasmic_iron_compound-binding_protein,_putative_2273245..2273475_NEGATIVE 264 79 38 190 150 NC_002967:TDE1004|5end_flagellar_filament_core_protein_1030136..1030366_NEGATIVE 251 95 70 54 29 NC_002967:TDE2356|5end_iron_compound_ABC_transporter,_periplasmic_iron_compound-binding_protein,_putative_2391089..2391319_POSITIVE 251 100 56 182 136 NC_002967:TDE0960|5end_neuB_family_protein_982376..982606_POSITIVE 250 98 62 157 119 NC_002967:TDE1100|5end_acetyltransferase,_GNAT_family_1134672..1134902_NEGATIVE 249 99 56 71 25 NC_002967:TDE2735|5end_surface_antigen,_putative_2790154..2790384_POSITIVE 249 84 58 59 34 NC_002967:TDE2491|5end_DNA_polymerase_domain_protein_2515499..2515729_NEGATIVE 244 100 52 65 21 NC_002967:TDE1067|5end_oligopeptide/dipeptide_ABC_transporter,_ATP-binding_protein_1095701..1095931_NEGATIVE 242 98 57 157 118 NC_002967:TDE2599|5end_thymidylate_kinase_2633963..2634193_NEGATIVE 240 90 41 184 138 NC_002967:TDE1335|5end_alginate_O-acetylation_protein,_putative_1370816..1371046_POSITIVE 239 79 39 205 162 NC_002967:TDE0855|5end_DNA-binding_response_regulator_876536..876766_POSITIVE 237 89 48 146 109 NC_002967:TDE0776|5end_ribosomal_protein_S17_810818..811048_POSITIVE 234 91 52 73 31 NC_002967:TDE0875|5end_ribosomal_large_subunit_pseudouridine_synthase_B_897489..897719_POSITIVE 233 79 48 217 188 NC_002967:TDE2603|5end_DNA_mismatch_repair_protein_2641476..2641706_POSITIVE 233 99 55 196 154 NC_002967:TDE1676|5end_ribosomal_protein_S18_1729642..1729872_NEGATIVE 229 78 40 110 68 NC_002967:TDE2314|5end_hypothetical_protein_2352054..2352284_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 264 78 35 117 79 NC_002967:TDE1718|3end_GMP_synthase_1773811..1773961_POSITIVE 251 95 70 30 5 NC_002967:TDE2355|3end_carbon_storage_regulator_2391145..2391295_POSITIVE 251 100 56 91 45 NC_002967:TDE0959|3end_hypothetical_protein_982365..982515_POSITIVE 249 80 35 148 103 NC_002967:TDE2635|3end_acetyltransferase,_GNAT_family_2676033..2676183_POSITIVE 249 84 58 49 24 NC_002967:TDE2492|3end_hypothetical_protein_2515509..2515659_NEGATIVE 244 100 52 72 28 NC_002967:TDE1068|3end_oligopeptide/dipeptide_ABC_transporter,_ATP-binding_protein_1095694..1095844_NEGATIVE 239 79 39 150 107 NC_002967:TDE0854|3end_regulatory_protein_RecX_876561..876711_POSITIVE 237 89 48 134 97 NC_002967:TDE0775|3end_ribosomal_protein_L29_810886..811036_POSITIVE 235 79 35 145 93 NC_002967:TDE1101|3end_acetyltransferase,_GNAT_family_1134663..1134813_NEGATIVE 234 100 52 63 12 NC_002967:TDE1844|3end_DNA_integrase_1873197..1873347_NEGATIVE 234 100 52 149 107 NC_002967:TDE0824|3end_lipoprotein,_putative_845226..845376_NEGATIVE 234 95 51 68 24 NC_002967:TDE0445|3end_amino_acid_permease_501104..501254_POSITIVE 228 91 57 38 3 NC_002967:TDE0874|3end_transcriptional_regulator,_putative_897534..897684_POSITIVE 227 99 70 86 54 NC_002967:TDE1358|3end_hypothetical_protein_1397910..1398060_POSITIVE 225 97 58 151 107 NC_002967:TDE2212|3end_galactokinase_2251482..2251632_NEGATIVE 222 99 64 77 36 NC_002967:TDE2281|3end_LysM_domain_protein_2317420..2317570_NEGATIVE 221 100 52 92 49 NC_002967:TDE2242|3end_antigen,_putative_2279569..2279719_NEGATIVE 220 93 62 83 40 NC_002967:TDE1892|3end_hypothetical_protein_1912237..1912387_POSITIVE 218 77 33 142 99 NC_002967:TDE1958|3end_surface_protein,_putative_1972309..1972459_NEGATIVE 217 78 31 137 92 NC_002967:TDE0452|3end_hypothetical_protein_509949..510099_NEGATIVE