Origin IGS: cgcaagtccattcatcattaaaatacaaattttcctttgaccgctttaatcgcggtcatttttattttccgtaaatcgtggtataataagacaatctagcagtgaaggaaaaggaa .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ttccttttccttcactgctagattgtcttattataccacgatttacggaaaataaaaatgaccgcgattaaagcggtcaaaggaaaatttgtattttaatgatgaatggacttgcg Mask Tandem Repeat Region ================================================ cgcaagtccattcatcattaaaatacaaattttcctttgaccgctttaatcgcggtcatttttattttccgtaaatcgtggtataataagacaatctagcagtgaaggaaaaggaa Find is-nt database================================================ Query_seq: SSA_1070:SSA_1072|SSA_1070:SSA_1072:Ribosomal large subunit pseudouridine synthase D, putative:Glutamate 5-kinase, putative:->->:1089779..1089894 116 cgcaagtccattcatcattaaaatacaaattttcctttgaccgctttaatcgcggtcatttttattttccgtaaatcgtggtataataagacaatctagcagtgaaggaaaaggaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1070:SSA_1072|SSA_1070:SSA_1072:Ribosomal large subunit pseudouridine synthase D, putative:Glutamate 5-kinase, putative:->->:1089779..1089894 116 cgcaagtccattcatcattaaaatacaaattttcctttgaccgctttaatcgcggtcatttttattttccgtaaatcgtggtataataagacaatctagcagtgaaggaaaaggaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1070:SSA_1072|SSA_1070:SSA_1072:Ribosomal large subunit pseudouridine synthase D, putative:Glutamate 5-kinase, putative:->->:1089779..1089894 116 cgcaagtccattcatcattaaaatacaaattttcctttgaccgctttaatcgcggtcatttttattttccgtaaatcgtggtataataagacaatctagcagtgaaggaaaaggaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 cgcaagtccattcatcattaaaatacaaattttcctttgaccgctttaatcgcggtcatttttattttccgtaaatcgtggtataataagacaatctagcagtgaaggaaaaggaa Predict ORF larger than 30AA ================================================ cgcaagtccattcatcattaaaatacaaattttcctttgaccgctttaatcgcggtcatttttattttccgtaaatcgtggtataataagacaatctagcagtgaaggaaaaggaa 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: 86 Start: 58 End: 87 .........................................................ATTTTTATTTTCCGTAAATCGTGGTATAAT............................. PromScan Matrix: RpoD-17 Strand: - Score: 82 Start: 83 End: 112 ..................................................................................TTTTCCTTCACTGCTAGATTGTCTTATTAT.... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ cgcaagtccattcatcattaaaatacaaattttcctttgaccgctttaatcgcggtcatttttattttccgtaaatcgtggtataataagacaatctagcagtgaaggaaaaggaa Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_1070:SSA_1072|SSA_1070:SSA_1072:Ribosomal large subunit pseudouridine synthase D, putative:Glutamate 5-kinase, putative:->->:1089779..1089894 116 cgcaagtccattcatcattaaaatacaaattttcctttgaccgctttaatcgcggtcatttttattttccgtaaatcgtggtataataagacaatctagcagtgaaggaaaaggaa Intra-Species Hit: Count: 1 Min: 1 Max: 116 Len: 116 Subject: NC_009009_SSA_1070_SSA_1072|Ribosomal large subunit pseudouridine synthase D, putative:Glutamate 5-kinase, putative|POSITIVE:POSITIVE|[1089779,1089894]|116 HSP 1 e-value: 8.0E-60 bit: 230.0 Len: 116 Query Start:1 Query End:116 Subject Strand: POSITIVE Subject Start: 1 Subject End: 116 cgcaagtccattcatcattaaaatacaaattttcctttgaccgctttaatcgcggtcatttttattttccgtaaatcgtggtataataagacaatctagcagtgaaggaaaaggaa cgcaagtccattcatcattaaaatacaaattttcctttgaccgctttaatcgcggtcatttttattttccgtaaatcgtggtataataagacaatctagcagtgaaggaaaaggaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CGCAAGUCCAUUCAUCAUUAAAAUACAAAUUUUCCUUUGACCGCUUUAAUCGCGGUCAUUUUUAUUUUCCGUAAAUCGUGGUAUAAUAAGACAAUCUAGCAGUGAAGGAAAAGGAA (....).......................(((((((((((((((.......))))))..(((((((..(((.......)))...)))))))............))))))))).... (-23.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUCCUUUUCCUUCACUGCUAGAUUGUCUUAUUAUACCACGAUUUACGGAAAAUAAAAAUGACCGCGAUUAAAGCGGUCAAAGGAAAAUUUGUAUUUUAAUGAUGAAUGGACUUGCG .(((.(((((((..(((.((((((((...........)))))))))))..........(((((((.......)))))))))))))).....((((.....))))...)))...... (-25.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 307 64 29 141 101 NC_009009:SSA_0871|5end_Cell_division_protein_FtsX,_putative_863621..863851_POSITIVE 279 79 35 72 22 NC_009009:SSA_1444|5end_Imidazole_glycerol-phosphate_synthase_subunit_hisH,_putative_1447267..1447497_NEGATIVE 268 48 2 106 56 NC_009009:SSA_0420|5end_Hydrolase,_HAD_superfamily,_putative_418620..418850_POSITIVE 263 80 31 211 172 NC_009009:SSA_0509|5end_Propanediol_utilization_protein,_putative_508024..508254_POSITIVE 262 104 67 45 10 NC_009009:SSA_1728|5end_ABC_transporter_membrane-spanning_permease-branched_chain_amino_acid_transport,_putative_1714293..1714523_NEGATIVE 260 79 31 145 102 NC_009009:SSA_1196|5end_Acetyltransferase,_GNAT_family,_putative_1222052..1222282_NEGATIVE 257 72 34 52 7 NC_009009:SSA_1618|5end_hypothetical_protein_1621574..1621804_NEGATIVE 248 69 25 217 170 NC_009009:SSA_1330|5end_hypothetical_protein_1346368..1346598_NEGATIVE 244 80 31 226 176 NC_009009:SSA_0603|5end_Cobalt_transporter,_putative_591596..591826_POSITIVE 243 80 31 172 115 NC_009009:SSA_2089|5end_L-xylulose-5-phosphate_3-epimerase,_putative_2094339..2094569_NEGATIVE 243 80 44 108 76 NC_009009:SSA_1188|5end_Ribonuclease_HII,_putative_1216819..1217049_NEGATIVE 242 66 25 166 120 NC_009009:SSA_0755|5end_hypothetical_protein_736212..736442_POSITIVE 240 66 21 106 57 NC_009009:SSA_2009|5end_Heat_shock_transcription_repressor_HrcA,_putative_2011132..2011362_NEGATIVE 237 84 51 229 198 NC_009009:SSA_1878|5end_Conserved_uncharacterized_protein_1872200..1872430_NEGATIVE 235 60 35 183 161 NC_009009:SSA_1560|5end_Structural_maintenance_of_chromosome_protein_(chromosome_segregation_ATPase),_putative_1565194..1565424_NEGATIVE 235 72 36 75 40 NC_009009:SSA_0852|5end_ATP-dependent_DNA_helicase,_putative_839050..839280_POSITIVE 235 45 1 214 162 NC_009009:SSA_0531|5end_Ethanolamine_utilization_protein_eutQ_(cobalamin-dependent_degradation_of_ethanolamine),_putative_527355..527585_POSITIVE 234 71 31 105 60 NC_009009:SSA_1585|5end_hypothetical_protein_1587604..1587834_NEGATIVE 233 71 31 156 111 NC_009009:SSA_0817|5end_Antirepressor_regulating_drug_resistance_(membrane-bound),_putative_797838..798068_POSITIVE 230 80 35 61 16 NC_009009:SSA_0114|5end_50S_ribosomal_protein_L16,_putative_111979..112209_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 307 64 29 148 108 NC_009009:SSA_0870|3end_Cell_division_protein_FtsE,_putative_863708..863858_POSITIVE 260 79 31 148 105 NC_009009:SSA_1197|3end_DNA_alkylation_repair_enzyme,_putative_1222049..1222199_NEGATIVE 251 96 51 51 5 NC_009009:SSA_1445|3end_Imidazole_glycerol-phosphate_dehydratase,_putative_1447302..1447452_NEGATIVE 248 69 25 112 65 NC_009009:SSA_1331|3end_Conserved_uncharacterized_protein_1346473..1346623_NEGATIVE 243 80 44 121 89 NC_009009:SSA_1189|3end_GTP-binding_protein,_putative_1216806..1216956_NEGATIVE 242 53 30 37 15 NC_009009:SSA_2184|3end_hypothetical_protein_2183284..2183434_NEGATIVE 234 83 42 144 109 NC_009009:SSA_0860|3end_N-acetylmuramidase/lysin,_putative_851738..851888_POSITIVE 233 71 31 140 95 NC_009009:SSA_0816|3end_Copper_transport_operon_or_penicillinase_transcription_repressor,_putative_797902..798052_POSITIVE 230 80 35 57 12 NC_009009:SSA_0113|3end_30S_ribosomal_protein_S3,_putative_112055..112205_POSITIVE 229 84 41 73 21 NC_009009:SSA_2281|3end_hypothetical_protein_2281912..2282062_NEGATIVE 228 84 41 140 103 NC_009009:SSA_2354|3end_hypothetical_protein_2355605..2355755_NEGATIVE 227 79 33 56 12 NC_009009:SSA_1642|3end_N-acetylglucosamine-1-phosphate_uridyltransferase,_putative_1643103..1643253_NEGATIVE 226 58 35 78 48 NC_009009:SSA_1069|3end_Lipoprotein_signal_peptidase,_putative_1088838..1088988_POSITIVE 223 78 35 77 21 NC_009009:SSA_0475|3end_CbiK_protein,_putative_478570..478720_POSITIVE 219 83 42 64 16 NC_009009:SSA_0371|3end_NADP-specific_glutamate_dehydrogenase,_putative_360413..360563_NEGATIVE 216 89 41 80 38 NC_009009:SSA_1673|3end_hypothetical_protein_1670603..1670753_POSITIVE 216 73 34 132 89 NC_009009:SSA_0186|3end_Competence_protein_ComYC,_putative_190458..190608_POSITIVE 214 78 31 60 14 NC_009009:SSA_2012|3end_hypothetical_protein_2012898..2013048_NEGATIVE 213 81 41 112 63 NC_009009:SSA_1951|3end_Penicillin-binding_protein_3,_putative_1948103..1948253_POSITIVE 213 86 42 65 17 NC_009009:SSA_1608|3end_hypothetical_protein_1613283..1613433_NEGATIVE