Origin IGS: attttctgcctcctttatttcgttattattattttatcataaatgaggttttaaagagtagtaaattatggtaaaataatgtgaagtaaaaatggagataatgaattagcaaagatttaaatt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aatttaaatctttgctaattcattatctccatttttacttcacattattttaccataatttactactctttaaaacctcatttatgataaaataataataacgaaataaaggaggcagaaaat Mask Tandem Repeat Region ================================================ attttctgcctcctttatttcgttattattattttatcataaatgaggttttaaagagtagtaaattatggtaaaataatgtgaagtaaaaatggagataatgaattagcaaagatttaaatt Find is-nt database================================================ Query_seq: SSA_1150:SSA_1151|SSA_1150:SSA_1151:Tautomerase, putative:Thymidine kinase, putative:<-->:1180167..1180289 123 attttctgcctcctttatttcgttattattattttatcataaatgaggttttaaagagtagtaaattatggtaaaataatgtgaagtaaaaatggagataatgaattagcaaagatttaaatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1150:SSA_1151|SSA_1150:SSA_1151:Tautomerase, putative:Thymidine kinase, putative:<-->:1180167..1180289 123 attttctgcctcctttatttcgttattattattttatcataaatgaggttttaaagagtagtaaattatggtaaaataatgtgaagtaaaaatggagataatgaattagcaaagatttaaatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1150:SSA_1151|SSA_1150:SSA_1151:Tautomerase, putative:Thymidine kinase, putative:<-->:1180167..1180289 123 attttctgcctcctttatttcgttattattattttatcataaatgaggttttaaagagtagtaaattatggtaaaataatgtgaagtaaaaatggagataatgaattagcaaagatttaaatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 attttctgcctcctttatttcgttattattattttatcataaatgaggttttaaagagtagtaaattatggtaaaataatgtgaagtaaaaatggagataatgaattagcaaagatttaaatt Predict ORF larger than 30AA ================================================ attttctgcctcctttatttcgttattattattttatcataaatgaggttttaaagagtagtaaattatggtaaaataatgtgaagtaaaaatggagataatgaattagcaaagatttaaatt 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================================================ attttctgcctcctttatttcgttattattattttatcataaatgaggttttaaagagtagtaaattatggtaaaataatgtgaagtaaaaatggagataatgaattagcaaagatttaaatt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_1150:SSA_1151|SSA_1150:SSA_1151:Tautomerase, putative:Thymidine kinase, putative:<-->:1180167..1180289 123 attttctgcctcctttatttcgttattattattttatcataaatgaggttttaaagagtagtaaattatggtaaaataatgtgaagtaaaaatggagataatgaattagcaaagatttaaatt Intra-Species Hit: Count: 1 Min: 1 Max: 123 Len: 123 Subject: NC_009009_SSA_1150_SSA_1151|Tautomerase, putative:Thymidine kinase, putative|NEGATIVE:POSITIVE|[1180167,1180289]|123 HSP 1 e-value: 6.0E-64 bit: 244.0 Len: 123 Query Start:1 Query End:123 Subject Strand: POSITIVE Subject Start: 1 Subject End: 123 attttctgcctcctttatttcgttattattattttatcataaatgaggttttaaagagtagtaaattatggtaaaataatgtgaagtaaaaatggagataatgaattagcaaagatttaaatt attttctgcctcctttatttcgttattattattttatcataaatgaggttttaaagagtagtaaattatggtaaaataatgtgaagtaaaaatggagataatgaattagcaaagatttaaatt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUUUUCUGCCUCCUUUAUUUCGUUAUUAUUAUUUUAUCAUAAAUGAGGUUUUAAAGAGUAGUAAAUUAUGGUAAAAUAAUGUGAAGUAAAAAUGGAGAUAAUGAAUUAGCAAAGAUUUAAAUU .........(((((((((((((....((((((((((((((((.......................)))))))))))))))))))))))))...))))....((((((......)))))).... (-22.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUUUAAAUCUUUGCUAAUUCAUUAUCUCCAUUUUUACUUCACAUUAUUUUACCAUAAUUUACUACUCUUUAAAACCUCAUUUAUGAUAAAAUAAUAAUAACGAAAUAAAGGAGGCAGAAAAU .........................(((((.((((((.(((..(((((((((.(((((.......................))))).)))))))))......))).)))))).)).))).... (-13.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 698 50 1 141 92 NC_009009:SSA_1150|5end_Tautomerase,_putative_1180076..1180306_NEGATIVE 258 58 11 133 75 NC_009009:SSA_1526|5end_hypothetical_protein_1533722..1533952_POSITIVE 245 22 2 115 93 NC_009009:SSA_0219|5end_PTS_system,_sugar-specific_enzyme_IIA_component,_putative_215367..215597_POSITIVE 242 117 77 71 38 NC_009009:SSA_1359|5end_Arginine/histidine_ABC_transporter,_permease_component,_putative_1374182..1374412_POSITIVE 236 23 3 204 182 NC_009009:SSA_2047|5end_hypothetical_protein_2049953..2050183_NEGATIVE 233 48 1 142 93 NC_009009:SSA_0076|5end_ABC_sugar_transporter,_permease_protein,_putative_79847..80077_POSITIVE 223 48 6 189 145 NC_009009:SSA_0924|5end_ABC-type_antimicrobial_peptide_transport_system,_permease_component,_putative_933738..933968_POSITIVE 223 50 8 148 108 NC_009009:SSA_0686|5end_Fe2+/Zn2+_uptake_regulation_protein,_putative_669556..669786_POSITIVE 216 40 1 138 90 NC_009009:SSA_0969|5end_hypothetical_protein_977212..977442_POSITIVE 213 109 70 181 132 NC_009009:SSA_0846|5end_DNA-polymerase_III_alpha-chain,_putative_830078..830308_POSITIVE 210 49 2 140 92 NC_009009:SSA_1586|5end_hypothetical_protein_1588182..1588412_NEGATIVE 210 25 2 69 39 NC_009009:SSA_0241|5end_Ribosomal_protein_L11_methyltransferase,_putative_234021..234251_POSITIVE 208 22 3 52 28 NC_009009:SSA_2184|5end_hypothetical_protein_2183754..2183984_NEGATIVE 207 49 2 155 111 NC_009009:SSA_1308|5end_hypothetical_protein_1326818..1327048_NEGATIVE 205 25 1 112 90 NC_009009:SSA_0254|5end_hypothetical_protein_247492..247722_NEGATIVE 205 57 11 141 96 NC_009009:SSA_0191|5end_Adenine-specific_DNA_methylase,_putative_191907..192137_POSITIVE 203 48 7 138 97 NC_009009:SSA_0798|5end_ABC_transporter_membrane-spanning_permease-macrolide_efflux,_putative_780463..780693_POSITIVE 202 33 4 120 93 NC_009009:SSA_0899|5end_Conserved_permease,_putative_889903..890133_POSITIVE 201 42 1 133 90 NC_009009:SSA_2284|5end_Histidyl-tRNA_synthetase,_putative_2287272..2287502_NEGATIVE 195 33 1 101 64 NC_009009:SSA_1901|5end_Conserved_uncharacterized_protein_1896599..1896829_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 233 48 1 142 93 NC_009009:SSA_0075|3end_ABC_sugar_transporter,_permease_protein,_putative_79927..80077_POSITIVE 223 48 6 69 25 NC_009009:SSA_0923|3end_Transcriptional_regulator,_TetR/AcrR_family,_putative_933698..933848_POSITIVE 210 49 2 84 36 NC_009009:SSA_1587|3end_hypothetical_protein_1588238..1588388_NEGATIVE 205 50 2 92 38 NC_009009:SSA_0568|3end_Aspartyl-tRNA_synthetase_1,_putative_563490..563640_POSITIVE 205 25 1 119 97 NC_009009:SSA_0255|3end_Multiple_antibiotic_resistance_operon_transcription_repressor_(MarR),_putative_247485..247635_NEGATIVE 205 57 11 59 14 NC_009009:SSA_0190|3end_hypothetical_protein_191905..192055_POSITIVE 203 48 7 59 18 NC_009009:SSA_0797|3end_Transcriptional_regulator,_putative_780464..780614_POSITIVE 201 58 11 75 21 NC_009009:SSA_1200|3end_Formate--tetrahydrofolate_ligase,_putative_1223921..1224071_NEGATIVE 197 42 5 66 32 NC_009009:SSA_0195|3end_hypothetical_protein_195831..195981_POSITIVE 195 100 51 151 116 NC_009009:SSA_2050|3end_Arabinose_efflux_permease,_putative_2054696..2054846_POSITIVE 193 40 15 88 60 NC_009009:SSA_0933|3end_Acetyltransferase,_GNAT_family,_putative_943257..943407_POSITIVE 192 51 13 92 51 NC_009009:SSA_1339|3end_Pneumococcal_histidine_triad_protein_D_precursor,_putative_1351879..1352029_NEGATIVE 190 50 6 120 79 NC_009009:SSA_0093|3end_V-type_sodium_ATPase,_subunit_D,_putative_94989..95139_POSITIVE 187 27 4 124 97 NC_009009:SSA_1836|3end_Superfamily_II_ATP-dependent_DNA/RNA_helicase_required_for_DNA_uptake_(late_competence_protein),_putative_1830938..1831088_NEGATIVE 183 29 9 128 107 NC_009009:SSA_0928|3end_ABC-type_multidrug_transporter,_ATPase_and_permease_components,_putative_938525..938675_POSITIVE 182 41 4 147 105 NC_009009:SSA_0468|3end_Precorrin-6y_C5,15-methyltransferase-like,_putative_472418..472568_POSITIVE 178 40 6 113 74 NC_009009:SSA_0817|3end_Antirepressor_regulating_drug_resistance_(membrane-bound),_putative_799375..799525_POSITIVE 175 41 8 35 2 NC_009009:SSA_1967|3end_Threonine_desaminase,_putative_1962309..1962459_NEGATIVE 175 50 6 148 108 NC_009009:SSA_1378|3end_hypothetical_protein_1397636..1397786_NEGATIVE 172 50 2 124 64 NC_009009:SSA_1991|3end_Pneumococcal_histidine_triad_protein_A,_putative_1986340..1986490_NEGATIVE