Origin IGS: gatgacaatcctttcatctatcagtctctgtttattttaacacaatatcaatcaaataagtatagggttgtgaaaatcaaaaacgaatgatggtcttagacttggcttgatcttcatcattcgttttattattttaaatcaaaatgtaagc .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gcttacattttgatttaaaataataaaacgaatgatgaagatcaagccaagtctaagaccatcattcgtttttgattttcacaaccctatacttatttgattgatattgtgttaaaataaacagagactgatagatgaaaggattgtcatc Mask Tandem Repeat Region ================================================ gatgacaatcctttcatctatcagtctctgtttattttaacacaatatcaatcaaataagtatagggttgtgaaaatcaaaaacgaatgatggtcttagacttggcttgatcttcatcattcgttttattattttaaatcaaaatgtaagc Find is-nt database================================================ Query_seq: SSA_1338:SSA_1339|SSA_1338:SSA_1339:hypothetical protein:Pneumococcal histidine triad protein D precursor, putative:<-<-:1351818..1351968 151 gatgacaatcctttcatctatcagtctctgtttattttaacacaatatcaatcaaataagtatagggttgtgaaaatcaaaaacgaatgatggtcttagacttggcttgatcttcatcattcgttttattattttaaatcaaaatgtaagc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1338:SSA_1339|SSA_1338:SSA_1339:hypothetical protein:Pneumococcal histidine triad protein D precursor, putative:<-<-:1351818..1351968 151 gatgacaatcctttcatctatcagtctctgtttattttaacacaatatcaatcaaataagtatagggttgtgaaaatcaaaaacgaatgatggtcttagacttggcttgatcttcatcattcgttttattattttaaatcaaaatgtaagc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1338:SSA_1339|SSA_1338:SSA_1339:hypothetical protein:Pneumococcal histidine triad protein D precursor, putative:<-<-:1351818..1351968 151 gatgacaatcctttcatctatcagtctctgtttattttaacacaatatcaatcaaataagtatagggttgtgaaaatcaaaaacgaatgatggtcttagacttggcttgatcttcatcattcgttttattattttaaatcaaaatgtaagc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gatgacaatcctttcatctatcagtctctgtttattttaacacaatatcaatcaaataagtatagggttgtgaaaatcaaaaacgaatgatggtcttagacttggcttgatcttcatcattcgttttattattttaaatcaaaatgtaagc Predict ORF larger than 30AA ================================================ gatgacaatcctttcatctatcagtctctgtttattttaacacaatatcaatcaaataagtatagggttgtgaaaatcaaaaacgaatgatggtcttagacttggcttgatcttcatcattcgttttattattttaaatcaaaatgtaagc 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================================================ gatgacaatcctttcatctatcagtctctgtttattttaacacaatatcaatcaaataagtatagggttgtgaaaatcaaaaacgaatgatggtcttagacttggcttgatcttcatcattcgttttattattttaaatcaaaatgtaagc Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_1338:SSA_1339|SSA_1338:SSA_1339:hypothetical protein:Pneumococcal histidine triad protein D precursor, putative:<-<-:1351818..1351968 151 gatgacaatcctttcatctatcagtctctgtttattttaacacaatatcaatcaaataagtatagggttgtgaaaatcaaaaacgaatgatggtcttagacttggcttgatcttcatcattcgttttattattttaaatcaaaatgtaagc Intra-Species Hit: Count: 1 Min: 1 Max: 151 Len: 151 Subject: NC_009009_SSA_1338_SSA_1339|hypothetical protein:Pneumococcal histidine triad protein D precursor, putative|NEGATIVE:NEGATIVE|[1351818,1351968]|151 HSP 1 e-value: 1.0E-80 bit: 299.0 Len: 151 Query Start:1 Query End:151 Subject Strand: POSITIVE Subject Start: 1 Subject End: 151 gatgacaatcctttcatctatcagtctctgtttattttaacacaatatcaatcaaataagtatagggttgtgaaaatcaaaaacgaatgatggtcttagacttggcttgatcttcatcattcgttttattattttaaatcaaaatgtaagc gatgacaatcctttcatctatcagtctctgtttattttaacacaatatcaatcaaataagtatagggttgtgaaaatcaaaaacgaatgatggtcttagacttggcttgatcttcatcattcgttttattattttaaatcaaaatgtaagc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAUGACAAUCCUUUCAUCUAUCAGUCUCUGUUUAUUUUAACACAAUAUCAAUCAAAUAAGUAUAGGGUUGUGAAAAUCAAAAACGAAUGAUGGUCUUAGACUUGGCUUGAUCUUCAUCAUUCGUUUUAUUAUUUUAAAUCAAAAUGUAAGC (((((........)))))...........((((((.....((((((......(......)......)))))).......((((((((((((((((..((......)).)))...)))))))))))))..................)))))) (-26.50) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GCUUACAUUUUGAUUUAAAAUAAUAAAACGAAUGAUGAAGAUCAAGCCAAGUCUAAGACCAUCAUUCGUUUUUGAUUUUCACAACCCUAUACUUAUUUGAUUGAUAUUGUGUUAAAAUAAACAGAGACUGAUAGAUGAAAGGAUUGUCAUC ................(((((...(((((((((((((.((((........)))).....)))))))))))))..))))).((((.(((....(((((((.((..(.((.((((......)))).)))..))))))))).))).)))).... (-24.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 827 110 61 201 152 NC_009009:SSA_1338|5end_hypothetical_protein_1351727..1351957_NEGATIVE 276 127 84 94 38 NC_009009:SSA_2237|5end_Dihydrofolate:folylpolyglutamate_synthetase,_putative_2236740..2236970_NEGATIVE 276 127 82 152 111 NC_009009:SSA_0833|5end_Accessory_secretory_protein_Asp1,_putative_817940..818170_POSITIVE 270 126 83 102 68 NC_009009:SSA_0102|5end_Kinase,_putative_104035..104265_POSITIVE 260 126 83 171 128 NC_009009:SSA_1805|5end_Primosomal_protein_DnaI,_putative_1789564..1789794_NEGATIVE 260 127 88 98 59 NC_009009:SSA_0553|5end_hypothetical_protein_548911..549141_POSITIVE 248 85 46 211 171 NC_009009:SSA_0264|5end_PEP_phosphonomutase-like_protein,_putative_258400..258630_POSITIVE 246 47 6 152 111 NC_009009:SSA_2091|5end_Phosphotransferase_system_sugar-specific_EII_component,_putative_2095562..2095792_NEGATIVE 241 140 91 102 60 NC_009009:SSA_1940|5end_3-oxoacyl-[acyl-carrier-protein]_synthase_III,_putative_1927129..1927359_NEGATIVE 241 126 82 93 32 NC_009009:SSA_1223|5end_30S_ribosomal_protein_S1,_putative_1246872..1247102_NEGATIVE 240 114 82 208 173 NC_009009:SSA_1343|5end_Aspartate_carbamoyltransferase,_putative_1361959..1362189_NEGATIVE 240 119 74 134 72 NC_009009:SSA_0672|5end_hypothetical_protein_655191..655421_POSITIVE 240 126 86 97 50 NC_009009:SSA_0601|5end_Phosphorylase,_Pnp/Udp_family,_putative_589147..589377_POSITIVE 239 110 64 167 117 NC_009009:SSA_1247|5end_hypothetical_protein_1272358..1272588_NEGATIVE 239 118 71 73 27 NC_009009:SSA_0071|5end_N-acetylmannosamine-6-p_hosphate_2-epimerase_1,_putative_75210..75440_POSITIVE 233 120 89 72 27 NC_009009:SSA_1344|5end_Xanthine/uracil_permeases,_putative_1363352..1363582_NEGATIVE 231 140 106 109 69 NC_009009:SSA_2299|5end_hypothetical_protein_2301545..2301775_NEGATIVE 229 44 5 139 92 NC_009009:SSA_1990|5end_Zn-porter_lipoprotein,_putative_1986319..1986549_NEGATIVE 229 118 88 156 122 NC_009009:SSA_1132|5end_TatC,_sec-independent_protein_translocase,_putative_1158645..1158875_POSITIVE 229 110 63 206 156 NC_009009:SSA_0304|5end_Bacterial_cell_wall_degradation_(CHAP/LysM_domains),_putative_301143..301373_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 276 127 82 143 102 NC_009009:SSA_0832|3end_SecY-like_protein,_putative_818011..818161_POSITIVE 270 126 83 100 66 NC_009009:SSA_0101|3end_Conserved_uncharacterized_protein_104113..104263_POSITIVE 241 140 91 102 60 NC_009009:SSA_1941|3end_hypothetical_protein_1927129..1927279_NEGATIVE 240 114 82 98 63 NC_009009:SSA_1344|3end_Xanthine/uracil_permeases,_putative_1362069..1362219_NEGATIVE 240 119 74 137 75 NC_009009:SSA_0671|3end_Methylenetetrahydrofolate_dehydrogenase/methenyltetrahydrofolate_cyclohydrolase,_putative_655274..655424_POSITIVE 233 120 89 63 18 NC_009009:SSA_1345|3end_Bifunctional_pyrimidine_operon_transcriptional_attenuation_protein/uracil_phosphoribosyltransferase,_putative_1363361..1363511_NEGATIVE 231 140 106 60 20 NC_009009:SSA_2300|3end_hypothetical_protein_2301594..2301744_NEGATIVE 229 44 5 118 71 NC_009009:SSA_1991|3end_Pneumococcal_histidine_triad_protein_A,_putative_1986340..1986490_NEGATIVE 228 120 76 144 93 NC_009009:SSA_0678|3end_Transcriptional_regulator,_ArgR_family,_putative_660785..660935_POSITIVE 225 130 84 111 55 NC_009009:SSA_1547|3end_HPr_kinase/phosphorylase,_putative_1550045..1550195_NEGATIVE 219 117 79 67 26 NC_009009:SSA_2261|3end_Transcriptional_repressor_(arginine_synthesis),_putative_2258229..2258379_NEGATIVE 219 118 77 46 9 NC_009009:SSA_0481|3end_Cobyric_acid_synthase,_putative_483541..483691_POSITIVE 216 107 68 79 38 NC_009009:SSA_1525|3end_Lyzozyme_M1_(1,4-beta-N-acetylmuramidase),_putative_1533683..1533833_POSITIVE 214 114 72 103 64 NC_009009:SSA_1031|3end_DNA_topology_modulation_protein_FlaR,_putative_1047734..1047884_NEGATIVE 213 126 88 89 41 NC_009009:SSA_0087|3end_V-type_sodium_ATPase,_subunit_E,_putative_88999..89149_POSITIVE 210 107 64 135 87 NC_009009:SSA_1573|3end_hypothetical_protein_1576054..1576204_NEGATIVE 208 128 88 107 64 NC_009009:SSA_2297|3end_hypothetical_protein_2298776..2298926_NEGATIVE 207 43 4 96 44 NC_009009:SSA_1618|3end_hypothetical_protein_1620720..1620870_NEGATIVE 207 106 65 122 86 NC_009009:SSA_1367|3end_hypothetical_protein_1383828..1383978_POSITIVE 207 119 88 32 1 NC_009009:SSA_0502|3end_Peptide_ABC_transporter,_permease_protein,_putative_502323..502473_POSITIVE