Origin IGS: tgaatatcactttcttttttgattacatagaattcgctaaaacctatcacaatttacaattaactcataatatacccccaaagaaatcatctaaatattttttctatagaatatagaagaaactcaatttttaacaacttaccaaactaattaaccagttaatcaactggttaatattttactcctcatcatctagtctgtcaagatttttttattagattgtaagaaaaatattatttattctttacttgtccaattatcataatacaaaaaagcctatcctttcggataaacttttttaaaaatatattaagcttc .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gaagcttaatatatttttaaaaaagtttatccgaaaggataggcttttttgtattatgataattggacaagtaaagaataaataatatttttcttacaatctaataaaaaaatcttgacagactagatgatgaggagtaaaatattaaccagttgattaactggttaattagtttggtaagttgttaaaaattgagtttcttctatattctatagaaaaaatatttagatgatttctttgggggtatattatgagttaattgtaaattgtgataggttttagcgaattctatgtaatcaaaaaagaaagtgatattca Mask Tandem Repeat Region ================================================ tgaatatcactttcttttttgattacatagaattcgctaaaacctatcacaatttacaattaactcataatatacccccaaagaaatcatctaaatattttttctatagaatatagaagaaactcaatttttaacaacttaccaaactaattaaccagttaatcaactggttaatattttactcctcatcatctagtctgtcaagatttttttattagattgtaagaaaaatattatttattctttacttgtccaattatcataatacaaaaaagcctatcctttcggataaacttttttaaaaatatattaagcttc Find is-nt database================================================ Query_seq: SSA_1991:SSA_1992|SSA_1991:SSA_1992:Pneumococcal histidine triad protein A, putative:Fructose-bisphosphate aldolase, putative:<-<-:1988863..1989180 318 tgaatatcactttcttttttgattacatagaattcgctaaaacctatcacaatttacaattaactcataatatacccccaaagaaatcatctaaatattttttctatagaatatagaagaaactcaatttttaacaacttaccaaactaattaaccagttaatcaactggttaatattttactcctcatcatctagtctgtcaagatttttttattagattgtaagaaaaatattatttattctttacttgtccaattatcataatacaaaaaagcctatcctttcggataaacttttttaaaaatatattaagcttc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1991:SSA_1992|SSA_1991:SSA_1992:Pneumococcal histidine triad protein A, putative:Fructose-bisphosphate aldolase, putative:<-<-:1988863..1989180 318 tgaatatcactttcttttttgattacatagaattcgctaaaacctatcacaatttacaattaactcataatatacccccaaagaaatcatctaaatattttttctatagaatatagaagaaactcaatttttaacaacttaccaaactaattaaccagttaatcaactggttaatattttactcctcatcatctagtctgtcaagatttttttattagattgtaagaaaaatattatttattctttacttgtccaattatcataatacaaaaaagcctatcctttcggataaacttttttaaaaatatattaagcttc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1991:SSA_1992|SSA_1991:SSA_1992:Pneumococcal histidine triad protein A, putative:Fructose-bisphosphate aldolase, putative:<-<-:1988863..1989180 318 tgaatatcactttcttttttgattacatagaattcgctaaaacctatcacaatttacaattaactcataatatacccccaaagaaatcatctaaatattttttctatagaatatagaagaaactcaatttttaacaacttaccaaactaattaaccagttaatcaactggttaatattttactcctcatcatctagtctgtcaagatttttttattagattgtaagaaaaatattatttattctttacttgtccaattatcataatacaaaaaagcctatcctttcggataaacttttttaaaaatatattaagcttc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgaatatcactttcttttttgattacatagaattcgctaaaacctatcacaatttacaattaactcataatatacccccaaagaaatcatctaaatattttttctatagaatatagaagaaactcaatttttaacaacttaccaaactaattaaccagttaatcaactggttaatattttactcctcatcatctagtctgtcaagatttttttattagattgtaagaaaaatattatttattctttacttgtccaattatcataatacaaaaaagcctatcctttcggataaacttttttaaaaatatattaagcttc Predict ORF larger than 30AA ================================================ Protein_Len: 36 Strand: + Start: 6 End: 113 ..... M T F F F D Y I E F A K T Y H N L Q L T H N I P P K K S S K Y F F Y R I ............................................................................................................................................................................................................. tgaatatcactttcttttttgattacatagaattcgctaaaacctatcacaatttacaattaactcataatatacccccaaagaaatcatctaaatattttttctatagaatatagaagaaactcaatttttaacaacttaccaaactaattaaccagttaatcaactggttaatattttactcctcatcatctagtctgtcaagatttttttattagattgtaagaaaaatattatttattctttacttgtccaattatcataatacaaaaaagcctatcctttcggataaacttttttaaaaatatattaagcttc 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: 89 Start: 176 End: 205 ...............................................................................................................................................................................CTTGACAGACTAGATGATGAGGAGTAAAAT................................................................................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tgaatatcactttcttttttgattacatagaattcgctaaaacctatcacaatttacaattaactcataatatacccccaaagaaatcatctaaatattttttctatagaatatagaagaaactcaatttttaacaacttaccaaactaattaaccagttaatcaactggttaatattttactcctcatcatctagtctgtcaagatttttttattagattgtaagaaaaatattatttattctttacttgtccaattatcataatacaaaaaagcctatcctttcggataaacttttttaaaaatatattaagcttc Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 80 HP_score: -8.6 Tail_Score: -4.32034 Start: 149 End: 176 Full_Region: ACAACTTACCAAACT AATTAACCAGTT AATC AACTGGTTAATA TTTTACTCCTCATCA ....................................................................................................................................................AATTAACCAGTTAATCAACTGGTTAATA.............................................................................................................................................. TransTerm Strand: + Conf: 95 HP_score: -11.2 Tail_Score: -3.76141 Start: 151 End: 174 Full_Region: AACTTACCAAACTAA TTAACCAGTT AATC AACTGGTTAA TATTTTACTCCTCAT ......................................................................................................................................................TTAACCAGTTAATCAACTGGTTAA................................................................................................................................................ TransTerm Strand: - Conf: 95 HP_score: -11.2 Tail_Score: -3.5782 Start: 151 End: 174 Full_Region: atgaggagtaaaata ttaaccagtt gatt aactggttaa ttagtttggtaagtt ......................................................................................................................................................ttaaccagttgattaactggttaa................................................................................................................................................ Find igs database================================================ Query_seq: SSA_1991:SSA_1992|SSA_1991:SSA_1992:Pneumococcal histidine triad protein A, putative:Fructose-bisphosphate aldolase, putative:<-<-:1988863..1989180 318 tgaatatcactttcttttttgattacatagaattcgctaaaacctatcacaatttacaattaactcataatatacccccaaagaaatcatctaaatattttttctatagaatatagaagaaactcaatttttaacaacttaccaaactaattaaccagttaatcaactggttaatattttactcctcatcatctagtctgtcaagatttttttattagattgtaagaaaaatattatttattctttacttgtccaattatcataatacaaaaaagcctatcctttcggataaacttttttaaaaatatattaagcttc Intra-Species Hit: Count: 1 Min: 1 Max: 318 Len: 318 Subject: NC_009009_SSA_1991_SSA_1992|Pneumococcal histidine triad protein A, putative:Fructose-bisphosphate aldolase, putative|NEGATIVE:NEGATIVE|[1988863,1989180]|318 HSP 1 e-value: 1.0E-167 bit: 589.0 Len: 318 Query Start:1 Query End:318 Subject Strand: POSITIVE Subject Start: 1 Subject End: 318 tgaatatcactttcttttttgattacatagaattcgctaaaacctatcacaatttacaattaactcataatatacccccaaagaaatcatctaaatattttttctatagaatatagaagaaactcaatttttaacaacttaccaaactaattaaccagttaatcaactggttaatattttactcctcatcatctagtctgtcaagannnnnnnattagattgtaagaaaaatattatttattctttacttgtccaattatcataatacaaaaaagcctatcctttcggataaacttttttaaaaatatattaagcttc tgaatatcactttcttttttgattacatagaattcgctaaaacctatcacaatttacaattaactcataatatacccccaaagaaatcatctaaatattttttctatagaatatagaagaaactcaatttttaacaacttaccaaactaattaaccagttaatcaactggttaatattttactcctcatcatctagtctgtcaagatttttttattagattgtaagaaaaatattatttattctttacttgtccaattatcataatacaaaaaagcctatcctttcggataaacttttttaaaaatatattaagcttc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGAAUAUCACUUUCUUUUUUGAUUACAUAGAAUUCGCUAAAACCUAUCACAAUUUACAAUUAACUCAUAAUAUACCCCCAAAGAAAUCAUCUAAAUAUUUUUUCUAUAGAAUAUAGAAGAAACUCAAUUUUUAACAACUUACCAAACUAAUUAACCAGUUAAUCAACUGGUUAAUAUUUUACUCCUCAUCAUCUAGUCUGUCAAGAUUUUUUUAUUAGAUUGUAAGAAAAAUAUUAUUUAUUCUUUACUUGUCCAAUUAUCAUAAUACAAAAAAGCCUAUCCUUUCGGAUAAACUUUUUUAAAAAUAUAUUAAGCUUC .(((((..........(((((((....((((....(.(((((.......................................(((.....))).....(((((((((((...)))))))))))......))))).)..............(((((((((((....)))))))))))................))))....)))))))(((((((((......)))))))))........))))).........................(((((((..(((((....)))))..))))))).................. (-43.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAAGCUUAAUAUAUUUUUAAAAAAGUUUAUCCGAAAGGAUAGGCUUUUUUGUAUUAUGAUAAUUGGACAAGUAAAGAAUAAAUAAUAUUUUUCUUACAAUCUAAUAAAAAAAUCUUGACAGACUAGAUGAUGAGGAGUAAAAUAUUAACCAGUUGAUUAACUGGUUAAUUAGUUUGGUAAGUUGUUAAAAAUUGAGUUUCUUCUAUAUUCUAUAGAAAAAAUAUUUAGAUGAUUUCUUUGGGGGUAUAUUAUGAGUUAAUUGUAAAUUGUGAUAGGUUUUAGCGAAUUCUAUGUAAUCAAAAAAGAAAGUGAUAUUCA ((((((((((.......(((((((((((((((....))))))))))))))).....((((((((...((((..................(((((((..(((((....................)))))..)))))))......(((((((((((....)))))))))))...))))...))))))))...)))))))))).((((((...))))))...((((((.......(((((((..(..(((((...(((((..(((.(((((......))))))))..))))).)))))..)...)))))))..)))))).. (-69.85) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 767 80 31 171 122 NC_009009:SSA_1991|5end_Pneumococcal_histidine_triad_protein_A,_putative_1988772..1989002_NEGATIVE 274 203 163 212 181 NC_009009:SSA_0931|5end_hypothetical_protein_940281..940511_POSITIVE 254 301 262 106 71 NC_009009:SSA_2054|5end_hypothetical_protein_2057899..2058129_NEGATIVE 253 207 162 78 26 NC_009009:SSA_1868|5end_ABC-type_arginine/histidine_transport_system,_permease_component,_putative_1863902..1864132_NEGATIVE 233 50 1 121 51 NC_009009:SSA_0401|5end_Two-component_response_transcriptional_regulator_(CheY-like_receiver_and_winged-helix_DNA-binding_domains),_putative_398462..398692_POSITIVE 232 230 183 111 51 NC_009009:SSA_0063|5end_Holliday_junction_DNA_helicase_ruvB,_putative_65335..65565_POSITIVE 230 203 166 119 71 NC_009009:SSA_0495|5end_ABC-type_oligopeptide/nickel_transport_system,_ATPase_component,_putative_495186..495416_POSITIVE 230 187 141 109 65 NC_009009:SSA_0042|5end_Amino_acid_recemase,_putative_47893..48123_POSITIVE 227 203 176 164 131 NC_009009:SSA_0269|5end_Phosphotransferase_system_(PTS)_cellobiose-specific_component_IIA,_putative_262550..262780_POSITIVE 226 200 157 127 82 NC_009009:SSA_1423|5end_Single-stranded_DNA-specific_exonuclease,_5'-3',_putative_1433783..1434013_NEGATIVE 222 220 176 118 76 NC_009009:SSA_2278|5end_Ukp_protein,_putative_2281669..2281899_NEGATIVE 222 207 175 144 111 NC_009009:SSA_0784|5end_Proton-translocating_ATPase,_F0_sector,_subunit_b,_putative_767550..767780_POSITIVE 219 48 1 124 75 NC_009009:SSA_0909|5end_Transcriptional_regulator,_AbrB_family_(stationary/sporulation_gene_expression),_putative_920887..921117_POSITIVE 215 202 166 172 136 NC_009009:SSA_1415|5end_Oxidoreductase,_putative_1426508..1426738_NEGATIVE 214 187 142 103 52 NC_009009:SSA_2216|5end_LPS_biosynthesis_protein,_putative_2218080..2218310_NEGATIVE 214 210 168 165 131 NC_009009:SSA_0245|5end_hypothetical_protein_239136..239366_POSITIVE 212 190 143 183 136 NC_009009:SSA_2356|5end_Replicative_DNA_helicase,_putative_2357958..2358188_NEGATIVE 212 202 168 225 192 NC_009009:SSA_2215|5end_Oligosaccharide_repeat_unit_polymerase_Wzy,_putative_2217157..2217387_NEGATIVE 212 194 151 80 33 NC_009009:SSA_1737|5end_Cystathionine_gamma-synthase,_putative_1723778..1724008_NEGATIVE 209 215 182 91 56 NC_009009:SSA_1617|5end_hypothetical_protein_1620651..1620881_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 284 206 163 140 96 NC_009009:SSA_1636|3end_ABC-type_antibiotic_exporter,_ATPase_component,_putative_1639364..1639514_NEGATIVE 274 203 163 114 83 NC_009009:SSA_0929|3end_ABC-type_multidrug_transporter,_ATPase_and_permease_components,_putative_940263..940413_POSITIVE 254 301 262 69 34 NC_009009:SSA_2055|3end_hypothetical_protein_2057936..2058086_NEGATIVE 250 198 153 111 63 NC_009009:SSA_1010|3end_UDP-glucose_4-epimerase,_putative_1013862..1014012_POSITIVE 247 214 177 124 89 NC_009009:SSA_2239|3end_Conserved_uncharacterized_cytosolic_protein_2236922..2237072_NEGATIVE 247 189 141 89 42 NC_009009:SSA_1672|3end_hypothetical_protein_1670291..1670441_NEGATIVE 245 289 241 70 16 NC_009009:SSA_0224|3end_hypothetical_protein_218518..218668_POSITIVE 234 200 160 114 79 NC_009009:SSA_1402|3end_ABC-type_multidrug_transport_system,_ATPase_and_permease_components,_putative_1414481..1414631_NEGATIVE 230 203 166 122 74 NC_009009:SSA_0494|3end_ABC-type_dipeptide/oligopeptide/nickel_transport_system,_ATPase_component,_putative_495269..495419_POSITIVE 230 187 141 105 61 NC_009009:SSA_0041|3end_hypothetical_protein_47969..48119_POSITIVE 222 220 176 116 74 NC_009009:SSA_2279|3end_hypothetical_protein_2281671..2281821_NEGATIVE 222 207 175 125 92 NC_009009:SSA_0783|3end_Proton-translocating_ATPase,_F0_sector,_subunit_a,_putative_767611..767761_POSITIVE 214 187 142 97 46 NC_009009:SSA_2217|3end_Cps9H,_putative_2218086..2218236_NEGATIVE 214 210 168 119 85 NC_009009:SSA_0244|3end_hypothetical_protein_239170..239320_POSITIVE 210 79 32 115 63 NC_009009:SSA_1457|3end_Neopullulanase,_putative_1462485..1462635_NEGATIVE 209 163 123 124 75 NC_009009:SSA_1284|3end_hypothetical_protein_1304446..1304596_NEGATIVE 208 263 226 116 83 NC_009009:SSA_1454|3end_hypothetical_protein_1460255..1460405_NEGATIVE 208 198 151 104 61 NC_009009:SSA_1087|3end_ABC-type_transporter_(antibiotic_resistance_protein),_ATPase_component,_putative_1106472..1106622_POSITIVE 208 212 185 51 26 NC_009009:SSA_0485|3end_Porphobilinogen_deaminase,_putative_486732..486882_POSITIVE 206 229 195 110 75 NC_009009:SSA_2143|3end_Conserved_uncharacterized_protein_2143590..2143740_NEGATIVE