Origin IGS: aaaactcctttgtgagaatggttttggatgggcccacctgtattattcggaaaacttatttgaaaatgatagtaaatttgaaaagccctgaatattttctgtctaaaataggcataatccactcaaaaaggagaaggctgaagacaacaataattacggcgatcatatagaagagatattctttttctcattagaatggaataaaacgaacgattatgatataatttagataaataattcgtaaaaatggcaatgatttttacgtgatgtgttagcttggtgcgtaagcgcctgtgatatttgatattgaggtatcttggct .........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 agccaagatacctcaatatcaaatatcacaggcgcttacgcaccaagctaacacatcacgtaaaaatcattgccatttttacgaattatttatctaaattatatcataatcgttcgttttattccattctaatgagaaaaagaatatctcttctatatgatcgccgtaattattgttgtcttcagccttctcctttttgagtggattatgcctattttagacagaaaatattcagggcttttcaaatttactatcattttcaaataagttttccgaataatacaggtgggcccatccaaaaccattctcacaaaggagtttt Mask Tandem Repeat Region ================================================ aaaactcctttgtgagaatggttttggatgggcccacctgtattattcggaaaacttatttgaaaatgatagtaaatttgaaaagccctgaatattttctgtctaaaataggcataatccactcaaaaaggagaaggctgaagacaacaataattacggcgatcatatagaagagatattctttttctcattagaatggaataaaacgaacgattatgatataatttagataaataattcgtaaaaatggcaatgatttttacgtgatgtgttagcttggtgcgtaagcgcctgtgatatttgatattgaggtatcttggct Find is-nt database================================================ Query_seq: SSA_0036:SSA_0037|SSA_0036:SSA_0037:Secreted protein, possible function in cell-wall metabolism (amidase), putative:Phosphoribosylamine-glycine ligase; phosphoribosyl glycinamide synthetase (GARS), putative:<-->:44090..44411 322 aaaactcctttgtgagaatggttttggatgggcccacctgtattattcggaaaacttatttgaaaatgatagtaaatttgaaaagccctgaatattttctgtctaaaataggcataatccactcaaaaaggagaaggctgaagacaacaataattacggcgatcatatagaagagatattctttttctcattagaatggaataaaacgaacgattatgatataatttagataaataattcgtaaaaatggcaatgatttttacgtgatgtgttagcttggtgcgtaagcgcctgtgatatttgatattgaggtatcttggct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0036:SSA_0037|SSA_0036:SSA_0037:Secreted protein, possible function in cell-wall metabolism (amidase), putative:Phosphoribosylamine-glycine ligase; phosphoribosyl glycinamide synthetase (GARS), putative:<-->:44090..44411 322 aaaactcctttgtgagaatggttttggatgggcccacctgtattattcggaaaacttatttgaaaatgatagtaaatttgaaaagccctgaatattttctgtctaaaataggcataatccactcaaaaaggagaaggctgaagacaacaataattacggcgatcatatagaagagatattctttttctcattagaatggaataaaacgaacgattatgatataatttagataaataattcgtaaaaatggcaatgatttttacgtgatgtgttagcttggtgcgtaagcgcctgtgatatttgatattgaggtatcttggct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0036:SSA_0037|SSA_0036:SSA_0037:Secreted protein, possible function in cell-wall metabolism (amidase), putative:Phosphoribosylamine-glycine ligase; phosphoribosyl glycinamide synthetase (GARS), putative:<-->:44090..44411 322 aaaactcctttgtgagaatggttttggatgggcccacctgtattattcggaaaacttatttgaaaatgatagtaaatttgaaaagccctgaatattttctgtctaaaataggcataatccactcaaaaaggagaaggctgaagacaacaataattacggcgatcatatagaagagatattctttttctcattagaatggaataaaacgaacgattatgatataatttagataaataattcgtaaaaatggcaatgatttttacgtgatgtgttagcttggtgcgtaagcgcctgtgatatttgatattgaggtatcttggct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aaaactcctttgtgagaatggttttggatgggcccacctgtattattcggaaaacttatttgaaaatgatagtaaatttgaaaagccctgaatattttctgtctaaaataggcataatccactcaaaaaggagaaggctgaagacaacaataattacggcgatcatatagaagagatattctttttctcattagaatggaataaaacgaacgattatgatataatttagataaataattcgtaaaaatggcaatgatttttacgtgatgtgttagcttggtgcgtaagcgcctgtgatatttgatattgaggtatcttggct Predict ORF larger than 30AA ================================================ Protein_Len: 52 Strand: + Start: 12 End: 167 ........... M R M V L D G P T C I I R K T Y L K M I V N L K S P E Y F L S K I G I I H S K R R R L K T T I I T A I I ........................................................................................................................................................... Protein_Len: 60 Strand: - Start: 126 End: 305 ............................................................................................................................. F P S P Q L C C Y N R R D Y L L S I R K R M L I S Y F S R N H Y L K S L Y N T F I A I I K V H H T L K T R L R R H Y K M ................. Protein_Len: 36 Strand: - Start: 59 End: 166 .......................................................... K F I I T F K F L G S Y K R D L I P M I W E F L L L S F V V I I V A I M ............................................................................................................................................................ Protein_Len: 40 Strand: - Start: 3 End: 122 .. V G K H S H N Q I P G G T N N P F S I Q F H Y Y I Q F A R F I K Q R F Y A Y D M ........................................................................................................................................................................................................ aaaactcctttgtgagaatggttttggatgggcccacctgtattattcggaaaacttatttgaaaatgatagtaaatttgaaaagccctgaatattttctgtctaaaataggcataatccactcaaaaaggagaaggctgaagacaacaataattacggcgatcatatagaagagatattctttttctcattagaatggaataaaacgaacgattatgatataatttagataaataattcgtaaaaatggcaatgatttttacgtgatgtgttagcttggtgcgtaagcgcctgtgatatttgatattgaggtatcttggct 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: 82 Start: 196 End: 225 ...................................................................................................................................................................................................ATGGAATAAAACGAACGATTATGATATAAT................................................................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aaaactcctttgtgagaatggttttggatgggcccacctgtattattcggaaaacttatttgaaaatgatagtaaatttgaaaagccctgaatattttctgtctaaaataggcataatccactcaaaaaggagaaggctgaagacaacaataattacggcgatcatatagaagagatattctttttctcattagaatggaataaaacgaacgattatgatataatttagataaataattcgtaaaaatggcaatgatttttacgtgatgtgttagcttggtgcgtaagcgcctgtgatatttgatattgaggtatcttggct Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 43 HP_score: -2.4 Tail_Score: -3.08696 Start: 239 End: 265 Full_Region: ccaagctaacacatc acgtaaaaat cattgcc atttttacga attatttatctaaat ..............................................................................................................................................................................................................................................acgtaaaaatcattgccatttttacga......................................................... TransTerm Strand: + Conf: 55 HP_score: -5.9 Tail_Score: -2.77036 Start: 240 End: 264 Full_Region: TTTAGATAAATAATT CGTAAAAAT GGCAATG ATTTTTACG TGATGTGTTAGCTTG ...............................................................................................................................................................................................................................................CGTAAAAATGGCAATGATTTTTACG.......................................................... Find igs database================================================ Query_seq: SSA_0036:SSA_0037|SSA_0036:SSA_0037:Secreted protein, possible function in cell-wall metabolism (amidase), putative:Phosphoribosylamine-glycine ligase; phosphoribosyl glycinamide synthetase (GARS), putative:<-->:44090..44411 322 aaaactcctttgtgagaatggttttggatgggcccacctgtattattcggaaaacttatttgaaaatgatagtaaatttgaaaagccctgaatattttctgtctaaaataggcataatccactcaaaaaggagaaggctgaagacaacaataattacggcgatcatatagaagagatattctttttctcattagaatggaataaaacgaacgattatgatataatttagataaataattcgtaaaaatggcaatgatttttacgtgatgtgttagcttggtgcgtaagcgcctgtgatatttgatattgaggtatcttggct Intra-Species Hit: Count: 1 Min: 1 Max: 322 Len: 322 Subject: NC_009009_SSA_0036_SSA_0037|Secreted protein, possible function in cell-wall metabolism (amidase), putative:Phosphoribosylamine-glycine ligase; phosphoribosyl glycinamide synthetase (GARS), putative|NEGATIVE:POSITIVE|[44090,44411]|322 HSP 1 e-value: 0.0 bit: 638.0 Len: 322 Query Start:1 Query End:322 Subject Strand: POSITIVE Subject Start: 1 Subject End: 322 aaaactcctttgtgagaatggttttggatgggcccacctgtattattcggaaaacttatttgaaaatgatagtaaatttgaaaagccctgaatattttctgtctaaaataggcataatccactcaaaaaggagaaggctgaagacaacaataattacggcgatcatatagaagagatattctttttctcattagaatggaataaaacgaacgattatgatataatttagataaataattcgtaaaaatggcaatgatttttacgtgatgtgttagcttggtgcgtaagcgcctgtgatatttgatattgaggtatcttggct aaaactcctttgtgagaatggttttggatgggcccacctgtattattcggaaaacttatttgaaaatgatagtaaatttgaaaagccctgaatattttctgtctaaaataggcataatccactcaaaaaggagaaggctgaagacaacaataattacggcgatcatatagaagagatattctttttctcattagaatggaataaaacgaacgattatgatataatttagataaataattcgtaaaaatggcaatgatttttacgtgatgtgttagcttggtgcgtaagcgcctgtgatatttgatattgaggtatcttggct Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAACUCCUUUGUGAGAAUGGUUUUGGAUGGGCCCACCUGUAUUAUUCGGAAAACUUAUUUGAAAAUGAUAGUAAAUUUGAAAAGCCCUGAAUAUUUUCUGUCUAAAAUAGGCAUAAUCCACUCAAAAAGGAGAAGGCUGAAGACAACAAUAAUUACGGCGAUCAUAUAGAAGAGAUAUUCUUUUUCUCAUUAGAAUGGAAUAAAACGAACGAUUAUGAUAUAAUUUAGAUAAAUAAUUCGUAAAAAUGGCAAUGAUUUUUACGUGAUGUGUUAGCUUGGUGCGUAAGCGCCUGUGAUAUUUGAUAUUGAGGUAUCUUGGCU ....(((((((.((((....(((((((((((((.((....(((((((((((.......))))).....))))))....))....)))).(((....))).))))))))).((......)).)))).)))))))..((((.(((..((((...((((((..((((((..........((((((..((((....)))).))))))..(((((..(((.(((......)))....)))..)))))..........))))))....)))))).))))..)))(((((....)))))...(((((((.......)))))))..)))) (-69.10) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGCCAAGAUACCUCAAUAUCAAAUAUCACAGGCGCUUACGCACCAAGCUAACACAUCACGUAAAAAUCAUUGCCAUUUUUACGAAUUAUUUAUCUAAAUUAUAUCAUAAUCGUUCGUUUUAUUCCAUUCUAAUGAGAAAAAGAAUAUCUCUUCUAUAUGAUCGCCGUAAUUAUUGUUGUCUUCAGCCUUCUCCUUUUUGAGUGGAUUAUGCCUAUUUUAGACAGAAAAUAUUCAGGGCUUUUCAAAUUUACUAUCAUUUUCAAAUAAGUUUUCCGAAUAAUACAGGUGGGCCCAUCCAAAACCAUUCUCACAAAGGAGUUUU .((.((((((...(((((............((.((....)).))..((..........(((((((((.......)))))))))...................((((((...........(((((..((((....))))...))))).........)))))).))......))))).))))))..))...(((((((.(((((((((...((((((((...........(((((.(((......(((((((..............)))))))))))))))....))))))))..)))))........)))).))))))).... (-51.85) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 911 50 1 141 92 NC_009009:SSA_0036|5end_Secreted_protein,_possible_function_in_cell-wall_metabolism_(amidase),_putative_43999..44229_NEGATIVE 337 317 271 54 2 NC_009009:SSA_2069|5end_Prolyl-tRNA_synthetase,_putative_2073252..2073482_NEGATIVE 332 49 2 202 149 NC_009009:SSA_0017|5end_Cell_shape_determining_protein_MreC,_putative_22811..23041_POSITIVE 329 170 129 106 66 NC_009009:SSA_0190|5end_hypothetical_protein_191481..191711_POSITIVE 313 320 275 171 123 NC_009009:SSA_0656|5end_Cell_division_protein_FtsZ,_putative_640159..640389_POSITIVE 311 320 271 208 149 NC_009009:SSA_0218|5end_Sugar-binding_periplasmic_protein,_putative_213863..214093_POSITIVE 288 320 275 157 115 NC_009009:SSA_0607|5end_ABC_transporter,_permease_component,_putative_596926..597156_NEGATIVE 286 50 5 149 97 NC_009009:SSA_2330|5end_Acetyltransferase,_putative_2333655..2333885_NEGATIVE 286 320 273 87 40 NC_009009:SSA_1741|5end_ABC-type_Fe3+-siderophores_transporter,_ATPase_component,_putative_1728007..1728237_POSITIVE 282 49 6 219 179 NC_009009:SSA_0258|5end_hypothetical_protein_251845..252075_POSITIVE 281 317 275 99 52 NC_009009:SSA_1746|5end_hypothetical_protein_1732945..1733175_NEGATIVE 281 160 118 139 101 NC_009009:SSA_1117|5end_hypothetical_protein_1142743..1142973_POSITIVE 279 305 266 47 4 NC_009009:SSA_2317|5end_Tfp_pilus_assembly_protein,_pilus_retraction_ATPase_PilT,_putative_2319410..2319640_NEGATIVE 273 294 253 135 90 NC_009009:SSA_0486|5end_Uroporphyrinogen-III_synthase,_putative_486637..486867_POSITIVE 269 48 5 152 100 NC_009009:SSA_0737|5end_Arginine_deiminase,_putative_718624..718854_POSITIVE 267 124 87 151 108 NC_009009:SSA_0242|5end_hypothetical_protein_234978..235208_POSITIVE 267 297 254 202 151 NC_009009:SSA_2391|5end_30S_ribosomal_protein_S14,_putative_114252..114482_POSITIVE 265 307 264 66 5 NC_009009:SSA_1163|5end_GMP_synthase_[glutamine-hydrolyzing],_putative_1190898..1191128_NEGATIVE 262 317 271 84 38 NC_009009:SSA_2131|5end_DNA-binding_protein,_putative_2133949..2134179_POSITIVE 262 42 3 46 8 NC_009009:SSA_0482|5end_ATP:cobalamin_adenosyl_transferase,_putative_483458..483688_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 329 170 129 68 28 NC_009009:SSA_0189|3end_Competence_protein_ComGF,_putative_191523..191673_POSITIVE 286 50 5 108 56 NC_009009:SSA_2331|3end_D-alanine_transfer_protein,_putative_2333696..2333846_NEGATIVE 282 49 6 134 94 NC_009009:SSA_0257|3end_N-acetylmuramidase/lysin,_putative_251840..251990_POSITIVE 281 317 275 106 59 NC_009009:SSA_1747|3end_hypothetical_protein_1732938..1733088_NEGATIVE 281 160 118 68 30 NC_009009:SSA_1116|3end_hypothetical_protein_1142752..1142902_POSITIVE 279 305 266 45 2 NC_009009:SSA_2318|3end_PilB-like_pili_biogenesis_ATPase,_putative_2319412..2319562_NEGATIVE 276 170 131 53 12 NC_009009:SSA_1409|3end_DTDP-glucose-4,6-dehydratase,_putative_1421209..1421359_NEGATIVE 273 294 253 150 105 NC_009009:SSA_0485|3end_Porphobilinogen_deaminase,_putative_486732..486882_POSITIVE 272 296 251 131 81 NC_009009:SSA_1622|3end_50S_ribosomal_protein_L1,_putative_1624752..1624902_NEGATIVE 268 295 254 43 3 NC_009009:SSA_1231|3end_hypothetical_protein_1253649..1253799_NEGATIVE 267 290 241 148 103 NC_009009:SSA_1262|3end_tRNA_modification_GTPase,_possibly_iron-binding,_putative_1289235..1289385_POSITIVE 267 124 87 150 107 NC_009009:SSA_0241|3end_Ribosomal_protein_L11_methyltransferase,_putative_235057..235207_POSITIVE 262 317 271 75 29 NC_009009:SSA_2130|3end_hypothetical_protein_2134020..2134170_POSITIVE 262 42 3 49 11 NC_009009:SSA_0481|3end_Cobyric_acid_synthase,_putative_483541..483691_POSITIVE 255 64 29 32 3 NC_009009:SSA_2336|3end_Transcriptional_regulator,_PadR_family,_putative_2338785..2338935_POSITIVE 254 165 122 63 19 NC_009009:SSA_0217|3end_Two-component_system_transcriptional_regulator_(CheY_domain_and_HTH-like_DNA-binding_domain),_putative_213946..214096_POSITIVE 253 303 263 150 103 NC_009009:SSA_0357|3end_Thioredoxin,_putative_351157..351307_POSITIVE 252 297 267 72 48 NC_009009:SSA_2215|3end_Oligosaccharide_repeat_unit_polymerase_Wzy,_putative_2215832..2215982_NEGATIVE 245 305 268 140 105 NC_009009:SSA_1595|3end_Tellurite_resistance,_putative_1600951..1601101_NEGATIVE 245 318 271 51 5 NC_009009:SSA_0331|3end_C3-degrading_proteinase,_putative_325992..326142_POSITIVE