Origin IGS: tccattttccctatctttcagccttttttaagaaaaaattcagtcctgtttaagtaaaaaactatatgataatgctattctagtgaaaggatgtgtattggatgacttgtaagctgcattagcttcttgcttgaaagaaagagtcagaaaaatttacaaaagaaagaaggtaatagattta .........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 taaatctattaccttctttcttttgtaaatttttctgactctttctttcaagcaagaagctaatgcagcttacaagtcatccaatacacatcctttcactagaatagcattatcatatagttttttacttaaacaggactgaattttttcttaaaaaaggctgaaagatagggaaaatgga Mask Tandem Repeat Region ================================================ tccattttccctatctttcagccttttttaagaaaaaattcagtcctgtttaagtaaaaaactatatgataatgctattctagtgaaaggatgtgtattggatgacttgtaagctgcattagcttcttgcttgaaagaaagagtcagaaaaatttacaaaagaaagaaggtaatagattta Find is-nt database================================================ Query_seq: SSA_0957:SSA_0958|SSA_0957:SSA_0958:Dehydrogenase, putative:hypothetical protein:->->:967232..967412 181 tccattttccctatctttcagccttttttaagaaaaaattcagtcctgtttaagtaaaaaactatatgataatgctattctagtgaaaggatgtgtattggatgacttgtaagctgcattagcttcttgcttgaaagaaagagtcagaaaaatttacaaaagaaagaaggtaatagattta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0957:SSA_0958|SSA_0957:SSA_0958:Dehydrogenase, putative:hypothetical protein:->->:967232..967412 181 tccattttccctatctttcagccttttttaagaaaaaattcagtcctgtttaagtaaaaaactatatgataatgctattctagtgaaaggatgtgtattggatgacttgtaagctgcattagcttcttgcttgaaagaaagagtcagaaaaatttacaaaagaaagaaggtaatagattta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0957:SSA_0958|SSA_0957:SSA_0958:Dehydrogenase, putative:hypothetical protein:->->:967232..967412 181 tccattttccctatctttcagccttttttaagaaaaaattcagtcctgtttaagtaaaaaactatatgataatgctattctagtgaaaggatgtgtattggatgacttgtaagctgcattagcttcttgcttgaaagaaagagtcagaaaaatttacaaaagaaagaaggtaatagattta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tccattttccctatctttcagccttttttaagaaaaaattcagtcctgtttaagtaaaaaactatatgataatgctattctagtgaaaggatgtgtattggatgacttgtaagctgcattagcttcttgcttgaaagaaagagtcagaaaaatttacaaaagaaagaaggtaatagattta Predict ORF larger than 30AA ================================================ Protein_Len: 37 Strand: - Start: 43 End: 153 .......................................... D Q K L L F S Y S L A I R T F P H T N S S K Y A A N A E Q K F S L T L F M ............................ tccattttccctatctttcagccttttttaagaaaaaattcagtcctgtttaagtaaaaaactatatgataatgctattctagtgaaaggatgtgtattggatgacttgtaagctgcattagcttcttgcttgaaagaaagagtcagaaaaatttacaaaagaaagaaggtaatagattta 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================================================ tccattttccctatctttcagccttttttaagaaaaaattcagtcctgtttaagtaaaaaactatatgataatgctattctagtgaaaggatgtgtattggatgacttgtaagctgcattagcttcttgcttgaaagaaagagtcagaaaaatttacaaaagaaagaaggtaatagattta Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_0957:SSA_0958|SSA_0957:SSA_0958:Dehydrogenase, putative:hypothetical protein:->->:967232..967412 181 tccattttccctatctttcagccttttttaagaaaaaattcagtcctgtttaagtaaaaaactatatgataatgctattctagtgaaaggatgtgtattggatgacttgtaagctgcattagcttcttgcttgaaagaaagagtcagaaaaatttacaaaagaaagaaggtaatagattta Intra-Species Hit: Count: 1 Min: 1 Max: 181 Len: 181 Subject: NC_009009_SSA_0957_SSA_0958|Dehydrogenase, putative:hypothetical protein|POSITIVE:POSITIVE|[967232,967412]|181 HSP 1 e-value: 2.0E-98 bit: 359.0 Len: 181 Query Start:1 Query End:181 Subject Strand: POSITIVE Subject Start: 1 Subject End: 181 tccattttccctatctttcagccttttttaagaaaaaattcagtcctgtttaagtaaaaaactatatgataatgctattctagtgaaaggatgtgtattggatgacttgtaagctgcattagcttcttgcttgaaagaaagagtcagaaaaatttacaaaagaaagaaggtaatagattta tccattttccctatctttcagccttttttaagaaaaaattcagtcctgtttaagtaaaaaactatatgataatgctattctagtgaaaggatgtgtattggatgacttgtaagctgcattagcttcttgcttgaaagaaagagtcagaaaaatttacaaaagaaagaaggtaatagattta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCCAUUUUCCCUAUCUUUCAGCCUUUUUUAAGAAAAAAUUCAGUCCUGUUUAAGUAAAAAACUAUAUGAUAAUGCUAUUCUAGUGAAAGGAUGUGUAUUGGAUGACUUGUAAGCUGCAUUAGCUUCUUGCUUGAAAGAAAGAGUCAGAAAAAUUUACAAAAGAAAGAAGGUAAUAGAUUUA .........(((.((((((..((((((...((((.....(((.....((((.......))))....)))........))))...)))))).((((.(((...(((((((((((..((....))..)))))..........))))))....))).))))...)))))))))........... (-32.42) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAAUCUAUUACCUUCUUUCUUUUGUAAAUUUUUCUGACUCUUUCUUUCAAGCAAGAAGCUAAUGCAGCUUACAAGUCAUCCAAUACACAUCCUUUCACUAGAAUAGCAUUAUCAUAUAGUUUUUUACUUAAACAGGACUGAAUUUUUUCUUAAAAAAGGCUGAAAGAUAGGGAAAAUGGA ....((((((.(((((((((.(((((((...........((((.((....)).)))).((....))...)))))))...............(((((....((((.....(((((....(((.....))).......)).))).....))))....)))))..)))))).)))...)))))) (-25.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 289 147 106 49 8 NC_009009:SSA_2117|5end_DNA_recombination_protein_RmuC,_putative_2119812..2120042_NEGATIVE 289 145 101 207 152 NC_009009:SSA_0138|5end_Metal-binding_(Zn)_permease,_putative_132533..132763_POSITIVE 284 134 93 60 15 NC_009009:SSA_1577|5end_Proline_dipeptidase,_putative_1580294..1580524_POSITIVE 270 147 101 49 5 NC_009009:SSA_2207|5end_hypothetical_protein_2207221..2207451_NEGATIVE 263 140 99 178 131 NC_009009:SSA_1514|5end_Cell-wall_biogenesis_glycosyltransferase,_putative_1521780..1522010_NEGATIVE 255 145 101 61 14 NC_009009:SSA_2050|5end_Arabinose_efflux_permease,_putative_2053255..2053485_POSITIVE 255 148 103 219 170 NC_009009:SSA_1035|5end_Pyrimidine_nucleoside_phosphorylase,_putative_1050174..1050404_POSITIVE 254 128 81 78 30 NC_009009:SSA_0322|5end_Transcriptional_activator,_TipA_family,_putative_314717..314947_POSITIVE 253 138 94 224 167 NC_009009:SSA_2055|5end_hypothetical_protein_2058160..2058390_NEGATIVE 252 130 84 44 3 NC_009009:SSA_1808|5end_hypothetical_protein_1792209..1792439_NEGATIVE 250 135 106 222 185 NC_009009:SSA_2082|5end_Carbohydrate_kinase,_FGGY_family,_putative_2086874..2087104_NEGATIVE 250 134 94 105 67 NC_009009:SSA_1628|5end_MutT/nudix_family_protein,_putative_1629864..1630094_POSITIVE 249 134 96 152 124 NC_009009:SSA_1149|5end_Glycosyl_hydrolase,_family_1,_putative_1178399..1178629_POSITIVE 249 150 102 115 68 NC_009009:SSA_0866|5end_Cation-transporting_ATPase,_E1-E_2_family,_putative_856983..857213_POSITIVE 248 145 103 178 133 NC_009009:SSA_2157|5end_ATP-dependent_serine_protease,_putative_2158241..2158471_NEGATIVE 248 117 73 186 135 NC_009009:SSA_1694|5end_PTS_system,_lactose-specific_IIA_component,_putative_1687128..1687358_NEGATIVE 245 138 92 230 180 NC_009009:SSA_2106|5end_Flavin_monoxygenase,_putative_2109064..2109294_NEGATIVE 245 50 2 138 88 NC_009009:SSA_1803|5end_GTP-binding_protein,_putative_1787909..1788139_NEGATIVE 245 131 93 220 189 NC_009009:SSA_0990|5end_hypothetical_protein_991733..991963_POSITIVE 244 130 89 187 145 NC_009009:SSA_0844|5end_hypothetical_protein_829324..829554_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 305 145 104 43 7 NC_009009:SSA_0274|3end_hypothetical_protein_268580..268730_NEGATIVE 300 129 89 117 78 NC_009009:SSA_0638|3end_Tryptophan_synthase_alpha_chain,_putative_627794..627944_POSITIVE 289 147 106 47 6 NC_009009:SSA_2118|3end_Thiamine_pyrophosphokinase,_putative_2119814..2119964_NEGATIVE 280 148 103 68 14 NC_009009:SSA_2210|3end_Ribosomal_large_subunit_pseudouridine_synthase_D,_putative_2211454..2211604_POSITIVE 250 135 106 146 109 NC_009009:SSA_2083|3end_hypothetical_protein_2086950..2087100_NEGATIVE 249 134 96 146 118 NC_009009:SSA_1148|3end_Beta-glucosides_PTS,_EIIC,_putative_1178473..1178623_POSITIVE 248 117 73 137 86 NC_009009:SSA_1695|3end_Transcriptional_antiterminator,_BglG/SacY_family_(induction_of_sugar_metabolism),_putative_1687177..1687327_NEGATIVE 245 50 2 95 45 NC_009009:SSA_1804|3end_NADPH-flavin_oxidoreductase,_putative_1787952..1788102_NEGATIVE 244 144 113 33 2 NC_009009:SSA_0172|3end_Transcriptional_regulator,_XRE_family,_putative_169672..169822_POSITIVE 243 133 97 78 40 NC_009009:SSA_0813|3end_Thioredoxin_reductase,_putative_794438..794588_NEGATIVE 239 124 87 79 39 NC_009009:SSA_1429|3end_hypothetical_protein_1436355..1436505_NEGATIVE 237 148 114 148 114 NC_009009:SSA_0620|3end_hypothetical_protein_611951..612101_NEGATIVE 234 130 90 139 106 NC_009009:SSA_1009|3end_Galactose-1-phosphate-uridylyltransferase,_putative_1012815..1012965_POSITIVE 233 131 112 60 41 NC_009009:SSA_1152|3end_Protein_chain_release_factor_A,_putative_1181918..1182068_POSITIVE 233 43 5 137 96 NC_009009:SSA_0502|3end_Peptide_ABC_transporter,_permease_protein,_putative_502323..502473_POSITIVE 232 150 101 140 86 NC_009009:SSA_1226|3end_ParC,_putative_1248783..1248933_NEGATIVE 230 133 92 126 66 NC_009009:SSA_1757|3end_hypothetical_protein_1745282..1745432_NEGATIVE 227 134 97 77 28 NC_009009:SSA_0689|3end_Penicillin-binding_protein_2B,_putative_674408..674558_POSITIVE 226 128 89 59 11 NC_009009:SSA_0465|3end_Precorrin-8X_methylmutase_/_precorrin_isomerase,_putative_469963..470113_POSITIVE 225 148 102 114 57 NC_009009:SSA_1191|3end_hypothetical_protein_1218222..1218372_NEGATIVE