Origin IGS: ttttatactcaaaaatggatttgcaaagagtattcaatagtatgaaaagaaatggttgcagatttgtagtcattttcttttatactaatagatgaaagaaggcgaatttttcagccttctttaagaaagcggtgataaaatcaacgttctcttacaatctagtaaaggaggttgcg .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 cgcaacctcctttactagattgtaagagaacgttgattttatcaccgctttcttaaagaaggctgaaaaattcgccttctttcatctattagtataaaagaaaatgactacaaatctgcaaccatttcttttcatactattgaatactctttgcaaatccatttttgagtataaaa Mask Tandem Repeat Region ================================================ ttttatactcaaaaatggatttgcaaagagtattcaatagtatgaaaagaaatggttgcagatttgtagtcattttcttttatactaatagatgaaagaaggcgaatttttcagccttctttaagaaagcggtgataaaatcaacgttctcttacaatctagtaaaggaggttgcg Find is-nt database================================================ Query_seq: SSA_0793:SSA_0794|SSA_0793:SSA_0794:DNA-entry nuclease, putative:Zn-dependent protease, putative:->->:775860..776035 176 ttttatactcaaaaatggatttgcaaagagtattcaatagtatgaaaagaaatggttgcagatttgtagtcattttcttttatactaatagatgaaagaaggcgaatttttcagccttctttaagaaagcggtgataaaatcaacgttctcttacaatctagtaaaggaggttgcg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0793:SSA_0794|SSA_0793:SSA_0794:DNA-entry nuclease, putative:Zn-dependent protease, putative:->->:775860..776035 176 ttttatactcaaaaatggatttgcaaagagtattcaatagtatgaaaagaaatggttgcagatttgtagtcattttcttttatactaatagatgaaagaaggcgaatttttcagccttctttaagaaagcggtgataaaatcaacgttctcttacaatctagtaaaggaggttgcg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0793:SSA_0794|SSA_0793:SSA_0794:DNA-entry nuclease, putative:Zn-dependent protease, putative:->->:775860..776035 176 ttttatactcaaaaatggatttgcaaagagtattcaatagtatgaaaagaaatggttgcagatttgtagtcattttcttttatactaatagatgaaagaaggcgaatttttcagccttctttaagaaagcggtgataaaatcaacgttctcttacaatctagtaaaggaggttgcg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttttatactcaaaaatggatttgcaaagagtattcaatagtatgaaaagaaatggttgcagatttgtagtcattttcttttatactaatagatgaaagaaggcgaatttttcagccttctttaagaaagcggtgataaaatcaacgttctcttacaatctagtaaaggaggttgcg Predict ORF larger than 30AA ================================================ Protein_Len: 32 Strand: - Start: 12 End: 107 ........... F H I Q L S Y E I T H F S I T A S K Y D N E K I S I S S L L R M ..................................................................... ttttatactcaaaaatggatttgcaaagagtattcaatagtatgaaaagaaatggttgcagatttgtagtcattttcttttatactaatagatgaaagaaggcgaatttttcagccttctttaagaaagcggtgataaaatcaacgttctcttacaatctagtaaaggaggttgcg 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================================================ ttttatactcaaaaatggatttgcaaagagtattcaatagtatgaaaagaaatggttgcagatttgtagtcattttcttttatactaatagatgaaagaaggcgaatttttcagccttctttaagaaagcggtgataaaatcaacgttctcttacaatctagtaaaggaggttgcg Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 70 HP_score: -8.2 Tail_Score: -3.16071 Start: 93 End: 124 Full_Region: tttatcaccgctttc ttaaagaaggctgaa aaa ttcgccttctttca tctattagtataaaa ............................................................................................ttaaagaaggctgaaaaattcgccttctttca.................................................... TransTerm Strand: + Conf: 73 HP_score: -8.1 Tail_Score: -3.53224 Start: 98 End: 119 Full_Region: TACTAATAGATGAAA GAAGGCGAA TTT TTCAGCCTTC TTTAAGAAAGCGGTG .................................................................................................GAAGGCGAATTTTTCAGCCTTC......................................................... TransTerm Strand: - Conf: 79 HP_score: -8.1 Tail_Score: -3.94333 Start: 98 End: 119 Full_Region: caccgctttcttaaa gaaggctgaa aaa ttcgccttc tttcatctattagta .................................................................................................gaaggctgaaaaattcgccttc......................................................... Find igs database================================================ Query_seq: SSA_0793:SSA_0794|SSA_0793:SSA_0794:DNA-entry nuclease, putative:Zn-dependent protease, putative:->->:775860..776035 176 ttttatactcaaaaatggatttgcaaagagtattcaatagtatgaaaagaaatggttgcagatttgtagtcattttcttttatactaatagatgaaagaaggcgaatttttcagccttctttaagaaagcggtgataaaatcaacgttctcttacaatctagtaaaggaggttgcg Intra-Species Hit: Count: 1 Min: 1 Max: 176 Len: 176 Subject: NC_009009_SSA_0793_SSA_0794|DNA-entry nuclease, putative:Zn-dependent protease, putative|POSITIVE:POSITIVE|[775860,776035]|176 HSP 1 e-value: 2.0E-95 bit: 349.0 Len: 176 Query Start:1 Query End:176 Subject Strand: POSITIVE Subject Start: 1 Subject End: 176 ttttatactcaaaaatggatttgcaaagagtattcaatagtatgaaaagaaatggttgcagatttgtagtcattttcttttatactaatagatgaaagaaggcgaatttttcagccttctttaagaaagcggtgataaaatcaacgttctcttacaatctagtaaaggaggttgcg ttttatactcaaaaatggatttgcaaagagtattcaatagtatgaaaagaaatggttgcagatttgtagtcattttcttttatactaatagatgaaagaaggcgaatttttcagccttctttaagaaagcggtgataaaatcaacgttctcttacaatctagtaaaggaggttgcg Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUUAUACUCAAAAAUGGAUUUGCAAAGAGUAUUCAAUAGUAUGAAAAGAAAUGGUUGCAGAUUUGUAGUCAUUUUCUUUUAUACUAAUAGAUGAAAGAAGGCGAAUUUUUCAGCCUUCUUUAAGAAAGCGGUGAUAAAAUCAACGUUCUCUUACAAUCUAGUAAAGGAGGUUGCG .......(((.....((((((....(((((..(((..((((((((((..(((((..(((......)))..)))))..)))))))))).......(((((((((..........)))))))))..))).(((.((((...)))).))).)))))..))))))......)))...... (-47.50) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CGCAACCUCCUUUACUAGAUUGUAAGAGAACGUUGAUUUUAUCACCGCUUUCUUAAAGAAGGCUGAAAAAUUCGCCUUCUUUCAUCUAUUAGUAUAAAAGAAAAUGACUACAAAUCUGCAACCAUUUCUUUUCAUACUAUUGAAUACUCUUUGCAAAUCCAUUUUUGAGUAUAAAA ...............(((((..(((((((.((.((((...)))).)).)))))))((((((((.((.....))))))))))..))))).((((((((((((((.((....((....))....)))))))))).))))))....((((((.................)))))).... (-33.93) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 282 122 88 88 50 NC_009009:SSA_1012|5end_Phosphoenolpyruvate_synthase,_putative_1014739..1014969_POSITIVE 279 150 101 64 12 NC_009009:SSA_1528|5end_Phosphoglycerate_mutase,_putative_1535135..1535365_POSITIVE 266 137 97 162 121 NC_009009:SSA_1044|5end_Homoserine_kinase,_putative_1059853..1060083_POSITIVE 257 147 102 63 9 NC_009009:SSA_0569|5end_Aspartyl/glutamyl-tRNA(Asn/Gln)_amidotransferase_subunit_C,_putative_563613..563843_POSITIVE 256 120 71 79 36 NC_009009:SSA_1901|5end_Conserved_uncharacterized_protein_1896599..1896829_NEGATIVE 256 50 7 195 147 NC_009009:SSA_0585|5end_hypothetical_protein_576937..577167_POSITIVE 255 133 97 176 139 NC_009009:SSA_0796|5end_ABC-NBD_transporters_with_duplicated_ATPase_domains,_putative_777085..777315_POSITIVE 253 170 128 115 71 NC_009009:SSA_1208|5end_23S_rRNA_pseudouridine_synthase,_putative_1233185..1233415_NEGATIVE 246 139 96 177 125 NC_009009:SSA_1349|5end_Transcriptional_regulator,_biotin_repressor_family,_putative_1365918..1366148_POSITIVE 242 147 102 56 20 NC_009009:SSA_2044|5end_Cysteinyl-tRNA_synthetase,_putative_2048409..2048639_NEGATIVE 240 149 101 163 112 NC_009009:SSA_0162|5end_hypothetical_protein_161391..161621_POSITIVE 238 147 101 222 169 NC_009009:SSA_0123|5end_50S_ribosomal_protein_L18P,_putative_116048..116278_POSITIVE 236 123 88 41 8 NC_009009:SSA_1153|5end_HemK_protein,_putative_1181838..1182068_POSITIVE 236 160 127 39 4 NC_009009:SSA_0749|5end_Competence_protein,_putative_730668..730898_POSITIVE 235 130 83 89 44 NC_009009:SSA_2358|5end_hypothetical_protein_2360497..2360727_NEGATIVE 235 146 101 128 71 NC_009009:SSA_1222|5end_NTP_pyrophosphohydrolases_including_oxidative_damage_repair_enzymes,_putative_1245454..1245684_NEGATIVE 235 131 91 210 182 NC_009009:SSA_0980|5end_3-isopropylmalate_dehydratase_large_subunit,_putative_984004..984234_POSITIVE 235 122 94 226 192 NC_009009:SSA_0460|5end_Multiple_antibiotic_resistance_operon_transcription_repressor_(MarR),_putative_462608..462838_POSITIVE 233 63 22 159 113 NC_009009:SSA_1137|5end_Dihydrolipoamide_dehydrogenase,_putative_1164375..1164605_POSITIVE 230 149 103 98 47 NC_009009:SSA_2071|5end_hypothetical_protein_2074766..2074996_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 348 87 45 53 10 NC_009009:SSA_0793|3end_DNA-entry_nuclease,_putative_775799..775949_POSITIVE 292 118 88 73 38 NC_009009:SSA_0564|3end_Potential_aminotransferase,_putative_556988..557138_POSITIVE 282 122 88 73 35 NC_009009:SSA_1011|3end_hypothetical_protein_1014804..1014954_POSITIVE 276 139 94 64 17 NC_009009:SSA_0459|3end_hypothetical_protein_462513..462663_POSITIVE 268 140 93 43 1 NC_009009:SSA_0314|3end_Nucleoside-diphosphate-sugar_epimerase,_putative_308967..309117_NEGATIVE 264 147 101 54 2 NC_009009:SSA_0863|3end_Cof_family_protein,_putative_854206..854356_NEGATIVE 255 133 97 76 39 NC_009009:SSA_0795|3end_hypothetical_protein_777065..777215_POSITIVE 253 170 128 118 74 NC_009009:SSA_1209|3end_Inorganic_polyphosphate/ATP-NAD_kinase,_putative_1233182..1233332_NEGATIVE 246 139 96 138 86 NC_009009:SSA_1348|3end_hypothetical_protein_1365959..1366109_POSITIVE 244 138 91 133 83 NC_009009:SSA_2050|3end_Arabinose_efflux_permease,_putative_2054696..2054846_POSITIVE 243 160 114 51 7 NC_009009:SSA_0255|3end_Multiple_antibiotic_resistance_operon_transcription_repressor_(MarR),_putative_247485..247635_NEGATIVE 242 147 102 38 2 NC_009009:SSA_2045|3end_Reductase,_putative_2048427..2048577_NEGATIVE 238 147 101 137 84 NC_009009:SSA_0122|3end_50S_ribosomal_protein_L6,_putative_116043..116193_POSITIVE 236 123 88 41 8 NC_009009:SSA_1152|3end_Protein_chain_release_factor_A,_putative_1181918..1182068_POSITIVE 230 149 103 64 13 NC_009009:SSA_2072|3end_Phosphatidate_cytidylyltransferase,_putative_2074800..2074950_NEGATIVE 230 142 103 55 11 NC_009009:SSA_1249|3end_hypothetical_protein_1273275..1273425_NEGATIVE 228 140 98 90 55 NC_009009:SSA_2283|3end_Conserved_uncharacterized_protein_2285537..2285687_NEGATIVE 227 96 54 123 69 NC_009009:SSA_2218|3end_Glycosyltransferase_(cell_wall_biogenesis)_Cps9G,_putative_2219123..2219273_NEGATIVE 224 152 116 143 109 NC_009009:SSA_1684|3end_Histidine_kinase,_putative_1677426..1677576_NEGATIVE 224 138 96 49 7 NC_009009:SSA_0536|3end_B12-dependent_diol_dehydratase_small_subunit,_putative_531937..532087_POSITIVE