Origin IGS: cctctccttcttctgggaaatatattttccctatcagcctgattaaaaatatttatcaaagcaaaataaaaaagctagactaagctagctttttcaaggcttttcagactctgctgaataaccttattttttgtaccctttttagataagtaccatatatattttctatggatgagataggtaatttttatcaaaaaactgctactccgatc .........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 gatcggagtagcagttttttgataaaaattacctatctcatccatagaaaatatatatggtacttatctaaaaagggtacaaaaaataaggttattcagcagagtctgaaaagccttgaaaaagctagcttagtctagcttttttattttgctttgataaatatttttaatcaggctgatagggaaaatatatttcccagaagaaggagagg Mask Tandem Repeat Region ================================================ cctctccttcttctgggaaatatattttccctatcagcctgattaaaaatatttatcaaagcaaaataaaaaagctagactaagctagctttttcaaggcttttcagactctgctgaataaccttattttttgtaccctttttagataagtaccatatatattttctatggatgagataggtaatttttatcaaaaaactgctactccgatc Find is-nt database================================================ Query_seq: SSA_2105:SSA_2106|SSA_2105:SSA_2106:hypothetical protein:Flavin monoxygenase, putative:<-<-:2107893..2108104 212 cctctccttcttctgggaaatatattttccctatcagcctgattaaaaatatttatcaaagcaaaataaaaaagctagactaagctagctttttcaaggcttttcagactctgctgaataaccttattttttgtaccctttttagataagtaccatatatattttctatggatgagataggtaatttttatcaaaaaactgctactccgatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_2105:SSA_2106|SSA_2105:SSA_2106:hypothetical protein:Flavin monoxygenase, putative:<-<-:2107893..2108104 212 cctctccttcttctgggaaatatattttccctatcagcctgattaaaaatatttatcaaagcaaaataaaaaagctagactaagctagctttttcaaggcttttcagactctgctgaataaccttattttttgtaccctttttagataagtaccatatatattttctatggatgagataggtaatttttatcaaaaaactgctactccgatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_2105:SSA_2106|SSA_2105:SSA_2106:hypothetical protein:Flavin monoxygenase, putative:<-<-:2107893..2108104 212 cctctccttcttctgggaaatatattttccctatcagcctgattaaaaatatttatcaaagcaaaataaaaaagctagactaagctagctttttcaaggcttttcagactctgctgaataaccttattttttgtaccctttttagataagtaccatatatattttctatggatgagataggtaatttttatcaaaaaactgctactccgatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 cctctccttcttctgggaaatatattttccctatcagcctgattaaaaatatttatcaaagcaaaataaaaaagctagactaagctagctttttcaaggcttttcagactctgctgaataaccttattttttgtaccctttttagataagtaccatatatattttctatggatgagataggtaatttttatcaaaaaactgctactccgatc Predict ORF larger than 30AA ================================================ Protein_Len: 39 Strand: - Start: 78 End: 194 ............................................................................. V L S A K E L S K L S Q Q I V K N K T G K K S L Y W I Y K R H I L Y T I K I M .................. cctctccttcttctgggaaatatattttccctatcagcctgattaaaaatatttatcaaagcaaaataaaaaagctagactaagctagctttttcaaggcttttcagactctgctgaataaccttattttttgtaccctttttagataagtaccatatatattttctatggatgagataggtaatttttatcaaaaaactgctactccgatc 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================================================ cctctccttcttctgggaaatatattttccctatcagcctgattaaaaatatttatcaaagcaaaataaaaaagctagactaagctagctttttcaaggcttttcagactctgctgaataaccttattttttgtaccctttttagataagtaccatatatattttctatggatgagataggtaatttttatcaaaaaactgctactccgatc Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 89 HP_score: -8.8 Tail_Score: -4.58773 Start: 67 End: 96 Full_Region: gagtctgaaaagcct tgaaaaagctag cttagt ctagctttttta ttttgctttgataaa ..................................................................tgaaaaagctagcttagtctagctttttta.................................................................................................................... TransTerm Strand: - Conf: 91 HP_score: -4.7 Tail_Score: -5.85244 Start: 74 End: 89 Full_Region: aaaagccttgaaaaa gctag cttagt ctagc ttttttattttgctt .........................................................................gctagcttagtctagc........................................................................................................................... Find igs database================================================ Query_seq: SSA_2105:SSA_2106|SSA_2105:SSA_2106:hypothetical protein:Flavin monoxygenase, putative:<-<-:2107893..2108104 212 cctctccttcttctgggaaatatattttccctatcagcctgattaaaaatatttatcaaagcaaaataaaaaagctagactaagctagctttttcaaggcttttcagactctgctgaataaccttattttttgtaccctttttagataagtaccatatatattttctatggatgagataggtaatttttatcaaaaaactgctactccgatc Intra-Species Hit: Count: 1 Min: 1 Max: 212 Len: 212 Subject: NC_009009_SSA_2105_SSA_2106|hypothetical protein:Flavin monoxygenase, putative|NEGATIVE:NEGATIVE|[2107893,2108104]|212 HSP 1 e-value: 1.0E-117 bit: 420.0 Len: 212 Query Start:1 Query End:212 Subject Strand: POSITIVE Subject Start: 1 Subject End: 212 cctctccttcttctgggaaatatattttccctatcagcctgattaaaaatatttatcaaagcaaaataaaaaagctagactaagctagctttttcaaggcttttcagactctgctgaataaccttattttttgtaccctttttagataagtaccatatatattttctatggatgagataggtaatttttatcaaaaaactgctactccgatc cctctccttcttctgggaaatatattttccctatcagcctgattaaaaatatttatcaaagcaaaataaaaaagctagactaagctagctttttcaaggcttttcagactctgctgaataaccttattttttgtaccctttttagataagtaccatatatattttctatggatgagataggtaatttttatcaaaaaactgctactccgatc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CCUCUCCUUCUUCUGGGAAAUAUAUUUUCCCUAUCAGCCUGAUUAAAAAUAUUUAUCAAAGCAAAAUAAAAAAGCUAGACUAAGCUAGCUUUUUCAAGGCUUUUCAGACUCUGCUGAAUAACCUUAUUUUUUGUACCCUUUUUAGAUAAGUACCAUAUAUAUUUUCUAUGGAUGAGAUAGGUAAUUUUUAUCAAAAAACUGCUACUCCGAUC ..............((((((.....))))))........((((.((((.((((((((...((((((..((((((((((......)))))))))).((((...(((((......)))))...))))...))))))..((....((((.(((((.......))))))))).))....)))))))).)))).))))................... (-44.00) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAUCGGAGUAGCAGUUUUUUGAUAAAAAUUACCUAUCUCAUCCAUAGAAAAUAUAUAUGGUACUUAUCUAAAAAGGGUACAAAAAAUAAGGUUAUUCAGCAGAGUCUGAAAAGCCUUGAAAAAGCUAGCUUAGUCUAGCUUUUUUAUUUUGCUUUGAUAAAUAUUUUUAAUCAGGCUGAUAGGGAAAAUAUAUUUCCCAGAAGAAGGAGAGG .(((.(((((((.((((((((....................(((((.........)))))....(((((.....)))))))))))))...))))))).....((((((((((((..((((((((((((......))))))))))))....)))))..((((....)))).)))))))))).((((((.....)))))).............. (-48.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 868 120 71 211 162 NC_009009:SSA_2105|5end_hypothetical_protein_2107802..2108032_NEGATIVE 312 124 82 198 160 NC_009009:SSA_0239|5end_7,8-dihydro-8-oxoguanine-triphosphatase,_putative_232961..233191_POSITIVE 311 40 2 48 4 NC_009009:SSA_0909|5end_Transcriptional_regulator,_AbrB_family_(stationary/sporulation_gene_expression),_putative_920887..921117_POSITIVE 301 122 83 78 44 NC_009009:SSA_0579|5end_Hydrolase,_HAD_superfamily,_putative_572220..572450_POSITIVE 287 119 73 192 142 NC_009009:SSA_0204|5end_Nisin_biosynthesis_two-component_response_transcriptional_regulator_nisR,_putative_202057..202287_POSITIVE 284 114 73 161 122 NC_009009:SSA_1726|5end_ABC_transporter_ATP-binding_protein-branched_chain_amino_acid_transport,_putative_1712467..1712697_NEGATIVE 283 117 71 162 107 NC_009009:SSA_0838|5end_GtfB,_putative_825406..825636_POSITIVE 283 108 61 194 139 NC_009009:SSA_0597|5end_hypothetical_protein_587566..587796_POSITIVE 283 116 72 219 163 NC_009009:SSA_0481|5end_Cobyric_acid_synthase,_putative_481962..482192_POSITIVE 281 41 5 198 163 NC_009009:SSA_1924|5end_Transcriptional_regulator,_TetR/AcrR_family,_putative_1913248..1913478_NEGATIVE 280 110 70 151 116 NC_009009:SSA_0319|5end_Branched-chain_amino_acid_permease_(L-methionine,_L-isoleucine,_leucine_and_valine),_putative_312721..312951_POSITIVE 274 110 61 221 175 NC_009009:SSA_0305|5end_hypothetical_protein_301985..302215_POSITIVE 273 119 72 151 106 NC_009009:SSA_2097|5end_Amino_acid_ABC_transporter,_ATP-binding_protein,_putative_2102918..2103148_NEGATIVE 272 107 67 195 146 NC_009009:SSA_1665|5end_hypothetical_protein_1665353..1665583_NEGATIVE 272 44 12 224 188 NC_009009:SSA_1644|5end_hypothetical_protein_1645617..1645847_NEGATIVE 271 113 73 162 129 NC_009009:SSA_2346|5end_3-oxoacyl-[acyl-carrier-protein]_synthase_III,_putative_2348546..2348776_NEGATIVE 270 117 71 74 21 NC_009009:SSA_0793|5end_DNA-entry_nuclease,_putative_774859..775089_POSITIVE 268 116 73 212 157 NC_009009:SSA_0187|5end_Competence_protein_ComYD,_putative_190350..190580_POSITIVE 265 119 80 73 25 NC_009009:SSA_0616|5end_YlbN-like_protein,_putative_609245..609475_POSITIVE 264 107 74 72 32 NC_009009:SSA_1317|5end_hypothetical_protein_1333544..1333774_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 303 110 68 85 39 NC_009009:SSA_0208|3end_Conserved_uncharacterized_protein_204968..205118_NEGATIVE 301 122 83 81 47 NC_009009:SSA_0578|3end_Nicotinate-nucleotide_adenylyltransferase,_putative_572303..572453_POSITIVE 280 110 70 141 106 NC_009009:SSA_0318|3end_Secreted_metalloendopeptidase_Gcp_312791..312941_POSITIVE 275 116 85 135 101 NC_009009:SSA_1206|3end_A/G-specific_adenine_glycosylase,_putative_1230071..1230221_NEGATIVE 273 119 72 138 93 NC_009009:SSA_2098|3end_ABC-type_arginine/histidine_transporter,_permease_protein,_putative_2102931..2103081_NEGATIVE 272 116 71 106 47 NC_009009:SSA_1960|3end_hypothetical_protein_1956571..1956721_NEGATIVE 271 113 73 61 28 NC_009009:SSA_2347|3end_Coenzyme_F390_synthetase,_putative_2348647..2348797_NEGATIVE 270 117 71 57 8 NC_009009:SSA_0304|3end_Bacterial_cell_wall_degradation_(CHAP/LysM_domains),_putative_301888..302038_POSITIVE 269 121 82 85 43 NC_009009:SSA_1379|3end_hypothetical_protein_1398178..1398328_NEGATIVE 261 114 75 53 13 NC_009009:SSA_0554|3end_hypothetical_protein_549692..549842_POSITIVE 251 118 74 45 9 NC_009009:SSA_1722|3end_Thymidylate_kinase,_putative_1708025..1708175_NEGATIVE 251 103 70 85 55 NC_009009:SSA_0827|3end_Conserved_uncharacterized_cytosolic_protein,_putative_806952..807102_POSITIVE 250 113 75 150 110 NC_009009:SSA_0494|3end_ABC-type_dipeptide/oligopeptide/nickel_transport_system,_ATPase_component,_putative_495269..495419_POSITIVE 250 113 79 35 1 NC_009009:SSA_0331|3end_C3-degrading_proteinase,_putative_325992..326142_POSITIVE 249 117 76 140 92 NC_009009:SSA_0420|3end_Hydrolase,_HAD_superfamily,_putative_419632..419782_POSITIVE 246 126 83 148 103 NC_009009:SSA_2264|3end_hypothetical_protein_2261239..2261389_NEGATIVE 246 116 71 109 41 NC_009009:SSA_1797|3end_Aminodeoxychorismate_lyase,_putative_1778448..1778598_NEGATIVE 245 93 66 74 43 NC_009009:SSA_0886|3end_Enolase,_putative_881057..881207_POSITIVE 244 102 71 107 78 NC_009009:SSA_0966|3end_Uridine_kinase,_putative_975790..975940_POSITIVE 243 44 2 72 18 NC_009009:SSA_2218|3end_Glycosyltransferase_(cell_wall_biogenesis)_Cps9G,_putative_2219123..2219273_NEGATIVE