Origin IGS: cttttattccttaaattgtgcttctatcattttaccatatttgccctattttctctggattcgggtataactaagaggctcatacttctaccatcttatatcccttgtcacgcatctcgttaaaagacataaaaaatgcccagctaaactgggcgaaatgg .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ccatttcgcccagtttagctgggcattttttatgtcttttaacgagatgcgtgacaagggatataagatggtagaagtatgagcctcttagttatacccgaatccagagaaaatagggcaaatatggtaaaatgatagaagcacaatttaaggaataaaag Mask Tandem Repeat Region ================================================ cttttattccttaaattgtgcttctatcattttaccatatttgccctattttctctggattcgggtataactaagaggctcatacttctaccatcttatatcccttgtcacgcatctcgttaaaagacataaaaaatgcccagctaaactgggcgaaatgg Find is-nt database================================================ Query_seq: SSA_1356:SSA_1357|SSA_1356:SSA_1357:Helicase subunit of the DNA excision repair complex, subunit B, putative:hypothetical protein:<-<-:1372006..1372166 161 cttttattccttaaattgtgcttctatcattttaccatatttgccctattttctctggattcgggtataactaagaggctcatacttctaccatcttatatcccttgtcacgcatctcgttaaaagacataaaaaatgcccagctaaactgggcgaaatgg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1356:SSA_1357|SSA_1356:SSA_1357:Helicase subunit of the DNA excision repair complex, subunit B, putative:hypothetical protein:<-<-:1372006..1372166 161 cttttattccttaaattgtgcttctatcattttaccatatttgccctattttctctggattcgggtataactaagaggctcatacttctaccatcttatatcccttgtcacgcatctcgttaaaagacataaaaaatgcccagctaaactgggcgaaatgg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1356:SSA_1357|SSA_1356:SSA_1357:Helicase subunit of the DNA excision repair complex, subunit B, putative:hypothetical protein:<-<-:1372006..1372166 161 cttttattccttaaattgtgcttctatcattttaccatatttgccctattttctctggattcgggtataactaagaggctcatacttctaccatcttatatcccttgtcacgcatctcgttaaaagacataaaaaatgcccagctaaactgggcgaaatgg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 cttttattccttaaattgtgcttctatcattttaccatatttgccctattttctctggattcgggtataactaagaggctcatacttctaccatcttatatcccttgtcacgcatctcgttaaaagacataaaaaatgcccagctaaactgggcgaaatgg Predict ORF larger than 30AA ================================================ Protein_Len: 35 Strand: + Start: 16 End: 120 ............... M C F Y H F T I F A L F S L D S G I T K R L I L L P S Y I P C H A S R ......................................... cttttattccttaaattgtgcttctatcattttaccatatttgccctattttctctggattcgggtataactaagaggctcatacttctaccatcttatatcccttgtcacgcatctcgttaaaagacataaaaaatgcccagctaaactgggcgaaatgg 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================================================ cttttattccttaaattgtgcttctatcattttaccatatttgccctattttctctggattcgggtataactaagaggctcatacttctaccatcttatatcccttgtcacgcatctcgttaaaagacataaaaaatgcccagctaaactgggcgaaatgg Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_1356:SSA_1357|SSA_1356:SSA_1357:Helicase subunit of the DNA excision repair complex, subunit B, putative:hypothetical protein:<-<-:1372006..1372166 161 cttttattccttaaattgtgcttctatcattttaccatatttgccctattttctctggattcgggtataactaagaggctcatacttctaccatcttatatcccttgtcacgcatctcgttaaaagacataaaaaatgcccagctaaactgggcgaaatgg Intra-Species Hit: Count: 1 Min: 1 Max: 161 Len: 161 Subject: NC_009009_SSA_1356_SSA_1357|Helicase subunit of the DNA excision repair complex, subunit B, putative:hypothetical protein|NEGATIVE:NEGATIVE|[1372006,1372166]|161 HSP 1 e-value: 2.0E-86 bit: 319.0 Len: 161 Query Start:1 Query End:161 Subject Strand: POSITIVE Subject Start: 1 Subject End: 161 cttttattccttaaattgtgcttctatcattttaccatatttgccctattttctctggattcgggtataactaagaggctcatacttctaccatcttatatcccttgtcacgcatctcgttaaaagacataaaaaatgcccagctaaactgggcgaaatgg cttttattccttaaattgtgcttctatcattttaccatatttgccctattttctctggattcgggtataactaagaggctcatacttctaccatcttatatcccttgtcacgcatctcgttaaaagacataaaaaatgcccagctaaactgggcgaaatgg Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUUUUAUUCCUUAAAUUGUGCUUCUAUCAUUUUACCAUAUUUGCCCUAUUUUCUCUGGAUUCGGGUAUAACUAAGAGGCUCAUACUUCUACCAUCUUAUAUCCCUUGUCACGCAUCUCGUUAAAAGACAUAAAAAAUGCCCAGCUAAACUGGGCGAAAUGG ..................................((((.(((((((..(((...((((....((((((((...(((((......)))))......))))))))..(((((((.....))).....))))..........))))..)))..))))))))))) (-32.10) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CCAUUUCGCCCAGUUUAGCUGGGCAUUUUUUAUGUCUUUUAACGAGAUGCGUGACAAGGGAUAUAAGAUGGUAGAAGUAUGAGCCUCUUAGUUAUACCCGAAUCCAGAGAAAAUAGGGCAAAUAUGGUAAAAUGAUAGAAGCACAAUUUAAGGAAUAAAAG ((.....((((((.....))))))...(((((((((((((.(((.....)))...)))))))))))))...........((.((.(((..(((.((((.....((..(.....)..)).......)))).)))...))).)).))......))........ (-35.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 936 120 71 211 162 NC_009009:SSA_1356|5end_Helicase_subunit_of_the_DNA_excision_repair_complex,_subunit_B,_putative_1371915..1372145_NEGATIVE 309 120 75 197 153 NC_009009:SSA_0926|5end_Histone_acetyltransferase_HPA2,_putative_935465..935695_POSITIVE 291 109 62 200 146 NC_009009:SSA_1374|5end_Multidrug_ABC_transporter,_ATPase_and_permease_components,_putative_1393095..1393325_NEGATIVE 288 102 62 58 7 NC_009009:SSA_2323|5end_Transporter,_putative_2327604..2327834_POSITIVE 277 145 103 54 16 NC_009009:SSA_0502|5end_Peptide_ABC_transporter,_permease_protein,_putative_501554..501784_POSITIVE 275 120 73 141 74 NC_009009:SSA_0817|5end_Antirepressor_regulating_drug_resistance_(membrane-bound),_putative_797838..798068_POSITIVE 275 113 71 125 81 NC_009009:SSA_0085|5end_V-type_sodium_ATPase,_subunit_I,_putative_85750..85980_POSITIVE 274 75 34 226 186 NC_009009:SSA_0167|5end_Hypothetical_protein_(Asparagine/proline-rich)_165254..165484_POSITIVE 273 109 61 217 154 NC_009009:SSA_1345|5end_Bifunctional_pyrimidine_operon_transcriptional_attenuation_protein/uracil_phosphoribosyltransferase,_putative_1363879..1364109_NEGATIVE 271 109 63 121 74 NC_009009:SSA_0596|5end_hypothetical_protein_586913..587143_POSITIVE 269 114 71 202 153 NC_009009:SSA_0240|5end_Acetyltransferase,_GNAT_family,_putative_233410..233640_POSITIVE 269 90 43 66 17 NC_009009:SSA_0200|5end_Bifunctional_folate_synthesis_protein,_putative_198918..199148_POSITIVE 266 87 41 95 33 NC_009009:SSA_0576|5end_Conserved_GTPase,_putative_570039..570269_POSITIVE 264 89 49 144 95 NC_009009:SSA_2082|5end_Carbohydrate_kinase,_FGGY_family,_putative_2086874..2087104_NEGATIVE 263 118 74 52 8 NC_009009:SSA_2304|5end_Conserved_uncharacterized_protein_2306270..2306500_NEGATIVE 263 57 13 210 158 NC_009009:SSA_2260|5end_DNA_mismatch_repair_protein_hexA,_putative_2258150..2258380_NEGATIVE 263 118 74 64 8 NC_009009:SSA_1176|5end_Acetoin_dehydrogenase,_E1_component,_beta_subunit,_putative_1205405..1205635_NEGATIVE 263 48 19 87 54 NC_009009:SSA_1001|5end_Arabinose_(multiple_sugar_metabolism)_operon_transcriptional_regulator,_putative_1001689..1001919_NEGATIVE 263 120 75 102 49 NC_009009:SSA_0671|5end_Methylenetetrahydrofolate_dehydrogenase/methenyltetrahydrofolate_cyclohydrolase,_putative_654340..654570_POSITIVE 262 117 78 53 8 NC_009009:SSA_1769|5end_hypothetical_protein_1757490..1757720_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 309 120 75 146 102 NC_009009:SSA_0925|3end_ABC-type_antimicrobial_peptide_transport_system,_ATPase_component,_putative_935494..935644_POSITIVE 305 92 52 139 99 NC_009009:SSA_0826|3end_hypothetical_protein_805516..805666_POSITIVE 275 120 73 125 58 NC_009009:SSA_0816|3end_Copper_transport_operon_or_penicillinase_transcription_repressor,_putative_797902..798052_POSITIVE 275 113 71 135 91 NC_009009:SSA_0083|3end_hypothetical_protein_85840..85990_POSITIVE 271 109 63 111 64 NC_009009:SSA_0595|3end_hypothetical_protein_586983..587133_POSITIVE 270 89 44 121 81 NC_009009:SSA_0641|3end_hypothetical_protein_629427..629577_POSITIVE 266 87 41 92 30 NC_009009:SSA_0575|3end_Hydrolase,_HAD_superfamily,_putative_570116..570266_POSITIVE 265 154 112 41 2 NC_009009:SSA_0068|3end_Alcohol-acetaldehyde_dehydrogenase,_putative_72848..72998_POSITIVE 264 89 49 68 19 NC_009009:SSA_2083|3end_hypothetical_protein_2086950..2087100_NEGATIVE 264 89 44 78 20 NC_009009:SSA_0446|3end_hypothetical_protein_444764..444914_NEGATIVE 263 57 13 131 79 NC_009009:SSA_2261|3end_Transcriptional_repressor_(arginine_synthesis),_putative_2258229..2258379_NEGATIVE 262 117 78 59 14 NC_009009:SSA_1770|3end_hypothetical_protein_1757484..1757634_NEGATIVE 261 146 103 43 2 NC_009009:SSA_2094|3end_Conserved_uncharacterized_protein_2097990..2098140_NEGATIVE 261 119 71 142 105 NC_009009:SSA_1260|3end_Phosphopentomutase,_putative_1285752..1285902_NEGATIVE 261 66 24 150 108 NC_009009:SSA_1153|3end_HemK_protein,_putative_1182748..1182898_POSITIVE 261 75 40 38 2 NC_009009:SSA_0166|3end_hypothetical_protein_165146..165296_POSITIVE 256 146 101 74 23 NC_009009:SSA_0355|3end_DNA_mismatch_repair_protein,_putative_349260..349410_POSITIVE 252 65 21 151 103 NC_009009:SSA_0240|3end_Acetyltransferase,_GNAT_family,_putative_233960..234110_POSITIVE 251 154 111 78 28 NC_009009:SSA_1504|3end_hypothetical_protein_1506459..1506609_NEGATIVE 249 154 123 74 44 NC_009009:SSA_0192|3end_Acetate_kinase,_putative_194182..194332_POSITIVE