Origin IGS: agctctattataccaaacaccgagactttaagccatttttaaaggcaagagaaggacgttttactgaaaaatgacctgaataaaggtcagatcattttatttctattcggt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 accgaatagaaataaaatgatctgacctttattcaggtcatttttcagtaaaacgtccttctcttgcctttaaaaatggcttaaagtctcggtgtttggtataatagagct Mask Tandem Repeat Region ================================================ agctctattataccaaacaccgagactttaagccatttttaaaggcaagagaaggacgttttactgaaaaatgacctgaataaaggtcagatcattttatttctattcggt Find is-nt database================================================ Query_seq: SSA_1239:SSA_1240|SSA_1239:SSA_1240:hypothetical protein:Orotate phosphoribosyltransferase, putative:<-<-:1264780..1264890 111 agctctattataccaaacaccgagactttaagccatttttaaaggcaagagaaggacgttttactgaaaaatgacctgaataaaggtcagatcattttatttctattcggt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1239:SSA_1240|SSA_1239:SSA_1240:hypothetical protein:Orotate phosphoribosyltransferase, putative:<-<-:1264780..1264890 111 agctctattataccaaacaccgagactttaagccatttttaaaggcaagagaaggacgttttactgaaaaatgacctgaataaaggtcagatcattttatttctattcggt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1239:SSA_1240|SSA_1239:SSA_1240:hypothetical protein:Orotate phosphoribosyltransferase, putative:<-<-:1264780..1264890 111 agctctattataccaaacaccgagactttaagccatttttaaaggcaagagaaggacgttttactgaaaaatgacctgaataaaggtcagatcattttatttctattcggt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 agctctattataccaaacaccgagactttaagccatttttaaaggcaagagaaggacgttttactgaaaaatgacctgaataaaggtcagatcattttatttctattcggt Predict ORF larger than 30AA ================================================ agctctattataccaaacaccgagactttaagccatttttaaaggcaagagaaggacgttttactgaaaaatgacctgaataaaggtcagatcattttatttctattcggt 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================================================ agctctattataccaaacaccgagactttaagccatttttaaaggcaagagaaggacgttttactgaaaaatgacctgaataaaggtcagatcattttatttctattcggt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_1239:SSA_1240|SSA_1239:SSA_1240:hypothetical protein:Orotate phosphoribosyltransferase, putative:<-<-:1264780..1264890 111 agctctattataccaaacaccgagactttaagccatttttaaaggcaagagaaggacgttttactgaaaaatgacctgaataaaggtcagatcattttatttctattcggt Intra-Species Hit: Count: 1 Min: 1 Max: 111 Len: 111 Subject: NC_009009_SSA_1239_SSA_1240|hypothetical protein:Orotate phosphoribosyltransferase, putative|NEGATIVE:NEGATIVE|[1264780,1264890]|111 HSP 1 e-value: 7.0E-57 bit: 220.0 Len: 111 Query Start:1 Query End:111 Subject Strand: POSITIVE Subject Start: 1 Subject End: 111 agctctattataccaaacaccgagactttaagccatttttaaaggcaagagaaggacgttttactgaaaaatgacctgaataaaggtcagatcattttatttctattcggt agctctattataccaaacaccgagactttaagccatttttaaaggcaagagaaggacgttttactgaaaaatgacctgaataaaggtcagatcattttatttctattcggt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGCUCUAUUAUACCAAACACCGAGACUUUAAGCCAUUUUUAAAGGCAAGAGAAGGACGUUUUACUGAAAAAUGACCUGAAUAAAGGUCAGAUCAUUUUAUUUCUAUUCGGU ..................(((((..((((..(((.........))).))))..(((.((.....(((....((((((......))))))..)))....)).)))..))))) (-20.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACCGAAUAGAAAUAAAAUGAUCUGACCUUUAUUCAGGUCAUUUUUCAGUAAAACGUCCUUCUCUUGCCUUUAAAAAUGGCUUAAAGUCUCGGUGUUUGGUAUAAUAGAGCU ((((((((.....((((((((((((.......)))))))))))).........((..(((.....(((.........)))...)))...)).))))))))........... (-23.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 868 60 11 151 102 NC_009009:SSA_1239|5end_hypothetical_protein_1264689..1264919_NEGATIVE 289 78 31 191 144 NC_009009:SSA_1748|5end_Inorganic_pyrophosphatase/exopolyphosphatase,_putative_1734478..1734708_NEGATIVE 280 60 20 204 163 NC_009009:SSA_0569|5end_Aspartyl/glutamyl-tRNA(Asn/Gln)_amidotransferase_subunit_C,_putative_563613..563843_POSITIVE 272 59 13 231 187 NC_009009:SSA_0293|5end_hypothetical_protein_287613..287843_NEGATIVE 257 64 21 155 113 NC_009009:SSA_1459|5end_RNA_methyltransferase,_putative_1467481..1467711_NEGATIVE 250 70 21 217 164 NC_009009:SSA_1804|5end_NADPH-flavin_oxidoreductase,_putative_1788668..1788898_NEGATIVE 243 90 49 142 112 NC_009009:SSA_0920|5end_hypothetical_protein_930896..931126_POSITIVE 242 52 12 52 9 NC_009009:SSA_1621|5end_Amino_acid_transporter,_putative_1624623..1624853_NEGATIVE 241 50 3 162 115 NC_009009:SSA_2184|5end_hypothetical_protein_2183754..2183984_NEGATIVE 240 88 45 56 13 NC_009009:SSA_2205|5end_Transcription_antitermination_factor_NusG,_putative_2206100..2206330_NEGATIVE 239 89 43 158 106 NC_009009:SSA_2097|5end_Amino_acid_ABC_transporter,_ATP-binding_protein,_putative_2102918..2103148_NEGATIVE 236 48 3 187 141 NC_009009:SSA_0373|5end_Dihydroorotate_dehydrogenase,_putative_362062..362292_POSITIVE 234 103 75 231 198 NC_009009:SSA_2012|5end_hypothetical_protein_2013470..2013700_NEGATIVE 233 46 13 203 172 NC_009009:SSA_1655|5end_hypothetical_protein_1651816..1652046_NEGATIVE 229 110 65 183 135 NC_009009:SSA_0894|5end_ATP-binding_cassette_protein,_putative_885779..886009_POSITIVE 229 36 1 215 180 NC_009009:SSA_0773|5end_PTS_enzyme_I,_putative_752603..752833_POSITIVE 227 79 32 84 32 NC_009009:SSA_1673|5end_hypothetical_protein_1670353..1670583_POSITIVE 225 75 32 188 150 NC_009009:SSA_1017|5end_hypothetical_protein_1022072..1022302_POSITIVE 224 49 1 70 23 NC_009009:SSA_2202|5end_Elongation_factor_Ts,_putative_2203350..2203580_NEGATIVE 224 67 26 225 184 NC_009009:SSA_1759|5end_hypothetical_protein_1746969..1747199_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 310 58 13 82 28 NC_009009:SSA_0294|3end_hypothetical_protein_287772..287922_NEGATIVE 289 78 31 52 5 NC_009009:SSA_1749|3end_Pyruvate_formate-lyase-activating_enzyme,_putative_1734617..1734767_NEGATIVE 257 64 21 70 28 NC_009009:SSA_1460|3end_Transcriptional_attenuator_LytR,_putative_1467566..1467716_NEGATIVE 243 90 49 111 81 NC_009009:SSA_0918|3end_Conserved_uncharacterized_protein_930945..931095_POSITIVE 243 46 1 68 8 NC_009009:SSA_0766|3end_hypothetical_protein_746975..747125_POSITIVE 239 89 43 145 93 NC_009009:SSA_2098|3end_ABC-type_arginine/histidine_transporter,_permease_protein,_putative_2102931..2103081_NEGATIVE 236 60 13 73 14 NC_009009:SSA_0903|3end_NAD(P)H_dehydrogenase_(quinone),_putative_893813..893963_POSITIVE 233 46 13 139 108 NC_009009:SSA_1656|3end_Nisin_resistance_protein,_putative_1651880..1652030_NEGATIVE 224 67 26 68 27 NC_009009:SSA_1760|3end_hypothetical_protein_1747126..1747276_NEGATIVE 223 54 19 41 10 NC_009009:SSA_0083|3end_hypothetical_protein_85840..85990_POSITIVE 218 62 26 113 78 NC_009009:SSA_2174|3end_2,3,4,5-tetrahydropyridine-2-carboxylate_N-succinyltransferase,_putative_2171991..2172141_NEGATIVE 217 48 1 85 35 NC_009009:SSA_1436|3end_hypothetical_protein_1442199..1442349_NEGATIVE 216 60 15 74 21 NC_009009:SSA_1731|3end_ATP-dependent_Clp_protease,_proteolytic_subunit,_putative_1716218..1716368_NEGATIVE 213 89 41 49 1 NC_009009:SSA_0842|3end_Effector_of_murein_hydrolase_LrgA/holin-like_protein,_putative_827790..827940_POSITIVE 212 104 62 143 98 NC_009009:SSA_1579|3end_ABC-type_Fe3+-siderophore_transport_system,_ATPase_component,_putative_1583686..1583836_POSITIVE 210 59 13 82 35 NC_009009:SSA_0832|3end_SecY-like_protein,_putative_818011..818161_POSITIVE 209 90 41 149 104 NC_009009:SSA_2269|3end_hypothetical_protein_2269392..2269542_NEGATIVE 209 57 20 42 1 NC_009009:SSA_0242|3end_hypothetical_protein_235810..235960_POSITIVE 207 48 4 61 11 NC_009009:SSA_1682|3end_hypothetical_protein_1676130..1676280_NEGATIVE 203 46 1 81 27 NC_009009:SSA_1930|3end_Acetyl-CoA_carboxylase_alpha_subunit,_putative_1917777..1917927_NEGATIVE