Origin IGS: gaaattagtctaaaagtcttgtcaaatcaatcagaatttgataaactatcaaagtaactaatctatggctcgcaaagagaccatggcagaaaggaaatttttgtaaa .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tttacaaaaatttcctttctgccatggtctctttgcgagccatagattagttactttgatagtttatcaaattctgattgatttgacaagacttttagactaatttc Mask Tandem Repeat Region ================================================ gaaattagtctaaaagtcttgtcaaatcaatcagaatttgataaactatcaaagtaactaatctatggctcgcaaagagaccatggcagaaaggaaatttttgtaaa Find is-nt database================================================ Query_seq: SSA_1271:SSA_1272|SSA_1271:SSA_1272:Conserved uncharacterized protein:50S ribosomal protein L31 type B, putative:->->:1295048..1295154 107 gaaattagtctaaaagtcttgtcaaatcaatcagaatttgataaactatcaaagtaactaatctatggctcgcaaagagaccatggcagaaaggaaatttttgtaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1271:SSA_1272|SSA_1271:SSA_1272:Conserved uncharacterized protein:50S ribosomal protein L31 type B, putative:->->:1295048..1295154 107 gaaattagtctaaaagtcttgtcaaatcaatcagaatttgataaactatcaaagtaactaatctatggctcgcaaagagaccatggcagaaaggaaatttttgtaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1271:SSA_1272|SSA_1271:SSA_1272:Conserved uncharacterized protein:50S ribosomal protein L31 type B, putative:->->:1295048..1295154 107 gaaattagtctaaaagtcttgtcaaatcaatcagaatttgataaactatcaaagtaactaatctatggctcgcaaagagaccatggcagaaaggaaatttttgtaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gaaattagtctaaaagtcttgtcaaatcaatcagaatttgataaactatcaaagtaactaatctatggctcgcaaagagaccatggcagaaaggaaatttttgtaaa Predict ORF larger than 30AA ================================================ gaaattagtctaaaagtcttgtcaaatcaatcagaatttgataaactatcaaagtaactaatctatggctcgcaaagagaccatggcagaaaggaaatttttgtaaa Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ PromScan Matrix: RpoD-17 Strand: + Score: 85 Start: 18 End: 47 .................CTTGTCAAATCAATCAGAATTTGATAAACT............................................................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gaaattagtctaaaagtcttgtcaaatcaatcagaatttgataaactatcaaagtaactaatctatggctcgcaaagagaccatggcagaaaggaaatttttgtaaa Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_1271:SSA_1272|SSA_1271:SSA_1272:Conserved uncharacterized protein:50S ribosomal protein L31 type B, putative:->->:1295048..1295154 107 gaaattagtctaaaagtcttgtcaaatcaatcagaatttgataaactatcaaagtaactaatctatggctcgcaaagagaccatggcagaaaggaaatttttgtaaa Intra-Species Hit: Count: 1 Min: 1 Max: 107 Len: 107 Subject: NC_009009_SSA_1271_SSA_1272|Conserved uncharacterized protein:50S ribosomal protein L31 type B, putative|POSITIVE:POSITIVE|[1295048,1295154]|107 HSP 1 e-value: 2.0E-54 bit: 212.0 Len: 107 Query Start:1 Query End:107 Subject Strand: POSITIVE Subject Start: 1 Subject End: 107 gaaattagtctaaaagtcttgtcaaatcaatcagaatttgataaactatcaaagtaactaatctatggctcgcaaagagaccatggcagaaaggaaatttttgtaaa gaaattagtctaaaagtcttgtcaaatcaatcagaatttgataaactatcaaagtaactaatctatggctcgcaaagagaccatggcagaaaggaaatttttgtaaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAAAUUAGUCUAAAAGUCUUGUCAAAUCAAUCAGAAUUUGAUAAACUAUCAAAGUAACUAAUCUAUGGCUCGCAAAGAGACCAUGGCAGAAAGGAAAUUUUUGUAAA ...((((((((...(((.(((((((((........)))))))))))).....))..))))))(((((((((.....))).))))))((((((.....)))))).... (-20.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUACAAAAAUUUCCUUUCUGCCAUGGUCUCUUUGCGAGCCAUAGAUUAGUUACUUUGAUAGUUUAUCAAAUUCUGAUUGAUUUGACAAGACUUUUAGACUAAUUUC .......................((((.(((.....))))))).((((((((....(((.(((((.(((((((......)))))))..))))).))))))))))).. (-18.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 368 95 66 61 30 NC_009009:SSA_0036|5end_Secreted_protein,_possible_function_in_cell-wall_metabolism_(amidase),_putative_43999..44229_NEGATIVE 298 89 45 210 159 NC_009009:SSA_1665|5end_hypothetical_protein_1665353..1665583_NEGATIVE 274 98 51 67 19 NC_009009:SSA_0458|5end_Formylmethionine_deformylase,_putative_461609..461839_POSITIVE 271 100 51 196 140 NC_009009:SSA_0342|5end_Pyruvate_formate-lyase,_putative_337206..337436_NEGATIVE 270 80 31 230 172 NC_009009:SSA_2175|5end_hypothetical_protein_2174042..2174272_NEGATIVE 264 95 63 162 123 NC_009009:SSA_0307|5end_Glutamine_synthetase_type_1,_putative_302987..303217_POSITIVE 262 91 54 209 162 NC_009009:SSA_1904|5end_ABC-type_multidrug_transport_system,_permease_component,_putative_1899279..1899509_NEGATIVE 257 86 52 165 123 NC_009009:SSA_0063|5end_Holliday_junction_DNA_helicase_ruvB,_putative_65335..65565_POSITIVE 254 93 57 134 83 NC_009009:SSA_0299|5end_hypothetical_protein_292759..292989_POSITIVE 252 94 67 226 197 NC_009009:SSA_0271|5end_Glycosylhydrolase,_family_35,_putative_264235..264465_POSITIVE 249 88 57 71 44 NC_009009:SSA_0188|5end_hypothetical_protein_190798..191028_POSITIVE 243 100 51 177 114 NC_009009:SSA_0238|5end_hypothetical_protein_232481..232711_POSITIVE 237 94 62 189 154 NC_009009:SSA_0776|5end_Glucose-1-phosphate_adenylyltransferase,_putative_758298..758528_POSITIVE 235 92 57 185 142 NC_009009:SSA_2279|5end_hypothetical_protein_2281910..2282140_NEGATIVE 231 69 21 70 15 NC_009009:SSA_1669|5end_hypothetical_protein_1668442..1668672_NEGATIVE 228 94 61 157 126 NC_009009:SSA_2340|5end_hypothetical_protein_2342843..2343073_NEGATIVE 228 40 8 147 119 NC_009009:SSA_0760|5end_Acetylornithine_aminotransferase,_putative_742581..742811_POSITIVE 223 59 17 102 58 NC_009009:SSA_1683|5end_NrdI_protein,_putative_1677405..1677635_NEGATIVE 221 88 57 51 20 NC_009009:SSA_0319|5end_Branched-chain_amino_acid_permease_(L-methionine,_L-isoleucine,_leucine_and_valine),_putative_312721..312951_POSITIVE 216 94 65 52 21 NC_009009:SSA_1015|5end_4-hydroxybenzoate_octaprenyltransferase,_putative_1018703..1018933_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 264 95 63 130 91 NC_009009:SSA_0306|3end_Transcription_regulator_(glutamine_synthetase_repressor),_putative_303035..303185_POSITIVE 249 88 57 45 18 NC_009009:SSA_0187|3end_Competence_protein_ComYD,_putative_190852..191002_POSITIVE 233 92 61 145 110 NC_009009:SSA_1927|3end_Exfoliative_toxin,_putative_1914956..1915106_NEGATIVE 228 40 8 144 116 NC_009009:SSA_0759|3end_Acetylglutamate_kinase,_putative_742658..742808_POSITIVE 224 94 65 74 39 NC_009009:SSA_0921|3end_Zn-dependeant_threonine_dehydrogenase,_putative_932164..932314_POSITIVE 223 59 17 81 37 NC_009009:SSA_1684|3end_Histidine_kinase,_putative_1677426..1677576_NEGATIVE 221 88 57 41 10 NC_009009:SSA_0318|3end_Secreted_metalloendopeptidase_Gcp_312791..312941_POSITIVE 217 94 57 140 93 NC_009009:SSA_1314|3end_Fe-S-cluster_oxidoreductase,_putative_1330746..1330896_NEGATIVE 217 86 61 121 93 NC_009009:SSA_0860|3end_N-acetylmuramidase/lysin,_putative_851738..851888_POSITIVE 216 94 65 67 36 NC_009009:SSA_1014|3end_Phosphatidylserine_decarboxylase_proenzyme_2,_putative_1018798..1018948_POSITIVE 214 96 67 55 26 NC_009009:SSA_1763|3end_ABC-type_molybdenum_transport_system,_ATPase_component,_putative_1750951..1751101_POSITIVE 214 89 46 151 96 NC_009009:SSA_1691|3end_Transcriptional_regulator,_XRE_family,_putative_1683570..1683720_POSITIVE 211 87 57 131 97 NC_009009:SSA_0606|3end_ABC-type_antimicrobial_peptide_transport_system,_ATPase_component,_putative_593789..593939_NEGATIVE 210 83 47 120 89 NC_009009:SSA_0398|3end_hypothetical_protein_394674..394824_NEGATIVE 209 92 68 38 4 NC_009009:SSA_0490|3end_Cobalamin_5'-phosphate_synthase,_putative_491044..491194_POSITIVE 208 94 58 85 44 NC_009009:SSA_1938|3end_Enoyl-acyl_carrier_protein(ACP)_reductase,_putative_1924764..1924914_NEGATIVE 208 93 61 132 89 NC_009009:SSA_1933|3end_(3R)-hydroxymyristoyl-[acyl_carrier_protein]_dehydratase,_putative_1920893..1921043_NEGATIVE 206 97 67 86 45 NC_009009:SSA_0673|3end_hypothetical_protein_656994..657144_POSITIVE 205 94 58 58 7 NC_009009:SSA_0805|3end_Collagen-binding_surface_protein,_putative_789232..789382_POSITIVE 204 90 47 71 19 NC_009009:SSA_1282|3end_Dipeptidase_V,_putative_1302246..1302396_NEGATIVE