Origin IGS: gaaagtagagaatatctgctttttttgtcatttgaggcacaaattaggacatttgaggggatttctaccagcttgctcttacttcttctataatgataagagaagaatggagagaat .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 attctctccattcttctcttatcattatagaagaagtaagagcaagctggtagaaatcccctcaaatgtcctaatttgtgcctcaaatgacaaaaaaagcagatattctctactttc Mask Tandem Repeat Region ================================================ gaaagtagagaatatctgctttttttgtcatttgaggcacaaattaggacatttgaggggatttctaccagcttgctcttacttcttctataatgataagagaagaatggagagaat Find is-nt database================================================ Query_seq: SSA_0193:SSA_0195|SSA_0193:SSA_0195:CAAX amino terminal protease family protein, putative:hypothetical protein:->->:195136..195252 117 gaaagtagagaatatctgctttttttgtcatttgaggcacaaattaggacatttgaggggatttctaccagcttgctcttacttcttctataatgataagagaagaatggagagaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0193:SSA_0195|SSA_0193:SSA_0195:CAAX amino terminal protease family protein, putative:hypothetical protein:->->:195136..195252 117 gaaagtagagaatatctgctttttttgtcatttgaggcacaaattaggacatttgaggggatttctaccagcttgctcttacttcttctataatgataagagaagaatggagagaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0193:SSA_0195|SSA_0193:SSA_0195:CAAX amino terminal protease family protein, putative:hypothetical protein:->->:195136..195252 117 gaaagtagagaatatctgctttttttgtcatttgaggcacaaattaggacatttgaggggatttctaccagcttgctcttacttcttctataatgataagagaagaatggagagaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gaaagtagagaatatctgctttttttgtcatttgaggcacaaattaggacatttgaggggatttctaccagcttgctcttacttcttctataatgataagagaagaatggagagaat Predict ORF larger than 30AA ================================================ Protein_Len: 34 Strand: + Start: 14 End: 115 ............. M C F F C H L R H K L G H L R G F L P A C S Y F F Y N D K R R M E R .. gaaagtagagaatatctgctttttttgtcatttgaggcacaaattaggacatttgaggggatttctaccagcttgctcttacttcttctataatgataagagaagaatggagagaat 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================================================ gaaagtagagaatatctgctttttttgtcatttgaggcacaaattaggacatttgaggggatttctaccagcttgctcttacttcttctataatgataagagaagaatggagagaat Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_0193:SSA_0195|SSA_0193:SSA_0195:CAAX amino terminal protease family protein, putative:hypothetical protein:->->:195136..195252 117 gaaagtagagaatatctgctttttttgtcatttgaggcacaaattaggacatttgaggggatttctaccagcttgctcttacttcttctataatgataagagaagaatggagagaat Intra-Species Hit: Count: 1 Min: 1 Max: 117 Len: 117 Subject: NC_009009_SSA_0193_SSA_0195|CAAX amino terminal protease family protein, putative:hypothetical protein|POSITIVE:POSITIVE|[195136,195252]|117 HSP 1 e-value: 7.0E-48 bit: 190.0 Len: 117 Query Start:1 Query End:117 Subject Strand: POSITIVE Subject Start: 1 Subject End: 117 gaaagtagagaatatctgcnnnnnnngtcatttgaggcacaaattaggacatttgaggggatttctaccagcttgctcttacttcttctataatgataagagaagaatggagagaat gaaagtagagaatatctgctttttttgtcatttgaggcacaaattaggacatttgaggggatttctaccagcttgctcttacttcttctataatgataagagaagaatggagagaat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAAAGUAGAGAAUAUCUGCUUUUUUUGUCAUUUGAGGCACAAAUUAGGACAUUUGAGGGGAUUUCUACCAGCUUGCUCUUACUUCUUCUAUAAUGAUAAGAGAAGAAUGGAGAGAAU ....(((((((...(((.(((....(((((((((.....)))))...))))...))).)))))))))).......(((((..(((((((...........)))))))..)))))... (-28.00) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUUCUCUCCAUUCUUCUCUUAUCAUUAUAGAAGAAGUAAGAGCAAGCUGGUAGAAAUCCCCUCAAAUGUCCUAAUUUGUGCCUCAAAUGACAAAAAAAGCAGAUAUUCUCUACUUUC ...((((...(((((((..((....)).)))))))...))))......((((((.(((..((....((((...(((((.....))))))))).....))..)))....))))))... (-19.00) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 316 89 46 51 8 NC_009009:SSA_0576|5end_Conserved_GTPase,_putative_570039..570269_POSITIVE 285 75 36 182 131 NC_009009:SSA_1501|5end_Cytidylate_kinase,_putative_1505772..1506002_NEGATIVE 274 69 21 231 178 NC_009009:SSA_0281|5end_hypothetical_protein_273404..273634_POSITIVE 273 69 21 58 20 NC_009009:SSA_1906|5end_Diadenosine_tetraphosphate_(Ap4A)_hydrolase_(histidine_triad_protein,_cell-cycle_regulation),_putative_1900026..1900256_POSITIVE 271 106 68 177 142 NC_009009:SSA_2252|5end_hypothetical_protein_2248649..2248879_NEGATIVE 268 75 44 230 192 NC_009009:SSA_1839|5end_Cysteine_synthase,_putative_1832976..1833206_POSITIVE 265 59 11 186 139 NC_009009:SSA_2148|5end_Alkaline_shock_stress_response_protein,_putative_2150039..2150269_NEGATIVE 264 77 31 179 137 NC_009009:SSA_1398|5end_Membrane_protein,_hemolysin_III-like,_putative_1410881..1411111_POSITIVE 263 79 46 198 154 NC_009009:SSA_0238|5end_hypothetical_protein_232481..232711_POSITIVE 260 72 31 226 180 NC_009009:SSA_0977|5end_3-isopropylmalate_dehydrogenase,_putative_982771..983001_POSITIVE 259 106 61 169 135 NC_009009:SSA_2157|5end_ATP-dependent_serine_protease,_putative_2158241..2158471_NEGATIVE 255 87 42 118 65 NC_009009:SSA_0327|5end_Glycosyltransferase,_putative_319979..320209_POSITIVE 251 50 1 66 15 NC_009009:SSA_2055|5end_hypothetical_protein_2058160..2058390_NEGATIVE 251 50 17 64 34 NC_009009:SSA_0035|5end_Bifunctional_purine_biosynthesis_protein_purH,_putative_40315..40545_POSITIVE 250 77 36 205 164 NC_009009:SSA_0432|5end_Formate--tetrahydrofolate_ligase,_putative_434991..435221_NEGATIVE 248 98 52 195 159 NC_009009:SSA_0504|5end_Peptide_ABC_transporter,_ATP-binding_protein,_putative_503009..503239_POSITIVE 246 110 69 184 139 NC_009009:SSA_2237|5end_Dihydrofolate:folylpolyglutamate_synthetase,_putative_2236740..2236970_NEGATIVE 246 85 45 98 61 NC_009009:SSA_1342|5end_Carbamoyl-phosphate_synthase_small_chain,_putative_1361017..1361247_NEGATIVE 243 89 44 192 131 NC_009009:SSA_1154|5end_hypothetical_protein_1182661..1182891_POSITIVE 240 88 47 160 123 NC_009009:SSA_0259|5end_Thiol_peroxidase,_putative_253543..253773_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 316 89 46 48 5 NC_009009:SSA_0575|3end_Hydrolase,_HAD_superfamily,_putative_570116..570266_POSITIVE 302 56 16 45 2 NC_009009:SSA_1092|3end_Dihydrofolate_reductase,_putative_1110191..1110341_POSITIVE 300 88 44 142 91 NC_009009:SSA_1837|3end_hypothetical_protein_1832955..1833105_POSITIVE 291 70 21 118 64 NC_009009:SSA_0279|3end_Sugar-binding_transcriptional_repressor_(DeoR),_putative_273370..273520_POSITIVE 260 72 31 144 98 NC_009009:SSA_0975|3end_2-isopropylmalate_synthase,_putative_982769..982919_POSITIVE 253 100 51 128 76 NC_009009:SSA_1314|3end_Fe-S-cluster_oxidoreductase,_putative_1330746..1330896_NEGATIVE 251 50 17 60 30 NC_009009:SSA_0034|3end_hypothetical_protein_40391..40541_POSITIVE 246 85 45 73 36 NC_009009:SSA_1343|3end_Aspartate_carbamoyltransferase,_putative_1361042..1361192_NEGATIVE 246 48 1 75 26 NC_009009:SSA_0683|3end_DNA-binding_protein_HU,_putative_664739..664889_POSITIVE 245 80 35 117 87 NC_009009:SSA_0272|3end_Oxidoreductase,_aldo/keto_reductase_family,_putative_267032..267182_POSITIVE 240 89 43 58 12 NC_009009:SSA_0949|3end_hypothetical_protein_956395..956545_POSITIVE 240 88 47 47 10 NC_009009:SSA_0260|3end_Manganese/Zinc_ABC_transporter_substrate-binding_lipoprotein_precursor,_putative_253656..253806_NEGATIVE 238 87 44 66 18 NC_009009:SSA_2361|3end_L-serine_dehydratase_beta_subunit_2364779..2364929_POSITIVE 238 84 44 134 101 NC_009009:SSA_0507|3end_hypothetical_protein_506442..506592_POSITIVE 236 80 33 64 25 NC_009009:SSA_0703|3end_Citrate_synthase,_putative_689352..689502_POSITIVE 235 80 34 79 36 NC_009009:SSA_1788|3end_Integral_membrane_protein,_possible_receptor,_putative_1771656..1771806_NEGATIVE 235 78 34 58 15 NC_009009:SSA_0795|3end_hypothetical_protein_777065..777215_POSITIVE 234 96 58 97 56 NC_009009:SSA_0484|3end_Glutamyl-tRNA_reductase,_putative_485825..485975_POSITIVE 234 93 60 55 22 NC_009009:SSA_0028|3end_Phosphoribosylaminoimidazole-succinocarboxamide_synthase,_putative_32670..32820_POSITIVE 233 83 55 87 59 NC_009009:SSA_0901|3end_Alpha-acetolactate_decarboxylase,_putative_893246..893396_POSITIVE