Origin IGS: tcggttctgattagcttcttttttgttaaataaattcaaaatattctaatattaaccatgtactgattttattttaaaaaataaatattcacaaaaataatataatgcataaaatattcaaagaaaacgctttaaagaagaatattataaaaatagaaatagaaaaaagcaaaggatttgacatttgcaatgtaggctttttcttgaaagcggtagcattaaatgctagaatagtacatgtaaacgggcttagaaaaacctaaaccgcaaagaaaaaggaggatagtag .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9 ctactatcctcctttttctttgcggtttaggtttttctaagcccgtttacatgtactattctagcatttaatgctaccgctttcaagaaaaagcctacattgcaaatgtcaaatcctttgcttttttctatttctatttttataatattcttctttaaagcgttttctttgaatattttatgcattatattatttttgtgaatatttattttttaaaataaaatcagtacatggttaatattagaatattttgaatttatttaacaaaaaagaagctaatcagaaccga Mask Tandem Repeat Region ================================================ tcggttctgattagcttcttttttgttaaataaattcaaaatattctaatattaaccatgtactgattttattttaaaaaataaatattcacaaaaataatataatgcataaaatattcaaagaaaacgctttaaagaagaatattataaaaatagaaatagaaaaaagcaaaggatttgacatttgcaatgtaggctttttcttgaaagcggtagcattaaatgctagaatagtacatgtaaacgggcttagaaaaacctaaaccgcaaagaaaaaggaggatagtag Find is-nt database================================================ Query_seq: SSA_0736:SSA_0737|SSA_0736:SSA_0737:Catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases, putative:Arginine deiminase, putative:->->:718475..718763 289 tcggttctgattagcttcttttttgttaaataaattcaaaatattctaatattaaccatgtactgattttattttaaaaaataaatattcacaaaaataatataatgcataaaatattcaaagaaaacgctttaaagaagaatattataaaaatagaaatagaaaaaagcaaaggatttgacatttgcaatgtaggctttttcttgaaagcggtagcattaaatgctagaatagtacatgtaaacgggcttagaaaaacctaaaccgcaaagaaaaaggaggatagtag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0736:SSA_0737|SSA_0736:SSA_0737:Catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases, putative:Arginine deiminase, putative:->->:718475..718763 289 tcggttctgattagcttcttttttgttaaataaattcaaaatattctaatattaaccatgtactgattttattttaaaaaataaatattcacaaaaataatataatgcataaaatattcaaagaaaacgctttaaagaagaatattataaaaatagaaatagaaaaaagcaaaggatttgacatttgcaatgtaggctttttcttgaaagcggtagcattaaatgctagaatagtacatgtaaacgggcttagaaaaacctaaaccgcaaagaaaaaggaggatagtag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0736:SSA_0737|SSA_0736:SSA_0737:Catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases, putative:Arginine deiminase, putative:->->:718475..718763 289 tcggttctgattagcttcttttttgttaaataaattcaaaatattctaatattaaccatgtactgattttattttaaaaaataaatattcacaaaaataatataatgcataaaatattcaaagaaaacgctttaaagaagaatattataaaaatagaaatagaaaaaagcaaaggatttgacatttgcaatgtaggctttttcttgaaagcggtagcattaaatgctagaatagtacatgtaaacgggcttagaaaaacctaaaccgcaaagaaaaaggaggatagtag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tcggttctgattagcttcttttttgttaaataaattcaaaatattctaatattaaccatgtactgattttattttaaaaaataaatattcacaaaaataatataatgcataaaatattcaaagaaaacgctttaaagaagaatattataaaaatagaaatagaaaaaagcaaaggatttgacatttgcaatgtaggctttttcttgaaagcggtagcattaaatgctagaatagtacatgtaaacgggcttagaaaaacctaaaccgcaaagaaaaaggaggatagtag Predict ORF larger than 30AA ================================================ Protein_Len: 60 Strand: + Start: 81 End: 260 ................................................................................ M N I H K N N I M H K I F K E N A L K K N I I K I E I E K S K G F D I C N V G F F L K A V A L N A R I V H V N G L R K T ............................. Protein_Len: 47 Strand: - Start: 92 End: 232 ........................................................................................... L F L I I C L I N L S F A K F F F I I F I S I S F L L P N S M Q L T P K K K F A T A N F A L M ......................................................... tcggttctgattagcttcttttttgttaaataaattcaaaatattctaatattaaccatgtactgattttattttaaaaaataaatattcacaaaaataatataatgcataaaatattcaaagaaaacgctttaaagaagaatattataaaaatagaaatagaaaaaagcaaaggatttgacatttgcaatgtaggctttttcttgaaagcggtagcattaaatgctagaatagtacatgtaaacgggcttagaaaaacctaaaccgcaaagaaaaaggaggatagtag 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: 86 Start: 144 End: 173 ...............................................................................................................................................TTTGCTTTTTTCTATTTCTATTTTTATAAT.................................................................................................................... PromScan Matrix: RpoD-17 Strand: + Score: 86 Start: 203 End: 232 ..........................................................................................................................................................................................................CTTGAAAGCGGTAGCATTAAATGCTAGAAT......................................................... PromScan Matrix: RpoD-17 Strand: - Score: 82 Start: 66 End: 95 .................................................................TTTGTGAATATTTATTTTTTAAAATAAAAT.................................................................................................................................................................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tcggttctgattagcttcttttttgttaaataaattcaaaatattctaatattaaccatgtactgattttattttaaaaaataaatattcacaaaaataatataatgcataaaatattcaaagaaaacgctttaaagaagaatattataaaaatagaaatagaaaaaagcaaaggatttgacatttgcaatgtaggctttttcttgaaagcggtagcattaaatgctagaatagtacatgtaaacgggcttagaaaaacctaaaccgcaaagaaaaaggaggatagtag Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 69 HP_score: -2.1 Tail_Score: -5.59879 Start: 169 End: 188 Full_Region: gaaaaagcctacatt gcaaatg tcaaat cctttgc ttttttctatttcta ........................................................................................................................................................................gcaaatgtcaaatcctttgc..................................................................................................... Find igs database================================================ Query_seq: SSA_0736:SSA_0737|SSA_0736:SSA_0737:Catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases, putative:Arginine deiminase, putative:->->:718475..718763 289 tcggttctgattagcttcttttttgttaaataaattcaaaatattctaatattaaccatgtactgattttattttaaaaaataaatattcacaaaaataatataatgcataaaatattcaaagaaaacgctttaaagaagaatattataaaaatagaaatagaaaaaagcaaaggatttgacatttgcaatgtaggctttttcttgaaagcggtagcattaaatgctagaatagtacatgtaaacgggcttagaaaaacctaaaccgcaaagaaaaaggaggatagtag Intra-Species Hit: Count: 1 Min: 1 Max: 289 Len: 289 Subject: NC_009009_SSA_0736_SSA_0737|Catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases, putative:Arginine deiminase, putative|POSITIVE:POSITIVE|[718475,718763]|289 HSP 1 e-value: 8.0E-59 bit: 228.0 Len: 115 Query Start:175 Query End:289 Subject Strand: POSITIVE Subject Start: 175 Subject End: 289 ..............................................................................................................................................................................gatttgacatttgcaatgtaggctttttcttgaaagcggtagcattaaatgctagaatagtacatgtaaacgggcttagaaaaacctaaaccgcaaagaaaaaggaggatagtag ..............................................................................................................................................................................gatttgacatttgcaatgtaggctttttcttgaaagcggtagcattaaatgctagaatagtacatgtaaacgggcttagaaaaacctaaaccgcaaagaaaaaggaggatagtag HSP 2 e-value: 2.0E-34 bit: 147.0 Len: 74 Query Start:1 Query End:74 Subject Strand: POSITIVE Subject Start: 1 Subject End: 74 tcggttctgattagcttcttttttgttaaataaattcaaaatattctaatattaaccatgtactgattttattt....................................................................................................................................................................................................................... tcggttctgattagcttcttttttgttaaataaattcaaaatattctaatattaaccatgtactgattttattt....................................................................................................................................................................................................................... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCGGUUCUGAUUAGCUUCUUUUUUGUUAAAUAAAUUCAAAAUAUUCUAAUAUUAACCAUGUACUGAUUUUAUUUUAAAAAAUAAAUAUUCACAAAAAUAAUAUAAUGCAUAAAAUAUUCAAAGAAAACGCUUUAAAGAAGAAUAUUAUAAAAAUAGAAAUAGAAAAAAGCAAAGGAUUUGACAUUUGCAAUGUAGGCUUUUUCUUGAAAGCGGUAGCAUUAAAUGCUAGAAUAGUACAUGUAAACGGGCUUAGAAAAACCUAAACCGCAAAGAAAAAGGAGGAUAGUAG .........((((.((((((((((.((.............................(((((((((..(((((((....))))))).................((((((........(((...)))..((((((.((((((((..(((((....((....)).......((((((.......).)))))..)))))..)))))))).))))))...))))))..........)))))))))....(((..((((......)))).)))..)).)))))))))).)))).. (-54.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUACUAUCCUCCUUUUUCUUUGCGGUUUAGGUUUUUCUAAGCCCGUUUACAUGUACUAUUCUAGCAUUUAAUGCUACCGCUUUCAAGAAAAAGCCUACAUUGCAAAUGUCAAAUCCUUUGCUUUUUUCUAUUUCUAUUUUUAUAAUAUUCUUCUUUAAAGCGUUUUCUUUGAAUAUUUUAUGCAUUAUAUUAUUUUUGUGAAUAUUUAUUUUUUAAAAUAAAAUCAGUACAUGGUUAAUAUUAGAAUAUUUUGAAUUUAUUUAACAAAAAAGAAGCUAAUCAGAACCGA ..................((((((((.(((((((((((((((..((........)).....((((((...))))))..))))...)).))))))))).)))))))).............((((((((.......((..((((.((((((((..(((((((......))))))).............((((((....((((....(((((((....))))))).....))))....)))))).)))))))).))))..)).........))))))))............. (-45.39) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 301 280 245 51 15 NC_009009:SSA_0213|5end_hypothetical_protein_210135..210365_NEGATIVE 296 249 202 183 144 NC_009009:SSA_2093|5end_PTS_system,_membrane_component,_putative_2097462..2097692_NEGATIVE 287 200 169 83 57 NC_009009:SSA_0334|5end_Diphosphomevalonate_decarboxylase,_putative_327855..328085_POSITIVE 278 237 197 148 107 NC_009009:SSA_0779|5end_Glycogen_phosphorylase,_putative_762209..762439_POSITIVE 276 217 180 67 23 NC_009009:SSA_0876|5end_4-methyl-5(B-hydroxyethyl)-thiazole_monophosphate_biosynthesis_protein,_putative_870233..870463_POSITIVE 263 218 172 168 124 NC_009009:SSA_0499|5end_ABC-type_dipeptide_transport_system,_periplasmic_component,_putative_498915..499145_POSITIVE 256 217 173 58 8 NC_009009:SSA_1943|5end_Aspartate_kinase,_putative_1928697..1928927_POSITIVE 249 220 185 192 149 NC_009009:SSA_1429|5end_hypothetical_protein_1437110..1437340_NEGATIVE 247 218 173 201 163 NC_009009:SSA_0618|5end_hypothetical_protein_611973..612203_NEGATIVE 244 207 166 80 36 NC_009009:SSA_0569|5end_Aspartyl/glutamyl-tRNA(Asn/Gln)_amidotransferase_subunit_C,_putative_563613..563843_POSITIVE 242 253 211 41 1 NC_009009:SSA_0354|5end_Uncharacterized_membrane_protein_346241..346471_POSITIVE 240 216 173 225 183 NC_009009:SSA_0621|5end_SOS_responce_UmuC_protein,_putative_613737..613967_NEGATIVE 236 215 182 69 32 NC_009009:SSA_2102|5end_Conserved_uncharacterized_protein_2106410..2106640_NEGATIVE 235 228 189 122 87 NC_009009:SSA_0606|5end_ABC-type_antimicrobial_peptide_transport_system,_ATPase_component,_putative_594532..594762_NEGATIVE 233 248 205 69 27 NC_009009:SSA_0962|5end_Lactoylglutathione_lyase,_putative_970965..971195_POSITIVE 232 217 176 187 137 NC_009009:SSA_2092|5end_Phosphotransferase_system_sugar-specific_EII_component,_putative_2095975..2096205_NEGATIVE 226 248 209 54 14 NC_009009:SSA_1304|5end_hypothetical_protein_1323449..1323679_NEGATIVE 224 280 246 191 148 NC_009009:SSA_0379|5end_PTS_system,_beta-glucoside-specific_EII_component,_putative_368822..369052_POSITIVE 223 235 191 76 27 NC_009009:SSA_1455|5end_Conserved_hypothetical_cytosolic_protein_1461676..1461906_NEGATIVE 221 206 161 82 30 NC_009009:SSA_1915|5end_hypothetical_protein_1905440..1905670_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 315 228 191 148 114 NC_009009:SSA_1865|3end_Thioredoxin_reductase,_putative_1860978..1861128_NEGATIVE 287 226 187 151 113 NC_009009:SSA_0615|3end_RggD,_putative_608326..608476_NEGATIVE 287 200 169 101 75 NC_009009:SSA_0333|3end_Mevalonate_kinase,_putative_327953..328103_POSITIVE 269 206 171 129 93 NC_009009:SSA_0935|3end_tRNA_pseudouridine_synthase_B,_putative_944973..945123_POSITIVE 247 229 184 59 9 NC_009009:SSA_0899|3end_Conserved_permease,_putative_891161..891311_POSITIVE 240 217 195 151 127 NC_009009:SSA_0796|3end_ABC-NBD_transporters_with_duplicated_ATPase_domains,_putative_779060..779210_POSITIVE 239 229 183 101 59 NC_009009:SSA_1942|3end_Enoyl-CoA_hydratase/carnithine_racemase,_putative_1927705..1927855_NEGATIVE 235 228 189 64 29 NC_009009:SSA_0607|3end_ABC_transporter,_permease_component,_putative_594590..594740_NEGATIVE 230 226 183 119 83 NC_009009:SSA_1680|3end_ABC-type_bacitracin_resistance_protein_A,_permease_component,_putative_1673200..1673350_NEGATIVE 229 229 195 132 95 NC_009009:SSA_0956|3end_surface_protein_D_965418..965568_POSITIVE 225 214 177 149 115 NC_009009:SSA_2061|3end_Peptide_deformylase,_putative_2063259..2063409_POSITIVE 225 230 182 58 4 NC_009009:SSA_1041|3end_Sugar_ABC_transporter,_permease_protein,_putative_1057434..1057584_POSITIVE 223 218 181 47 8 NC_009009:SSA_2108|3end_Glyceraldehyde_3-phosphate_dehydrogenase,_putative_2111457..2111607_NEGATIVE 223 228 185 148 109 NC_009009:SSA_2076|3end_Conserved_uncharacterized_protein_2079390..2079540_NEGATIVE 221 218 173 88 32 NC_009009:SSA_1797|3end_Aminodeoxychorismate_lyase,_putative_1778448..1778598_NEGATIVE 220 230 183 83 38 NC_009009:SSA_1952|3end_ABC-type_Fe-S_cluster_assembly_transporter,_permease_component,_putative_1948212..1948362_NEGATIVE 219 228 183 151 93 NC_009009:SSA_1501|3end_Cytidylate_kinase,_putative_1505095..1505245_NEGATIVE 218 239 194 76 39 NC_009009:SSA_0554|3end_hypothetical_protein_549692..549842_POSITIVE 217 227 182 62 2 NC_009009:SSA_2275|3end_hypothetical_protein_2275225..2275375_NEGATIVE 217 235 198 46 12 NC_009009:SSA_2383|3end_Prophage_maintenance_system_killer_protein_(DOC:_death-on-curing),_putative_1461706..1461856_NEGATIVE