Origin IGS: aggtctattatagcagaaaagaatagcatacaacagaaagacgttagaatgttagaaaatcataagttggattcctttcataggtaatactgaactttaacttgtctttatatcttcttgcaagtatcaaaaatatattgcgaatgagacaatattctcttcataataaagcgctttctaagtaaaaatcaagcaagcgattgcacagctattttaataggctttgattaaataaacagaaataaaatagaaaaattttagaaaaattaatatatttttaaaaaaatttcaaaaaaagacttgacaaaaattgcaaacggttgcataataggattgtaaataaaaattccgggaggaaatagga .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9 tcctatttcctcccggaatttttatttacaatcctattatgcaaccgtttgcaatttttgtcaagtctttttttgaaatttttttaaaaatatattaatttttctaaaatttttctattttatttctgtttatttaatcaaagcctattaaaatagctgtgcaatcgcttgcttgatttttacttagaaagcgctttattatgaagagaatattgtctcattcgcaatatatttttgatacttgcaagaagatataaagacaagttaaagttcagtattacctatgaaaggaatccaacttatgattttctaacattctaacgtctttctgttgtatgctattcttttctgctataatagacct Mask Tandem Repeat Region ================================================ aggtctattatagcagaaaagaatagcatacaacagaaagacgttagaatgttagaaaatcataagttggattcctttcataggtaatactgaactttaacttgtctttatatcttcttgcaagtatcaaaaatatattgcgaatgagacaatattctcttcataataaagcgctttctaagtaaaaatcaagcaagcgattgcacagctattttaataggctttgattaaataaacagaaataaaatagaaaaattttagaaaaattaatatatttttaaaaaaatttcaaaaaaagacttgacaaaaattgcaaacggttgcataataggattgtaaataaaaattccgggaggaaatagga Find is-nt database================================================ Query_seq: SSA_1297:SSA_1298|SSA_1297:SSA_1298:Nuclease subunit of the excinuclease complex, subunit C, putative:Maltose/maltodextrin ABC transporter, sugar-binding protein MalX, putative:<-->:1315067..1315430 364 aggtctattatagcagaaaagaatagcatacaacagaaagacgttagaatgttagaaaatcataagttggattcctttcataggtaatactgaactttaacttgtctttatatcttcttgcaagtatcaaaaatatattgcgaatgagacaatattctcttcataataaagcgctttctaagtaaaaatcaagcaagcgattgcacagctattttaataggctttgattaaataaacagaaataaaatagaaaaattttagaaaaattaatatatttttaaaaaaatttcaaaaaaagacttgacaaaaattgcaaacggttgcataataggattgtaaataaaaattccgggaggaaatagga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1297:SSA_1298|SSA_1297:SSA_1298:Nuclease subunit of the excinuclease complex, subunit C, putative:Maltose/maltodextrin ABC transporter, sugar-binding protein MalX, putative:<-->:1315067..1315430 364 aggtctattatagcagaaaagaatagcatacaacagaaagacgttagaatgttagaaaatcataagttggattcctttcataggtaatactgaactttaacttgtctttatatcttcttgcaagtatcaaaaatatattgcgaatgagacaatattctcttcataataaagcgctttctaagtaaaaatcaagcaagcgattgcacagctattttaataggctttgattaaataaacagaaataaaatagaaaaattttagaaaaattaatatatttttaaaaaaatttcaaaaaaagacttgacaaaaattgcaaacggttgcataataggattgtaaataaaaattccgggaggaaatagga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1297:SSA_1298|SSA_1297:SSA_1298:Nuclease subunit of the excinuclease complex, subunit C, putative:Maltose/maltodextrin ABC transporter, sugar-binding protein MalX, putative:<-->:1315067..1315430 364 aggtctattatagcagaaaagaatagcatacaacagaaagacgttagaatgttagaaaatcataagttggattcctttcataggtaatactgaactttaacttgtctttatatcttcttgcaagtatcaaaaatatattgcgaatgagacaatattctcttcataataaagcgctttctaagtaaaaatcaagcaagcgattgcacagctattttaataggctttgattaaataaacagaaataaaatagaaaaattttagaaaaattaatatatttttaaaaaaatttcaaaaaaagacttgacaaaaattgcaaacggttgcataataggattgtaaataaaaattccgggaggaaatagga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aggtctattatagcagaaaagaatagcatacaacagaaagacgttagaatgttagaaaatcataagttggattcctttcataggtaatactgaactttaacttgtctttatatcttcttgcaagtatcaaaaatatattgcgaatgagacaatattctcttcataataaagcgctttctaagtaaaaatcaagcaagcgattgcacagctattttaataggctttgattaaataaacagaaataaaatagaaaaattttagaaaaattaatatatttttaaaaaaatttcaaaaaaagacttgacaaaaattgcaaacggttgcataataggattgtaaataaaaattccgggaggaaatagga Predict ORF larger than 30AA ================================================ Protein_Len: 32 Strand: + Start: 87 End: 182 ...................................................................................... M L N F N L S L Y L L A S I K N I L R M R Q Y S L H N K A L S K ...................................................................................................................................................................................... Protein_Len: 33 Strand: - Start: 47 End: 145 .............................................. F T L F D Y T P N R E Y T I S F K L K D K Y R R A L I L F I N R M ........................................................................................................................................................................................................................... aggtctattatagcagaaaagaatagcatacaacagaaagacgttagaatgttagaaaatcataagttggattcctttcataggtaatactgaactttaacttgtctttatatcttcttgcaagtatcaaaaatatattgcgaatgagacaatattctcttcataataaagcgctttctaagtaaaaatcaagcaagcgattgcacagctattttaataggctttgattaaataaacagaaataaaatagaaaaattttagaaaaattaatatatttttaaaaaaatttcaaaaaaagacttgacaaaaattgcaaacggttgcataataggattgtaaataaaaattccgggaggaaatagga 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: 88 Start: 300 End: 329 ...........................................................................................................................................................................................................................................................................................................CTTGACAAAAATTGCAAACGGTTGCATAAT................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aggtctattatagcagaaaagaatagcatacaacagaaagacgttagaatgttagaaaatcataagttggattcctttcataggtaatactgaactttaacttgtctttatatcttcttgcaagtatcaaaaatatattgcgaatgagacaatattctcttcataataaagcgctttctaagtaaaaatcaagcaagcgattgcacagctattttaataggctttgattaaataaacagaaataaaatagaaaaattttagaaaaattaatatatttttaaaaaaatttcaaaaaaagacttgacaaaaattgcaaacggttgcataataggattgtaaataaaaattccgggaggaaatagga Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 42 HP_score: -2.4 Tail_Score: -3.21099 Start: 146 End: 159 Full_Region: AAATATATTGCGAAT GAGA CAATAT TCTC TTCATAATAAAGCGC .................................................................................................................................................GAGACAATATTCTC............................................................................................................................................................................................................. Find igs database================================================ Query_seq: SSA_1297:SSA_1298|SSA_1297:SSA_1298:Nuclease subunit of the excinuclease complex, subunit C, putative:Maltose/maltodextrin ABC transporter, sugar-binding protein MalX, putative:<-->:1315067..1315430 364 aggtctattatagcagaaaagaatagcatacaacagaaagacgttagaatgttagaaaatcataagttggattcctttcataggtaatactgaactttaacttgtctttatatcttcttgcaagtatcaaaaatatattgcgaatgagacaatattctcttcataataaagcgctttctaagtaaaaatcaagcaagcgattgcacagctattttaataggctttgattaaataaacagaaataaaatagaaaaattttagaaaaattaatatatttttaaaaaaatttcaaaaaaagacttgacaaaaattgcaaacggttgcataataggattgtaaataaaaattccgggaggaaatagga Intra-Species Hit: Count: 1 Min: 1 Max: 364 Len: 364 Subject: NC_009009_SSA_1297_SSA_1298|Nuclease subunit of the excinuclease complex, subunit C, putative:Maltose/maltodextrin ABC transporter, sugar-binding protein MalX, putative|NEGATIVE:POSITIVE|[1315067,1315430]|364 HSP 1 e-value: 1.0E-125 bit: 448.0 Len: 226 Query Start:1 Query End:226 Subject Strand: POSITIVE Subject Start: 1 Subject End: 226 aggtctattatagcagaaaagaatagcatacaacagaaagacgttagaatgttagaaaatcataagttggattcctttcataggtaatactgaactttaacttgtctttatatcttcttgcaagtatcaaaaatatattgcgaatgagacaatattctcttcataataaagcgctttctaagtaaaaatcaagcaagcgattgcacagctattttaataggctttg.......................................................................................................................................... aggtctattatagcagaaaagaatagcatacaacagaaagacgttagaatgttagaaaatcataagttggattcctttcataggtaatactgaactttaacttgtctttatatcttcttgcaagtatcaaaaatatattgcgaatgagacaatattctcttcataataaagcgctttctaagtaaaaatcaagcaagcgattgcacagctattttaataggctttg.......................................................................................................................................... HSP 2 e-value: 4.0E-18 bit: 93.7 Len: 47 Query Start:318 Query End:364 Subject Strand: POSITIVE Subject Start: 318 Subject End: 364 .............................................................................................................................................................................................................................................................................................................................cggttgcataataggattgtaaataaaaattccgggaggaaatagga .............................................................................................................................................................................................................................................................................................................................cggttgcataataggattgtaaataaaaattccgggaggaaatagga Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGGUCUAUUAUAGCAGAAAAGAAUAGCAUACAACAGAAAGACGUUAGAAUGUUAGAAAAUCAUAAGUUGGAUUCCUUUCAUAGGUAAUACUGAACUUUAACUUGUCUUUAUAUCUUCUUGCAAGUAUCAAAAAUAUAUUGCGAAUGAGACAAUAUUCUCUUCAUAAUAAAGCGCUUUCUAAGUAAAAAUCAAGCAAGCGAUUGCACAGCUAUUUUAAUAGGCUUUGAUUAAAUAAACAGAAAUAAAAUAGAAAAAUUUUAGAAAAAUUAAUAUAUUUUUAAAAAAAUUUCAAAAAAAGACUUGACAAAAAUUGCAAACGGUUGCAUAAUAGGAUUGUAAAUAAAAAUUCCGGGAGGAAAUAGGA ((((((.(((.(((.....((((((((.(((...((((((.((((((((((((.((.......(((((((((((((.....))).))).)).))))).......))......((((.((((((((((.....)))).))))))..)))).))))))))...........))))))))))..)))........((((....))))...)))))))).....))).)))......................((((..(((((((((.((....)).)))))))))...))))......)))))).........(((((....))))).....................((((....))))...... (-61.84) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCCUAUUUCCUCCCGGAAUUUUUAUUUACAAUCCUAUUAUGCAACCGUUUGCAAUUUUUGUCAAGUCUUUUUUUGAAAUUUUUUUAAAAAUAUAUUAAUUUUUCUAAAAUUUUUCUAUUUUAUUUCUGUUUAUUUAAUCAAAGCCUAUUAAAAUAGCUGUGCAAUCGCUUGCUUGAUUUUUACUUAGAAAGCGCUUUAUUAUGAAGAGAAUAUUGUCUCAUUCGCAAUAUAUUUUUGAUACUUGCAAGAAGAUAUAAAGACAAGUUAAAGUUCAGUAUUACCUAUGAAAGGAAUCCAACUUAUGAUUUUCUAACAUUCUAACGUCUUUCUGUUGUAUGCUAUUCUUUUCUGCUAUAAUAGACCU ((((..((((....))))........(((..........(((((....)))))...((((((..((.((((((((........(((((((((((((...((((((((.......((((((((.....((((.........))))....))))))))....((((....))))...........))))))))...........(((((((......)))).)))..)))))))))))))......)))))))).))...))))))..........)))...........))))...................................(((((((((.((...........)))))))))))... (-55.74) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 799 50 1 141 92 NC_009009:SSA_1297|5end_Nuclease_subunit_of_the_excinuclease_complex,_subunit_C,_putative_1314976..1315206_NEGATIVE 285 229 185 173 131 NC_009009:SSA_0809|5end_Translation_initiation_inhibitor,_yjgF_family_/_endoribonuclease_L-PSP,_putative_791146..791376_POSITIVE 279 240 195 213 172 NC_009009:SSA_1378|5end_hypothetical_protein_1397998..1398228_NEGATIVE 271 227 191 229 183 NC_009009:SSA_0915|5end_hypothetical_protein_927542..927772_POSITIVE 270 50 1 222 168 NC_009009:SSA_2360|5end_tRNA_(5-methylaminomethyl-2-thiouridylate)-methyltransferase,_putative_2363779..2364009_NEGATIVE 255 179 139 102 66 NC_009009:SSA_1468|5end_3-dehydroquinate_synthase,_putative_1475452..1475682_NEGATIVE 255 120 72 120 74 NC_009009:SSA_0720|5end_hypothetical_protein_705106..705336_POSITIVE 254 179 138 70 22 NC_009009:SSA_1901|5end_Conserved_uncharacterized_protein_1896599..1896829_NEGATIVE 251 210 161 181 124 NC_009009:SSA_1107|5end_Lipid/multidrug/protein-type_ABC_exporter,_ATP_binding/membrane-spanning_protein,_putative_1131968..1132198_POSITIVE 250 171 136 218 177 NC_009009:SSA_0183|5end_hypothetical_protein_187646..187876_POSITIVE 247 226 181 179 125 NC_009009:SSA_0643|5end_hypothetical_protein_630194..630424_NEGATIVE 243 115 74 190 152 NC_009009:SSA_0385|5end_ABC_transporter,_glycine-betaine/proline_permease_protein,_putative_380250..380480_NEGATIVE 239 209 170 94 51 NC_009009:SSA_2207|5end_hypothetical_protein_2207221..2207451_NEGATIVE 238 205 172 210 180 NC_009009:SSA_2259|5end_hypothetical_protein_2255422..2255652_NEGATIVE 234 207 170 160 118 NC_009009:SSA_2097|5end_Amino_acid_ABC_transporter,_ATP-binding_protein,_putative_2102918..2103148_NEGATIVE 234 213 173 70 27 NC_009009:SSA_1891|5end_Oxidoreductase,_aldo/keto_reductase_family,_putative_1888991..1889221_NEGATIVE 234 33 4 185 155 NC_009009:SSA_1310|5end_30S_ribosomal_protein_S16,_putative_1327610..1327840_NEGATIVE 234 222 182 229 187 NC_009009:SSA_0222|5end_PTS_system,_mannose-specific_IID_component,_putative_217217..217447_POSITIVE 228 217 172 146 102 NC_009009:SSA_1136|5end_ATPases_with_chaperone_activity,_ATP-binding_subunit,_putative_1161924..1162154_POSITIVE 228 209 171 196 152 NC_009009:SSA_0807|5end_GTP-binding_protein,_putative_789449..789679_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 260 240 191 82 43 NC_009009:SSA_0208|3end_Conserved_uncharacterized_protein_204968..205118_NEGATIVE 255 179 139 91 55 NC_009009:SSA_1469|3end_Shikimate_dehydrogenase,_putative_1475463..1475613_NEGATIVE 238 205 172 31 1 NC_009009:SSA_2260|3end_DNA_mismatch_repair_protein_hexA,_putative_2255601..2255751_NEGATIVE 235 358 311 146 106 NC_009009:SSA_2010|3end_ABC-type_multidrug_transport_system,_permease_component,_putative_2011296..2011446_NEGATIVE 234 207 170 147 105 NC_009009:SSA_2098|3end_ABC-type_arginine/histidine_transporter,_permease_protein,_putative_2102931..2103081_NEGATIVE 228 209 171 145 101 NC_009009:SSA_0806|3end_hypothetical_protein_789478..789628_POSITIVE 228 198 157 68 31 NC_009009:SSA_0567|3end_Isochorismitase_family_protein,_putative_561442..561592_POSITIVE 225 227 195 44 3 NC_009009:SSA_0914|3end_Phenylalanyl-tRNA_synthetase_beta_chain,_putative_927437..927587_POSITIVE 222 228 191 106 67 NC_009009:SSA_0207|3end_hypothetical_protein_204944..205094_POSITIVE 221 211 172 55 15 NC_009009:SSA_1593|3end_Dipeptidase,_putative_1596390..1596540_NEGATIVE 219 213 172 82 35 NC_009009:SSA_0141|3end_Copper_chaperone,_putative_137191..137341_POSITIVE 217 209 161 150 98 NC_009009:SSA_0319|3end_Branched-chain_amino_acid_permease_(L-methionine,_L-isoleucine,_leucine_and_valine),_putative_313496..313646_POSITIVE 216 57 12 145 99 NC_009009:SSA_2072|3end_Phosphatidate_cytidylyltransferase,_putative_2074800..2074950_NEGATIVE 216 226 186 50 12 NC_009009:SSA_1015|3end_4-hydroxybenzoate_octaprenyltransferase,_putative_1019682..1019832_POSITIVE 215 210 170 62 26 NC_009009:SSA_1592|3end_hypothetical_protein_1595576..1595726_NEGATIVE 215 90 46 99 58 NC_009009:SSA_0400|3end_hypothetical_protein_396470..396620_NEGATIVE 212 222 191 80 41 NC_009009:SSA_2083|3end_hypothetical_protein_2086950..2087100_NEGATIVE 212 215 175 140 99 NC_009009:SSA_1165|3end_Transcriptional_regulator,_GntR_family,_putative_1191865..1192015_POSITIVE 212 229 195 81 49 NC_009009:SSA_0243|3end_Cyclo-nucleotide_phosphodiesterase,_putative_235824..235974_NEGATIVE 211 178 138 144 104 NC_009009:SSA_0512|3end_Nicotinate-nucleotide--dimethylbenzimidazole_phosphoribosyltransferase,_putative_511625..511775_POSITIVE