Origin IGS: atagaggattctgccagtttaagtttcttaaaagcttagactggtagaattttattatcttctcaaagggggatttgacaatccgccaagagcagttggtcatcagtttatctttattttaggtcgattttgcttacagtttgtacttcgtttcctaataccaaaaacaaactgaaagattatttatcttttttcttgacattcacaaacgacaattgtagaatatacttataaactacatttgtagaatgtttttgaaaaatactgcttggaagggagaagaaagcaaagcttatccagacgcttgtaggatgcagagcggaagctctatttcttttaaaagcacaaactacatttgtagaatcaaaggagaattcaa .........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 ttgaattctcctttgattctacaaatgtagtttgtgcttttaaaagaaatagagcttccgctctgcatcctacaagcgtctggataagctttgctttcttctcccttccaagcagtatttttcaaaaacattctacaaatgtagtttataagtatattctacaattgtcgtttgtgaatgtcaagaaaaaagataaataatctttcagtttgtttttggtattaggaaacgaagtacaaactgtaagcaaaatcgacctaaaataaagataaactgatgaccaactgctcttggcggattgtcaaatccccctttgagaagataataaaattctaccagtctaagcttttaagaaacttaaactggcagaatcctctat Mask Tandem Repeat Region ================================================ atagaggattctgccagtttaagtttcttaaaagcttagactggtagaattttattatcttctcaaagggggatttgacaatccgccaagagcagttggtcatcagtttatctttattttaggtcgattttgcttacagtttgtacttcgtttcctaataccaaaaacaaactgaaagattatttatcttttttcttgacattcacaaacgacaattgtagaatatacttataaactacatttgtagaatgtttttgaaaaatactgcttggaagggagaagaaagcaaagcttatccagacgcttgtaggatgcagagcggaagctctatttcttttaaaagcacaaactacatttgtagaatcaaaggagaattcaa Find is-nt database================================================ Query_seq: SSA_0817:SSA_0818|SSA_0817:SSA_0818:Antirepressor regulating drug resistance (membrane-bound), putative:SPX domain-like protein, putative:->->:799436..799814 379 atagaggattctgccagtttaagtttcttaaaagcttagactggtagaattttattatcttctcaaagggggatttgacaatccgccaagagcagttggtcatcagtttatctttattttaggtcgattttgcttacagtttgtacttcgtttcctaataccaaaaacaaactgaaagattatttatcttttttcttgacattcacaaacgacaattgtagaatatacttataaactacatttgtagaatgtttttgaaaaatactgcttggaagggagaagaaagcaaagcttatccagacgcttgtaggatgcagagcggaagctctatttcttttaaaagcacaaactacatttgtagaatcaaaggagaattcaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0817:SSA_0818|SSA_0817:SSA_0818:Antirepressor regulating drug resistance (membrane-bound), putative:SPX domain-like protein, putative:->->:799436..799814 379 atagaggattctgccagtttaagtttcttaaaagcttagactggtagaattttattatcttctcaaagggggatttgacaatccgccaagagcagttggtcatcagtttatctttattttaggtcgattttgcttacagtttgtacttcgtttcctaataccaaaaacaaactgaaagattatttatcttttttcttgacattcacaaacgacaattgtagaatatacttataaactacatttgtagaatgtttttgaaaaatactgcttggaagggagaagaaagcaaagcttatccagacgcttgtaggatgcagagcggaagctctatttcttttaaaagcacaaactacatttgtagaatcaaaggagaattcaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0817:SSA_0818|SSA_0817:SSA_0818:Antirepressor regulating drug resistance (membrane-bound), putative:SPX domain-like protein, putative:->->:799436..799814 379 atagaggattctgccagtttaagtttcttaaaagcttagactggtagaattttattatcttctcaaagggggatttgacaatccgccaagagcagttggtcatcagtttatctttattttaggtcgattttgcttacagtttgtacttcgtttcctaataccaaaaacaaactgaaagattatttatcttttttcttgacattcacaaacgacaattgtagaatatacttataaactacatttgtagaatgtttttgaaaaatactgcttggaagggagaagaaagcaaagcttatccagacgcttgtaggatgcagagcggaagctctatttcttttaaaagcacaaactacatttgtagaatcaaaggagaattcaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 atagaggattctgccagtttaagtttcttaaaagcttagactggtagaattttattatcttctcaaagggggatttgacaatccgccaagagcagttggtcatcagtttatctttattttaggtcgattttgcttacagtttgtacttcgtttcctaataccaaaaacaaactgaaagattatttatcttttttcttgacattcacaaacgacaattgtagaatatacttataaactacatttgtagaatgtttttgaaaaatactgcttggaagggagaagaaagcaaagcttatccagacgcttgtaggatgcagagcggaagctctatttcttttaaaagcacaaactacatttgtagaatcaaaggagaattcaa Predict ORF larger than 30AA ================================================ Protein_Len: 44 Strand: + Start: 41 End: 172 ........................................ M V E F Y Y L L K G G F D N P P R A V G H Q F I F I L G R F C L Q F V L R F L I P K T N ............................................................................................................................................................................................................... Protein_Len: 35 Strand: + Start: 127 End: 231 .............................................................................................................................. M L L T V C T S F P N T K N K L K D Y L S F F L T F T N D N C R I Y L .................................................................................................................................................... Protein_Len: 51 Strand: + Start: 225 End: 377 ................................................................................................................................................................................................................................ M L I N Y I C R M F L K N T A W K G E E S K A Y P D A C R M Q S G S S I S F K S T N Y I C R I K G E F .. Protein_Len: 39 Strand: + Start: 262 End: 378 ..................................................................................................................................................................................................................................................................... M L L G R E K K A K L I Q T L V G C R A E A L F L L K A Q T T F V E S K E N S . Protein_Len: 45 Strand: - Start: 183 End: 317 ...................................................................................................................................................................................... K D K K K V N V F S L Q L I Y K Y V V N T S H K Q F I S S P L S F F A F S I W V S T P H M .............................................................. Protein_Len: 35 Strand: - Start: 2 End: 106 . L P N Q W N L N R L L K S Q Y F K I I K E F P S K V I R W S C N T M M ................................................................................................................................................................................................................................................................................. atagaggattctgccagtttaagtttcttaaaagcttagactggtagaattttattatcttctcaaagggggatttgacaatccgccaagagcagttggtcatcagtttatctttattttaggtcgattttgcttacagtttgtacttcgtttcctaataccaaaaacaaactgaaagattatttatcttttttcttgacattcacaaacgacaattgtagaatatacttataaactacatttgtagaatgtttttgaaaaatactgcttggaagggagaagaaagcaaagcttatccagacgcttgtaggatgcagagcggaagctctatttcttttaaaagcacaaactacatttgtagaatcaaaggagaattcaa 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: 195 End: 224 ..................................................................................................................................................................................................CTTGACATTCACAAACGACAATTGTAGAAT........................................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ atagaggattctgccagtttaagtttcttaaaagcttagactggtagaattttattatcttctcaaagggggatttgacaatccgccaagagcagttggtcatcagtttatctttattttaggtcgattttgcttacagtttgtacttcgtttcctaataccaaaaacaaactgaaagattatttatcttttttcttgacattcacaaacgacaattgtagaatatacttataaactacatttgtagaatgtttttgaaaaatactgcttggaagggagaagaaagcaaagcttatccagacgcttgtaggatgcagagcggaagctctatttcttttaaaagcacaaactacatttgtagaatcaaaggagaattcaa Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_0817:SSA_0818|SSA_0817:SSA_0818:Antirepressor regulating drug resistance (membrane-bound), putative:SPX domain-like protein, putative:->->:799436..799814 379 atagaggattctgccagtttaagtttcttaaaagcttagactggtagaattttattatcttctcaaagggggatttgacaatccgccaagagcagttggtcatcagtttatctttattttaggtcgattttgcttacagtttgtacttcgtttcctaataccaaaaacaaactgaaagattatttatcttttttcttgacattcacaaacgacaattgtagaatatacttataaactacatttgtagaatgtttttgaaaaatactgcttggaagggagaagaaagcaaagcttatccagacgcttgtaggatgcagagcggaagctctatttcttttaaaagcacaaactacatttgtagaatcaaaggagaattcaa Intra-Species Hit: Count: 1 Min: 1 Max: 379 Len: 379 Subject: NC_009009_SSA_0817_SSA_0818|Antirepressor regulating drug resistance (membrane-bound), putative:SPX domain-like protein, putative|POSITIVE:POSITIVE|[799436,799814]|379 HSP 1 e-value: 0.0 bit: 751.0 Len: 379 Query Start:1 Query End:379 Subject Strand: POSITIVE Subject Start: 1 Subject End: 379 atagaggattctgccagtttaagtttcttaaaagcttagactggtagaattttattatcttctcaaagggggatttgacaatccgccaagagcagttggtcatcagtttatctttattttaggtcgattttgcttacagtttgtacttcgtttcctaataccaaaaacaaactgaaagattatttatcttttttcttgacattcacaaacgacaattgtagaatatacttataaactacatttgtagaatgtttttgaaaaatactgcttggaagggagaagaaagcaaagcttatccagacgcttgtaggatgcagagcggaagctctatttcttttaaaagcacaaactacatttgtagaatcaaaggagaattcaa atagaggattctgccagtttaagtttcttaaaagcttagactggtagaattttattatcttctcaaagggggatttgacaatccgccaagagcagttggtcatcagtttatctttattttaggtcgattttgcttacagtttgtacttcgtttcctaataccaaaaacaaactgaaagattatttatcttttttcttgacattcacaaacgacaattgtagaatatacttataaactacatttgtagaatgtttttgaaaaatactgcttggaagggagaagaaagcaaagcttatccagacgcttgtaggatgcagagcggaagctctatttcttttaaaagcacaaactacatttgtagaatcaaaggagaattcaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUAGAGGAUUCUGCCAGUUUAAGUUUCUUAAAAGCUUAGACUGGUAGAAUUUUAUUAUCUUCUCAAAGGGGGAUUUGACAAUCCGCCAAGAGCAGUUGGUCAUCAGUUUAUCUUUAUUUUAGGUCGAUUUUGCUUACAGUUUGUACUUCGUUUCCUAAUACCAAAAACAAACUGAAAGAUUAUUUAUCUUUUUUCUUGACAUUCACAAACGACAAUUGUAGAAUAUACUUAUAAACUACAUUUGUAGAAUGUUUUUGAAAAAUACUGCUUGGAAGGGAGAAGAAAGCAAAGCUUAUCCAGACGCUUGUAGGAUGCAGAGCGGAAGCUCUAUUUCUUUUAAAAGCACAAACUACAUUUGUAGAAUCAAAGGAGAAUUCAA ....((((((((((((((((((((((.....))))))))))))))))))))))....(((((((...((.(((((....))))).))..((((((((((((.(((((((.........(((((.(((...(((.........)))..)))...)))))..........)))))))..))))).......((((((..(((((((.......((((.(((((..(((....)))..))))).)))).)))))))...)))))).)))))))......)))))))............(((....((((..((((...(((((....)))))...))))....)))).....((((....)))).......)))........ (-112.31) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUGAAUUCUCCUUUGAUUCUACAAAUGUAGUUUGUGCUUUUAAAAGAAAUAGAGCUUCCGCUCUGCAUCCUACAAGCGUCUGGAUAAGCUUUGCUUUCUUCUCCCUUCCAAGCAGUAUUUUUCAAAAACAUUCUACAAAUGUAGUUUAUAAGUAUAUUCUACAAUUGUCGUUUGUGAAUGUCAAGAAAAAAGAUAAAUAAUCUUUCAGUUUGUUUUUGGUAUUAGGAAACGAAGUACAAACUGUAAGCAAAAUCGACCUAAAAUAAAGAUAAACUGAUGACCAACUGCUCUUGGCGGAUUGUCAAAUCCCCCUUUGAGAAGAUAAUAAAAUUCUACCAGUCUAAGCUUUUAAGAAACUUAAACUGGCAGAAUCCUCUAU ........(((...(((.((.....(((((..(((.(((....)))....(((((....))))))))..))))))).))).)))............(((((((.......((((((...........(((..(.((((.(((((..(((....)))..))))).)))).)..)))....((((.....((((((.....))))))(((((((((((((...(((((...(((..(((.....))).......))).)))))..))))))))))))).))))..))))))...((.(((((....))))).))...))))))).......(((((.(((((.((((.(((....))))))).))))).)))))....... (-89.00) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 371 108 68 47 11 NC_009009:SSA_1156|5end_hypothetical_protein_1184562..1184792_POSITIVE 370 104 72 223 187 NC_009009:SSA_0605|5end_Methyltransferase_gidB,_putative_593707..593937_NEGATIVE 362 110 61 173 117 NC_009009:SSA_1367|5end_hypothetical_protein_1383593..1383823_POSITIVE 347 320 271 200 147 NC_009009:SSA_0307|5end_Glutamine_synthetase_type_1,_putative_302987..303217_POSITIVE 327 339 297 81 31 NC_009009:SSA_1734|5end_Cation_(Mg/Ni_uptake)_transport_ATPase,_putative_1720303..1720533_NEGATIVE 324 329 282 205 145 NC_009009:SSA_0812|5end_hypothetical_protein_793443..793673_POSITIVE 320 320 276 187 140 NC_009009:SSA_0516|5end_AmiR_two-component_response_regulator_with_transcriptional_antiterminator_output_domain,_putative_514485..514715_POSITIVE 318 319 274 221 169 NC_009009:SSA_0543|5end_SecA,_putative_537279..537509_POSITIVE 310 329 291 62 14 NC_009009:SSA_2165|5end_ABC-type_oligopeptide_transporter,_periplasmic_component,_putative_2161734..2161964_POSITIVE 306 347 304 223 176 NC_009009:SSA_1620|5end_Uridylate_kinase,_putative_1622981..1623211_NEGATIVE 300 100 58 141 101 NC_009009:SSA_1208|5end_23S_rRNA_pseudouridine_synthase,_putative_1233185..1233415_NEGATIVE 298 100 55 212 151 NC_009009:SSA_0618|5end_hypothetical_protein_611973..612203_NEGATIVE 297 319 274 63 18 NC_009009:SSA_0085|5end_V-type_sodium_ATPase,_subunit_I,_putative_85750..85980_POSITIVE 296 320 271 227 161 NC_009009:SSA_1569|5end_ABC_transporter_membrane-spanning_permease,_arginine/histidine_transport,_putative_1571891..1572121_POSITIVE 295 329 281 67 13 NC_009009:SSA_1971|5end_hypothetical_protein_1967167..1967397_POSITIVE 294 336 291 130 86 NC_009009:SSA_0920|5end_hypothetical_protein_930896..931126_POSITIVE 292 106 67 220 178 NC_009009:SSA_0944|5end_Phosphate_import_ATP-binding_protein_pstB_2,_putative_951741..951971_POSITIVE 291 328 292 204 162 NC_009009:SSA_2277|5end_DNA_segregation_ATPase_FtsK/SpoIIIE_family_protein,_putative_2280407..2280637_NEGATIVE 290 335 297 228 189 NC_009009:SSA_1500|5end_Translation_initiation_factor_IF-3,_putative_1504921..1505151_NEGATIVE 290 330 292 50 2 NC_009009:SSA_1466|5end_Prephenate_dehydrogenase,_putative_1473111..1473341_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 491 50 5 83 38 NC_009009:SSA_0817|3end_Antirepressor_regulating_drug_resistance_(membrane-bound),_putative_799375..799525_POSITIVE 371 108 68 45 9 NC_009009:SSA_1155|3end_Serine_hydroxymethyltransferase,_putative_1184640..1184790_POSITIVE 370 104 72 141 105 NC_009009:SSA_0606|3end_ABC-type_antimicrobial_peptide_transport_system,_ATPase_component,_putative_593789..593939_NEGATIVE 325 127 81 81 41 NC_009009:SSA_1280|3end_hypothetical_protein_1301108..1301258_NEGATIVE 300 100 58 144 104 NC_009009:SSA_1209|3end_Inorganic_polyphosphate/ATP-NAD_kinase,_putative_1233182..1233332_NEGATIVE 297 319 274 73 28 NC_009009:SSA_0083|3end_hypothetical_protein_85840..85990_POSITIVE 294 336 291 99 55 NC_009009:SSA_0918|3end_Conserved_uncharacterized_protein_930945..931095_POSITIVE 294 130 81 99 47 NC_009009:SSA_0756|3end_Alanyl-tRNA_synthetase,_putative_739434..739584_POSITIVE 290 335 297 54 15 NC_009009:SSA_1501|3end_Cytidylate_kinase,_putative_1505095..1505245_NEGATIVE 290 338 296 68 20 NC_009009:SSA_0644|3end_DNA_Protection_System,_DNA-binding_ferritin-like_protein_(oxidative_damage_protectant),_putative_630765..630915_POSITIVE 288 336 291 99 50 NC_009009:SSA_1713|3end_D-3-phosphoglycerate_dehydrogenase,_putative_1700209..1700359_NEGATIVE 284 300 265 45 8 NC_009009:SSA_0646|3end_hypothetical_protein_631076..631226_POSITIVE 283 79 36 49 8 NC_009009:SSA_2007|3end_Chaperone_protein_dnaK/HSP70,_putative_2007443..2007593_NEGATIVE 282 329 286 78 26 NC_009009:SSA_2282|3end_Phage_infection_protein,_putative_2282377..2282527_NEGATIVE 282 338 297 113 71 NC_009009:SSA_0187|3end_Competence_protein_ComYD,_putative_190852..191002_POSITIVE 281 106 65 74 34 NC_009009:SSA_0683|3end_DNA-binding_protein_HU,_putative_664739..664889_POSITIVE 279 333 291 47 9 NC_009009:SSA_0807|3end_GTP-binding_protein,_putative_790839..790989_POSITIVE 275 337 293 123 66 NC_009009:SSA_2060|3end_Arabinose_efflux_permease,_putative_2061234..2061384_NEGATIVE 272 327 286 138 98 NC_009009:SSA_1569|3end_ABC_transporter_membrane-spanning_permease,_arginine/histidine_transport,_putative_1572630..1572780_POSITIVE 272 325 281 63 26 NC_009009:SSA_0407|3end_ABC-type_multidrug_transport_system_(3-component_subtilin_immunity_exporter),_ATPase_component,_putative_402911..403061_NEGATIVE