Origin IGS: aagagttccctcttcttcctatccgtatttcttatacttattatactttattttacagctgatttcaaacgcttccaagttctttgcctaagttttcaaaatttagaaaaatcccgcgattggaaaaattgaagatggacaatggctagatatactattttaagcatctaagagaagaaaaaaggtccaatggaccttttcaaaatgttaagttactaccataactttctatcaaaaacctaaaaatgtctcccagacattttgaagaaaactcgctgccgtgagtttccatctgcaacctgaaacaatttcctggccatcttgacgaaaaccttgttttctttatctgcaacttaaaaaggtccaatggaccttttcaaaacgttaagttactatcgtaactttctatccacaacctaaaaatgtctcccagacattt .........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 aaatgtctgggagacatttttaggttgtggatagaaagttacgatagtaacttaacgttttgaaaaggtccattggacctttttaagttgcagataaagaaaacaaggttttcgtcaagatggccaggaaattgtttcaggttgcagatggaaactcacggcagcgagttttcttcaaaatgtctgggagacatttttaggtttttgatagaaagttatggtagtaacttaacattttgaaaaggtccattggaccttttttcttctcttagatgcttaaaatagtatatctagccattgtccatcttcaatttttccaatcgcgggatttttctaaattttgaaaacttaggcaaagaacttggaagcgtttgaaatcagctgtaaaataaagtataataagtataagaaatacggataggaagaagagggaactctt Mask Tandem Repeat Region ================================================ aagagttccctcttcttcctatccgtatttcttatacttattatactttattttacagctgatttcaaacgcttccaagttctttgcctaagttttcaaaatttagaaaaatcccgcgattggaaaaattgaagatggacaatggctagatatactattttaagcatctaagagaagaaaaaaggtccaatggaccttttcaaaatgttaagttactaccataactttctatcaaaaacctaaaaatgtctcccagacattttgaagaaaactcgctgccgtgagtttccatctgcaacctgaaacaatttcctggccatcttgacgaaaaccttgttttctttatctgcaacttaaaaaggtccaatggaccttttcaaaacgttaagttactatcgtaactttctatccacaacctaaaaatgtctcccagacattt Find is-nt database================================================ Query_seq: SSA_1724:SSA_1725|SSA_1724:SSA_1725:CBS domain protein, putative:Branched-chain amino acid ABC transporter, ATP-binding protein, putative:<-<-:1710644..1711082 439 aagagttccctcttcttcctatccgtatttcttatacttattatactttattttacagctgatttcaaacgcttccaagttctttgcctaagttttcaaaatttagaaaaatcccgcgattggaaaaattgaagatggacaatggctagatatactattttaagcatctaagagaagaaaaaaggtccaatggaccttttcaaaatgttaagttactaccataactttctatcaaaaacctaaaaatgtctcccagacattttgaagaaaactcgctgccgtgagtttccatctgcaacctgaaacaatttcctggccatcttgacgaaaaccttgttttctttatctgcaacttaaaaaggtccaatggaccttttcaaaacgttaagttactatcgtaactttctatccacaacctaaaaatgtctcccagacattt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1724:SSA_1725|SSA_1724:SSA_1725:CBS domain protein, putative:Branched-chain amino acid ABC transporter, ATP-binding protein, putative:<-<-:1710644..1711082 439 aagagttccctcttcttcctatccgtatttcttatacttattatactttattttacagctgatttcaaacgcttccaagttctttgcctaagttttcaaaatttagaaaaatcccgcgattggaaaaattgaagatggacaatggctagatatactattttaagcatctaagagaagaaaaaaggtccaatggaccttttcaaaatgttaagttactaccataactttctatcaaaaacctaaaaatgtctcccagacattttgaagaaaactcgctgccgtgagtttccatctgcaacctgaaacaatttcctggccatcttgacgaaaaccttgttttctttatctgcaacttaaaaaggtccaatggaccttttcaaaacgttaagttactatcgtaactttctatccacaacctaaaaatgtctcccagacattt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1724:SSA_1725|SSA_1724:SSA_1725:CBS domain protein, putative:Branched-chain amino acid ABC transporter, ATP-binding protein, putative:<-<-:1710644..1711082 439 aagagttccctcttcttcctatccgtatttcttatacttattatactttattttacagctgatttcaaacgcttccaagttctttgcctaagttttcaaaatttagaaaaatcccgcgattggaaaaattgaagatggacaatggctagatatactattttaagcatctaagagaagaaaaaaggtccaatggaccttttcaaaatgttaagttactaccataactttctatcaaaaacctaaaaatgtctcccagacattttgaagaaaactcgctgccgtgagtttccatctgcaacctgaaacaatttcctggccatcttgacgaaaaccttgttttctttatctgcaacttaaaaaggtccaatggaccttttcaaaacgttaagttactatcgtaactttctatccacaacctaaaaatgtctcccagacattt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aagagttccctcttcttcctatccgtatttcttatacttattatactttattttacagctgatttcaaacgcttccaagttctttgcctaagttttcaaaatttagaaaaatcccgcgattggaaaaattgaagatggacaatggctagatatactattttaagcatctaagagaagaaaaaaggtccaatggaccttttcaaaatgttaagttactaccataactttctatcaaaaacctaaaaatgtctcccagacattttgaagaaaactcgctgccgtgagtttccatctgcaacctgaaacaatttcctggccatcttgacgaaaaccttgttttctttatctgcaacttaaaaaggtccaatggaccttttcaaaacgttaagttactatcgtaactttctatccacaacctaaaaatgtctcccagacattt Predict ORF larger than 30AA ================================================ Protein_Len: 32 Strand: + Start: 34 End: 129 ................................. M L I I L Y F T A D F K R F Q V L C L S F Q N L E K S R D W K N ...................................................................................................................................................................................................................................................................................................................... Protein_Len: 36 Strand: + Start: 291 End: 398 .................................................................................................................................................................................................................................................................................................. M C N L K Q F P G H L D E N L V F F I C N L K R S N G P F Q N V K L L S ......................................... Protein_Len: 55 Strand: - Start: 203 End: 367 .......................................................................................................................................................................................................... F T L N S G Y S E I L F R F I D G L C K S S F E S G H T E M Q L R F C N G P W R S S F R T K K I Q L K F L D M ........................................................................ aagagttccctcttcttcctatccgtatttcttatacttattatactttattttacagctgatttcaaacgcttccaagttctttgcctaagttttcaaaatttagaaaaatcccgcgattggaaaaattgaagatggacaatggctagatatactattttaagcatctaagagaagaaaaaaggtccaatggaccttttcaaaatgttaagttactaccataactttctatcaaaaacctaaaaatgtctcccagacattttgaagaaaactcgctgccgtgagtttccatctgcaacctgaaacaatttcctggccatcttgacgaaaaccttgttttctttatctgcaacttaaaaaggtccaatggaccttttcaaaacgttaagttactatcgtaactttctatccacaacctaaaaatgtctcccagacattt 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: 40 End: 69 .......................................TTTGAAATCAGCTGTAAAATAAAGTATAAT.................................................................................................................................................................................................................................................................................................................................................................................. PromScan Matrix: RpoD-17 Strand: - Score: 83 Start: 50 End: 79 .................................................CTTGGAAGCGTTTGAAATCAGCTGTAAAAT........................................................................................................................................................................................................................................................................................................................................................................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aagagttccctcttcttcctatccgtatttcttatacttattatactttattttacagctgatttcaaacgcttccaagttctttgcctaagttttcaaaatttagaaaaatcccgcgattggaaaaattgaagatggacaatggctagatatactattttaagcatctaagagaagaaaaaaggtccaatggaccttttcaaaatgttaagttactaccataactttctatcaaaaacctaaaaatgtctcccagacattttgaagaaaactcgctgccgtgagtttccatctgcaacctgaaacaatttcctggccatcttgacgaaaaccttgttttctttatctgcaacttaaaaaggtccaatggaccttttcaaaacgttaagttactatcgtaactttctatccacaacctaaaaatgtctcccagacattt Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 89 HP_score: -9.1 Tail_Score: -4.14472 Start: 184 End: 196 Full_Region: TAAGAGAAGAAAAAA GGTCC AAT GGACC TTTTCAAAATGTTAA .......................................................................................................................................................................................GGTCCAATGGACC................................................................................................................................................................................................................................................... TransTerm Strand: - Conf: 100 HP_score: -9.1 Tail_Score: -5.64304 Start: 184 End: 196 Full_Region: ttaacattttgaaaa ggtcc att ggacc ttttttcttctctta .......................................................................................................................................................................................ggtccattggacc................................................................................................................................................................................................................................................... TransTerm Strand: - Conf: 86 HP_score: -8.3 Tail_Score: -4.7254 Start: 239 End: 267 Full_Region: acggcagcgagtttt cttcaaaatgtct ggg agacatttttagg tttttgatagaaagt ..............................................................................................................................................................................................................................................cttcaaaatgtctgggagacatttttagg............................................................................................................................................................................ TransTerm Strand: - Conf: 83 HP_score: -6.3 Tail_Score: -4.92239 Start: 247 End: 259 Full_Region: gagttttcttcaaaa tgtct ggg agaca tttttaggtttttga ......................................................................................................................................................................................................................................................tgtctgggagaca.................................................................................................................................................................................... TransTerm Strand: + Conf: 73 HP_score: -7.2 Tail_Score: -4.0492 Start: 327 End: 341 Full_Region: CCTGGCCATCTTGAC GAAAAC CTT GTTTTC TTTATCTGCAACTTA ......................................................................................................................................................................................................................................................................................................................................GAAAACCTTGTTTTC.................................................................................................. TransTerm Strand: + Conf: 89 HP_score: -9.1 Tail_Score: -4.09739 Start: 361 End: 373 Full_Region: TCTGCAACTTAAAAA GGTCC AAT GGACC TTTTCAAAACGTTAA ........................................................................................................................................................................................................................................................................................................................................................................GGTCCAATGGACC.................................................................. TransTerm Strand: - Conf: 100 HP_score: -9.1 Tail_Score: -4.74103 Start: 361 End: 373 Full_Region: ttaacgttttgaaaa ggtcc att ggacc tttttaagttgcaga ........................................................................................................................................................................................................................................................................................................................................................................ggtccattggacc.................................................................. Find igs database================================================ Query_seq: SSA_1724:SSA_1725|SSA_1724:SSA_1725:CBS domain protein, putative:Branched-chain amino acid ABC transporter, ATP-binding protein, putative:<-<-:1710644..1711082 439 aagagttccctcttcttcctatccgtatttcttatacttattatactttattttacagctgatttcaaacgcttccaagttctttgcctaagttttcaaaatttagaaaaatcccgcgattggaaaaattgaagatggacaatggctagatatactattttaagcatctaagagaagaaaaaaggtccaatggaccttttcaaaatgttaagttactaccataactttctatcaaaaacctaaaaatgtctcccagacattttgaagaaaactcgctgccgtgagtttccatctgcaacctgaaacaatttcctggccatcttgacgaaaaccttgttttctttatctgcaacttaaaaaggtccaatggaccttttcaaaacgttaagttactatcgtaactttctatccacaacctaaaaatgtctcccagacattt Intra-Species Hit: Count: 1 Min: 1 Max: 439 Len: 439 Subject: NC_009009_SSA_1724_SSA_1725|CBS domain protein, putative:Branched-chain amino acid ABC transporter, ATP-binding protein, putative|NEGATIVE:NEGATIVE|[1710644,1711082]|439 HSP 1 e-value: 0.0 bit: 870.0 Len: 439 Query Start:1 Query End:439 Subject Strand: POSITIVE Subject Start: 1 Subject End: 439 aagagttccctcttcttcctatccgtatttcttatacttattatactttattttacagctgatttcaaacgcttccaagttctttgcctaagttttcaaaatttagaaaaatcccgcgattggaaaaattgaagatggacaatggctagatatactattttaagcatctaagagaagaaaaaaggtccaatggaccttttcaaaatgttaagttactaccataactttctatcaaaaacctaaaaatgtctcccagacattttgaagaaaactcgctgccgtgagtttccatctgcaacctgaaacaatttcctggccatcttgacgaaaaccttgttttctttatctgcaacttaaaaaggtccaatggaccttttcaaaacgttaagttactatcgtaactttctatccacaacctaaaaatgtctcccagacattt aagagttccctcttcttcctatccgtatttcttatacttattatactttattttacagctgatttcaaacgcttccaagttctttgcctaagttttcaaaatttagaaaaatcccgcgattggaaaaattgaagatggacaatggctagatatactattttaagcatctaagagaagaaaaaaggtccaatggaccttttcaaaatgttaagttactaccataactttctatcaaaaacctaaaaatgtctcccagacattttgaagaaaactcgctgccgtgagtttccatctgcaacctgaaacaatttcctggccatcttgacgaaaaccttgttttctttatctgcaacttaaaaaggtccaatggaccttttcaaaacgttaagttactatcgtaactttctatccacaacctaaaaatgtctcccagacattt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAGAGUUCCCUCUUCUUCCUAUCCGUAUUUCUUAUACUUAUUAUACUUUAUUUUACAGCUGAUUUCAAACGCUUCCAAGUUCUUUGCCUAAGUUUUCAAAAUUUAGAAAAAUCCCGCGAUUGGAAAAAUUGAAGAUGGACAAUGGCUAGAUAUACUAUUUUAAGCAUCUAAGAGAAGAAAAAAGGUCCAAUGGACCUUUUCAAAAUGUUAAGUUACUACCAUAACUUUCUAUCAAAAACCUAAAAAUGUCUCCCAGACAUUUUGAAGAAAACUCGCUGCCGUGAGUUUCCAUCUGCAACCUGAAACAAUUUCCUGGCCAUCUUGACGAAAACCUUGUUUUCUUUAUCUGCAACUUAAAAAGGUCCAAUGGACCUUUUCAAAACGUUAAGUUACUAUCGUAACUUUCUAUCCACAACCUAAAAAUGUCUCCCAGACAUUU (((((....))))).........(((.(((((((..((((..(((...(((((..((.(((.((((((....((((((.....((((.....(((((........))))).....))))))))))...)))))).)))....))...)))))...)))..))))....)))))))....((((((((((.((((((((((....(((..((((((......))))))..)))..........((((((((.....))))))))...(.((((((((....)))))))).)...((((.((.(((.....)))..))..........((((((...))))))......)))).....)))))))))).))))))))))....)))..(((((((....)))))))................(((((((.....))))))) (-93.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAUGUCUGGGAGACAUUUUUAGGUUGUGGAUAGAAAGUUACGAUAGUAACUUAACGUUUUGAAAAGGUCCAUUGGACCUUUUUAAGUUGCAGAUAAAGAAAACAAGGUUUUCGUCAAGAUGGCCAGGAAAUUGUUUCAGGUUGCAGAUGGAAACUCACGGCAGCGAGUUUUCUUCAAAAUGUCUGGGAGACAUUUUUAGGUUUUUGAUAGAAAGUUAUGGUAGUAACUUAACAUUUUGAAAAGGUCCAUUGGACCUUUUUUCUUCUCUUAGAUGCUUAAAAUAGUAUAUCUAGCCAUUGUCCAUCUUCAAUUUUUCCAAUCGCGGGAUUUUUCUAAAUUUUGAAAACUUAGGCAAAGAACUUGGAAGCGUUUGAAAUCAGCUGUAAAAUAAAGUAUAAUAAGUAUAAGAAAUACGGAUAGGAAGAAGAGGGAACUCUU (((((((.....)))))))...((..((((((((.(((((((....)))))))...(....(((((((((((.((((((((((((((.((((((..((((((((..(((..((.....))..)))...............(((((.((.(....)))...)))))..)))))))).((((((((.....))))))))......)))).....(((((((....)))))))..)).)))))))))))))).)))))))))))....)..(((((((((......)))..))))))...))))))))..))..(((((((.(((.((.....(((((..((((..((..(((...(((.....))).)))..))..))))..(((.........)))............)))))..))))).)))))))(((....))).. (-117.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 816 120 71 211 162 NC_009009:SSA_1724|5end_CBS_domain_protein,_putative_1710553..1710783_NEGATIVE 453 307 262 226 181 NC_009009:SSA_1268|5end_Chorismate_mutase/prephenate_dehydratase,_putative_1291610..1291840_NEGATIVE 367 319 272 179 130 NC_009009:SSA_0785|5end_Proton-translocating_ATPase,_F1_sector,_delta_subunit,_putative_768044..768274_POSITIVE 348 289 250 67 31 NC_009009:SSA_0086|5end_V-type_sodium_ATPase,_subunit_K,_putative_87839..88069_POSITIVE 345 290 247 63 13 NC_009009:SSA_0219|5end_PTS_system,_sugar-specific_enzyme_IIA_component,_putative_215367..215597_POSITIVE 311 320 273 73 1 NC_009009:SSA_0257|5end_N-acetylmuramidase/lysin,_putative_248878..249108_POSITIVE 308 320 272 76 27 NC_009009:SSA_0481|5end_Cobyric_acid_synthase,_putative_481962..482192_POSITIVE 293 318 271 202 143 NC_009009:SSA_1448|5end_ATP_phosphoribosyltransferase_regulatory_subunit,_putative_1450817..1451047_NEGATIVE 293 340 294 184 135 NC_009009:SSA_0987|5end_ABC-type_choline_transporter,_membrane-spanning_permease,_putative_988994..989224_POSITIVE 292 318 271 163 115 NC_009009:SSA_1196|5end_Acetyltransferase,_GNAT_family,_putative_1222052..1222282_NEGATIVE 292 279 240 73 21 NC_009009:SSA_0778|5end_Glycogen_synthase,_putative_760566..760796_POSITIVE 292 311 272 49 19 NC_009009:SSA_0345|5end_hypothetical_protein_338803..339033_POSITIVE 288 259 225 141 103 NC_009009:SSA_0928|5end_ABC-type_multidrug_transporter,_ATPase_and_permease_components,_putative_936679..936909_POSITIVE 288 320 272 91 32 NC_009009:SSA_0489|5end_Adenosylcobinamide_kinase_/_adenosylcobinamide_phosphate_guanyltransferase,_putative_489655..489885_POSITIVE 285 319 271 62 11 NC_009009:SSA_1070|5end_Ribosomal_large_subunit_pseudouridine_synthase_D,_putative_1088742..1088972_POSITIVE 284 327 286 216 176 NC_009009:SSA_0216|5end_Histidine_kinase,_putative_211877..212107_POSITIVE 283 318 271 127 72 NC_009009:SSA_2161|5end_NTP_pyrophosphohydrolases_including_oxidative_damage_repair_enzymes,_putative_2160600..2160830_NEGATIVE 283 310 266 70 15 NC_009009:SSA_1390|5end_hypothetical_protein_1406118..1406348_NEGATIVE 283 318 273 219 176 NC_009009:SSA_0198|5end_Dihydrofolate_synthetase,_putative_196901..197131_POSITIVE 278 317 272 53 2 NC_009009:SSA_2106|5end_Flavin_monoxygenase,_putative_2109064..2109294_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 466 316 271 84 39 NC_009009:SSA_1269|3end_hypothetical_protein_1291970..1292120_NEGATIVE 352 313 272 150 117 NC_009009:SSA_1960|3end_hypothetical_protein_1956571..1956721_NEGATIVE 308 320 272 91 42 NC_009009:SSA_0480|3end_Cobalt_ABC_transporter,_ATP-binding_protein,_putative_482057..482207_POSITIVE 307 297 252 86 34 NC_009009:SSA_0812|3end_hypothetical_protein_794434..794584_POSITIVE 294 31 2 151 123 NC_009009:SSA_1719|3end_Conserved_uncharacterized_protein_1705924..1706074_NEGATIVE 293 318 271 146 87 NC_009009:SSA_1449|3end_Histidinol-phosphate/aromatic_aminotransferase_and_cobyric_acid_decarboxylase,_putative_1450873..1451023_NEGATIVE 292 279 240 76 24 NC_009009:SSA_0777|3end_Glycogen_biosynthesis_protein_GlgD,_putative_760649..760799_POSITIVE 291 300 251 146 106 NC_009009:SSA_1197|3end_DNA_alkylation_repair_enzyme,_putative_1222049..1222199_NEGATIVE 288 259 225 122 84 NC_009009:SSA_0927|3end_Transcriptional_regulator,_TetR/AcrR_family,_putative_936740..936890_POSITIVE 288 320 272 98 39 NC_009009:SSA_0488|3end_Glutamate-1-semialdehyde_2,1-aminotransferase,_putative_489742..489892_POSITIVE 285 319 271 78 27 NC_009009:SSA_1069|3end_Lipoprotein_signal_peptidase,_putative_1088838..1088988_POSITIVE 285 322 281 145 105 NC_009009:SSA_0999|3end_Biotin--[acetyl-CoA-carboxylase]_ligase,_putative_998781..998931_NEGATIVE 278 296 251 85 25 NC_009009:SSA_0486|3end_Uroporphyrinogen-III_synthase,_putative_487442..487592_POSITIVE 274 319 271 43 3 NC_009009:SSA_1933|3end_(3R)-hydroxymyristoyl-[acyl_carrier_protein]_dehydratase,_putative_1920893..1921043_NEGATIVE 274 320 271 61 2 NC_009009:SSA_1532|3end_Membrane-fusion_protein_/_periplasmic_component_of_efflux_system,_putative_1539460..1539610_NEGATIVE 272 319 276 48 7 NC_009009:SSA_0050|3end_Dihydroxyacetone_kinase,_phosphatase_domain_(Dak2),_putative_55270..55420_POSITIVE 270 318 273 70 29 NC_009009:SSA_1909|3end_Transcriptional_attenuator_LytR,_putative_1900904..1901054_NEGATIVE 270 44 3 53 7 NC_009009:SSA_0040|3end_Phosphoribosylaminoimidazole_carboxylase,_ATPase_subunit,_putative_47479..47629_POSITIVE 264 388 355 101 69 NC_009009:SSA_2355|3end_Conserved_uncharacterized_protein_2356325..2356475_NEGATIVE 264 318 272 111 71 NC_009009:SSA_1439|3end_hypothetical_protein_1443624..1443774_NEGATIVE