Origin IGS: atcaaaatactaagaaaattggaagaagcgagacctaccttgcttctttttctttttttgctaataaactccaaaaataatccagcatattaaaaattttcagaaaatatcgactttttcttgacaggtttatgatactgtgttaaaatactaaacaataagaaaccatctcaaaaaggagttagtcaaacatgaagtcaacccaatcttcaaactttgctttgttgttgcgttactcgggctagtgcaaaagcattagtcctgtttggcttaccaagcgggagtaaatcaacatctcgcttgttcctcaagtgagatgttttttatttcacctatcttacctcaagctctgatgaggaagaa .........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 ttcttcctcatcagagcttgaggtaagataggtgaaataaaaaacatctcacttgaggaacaagcgagatgttgatttactcccgcttggtaagccaaacaggactaatgcttttgcactagcccgagtaacgcaacaacaaagcaaagtttgaagattgggttgacttcatgtttgactaactcctttttgagatggtttcttattgtttagtattttaacacagtatcataaacctgtcaagaaaaagtcgatattttctgaaaatttttaatatgctggattatttttggagtttattagcaaaaaaagaaaaagaagcaaggtaggtctcgcttcttccaattttcttagtattttgat Mask Tandem Repeat Region ================================================ atcaaaatactaagaaaattggaagaagcgagacctaccttgcttctttttctttttttgctaataaactccaaaaataatccagcatattaaaaattttcagaaaatatcgactttttcttgacaggtttatgatactgtgttaaaatactaaacaataagaaaccatctcaaaaaggagttagtcaaacatgaagtcaacccaatcttcaaactttgctttgttgttgcgttactcgggctagtgcaaaagcattagtcctgtttggcttaccaagcgggagtaaatcaacatctcgcttgttcctcaagtgagatgttttttatttcacctatcttacctcaagctctgatgaggaagaa Find is-nt database================================================ Query_seq: SSA_0973:SSA_0975|SSA_0973:SSA_0975:hypothetical protein:2-isopropylmalate synthase, putative:->->:980748..981110 363 atcaaaatactaagaaaattggaagaagcgagacctaccttgcttctttttctttttttgctaataaactccaaaaataatccagcatattaaaaattttcagaaaatatcgactttttcttgacaggtttatgatactgtgttaaaatactaaacaataagaaaccatctcaaaaaggagttagtcaaacatgaagtcaacccaatcttcaaactttgctttgttgttgcgttactcgggctagtgcaaaagcattagtcctgtttggcttaccaagcgggagtaaatcaacatctcgcttgttcctcaagtgagatgttttttatttcacctatcttacctcaagctctgatgaggaagaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0973:SSA_0975|SSA_0973:SSA_0975:hypothetical protein:2-isopropylmalate synthase, putative:->->:980748..981110 363 atcaaaatactaagaaaattggaagaagcgagacctaccttgcttctttttctttttttgctaataaactccaaaaataatccagcatattaaaaattttcagaaaatatcgactttttcttgacaggtttatgatactgtgttaaaatactaaacaataagaaaccatctcaaaaaggagttagtcaaacatgaagtcaacccaatcttcaaactttgctttgttgttgcgttactcgggctagtgcaaaagcattagtcctgtttggcttaccaagcgggagtaaatcaacatctcgcttgttcctcaagtgagatgttttttatttcacctatcttacctcaagctctgatgaggaagaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0973:SSA_0975|SSA_0973:SSA_0975:hypothetical protein:2-isopropylmalate synthase, putative:->->:980748..981110 363 atcaaaatactaagaaaattggaagaagcgagacctaccttgcttctttttctttttttgctaataaactccaaaaataatccagcatattaaaaattttcagaaaatatcgactttttcttgacaggtttatgatactgtgttaaaatactaaacaataagaaaccatctcaaaaaggagttagtcaaacatgaagtcaacccaatcttcaaactttgctttgttgttgcgttactcgggctagtgcaaaagcattagtcctgtttggcttaccaagcgggagtaaatcaacatctcgcttgttcctcaagtgagatgttttttatttcacctatcttacctcaagctctgatgaggaagaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 atcaaaatactaagaaaattggaagaagcgagacctaccttgcttctttttctttttttgctaataaactccaaaaataatccagcatattaaaaattttcagaaaatatcgactttttcttgacaggtttatgatactgtgttaaaatactaaacaataagaaaccatctcaaaaaggagttagtcaaacatgaagtcaacccaatcttcaaactttgctttgttgttgcgttactcgggctagtgcaaaagcattagtcctgtttggcttaccaagcgggagtaaatcaacatctcgcttgttcctcaagtgagatgttttttatttcacctatcttacctcaagctctgatgaggaagaa Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: + Start: 1 End: 90 M K I L R K L E E A R P T L L L F L F L L I N S K N N P A Y ................................................................................................................................................................................................................................................................................. Protein_Len: 33 Strand: + Start: 158 End: 256 ............................................................................................................................................................. M R N H L K K E L V K H E V N P I F K L C F V V A L L G L V Q K H ........................................................................................................... Protein_Len: 32 Strand: + Start: 217 End: 312 ........................................................................................................................................................................................................................ M L C C C V T R A S A K A L V L F G L P S G S K S T S R L F L K ................................................... Protein_Len: 32 Strand: + Start: 266 End: 361 ......................................................................................................................................................................................................................................................................... M A Y Q A G V N Q H L A C S S S E M F F I S P I L P Q A L M R K .. Protein_Len: 33 Strand: - Start: 213 End: 311 .................................................................................................................................................................................................................... V K S Q Q Q T V R A L A F A N T R N P K G L P L L D V D R K N R M .................................................... Protein_Len: 33 Strand: - Start: 38 End: 136 ..................................... R A E K E K K A L L S W F Y D L M N F I K L F Y R S K R S L N I M ................................................................................................................................................................................................................................... atcaaaatactaagaaaattggaagaagcgagacctaccttgcttctttttctttttttgctaataaactccaaaaataatccagcatattaaaaattttcagaaaatatcgactttttcttgacaggtttatgatactgtgttaaaatactaaacaataagaaaccatctcaaaaaggagttagtcaaacatgaagtcaacccaatcttcaaactttgctttgttgttgcgttactcgggctagtgcaaaagcattagtcctgtttggcttaccaagcgggagtaaatcaacatctcgcttgttcctcaagtgagatgttttttatttcacctatcttacctcaagctctgatgaggaagaa 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: 90 Start: 120 End: 149 .......................................................................................................................CTTGACAGGTTTATGATACTGTGTTAAAAT...................................................................................................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ atcaaaatactaagaaaattggaagaagcgagacctaccttgcttctttttctttttttgctaataaactccaaaaataatccagcatattaaaaattttcagaaaatatcgactttttcttgacaggtttatgatactgtgttaaaatactaaacaataagaaaccatctcaaaaaggagttagtcaaacatgaagtcaacccaatcttcaaactttgctttgttgttgcgttactcgggctagtgcaaaagcattagtcctgtttggcttaccaagcgggagtaaatcaacatctcgcttgttcctcaagtgagatgttttttatttcacctatcttacctcaagctctgatgaggaagaa Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 81 HP_score: -9.6 Tail_Score: -3.46068 Start: 239 End: 262 Full_Region: GTTGTTGCGTTACTC GGGCTAGTGC AAAA GCATTAGTCC TGTTTGGCTTACCAA ..............................................................................................................................................................................................................................................GGGCTAGTGCAAAAGCATTAGTCC..................................................................................................... TransTerm Strand: + Conf: 59 HP_score: -6.1 Tail_Score: -3.16683 Start: 275 End: 303 Full_Region: TCCTGTTTGGCTTAC CAAGCGGGAGT AAATCA ACATCTCGCTTG TTCCTCAAGTGAGAT ..................................................................................................................................................................................................................................................................................CAAGCGGGAGTAAATCAACATCTCGCTTG............................................................ TransTerm Strand: + Conf: 50 HP_score: -2.0 Tail_Score: -3.7282 Start: 278 End: 300 Full_Region: TGTTTGGCTTACCAA GCGGGAGT AAATCA ACATCTCGC TTGTTCCTCAAGTGA .....................................................................................................................................................................................................................................................................................GCGGGAGTAAATCAACATCTCGC............................................................... TransTerm Strand: + Conf: 100 HP_score: -11.7 Tail_Score: -5.64421 Start: 293 End: 319 Full_Region: GCGGGAGTAAATCAA CATCTCGCTTG TTCCT CAAGTGAGATG TTTTTTATTTCACCT ....................................................................................................................................................................................................................................................................................................CATCTCGCTTGTTCCTCAAGTGAGATG............................................ TransTerm Strand: - Conf: 80 HP_score: -9.5 Tail_Score: -3.56704 Start: 293 End: 319 Full_Region: aggtgaaataaaaaa catctcacttg aggaa caagcgagatg ttgatttactcccgc ....................................................................................................................................................................................................................................................................................................catctcacttgaggaacaagcgagatg............................................ Find igs database================================================ Query_seq: SSA_0973:SSA_0975|SSA_0973:SSA_0975:hypothetical protein:2-isopropylmalate synthase, putative:->->:980748..981110 363 atcaaaatactaagaaaattggaagaagcgagacctaccttgcttctttttctttttttgctaataaactccaaaaataatccagcatattaaaaattttcagaaaatatcgactttttcttgacaggtttatgatactgtgttaaaatactaaacaataagaaaccatctcaaaaaggagttagtcaaacatgaagtcaacccaatcttcaaactttgctttgttgttgcgttactcgggctagtgcaaaagcattagtcctgtttggcttaccaagcgggagtaaatcaacatctcgcttgttcctcaagtgagatgttttttatttcacctatcttacctcaagctctgatgaggaagaa Intra-Species Hit: Count: 1 Min: 1 Max: 363 Len: 363 Subject: NC_009009_SSA_0973_SSA_0975|hypothetical protein:2-isopropylmalate synthase, putative|POSITIVE:POSITIVE|[980748,981110]|363 HSP 1 e-value: 1.0E-171 bit: 603.0 Len: 304 Query Start:60 Query End:363 Subject Strand: POSITIVE Subject Start: 60 Subject End: 363 ...........................................................gctaataaactccaaaaataatccagcatattaaaaattttcagaaaatatcgactttttcttgacaggtttatgatactgtgttaaaatactaaacaataagaaaccatctcaaaaaggagttagtcaaacatgaagtcaacccaatcttcaaactttgctttgttgttgcgttactcgggctagtgcaaaagcattagtcctgtttggcttaccaagcgggagtaaatcaacatctcgcttgttcctcaagtgagatgttttttatttcacctatcttacctcaagctctgatgaggaagaa ...........................................................gctaataaactccaaaaataatccagcatattaaaaattttcagaaaatatcgactttttcttgacaggtttatgatactgtgttaaaatactaaacaataagaaaccatctcaaaaaggagttagtcaaacatgaagtcaacccaatcttcaaactttgctttgttgttgcgttactcgggctagtgcaaaagcattagtcctgtttggcttaccaagcgggagtaaatcaacatctcgcttgttcctcaagtgagatgttttttatttcacctatcttacctcaagctctgatgaggaagaa HSP 2 e-value: 2.0E-17 bit: 91.7 Len: 46 Query Start:1 Query End:46 Subject Strand: POSITIVE Subject Start: 1 Subject End: 46 atcaaaatactaagaaaattggaagaagcgagacctaccttgcttc............................................................................................................................................................................................................................................................................................................................. atcaaaatactaagaaaattggaagaagcgagacctaccttgcttc............................................................................................................................................................................................................................................................................................................................. Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUCAAAAUACUAAGAAAAUUGGAAGAAGCGAGACCUACCUUGCUUCUUUUUCUUUUUUUGCUAAUAAACUCCAAAAAUAAUCCAGCAUAUUAAAAAUUUUCAGAAAAUAUCGACUUUUUCUUGACAGGUUUAUGAUACUGUGUUAAAAUACUAAACAAUAAGAAACCAUCUCAAAAAGGAGUUAGUCAAACAUGAAGUCAACCCAAUCUUCAAACUUUGCUUUGUUGUUGCGUUACUCGGGCUAGUGCAAAAGCAUUAGUCCUGUUUGGCUUACCAAGCGGGAGUAAAUCAACAUCUCGCUUGUUCCUCAAGUGAGAUGUUUUUUAUUUCACCUAUCUUACCUCAAGCUCUGAUGAGGAAGAA ...........(((((((..((((((((((((......))))))))))))..)))))))(((....((((((.....(((..(((..(((((.((((((((((((((........))))).))).)))))).))))))))..)))...............(((.....)))......)))))).(((((((....(((.(((.((((...((((......))))..)))).)))))).((((((((((....)))))))))).)))))))......))).((((((((..(((((((((((((.....))))))))))))).)))))))).....((((.(((((........))))))))). (-103.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUCUUCCUCAUCAGAGCUUGAGGUAAGAUAGGUGAAAUAAAAAACAUCUCACUUGAGGAACAAGCGAGAUGUUGAUUUACUCCCGCUUGGUAAGCCAAACAGGACUAAUGCUUUUGCACUAGCCCGAGUAACGCAACAACAAAGCAAAGUUUGAAGAUUGGGUUGACUUCAUGUUUGACUAACUCCUUUUUGAGAUGGUUUCUUAUUGUUUAGUAUUUUAACACAGUAUCAUAAACCUGUCAAGAAAAAGUCGAUAUUUUCUGAAAAUUUUUAAUAUGCUGGAUUAUUUUUGGAGUUUAUUAGCAAAAAAAGAAAAAGAAGCAAGGUAGGUCUCGCUUCUUCCAAUUUUCUUAGUAUUUUGAU .(((((((((........))))).))))...(((........((((((((.((((.....)))).))))))))...((((((..(.((((....)))).).((.(((.(((....))).))))).)))))))))..........((((((..(((((((((......(((...((((((...(((......)))..(((((..((((((((((....)))).))))))....))))).)))))).....((..(((..(((..(((((.((((......))))..)))))..)))..)))..)).......))).(((((((.(((....))).)))))))))))))))).....)))))).. (-92.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 350 226 181 86 41 NC_009009:SSA_1072|5end_Glutamate_5-kinase,_putative_1089755..1089985_POSITIVE 337 280 238 218 160 NC_009009:SSA_2042|5end_hypothetical_protein_2047073..2047303_NEGATIVE 326 279 231 163 92 NC_009009:SSA_0760|5end_Acetylornithine_aminotransferase,_putative_742581..742811_POSITIVE 321 248 202 63 15 NC_009009:SSA_1606|5end_Dephospho-CoA_kinase,_putative_1612425..1612655_NEGATIVE 318 280 231 146 98 NC_009009:SSA_1605|5end_Major_facilitator_superfamily_multi-drug_resistance_efflux_pump_pmrA,_putative_1611732..1611962_NEGATIVE 317 286 242 203 155 NC_009009:SSA_1179|5end_Carbamoylphosphate_synthase_large_subunit_/_biotin_carboxylase,_putative_1207806..1208036_NEGATIVE 316 70 21 167 118 NC_009009:SSA_1010|5end_UDP-glucose_4-epimerase,_putative_1012739..1012969_POSITIVE 314 309 261 158 101 NC_009009:SSA_1040|5end_Sugar_ABC_transporter,_permease_protein,_putative_1055302..1055532_POSITIVE 313 286 241 202 166 NC_009009:SSA_2275|5end_hypothetical_protein_2275590..2275820_NEGATIVE 313 63 23 96 51 NC_009009:SSA_1901|5end_Conserved_uncharacterized_protein_1896599..1896829_NEGATIVE 311 279 232 202 150 NC_009009:SSA_0102|5end_Kinase,_putative_104035..104265_POSITIVE 307 299 252 204 162 NC_009009:SSA_1694|5end_PTS_system,_lactose-specific_IIA_component,_putative_1687128..1687358_NEGATIVE 304 266 221 155 117 NC_009009:SSA_0143|5end_Conserved_uncharacterized_protein_137465..137695_POSITIVE 300 280 242 44 1 NC_009009:SSA_0282|5end_Phosphotransferase_system_(PTS),_cellobiose-specific_IIA_component,_putative_274215..274445_POSITIVE 297 299 253 213 158 NC_009009:SSA_1769|5end_hypothetical_protein_1757490..1757720_NEGATIVE 297 275 236 80 43 NC_009009:SSA_1650|5end_3-Ketoacyl-ACP_reductase,_putative_1649594..1649824_NEGATIVE 297 308 269 185 143 NC_009009:SSA_0875|5end_Rod_shape_determining_protein_(cell-cycle_protein),_putative_868928..869158_POSITIVE 295 278 231 167 113 NC_009009:SSA_1804|5end_NADPH-flavin_oxidoreductase,_putative_1788668..1788898_NEGATIVE 293 239 196 114 59 NC_009009:SSA_2125|5end_Small_primase-like_protein_(Toprim_domain),_putative_2130019..2130249_NEGATIVE 291 232 197 73 30 NC_009009:SSA_2014|5end_D-alanyl-D-alanine_carboxypeptidase,_putative_2014807..2015037_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 321 248 202 57 9 NC_009009:SSA_1607|3end_Formamidopyrimidine-DNA_glycosylase,_putative_1612431..1612581_NEGATIVE 318 280 231 49 1 NC_009009:SSA_1606|3end_Dephospho-CoA_kinase,_putative_1611829..1611979_NEGATIVE 304 266 221 99 61 NC_009009:SSA_0142|3end_hypothetical_protein_137489..137639_POSITIVE 297 275 236 87 50 NC_009009:SSA_1651|3end_hypothetical_protein_1649587..1649737_NEGATIVE 293 239 196 148 93 NC_009009:SSA_2126|3end_hypothetical_protein_2129985..2130135_NEGATIVE 291 232 197 86 43 NC_009009:SSA_2015|3end_Phosphoglycerate_mutase,_putative_2014794..2014944_NEGATIVE 288 279 239 145 88 NC_009009:SSA_2198|3end_hypothetical_protein_2197842..2197992_NEGATIVE 287 248 202 147 86 NC_009009:SSA_1380|3end_hypothetical_protein_1398538..1398688_NEGATIVE 287 279 231 73 16 NC_009009:SSA_0488|3end_Glutamate-1-semialdehyde_2,1-aminotransferase,_putative_489742..489892_POSITIVE 283 62 28 112 71 NC_009009:SSA_2139|3end_Membrane_protein_(preprotein_translocase)_oxaA_1_precursor,_putative_2139509..2139659_NEGATIVE 282 308 266 60 21 NC_009009:SSA_0863|3end_Cof_family_protein,_putative_854206..854356_NEGATIVE 281 310 263 57 8 NC_009009:SSA_2318|3end_PilB-like_pili_biogenesis_ATPase,_putative_2319412..2319562_NEGATIVE 280 283 258 59 36 NC_009009:SSA_1529|3end_Lysyl-tRNA_synthetase,_putative_1537441..1537591_POSITIVE 280 319 276 112 64 NC_009009:SSA_1309|3end_RNA-binding_protein_(KH_domain),_putative_1327079..1327229_NEGATIVE 279 44 9 39 4 NC_009009:SSA_1131|3end_High-affinity_Fe_2+/Pb2+_permease,_putative_1158768..1158918_POSITIVE 277 48 2 89 47 NC_009009:SSA_1870|3end_Phospho-N-acetylmuramoyl-pentapeptide-_transferase,_putative_1865600..1865750_NEGATIVE 276 308 273 77 48 NC_009009:SSA_0415|3end_Permease,_putative_411730..411880_POSITIVE 275 309 262 108 51 NC_009009:SSA_2334|3end_D-alanine--D-alanyl_carrier_protein_ligase,_putative_2336457..2336607_NEGATIVE 274 349 306 106 60 NC_009009:SSA_2364|3end_Immunodominant_staphylococcal_antigen_A_precursor,_putative_2366442..2366592_NEGATIVE 274 246 206 74 27 NC_009009:SSA_1013|3end_Phosphatidylserine_synthase,_putative_1017933..1018083_POSITIVE