Origin IGS: aaaatcactttcttcatgggtgtaatatttattaaaagtttaagggctattctggctggaaagtacatttgaagccacttttacttttctgctattctatatttgtcttagaatgtgtttatattataacatagttatagacaaataaaccgtttgcaagactgaaacttatcaagagtgtacagctgagactgatttgtaagtattgaaatgaatcaaatctatatcggcttttcctatcagtttgagatgcctgtttagtaatctctgactgtttttctgaaaatatgttataatttatgcaagtacgaagctgtattcctgaagatgatttgccagatggttggactgtcagccaggaatgcagattttaaaatccgttttcgaaggtttttgaaaacgagggggtgaatag .........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 ctattcaccccctcgttttcaaaaaccttcgaaaacggattttaaaatctgcattcctggctgacagtccaaccatctggcaaatcatcttcaggaatacagcttcgtacttgcataaattataacatattttcagaaaaacagtcagagattactaaacaggcatctcaaactgataggaaaagccgatatagatttgattcatttcaatacttacaaatcagtctcagctgtacactcttgataagtttcagtcttgcaaacggtttatttgtctataactatgttataatataaacacattctaagacaaatatagaatagcagaaaagtaaaagtggcttcaaatgtactttccagccagaatagcccttaaacttttaataaatattacacccatgaagaaagtgatttt Mask Tandem Repeat Region ================================================ aaaatcactttcttcatgggtgtaatatttattaaaagtttaagggctattctggctggaaagtacatttgaagccacttttacttttctgctattctatatttgtcttagaatgtgtttatattataacatagttatagacaaataaaccgtttgcaagactgaaacttatcaagagtgtacagctgagactgatttgtaagtattgaaatgaatcaaatctatatcggcttttcctatcagtttgagatgcctgtttagtaatctctgactgtttttctgaaaatatgttataatttatgcaagtacgaagctgtattcctgaagatgatttgccagatggttggactgtcagccaggaatgcagattttaaaatccgttttcgaaggtttttgaaaacgagggggtgaatag Find is-nt database================================================ Query_seq: SSA_0081:SSA_0083|SSA_0081:SSA_0083:Transcriptional regulator, RpiR family (phosphosugar-binding), putative:hypothetical protein:<-->:85162..85576 415 aaaatcactttcttcatgggtgtaatatttattaaaagtttaagggctattctggctggaaagtacatttgaagccacttttacttttctgctattctatatttgtcttagaatgtgtttatattataacatagttatagacaaataaaccgtttgcaagactgaaacttatcaagagtgtacagctgagactgatttgtaagtattgaaatgaatcaaatctatatcggcttttcctatcagtttgagatgcctgtttagtaatctctgactgtttttctgaaaatatgttataatttatgcaagtacgaagctgtattcctgaagatgatttgccagatggttggactgtcagccaggaatgcagattttaaaatccgttttcgaaggtttttgaaaacgagggggtgaatag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0081:SSA_0083|SSA_0081:SSA_0083:Transcriptional regulator, RpiR family (phosphosugar-binding), putative:hypothetical protein:<-->:85162..85576 415 aaaatcactttcttcatgggtgtaatatttattaaaagtttaagggctattctggctggaaagtacatttgaagccacttttacttttctgctattctatatttgtcttagaatgtgtttatattataacatagttatagacaaataaaccgtttgcaagactgaaacttatcaagagtgtacagctgagactgatttgtaagtattgaaatgaatcaaatctatatcggcttttcctatcagtttgagatgcctgtttagtaatctctgactgtttttctgaaaatatgttataatttatgcaagtacgaagctgtattcctgaagatgatttgccagatggttggactgtcagccaggaatgcagattttaaaatccgttttcgaaggtttttgaaaacgagggggtgaatag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0081:SSA_0083|SSA_0081:SSA_0083:Transcriptional regulator, RpiR family (phosphosugar-binding), putative:hypothetical protein:<-->:85162..85576 415 aaaatcactttcttcatgggtgtaatatttattaaaagtttaagggctattctggctggaaagtacatttgaagccacttttacttttctgctattctatatttgtcttagaatgtgtttatattataacatagttatagacaaataaaccgtttgcaagactgaaacttatcaagagtgtacagctgagactgatttgtaagtattgaaatgaatcaaatctatatcggcttttcctatcagtttgagatgcctgtttagtaatctctgactgtttttctgaaaatatgttataatttatgcaagtacgaagctgtattcctgaagatgatttgccagatggttggactgtcagccaggaatgcagattttaaaatccgttttcgaaggtttttgaaaacgagggggtgaatag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aaaatcactttcttcatgggtgtaatatttattaaaagtttaagggctattctggctggaaagtacatttgaagccacttttacttttctgctattctatatttgtcttagaatgtgtttatattataacatagttatagacaaataaaccgtttgcaagactgaaacttatcaagagtgtacagctgagactgatttgtaagtattgaaatgaatcaaatctatatcggcttttcctatcagtttgagatgcctgtttagtaatctctgactgtttttctgaaaatatgttataatttatgcaagtacgaagctgtattcctgaagatgatttgccagatggttggactgtcagccaggaatgcagattttaaaatccgttttcgaaggtttttgaaaacgagggggtgaatag Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: + Start: 56 End: 145 ....................................................... M E S T F E A T F T F L L F Y I C L R M C L Y Y N I V I D K .............................................................................................................................................................................................................................................................................. Protein_Len: 47 Strand: + Start: 268 End: 408 ........................................................................................................................................................................................................................................................................... M T V F L K I C Y N L C K Y E A V F L K M I C Q M V G L S A R N A D F K I R F R R F L K T R G ....... Protein_Len: 40 Strand: - Start: 294 End: 413 ..................................................................................................................................................................................................................................................................................................... L K H L Y S A T N R F I I Q W I T P S D A L F A S K L I R K R L N K F V L P H M .. Protein_Len: 41 Strand: - Start: 175 End: 297 .............................................................................................................................................................................. S H V A S V S K Y T N F H I L D I D A K G I L K L H R N L L R Q S N K Q F Y T I M ...................................................................................................................... Protein_Len: 60 Strand: - Start: 122 End: 367 ......................................................................................................................... L S I Q L Y Q F S D F R Y R S K R D T Q S A Q K T I E S Q K E S F I N Y N I C T R L Q I G S S S K G S P Q V T L W S H M ................................................ aaaatcactttcttcatgggtgtaatatttattaaaagtttaagggctattctggctggaaagtacatttgaagccacttttacttttctgctattctatatttgtcttagaatgtgtttatattataacatagttatagacaaataaaccgtttgcaagactgaaacttatcaagagtgtacagctgagactgatttgtaagtattgaaatgaatcaaatctatatcggcttttcctatcagtttgagatgcctgtttagtaatctctgactgtttttctgaaaatatgttataatttatgcaagtacgaagctgtattcctgaagatgatttgccagatggttggactgtcagccaggaatgcagattttaaaatccgttttcgaaggtttttgaaaacgagggggtgaatag Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aaaatcactttcttcatgggtgtaatatttattaaaagtttaagggctattctggctggaaagtacatttgaagccacttttacttttctgctattctatatttgtcttagaatgtgtttatattataacatagttatagacaaataaaccgtttgcaagactgaaacttatcaagagtgtacagctgagactgatttgtaagtattgaaatgaatcaaatctatatcggcttttcctatcagtttgagatgcctgtttagtaatctctgactgtttttctgaaaatatgttataatttatgcaagtacgaagctgtattcctgaagatgatttgccagatggttggactgtcagccaggaatgcagattttaaaatccgttttcgaaggtttttgaaaacgagggggtgaatag Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_0081:SSA_0083|SSA_0081:SSA_0083:Transcriptional regulator, RpiR family (phosphosugar-binding), putative:hypothetical protein:<-->:85162..85576 415 aaaatcactttcttcatgggtgtaatatttattaaaagtttaagggctattctggctggaaagtacatttgaagccacttttacttttctgctattctatatttgtcttagaatgtgtttatattataacatagttatagacaaataaaccgtttgcaagactgaaacttatcaagagtgtacagctgagactgatttgtaagtattgaaatgaatcaaatctatatcggcttttcctatcagtttgagatgcctgtttagtaatctctgactgtttttctgaaaatatgttataatttatgcaagtacgaagctgtattcctgaagatgatttgccagatggttggactgtcagccaggaatgcagattttaaaatccgttttcgaaggtttttgaaaacgagggggtgaatag Intra-Species Hit: Count: 1 Min: 1 Max: 415 Len: 415 Subject: NC_009009_SSA_0081_SSA_0083|Transcriptional regulator, RpiR family (phosphosugar-binding), putative:hypothetical protein|NEGATIVE:POSITIVE|[85162,85576]|415 HSP 1 e-value: 0.0 bit: 823.0 Len: 415 Query Start:1 Query End:415 Subject Strand: POSITIVE Subject Start: 1 Subject End: 415 aaaatcactttcttcatgggtgtaatatttattaaaagtttaagggctattctggctggaaagtacatttgaagccacttttacttttctgctattctatatttgtcttagaatgtgtttatattataacatagttatagacaaataaaccgtttgcaagactgaaacttatcaagagtgtacagctgagactgatttgtaagtattgaaatgaatcaaatctatatcggcttttcctatcagtttgagatgcctgtttagtaatctctgactgtttttctgaaaatatgttataatttatgcaagtacgaagctgtattcctgaagatgatttgccagatggttggactgtcagccaggaatgcagattttaaaatccgttttcgaaggtttttgaaaacgagggggtgaatag aaaatcactttcttcatgggtgtaatatttattaaaagtttaagggctattctggctggaaagtacatttgaagccacttttacttttctgctattctatatttgtcttagaatgtgtttatattataacatagttatagacaaataaaccgtttgcaagactgaaacttatcaagagtgtacagctgagactgatttgtaagtattgaaatgaatcaaatctatatcggcttttcctatcagtttgagatgcctgtttagtaatctctgactgtttttctgaaaatatgttataatttatgcaagtacgaagctgtattcctgaagatgatttgccagatggttggactgtcagccaggaatgcagattttaaaatccgttttcgaaggtttttgaaaacgagggggtgaatag Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAAUCACUUUCUUCAUGGGUGUAAUAUUUAUUAAAAGUUUAAGGGCUAUUCUGGCUGGAAAGUACAUUUGAAGCCACUUUUACUUUUCUGCUAUUCUAUAUUUGUCUUAGAAUGUGUUUAUAUUAUAACAUAGUUAUAGACAAAUAAACCGUUUGCAAGACUGAAACUUAUCAAGAGUGUACAGCUGAGACUGAUUUGUAAGUAUUGAAAUGAAUCAAAUCUAUAUCGGCUUUUCCUAUCAGUUUGAGAUGCCUGUUUAGUAAUCUCUGACUGUUUUUCUGAAAAUAUGUUAUAAUUUAUGCAAGUACGAAGCUGUAUUCCUGAAGAUGAUUUGCCAGAUGGUUGGACUGUCAGCCAGGAAUGCAGAUUUUAAAAUCCGUUUUCGAAGGUUUUUGAAAACGAGGGGGUGAAUAG ....(((((..(..((((((((((((((.......((((((.((.((.....((((.((((((((.(..((....))..).)))))))).)))).....(((((((((.....((((((........)))))).....)))))))))........))....)).)))))).(((.(((.....((((((....((((((....(((....)))...))))))....))))))........(((((.(((((..((....))..))))).)))))...))))))....))))))).))))))).......(((((((((((((((....((((...((((....))))...))))..))))))))))).))))......((((((((((....)))))))))).)..))))).... (-107.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUAUUCACCCCCUCGUUUUCAAAAACCUUCGAAAACGGAUUUUAAAAUCUGCAUUCCUGGCUGACAGUCCAACCAUCUGGCAAAUCAUCUUCAGGAAUACAGCUUCGUACUUGCAUAAAUUAUAACAUAUUUUCAGAAAAACAGUCAGAGAUUACUAAACAGGCAUCUCAAACUGAUAGGAAAAGCCGAUAUAGAUUUGAUUCAUUUCAAUACUUACAAAUCAGUCUCAGCUGUACACUCUUGAUAAGUUUCAGUCUUGCAAACGGUUUAUUUGUCUAUAACUAUGUUAUAAUAUAAACACAUUCUAAGACAAAUAUAGAAUAGCAGAAAAGUAAAAGUGGCUUCAAAUGUACUUUCCAGCCAGAAUAGCCCUUAAACUUUUAAUAAAUAUUACACCCAUGAAGAAAGUGAUUUU ....((((....((((((((..........))))))))..........(((.((((((((.(((....(((......)))....)))...)))))))).)))((((((...(((....(((((((((((.((..(((....((((..(((((..((....))..)))))..)))).......((((((.....((((((.................)))))).((....((((...(((.......)))..))))...))...)))))).....)))..)).)))))))))))........((((((.........)))))).))).((((((..(((.((((......((........))......)))))))..))))))................))))))...)))).... (-80.23) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 856 90 41 181 132 NC_009009:SSA_0081|5end_Transcriptional_regulator,_RpiR_family_(phosphosugar-binding),_putative_85071..85301_NEGATIVE 378 380 337 211 171 NC_009009:SSA_0346|5end_hypothetical_protein_339448..339678_POSITIVE 336 357 312 188 149 NC_009009:SSA_0143|5end_Conserved_uncharacterized_protein_137465..137695_POSITIVE 330 360 311 51 3 NC_009009:SSA_2363|5end_Phosphoglycolate_phosphatase,_putative_2365632..2365862_POSITIVE 327 90 42 223 171 NC_009009:SSA_1712|5end_Arsenate_reductase_(ArsC),_glutaredoxin_family,_putative_1700084..1700314_NEGATIVE 325 347 306 208 169 NC_009009:SSA_1974|5end_ABC-type_multidrug_transport_system,_permease_component,_putative_1970246..1970476_NEGATIVE 319 360 311 60 7 NC_009009:SSA_1379|5end_hypothetical_protein_1398528..1398758_NEGATIVE 318 387 341 60 16 NC_009009:SSA_1577|5end_Proline_dipeptidase,_putative_1580294..1580524_POSITIVE 314 379 334 62 1 NC_009009:SSA_0838|5end_GtfB,_putative_825406..825636_POSITIVE 311 200 151 61 13 NC_009009:SSA_2364|5end_Immunodominant_staphylococcal_antigen_A_precursor,_putative_2367032..2367262_NEGATIVE 310 358 311 228 165 NC_009009:SSA_0884|5end_hypothetical_protein_879063..879293_NEGATIVE 308 283 242 222 176 NC_009009:SSA_0218|5end_Sugar-binding_periplasmic_protein,_putative_213863..214093_POSITIVE 306 360 311 74 20 NC_009009:SSA_0190|5end_hypothetical_protein_191481..191711_POSITIVE 301 358 312 170 121 NC_009009:SSA_0978|5end_hypothetical_protein_983736..983966_POSITIVE 299 356 312 41 7 NC_009009:SSA_2353|5end_ABC-type_nitrate/sulfonate/bicarbonate_transport_system,_permease_component,_putative_2355302..2355532_NEGATIVE 298 86 41 170 122 NC_009009:SSA_2366|5end_ABC-type_cobalt_transport_system,_ATPase_component,_putative_2368869..2369099_NEGATIVE 297 359 312 40 1 NC_009009:SSA_2228|5end_Acetyltransferase_(GNAT)_family,_putative_2228768..2228998_NEGATIVE 296 367 321 45 4 NC_009009:SSA_1738|5end_Polysaccharide_biosynthesis_protein,_putative_1725503..1725733_NEGATIVE 293 360 319 228 174 NC_009009:SSA_2340|5end_hypothetical_protein_2342843..2343073_NEGATIVE 293 259 216 159 114 NC_009009:SSA_2217|5end_Cps9H,_putative_2219045..2219275_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 379 369 321 146 102 NC_009009:SSA_0390|3end_hypothetical_protein_385714..385864_POSITIVE 336 357 312 132 93 NC_009009:SSA_0142|3end_hypothetical_protein_137489..137639_POSITIVE 327 90 42 98 46 NC_009009:SSA_1713|3end_D-3-phosphoglycerate_dehydrogenase,_putative_1700209..1700359_NEGATIVE 314 379 334 78 17 NC_009009:SSA_0837|3end_Glucosyltransferase,_putative_825502..825652_POSITIVE 308 366 329 151 113 NC_009009:SSA_2268|3end_Type_II_secretory_pathway,_pullulanase_PulA_glycosidase,_putative_2269386..2269536_POSITIVE 293 259 216 81 36 NC_009009:SSA_2218|3end_Glycosyltransferase_(cell_wall_biogenesis)_Cps9G,_putative_2219123..2219273_NEGATIVE 291 256 213 114 58 NC_009009:SSA_0509|3end_Propanediol_utilization_protein,_putative_508538..508688_POSITIVE 291 80 39 148 106 NC_009009:SSA_0453|3end_Type_II_secretory_pathway,_pullulanase_PulA_glycosidase,_putative_455993..456143_POSITIVE 290 357 311 59 10 NC_009009:SSA_0776|3end_Glucose-1-phosphate_adenylyltransferase,_putative_759520..759670_POSITIVE 287 369 321 86 36 NC_009009:SSA_1778|3end_Segregation_and_condensation_protein_B,_putative_1765142..1765292_NEGATIVE 287 358 319 140 112 NC_009009:SSA_1722|3end_Thymidylate_kinase,_putative_1708025..1708175_NEGATIVE 286 365 336 34 5 NC_009009:SSA_1299|3end_Maltose/maltodextrin_ABC_transport_system,_putative_1318067..1318217_POSITIVE 284 346 305 44 7 NC_009009:SSA_1912|3end_hypothetical_protein_1903113..1903263_NEGATIVE 284 270 221 136 84 NC_009009:SSA_0466|3end_Precorrin-8X_methylmutase_/_precorrin_isomerase,_putative_470668..470818_POSITIVE 280 369 335 146 115 NC_009009:SSA_1958|3end_Adapter_protein_mecA,_putative_1954661..1954811_NEGATIVE 279 257 226 94 63 NC_009009:SSA_0486|3end_Uroporphyrinogen-III_synthase,_putative_487442..487592_POSITIVE 278 360 312 137 85 NC_009009:SSA_0944|3end_Phosphate_import_ATP-binding_protein_pstB_2,_putative_952624..952774_POSITIVE 278 367 321 56 7 NC_009009:SSA_0497|3end_Nickel_ABC_transporter,_putative_497997..498147_POSITIVE 276 395 351 53 7 NC_009009:SSA_1697|3end_Tagatose-6-phosphate_kinase,_putative_1689191..1689341_NEGATIVE 275 77 43 132 98 NC_009009:SSA_2145|3end_Tributyrin_esterase,_putative_2145879..2146029_NEGATIVE