Origin IGS: ctcattcctccttatattctatctatcatatcaaaaaatagtaaaattttctagtttaattctaaataaaaaggtccactggaccttgattaaagggaactcgcaagggcgagtctttatctgcaacctaaaacagctcctatctatagattaaaaaggttccccgaaccttattaaagagcactcgcttaaccgagtgcttagccacaacctaaaaatacccgttaggcttgtctcagggtaaaccgactaccgtcggttctcatccgcagattaaaaaagtccaccgaaccttggattaaggagaactcgcaaaagcgagtttttatctgcaacctaaaacagtcctctggactgtt .........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 aacagtccagaggactgttttaggttgcagataaaaactcgcttttgcgagttctccttaatccaaggttcggtggacttttttaatctgcggatgagaaccgacggtagtcggtttaccctgagacaagcctaacgggtatttttaggttgtggctaagcactcggttaagcgagtgctctttaataaggttcggggaacctttttaatctatagataggagctgttttaggttgcagataaagactcgcccttgcgagttccctttaatcaaggtccagtggacctttttatttagaattaaactagaaaattttactattttttgatatgatagatagaatataaggaggaatgag Mask Tandem Repeat Region ================================================ ctcattcctccttatattctatctatcatatcaaaaaatagtaaaattttctagtttaattctaaataaaaaggtccactggaccttgattaaagggaactcgcaagggcgagtctttatctgcaacctaaaacagctcctatctatagattaaaaaggttccccgaaccttattaaagagcactcgcttaaccgagtgcttagccacaacctaaaaatacccgttaggcttgtctcagggtaaaccgactaccgtcggttctcatccgcagattaaaaaagtccaccgaaccttggattaaggagaactcgcaaaagcgagtttttatctgcaacctaaaacagtcctctggactgtt Find is-nt database================================================ Query_seq: SSA_1268:SSA_1269|SSA_1268:SSA_1269:Chorismate mutase/prephenate dehydratase, putative:hypothetical protein:<-<-:1291701..1292059 359 ctcattcctccttatattctatctatcatatcaaaaaatagtaaaattttctagtttaattctaaataaaaaggtccactggaccttgattaaagggaactcgcaagggcgagtctttatctgcaacctaaaacagctcctatctatagattaaaaaggttccccgaaccttattaaagagcactcgcttaaccgagtgcttagccacaacctaaaaatacccgttaggcttgtctcagggtaaaccgactaccgtcggttctcatccgcagattaaaaaagtccaccgaaccttggattaaggagaactcgcaaaagcgagtttttatctgcaacctaaaacagtcctctggactgtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1268:SSA_1269|SSA_1268:SSA_1269:Chorismate mutase/prephenate dehydratase, putative:hypothetical protein:<-<-:1291701..1292059 359 ctcattcctccttatattctatctatcatatcaaaaaatagtaaaattttctagtttaattctaaataaaaaggtccactggaccttgattaaagggaactcgcaagggcgagtctttatctgcaacctaaaacagctcctatctatagattaaaaaggttccccgaaccttattaaagagcactcgcttaaccgagtgcttagccacaacctaaaaatacccgttaggcttgtctcagggtaaaccgactaccgtcggttctcatccgcagattaaaaaagtccaccgaaccttggattaaggagaactcgcaaaagcgagtttttatctgcaacctaaaacagtcctctggactgtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1268:SSA_1269|SSA_1268:SSA_1269:Chorismate mutase/prephenate dehydratase, putative:hypothetical protein:<-<-:1291701..1292059 359 ctcattcctccttatattctatctatcatatcaaaaaatagtaaaattttctagtttaattctaaataaaaaggtccactggaccttgattaaagggaactcgcaagggcgagtctttatctgcaacctaaaacagctcctatctatagattaaaaaggttccccgaaccttattaaagagcactcgcttaaccgagtgcttagccacaacctaaaaatacccgttaggcttgtctcagggtaaaccgactaccgtcggttctcatccgcagattaaaaaagtccaccgaaccttggattaaggagaactcgcaaaagcgagtttttatctgcaacctaaaacagtcctctggactgtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ctcattcctccttatattctatctatcatatcaaaaaatagtaaaattttctagtttaattctaaataaaaaggtccactggaccttgattaaagggaactcgcaagggcgagtctttatctgcaacctaaaacagctcctatctatagattaaaaaggttccccgaaccttattaaagagcactcgcttaaccgagtgcttagccacaacctaaaaatacccgttaggcttgtctcagggtaaaccgactaccgtcggttctcatccgcagattaaaaaagtccaccgaaccttggattaaggagaactcgcaaaagcgagtttttatctgcaacctaaaacagtcctctggactgtt Predict ORF larger than 30AA ================================================ Protein_Len: 46 Strand: + Start: 14 End: 151 ............. M F Y L S Y Q K I V K F S S L I L N K K V H W T L I K G N S Q G R V F I C N L K Q L L S I D ................................................................................................................................................................................................................ Protein_Len: 31 Strand: + Start: 265 End: 357 ........................................................................................................................................................................................................................................................................ M R R L K K S T E P W I K E N S Q K R V F I C N L K Q S S G L .. Protein_Len: 36 Strand: - Start: 228 End: 335 ................................................................................................................................................................................................................................... A Q R L T F R S G D T R M R L N F F D V S G Q I L S F E C F R T K I Q M ........................ Protein_Len: 38 Strand: - Start: 34 End: 147 ................................. F I T F N E L K I R F L F T W Q V K I L P F E C P R T K I Q L R F C S R D M .................................................................................................................................................................................................................... ctcattcctccttatattctatctatcatatcaaaaaatagtaaaattttctagtttaattctaaataaaaaggtccactggaccttgattaaagggaactcgcaagggcgagtctttatctgcaacctaaaacagctcctatctatagattaaaaaggttccccgaaccttattaaagagcactcgcttaaccgagtgcttagccacaacctaaaaatacccgttaggcttgtctcagggtaaaccgactaccgtcggttctcatccgcagattaaaaaagtccaccgaaccttggattaaggagaactcgcaaaagcgagtttttatctgcaacctaaaacagtcctctggactgtt 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: 84 Start: 25 End: 54 ........................CTAGAAAATTTTACTATTTTTTGATATGAT................................................................................................................................................................................................................................................................................................................. PromScan Matrix: RpoD-17 Strand: - Score: 81 Start: 38 End: 67 .....................................ATTTAGAATTAAACTAGAAAATTTTACTAT.................................................................................................................................................................................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ctcattcctccttatattctatctatcatatcaaaaaatagtaaaattttctagtttaattctaaataaaaaggtccactggaccttgattaaagggaactcgcaagggcgagtctttatctgcaacctaaaacagctcctatctatagattaaaaaggttccccgaaccttattaaagagcactcgcttaaccgagtgcttagccacaacctaaaaatacccgttaggcttgtctcagggtaaaccgactaccgtcggttctcatccgcagattaaaaaagtccaccgaaccttggattaaggagaactcgcaaaagcgagtttttatctgcaacctaaaacagtcctctggactgtt Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 72 HP_score: -9.1 Tail_Score: -3.33696 Start: 73 End: 85 Full_Region: AATTCTAAATAAAAA GGTCC ACT GGACC TTGATTAAAGGGAAC ........................................................................GGTCCACTGGACC.................................................................................................................................................................................................................................................................................. TransTerm Strand: - Conf: 93 HP_score: -9.1 Tail_Score: -5.29846 Start: 73 End: 85 Full_Region: gttccctttaatcaa ggtcc agt ggacc tttttatttagaatt ........................................................................ggtccagtggacc.................................................................................................................................................................................................................................................................................. TransTerm Strand: - Conf: 71 HP_score: -9.6 Tail_Score: -2.91264 Start: 151 End: 177 Full_Region: ttaagcgagtgctct ttaataaggttc ggg gaacctttttaa tctatagataggagc ......................................................................................................................................................ttaataaggttcggggaacctttttaa...................................................................................................................................................................................... TransTerm Strand: - Conf: 86 HP_score: -7.7 Tail_Score: -4.84527 Start: 158 End: 170 Full_Region: agtgctctttaataa ggttc ggg gaacc tttttaatctataga .............................................................................................................................................................ggttcggggaacc............................................................................................................................................................................................. TransTerm Strand: - Conf: 66 HP_score: -6.7 Tail_Score: -3.76492 Start: 179 End: 202 Full_Region: ttttaggttgtggct aagcactcg gttaag cgagtgctc tttaataaggttcgg ..................................................................................................................................................................................aagcactcggttaagcgagtgctc............................................................................................................................................................. TransTerm Strand: - Conf: 74 HP_score: -9.3 Tail_Score: -3.46534 Start: 181 End: 200 Full_Region: ttaggttgtggctaa gcactcg gttaag cgagtgc tctttaataaggttc ....................................................................................................................................................................................gcactcggttaagcgagtgc............................................................................................................................................................... TransTerm Strand: - Conf: 76 HP_score: -3.2 Tail_Score: -5.21709 Start: 282 End: 292 Full_Region: tctccttaatccaag gttc ggt ggac ttttttaatctgcgg .........................................................................................................................................................................................................................................................................................gttcggtggac................................................................... TransTerm Strand: + Conf: 86 HP_score: -8.1 Tail_Score: -4.96848 Start: 309 End: 322 Full_Region: TTGGATTAAGGAGAA CTCGC AAAA GCGAG TTTTTATCTGCAACC ....................................................................................................................................................................................................................................................................................................................CTCGCAAAAGCGAG..................................... Find igs database================================================ Query_seq: SSA_1268:SSA_1269|SSA_1268:SSA_1269:Chorismate mutase/prephenate dehydratase, putative:hypothetical protein:<-<-:1291701..1292059 359 ctcattcctccttatattctatctatcatatcaaaaaatagtaaaattttctagtttaattctaaataaaaaggtccactggaccttgattaaagggaactcgcaagggcgagtctttatctgcaacctaaaacagctcctatctatagattaaaaaggttccccgaaccttattaaagagcactcgcttaaccgagtgcttagccacaacctaaaaatacccgttaggcttgtctcagggtaaaccgactaccgtcggttctcatccgcagattaaaaaagtccaccgaaccttggattaaggagaactcgcaaaagcgagtttttatctgcaacctaaaacagtcctctggactgtt Intra-Species Hit: Count: 1 Min: 1 Max: 359 Len: 359 Subject: NC_009009_SSA_1268_SSA_1269|Chorismate mutase/prephenate dehydratase, putative:hypothetical protein|NEGATIVE:NEGATIVE|[1291701,1292059]|359 HSP 1 e-value: 0.0 bit: 712.0 Len: 359 Query Start:1 Query End:359 Subject Strand: POSITIVE Subject Start: 1 Subject End: 359 ctcattcctccttatattctatctatcatatcaaaaaatagtaaaattttctagtttaattctaaataaaaaggtccactggaccttgattaaagggaactcgcaagggcgagtctttatctgcaacctaaaacagctcctatctatagattaaaaaggttccccgaaccttattaaagagcactcgcttaaccgagtgcttagccacaacctaaaaatacccgttaggcttgtctcagggtaaaccgactaccgtcggttctcatccgcagattaaaaaagtccaccgaaccttggattaaggagaactcgcaaaagcgagtttttatctgcaacctaaaacagtcctctggactgtt ctcattcctccttatattctatctatcatatcaaaaaatagtaaaattttctagtttaattctaaataaaaaggtccactggaccttgattaaagggaactcgcaagggcgagtctttatctgcaacctaaaacagctcctatctatagattaaaaaggttccccgaaccttattaaagagcactcgcttaaccgagtgcttagccacaacctaaaaatacccgttaggcttgtctcagggtaaaccgactaccgtcggttctcatccgcagattaaaaaagtccaccgaaccttggattaaggagaactcgcaaaagcgagtttttatctgcaacctaaaacagtcctctggactgtt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUCAUUCCUCCUUAUAUUCUAUCUAUCAUAUCAAAAAAUAGUAAAAUUUUCUAGUUUAAUUCUAAAUAAAAAGGUCCACUGGACCUUGAUUAAAGGGAACUCGCAAGGGCGAGUCUUUAUCUGCAACCUAAAACAGCUCCUAUCUAUAGAUUAAAAAGGUUCCCCGAACCUUAUUAAAGAGCACUCGCUUAACCGAGUGCUUAGCCACAACCUAAAAAUACCCGUUAGGCUUGUCUCAGGGUAAACCGACUACCGUCGGUUCUCAUCCGCAGAUUAAAAAAGUCCACCGAACCUUGGAUUAAGGAGAACUCGCAAAAGCGAGUUUUUAUCUGCAACCUAAAACAGUCCUCUGGACUGUU .......(((((((...((((....((...........................(((((((.........(((((((...)))))))))))))).(((((((((....))))))....((((((.((((......((.............((((.(((((((...))))))).)))).(((((((((......))))))))).)).(((((((((.........))))).))))....)))).(((((((....))))))).......))))))........)))...))....)))).))))))).((((((....)))))).................((((((((...)))))))) (-98.50) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AACAGUCCAGAGGACUGUUUUAGGUUGCAGAUAAAAACUCGCUUUUGCGAGUUCUCCUUAAUCCAAGGUUCGGUGGACUUUUUUAAUCUGCGGAUGAGAACCGACGGUAGUCGGUUUACCCUGAGACAAGCCUAACGGGUAUUUUUAGGUUGUGGCUAAGCACUCGGUUAAGCGAGUGCUCUUUAAUAAGGUUCGGGGAACCUUUUUAAUCUAUAGAUAGGAGCUGUUUUAGGUUGCAGAUAAAGACUCGCCCUUGCGAGUUCCCUUUAAUCAAGGUCCAGUGGACCUUUUUAUUUAGAAUUAAACUAGAAAAUUUUACUAUUUUUUGAUAUGAUAGAUAGAAUAUAAGGAGGAAUGAG ((((((((...))))))))................(((((((....)))))))(((((((....((((((((.((((((((....(((((((.....((((((((....))))))))..(((((((((..((....)).(((((.(((((((......((((((((......)))))))).......(((((((...)))))))..))))))).))))).....))))))))).)))))))...(((((((....)))))))..........)))))))).))))))))((((((((..((.....((((((((......))))))))..))..))))))))...)))))))....... (-124.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 969 120 71 211 162 NC_009009:SSA_1268|5end_Chorismate_mutase/prephenate_dehydratase,_putative_1291610..1291840_NEGATIVE 493 267 221 52 3 NC_009009:SSA_0263|5end_Zinc_metalloproteinase_in_scaA_5'region,_putative_256274..256504_POSITIVE 398 206 161 231 191 NC_009009:SSA_1680|5end_ABC-type_bacitracin_resistance_protein_A,_permease_component,_putative_1675200..1675430_NEGATIVE 386 270 223 154 115 NC_009009:SSA_1242|5end_Dihydroorotate_dehydrogenase_B,_putative_1267386..1267616_NEGATIVE 365 205 161 231 192 NC_009009:SSA_1659|5end_ABC-type_antimicrobial_peptide_transport_system,_permease_component,_putative_1656819..1657049_NEGATIVE 336 270 222 77 28 NC_009009:SSA_1066|5end_ABC-type_oligopeptide_transport_system,_putative_1084335..1084565_POSITIVE 323 330 281 198 151 NC_009009:SSA_0579|5end_Hydrolase,_HAD_superfamily,_putative_572220..572450_POSITIVE 319 270 221 89 27 NC_009009:SSA_0508|5end_Conserved_uncharacterized_protein,_possible_phosphoserine_phosphatase_506668..506898_POSITIVE 318 270 225 73 15 NC_009009:SSA_0788|5end_Proton-translocating_ATPase,_F1_sector,_beta_subunit,_putative_771037..771267_POSITIVE 317 118 71 53 8 NC_009009:SSA_1711|5end_Endonuclease_III,_putative_1699636..1699866_NEGATIVE 315 268 222 101 48 NC_009009:SSA_0283|5end_Phosphotransferase_system_(PTS),_cellobiose-specific_IIB_component,_putative_274559..274789_POSITIVE 314 270 221 105 51 NC_009009:SSA_1606|5end_Dephospho-CoA_kinase,_putative_1612425..1612655_NEGATIVE 314 280 236 48 1 NC_009009:SSA_0421|5end_Phosphoglycerate_mutase_family_protein,_putative_419564..419794_POSITIVE 314 260 222 208 156 NC_009009:SSA_0377|5end_ABC-type_methionine_transporter,_permease_component,_putative_366446..366676_POSITIVE 310 87 67 177 157 NC_009009:SSA_2354|5end_hypothetical_protein_2356237..2356467_NEGATIVE 308 270 222 186 137 NC_009009:SSA_0978|5end_hypothetical_protein_983736..983966_POSITIVE 306 140 96 58 11 NC_009009:SSA_0036|5end_Secreted_protein,_possible_function_in_cell-wall_metabolism_(amidase),_putative_43999..44229_NEGATIVE 305 227 181 231 182 NC_009009:SSA_2208|5end_Preprotein_translocase_secE_component,_putative_2207913..2208143_NEGATIVE 304 240 192 66 17 NC_009009:SSA_0335|5end_Phosphomevalonate_kinase,_putative_328792..329022_POSITIVE 303 206 177 64 39 NC_009009:SSA_0735|5end_Integral_membrane_protein,_putative_717103..717333_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 386 270 223 142 103 NC_009009:SSA_1243|3end_Dihydroorotate_dehydrogenase_electron_transfer_subunit,_putative_1267398..1267548_NEGATIVE 356 270 223 125 77 NC_009009:SSA_1960|3end_hypothetical_protein_1956571..1956721_NEGATIVE 315 268 222 80 27 NC_009009:SSA_0282|3end_Phosphotransferase_system_(PTS),_cellobiose-specific_IIA_component,_putative_274618..274768_POSITIVE 314 270 221 99 45 NC_009009:SSA_1607|3end_Formamidopyrimidine-DNA_glycosylase,_putative_1612431..1612581_NEGATIVE 314 289 247 52 1 NC_009009:SSA_0420|3end_Hydrolase,_HAD_superfamily,_putative_419632..419782_POSITIVE 313 144 101 75 29 NC_009009:SSA_1501|3end_Cytidylate_kinase,_putative_1505095..1505245_NEGATIVE 310 87 67 89 69 NC_009009:SSA_2355|3end_Conserved_uncharacterized_protein_2356325..2356475_NEGATIVE 307 151 111 123 77 NC_009009:SSA_1235|3end_Dihydroorotase,_putative_1259959..1260109_NEGATIVE 304 240 192 76 27 NC_009009:SSA_0334|3end_Diphosphomevalonate_decarboxylase,_putative_328882..329032_POSITIVE 303 206 177 77 52 NC_009009:SSA_0734|3end_Arsenical_resistance_operon_transcription_repressor_(ArsR),_putative_717196..717346_POSITIVE 300 270 223 131 81 NC_009009:SSA_0810|3end_P-loop_ATPase,_putative_792552..792702_POSITIVE 294 270 223 65 16 NC_009009:SSA_0198|3end_Dihydrofolate_synthetase,_putative_198375..198525_POSITIVE 293 259 228 123 88 NC_009009:SSA_2077|3end_hypothetical_protein_2081352..2081502_NEGATIVE 293 268 221 59 1 NC_009009:SSA_1443|3end_1-(5-phosphoribosyl)-5-[(5-_phosphoribosylamino)methylideneamino]_imidazole-4-carboxamide_isomerase,_putative_1445944..1446094_NEGATIVE 292 269 226 69 30 NC_009009:SSA_0467|3end_Cobalt-precorrin-6A_synthase_[deacetylating],_putative_471795..471945_POSITIVE 291 230 181 110 46 NC_009009:SSA_2318|3end_PilB-like_pili_biogenesis_ATPase,_putative_2319412..2319562_NEGATIVE 286 144 106 92 52 NC_009009:SSA_2122|3end_hypothetical_protein_2127200..2127350_NEGATIVE 283 269 224 149 103 NC_009009:SSA_1852|3end_Metal_dependent_phosphohydrolase_(HD_motif),_putative_1846869..1847019_NEGATIVE 283 261 222 139 107 NC_009009:SSA_0314|3end_Nucleoside-diphosphate-sugar_epimerase,_putative_308967..309117_NEGATIVE 281 270 227 62 18 NC_009009:SSA_1448|3end_ATP_phosphoribosyltransferase_regulatory_subunit,_putative_1449828..1449978_NEGATIVE