Origin IGS: aaacttaccttctttctgctccctattttatcactttttgcggtaaatgagtaggaaaatcttatagcttgcctgaatcaagaggactgcccgcttaggaatccagcttctcccaggaaaatctggaatattgtttgtcgcctctgctcttttgtgttaaaatattctac .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gtagaatattttaacacaaaagagcagaggcgacaaacaatattccagattttcctgggagaagctggattcctaagcgggcagtcctcttgattcaggcaagctataagattttcctactcatttaccgcaaaaagtgataaaatagggagcagaaagaaggtaagttt Mask Tandem Repeat Region ================================================ aaacttaccttctttctgctccctattttatcactttttgcggtaaatgagtaggaaaatcttatagcttgcctgaatcaagaggactgcccgcttaggaatccagcttctcccaggaaaatctggaatattgtttgtcgcctctgctcttttgtgttaaaatattctac Find is-nt database================================================ Query_seq: SSA_0209:SSA_0210|SSA_0209:SSA_0210:Glutamyl aminopeptidase, putative:hypothetical protein:<-->:207727..207896 170 aaacttaccttctttctgctccctattttatcactttttgcggtaaatgagtaggaaaatcttatagcttgcctgaatcaagaggactgcccgcttaggaatccagcttctcccaggaaaatctggaatattgtttgtcgcctctgctcttttgtgttaaaatattctac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0209:SSA_0210|SSA_0209:SSA_0210:Glutamyl aminopeptidase, putative:hypothetical protein:<-->:207727..207896 170 aaacttaccttctttctgctccctattttatcactttttgcggtaaatgagtaggaaaatcttatagcttgcctgaatcaagaggactgcccgcttaggaatccagcttctcccaggaaaatctggaatattgtttgtcgcctctgctcttttgtgttaaaatattctac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0209:SSA_0210|SSA_0209:SSA_0210:Glutamyl aminopeptidase, putative:hypothetical protein:<-->:207727..207896 170 aaacttaccttctttctgctccctattttatcactttttgcggtaaatgagtaggaaaatcttatagcttgcctgaatcaagaggactgcccgcttaggaatccagcttctcccaggaaaatctggaatattgtttgtcgcctctgctcttttgtgttaaaatattctac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aaacttaccttctttctgctccctattttatcactttttgcggtaaatgagtaggaaaatcttatagcttgcctgaatcaagaggactgcccgcttaggaatccagcttctcccaggaaaatctggaatattgtttgtcgcctctgctcttttgtgttaaaatattctac Predict ORF larger than 30AA ================================================ Protein_Len: 35 Strand: + Start: 64 End: 168 ............................................................... M A C L N Q E D C P L R N P A S P R K I W N I V C R L C S F V L K Y S .. Protein_Len: 32 Strand: - Start: 34 End: 129 ................................. K K R Y I L L F I K Y S A Q I L L V A R K P I W S R G P F D P M ......................................... aaacttaccttctttctgctccctattttatcactttttgcggtaaatgagtaggaaaatcttatagcttgcctgaatcaagaggactgcccgcttaggaatccagcttctcccaggaaaatctggaatattgtttgtcgcctctgctcttttgtgttaaaatattctac 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: 87 Start: 134 End: 163 .....................................................................................................................................TTTGTCGCCTCTGCTCTTTTGTGTTAAAAT....... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aaacttaccttctttctgctccctattttatcactttttgcggtaaatgagtaggaaaatcttatagcttgcctgaatcaagaggactgcccgcttaggaatccagcttctcccaggaaaatctggaatattgtttgtcgcctctgctcttttgtgttaaaatattctac Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_0209:SSA_0210|SSA_0209:SSA_0210:Glutamyl aminopeptidase, putative:hypothetical protein:<-->:207727..207896 170 aaacttaccttctttctgctccctattttatcactttttgcggtaaatgagtaggaaaatcttatagcttgcctgaatcaagaggactgcccgcttaggaatccagcttctcccaggaaaatctggaatattgtttgtcgcctctgctcttttgtgttaaaatattctac Intra-Species Hit: Count: 1 Min: 1 Max: 170 Len: 170 Subject: NC_009009_SSA_0209_SSA_0210|Glutamyl aminopeptidase, putative:hypothetical protein|NEGATIVE:POSITIVE|[207727,207896]|170 HSP 1 e-value: 7.0E-92 bit: 337.0 Len: 170 Query Start:1 Query End:170 Subject Strand: POSITIVE Subject Start: 1 Subject End: 170 aaacttaccttctttctgctccctattttatcactttttgcggtaaatgagtaggaaaatcttatagcttgcctgaatcaagaggactgcccgcttaggaatccagcttctcccaggaaaatctggaatattgtttgtcgcctctgctcttttgtgttaaaatattctac aaacttaccttctttctgctccctattttatcactttttgcggtaaatgagtaggaaaatcttatagcttgcctgaatcaagaggactgcccgcttaggaatccagcttctcccaggaaaatctggaatattgtttgtcgcctctgctcttttgtgttaaaatattctac Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAACUUACCUUCUUUCUGCUCCCUAUUUUAUCACUUUUUGCGGUAAAUGAGUAGGAAAAUCUUAUAGCUUGCCUGAAUCAAGAGGACUGCCCGCUUAGGAAUCCAGCUUCUCCCAGGAAAAUCUGGAAUAUUGUUUGUCGCCUCUGCUCUUUUGUGUUAAAAUAUUCUAC ............(((((((((.....((((((.(.....).)))))).))))))))).......((((......((....(((((.....((.....))..(((((.((.((....)).)).))))).............)))))..))......))))........... (-32.00) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUAGAAUAUUUUAACACAAAAGAGCAGAGGCGACAAACAAUAUUCCAGAUUUUCCUGGGAGAAGCUGGAUUCCUAAGCGGGCAGUCCUCUUGAUUCAGGCAAGCUAUAAGAUUUUCCUACUCAUUUACCGCAAAAAGUGAUAAAAUAGGGAGCAGAAAGAAGGUAAGUUU ((((((.((((((........(((..((((.(((.........(((((.(((((....))))).))))).(((.....)))..))).))))..))).((....)).)))))).)).))))..(((((((................................))))))).. (-30.15) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 1040 120 71 211 162 NC_009009:SSA_0209|5end_Glutamyl_aminopeptidase,_putative_207636..207866_NEGATIVE 364 110 66 106 66 NC_009009:SSA_0977|5end_3-isopropylmalate_dehydrogenase,_putative_982771..983001_POSITIVE 359 95 52 204 152 NC_009009:SSA_1892|5end_hypothetical_protein_1889262..1889492_NEGATIVE 354 118 71 54 13 NC_009009:SSA_2323|5end_Transporter,_putative_2327604..2327834_POSITIVE 348 118 72 60 7 NC_009009:SSA_0188|5end_hypothetical_protein_190798..191028_POSITIVE 345 109 67 49 3 NC_009009:SSA_0488|5end_Glutamate-1-semialdehyde_2,1-aminotransferase,_putative_488364..488594_POSITIVE 345 118 71 62 9 NC_009009:SSA_0468|5end_Precorrin-6y_C5,15-methyltransferase-like,_putative_471706..471936_POSITIVE 344 149 103 168 115 NC_009009:SSA_0299|5end_hypothetical_protein_292759..292989_POSITIVE 331 117 71 71 21 NC_009009:SSA_1447|5end_ATP_phosphoribosyltransferase,_putative_1449831..1450061_NEGATIVE 328 156 113 43 7 NC_009009:SSA_1459|5end_RNA_methyltransferase,_putative_1467481..1467711_NEGATIVE 326 150 101 57 1 NC_009009:SSA_0852|5end_ATP-dependent_DNA_helicase,_putative_839050..839280_POSITIVE 322 47 9 39 1 NC_009009:SSA_1328|5end_hypothetical_protein_1344896..1345126_NEGATIVE 320 110 65 73 28 NC_009009:SSA_1585|5end_hypothetical_protein_1587604..1587834_NEGATIVE 318 113 73 171 126 NC_009009:SSA_1751|5end_Dextran_glucosidase,_alpha_amylase_family,_putative_1739801..1740031_NEGATIVE 315 119 78 49 3 NC_009009:SSA_0620|5end_hypothetical_protein_612325..612555_NEGATIVE 312 117 78 68 31 NC_009009:SSA_0219|5end_PTS_system,_sugar-specific_enzyme_IIA_component,_putative_215367..215597_POSITIVE 309 110 61 184 106 NC_009009:SSA_2101|5end_Amino_acid_ABC_transporter,_periplasmic_amino_acid-binding_protein,_putative_2105393..2105623_NEGATIVE 307 119 74 230 172 NC_009009:SSA_0330|5end_hypothetical_protein_323799..324029_POSITIVE 307 109 66 67 18 NC_009009:SSA_0308|5end_hypothetical_protein_304385..304615_POSITIVE 306 113 71 100 54 NC_009009:SSA_1413|5end_GufA-like_protein,_putative_1424919..1425149_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 384 120 72 86 22 NC_009009:SSA_0673|3end_hypothetical_protein_656994..657144_POSITIVE 345 118 71 71 18 NC_009009:SSA_0467|3end_Cobalt-precorrin-6A_synthase_[deacetylating],_putative_471795..471945_POSITIVE 336 95 54 45 1 NC_009009:SSA_1893|3end_N-acetylglucosamine-6-phosphate_deacetylase,_putative_1889421..1889571_NEGATIVE 333 115 75 113 72 NC_009009:SSA_2068|3end_Superfamily_I_DNA_and_RNA_helicases,_putative_2070931..2071081_NEGATIVE 331 117 71 74 24 NC_009009:SSA_1448|3end_ATP_phosphoribosyltransferase_regulatory_subunit,_putative_1449828..1449978_NEGATIVE 316 127 84 48 5 NC_009009:SSA_1189|3end_GTP-binding_protein,_putative_1216806..1216956_NEGATIVE 315 119 78 52 6 NC_009009:SSA_0621|3end_SOS_responce_UmuC_protein,_putative_612322..612472_NEGATIVE 311 107 66 49 4 NC_009009:SSA_0624|3end_hypothetical_protein_615698..615848_POSITIVE 306 113 71 77 31 NC_009009:SSA_1414|3end_hypothetical_protein_1424942..1425092_NEGATIVE 304 125 83 142 103 NC_009009:SSA_2340|3end_hypothetical_protein_2341539..2341689_NEGATIVE 297 127 83 80 36 NC_009009:SSA_2242|3end_hypothetical_protein_2238121..2238271_NEGATIVE 296 108 61 48 5 NC_009009:SSA_0728|3end_Protease,_putative_714523..714673_POSITIVE 295 96 56 59 11 NC_009009:SSA_0934|3end_HydD,_putative_944091..944241_POSITIVE 292 100 54 145 99 NC_009009:SSA_0685|3end_hypothetical_protein_669432..669582_POSITIVE 292 113 73 106 58 NC_009009:SSA_0239|3end_7,8-dihydro-8-oxoguanine-triphosphatase,_putative_233493..233643_POSITIVE 291 118 80 45 3 NC_009009:SSA_2357|3end_50S_ribosomal_protein_L9,_putative_2357985..2358135_NEGATIVE 290 110 68 48 4 NC_009009:SSA_0473|3end_Precorrin-6x_reductase,_putative_476331..476481_POSITIVE 289 149 104 59 15 NC_009009:SSA_2000|3end_hypothetical_protein_1996987..1997137_NEGATIVE 289 114 73 139 86 NC_009009:SSA_0263|3end_Zinc_metalloproteinase_in_scaA_5'region,_putative_258246..258396_POSITIVE 288 116 78 138 91 NC_009009:SSA_1763|3end_ABC-type_molybdenum_transport_system,_ATPase_component,_putative_1750951..1751101_POSITIVE