Origin IGS: gatgtaattctcctttatatgaaagaatgagggcttccagagtgctgcaagtaaggtcgctctgagagcaagctatttttgaacgaaagttaatgatttagcacctagc .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gctaggtgctaaatcattaactttcgttcaaaaatagcttgctctcagagcgaccttacttgcagcactctggaagccctcattctttcatataaaggagaattacatc Mask Tandem Repeat Region ================================================ gatgtaattctcctttatatgaaagaatgagggcttccagagtgctgcaagtaaggtcgctctgagagcaagctatttttgaacgaaagttaatgatttagcacctagc Find is-nt database================================================ Query_seq: SSA_1343:SSA_1344|SSA_1343:SSA_1344:Aspartate carbamoyltransferase, putative:Xanthine/uracil permeases, putative:<-<-:1362050..1362158 109 gatgtaattctcctttatatgaaagaatgagggcttccagagtgctgcaagtaaggtcgctctgagagcaagctatttttgaacgaaagttaatgatttagcacctagc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1343:SSA_1344|SSA_1343:SSA_1344:Aspartate carbamoyltransferase, putative:Xanthine/uracil permeases, putative:<-<-:1362050..1362158 109 gatgtaattctcctttatatgaaagaatgagggcttccagagtgctgcaagtaaggtcgctctgagagcaagctatttttgaacgaaagttaatgatttagcacctagc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1343:SSA_1344|SSA_1343:SSA_1344:Aspartate carbamoyltransferase, putative:Xanthine/uracil permeases, putative:<-<-:1362050..1362158 109 gatgtaattctcctttatatgaaagaatgagggcttccagagtgctgcaagtaaggtcgctctgagagcaagctatttttgaacgaaagttaatgatttagcacctagc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gatgtaattctcctttatatgaaagaatgagggcttccagagtgctgcaagtaaggtcgctctgagagcaagctatttttgaacgaaagttaatgatttagcacctagc Predict ORF larger than 30AA ================================================ Protein_Len: 32 Strand: - Start: 2 End: 97 . H L E G K Y S L I L A E L T S C T L D S Q S C A I K S R F N I M ............ gatgtaattctcctttatatgaaagaatgagggcttccagagtgctgcaagtaaggtcgctctgagagcaagctatttttgaacgaaagttaatgatttagcacctagc 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================================================ gatgtaattctcctttatatgaaagaatgagggcttccagagtgctgcaagtaaggtcgctctgagagcaagctatttttgaacgaaagttaatgatttagcacctagc Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_1343:SSA_1344|SSA_1343:SSA_1344:Aspartate carbamoyltransferase, putative:Xanthine/uracil permeases, putative:<-<-:1362050..1362158 109 gatgtaattctcctttatatgaaagaatgagggcttccagagtgctgcaagtaaggtcgctctgagagcaagctatttttgaacgaaagttaatgatttagcacctagc Intra-Species Hit: Count: 1 Min: 1 Max: 109 Len: 109 Subject: NC_009009_SSA_1343_SSA_1344|Aspartate carbamoyltransferase, putative:Xanthine/uracil permeases, putative|NEGATIVE:NEGATIVE|[1362050,1362158]|109 HSP 1 e-value: 1.0E-55 bit: 216.0 Len: 109 Query Start:1 Query End:109 Subject Strand: POSITIVE Subject Start: 1 Subject End: 109 gatgtaattctcctttatatgaaagaatgagggcttccagagtgctgcaagtaaggtcgctctgagagcaagctatttttgaacgaaagttaatgatttagcacctagc gatgtaattctcctttatatgaaagaatgagggcttccagagtgctgcaagtaaggtcgctctgagagcaagctatttttgaacgaaagttaatgatttagcacctagc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAUGUAAUUCUCCUUUAUAUGAAAGAAUGAGGGCUUCCAGAGUGCUGCAAGUAAGGUCGCUCUGAGAGCAAGCUAUUUUUGAACGAAAGUUAAUGAUUUAGCACCUAGC .((((((.......)))))).........((((((..(((((((((........)).)))))))..)))..((((..((..(((....)))...))..)))).)))... (-30.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GCUAGGUGCUAAAUCAUUAACUUUCGUUCAAAAAUAGCUUGCUCUCAGAGCGACCUUACUUGCAGCACUCUGGAAGCCCUCAUUCUUUCAUAUAAAGGAGAAUUACAUC .(((((((((........(((....))).......((.((((((...)))))).)).......))))).))))........(((((((........)))))))...... (-18.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 1021 70 21 161 112 NC_009009:SSA_1343|5end_Aspartate_carbamoyltransferase,_putative_1361959..1362189_NEGATIVE 395 73 33 59 14 NC_009009:SSA_2165|5end_ABC-type_oligopeptide_transporter,_periplasmic_component,_putative_2161734..2161964_POSITIVE 327 80 31 184 118 NC_009009:SSA_2090|5end_Hexulose-6-phosphate_synthase,_putative_2095038..2095268_NEGATIVE 324 58 24 86 52 NC_009009:SSA_0778|5end_Glycogen_synthase,_putative_760566..760796_POSITIVE 322 72 32 49 9 NC_009009:SSA_1948|5end_Oligopeptide-binding_lipoprotein_precursor,_putative_1942170..1942400_NEGATIVE 320 69 26 172 119 NC_009009:SSA_0293|5end_hypothetical_protein_287613..287843_NEGATIVE 319 69 23 80 38 NC_009009:SSA_2207|5end_hypothetical_protein_2207221..2207451_NEGATIVE 319 78 32 209 151 NC_009009:SSA_1558|5end_Hydrolase,_HAD_superfamily_1560862..1561092_NEGATIVE 317 80 31 106 58 NC_009009:SSA_1996|5end_DNA-directed_RNA_polymerase_delta_subunit,_putative_1994024..1994254_NEGATIVE 312 77 32 65 17 NC_009009:SSA_1729|5end_ABC_transporter_substrate-binding_protein-branched_chain_amino_acid_transport,_putative_1715699..1715929_NEGATIVE 307 62 22 218 170 NC_009009:SSA_2173|5end_Aminoacylase/N-acyl-L-amino_acid_amidohydrolase/hippurate_hydrolase,_putative_2171914..2172144_NEGATIVE 306 70 26 192 137 NC_009009:SSA_0492|5end_NADH-dependent_flavin_oxidoreductase,_putative_491588..491818_POSITIVE 306 78 35 57 2 NC_009009:SSA_0461|5end_ABC-type_multidrug_transport_system,_ATPase_and_permease_components,_putative_463059..463289_POSITIVE 303 89 42 188 132 NC_009009:SSA_2360|5end_tRNA_(5-methylaminomethyl-2-thiouridylate)-methyltransferase,_putative_2363779..2364009_NEGATIVE 300 72 33 223 174 NC_009009:SSA_1462|5end_Prephenate_dehydratase,_putative_1469767..1469997_NEGATIVE 299 78 32 65 8 NC_009009:SSA_1861|5end_Aminopeptidase_C,_putative_1857902..1858132_NEGATIVE 294 69 31 206 165 NC_009009:SSA_1364|5end_hypothetical_protein_1381297..1381527_NEGATIVE 293 75 33 96 46 NC_009009:SSA_2039|5end_Aminoacid_specific_permease,_putative_2044455..2044685_NEGATIVE 291 69 28 213 167 NC_009009:SSA_1875|5end_hypothetical_protein_1870558..1870788_POSITIVE 291 74 39 174 140 NC_009009:SSA_0714|5end_hypothetical_protein_700042..700272_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 377 50 4 130 82 NC_009009:SSA_0780|3end_Acid_phosphatase_(PAP2_family),_putative_765328..765478_POSITIVE 324 58 24 89 55 NC_009009:SSA_0777|3end_Glycogen_biosynthesis_protein_GlgD,_putative_760649..760799_POSITIVE 310 78 31 66 12 NC_009009:SSA_1436|3end_hypothetical_protein_1442199..1442349_NEGATIVE 307 62 22 141 93 NC_009009:SSA_2174|3end_2,3,4,5-tetrahydropyridine-2-carboxylate_N-succinyltransferase,_putative_2171991..2172141_NEGATIVE 306 69 21 146 107 NC_009009:SSA_0956|3end_surface_protein_D_965418..965568_POSITIVE 306 70 26 137 82 NC_009009:SSA_0491|3end_Alpha-ribazole-5'-phosphate_phosphatase,_putative_491613..491763_POSITIVE 306 78 35 64 9 NC_009009:SSA_0460|3end_Multiple_antibiotic_resistance_operon_transcription_repressor_(MarR),_putative_463146..463296_POSITIVE 294 69 31 151 110 NC_009009:SSA_1365|3end_FmtA-like_protein,_putative_1381352..1381502_NEGATIVE 291 74 39 80 46 NC_009009:SSA_0713|3end_1-acyl-sn-glycerol-3-phosphate_acyltransferase,_putative_700028..700178_POSITIVE 290 80 43 72 36 NC_009009:SSA_0389|3end_hypothetical_protein_385082..385232_POSITIVE 287 69 24 62 3 NC_009009:SSA_0715|3end_DNA_uptake_protein,_putative_701486..701636_POSITIVE 285 60 30 144 104 NC_009009:SSA_1013|3end_Phosphatidylserine_synthase,_putative_1017933..1018083_POSITIVE 284 69 30 150 93 NC_009009:SSA_2091|3end_Phosphotransferase_system_sugar-specific_EII_component,_putative_2095062..2095212_NEGATIVE 284 48 8 145 102 NC_009009:SSA_0500|3end_Peptide_ABC_transporter,_permease_protein,_putative_501524..501674_POSITIVE 284 77 31 126 74 NC_009009:SSA_0187|3end_Competence_protein_ComYD,_putative_190852..191002_POSITIVE 283 69 23 151 103 NC_009009:SSA_0341|3end_hypothetical_protein_333955..334105_NEGATIVE 281 85 43 140 110 NC_009009:SSA_1383|3end_Aspartate_aminotransferase,_putative_1400537..1400687_NEGATIVE 281 74 34 50 1 NC_009009:SSA_0316|3end_hypothetical_protein_311342..311492_POSITIVE 278 48 8 141 103 NC_009009:SSA_0791|3end_UDP-N-acetylglucosamine-like_protein,_putative_774705..774855_POSITIVE 274 62 26 87 46 NC_009009:SSA_1267|3end_crcB-like_protein_2,_putative_1290973..1291123_NEGATIVE