Origin IGS: gaaaatatctccttcaatcgttagaaaggcttggaaatacttttccagcctattctttgtttatccaatgtactttcattatactgaaaggagatatagttttcaattatactttttctctaactagatatagttagaaactatgta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tacatagtttctaactatatctagttagagaaaaagtataattgaaaactatatctcctttcagtataatgaaagtacattggataaacaaagaataggctggaaaagtatttccaagcctttctaacgattgaaggagatattttc Mask Tandem Repeat Region ================================================ gaaaatatctccttcaatcgttagaaaggcttggaaatacttttccagcctattctttgtttatccaatgtactttcattatactgaaaggagatatagttttcaattatactttttctctaactagatatagttagaaactatgta Find is-nt database================================================ Query_seq: SSA_1420:SSA_1421|SSA_1420:SSA_1421:Homoserine O-succinyltransferase, putative:Adenine phosphoribosyltransferase, putative:<-<-:1430716..1430862 147 gaaaatatctccttcaatcgttagaaaggcttggaaatacttttccagcctattctttgtttatccaatgtactttcattatactgaaaggagatatagttttcaattatactttttctctaactagatatagttagaaactatgta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1420:SSA_1421|SSA_1420:SSA_1421:Homoserine O-succinyltransferase, putative:Adenine phosphoribosyltransferase, putative:<-<-:1430716..1430862 147 gaaaatatctccttcaatcgttagaaaggcttggaaatacttttccagcctattctttgtttatccaatgtactttcattatactgaaaggagatatagttttcaattatactttttctctaactagatatagttagaaactatgta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1420:SSA_1421|SSA_1420:SSA_1421:Homoserine O-succinyltransferase, putative:Adenine phosphoribosyltransferase, putative:<-<-:1430716..1430862 147 gaaaatatctccttcaatcgttagaaaggcttggaaatacttttccagcctattctttgtttatccaatgtactttcattatactgaaaggagatatagttttcaattatactttttctctaactagatatagttagaaactatgta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gaaaatatctccttcaatcgttagaaaggcttggaaatacttttccagcctattctttgtttatccaatgtactttcattatactgaaaggagatatagttttcaattatactttttctctaactagatatagttagaaactatgta Predict ORF larger than 30AA ================================================ Protein_Len: 40 Strand: + Start: 5 End: 124 .... M S P S I V R K A W K Y F S S L F F V Y P M Y F H Y T E R R Y S F Q L Y F F S N ....................... gaaaatatctccttcaatcgttagaaaggcttggaaatacttttccagcctattctttgtttatccaatgtactttcattatactgaaaggagatatagttttcaattatactttttctctaactagatatagttagaaactatgta 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: 78 End: 107 .............................................................................ATTGAAAACTATATCTCCTTTCAGTATAAT........................................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gaaaatatctccttcaatcgttagaaaggcttggaaatacttttccagcctattctttgtttatccaatgtactttcattatactgaaaggagatatagttttcaattatactttttctctaactagatatagttagaaactatgta Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 74 HP_score: -7.1 Tail_Score: -3.89614 Start: 28 End: 50 Full_Region: gataaacaaagaata ggctggaaa agta tttccaagcc tttctaacgattgaa ...........................ggctggaaaagtatttccaagcc................................................................................................. Find igs database================================================ Query_seq: SSA_1420:SSA_1421|SSA_1420:SSA_1421:Homoserine O-succinyltransferase, putative:Adenine phosphoribosyltransferase, putative:<-<-:1430716..1430862 147 gaaaatatctccttcaatcgttagaaaggcttggaaatacttttccagcctattctttgtttatccaatgtactttcattatactgaaaggagatatagttttcaattatactttttctctaactagatatagttagaaactatgta Intra-Species Hit: Count: 1 Min: 1 Max: 147 Len: 147 Subject: NC_009009_SSA_1420_SSA_1421|Homoserine O-succinyltransferase, putative:Adenine phosphoribosyltransferase, putative|NEGATIVE:NEGATIVE|[1430716,1430862]|147 HSP 1 e-value: 3.0E-78 bit: 291.0 Len: 147 Query Start:1 Query End:147 Subject Strand: POSITIVE Subject Start: 1 Subject End: 147 gaaaatatctccttcaatcgttagaaaggcttggaaatacttttccagcctattctttgtttatccaatgtactttcattatactgaaaggagatatagttttcaattatactttttctctaactagatatagttagaaactatgta gaaaatatctccttcaatcgttagaaaggcttggaaatacttttccagcctattctttgtttatccaatgtactttcattatactgaaaggagatatagttttcaattatactttttctctaactagatatagttagaaactatgta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAAAAUAUCUCCUUCAAUCGUUAGAAAGGCUUGGAAAUACUUUUCCAGCCUAUUCUUUGUUUAUCCAAUGUACUUUCAUUAUACUGAAAGGAGAUAUAGUUUUCAAUUAUACUUUUUCUCUAACUAGAUAUAGUUAGAAACUAUGUA ((((((((((((((((......(((((((((.(((((....)))))))))).))))..........((((......))))....)).))))))))))...)))).....(((......((((((((....))))))))......))) (-38.50) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UACAUAGUUUCUAACUAUAUCUAGUUAGAGAAAAAGUAUAAUUGAAAACUAUAUCUCCUUUCAGUAUAAUGAAAGUACAUUGGAUAAACAAAGAAUAGGCUGGAAAAGUAUUUCCAAGCCUUUCUAACGAUUGAAGGAGAUAUUUUC (((....((((((((((....))))))))))....))).....((((...((((((((((.((((.(((((......))))).........((((.((((((((((....))))).)))))))))....)))))))))))))))))) (-41.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 847 60 11 151 102 NC_009009:SSA_1420|5end_Homoserine_O-succinyltransferase,_putative_1430625..1430855_NEGATIVE 322 77 32 54 6 NC_009009:SSA_2229|5end_hypothetical_protein_2228994..2229224_NEGATIVE 281 55 11 219 172 NC_009009:SSA_0254|5end_hypothetical_protein_247492..247722_NEGATIVE 271 60 12 88 40 NC_009009:SSA_1210|5end_GTP_pyrophosphokinase,_putative_1234655..1234885_NEGATIVE 266 50 8 137 95 NC_009009:SSA_0006|5end_Peptidyl-tRNA_hydrolase,_putative_5009..5239_POSITIVE 262 70 25 56 8 NC_009009:SSA_2304|5end_Conserved_uncharacterized_protein_2306270..2306500_NEGATIVE 260 90 41 198 153 NC_009009:SSA_1795|5end_Guanosine_3',5'-bis-pyrophosphate_(ppGpp)_synthetase,_putative_1777671..1777901_NEGATIVE 254 90 42 140 86 NC_009009:SSA_1892|5end_hypothetical_protein_1889262..1889492_NEGATIVE 252 133 96 118 81 NC_009009:SSA_0758|5end_Ornithine_acetyltransferase_/_amino-acid_acetyltransferase,_putative_740636..740866_POSITIVE 250 58 11 56 5 NC_009009:SSA_1153|5end_HemK_protein,_putative_1181838..1182068_POSITIVE 248 58 12 102 46 NC_009009:SSA_1466|5end_Prephenate_dehydrogenase,_putative_1473111..1473341_NEGATIVE 248 58 11 191 132 NC_009009:SSA_0911|5end_hypothetical_protein_922078..922308_POSITIVE 247 50 8 130 97 NC_009009:SSA_1490|5end_Ribonuclease_BN,_putative_1496732..1496962_NEGATIVE 246 52 11 203 155 NC_009009:SSA_1658|5end_Cationic_amino_acid_transporter,_putative_1654674..1654904_NEGATIVE 244 65 26 165 121 NC_009009:SSA_1260|5end_Phosphopentomutase,_putative_1286963..1287193_NEGATIVE 244 50 4 201 145 NC_009009:SSA_0765|5end_hypothetical_protein_745519..745749_POSITIVE 240 67 26 154 106 NC_009009:SSA_1432|5end_HflX_GTPase,_putative_1439901..1440131_NEGATIVE 239 49 7 134 99 NC_009009:SSA_1139|5end_Pyruvate_dehydrogenase_E1_component_beta_subunit,_putative_1166823..1167053_POSITIVE 239 50 11 55 24 NC_009009:SSA_0374|5end_Peptide_methionine_sulfoxide_reductase_msrA/msrB,_putative_363163..363393_POSITIVE 237 67 23 66 18 NC_009009:SSA_1722|5end_Thymidylate_kinase,_putative_1708663..1708893_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 322 77 32 85 37 NC_009009:SSA_2230|3end_Ribonucleotide_reductase,_class_III,_anaerobic,_putative_2228963..2229113_NEGATIVE 313 68 21 101 52 NC_009009:SSA_0876|3end_4-methyl-5(B-hydroxyethyl)-thiazole_monophosphate_biosynthesis_protein,_putative_870861..871011_POSITIVE 313 50 7 123 78 NC_009009:SSA_0507|3end_hypothetical_protein_506442..506592_POSITIVE 292 70 27 112 57 NC_009009:SSA_1554|3end_hypothetical_protein_1556847..1556997_POSITIVE 283 66 23 85 47 NC_009009:SSA_0564|3end_Potential_aminotransferase,_putative_556988..557138_POSITIVE 266 50 8 64 22 NC_009009:SSA_0005|3end_GTP-binding_protein,_putative_5016..5166_POSITIVE 261 58 13 99 55 NC_009009:SSA_0798|3end_ABC_transporter_membrane-spanning_permease-macrolide_efflux,_putative_781724..781874_POSITIVE 252 133 96 100 63 NC_009009:SSA_0757|3end_N-acetyl-gamma-glutamyl-phosphate_reductase,_putative_740698..740848_POSITIVE 250 58 11 56 5 NC_009009:SSA_1152|3end_Protein_chain_release_factor_A,_putative_1181918..1182068_POSITIVE 248 58 12 86 30 NC_009009:SSA_1467|3end_Chorismate_synthase,_putative_1473127..1473277_NEGATIVE 247 50 8 82 49 NC_009009:SSA_1491|3end_Methionine_aminopeptidase_A,_putative_1496780..1496930_NEGATIVE 244 65 26 151 107 NC_009009:SSA_1261|3end_Ribose-5-phosphate_isomerase_A,_putative_1286977..1287127_NEGATIVE 242 90 43 44 1 NC_009009:SSA_1796|3end_Transcription_elongation_factor_GreA,_putative_1777825..1777975_NEGATIVE 240 67 26 122 74 NC_009009:SSA_1433|3end_tRNA_delta(2)-isopentenylpyrophosphate_transferase,_putative_1439933..1440083_NEGATIVE 239 52 17 46 13 NC_009009:SSA_1659|3end_ABC-type_antimicrobial_peptide_transport_system,_permease_component,_putative_1654831..1654981_NEGATIVE 239 49 7 115 80 NC_009009:SSA_1138|3end_Pyruvate_dehydrogenase,_TPP-dependent_E1_component_alpha-subunit,_putative_1166884..1167034_POSITIVE 236 68 23 56 1 NC_009009:SSA_0963|3end_Peptidoglycan_N-acetylglucosamine_deacetylase_A,_putative_972890..973040_POSITIVE 236 50 7 68 15 NC_009009:SSA_0451|3end_Conserved_uncharacterized_protein_451636..451786_POSITIVE 233 50 12 34 4 NC_009009:SSA_0268|3end_Phosphotransferase_system_(PTS)_cellobiose-specific_component_IIB,_putative_262621..262771_POSITIVE 230 56 11 149 99 NC_009009:SSA_0093|3end_V-type_sodium_ATPase,_subunit_D,_putative_94989..95139_POSITIVE