Origin IGS: agcagcatacctccatcttttctttattaaattttattagtattctacaccttccgaacttatatttcaaggaatattaaaagaaacaagggatttcgtcccttgtttcttttggttgat .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 atcaaccaaaagaaacaagggacgaaatcccttgtttcttttaatattccttgaaatataagttcggaaggtgtagaatactaataaaatttaataaagaaaagatggaggtatgctgct Mask Tandem Repeat Region ================================================ agcagcatacctccatcttttctttattaaattttattagtattctacaccttccgaacttatatttcaaggaatattaaaagaaacaagggatttcgtcccttgtttcttttggttgat Find is-nt database================================================ Query_seq: SSA_1995:SSA_1996|SSA_1995:SSA_1996:hypothetical protein:DNA-directed RNA polymerase delta subunit, putative:<-<-:1993449..1993568 120 agcagcatacctccatcttttctttattaaattttattagtattctacaccttccgaacttatatttcaaggaatattaaaagaaacaagggatttcgtcccttgtttcttttggttgat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1995:SSA_1996|SSA_1995:SSA_1996:hypothetical protein:DNA-directed RNA polymerase delta subunit, putative:<-<-:1993449..1993568 120 agcagcatacctccatcttttctttattaaattttattagtattctacaccttccgaacttatatttcaaggaatattaaaagaaacaagggatttcgtcccttgtttcttttggttgat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1995:SSA_1996|SSA_1995:SSA_1996:hypothetical protein:DNA-directed RNA polymerase delta subunit, putative:<-<-:1993449..1993568 120 agcagcatacctccatcttttctttattaaattttattagtattctacaccttccgaacttatatttcaaggaatattaaaagaaacaagggatttcgtcccttgtttcttttggttgat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 agcagcatacctccatcttttctttattaaattttattagtattctacaccttccgaacttatatttcaaggaatattaaaagaaacaagggatttcgtcccttgtttcttttggttgat Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: + Start: 31 End: 120 .............................. M L L V F Y T F R T Y I S R N I K R N K G F R P L F L L V D agcagcatacctccatcttttctttattaaattttattagtattctacaccttccgaacttatatttcaaggaatattaaaagaaacaagggatttcgtcccttgtttcttttggttgat 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: 88 Start: 42 End: 71 .........................................CTTGAAATATAAGTTCGGAAGGTGTAGAAT................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ agcagcatacctccatcttttctttattaaattttattagtattctacaccttccgaacttatatttcaaggaatattaaaagaaacaagggatttcgtcccttgtttcttttggttgat Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 70 HP_score: -5.5 Tail_Score: -4.47163 Start: 90 End: 102 Full_Region: TATTAAAAGAAACAA GGGAT TTC GTCCC TTGTTTCTTTTGGTT .........................................................................................GGGATTTCGTCCC.................. Find igs database================================================ Query_seq: SSA_1995:SSA_1996|SSA_1995:SSA_1996:hypothetical protein:DNA-directed RNA polymerase delta subunit, putative:<-<-:1993449..1993568 120 agcagcatacctccatcttttctttattaaattttattagtattctacaccttccgaacttatatttcaaggaatattaaaagaaacaagggatttcgtcccttgtttcttttggttgat Intra-Species Hit: Count: 1 Min: 1 Max: 120 Len: 120 Subject: NC_009009_SSA_1995_SSA_1996|hypothetical protein:DNA-directed RNA polymerase delta subunit, putative|NEGATIVE:NEGATIVE|[1993449,1993568]|120 HSP 1 e-value: 3.0E-62 bit: 238.0 Len: 120 Query Start:1 Query End:120 Subject Strand: POSITIVE Subject Start: 1 Subject End: 120 agcagcatacctccatcttttctttattaaattttattagtattctacaccttccgaacttatatttcaaggaatattaaaagaaacaagggatttcgtcccttgtttcttttggttgat agcagcatacctccatcttttctttattaaattttattagtattctacaccttccgaacttatatttcaaggaatattaaaagaaacaagggatttcgtcccttgtttcttttggttgat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGCAGCAUACCUCCAUCUUUUCUUUAUUAAAUUUUAUUAGUAUUCUACACCUUCCGAACUUAUAUUUCAAGGAAUAUUAAAAGAAACAAGGGAUUUCGUCCCUUGUUUCUUUUGGUUGAU ..((((.....(((..........((((((......)))))).............(((.......)))..)))....(((((((((((((((((...))))))))))))))))))))).. (-28.50) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUCAACCAAAAGAAACAAGGGACGAAAUCCCUUGUUUCUUUUAAUAUUCCUUGAAAUAUAAGUUCGGAAGGUGUAGAAUACUAAUAAAAUUUAAUAAAGAAAAGAUGGAGGUAUGCUGCU .......(((((((((((((((.....)))))))))))))))....((((..(((.......)))))))...((((.(((((..((...(((........)))..))..))))).)))). (-28.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 787 120 71 211 162 NC_009009:SSA_1995|5end_hypothetical_protein_1993358..1993588_NEGATIVE 245 110 63 168 120 NC_009009:SSA_1100|5end_Hemolysin_exporter,_ATPase_component,_putative_1119873..1120103_POSITIVE 244 50 2 134 87 NC_009009:SSA_1128|5end_Voltage_gated_chloride_channel_EriC,_putative_1153250..1153480_POSITIVE 240 55 11 131 98 NC_009009:SSA_0367|5end_hypothetical_protein_358309..358539_POSITIVE 235 119 79 123 68 NC_009009:SSA_0817|5end_Antirepressor_regulating_drug_resistance_(membrane-bound),_putative_797838..798068_POSITIVE 229 110 67 207 157 NC_009009:SSA_0927|5end_Transcriptional_regulator,_TetR/AcrR_family,_putative_936049..936279_POSITIVE 220 113 86 107 78 NC_009009:SSA_0219|5end_PTS_system,_sugar-specific_enzyme_IIA_component,_putative_215367..215597_POSITIVE 218 75 32 229 185 NC_009009:SSA_1275|5end_hypothetical_protein_1297606..1297836_NEGATIVE 217 57 12 106 43 NC_009009:SSA_1291|5end_hypothetical_protein_1311102..1311332_NEGATIVE 211 120 82 51 1 NC_009009:SSA_1459|5end_RNA_methyltransferase,_putative_1467481..1467711_NEGATIVE 208 75 31 143 98 NC_009009:SSA_1697|5end_Tagatose-6-phosphate_kinase,_putative_1690120..1690350_NEGATIVE 208 106 69 45 9 NC_009009:SSA_0597|5end_hypothetical_protein_587566..587796_POSITIVE 208 29 3 118 86 NC_009009:SSA_0195|5end_hypothetical_protein_195113..195343_POSITIVE 207 119 87 222 187 NC_009009:SSA_1480|5end_hypothetical_protein_1484811..1485041_NEGATIVE 206 118 79 168 124 NC_009009:SSA_0650|5end_GTP-binding_protein_TypA/BipA,_putative_632548..632778_POSITIVE 205 93 51 217 174 NC_009009:SSA_1986|5end_Acetyltransferase,_GNAT_family,_putative_1982531..1982761_NEGATIVE 204 16 1 211 193 NC_009009:SSA_1468|5end_3-dehydroquinate_synthase,_putative_1475452..1475682_NEGATIVE 204 24 1 115 87 NC_009009:SSA_0894|5end_ATP-binding_cassette_protein,_putative_885779..886009_POSITIVE 203 118 88 197 169 NC_009009:SSA_1934|5end_Biotin_carboxyl_carrier_protein_of_acetyl-CoA_carboxylase,_putative_1921800..1922030_NEGATIVE 203 120 89 79 49 NC_009009:SSA_0935|5end_tRNA_pseudouridine_synthase_B,_putative_944015..944245_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 285 104 64 72 25 NC_009009:SSA_0427|3end_DNA-binding_transcriptional_activator,_SARP_family,_putative_427615..427765_POSITIVE 245 110 63 89 41 NC_009009:SSA_1099|3end_Calcium_binding_hemolysin-like_protein,_putative_1119874..1120024_POSITIVE 235 119 79 107 52 NC_009009:SSA_0816|3end_Copper_transport_operon_or_penicillinase_transcription_repressor,_putative_797902..798052_POSITIVE 233 116 77 85 38 NC_009009:SSA_1796|3end_Transcription_elongation_factor_GreA,_putative_1777825..1777975_NEGATIVE 229 17 3 116 102 NC_009009:SSA_1766|3end_Bacitracin_ABC_transporter,_permease_protein,_putative_1754388..1754538_NEGATIVE 222 36 1 107 76 NC_009009:SSA_1707|3end_Conserved_uncharacterized_protein_1698248..1698398_POSITIVE 217 57 12 109 46 NC_009009:SSA_1292|3end_hypothetical_protein_1311099..1311249_NEGATIVE 216 120 73 82 33 NC_009009:SSA_2136|3end_50S_ribosomal_protein_L34,_putative_2137507..2137657_NEGATIVE 213 117 82 81 42 NC_009009:SSA_0492|3end_NADH-dependent_flavin_oxidoreductase,_putative_492771..492921_POSITIVE 213 56 11 82 33 NC_009009:SSA_0375|3end_D-methionine-binding_lipoprotein_(ABC-type_transporter),_putative_365209..365359_POSITIVE 208 75 31 130 85 NC_009009:SSA_1698|3end_Galactose-6-phosphate_isomerase,_LacB_subunit,_putative_1690133..1690283_NEGATIVE 204 24 1 128 100 NC_009009:SSA_0893|3end_ATP-binding_cassette_transporter-like_protein,_putative_885872..886022_POSITIVE 203 120 89 75 45 NC_009009:SSA_0934|3end_HydD,_putative_944091..944241_POSITIVE 202 111 71 92 55 NC_009009:SSA_1825|3end_hypothetical_protein_1814458..1814608_POSITIVE 201 101 68 56 18 NC_009009:SSA_1588|3end_Conserved_ABC-type_antimicrobial_permease-like_protein,_putative_1589182..1589332_NEGATIVE 201 116 87 150 117 NC_009009:SSA_0449|3end_Aminopeptidase_P;_XAA-pro_aminopeptidase,_putative_450605..450755_POSITIVE 200 117 89 116 88 NC_009009:SSA_2286|3end_Dihydroxy-acid_dehydratase,_putative_2287878..2288028_NEGATIVE 199 47 4 101 61 NC_009009:SSA_0559|3end_hypothetical_protein_553119..553269_POSITIVE 197 119 71 89 35 NC_009009:SSA_1788|3end_Integral_membrane_protein,_possible_receptor,_putative_1771656..1771806_NEGATIVE 197 108 64 66 15 NC_009009:SSA_1162|3end_Possible_fimbrial_assembly_protein_fimC,_putative_1188489..1188639_NEGATIVE