Origin IGS: caagatagtttttccagcttgcttcttgtatggtataatagtctcgaatatctcaaaggaggacagctttgtttttagcttttaaagagattgtctacagtcgcggacgctatcgttta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taaacgatagcgtccgcgactgtagacaatctctttaaaagctaaaaacaaagctgtcctcctttgagatattcgagactattataccatacaagaagcaagctggaaaaactatcttg Mask Tandem Repeat Region ================================================ caagatagtttttccagcttgcttcttgtatggtataatagtctcgaatatctcaaaggaggacagctttgtttttagcttttaaagagattgtctacagtcgcggacgctatcgttta Find is-nt database================================================ Query_seq: SSA_0923:SSA_0924|SSA_0923:SSA_0924:Transcriptional regulator, TetR/AcrR family, putative:ABC-type antimicrobial peptide transport system, permease component, putative:->->:933759..933877 119 caagatagtttttccagcttgcttcttgtatggtataatagtctcgaatatctcaaaggaggacagctttgtttttagcttttaaagagattgtctacagtcgcggacgctatcgttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0923:SSA_0924|SSA_0923:SSA_0924:Transcriptional regulator, TetR/AcrR family, putative:ABC-type antimicrobial peptide transport system, permease component, putative:->->:933759..933877 119 caagatagtttttccagcttgcttcttgtatggtataatagtctcgaatatctcaaaggaggacagctttgtttttagcttttaaagagattgtctacagtcgcggacgctatcgttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0923:SSA_0924|SSA_0923:SSA_0924:Transcriptional regulator, TetR/AcrR family, putative:ABC-type antimicrobial peptide transport system, permease component, putative:->->:933759..933877 119 caagatagtttttccagcttgcttcttgtatggtataatagtctcgaatatctcaaaggaggacagctttgtttttagcttttaaagagattgtctacagtcgcggacgctatcgttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 caagatagtttttccagcttgcttcttgtatggtataatagtctcgaatatctcaaaggaggacagctttgtttttagcttttaaagagattgtctacagtcgcggacgctatcgttta Predict ORF larger than 30AA ================================================ caagatagtttttccagcttgcttcttgtatggtataatagtctcgaatatctcaaaggaggacagctttgtttttagcttttaaagagattgtctacagtcgcggacgctatcgttta 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: 10 End: 39 .........TTTTCCAGCTTGCTTCTTGTATGGTATAAT................................................................................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ caagatagtttttccagcttgcttcttgtatggtataatagtctcgaatatctcaaaggaggacagctttgtttttagcttttaaagagattgtctacagtcgcggacgctatcgttta Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_0923:SSA_0924|SSA_0923:SSA_0924:Transcriptional regulator, TetR/AcrR family, putative:ABC-type antimicrobial peptide transport system, permease component, putative:->->:933759..933877 119 caagatagtttttccagcttgcttcttgtatggtataatagtctcgaatatctcaaaggaggacagctttgtttttagcttttaaagagattgtctacagtcgcggacgctatcgttta Intra-Species Hit: Count: 1 Min: 1 Max: 119 Len: 119 Subject: NC_009009_SSA_0923_SSA_0924|Transcriptional regulator, TetR/AcrR family, putative:ABC-type antimicrobial peptide transport system, permease component, putative|POSITIVE:POSITIVE|[933759,933877]|119 HSP 1 e-value: 1.0E-61 bit: 236.0 Len: 119 Query Start:1 Query End:119 Subject Strand: POSITIVE Subject Start: 1 Subject End: 119 caagatagtttttccagcttgcttcttgtatggtataatagtctcgaatatctcaaaggaggacagctttgtttttagcttttaaagagattgtctacagtcgcggacgctatcgttta caagatagtttttccagcttgcttcttgtatggtataatagtctcgaatatctcaaaggaggacagctttgtttttagcttttaaagagattgtctacagtcgcggacgctatcgttta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CAAGAUAGUUUUUCCAGCUUGCUUCUUGUAUGGUAUAAUAGUCUCGAAUAUCUCAAAGGAGGACAGCUUUGUUUUUAGCUUUUAAAGAGAUUGUCUACAGUCGCGGACGCUAUCGUUUA ...((((((...(((.((.(((.....)))..(((..((((((((.....((((....))))..((((........))))......)))))))).)))....))))).))))))..... (-26.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAACGAUAGCGUCCGCGACUGUAGACAAUCUCUUUAAAAGCUAAAAACAAAGCUGUCCUCCUUUGAGAUAUUCGAGACUAUUAUACCAUACAAGAAGCAAGCUGGAAAAACUAUCUUG .....(((((..(((((...((....)).((((......((((........))))...(((....)))......)))).......................)).)))....)))))... (-17.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 317 59 14 223 181 NC_009009:SSA_0583|5end_Nucleotidyltransferase,_putative_574505..574735_POSITIVE 290 88 41 69 21 NC_009009:SSA_2031|5end_Conserved_domain_uncharacterized_protein_2037153..2037383_POSITIVE 278 107 61 198 141 NC_009009:SSA_0346|5end_hypothetical_protein_339448..339678_POSITIVE 276 110 63 172 122 NC_009009:SSA_1373|5end_ATPase_components_of_ABC_transporters_with_duplicated_ATPase_domains,_multidrug_transport_system,_putative_1389707..1389937_POSITIVE 272 44 11 107 68 NC_009009:SSA_1311|5end_Hydrolase,_haloacid_dehalogenase-like_family,_putative_1328393..1328623_NEGATIVE 271 110 61 185 132 NC_009009:SSA_0279|5end_Sugar-binding_transcriptional_repressor_(DeoR),_putative_272319..272549_POSITIVE 263 109 61 195 138 NC_009009:SSA_0125|5end_50S_ribosomal_protein_L30,_putative_116930..117160_POSITIVE 257 100 51 168 107 NC_009009:SSA_2048|5end_Serine_acetyltransferase,_putative_2050601..2050831_NEGATIVE 256 110 61 55 1 NC_009009:SSA_1897|5end_Ribosomal_protein_HS6-type_(S12/L30/L7a),_putative_1894450..1894680_NEGATIVE 256 107 66 47 6 NC_009009:SSA_1676|5end_Transcriptional_regulator,_LytTr_family,_putative_1671313..1671543_NEGATIVE 256 81 42 228 191 NC_009009:SSA_0420|5end_Hydrolase,_HAD_superfamily,_putative_418620..418850_POSITIVE 255 55 11 219 164 NC_009009:SSA_1044|5end_Homoserine_kinase,_putative_1059853..1060083_POSITIVE 253 89 46 229 194 NC_009009:SSA_0616|5end_YlbN-like_protein,_putative_609245..609475_POSITIVE 250 58 13 195 142 NC_009009:SSA_2101|5end_Amino_acid_ABC_transporter,_periplasmic_amino_acid-binding_protein,_putative_2105393..2105623_NEGATIVE 250 43 11 220 192 NC_009009:SSA_0567|5end_Isochorismitase_family_protein,_putative_560805..561035_POSITIVE 250 110 61 229 181 NC_009009:SSA_0221|5end_PTS_system,_mannose-specific_IIC_component,_putative_216370..216600_POSITIVE 248 110 61 61 16 NC_009009:SSA_1541|5end_Peptidase,_U32_family,_putative_1546600..1546830_NEGATIVE 248 110 64 212 155 NC_009009:SSA_1069|5end_Lipoprotein_signal_peptidase,_putative_1088291..1088521_POSITIVE 248 110 66 162 114 NC_009009:SSA_0025|5end_DNA_repair_protein_recO,_putative_29694..29924_POSITIVE 245 54 11 217 169 NC_009009:SSA_1398|5end_Membrane_protein,_hemolysin_III-like,_putative_1410881..1411111_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 265 109 61 126 74 NC_009009:SSA_0343|3end_DNA-damage-inducible_protein_P,_putative_338669..338819_POSITIVE 260 96 58 114 74 NC_009009:SSA_1018|3end_Zinc_metalloprotease_zmpC_precursor,_putative_1032569..1032719_POSITIVE 257 100 51 76 15 NC_009009:SSA_2049|3end_Polyribonucleotide_nucleotidyltransferase,_putative_2050693..2050843_NEGATIVE 256 110 61 62 8 NC_009009:SSA_1899|3end_hypothetical_protein_1894443..1894593_NEGATIVE 256 81 42 58 21 NC_009009:SSA_0419|3end_Alpha-galactosidase,_putative_418530..418680_POSITIVE 248 110 64 85 41 NC_009009:SSA_2101|3end_Amino_acid_ABC_transporter,_periplasmic_amino_acid-binding_protein,_putative_2104509..2104659_NEGATIVE 245 110 64 150 100 NC_009009:SSA_0473|3end_Precorrin-6x_reductase,_putative_476331..476481_POSITIVE 245 45 3 58 16 NC_009009:SSA_0239|3end_7,8-dihydro-8-oxoguanine-triphosphatase,_putative_233493..233643_POSITIVE 244 66 40 82 58 NC_009009:SSA_1364|3end_hypothetical_protein_1380482..1380632_NEGATIVE 244 95 53 46 2 NC_009009:SSA_0825|3end_DNA-directed_RNA_polymerase,_sigma_subunit_(sigma70/sigma32),_putative_805056..805206_POSITIVE 241 76 39 42 6 NC_009009:SSA_1433|3end_tRNA_delta(2)-isopentenylpyrophosphate_transferase,_putative_1439933..1440083_NEGATIVE 240 44 14 109 73 NC_009009:SSA_1870|3end_Phospho-N-acetylmuramoyl-pentapeptide-_transferase,_putative_1865600..1865750_NEGATIVE 236 47 2 74 21 NC_009009:SSA_0494|3end_ABC-type_dipeptide/oligopeptide/nickel_transport_system,_ATPase_component,_putative_495269..495419_POSITIVE 235 81 41 77 28 NC_009009:SSA_0102|3end_Kinase,_putative_104627..104777_POSITIVE 234 60 18 151 105 NC_009009:SSA_0873|3end_ATP-dependent_DNA_helicase;_DNA_polymerase_III,_epsilon_subunit,_putative_867915..868065_POSITIVE 232 69 21 58 2 NC_009009:SSA_1694|3end_PTS_system,_lactose-specific_IIA_component,_putative_1686811..1686961_NEGATIVE 232 110 62 137 86 NC_009009:SSA_1607|3end_Formamidopyrimidine-DNA_glycosylase,_putative_1612431..1612581_NEGATIVE 232 47 7 103 56 NC_009009:SSA_1065|3end_Beta-hexosamidase_A,_putative_1084130..1084280_POSITIVE 232 49 2 126 72 NC_009009:SSA_0345|3end_hypothetical_protein_339209..339359_POSITIVE 231 110 65 131 82 NC_009009:SSA_0854|3end_hypothetical_protein_841813..841963_POSITIVE