Origin IGS: agttttctctctttctctttttaaaattttctatcaaactagggaatagaatttcaaattacgagactattatatccttttggtcaaaaaaggtcaaatagaaactt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aagtttctatttgaccttttttgaccaaaaggatataatagtctcgtaatttgaaattctattccctagtttgatagaaaattttaaaaagagaaagagagaaaact Mask Tandem Repeat Region ================================================ agttttctctctttctctttttaaaattttctatcaaactagggaatagaatttcaaattacgagactattatatccttttggtcaaaaaaggtcaaatagaaactt Find is-nt database================================================ Query_seq: SSA_1731:SSA_1732|SSA_1731:SSA_1732:ATP-dependent Clp protease, proteolytic subunit, putative:Uracil phosphoribosyltransferase, putative:<-<-:1716899..1717005 107 agttttctctctttctctttttaaaattttctatcaaactagggaatagaatttcaaattacgagactattatatccttttggtcaaaaaaggtcaaatagaaactt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1731:SSA_1732|SSA_1731:SSA_1732:ATP-dependent Clp protease, proteolytic subunit, putative:Uracil phosphoribosyltransferase, putative:<-<-:1716899..1717005 107 agttttctctctttctctttttaaaattttctatcaaactagggaatagaatttcaaattacgagactattatatccttttggtcaaaaaaggtcaaatagaaactt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1731:SSA_1732|SSA_1731:SSA_1732:ATP-dependent Clp protease, proteolytic subunit, putative:Uracil phosphoribosyltransferase, putative:<-<-:1716899..1717005 107 agttttctctctttctctttttaaaattttctatcaaactagggaatagaatttcaaattacgagactattatatccttttggtcaaaaaaggtcaaatagaaactt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 agttttctctctttctctttttaaaattttctatcaaactagggaatagaatttcaaattacgagactattatatccttttggtcaaaaaaggtcaaatagaaactt Predict ORF larger than 30AA ================================================ agttttctctctttctctttttaaaattttctatcaaactagggaatagaatttcaaattacgagactattatatccttttggtcaaaaaaggtcaaatagaaactt 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: 89 Start: 69 End: 98 ....................................................................TTTGACCTTTTTTGACCAAAAGGATATAAT......... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ agttttctctctttctctttttaaaattttctatcaaactagggaatagaatttcaaattacgagactattatatccttttggtcaaaaaaggtcaaatagaaactt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_1731:SSA_1732|SSA_1731:SSA_1732:ATP-dependent Clp protease, proteolytic subunit, putative:Uracil phosphoribosyltransferase, putative:<-<-:1716899..1717005 107 agttttctctctttctctttttaaaattttctatcaaactagggaatagaatttcaaattacgagactattatatccttttggtcaaaaaaggtcaaatagaaactt Intra-Species Hit: Count: 1 Min: 1 Max: 107 Len: 107 Subject: NC_009009_SSA_1731_SSA_1732|ATP-dependent Clp protease, proteolytic subunit, putative:Uracil phosphoribosyltransferase, putative|NEGATIVE:NEGATIVE|[1716899,1717005]|107 HSP 1 e-value: 2.0E-54 bit: 212.0 Len: 107 Query Start:1 Query End:107 Subject Strand: POSITIVE Subject Start: 1 Subject End: 107 agttttctctctttctctttttaaaattttctatcaaactagggaatagaatttcaaattacgagactattatatccttttggtcaaaaaaggtcaaatagaaactt agttttctctctttctctttttaaaattttctatcaaactagggaatagaatttcaaattacgagactattatatccttttggtcaaaaaaggtcaaatagaaactt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGUUUUCUCUCUUUCUCUUUUUAAAAUUUUCUAUCAAACUAGGGAAUAGAAUUUCAAAUUACGAGACUAUUAUAUCCUUUUGGUCAAAAAAGGUCAAAUAGAAACUU .............((((........(((..(((......)))..))).(.....).......))))(((((....((((((......))))))...)))))...... (-13.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAGUUUCUAUUUGACCUUUUUUGACCAAAAGGAUAUAAUAGUCUCGUAAUUUGAAAUUCUAUUCCCUAGUUUGAUAGAAAAUUUUAAAAAGAGAAAGAGAGAAAACU ...(((((......((((((......)))))).........((((....((((((((((((((.........))))))..))))))))..))))...)))))..... (-17.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 744 80 31 171 122 NC_009009:SSA_1731|5end_ATP-dependent_Clp_protease,_proteolytic_subunit,_putative_1716808..1717038_NEGATIVE 313 50 3 152 96 NC_009009:SSA_1100|5end_Hemolysin_exporter,_ATPase_component,_putative_1119873..1120103_POSITIVE 234 49 1 183 119 NC_009009:SSA_2218|5end_Glycosyltransferase_(cell_wall_biogenesis)_Cps9G,_putative_2219941..2220171_NEGATIVE 228 55 13 136 96 NC_009009:SSA_1244|5end_hypothetical_protein_1268704..1268934_NEGATIVE 220 50 1 135 92 NC_009009:SSA_2174|5end_2,3,4,5-tetrahydropyridine-2-carboxylate_N-succinyltransferase,_putative_2172689..2172919_NEGATIVE 217 45 4 140 91 NC_009009:SSA_1396|5end_hypothetical_protein_1410374..1410604_NEGATIVE 217 45 1 170 123 NC_009009:SSA_1056|5end_Firmicute_fructose-1,6-bisphosphatase,_putative_1071760..1071990_POSITIVE 213 42 8 131 96 NC_009009:SSA_0690|5end_Recombinational_DNA_repair_protein_(RecF_pathway),_putative_674432..674662_POSITIVE 213 56 12 143 98 NC_009009:SSA_0567|5end_Isochorismitase_family_protein,_putative_560805..561035_POSITIVE 212 46 1 141 92 NC_009009:SSA_0903|5end_NAD(P)H_dehydrogenase_(quinone),_putative_893242..893472_POSITIVE 209 50 2 140 93 NC_009009:SSA_0527|5end_Propanediol_utilization_protein_PduL_524625..524855_POSITIVE 202 32 3 75 52 NC_009009:SSA_1381|5end_hypothetical_protein_1399565..1399795_NEGATIVE 200 50 1 152 93 NC_009009:SSA_0357|5end_Thioredoxin,_putative_350763..350993_POSITIVE 199 43 2 144 96 NC_009009:SSA_1237|5end_Uracil-DNA_glycosylase,_putative_1262366..1262596_NEGATIVE 196 36 1 130 95 NC_009009:SSA_1411|5end_Glucose-1-phosphate_thymidylytransferase,_putative_1423960..1424190_NEGATIVE 194 51 14 54 19 NC_009009:SSA_0080|5end_Superfamily_I_DNA_and_RNA_helicases,_putative_83785..84015_POSITIVE 193 36 1 127 92 NC_009009:SSA_1543|5end_hypothetical_protein_1547835..1548065_POSITIVE 192 78 33 230 185 NC_009009:SSA_1726|5end_ABC_transporter_ATP-binding_protein-branched_chain_amino_acid_transport,_putative_1712467..1712697_NEGATIVE 191 44 10 143 98 NC_009009:SSA_1967|5end_Threonine_desaminase,_putative_1963559..1963789_NEGATIVE 191 95 53 65 24 NC_009009:SSA_1867|5end_ABC-type_polar_amino_acid_transport_system,_ATPase_component,_putative_1863096..1863326_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 313 50 3 73 17 NC_009009:SSA_1099|3end_Calcium_binding_hemolysin-like_protein,_putative_1119874..1120024_POSITIVE 236 50 3 143 99 NC_009009:SSA_0415|3end_Permease,_putative_411730..411880_POSITIVE 217 45 1 127 80 NC_009009:SSA_1055|3end_Conserved_uncharacterized_protein_1071797..1071947_POSITIVE 213 56 12 143 98 NC_009009:SSA_0566|3end_GTP-sensing_transcriptional_pleiotropic_repressor,_putative_560885..561035_POSITIVE 212 46 1 65 16 NC_009009:SSA_0901|3end_Alpha-acetolactate_decarboxylase,_putative_893246..893396_POSITIVE 209 50 2 116 69 NC_009009:SSA_0526|3end_hypothetical_protein_524681..524831_POSITIVE 200 50 1 66 7 NC_009009:SSA_0356|3end_Dipeptidase,_putative_350757..350907_POSITIVE 199 43 2 108 60 NC_009009:SSA_1238|3end_hypothetical_protein_1262402..1262552_NEGATIVE 197 59 15 125 85 NC_009009:SSA_1610|3end_hypothetical_protein_1614004..1614154_NEGATIVE 196 36 1 96 61 NC_009009:SSA_1412|3end_hypothetical_protein_1423994..1424144_NEGATIVE 192 43 7 83 44 NC_009009:SSA_1501|3end_Cytidylate_kinase,_putative_1505095..1505245_NEGATIVE 191 95 53 65 24 NC_009009:SSA_1868|3end_ABC-type_arginine/histidine_transport_system,_permease_component,_putative_1863096..1863246_NEGATIVE 188 44 3 41 1 NC_009009:SSA_2103|3end_hypothetical_protein_2106500..2106650_NEGATIVE 188 81 54 36 2 NC_009009:SSA_0074|3end_ABC_transporter_substrate-binding_protein-sugar_transport,_putative_78975..79125_POSITIVE 186 56 15 120 79 NC_009009:SSA_2209|3end_Penicillin-binding_protein_2A,_putative_2208144..2208294_NEGATIVE 185 97 51 131 83 NC_009009:SSA_0623|3end_hypothetical_protein_615080..615230_POSITIVE 183 50 3 74 15 NC_009009:SSA_1133|3end_TatA,_sec-independent_protein_secretion_pathway_component,_putative_1159665..1159815_POSITIVE 181 47 4 140 94 NC_009009:SSA_0025|3end_DNA_repair_protein_recO,_putative_30547..30697_POSITIVE 178 44 5 43 1 NC_009009:SSA_1968|3end_Ketol-acid_reductoisomerase,_putative_1963659..1963809_NEGATIVE 176 44 2 106 63 NC_009009:SSA_0825|3end_DNA-directed_RNA_polymerase,_sigma_subunit_(sigma70/sigma32),_putative_805056..805206_POSITIVE