Origin IGS: cgctgtttacaatgtaaaaaaagatgaaaaagaaagtccctgtctagttccaagtgtttttataactgacaaagggcttcttttttgatataatacaatgaggtgatttt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aaaatcacctcattgtattatatcaaaaaagaagccctttgtcagttataaaaacacttggaactagacagggactttctttttcatctttttttacattgtaaacagcg Mask Tandem Repeat Region ================================================ cgctgtttacaatgtaaaaaaagatgaaaaagaaagtccctgtctagttccaagtgtttttataactgacaaagggcttcttttttgatataatacaatgaggtgatttt Find is-nt database================================================ Query_seq: SSA_0352:SSA_0353|SSA_0352:SSA_0353:Ribonuclease HIII, putative:Conserved uncharacterized protein:<-->:345970..346079 110 cgctgtttacaatgtaaaaaaagatgaaaaagaaagtccctgtctagttccaagtgtttttataactgacaaagggcttcttttttgatataatacaatgaggtgatttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0352:SSA_0353|SSA_0352:SSA_0353:Ribonuclease HIII, putative:Conserved uncharacterized protein:<-->:345970..346079 110 cgctgtttacaatgtaaaaaaagatgaaaaagaaagtccctgtctagttccaagtgtttttataactgacaaagggcttcttttttgatataatacaatgaggtgatttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0352:SSA_0353|SSA_0352:SSA_0353:Ribonuclease HIII, putative:Conserved uncharacterized protein:<-->:345970..346079 110 cgctgtttacaatgtaaaaaaagatgaaaaagaaagtccctgtctagttccaagtgtttttataactgacaaagggcttcttttttgatataatacaatgaggtgatttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 cgctgtttacaatgtaaaaaaagatgaaaaagaaagtccctgtctagttccaagtgtttttataactgacaaagggcttcttttttgatataatacaatgaggtgatttt Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: - Start: 10 End: 99 ......... L T F F S S F S L G Q R T G L T K I V S L P S R K Q Y L V M ........... cgctgtttacaatgtaaaaaaagatgaaaaagaaagtccctgtctagttccaagtgtttttataactgacaaagggcttcttttttgatataatacaatgaggtgatttt 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: 65 End: 94 ................................................................ACTGACAAAGGGCTTCTTTTTTGATATAAT................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ cgctgtttacaatgtaaaaaaagatgaaaaagaaagtccctgtctagttccaagtgtttttataactgacaaagggcttcttttttgatataatacaatgaggtgatttt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_0352:SSA_0353|SSA_0352:SSA_0353:Ribonuclease HIII, putative:Conserved uncharacterized protein:<-->:345970..346079 110 cgctgtttacaatgtaaaaaaagatgaaaaagaaagtccctgtctagttccaagtgtttttataactgacaaagggcttcttttttgatataatacaatgaggtgatttt Intra-Species Hit: Count: 1 Min: 1 Max: 110 Len: 110 Subject: NC_009009_SSA_0352_SSA_0353|Ribonuclease HIII, putative:Conserved uncharacterized protein|NEGATIVE:POSITIVE|[345970,346079]|110 HSP 1 e-value: 9.0E-44 bit: 176.0 Len: 110 Query Start:1 Query End:110 Subject Strand: POSITIVE Subject Start: 1 Subject End: 110 cgctgtttacaatgtnnnnnnngatgaaaaagaaagtccctgtctagttccaagtgtttttataactgacaaagggcttcttttttgatataatacaatgaggtgatttt cgctgtttacaatgtaaaaaaagatgaaaaagaaagtccctgtctagttccaagtgtttttataactgacaaagggcttcttttttgatataatacaatgaggtgatttt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CGCUGUUUACAAUGUAAAAAAAGAUGAAAAAGAAAGUCCCUGUCUAGUUCCAAGUGUUUUUAUAACUGACAAAGGGCUUCUUUUUUGAUAUAAUACAAUGAGGUGAUUUU ((((.....((.((((.........(((((((((.((((.((((.((((..(((....)))..))))))))..))))))))))))).......)))).)).))))..... (-21.59) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAAUCACCUCAUUGUAUUAUAUCAAAAAAGAAGCCCUUUGUCAGUUAUAAAAACACUUGGAACUAGACAGGGACUUUCUUUUUCAUCUUUUUUUACAUUGUAAACAGCG ..........((.((((........(((((((((..(((((((((((.(((......))).)))).)))))))..)))))))))..........)))).))......... (-19.17) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 865 80 31 171 122 NC_009009:SSA_0352|5end_Ribonuclease_HIII,_putative_345879..346109_NEGATIVE 280 89 41 189 146 NC_009009:SSA_1976|5end_Conserved_uncharacterized_protein_1972158..1972388_NEGATIVE 267 77 38 134 88 NC_009009:SSA_0271|5end_Glycosylhydrolase,_family_35,_putative_264235..264465_POSITIVE 254 77 35 65 25 NC_009009:SSA_0377|5end_ABC-type_methionine_transporter,_permease_component,_putative_366446..366676_POSITIVE 252 78 31 97 47 NC_009009:SSA_0563|5end_Universal_stress_protein_family,_putative_555399..555629_NEGATIVE 244 77 34 211 171 NC_009009:SSA_1986|5end_Acetyltransferase,_GNAT_family,_putative_1982531..1982761_NEGATIVE 244 77 37 206 164 NC_009009:SSA_1085|5end_Dihydrodipicolinate_reductase,_putative_1102564..1102794_POSITIVE 244 79 31 55 6 NC_009009:SSA_0715|5end_DNA_uptake_protein,_putative_700726..700956_POSITIVE 241 77 37 46 9 NC_009009:SSA_0274|5end_hypothetical_protein_269557..269787_NEGATIVE 238 78 36 63 19 NC_009009:SSA_1721|5end_DNA_polymerase_III,_delta'_subunit,_putative_1708028..1708258_NEGATIVE 236 80 31 188 143 NC_009009:SSA_2270|5end_Aspartyl-tRNA_synthetase,_putative_2272068..2272298_NEGATIVE 236 80 41 182 145 NC_009009:SSA_0591|5end_Conserved_uncharacterized_protein_582769..582999_POSITIVE 235 80 35 195 145 NC_009009:SSA_1840|5end_RNA_binding_protein,_putative_1834422..1834652_NEGATIVE 232 77 38 40 6 NC_009009:SSA_1726|5end_ABC_transporter_ATP-binding_protein-branched_chain_amino_acid_transport,_putative_1712467..1712697_NEGATIVE 231 80 36 178 125 NC_009009:SSA_0978|5end_hypothetical_protein_983736..983966_POSITIVE 231 80 36 103 51 NC_009009:SSA_0518|5end_Ethanolamine_utilization_protein_EutA,_putative_516610..516840_POSITIVE 225 87 41 154 111 NC_009009:SSA_1996|5end_DNA-directed_RNA_polymerase_delta_subunit,_putative_1994024..1994254_NEGATIVE 225 77 40 151 114 NC_009009:SSA_1481|5end_FmtA-like_protein,_putative_1486622..1486852_NEGATIVE 223 78 36 73 11 NC_009009:SSA_0826|5end_hypothetical_protein_805098..805328_POSITIVE 223 80 34 217 168 NC_009009:SSA_0363|5end_D-alanine/glycine/Na_permease,_putative_353858..354088_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 283 78 31 91 34 NC_009009:SSA_1453|3end_hypothetical_protein_1459897..1460047_NEGATIVE 280 89 41 78 35 NC_009009:SSA_1978|3end_Dihydroxyacetone_kinase_family_protein_(Dak2_domain),_putative_1972269..1972419_NEGATIVE 267 77 38 133 87 NC_009009:SSA_0270|3end_Phosphotransferase_system_(PTS)_cellobiose-specific,_IIC_component,_putative_264314..264464_POSITIVE 254 77 35 65 25 NC_009009:SSA_0376|3end_ABC-type_methionine_transporter,_ATPase_component,_putative_366526..366676_POSITIVE 238 78 36 66 22 NC_009009:SSA_1722|3end_Thymidylate_kinase,_putative_1708025..1708175_NEGATIVE 236 87 43 151 110 NC_009009:SSA_1808|3end_hypothetical_protein_1791394..1791544_NEGATIVE 236 80 41 150 113 NC_009009:SSA_0590|3end_hypothetical_protein_582817..582967_POSITIVE 232 77 38 40 6 NC_009009:SSA_1727|3end_ABC_transporter_membrane-spanning_permease-branched_chain_amino_acid_transport,_putative_1712467..1712617_NEGATIVE 228 76 31 82 45 NC_009009:SSA_1582|3end_Esterase,_alpha/beta_hydrolase_superfamily,_putative_1585443..1585593_POSITIVE 220 85 44 137 105 NC_009009:SSA_0796|3end_ABC-NBD_transporters_with_duplicated_ATPase_domains,_putative_779060..779210_POSITIVE 219 56 11 70 17 NC_009009:SSA_1878|3end_Conserved_uncharacterized_protein_1871943..1872093_NEGATIVE 219 77 35 126 95 NC_009009:SSA_1559|3end_Conserved_uncharacterized_protein_1560862..1561012_NEGATIVE 219 78 36 70 30 NC_009009:SSA_0388|3end_Mismatch_repair_ATPase_(MutS_family),_putative_384248..384398_POSITIVE 218 88 43 143 99 NC_009009:SSA_1068|3end_Transcriptional_regulator,_LysR_family_(capsular_polysaccharide_biosynthesis_regulation),_putative_1088367..1088517_POSITIVE 217 47 2 59 7 NC_009009:SSA_0704|3end_Isocitrate_dehydrogenase_[NADP],_putative_690550..690700_POSITIVE 214 77 31 99 57 NC_009009:SSA_1680|3end_ABC-type_bacitracin_resistance_protein_A,_permease_component,_putative_1673200..1673350_NEGATIVE 213 78 35 81 43 NC_009009:SSA_2002|3end_tRNA_pseudouridine_synthase_A,_putative_1998210..1998360_NEGATIVE 212 89 41 81 34 NC_009009:SSA_0677|3end_rRNA_methylase,_putative_660361..660511_POSITIVE 210 80 34 123 77 NC_009009:SSA_0751|3end_Oligoendopeptidase_F,_putative_734249..734399_POSITIVE 210 78 31 58 2 NC_009009:SSA_0489|3end_Adenosylcobinamide_kinase_/_adenosylcobinamide_phosphate_guanyltransferase,_putative_490319..490469_POSITIVE