Origin IGS: aaatttcctcaatcttttttaaaataaactagcattattgtaccacaaaagggggttgaaatgtaagcaaatgttttaaagacatctaaaaagccccattaggggcttaaaa .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ttttaagcccctaatggggctttttagatgtctttaaaacatttgcttacatttcaacccccttttgtggtacaataatgctagtttattttaaaaaagattgaggaaattt Mask Tandem Repeat Region ================================================ aaatttcctcaatcttttttaaaataaactagcattattgtaccacaaaagggggttgaaatgtaagcaaatgttttaaagacatctaaaaagccccattaggggcttaaaa Find is-nt database================================================ Query_seq: SSA_0813:SSA_0814|SSA_0813:SSA_0814:Thioredoxin reductase, putative:Oxidoreductase, pyridine nucleotide-disulfide, class I, putative:<-<-:795497..795608 112 aaatttcctcaatcttttttaaaataaactagcattattgtaccacaaaagggggttgaaatgtaagcaaatgttttaaagacatctaaaaagccccattaggggcttaaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0813:SSA_0814|SSA_0813:SSA_0814:Thioredoxin reductase, putative:Oxidoreductase, pyridine nucleotide-disulfide, class I, putative:<-<-:795497..795608 112 aaatttcctcaatcttttttaaaataaactagcattattgtaccacaaaagggggttgaaatgtaagcaaatgttttaaagacatctaaaaagccccattaggggcttaaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0813:SSA_0814|SSA_0813:SSA_0814:Thioredoxin reductase, putative:Oxidoreductase, pyridine nucleotide-disulfide, class I, putative:<-<-:795497..795608 112 aaatttcctcaatcttttttaaaataaactagcattattgtaccacaaaagggggttgaaatgtaagcaaatgttttaaagacatctaaaaagccccattaggggcttaaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aaatttcctcaatcttttttaaaataaactagcattattgtaccacaaaagggggttgaaatgtaagcaaatgttttaaagacatctaaaaagccccattaggggcttaaaa Predict ORF larger than 30AA ================================================ aaatttcctcaatcttttttaaaataaactagcattattgtaccacaaaagggggttgaaatgtaagcaaatgttttaaagacatctaaaaagccccattaggggcttaaaa Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aaatttcctcaatcttttttaaaataaactagcattattgtaccacaaaagggggttgaaatgtaagcaaatgttttaaagacatctaaaaagccccattaggggcttaaaa Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_0813:SSA_0814|SSA_0813:SSA_0814:Thioredoxin reductase, putative:Oxidoreductase, pyridine nucleotide-disulfide, class I, putative:<-<-:795497..795608 112 aaatttcctcaatcttttttaaaataaactagcattattgtaccacaaaagggggttgaaatgtaagcaaatgttttaaagacatctaaaaagccccattaggggcttaaaa Intra-Species Hit: Count: 1 Min: 1 Max: 112 Len: 112 Subject: NC_009009_SSA_0813_SSA_0814|Thioredoxin reductase, putative:Oxidoreductase, pyridine nucleotide-disulfide, class I, putative|NEGATIVE:NEGATIVE|[795497,795608]|112 HSP 1 e-value: 2.0E-57 bit: 222.0 Len: 112 Query Start:1 Query End:112 Subject Strand: POSITIVE Subject Start: 1 Subject End: 112 aaatttcctcaatcttttttaaaataaactagcattattgtaccacaaaagggggttgaaatgtaagcaaatgttttaaagacatctaaaaagccccattaggggcttaaaa aaatttcctcaatcttttttaaaataaactagcattattgtaccacaaaagggggttgaaatgtaagcaaatgttttaaagacatctaaaaagccccattaggggcttaaaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAUUUCCUCAAUCUUUUUUAAAAUAAACUAGCAUUAUUGUACCACAAAAGGGGGUUGAAAUGUAAGCAAAUGUUUUAAAGACAUCUAAAAAGCCCCAUUAGGGGCUUAAAA ...............(((((((((((..((.(((((.....(((.(......))))...))))).))....)))))))))))........(((((((....))))))).... (-23.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUUAAGCCCCUAAUGGGGCUUUUUAGAUGUCUUUAAAACAUUUGCUUACAUUUCAACCCCCUUUUGUGGUACAAUAAUGCUAGUUUAUUUUAAAAAAGAUUGAGGAAAUUU ....(((((((....)))))))(((....((((((.........(((..((((.......((......))......))))..)))..........))))))....))).... (-20.63) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 816 100 51 191 142 NC_009009:SSA_0813|5end_Thioredoxin_reductase,_putative_795406..795636_NEGATIVE 355 60 13 148 100 NC_009009:SSA_1921|5end_hypothetical_protein_1910875..1911105_POSITIVE 314 70 30 167 116 NC_009009:SSA_1971|5end_hypothetical_protein_1967167..1967397_POSITIVE 260 107 80 226 199 NC_009009:SSA_0334|5end_Diphosphomevalonate_decarboxylase,_putative_327855..328085_POSITIVE 254 100 52 108 44 NC_009009:SSA_0320|5end_hypothetical_protein_313406..313636_POSITIVE 232 48 4 130 81 NC_009009:SSA_0843|5end_hypothetical_protein_827682..827912_POSITIVE 223 69 35 157 124 NC_009009:SSA_1522|5end_Cell_division_protein_FtsW,_putative_1531962..1532192_NEGATIVE 221 70 30 43 1 NC_009009:SSA_0253|5end_CAAX_amino_terminal_protease_family_protein,_putative_246289..246519_POSITIVE 218 100 51 92 29 NC_009009:SSA_1953|5end_NifU_family_protein,_putative_1950079..1950309_NEGATIVE 215 106 61 223 178 NC_009009:SSA_1423|5end_Single-stranded_DNA-specific_exonuclease,_5'-3',_putative_1433783..1434013_NEGATIVE 214 109 92 18 3 NC_009009:SSA_1183|5end_hypothetical_protein_1211453..1211683_NEGATIVE 212 108 61 202 142 NC_009009:SSA_2204|5end_hypothetical_protein_2204663..2204893_POSITIVE 211 64 27 174 139 NC_009009:SSA_1264|5end_hypothetical_protein_1290042..1290272_NEGATIVE 209 108 72 225 193 NC_009009:SSA_1189|5end_GTP-binding_protein,_putative_1217657..1217887_NEGATIVE 209 76 31 167 116 NC_009009:SSA_1076|5end_hypothetical_protein_1094227..1094457_POSITIVE 206 109 80 206 175 NC_009009:SSA_2211|5end_Transmembrane_protein,_putative_2212473..2212703_NEGATIVE 206 88 43 94 55 NC_009009:SSA_0544|5end_Phospho-2-dehydro-3-deoxyheptonate_aldolase,_putative_539819..540049_POSITIVE 206 45 3 135 90 NC_009009:SSA_0341|5end_hypothetical_protein_334731..334961_NEGATIVE 204 83 61 70 44 NC_009009:SSA_2195|5end_ATPase/kinase,_putative_2196743..2196973_NEGATIVE 204 69 28 69 35 NC_009009:SSA_1909|5end_Transcriptional_attenuator_LytR,_putative_1902142..1902372_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 355 60 13 77 29 NC_009009:SSA_1920|3end_Phosphotransferase_system,_mannose-specific_EIID,_putative_1910884..1911034_POSITIVE 255 108 63 73 26 NC_009009:SSA_0144|3end_Transcriptional_regulator,_TetR_family,_putative_137993..138143_NEGATIVE 254 100 52 118 54 NC_009009:SSA_0319|3end_Branched-chain_amino_acid_permease_(L-methionine,_L-isoleucine,_leucine_and_valine),_putative_313496..313646_POSITIVE 220 108 66 85 42 NC_009009:SSA_0362|3end_Thioredoxin,_putative_353594..353744_POSITIVE 218 100 51 105 42 NC_009009:SSA_1954|3end_Aminotransferase,_class-V,_putative_1950066..1950216_NEGATIVE 215 106 61 117 72 NC_009009:SSA_1424|3end_Hydrolase,_putative_1433889..1434039_NEGATIVE 211 59 29 63 24 NC_009009:SSA_2076|3end_Conserved_uncharacterized_protein_2079390..2079540_NEGATIVE 209 108 72 83 51 NC_009009:SSA_1190|3end_Conserved_uncharacterized_protein_1217799..1217949_NEGATIVE 208 107 63 53 8 NC_009009:SSA_1621|3end_Amino_acid_transporter,_putative_1623172..1623322_NEGATIVE 206 109 80 52 21 NC_009009:SSA_2212|3end_Possible_polysaccharide_transport_protein,_putative_2212627..2212777_NEGATIVE 206 88 43 73 34 NC_009009:SSA_0543|3end_SecA,_putative_539878..540028_POSITIVE 204 109 66 62 11 NC_009009:SSA_2107|3end_Glucosamine--fructose-6-phosphate_aminotransferase_[isomerizing],_putative_2109295..2109445_NEGATIVE 204 69 28 60 26 NC_009009:SSA_1910|3end_hypothetical_protein_1902151..1902301_NEGATIVE 203 108 74 76 40 NC_009009:SSA_0192|3end_Acetate_kinase,_putative_194182..194332_POSITIVE 202 108 77 89 58 NC_009009:SSA_0337|3end_Hydroxymethylglutaryl-CoA_reductase,_putative_330889..331039_NEGATIVE 201 74 32 63 11 NC_009009:SSA_1788|3end_Integral_membrane_protein,_possible_receptor,_putative_1771656..1771806_NEGATIVE 201 84 43 47 1 NC_009009:SSA_1416|3end_hypothetical_protein_1426520..1426670_NEGATIVE 199 105 79 76 44 NC_009009:SSA_1221|3end_L-lactate_dehydrogenase,_putative_1245022..1245172_POSITIVE 198 106 72 78 41 NC_009009:SSA_1377|3end_Asparaginyl-tRNA_synthetase,_putative_1396268..1396418_NEGATIVE 196 58 13 134 89 NC_009009:SSA_1398|3end_Membrane_protein,_hemolysin_III-like,_putative_1411626..1411776_POSITIVE