Origin IGS: tcaataaaaagctgacctttctcagctttttatttgtaatctatcgtaaatgctatagatttttgatataatagagtgtattttgtttacataaaagagagaaaatc .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gattttctctcttttatgtaaacaaaatacactctattatatcaaaaatctatagcatttacgatagattacaaataaaaagctgagaaaggtcagctttttattga Mask Tandem Repeat Region ================================================ tcaataaaaagctgacctttctcagctttttatttgtaatctatcgtaaatgctatagatttttgatataatagagtgtattttgtttacataaaagagagaaaatc Find is-nt database================================================ Query_seq: SSA_1045:SSA_1047|SSA_1045:SSA_1047:hypothetical protein:UDP-N-acetylenolpyruvoylglucosamine reductase, putative:->->:1061893..1061999 107 tcaataaaaagctgacctttctcagctttttatttgtaatctatcgtaaatgctatagatttttgatataatagagtgtattttgtttacataaaagagagaaaatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1045:SSA_1047|SSA_1045:SSA_1047:hypothetical protein:UDP-N-acetylenolpyruvoylglucosamine reductase, putative:->->:1061893..1061999 107 tcaataaaaagctgacctttctcagctttttatttgtaatctatcgtaaatgctatagatttttgatataatagagtgtattttgtttacataaaagagagaaaatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1045:SSA_1047|SSA_1045:SSA_1047:hypothetical protein:UDP-N-acetylenolpyruvoylglucosamine reductase, putative:->->:1061893..1061999 107 tcaataaaaagctgacctttctcagctttttatttgtaatctatcgtaaatgctatagatttttgatataatagagtgtattttgtttacataaaagagagaaaatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tcaataaaaagctgacctttctcagctttttatttgtaatctatcgtaaatgctatagatttttgatataatagagtgtattttgtttacataaaagagagaaaatc Predict ORF larger than 30AA ================================================ tcaataaaaagctgacctttctcagctttttatttgtaatctatcgtaaatgctatagatttttgatataatagagtgtattttgtttacataaaagagagaaaatc 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================================================ tcaataaaaagctgacctttctcagctttttatttgtaatctatcgtaaatgctatagatttttgatataatagagtgtattttgtttacataaaagagagaaaatc Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_1045:SSA_1047|SSA_1045:SSA_1047:hypothetical protein:UDP-N-acetylenolpyruvoylglucosamine reductase, putative:->->:1061893..1061999 107 tcaataaaaagctgacctttctcagctttttatttgtaatctatcgtaaatgctatagatttttgatataatagagtgtattttgtttacataaaagagagaaaatc Intra-Species Hit: Count: 1 Min: 1 Max: 107 Len: 107 Subject: NC_009009_SSA_1045_SSA_1047|hypothetical protein:UDP-N-acetylenolpyruvoylglucosamine reductase, putative|POSITIVE:POSITIVE|[1061893,1061999]|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 tcaataaaaagctgacctttctcagctttttatttgtaatctatcgtaaatgctatagatttttgatataatagagtgtattttgtttacataaaagagagaaaatc tcaataaaaagctgacctttctcagctttttatttgtaatctatcgtaaatgctatagatttttgatataatagagtgtattttgtttacataaaagagagaaaatc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCAAUAAAAAGCUGACCUUUCUCAGCUUUUUAUUUGUAAUCUAUCGUAAAUGCUAUAGAUUUUUGAUAUAAUAGAGUGUAUUUUGUUUACAUAAAAGAGAGAAAAUC ..(((((((((((((......)))))))))))))...........(((((((..(((.(((((.........))))).)))..)))))))................. (-21.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAUUUUCUCUCUUUUAUGUAAACAAAAUACACUCUAUUAUAUCAAAAAUCUAUAGCAUUUACGAUAGAUUACAAAUAAAAAGCUGAGAAAGGUCAGCUUUUUAUUGA ................((((.......))))...............(((((((.(......).)))))))...(((((((((((((......))))))))))))).. (-18.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 276 68 21 80 27 NC_009009:SSA_0594|5end_Transcriptional_regulator,_AraC_family,_putative_585630..585860_POSITIVE 271 56 12 142 95 NC_009009:SSA_2284|5end_Histidyl-tRNA_synthetase,_putative_2287272..2287502_NEGATIVE 261 46 2 169 128 NC_009009:SSA_0668|5end_hypothetical_protein_650737..650967_POSITIVE 256 48 4 168 127 NC_009009:SSA_0213|5end_hypothetical_protein_210135..210365_NEGATIVE 248 47 11 91 44 NC_009009:SSA_2105|5end_hypothetical_protein_2107802..2108032_NEGATIVE 247 29 10 56 32 NC_009009:SSA_0835|5end_Accessory_secretory_protein_Asp3,_putative_821036..821266_POSITIVE 235 46 1 150 106 NC_009009:SSA_1777|5end_Ribosomal_large_subunit_pseudouridine_synthase_B,_putative_1765155..1765385_NEGATIVE 232 59 11 226 188 NC_009009:SSA_0929|5end_ABC-type_multidrug_transporter,_ATPase_and_permease_components,_putative_938438..938668_POSITIVE 231 54 18 72 30 NC_009009:SSA_2140|5end_Ribonuclease_P_protein_component,_putative_2140574..2140804_NEGATIVE 229 29 9 169 149 NC_009009:SSA_0803|5end_hypothetical_protein_785145..785375_POSITIVE 223 58 16 148 101 NC_009009:SSA_0467|5end_Cobalt-precorrin-6A_synthase_[deacetylating],_putative_470588..470818_POSITIVE 221 44 1 62 24 NC_009009:SSA_2226|5end_Organic_radical_activating_chaperone,_putative_2227756..2227986_NEGATIVE 219 88 44 106 60 NC_009009:SSA_1279|5end_Oxidoreductase,_putative_1300832..1301062_NEGATIVE 219 45 11 219 183 NC_009009:SSA_0792|5end_hypothetical_protein_774618..774848_POSITIVE 216 53 11 193 139 NC_009009:SSA_2001|5end_Hydroxymethylpyrimidine/phosphomethylpyrimidine_kinase,_putative_1998220..1998450_NEGATIVE 212 37 9 231 203 NC_009009:SSA_0529|5end_Ethanolamine_utilization_protein,_putative_525945..526175_POSITIVE 209 58 19 140 96 NC_009009:SSA_1787|5end_Diaminopimelate_decarboxylase,_putative_1771551..1771781_NEGATIVE 208 31 11 231 213 NC_009009:SSA_1438|5end_Acetyltransferase,_putative_1443612..1443842_NEGATIVE 206 69 21 124 75 NC_009009:SSA_2169|5end_Glucose-1-phosphate_uridylyltransferase,_putative_2168446..2168676_POSITIVE 206 40 1 143 103 NC_009009:SSA_1490|5end_Ribonuclease_BN,_putative_1496732..1496962_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 274 50 3 111 57 NC_009009:SSA_1045|3end_hypothetical_protein_1061832..1061982_POSITIVE 261 46 2 109 68 NC_009009:SSA_0667|3end_Transcriptional_regulator,_putative_650757..650907_POSITIVE 249 48 9 113 77 NC_009009:SSA_0551|3end_L-asparaginase,_putative_546331..546481_NEGATIVE 247 29 10 59 35 NC_009009:SSA_0834|3end_Accessory_secretory_protein_Asp2,_putative_821119..821269_POSITIVE 223 58 16 148 101 NC_009009:SSA_0466|3end_Precorrin-8X_methylmutase_/_precorrin_isomerase,_putative_470668..470818_POSITIVE 221 44 1 102 64 NC_009009:SSA_2227|3end_Acetyl_transferase,_putative_2227716..2227866_NEGATIVE 214 39 10 142 113 NC_009009:SSA_2212|3end_Possible_polysaccharide_transport_protein,_putative_2212627..2212777_NEGATIVE 206 40 1 95 55 NC_009009:SSA_1491|3end_Methionine_aminopeptidase_A,_putative_1496780..1496930_NEGATIVE 205 26 1 144 119 NC_009009:SSA_1778|3end_Segregation_and_condensation_protein_B,_putative_1765142..1765292_NEGATIVE 205 64 21 140 90 NC_009009:SSA_0557|3end_hypothetical_protein_552393..552543_POSITIVE 200 67 22 74 36 NC_009009:SSA_2372|3end_hypothetical_protein_2374285..2374435_POSITIVE 200 42 8 98 67 NC_009009:SSA_1772|3end_hypothetical_protein_1758895..1759045_NEGATIVE 199 58 11 75 23 NC_009009:SSA_0334|3end_Diphosphomevalonate_decarboxylase,_putative_328882..329032_POSITIVE 199 31 2 65 28 NC_009009:SSA_0234|3end_hypothetical_protein_228423..228573_NEGATIVE 194 42 15 107 75 NC_009009:SSA_1879|3end_Glycyl-tRNA_synthetase_beta_chain,_putative_1872223..1872373_NEGATIVE 193 47 17 126 86 NC_009009:SSA_2308|3end_hypothetical_protein_2309893..2310043_NEGATIVE 193 66 21 88 38 NC_009009:SSA_1883|3end_hypothetical_protein_1881574..1881724_NEGATIVE 193 31 6 31 3 NC_009009:SSA_0051|3end_Dihydroxyacetone_kinase_phosphotransfer_protein,_putative_55644..55794_POSITIVE 192 54 17 108 72 NC_009009:SSA_0894|3end_ATP-binding_cassette_protein,_putative_886533..886683_POSITIVE 191 29 6 58 35 NC_009009:SSA_0597|3end_hypothetical_protein_588563..588713_POSITIVE