Origin IGS: ttagtttgtttattgaatttacaggagatttcaatcaagtccgcattagacaataaaatgctattgcaatcaaatacaaagaagaccttgagaaaattttctcaaggtcttttg .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 caaaagaccttgagaaaattttctcaaggtcttctttgtatttgattgcaatagcattttattgtctaatgcggacttgattgaaatctcctgtaaattcaataaacaaactaa Mask Tandem Repeat Region ================================================ ttagtttgtttattgaatttacaggagatttcaatcaagtccgcattagacaataaaatgctattgcaatcaaatacaaagaagaccttgagaaaattttctcaaggtcttttg Find is-nt database================================================ Query_seq: SSA_0289:SSA_0290|SSA_0289:SSA_0290:Leucyl-tRNA synthetase, putative:hypothetical protein:-><-:284060..284173 114 ttagtttgtttattgaatttacaggagatttcaatcaagtccgcattagacaataaaatgctattgcaatcaaatacaaagaagaccttgagaaaattttctcaaggtcttttg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0289:SSA_0290|SSA_0289:SSA_0290:Leucyl-tRNA synthetase, putative:hypothetical protein:-><-:284060..284173 114 ttagtttgtttattgaatttacaggagatttcaatcaagtccgcattagacaataaaatgctattgcaatcaaatacaaagaagaccttgagaaaattttctcaaggtcttttg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0289:SSA_0290|SSA_0289:SSA_0290:Leucyl-tRNA synthetase, putative:hypothetical protein:-><-:284060..284173 114 ttagtttgtttattgaatttacaggagatttcaatcaagtccgcattagacaataaaatgctattgcaatcaaatacaaagaagaccttgagaaaattttctcaaggtcttttg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttagtttgtttattgaatttacaggagatttcaatcaagtccgcattagacaataaaatgctattgcaatcaaatacaaagaagaccttgagaaaattttctcaaggtcttttg Predict ORF larger than 30AA ================================================ Protein_Len: 34 Strand: + Start: 13 End: 114 ............ M N L Q E I S I K S A L D N K M L L Q S N T K K T L R K F S Q G L L ttagtttgtttattgaatttacaggagatttcaatcaagtccgcattagacaataaaatgctattgcaatcaaatacaaagaagaccttgagaaaattttctcaaggtcttttg 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: 81 Start: 45 End: 74 ............................................TTTGATTGCAATAGCATTTTATTGTCTAAT........................................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ttagtttgtttattgaatttacaggagatttcaatcaagtccgcattagacaataaaatgctattgcaatcaaatacaaagaagaccttgagaaaattttctcaaggtcttttg Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_0289:SSA_0290|SSA_0289:SSA_0290:Leucyl-tRNA synthetase, putative:hypothetical protein:-><-:284060..284173 114 ttagtttgtttattgaatttacaggagatttcaatcaagtccgcattagacaataaaatgctattgcaatcaaatacaaagaagaccttgagaaaattttctcaaggtcttttg Intra-Species Hit: Count: 1 Min: 1 Max: 114 Len: 114 Subject: NC_009009_SSA_0289_SSA_0290|Leucyl-tRNA synthetase, putative:hypothetical protein|POSITIVE:NEGATIVE|[284060,284173]|114 HSP 1 e-value: 1.0E-58 bit: 226.0 Len: 114 Query Start:1 Query End:114 Subject Strand: POSITIVE Subject Start: 1 Subject End: 114 ttagtttgtttattgaatttacaggagatttcaatcaagtccgcattagacaataaaatgctattgcaatcaaatacaaagaagaccttgagaaaattttctcaaggtcttttg ttagtttgtttattgaatttacaggagatttcaatcaagtccgcattagacaataaaatgctattgcaatcaaatacaaagaagaccttgagaaaattttctcaaggtcttttg HSP 2 e-value: 2.0E-8 bit: 60.0 Len: 30 Query Start:82 Query End:111 Subject Strand: NEGATIVE Subject Start: 82 Subject End: 111 .................................................................................aagaccttgagaaaattttctcaaggtctt... .................................................................................aagaccttgagaaaattttctcaaggtctt... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUAGUUUGUUUAUUGAAUUUACAGGAGAUUUCAAUCAAGUCCGCAUUAGACAAUAAAAUGCUAUUGCAAUCAAAUACAAAGAAGACCUUGAGAAAAUUUUCUCAAGGUCUUUUG ...(((((...((((((.((......)).)))))).......(((.(((.((......))))).)))...)))))....(((((((((((((((....))))))))))))))). (-31.50) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CAAAAGACCUUGAGAAAAUUUUCUCAAGGUCUUCUUUGUAUUUGAUUGCAAUAGCAUUUUAUUGUCUAAUGCGGACUUGAUUGAAAUCUCCUGUAAAUUCAAUAAACAAACUAA ...(((((((((((((....))))))))))))).(((((..(((((((((..((.((((((..((((.....)))).....))))))))..)))))..))))...))))).... (-31.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 285 65 22 92 44 NC_009009:SSA_1558|5end_Hydrolase,_HAD_superfamily_1560862..1561092_NEGATIVE 274 67 22 183 143 NC_009009:SSA_1727|5end_ABC_transporter_membrane-spanning_permease-branched_chain_amino_acid_transport,_putative_1713420..1713650_NEGATIVE 241 67 23 182 132 NC_009009:SSA_1345|5end_Bifunctional_pyrimidine_operon_transcriptional_attenuation_protein/uracil_phosphoribosyltransferase,_putative_1363879..1364109_NEGATIVE 239 90 41 181 129 NC_009009:SSA_2087|5end_Conserved_uncharacterized_protein_2092657..2092887_NEGATIVE 224 65 22 222 176 NC_009009:SSA_1613|5end_hypothetical_protein_1616975..1617205_NEGATIVE 222 49 2 96 44 NC_009009:SSA_2166|5end_ABC-type_multidrug_transporter,_ATPase_and_permease_components,_putative_2165642..2165872_NEGATIVE 222 67 24 54 16 NC_009009:SSA_2031|5end_Conserved_domain_uncharacterized_protein_2037153..2037383_POSITIVE 218 67 26 181 131 NC_009009:SSA_1923|5end_NADPH-q_uinone_reductase_(modulator_of_drug_activity_B),_putative_1912698..1912928_NEGATIVE 212 44 14 145 116 NC_009009:SSA_0239|5end_7,8-dihydro-8-oxoguanine-triphosphatase,_putative_232961..233191_POSITIVE 209 48 3 47 7 NC_009009:SSA_1511|5end_Glycosyltransferase,_putative_1516697..1516927_NEGATIVE 209 45 23 148 118 NC_009009:SSA_0584|5end_hypothetical_protein_575806..576036_POSITIVE 206 63 22 57 17 NC_009009:SSA_1669|5end_hypothetical_protein_1668442..1668672_NEGATIVE 206 68 23 57 21 NC_009009:SSA_0458|5end_Formylmethionine_deformylase,_putative_461609..461839_POSITIVE 205 45 6 71 33 NC_009009:SSA_1916|5end_hypothetical_protein_1905487..1905717_POSITIVE 203 108 70 219 184 NC_009009:SSA_1703|5end_Methionyl-tRNA_synthetase,_putative_1695640..1695870_NEGATIVE 203 43 3 103 66 NC_009009:SSA_0846|5end_DNA-polymerase_III_alpha-chain,_putative_830078..830308_POSITIVE 202 64 21 187 127 NC_009009:SSA_0299|5end_hypothetical_protein_292759..292989_POSITIVE 201 95 52 218 169 NC_009009:SSA_1760|5end_hypothetical_protein_1747284..1747514_NEGATIVE 201 67 26 139 94 NC_009009:SSA_1188|5end_Ribonuclease_HII,_putative_1216819..1217049_NEGATIVE 200 77 38 114 83 NC_009009:SSA_1301|5end_Conserved_uncharacterized_protein,_possible_surface_protein_1321571..1321801_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 285 65 22 92 44 NC_009009:SSA_1559|3end_Conserved_uncharacterized_protein_1560862..1561012_NEGATIVE 239 90 41 72 20 NC_009009:SSA_2088|3end_Carbohydrate_isomerase,_AraD/FucA_family,_putative_2092766..2092916_NEGATIVE 234 53 24 146 118 NC_009009:SSA_0243|3end_Cyclo-nucleotide_phosphodiesterase,_putative_235824..235974_NEGATIVE 222 49 2 94 42 NC_009009:SSA_2167|3end_ABC-type_multidrug_transporter,_ATPase_and_permease_components,_putative_2165644..2165794_NEGATIVE 219 67 22 86 34 NC_009009:SSA_0337|3end_Hydroxymethylglutaryl-CoA_reductase,_putative_330889..331039_NEGATIVE 217 110 76 78 48 NC_009009:SSA_0773|3end_PTS_enzyme_I,_putative_754416..754566_POSITIVE 212 44 14 135 106 NC_009009:SSA_0238|3end_hypothetical_protein_233031..233181_POSITIVE 209 48 3 43 3 NC_009009:SSA_1512|3end_hypothetical_protein_1516701..1516851_NEGATIVE 203 108 70 90 55 NC_009009:SSA_1704|3end_Conserved_uncharacterized_protein_1695769..1695919_NEGATIVE 201 95 52 65 16 NC_009009:SSA_1761|3end_Hemolysin_(containing_CBS_domains),_putative_1747437..1747587_NEGATIVE 199 51 21 27 3 NC_009009:SSA_0910|3end_ABC-type_multidrug_transporter,_ATPase_component,_putative_922161..922311_POSITIVE 199 49 5 114 75 NC_009009:SSA_0731|3end_Integral_membrane_protein,_putative_715654..715804_POSITIVE 198 51 23 134 109 NC_009009:SSA_1140|3end_Dihydrolipoamide_acetyl_transferase,_E2_component,_putative_1169207..1169357_POSITIVE 195 103 67 66 30 NC_009009:SSA_2244|3end_Arsenate_reductase,_putative_2239477..2239627_NEGATIVE 192 67 21 75 27 NC_009009:SSA_0200|3end_Bifunctional_folate_synthesis_protein,_putative_199810..199960_POSITIVE 191 50 8 46 12 NC_009009:SSA_1621|3end_Amino_acid_transporter,_putative_1623172..1623322_NEGATIVE 191 53 17 141 108 NC_009009:SSA_0642|3end_Type_4_prepilin_peptidase,_putative_629391..629541_NEGATIVE 189 109 78 39 7 NC_009009:SSA_1567|3end_Polar_amino_acid_ABC_transporter,_amino_acid-binding_protein,_putative_1571267..1571417_POSITIVE 189 83 41 44 7 NC_009009:SSA_1054|3end_CBS_domain_protein,_putative_1070973..1071123_POSITIVE 188 110 61 71 27 NC_009009:SSA_1909|3end_Transcriptional_attenuator_LytR,_putative_1900904..1901054_NEGATIVE