Origin IGS: taacgctcccttaaaagaaaaggctaatccgcttttttattatagtaaaaggtagaaaaaaaacggcgtgaggcgtatcatatccgacaaatttaatctgattttattgtgggagagtt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aactctcccacaataaaatcagattaaatttgtcggatatgatacgcctcacgccgttttttttctaccttttactataataaaaaagcggattagccttttcttttaagggagcgtta Mask Tandem Repeat Region ================================================ taacgctcccttaaaagaaaaggctaatccgcttttttattatagtaaaaggtagaaaaaaaacggcgtgaggcgtatcatatccgacaaatttaatctgattttattgtgggagagtt Find is-nt database================================================ Query_seq: AA01220:AA01221|AA01220:AA01221:competence protein F; amidophosphoribosyltransferase:transformation locus protein orfG homolog:->->:833599..833717 119 taacgctcccttaaaagaaaaggctaatccgcttttttattatagtaaaaggtagaaaaaaaacggcgtgaggcgtatcatatccgacaaatttaatctgattttattgtgggagagtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: AA01220:AA01221|AA01220:AA01221:competence protein F; amidophosphoribosyltransferase:transformation locus protein orfG homolog:->->:833599..833717 119 taacgctcccttaaaagaaaaggctaatccgcttttttattatagtaaaaggtagaaaaaaaacggcgtgaggcgtatcatatccgacaaatttaatctgattttattgtgggagagtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: AA01220:AA01221|AA01220:AA01221:competence protein F; amidophosphoribosyltransferase:transformation locus protein orfG homolog:->->:833599..833717 119 taacgctcccttaaaagaaaaggctaatccgcttttttattatagtaaaaggtagaaaaaaaacggcgtgaggcgtatcatatccgacaaatttaatctgattttattgtgggagagtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taacgctcccttaaaagaaaaggctaatccgcttttttattatagtaaaaggtagaaaaaaaacggcgtgaggcgtatcatatccgacaaatttaatctgattttattgtgggagagtt Predict ORF larger than 30AA ================================================ taacgctcccttaaaagaaaaggctaatccgcttttttattatagtaaaaggtagaaaaaaaacggcgtgaggcgtatcatatccgacaaatttaatctgattttattgtgggagagtt 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: 82 Start: 52 End: 81 ...................................................GTAGAAAAAAAACGGCGTGAGGCGTATCAT...................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ taacgctcccttaaaagaaaaggctaatccgcttttttattatagtaaaaggtagaaaaaaaacggcgtgaggcgtatcatatccgacaaatttaatctgattttattgtgggagagtt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: AA01220:AA01221|AA01220:AA01221:competence protein F; amidophosphoribosyltransferase:transformation locus protein orfG homolog:->->:833599..833717 119 taacgctcccttaaaagaaaaggctaatccgcttttttattatagtaaaaggtagaaaaaaaacggcgtgaggcgtatcatatccgacaaatttaatctgattttattgtgggagagtt Intra-Species Hit: Count: 1 Min: 1 Max: 119 Len: 119 Subject: aact_AA01220_AA01221|competence protein F; amidophosphoribosyltransferase:transformation locus protein orfG homolog|POSITIVE:POSITIVE|[833599,833717]|119 HSP 1 e-value: 3.0E-47 bit: 188.0 Len: 119 Query Start:1 Query End:119 Subject Strand: POSITIVE Subject Start: 1 Subject End: 119 taacgctcccttaaaagaaaaggctaatccgcttttttattatagtaaaaggtagnnnnnnnncggcgtgaggcgtatcatatccgacaaatttaatctgattttattgtgggagagtt taacgctcccttaaaagaaaaggctaatccgcttttttattatagtaaaaggtagaaaaaaaacggcgtgaggcgtatcatatccgacaaatttaatctgattttattgtgggagagtt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAACGCUCCCUUAAAAGAAAAGGCUAAUCCGCUUUUUUAUUAUAGUAAAAGGUAGAAAAAAAACGGCGUGAGGCGUAUCAUAUCCGACAAAUUUAAUCUGAUUUUAUUGUGGGAGAGUU .(((.(((((......((((((((......))))))))...(((((((((..((((......(((.(....).))).((......)).........)))).)))))))))))))).))) (-30.20) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AACUCUCCCACAAUAAAAUCAGAUUAAAUUUGUCGGAUAUGAUACGCCUCACGCCGUUUUUUUUCUACCUUUUACUAUAAUAAAAAAGCGGAUUAGCCUUUUCUUUUAAGGGAGCGUUA (((.(((((........(((.(((.......))).))).......((......((((((((((..................))))))))))....))............))))).))). (-23.07) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 291 87 43 146 98 aact:AA00819|5end_D-alanyl-D-alanine_carboxypeptidase_562644..562874_POSITIVE 285 100 63 179 132 aact:AA00012|5end_conserved_hypothetical_protein_6433..6663_POSITIVE 281 87 51 150 107 aact:AA00252|5end_conserved_hypothetical_protein_177207..177437_POSITIVE 275 98 65 96 60 aact:AA02162|5end_lipoprotein_1478950..1479180_POSITIVE 270 90 64 176 139 aact:AA02992|5end_RNA_methyltransferase_2090638..2090868_POSITIVE 260 87 61 160 129 aact:AA00578|5end_DNA_topoisomerase_394576..394806_POSITIVE 258 110 61 84 27 aact:AA02439|5end_integral_membrane_protein;_possible_ABC_transporter_permease_1683902..1684132_POSITIVE 255 109 65 70 23 aact:AA02910|5end_ribonuclease_E_2036137..2036367_POSITIVE 255 70 30 119 82 aact:AA00863|5end_conserved_hypothetical_protein_596679..596909_POSITIVE 253 88 61 198 172 aact:AA01807|5end_electron_transport_complex_protein_1216696..1216926_POSITIVE 252 89 49 218 161 aact:AA02217|5end_deoxyribose-phosphate_aldolase_1509135..1509365_POSITIVE 251 106 64 157 112 aact:AA02742|5end_tRNA_nucleotidyltransferase_1921308..1921538_POSITIVE 249 68 22 198 156 aact:AA02014|5end_probable_hemolysin_1370406..1370636_POSITIVE 248 91 64 183 161 aact:AA02830|5end_colicin_tolerance_protein_1988729..1988959_POSITIVE 248 88 58 65 28 aact:AA01588|5end_N-acetylmuramoyl-L-alanine_amidase_II_1068816..1069046_POSITIVE 243 94 51 121 69 aact:AA00715|5end_[2Fe-2S]_ferredoxin_490632..490862_POSITIVE 242 75 31 76 41 aact:AA02605|5end_hypothetical_protein_1816555..1816785_POSITIVE 241 109 64 222 162 aact:AA02375|5end_D-3-phosphoglycerate_dehydrogenase_1626514..1626744_POSITIVE 240 88 51 117 82 aact:AA01276|5end_heptosyltransferase_III_864730..864960_POSITIVE 239 91 64 153 126 aact:AA02524|5end_orotidine_5'-phosphate_decarboxylase_1753313..1753543_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 281 87 51 101 58 aact:AA00251|3end_lipoate_biosynthesis_protein_B_177238..177388_POSITIVE 270 90 64 54 17 aact:AA02990|3end_beta_hexosaminadase_2090596..2090746_POSITIVE 258 110 61 94 37 aact:AA02438|3end_membrane_protein;_possible_ABC_transporter_permease_protein_1683992..1684142_POSITIVE 255 70 30 75 38 aact:AA00862|3end_conserved_hypothetical_protein_596715..596865_POSITIVE 249 68 22 86 44 aact:AA02013|3end_carbonic_anhydrase_1370374..1370524_POSITIVE 248 88 58 62 25 aact:AA01586|3end_DNA_mismatch_repair_protein_1068893..1069043_POSITIVE 244 75 51 117 96 aact:AA02566|3end_PTS_system,_IIC_component_1788179..1788329_POSITIVE 244 86 61 151 121 aact:AA00576|3end_conserved_hypothetical_protein_(possible_translation_factor)_394648..394798_POSITIVE 243 94 51 106 54 aact:AA00713|3end_chaperone_protein_hscA,_heat_shock_cognate_66_490697..490847_POSITIVE 240 88 51 139 104 aact:AA01274|3end_hypothetical_protein_864832..864982_POSITIVE 239 91 64 144 117 aact:AA02523|3end_conserved_hypothetical_protein_1753384..1753534_POSITIVE 238 59 16 73 21 aact:AA01599|3end_phosphocarrier_protein_HPr_1080444..1080594_POSITIVE 234 38 3 88 57 aact:AA02763|3end_DNA_polymerase_III,_epsilon_subunit_1934477..1934627_POSITIVE 232 109 65 59 14 aact:AA00148|3end_ATP-dependent_RNA_helicase_107843..107993_POSITIVE 231 34 2 45 4 aact:AA01358|3end_conserved_hypothetical_protein_920387..920537_POSITIVE 230 70 21 142 86 aact:AA01890|3end_cell-cycle_protein_1275967..1276117_POSITIVE 229 80 31 133 61 aact:AA01968|3end_hypothetical_protein_1331949..1332099_POSITIVE 229 99 51 102 63 aact:AA00568|3end_hypothetical_protein_391276..391426_POSITIVE 226 89 64 92 69 aact:AA02970|3end_tyrosine_phenol-lyase_2077391..2077541_POSITIVE 226 75 48 23 1 aact:AA02604|3end_thioredoxin_reductase_1816582..1816732_POSITIVE