Origin IGS: aaataaaaaatccgttaatcaagtttgcttatttagcaatgtcctatacaatgtcgggcaattgtaacccatttatcatttttcgtaaaaataaggattctatcca .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tggatagaatccttatttttacgaaaaatgataaatgggttacaattgcccgacattgtataggacattgctaaataagcaaacttgattaacggattttttattt Mask Tandem Repeat Region ================================================ aaataaaaaatccgttaatcaagtttgcttatttagcaatgtcctatacaatgtcgggcaattgtaacccatttatcatttttcgtaaaaataaggattctatcca Find is-nt database================================================ Query_seq: AA01355:AA01356|AA01355:AA01356:large subunit pseudouridylate synthase D:lipooligosaccharide galactosyltransferase II (comL related):->->:918340..918445 106 aaataaaaaatccgttaatcaagtttgcttatttagcaatgtcctatacaatgtcgggcaattgtaacccatttatcatttttcgtaaaaataaggattctatcca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: AA01355:AA01356|AA01355:AA01356:large subunit pseudouridylate synthase D:lipooligosaccharide galactosyltransferase II (comL related):->->:918340..918445 106 aaataaaaaatccgttaatcaagtttgcttatttagcaatgtcctatacaatgtcgggcaattgtaacccatttatcatttttcgtaaaaataaggattctatcca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: AA01355:AA01356|AA01355:AA01356:large subunit pseudouridylate synthase D:lipooligosaccharide galactosyltransferase II (comL related):->->:918340..918445 106 aaataaaaaatccgttaatcaagtttgcttatttagcaatgtcctatacaatgtcgggcaattgtaacccatttatcatttttcgtaaaaataaggattctatcca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aaataaaaaatccgttaatcaagtttgcttatttagcaatgtcctatacaatgtcgggcaattgtaacccatttatcatttttcgtaaaaataaggattctatcca Predict ORF larger than 30AA ================================================ Protein_Len: 34 Strand: + Start: 3 End: 104 .. M K N P L I K F A Y L A M S Y T M S G N C N P F I I F R K N K D S I .. aaataaaaaatccgttaatcaagtttgcttatttagcaatgtcctatacaatgtcgggcaattgtaacccatttatcatttttcgtaaaaataaggattctatcca 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: 84 Start: 61 End: 90 ............................................................TTTTACGAAAAATGATAAATGGGTTACAAT................ PromScan Matrix: RpoD-17 Strand: + Score: 81 Start: 23 End: 52 ......................GTTTGCTTATTTAGCAATGTCCTATACAAT...................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aaataaaaaatccgttaatcaagtttgcttatttagcaatgtcctatacaatgtcgggcaattgtaacccatttatcatttttcgtaaaaataaggattctatcca Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: AA01355:AA01356|AA01355:AA01356:large subunit pseudouridylate synthase D:lipooligosaccharide galactosyltransferase II (comL related):->->:918340..918445 106 aaataaaaaatccgttaatcaagtttgcttatttagcaatgtcctatacaatgtcgggcaattgtaacccatttatcatttttcgtaaaaataaggattctatcca Intra-Species Hit: Count: 1 Min: 1 Max: 106 Len: 106 Subject: aact_AA01355_AA01356|large subunit pseudouridylate synthase D:lipooligosaccharide galactosyltransferase II (comL related)|POSITIVE:POSITIVE|[918340,918445]|106 HSP 1 e-value: 6.0E-54 bit: 210.0 Len: 106 Query Start:1 Query End:106 Subject Strand: POSITIVE Subject Start: 1 Subject End: 106 aaataaaaaatccgttaatcaagtttgcttatttagcaatgtcctatacaatgtcgggcaattgtaacccatttatcatttttcgtaaaaataaggattctatcca aaataaaaaatccgttaatcaagtttgcttatttagcaatgtcctatacaatgtcgggcaattgtaacccatttatcatttttcgtaaaaataaggattctatcca Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAUAAAAAAUCCGUUAAUCAAGUUUGCUUAUUUAGCAAUGUCCUAUACAAUGUCGGGCAAUUGUAACCCAUUUAUCAUUUUUCGUAAAAAUAAGGAUUCUAUCCA ..(..((((((..(((((..(((....)))..)))))..(((((.((.....)).))))).................))))))..)........((((...)))). (-13.50) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGGAUAGAAUCCUUAUUUUUACGAAAAAUGAUAAAUGGGUUACAAUUGCCCGACAUUGUAUAGGACAUUGCUAAAUAAGCAAACUUGAUUAACGGAUUUUUUAUUU .....(((((((.......................(((((.......)))))........((((...(((((.....))))).))))......)))))))...... (-16.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 281 66 21 83 38 aact:AA01834|5end_hypothetical_protein_1234640..1234870_POSITIVE 276 60 11 166 112 aact:AA00199|5end_hypothetical_protein_138575..138805_POSITIVE 257 64 24 121 83 aact:AA00880|5end_tight_adherence_protein_G_610628..610858_POSITIVE 252 60 11 82 20 aact:AA02220|5end_ABC_transport_system_permease_protein_1511155..1511385_POSITIVE 243 73 35 109 54 aact:AA02490|5end_hypothetical_protein_1726610..1726840_POSITIVE 237 60 13 203 149 aact:AA01203|5end_diaminopimelate_epimerase_824140..824370_POSITIVE 234 56 11 133 81 aact:AA00908|5end_probable_sigma-E_factor_regulatory_protein_626076..626306_POSITIVE 232 68 24 146 102 aact:AA01700|5end_hexulose-6-phosphate_isomerase_1154535..1154765_POSITIVE 231 69 26 178 132 aact:AA02634|5end_rhamnosyltransferase;_glycosyltransferase_homolog_2_1832816..1833046_POSITIVE 230 70 26 101 51 aact:AA01239|5end_30S_ribosomal_protein_S13_844503..844733_POSITIVE 229 88 43 179 136 aact:AA01727|5end_conserved_hypothetical_protein_(possible_HipA_protein)_1168227..1168457_POSITIVE 229 88 43 57 14 aact:AA01726|5end_conserved_hypothetical_protein_(possible_HipA-like_protein_1168105..1168335_POSITIVE 224 78 52 72 42 aact:AA00054|5end_cytochrome_c_biogenesis_protein_41393..41623_POSITIVE 222 75 33 192 134 aact:AA02738|5end_phosphate_permease_1919372..1919602_POSITIVE 222 70 23 174 133 aact:AA00782|5end_conserved_hypothetical_protein_538723..538953_POSITIVE 221 57 11 81 38 aact:AA02088|5end_glycogen_operon_protein_1421282..1421512_POSITIVE 219 60 12 54 1 aact:AA02270|5end_endopeptidase_La;_lon_protease;_protease_La_homolog;_ATP-dependent_protease_LA_(lon-1)_1546870..1547100_POSITIVE 219 60 11 67 11 aact:AA01054|5end_conserved_hypothetical_protein_733678..733908_POSITIVE 218 88 52 91 55 aact:AA02119|5end_hypothetical_protein_1446372..1446602_POSITIVE 218 59 11 99 60 aact:AA01724|5end_valyl-tRNA_synthetase_1164446..1164676_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 257 64 24 101 63 aact:AA00879|3end_tight_adherence_protein_F_610688..610838_POSITIVE 252 79 37 137 89 aact:AA01271|3end_hypothetical_protein_863981..864131_POSITIVE 252 79 37 53 5 aact:AA01270|3end_hydrolase_(possible_2-haloalkanoic_acid_dehalogenase_I)_863897..864047_POSITIVE 234 56 11 120 68 aact:AA00906|3end_sigma-E_factor_regulatory_protein_626143..626293_POSITIVE 232 68 24 102 58 aact:AA01698|3end_probable_transcriptional_regulator_(DeoR_family)_1154571..1154721_POSITIVE 229 88 43 54 11 aact:AA01725|3end_hypothetical_protein_1168182..1168332_POSITIVE 226 89 41 87 21 aact:AA02076|3end_conserved_hypothetical_protein_1411094..1411244_POSITIVE 224 85 42 54 3 aact:AA02489|3end_hypothetical_protein_1726629..1726779_POSITIVE 224 78 52 69 39 aact:AA00052|3end_cytochrome_c-type_biogenesis_protein_precursor_41470..41620_POSITIVE 219 70 37 38 3 aact:AA00861|3end_transcription_repair_coupling_factor_596150..596300_POSITIVE 218 80 31 142 91 aact:AA01466|3end_mannose-specific_phosphotransferase_system_IIC_986362..986512_POSITIVE 217 59 13 116 84 aact:AA01501|3end_hypothetical_protein_1010040..1010190_POSITIVE 216 58 13 65 19 aact:AA00962|3end_exopolyphosphatase_(metaphosphatase)_672684..672834_POSITIVE 215 70 23 62 2 aact:AA01840|3end_conserved_hypothetical_protein_1237554..1237704_POSITIVE 214 67 21 130 84 aact:AA02315|3end_conserved_hypothetical_protein_1581752..1581902_POSITIVE 212 66 31 142 99 aact:AA01765|3end_Mu-like_prophage_FluMu_transposase_A_1192636..1192786_POSITIVE 208 56 11 145 99 aact:AA01342|3end_conserved_hypotheticl_protein_(possible_ribosomal_RNA_adenine_dimethylase)_911085..911235_POSITIVE 208 69 26 137 92 aact:AA01181|3end_conserved_hypothetical_protein_809294..809444_POSITIVE 208 60 13 98 45 aact:AA00425|3end_N-terminal_region_of_competence_protein_M_288073..288223_POSITIVE 207 61 24 145 106 aact:AA02950|3end_isoleucyl-tRNA_synthetase_2065113..2065263_POSITIVE