Origin IGS: taaaatccaccgcacttttagataaattttagctttaatgtaagcaaattcaggatttaggcttgagaatacaagataaagtgagtataatgcacgacctttaatatagtacgcgggtcgggttgcgacctgacgaggtcactctcaaaagttatttttgaagtattccgaaccgtaagctcgagcttatatttcattattggagattaat .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 attaatctccaataatgaaatataagctcgagcttacggttcggaatacttcaaaaataacttttgagagtgacctcgtcaggtcgcaacccgacccgcgtactatattaaaggtcgtgcattatactcactttatcttgtattctcaagcctaaatcctgaatttgcttacattaaagctaaaatttatctaaaagtgcggtggatttta Mask Tandem Repeat Region ================================================ taaaatccaccgcacttttagataaattttagctttaatgtaagcaaattcaggatttaggcttgagaatacaagataaagtgagtataatgcacgacctttaatatagtacgcgggtcgggttgcgacctgacgaggtcactctcaaaagttatttttgaagtattccgaaccgtaagctcgagcttatatttcattattggagattaat Find is-nt database================================================ Query_seq: AA01321:AA01323|AA01321:AA01323:DNA repair protein:50S ribosomal protein L28:->->:894176..894386 211 taaaatccaccgcacttttagataaattttagctttaatgtaagcaaattcaggatttaggcttgagaatacaagataaagtgagtataatgcacgacctttaatatagtacgcgggtcgggttgcgacctgacgaggtcactctcaaaagttatttttgaagtattccgaaccgtaagctcgagcttatatttcattattggagattaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: AA01321:AA01323|AA01321:AA01323:DNA repair protein:50S ribosomal protein L28:->->:894176..894386 211 taaaatccaccgcacttttagataaattttagctttaatgtaagcaaattcaggatttaggcttgagaatacaagataaagtgagtataatgcacgacctttaatatagtacgcgggtcgggttgcgacctgacgaggtcactctcaaaagttatttttgaagtattccgaaccgtaagctcgagcttatatttcattattggagattaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: AA01321:AA01323|AA01321:AA01323:DNA repair protein:50S ribosomal protein L28:->->:894176..894386 211 taaaatccaccgcacttttagataaattttagctttaatgtaagcaaattcaggatttaggcttgagaatacaagataaagtgagtataatgcacgacctttaatatagtacgcgggtcgggttgcgacctgacgaggtcactctcaaaagttatttttgaagtattccgaaccgtaagctcgagcttatatttcattattggagattaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taaaatccaccgcacttttagataaattttagctttaatgtaagcaaattcaggatttaggcttgagaatacaagataaagtgagtataatgcacgacctttaatatagtacgcgggtcgggttgcgacctgacgaggtcactctcaaaagttatttttgaagtattccgaaccgtaagctcgagcttatatttcattattggagattaat Predict ORF larger than 30AA ================================================ Protein_Len: 35 Strand: + Start: 106 End: 207 ......................................................................................................... M V R G S G C D L T R S L S K V I F E V F R T V S S S L Y F I I G D * .... Protein_Len: 47 Strand: - Start: 60 End: 200 ........................................................... A Q S Y L I F H T Y H V V K L I T R P D P Q S R V L D S E F T I K S T N R V T L E L K Y K M M ........... Protein_Len: 35 Strand: - Start: 1 End: 105 L I W R V K L Y I K A K I Y A F E P N L S S F V L Y L S Y L A R G K M .......................................................................................................... taaaatccaccgcacttttagataaattttagctttaatgtaagcaaattcaggatttaggcttgagaatacaagataaagtgagtataatgcacgacctttaatatagtacgcgggtcgggttgcgacctgacgaggtcactctcaaaagttatttttgaagtattccgaaccgtaagctcgagcttatatttcattattggagattaat 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: 86 Start: 62 End: 91 .............................................................CTTGAGAATACAAGATAAAGTGAGTATAAT........................................................................................................................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ taaaatccaccgcacttttagataaattttagctttaatgtaagcaaattcaggatttaggcttgagaatacaagataaagtgagtataatgcacgacctttaatatagtacgcgggtcgggttgcgacctgacgaggtcactctcaaaagttatttttgaagtattccgaaccgtaagctcgagcttatatttcattattggagattaat Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: AA01321:AA01323|AA01321:AA01323:DNA repair protein:50S ribosomal protein L28:->->:894176..894386 211 taaaatccaccgcacttttagataaattttagctttaatgtaagcaaattcaggatttaggcttgagaatacaagataaagtgagtataatgcacgacctttaatatagtacgcgggtcgggttgcgacctgacgaggtcactctcaaaagttatttttgaagtattccgaaccgtaagctcgagcttatatttcattattggagattaat Intra-Species Hit: Count: 1 Min: 1 Max: 211 Len: 211 Subject: aact_AA01321_AA01323|DNA repair protein:50S ribosomal protein L28|POSITIVE:POSITIVE|[894176,894386]|211 HSP 1 e-value: 1.0E-116 bit: 418.0 Len: 211 Query Start:1 Query End:211 Subject Strand: POSITIVE Subject Start: 1 Subject End: 211 taaaatccaccgcacttttagataaattttagctttaatgtaagcaaattcaggatttaggcttgagaatacaagataaagtgagtataatgcacgacctttaatatagtacgcgggtcgggttgcgacctgacgaggtcactctcaaaagttatttttgaagtattccgaaccgtaagctcgagcttatatttcattattggagattaat taaaatccaccgcacttttagataaattttagctttaatgtaagcaaattcaggatttaggcttgagaatacaagataaagtgagtataatgcacgacctttaatatagtacgcgggtcgggttgcgacctgacgaggtcactctcaaaagttatttttgaagtattccgaaccgtaagctcgagcttatatttcattattggagattaat Inter-species Hit: Count: 5 Min: 55 Max: 211 Len: 157 Subject: NC_002663_PM1151_PM1152|50S ribosomal protein L28:DNA repair protein RadC|NEGATIVE:NEGATIVE|[1349612,1349852]|241 HSP 1 e-value: 2.0E-21 bit: 103.0 Len: 85 Query Start:55 Query End:139 Subject Strand: NEGATIVE Subject Start: 93 Subject End: 179 ......................................................atttaggcttgagaatacaagataaagtgagtataatgcacgacctttaatatagtacgcgggtcgggt--tgcgacctgacgaggt........................................................................ ......................................................atttaggcttgagaataaaagataaagtgagtataattcaccacctttaatatagtatgcgggtcggttacagcgacctgacgaggt........................................................................ HSP 2 e-value: 3.0E-8 bit: 60.0 Len: 45 Query Start:167 Query End:211 Subject Strand: NEGATIVE Subject Start: 1 Subject End: 46 ......................................................................................................................................................................tccgaaccgtaagctcgagcttatatttca-ttattggagattaat ......................................................................................................................................................................tccgaaccctaagctcgagcttatatttgatttattggagattaat Subject: NC_007146_NTHI1124_NTHI1125|50S ribosomal protein L28:DNA repair protein RadC|NEGATIVE:NEGATIVE|[1069692,1069904]|213 HSP 1 e-value: 1.0E-13 bit: 77.8 Len: 43 Query Start:167 Query End:209 Subject Strand: NEGATIVE Subject Start: 3 Subject End: 45 ......................................................................................................................................................................tccgaaccgtaagctcgagcttatatttcattattggagatta.. ......................................................................................................................................................................tccgaaccgtaagctcgagcttatatttaattattggagatta.. HSP 2 e-value: 2.0E-6 bit: 54.0 Len: 62 Query Start:78 Query End:139 Subject Strand: NEGATIVE Subject Start: 76 Subject End: 140 .............................................................................aaagtgagtataatgcacgacctttaatatagtacgcgggtcgggtt---gcgacctgacgaggt........................................................................ .............................................................................aaagtcagtataatttgcgacctttaatatagtaagcgggtcggattagcgcgacctgacgaggt........................................................................ Subject: NC_000907_HI0951_HI0952|50S ribosomal protein L28:DNA repair protein RadC|NEGATIVE:NEGATIVE|[1011094,1011306]|213 HSP 1 e-value: 1.0E-13 bit: 77.8 Len: 43 Query Start:167 Query End:209 Subject Strand: NEGATIVE Subject Start: 3 Subject End: 45 ......................................................................................................................................................................tccgaaccgtaagctcgagcttatatttcattattggagatta.. ......................................................................................................................................................................tccgaaccgtaagctcgagcttatatttaattattggagatta.. HSP 2 e-value: 2.0E-6 bit: 54.0 Len: 62 Query Start:78 Query End:139 Subject Strand: NEGATIVE Subject Start: 76 Subject End: 140 .............................................................................aaagtgagtataatgcacgacctttaatatagtacgcgggtcgggtt---gcgacctgacgaggt........................................................................ .............................................................................aaagtcagtataatttgcgacctttaatatagtaagcgggtcggattagcgcgacctgacgaggt........................................................................ Subject: NC_006300_MS1941_MS1942|RadC protein:50S ribosomal protein L28|POSITIVE:POSITIVE|[1920128,1920429]|302 HSP 1 e-value: 8.0E-12 bit: 71.9 Len: 138 Query Start:62 Query End:199 Subject Strand: POSITIVE Subject Start: 159 Subject End: 302 .............................................................cttgagaatacaagataaagtgagtataatgcacgacctttaatatagtacgcgggtcgggt--tgcgacctgacgaggtcactctcaaaa----gttatttttgaagtattccgaaccgtaagctcgagcttatatttcatta............ .............................................................cttgagaatagcagataaagtaagtataatcagcgacctttgatatagttagcgggtcggatactgcgacctgacgaggtggcttacaaaatcaagctgattttgaagtagtccgaaccctaagctcgagcttatatttaatta............ Subject: NC_008309_HS_0144_HS_0145|DNA repair protein:50S ribosomal protein L28|POSITIVE:POSITIVE|[129913,130132]|220 HSP 1 e-value: 3.0E-11 bit: 69.9 Len: 127 Query Start:85 Query End:211 Subject Strand: POSITIVE Subject Start: 97 Subject End: 220 ....................................................................................gtataatgcacgacctttaatatagtacgcgggtcgggt-tgcgacctgacgaggtcactctcaaaagtt--atttttgaagtattccgaaccgtaagctcgagcttatatttcattattggagattaat ....................................................................................gtataattcacgacctttaatatagt----gggtcggctatgcgacctgacgaggtagccttcaaaatcttgaattttgaagtggtccgaaccctaagctcgagcttatattt--ttattggagattaat Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUUUAGGCUUGAGAAUACAAGAUAAAGUGAGUAUAAUGCACGACCUUUAAUAUAGUACGCGGGUCGGGUUGCGACCUGACGAGGUCACUCUCAAAAGUUAUUUUUGAAGUAUUCCGAACCGUAAGCUCGAGCUUAUAUUUCAUUAUUGGAGAUUAAU ...((((((((((..(((........(.((((((.......(((((...........(((((((((.....))))))).)))))))....(((((((...))))))).))))))).....)))..))))))))))..(((((....)))))...... (-40.52) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUUAAUCUCCAAUAAUGAAAUAUAAGCUCGAGCUUACGGUUCGGAAUACUUCAAAAAUAACUUUUGAGAGUGACCUCGUCAGGUCGCAACCCGACCCGCGUACUAUAUUAAAGGUCGUGCAUUAUACUCACUUUAUCUUGUAUUCUCAAGCCUAAAU ...............(((..(((((((.(((.(((.(((.((((.....(((((((.....))))))).(((((((....)))))))...)))).)))............))).))).)).))))).)))......((((......))))....... (-34.32) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 336 84 41 191 143 aact:AA01841|5end_conserved_hypothetical_protein_1237514..1237744_POSITIVE 323 77 32 179 140 aact:AA02634|5end_rhamnosyltransferase;_glycosyltransferase_homolog_2_1832816..1833046_POSITIVE 315 85 45 156 118 aact:AA01842|5end_conserved_hypothetical_protein_1238271..1238501_POSITIVE 313 85 45 196 151 aact:AA01815|5end_probable_sodium-dependent_transmembrane_transport_protein_1222541..1222771_POSITIVE 308 84 58 196 163 aact:AA00918|5end_hypothetical_protein_630044..630274_POSITIVE 306 85 59 200 162 aact:AA00578|5end_DNA_topoisomerase_394576..394806_POSITIVE 305 84 59 231 190 aact:AA00719|5end_hypothetical_protein_494627..494857_POSITIVE 302 89 58 171 134 aact:AA02440|5end_ABC_transporter,_ATP-binding_protein_1685043..1685273_POSITIVE 300 79 37 60 22 aact:AA01868|5end_biotin_synthetase_1255545..1255775_POSITIVE 298 100 53 152 102 aact:AA02898|5end_oligopeptide_transport_ATP-binding_protein_2029083..2029313_POSITIVE 297 87 44 68 26 aact:AA03012|5end_conserved_hypothetical_protein_2104216..2104446_POSITIVE 296 85 54 179 144 aact:AA00002|5end_DNA_polymerase_III,_beta_subunit_1233..1463_POSITIVE 294 84 41 144 92 aact:AA01866|5end_thiamin_ABC_transporter,_permease_protein_1253313..1253543_POSITIVE 293 93 59 41 3 aact:AA00229|5end_DNA_polymerase_III,_alpha_subunit_156863..157093_POSITIVE 289 67 30 231 182 aact:AA00135|5end_S-adenosylmethionine:_2-demethylmenaquinone_methyltransferase_(menaquinone_biosynthesis_protein)_96303..96533_POSITIVE 288 94 59 168 133 aact:AA02206|5end_tryptophan_synthase,_beta_chain_1501917..1502147_POSITIVE 287 96 53 57 3 aact:AA01289|5end_hypothetical_protein_872385..872615_POSITIVE 287 86 41 46 1 aact:AA00715|5end_[2Fe-2S]_ferredoxin_490632..490862_POSITIVE 286 99 58 49 7 aact:AA00251|5end_lipoate_biosynthesis_protein_B_176523..176753_POSITIVE 283 94 59 107 57 aact:AA01117|5end_signal_recognition_particle_protein_54_(GTP-binding_export_factor)_767919..768149_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 336 84 41 151 103 aact:AA01840|3end_conserved_hypothetical_protein_1237554..1237704_POSITIVE 311 87 59 116 80 aact:AA01394|3end_transcriptional_regulator_(mtr_efflux_pump)_943211..943361_POSITIVE 298 100 53 139 89 aact:AA02897|3end_oligopeptide_ABC_transporter;_permease_protein_2029150..2029300_POSITIVE 297 87 44 65 23 aact:AA03011|3end_inner_membrane_protein,_60_kDa_2104293..2104443_POSITIVE 294 84 41 60 8 aact:AA01865|3end_thiamin_ABC_transporter,_periplasmic-binding_protein_1253309..1253459_POSITIVE 292 97 57 39 1 aact:AA02564|3end_transketolase_N-terminal_section_1786783..1786933_POSITIVE 286 89 44 151 106 aact:AA02205|3end_short_chain_dehydrogenase/reductase_1501984..1502134_POSITIVE 284 104 62 57 19 aact:AA00839|3end_UDP-MurNAc-pentapeptide_phosphotransferase_579784..579934_POSITIVE 282 90 42 77 13 aact:AA01675|3end_probable_multidrug_resistance_protein;_multidrug-efflux_transporter_1133589..1133739_POSITIVE 281 85 53 84 46 aact:AA02703|3end_hypothetical_protein_1885582..1885732_POSITIVE 280 87 44 140 98 aact:AA00796|3end_iron(III)_dicitrate_transport_system_permease_protein_546752..546902_POSITIVE 279 106 61 73 14 aact:AA02918|3end_hypothetical_protein_2043501..2043651_POSITIVE 276 79 32 71 18 aact:AA01172|3end_conserved_hypothetical_protein_803847..803997_POSITIVE 276 60 11 49 3 aact:AA00603|3end_undecaprenyl_pyrophosphate_synthetase_(UPPS)_410992..411142_POSITIVE 274 86 57 146 107 aact:AA02911|3end_hypothetical_protein_2039235..2039385_POSITIVE 274 79 37 62 16 aact:AA02684|3end_hydrogenase_4_membrane_subunit_1871612..1871762_POSITIVE 270 79 37 69 26 aact:AA02324|3end_ABC_transporter_ATP_binding_protein_1587392..1587542_POSITIVE 268 88 47 149 112 aact:AA01869|3end_periplasmic_serine_protease_do;_hhoA-like_precursor;_heat_shock_protein_1258109..1258259_POSITIVE 266 86 57 32 5 aact:AA00271|3end_hypothetical_protein_190469..190619_POSITIVE 265 87 41 77 25 aact:AA00407|3end_trk_system_potassium_uptake_protein_272309..272459_POSITIVE