Origin IGS: acatgcacaaaaacatatcttttgcgcaaaaatacacaaaaagccataaaacgagcaaacgacaccctgacgatagtgagacgaccgaatcaaaaggcgagcagcatcttcaagtggttttgtcagaaaacggctttatcccggatttgtcatttagaaaagtaagacctaacgacaatccgggtttatgcggaagaacgcttcaagcgtatgaagccctcatttcttcgacccaataacctcggggtggaggcagcgggggaagcttcgcaaaccgtaaaggactcggagctcggattcggaattatcggaaatgaaagacccgaatgcttctaaagcttctccatgacccgtacgacacgctcaataggtgagcaaaaaagatacttcttgataatcttctctttttgcaaaggtttctataattctattggagaaggtgcaatctgtagagcagggagagcgaggcggggg .........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.........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 cccccgcctcgctctccctgctctacagattgcaccttctccaatagaattatagaaacctttgcaaaaagagaagattatcaagaagtatcttttttgctcacctattgagcgtgtcgtacgggtcatggagaagctttagaagcattcgggtctttcatttccgataattccgaatccgagctccgagtcctttacggtttgcgaagcttcccccgctgcctccaccccgaggttattgggtcgaagaaatgagggcttcatacgcttgaagcgttcttccgcataaacccggattgtcgttaggtcttacttttctaaatgacaaatccgggataaagccgttttctgacaaaaccacttgaagatgctgctcgccttttgattcggtcgtctcactatcgtcagggtgtcgtttgctcgttttatggctttttgtgtatttttgcgcaaaagatatgtttttgtgcatgt Mask Tandem Repeat Region ================================================ acatgcacaaaaacatatcttttgcgcaaaaatacacaaaaagccataaaacgagcaaacgacaccctgacgatagtgagacgaccgaatcaaaaggcgagcagcatcttcaagtggttttgtcagaaaacggctttatcccggatttgtcatttagaaaagtaagacctaacgacaatccgggtttatgcggaagaacgcttcaagcgtatgaagccctcatttcttcgacccaataacctcggggtggaggcagcgggggaagcttcgcaaaccgtaaaggactcggagctcggattcggaattatcggaaatgaaagacccgaatgcttctaaagcttctccatgacccgtacgacacgctcaataggtgagcaaaaaagatacttcttgataatcttctctttttgcaaaggtttctataattctattggagaaggtgcaatctgtagagcagggagagcgaggcggggg Find is-nt database================================================ Query_seq: PG1829:PG1831|PG1829:PG1831:long-chain-fatty-acid--CoA ligase, putative:ATP-dependent DNA helicase RecQ:<-<-:1923071..1923544 474 acatgcacaaaaacatatcttttgcgcaaaaatacacaaaaagccataaaacgagcaaacgacaccctgacgatagtgagacgaccgaatcaaaaggcgagcagcatcttcaagtggttttgtcagaaaacggctttatcccggatttgtcatttagaaaagtaagacctaacgacaatccgggtttatgcggaagaacgcttcaagcgtatgaagccctcatttcttcgacccaataacctcggggtggaggcagcgggggaagcttcgcaaaccgtaaaggactcggagctcggattcggaattatcggaaatgaaagacccgaatgcttctaaagcttctccatgacccgtacgacacgctcaataggtgagcaaaaaagatacttcttgataatcttctctttttgcaaaggtttctataattctattggagaaggtgcaatctgtagagcagggagagcgaggcggggg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG1829:PG1831|PG1829:PG1831:long-chain-fatty-acid--CoA ligase, putative:ATP-dependent DNA helicase RecQ:<-<-:1923071..1923544 474 acatgcacaaaaacatatcttttgcgcaaaaatacacaaaaagccataaaacgagcaaacgacaccctgacgatagtgagacgaccgaatcaaaaggcgagcagcatcttcaagtggttttgtcagaaaacggctttatcccggatttgtcatttagaaaagtaagacctaacgacaatccgggtttatgcggaagaacgcttcaagcgtatgaagccctcatttcttcgacccaataacctcggggtggaggcagcgggggaagcttcgcaaaccgtaaaggactcggagctcggattcggaattatcggaaatgaaagacccgaatgcttctaaagcttctccatgacccgtacgacacgctcaataggtgagcaaaaaagatacttcttgataatcttctctttttgcaaaggtttctataattctattggagaaggtgcaatctgtagagcagggagagcgaggcggggg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG1829:PG1831|PG1829:PG1831:long-chain-fatty-acid--CoA ligase, putative:ATP-dependent DNA helicase RecQ:<-<-:1923071..1923544 474 acatgcacaaaaacatatcttttgcgcaaaaatacacaaaaagccataaaacgagcaaacgacaccctgacgatagtgagacgaccgaatcaaaaggcgagcagcatcttcaagtggttttgtcagaaaacggctttatcccggatttgtcatttagaaaagtaagacctaacgacaatccgggtttatgcggaagaacgcttcaagcgtatgaagccctcatttcttcgacccaataacctcggggtggaggcagcgggggaagcttcgcaaaccgtaaaggactcggagctcggattcggaattatcggaaatgaaagacccgaatgcttctaaagcttctccatgacccgtacgacacgctcaataggtgagcaaaaaagatacttcttgataatcttctctttttgcaaaggtttctataattctattggagaaggtgcaatctgtagagcagggagagcgaggcggggg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 acatgcacaaaaacatatcttttgcgcaaaaatacacaaaaagccataaaacgagcaaacgacaccctgacgatagtgagacgaccgaatcaaaaggcgagcagcatcttcaagtggttttgtcagaaaacggctttatcccggatttgtcatttagaaaagtaagacctaacgacaatccgggtttatgcggaagaacgcttcaagcgtatgaagccctcatttcttcgacccaataacctcggggtggaggcagcgggggaagcttcgcaaaccgtaaaggactcggagctcggattcggaattatcggaaatgaaagacccgaatgcttctaaagcttctccatgacccgtacgacacgctcaataggtgagcaaaaaagatacttcttgataatcttctctttttgcaaaggtttctataattctattggagaaggtgcaatctgtagagcagggagagcgaggcggggg Predict ORF larger than 30AA ================================================ Protein_Len: 47 Strand: + Start: 22 End: 162 ..................... M R K N T Q K A I K R A N D T L T I V R R P N Q K A S S I F K W F C Q K T A L S R I C H L E K ........................................................................................................................................................................................................................................................................................................................ Protein_Len: 60 Strand: + Start: 3 End: 236 .. M H K N I S F A Q K Y T K S H K T S K R H P D D S E T T E S K G E Q H L Q V V L S E N G F I P D L S F R K V R P N D N P .............................................................................................................................................................................................................................................. Protein_Len: 52 Strand: + Start: 178 End: 333 ................................................................................................................................................................................. M R V Y A E E R F K R M K P S F L R P N N L G V E A A G E A S Q T V K D S E L G F G I I G N E R P E C F ............................................................................................................................................. Protein_Len: 43 Strand: + Start: 346 End: 474 ......................................................................................................................................................................................................................................................................................................................................................... M T R T T R S I G E Q K R Y F L I I F S F C K G F Y N S I G E G A I C R A G R A R R G Protein_Len: 31 Strand: - Start: 223 End: 315 .............................................................................................................................................................................................................................. K K S G I V E P H L C R P F S R L G Y L V R L E S E S N D S M ............................................................................................................................................................... Protein_Len: 31 Strand: - Start: 206 End: 298 ............................................................................................................................................................................................................. A Y S A R M E E V W Y G R P P P L P P L K A F R L P S P A R M ................................................................................................................................................................................ Protein_Len: 40 Strand: - Start: 189 End: 308 ............................................................................................................................................................................................ A S S R K L R I F G E N R R G L L R P T S A A P S A E C V T F S E S S P N P I M ...................................................................................................................................................................... Protein_Len: 42 Strand: - Start: 1 End: 126 C A C F C I K Q A F I C L F G Y F S C V V G Q R Y H S S R I L L R A A D E L P K T M ............................................................................................................................................................................................................................................................................................................................................................ acatgcacaaaaacatatcttttgcgcaaaaatacacaaaaagccataaaacgagcaaacgacaccctgacgatagtgagacgaccgaatcaaaaggcgagcagcatcttcaagtggttttgtcagaaaacggctttatcccggatttgtcatttagaaaagtaagacctaacgacaatccgggtttatgcggaagaacgcttcaagcgtatgaagccctcatttcttcgacccaataacctcggggtggaggcagcgggggaagcttcgcaaaccgtaaaggactcggagctcggattcggaattatcggaaatgaaagacccgaatgcttctaaagcttctccatgacccgtacgacacgctcaataggtgagcaaaaaagatacttcttgataatcttctctttttgcaaaggtttctataattctattggagaaggtgcaatctgtagagcagggagagcgaggcggggg 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================================================ acatgcacaaaaacatatcttttgcgcaaaaatacacaaaaagccataaaacgagcaaacgacaccctgacgatagtgagacgaccgaatcaaaaggcgagcagcatcttcaagtggttttgtcagaaaacggctttatcccggatttgtcatttagaaaagtaagacctaacgacaatccgggtttatgcggaagaacgcttcaagcgtatgaagccctcatttcttcgacccaataacctcggggtggaggcagcgggggaagcttcgcaaaccgtaaaggactcggagctcggattcggaattatcggaaatgaaagacccgaatgcttctaaagcttctccatgacccgtacgacacgctcaataggtgagcaaaaaagatacttcttgataatcttctctttttgcaaaggtttctataattctattggagaaggtgcaatctgtagagcagggagagcgaggcggggg Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PG1829:PG1831|PG1829:PG1831:long-chain-fatty-acid--CoA ligase, putative:ATP-dependent DNA helicase RecQ:<-<-:1923071..1923544 474 acatgcacaaaaacatatcttttgcgcaaaaatacacaaaaagccataaaacgagcaaacgacaccctgacgatagtgagacgaccgaatcaaaaggcgagcagcatcttcaagtggttttgtcagaaaacggctttatcccggatttgtcatttagaaaagtaagacctaacgacaatccgggtttatgcggaagaacgcttcaagcgtatgaagccctcatttcttcgacccaataacctcggggtggaggcagcgggggaagcttcgcaaaccgtaaaggactcggagctcggattcggaattatcggaaatgaaagacccgaatgcttctaaagcttctccatgacccgtacgacacgctcaataggtgagcaaaaaagatacttcttgataatcttctctttttgcaaaggtttctataattctattggagaaggtgcaatctgtagagcagggagagcgaggcggggg Intra-Species Hit: Count: 1 Min: 1 Max: 474 Len: 474 Subject: NC_002950_PG1829_PG1831|long-chain-fatty-acid--CoA ligase, putative:ATP-dependent DNA helicase RecQ|NEGATIVE:NEGATIVE|[1923071,1923544]|474 HSP 1 e-value: 0.0 bit: 940.0 Len: 474 Query Start:1 Query End:474 Subject Strand: POSITIVE Subject Start: 1 Subject End: 474 acatgcacaaaaacatatcttttgcgcaaaaatacacaaaaagccataaaacgagcaaacgacaccctgacgatagtgagacgaccgaatcaaaaggcgagcagcatcttcaagtggttttgtcagaaaacggctttatcccggatttgtcatttagaaaagtaagacctaacgacaatccgggtttatgcggaagaacgcttcaagcgtatgaagccctcatttcttcgacccaataacctcggggtggaggcagcgggggaagcttcgcaaaccgtaaaggactcggagctcggattcggaattatcggaaatgaaagacccgaatgcttctaaagcttctccatgacccgtacgacacgctcaataggtgagcaaaaaagatacttcttgataatcttctctttttgcaaaggtttctataattctattggagaaggtgcaatctgtagagcagggagagcgaggcggggg acatgcacaaaaacatatcttttgcgcaaaaatacacaaaaagccataaaacgagcaaacgacaccctgacgatagtgagacgaccgaatcaaaaggcgagcagcatcttcaagtggttttgtcagaaaacggctttatcccggatttgtcatttagaaaagtaagacctaacgacaatccgggtttatgcggaagaacgcttcaagcgtatgaagccctcatttcttcgacccaataacctcggggtggaggcagcgggggaagcttcgcaaaccgtaaaggactcggagctcggattcggaattatcggaaatgaaagacccgaatgcttctaaagcttctccatgacccgtacgacacgctcaataggtgagcaaaaaagatacttcttgataatcttctctttttgcaaaggtttctataattctattggagaaggtgcaatctgtagagcagggagagcgaggcggggg Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACAUGCACAAAAACAUAUCUUUUGCGCAAAAAUACACAAAAAGCCAUAAAACGAGCAAACGACACCCUGACGAUAGUGAGACGACCGAAUCAAAAGGCGAGCAGCAUCUUCAAGUGGUUUUGUCAGAAAACGGCUUUAUCCCGGAUUUGUCAUUUAGAAAAGUAAGACCUAACGACAAUCCGGGUUUAUGCGGAAGAACGCUUCAAGCGUAUGAAGCCCUCAUUUCUUCGACCCAAUAACCUCGGGGUGGAGGCAGCGGGGGAAGCUUCGCAAACCGUAAAGGACUCGGAGCUCGGAUUCGGAAUUAUCGGAAAUGAAAGACCCGAAUGCUUCUAAAGCUUCUCCAUGACCCGUACGACACGCUCAAUAGGUGAGCAAAAAAGAUACUUCUUGAUAAUCUUCUCUUUUUGCAAAGGUUUCUAUAAUUCUAUUGGAGAAGGUGCAAUCUGUAGAGCAGGGAGAGCGAGGCGGGGG ...(((.(((((.......))))).)))..............(((......((......)).(((((((((((.((((((..(((.((((((...((.((......)).))...)))))).))).......(((((((.((((((((.(((..((((...........)))).)))))))))))..(((((.((((....))))..))))))))))))))))))...)))...........))))))))..)))....((((((((((......((.....))....(((((....((((((..((.(((....))).))..)))))))))))..))))))))))....(((((.((.(..(((((.....)))))..........(((((((....(((...(...(((((....((((((.........))))))...)))))...).))).))))))).)))..))))).. (-137.00) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CCCCCGCCUCGCUCUCCCUGCUCUACAGAUUGCACCUUCUCCAAUAGAAUUAUAGAAACCUUUGCAAAAAGAGAAGAUUAUCAAGAAGUAUCUUUUUUGCUCACCUAUUGAGCGUGUCGUACGGGUCAUGGAGAAGCUUUAGAAGCAUUCGGGUCUUUCAUUUCCGAUAAUUCCGAAUCCGAGCUCCGAGUCCUUUACGGUUUGCGAAGCUUCCCCCGCUGCCUCCACCCCGAGGUUAUUGGGUCGAAGAAAUGAGGGCUUCAUACGCUUGAAGCGUUCUUCCGCAUAAACCCGGAUUGUCGUUAGGUCUUACUUUUCUAAAUGACAAAUCCGGGAUAAAGCCGUUUUCUGACAAAACCACUUGAAGAUGCUGCUCGCCUUUUGAUUCGGUCGUCUCACUAUCGUCAGGGUGUCGUUUGCUCGUUUUAUGGCUUUUUGUGUAUUUUUGCGCAAAAGAUAUGUUUUUGUGCAUGU .....(((..((((.....((((((.((.......((((((((.((......))...((((.(((....(((((((((...........)))))))))(((((.....))))).....))).))))..)))))))))).))).))).((((((....((......))....))))))...))))..(((((.....((((((((((...((((.((((..(((((......)))))...))))..))))....(((.((((((......)))))).)))...))).....(((((((((((((((((.........))).)))))).))))))))...))))))).....((((......(((((.((((.((..((((.........)).))...)).)))).))))).))))....)))))......))).(((((((((....))))))))).((((((......)))))) (-139.51) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 1014 110 61 201 152 NC_002950:PG1829|5end_long-chain-fatty-acid--CoA_ligase,_putative_1922980..1923210_NEGATIVE 436 278 238 176 117 NC_002950:PG1242|5end_replicative_DNA_helicase_1317435..1317665_POSITIVE 428 290 244 57 11 NC_002950:PG0740|5end_NLP/P60_family_protein_787836..788066_POSITIVE 403 289 242 181 127 NC_002950:PG0735|5end_aminotransferase,_class_V_784383..784613_POSITIVE 396 289 244 151 106 NC_002950:PG0800|5end_hypothetical_protein_856278..856508_NEGATIVE 385 289 243 198 152 NC_002950:PG0227|5end_DNA_repair_protein_RadA_263978..264208_NEGATIVE 383 288 244 86 37 NC_002950:PG1006|5end_hypothetical_protein_1066478..1066708_NEGATIVE 381 290 241 163 87 NC_002950:PG0145|5end_hypothetical_protein_167831..168061_POSITIVE 378 270 229 215 171 NC_002950:PG1932|5end_ribosomal_protein_S3_2021610..2021840_NEGATIVE 373 290 241 66 14 NC_002950:PG1868|5end_hypothetical_protein_1965619..1965849_NEGATIVE 371 259 216 58 22 NC_002950:PG0638|5end_tetraacyldisaccharide_4'-kinase_691183..691413_NEGATIVE 369 270 221 219 166 NC_002950:PG2065|5end_conserved_hypothetical_protein_TIGR00048_2161000..2161230_POSITIVE 369 470 431 182 143 NC_002950:PG1648|5end_RelA/SpoT_family_protein_1727762..1727992_POSITIVE 369 277 231 131 75 NC_002950:PG1402|5end_AP_endonuclease_domain_protein_1485963..1486193_NEGATIVE 368 270 222 230 173 NC_002950:PG1634|5end_hypothetical_protein_1715148..1715378_NEGATIVE 367 287 244 124 78 NC_002950:PG0328|5end_imidazolonepropionase_363426..363656_NEGATIVE 366 288 243 157 103 NC_002950:PG1173|5end_YkgG_family_protein_1252435..1252665_POSITIVE 364 150 101 164 107 NC_002950:PG1719|5end_ABC_transporter,_ATP-binding_protein,_MsbA_family_1806749..1806979_POSITIVE 364 288 242 86 31 NC_002950:PG0562|5end_potassium_uptake_protein_TrkA,_putative_619222..619452_POSITIVE 363 289 242 195 150 NC_002950:PG2107|5end_thiamine_biosynthesis_protein_ThiH_2216658..2216888_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 436 278 238 141 82 NC_002950:PG1241|3end_GTP-binding_protein_LepA_1317480..1317630_POSITIVE 428 290 244 82 36 NC_002950:PG0739|3end_ribonuclease_Z_787941..788091_POSITIVE 412 290 242 109 65 NC_002950:PG0046|3end_phosphatidate_cytidylyltransferase_56346..56496_NEGATIVE 405 270 225 90 45 NC_002950:PG0324|3end_histidine_ammonia-lyase_357589..357739_NEGATIVE 403 289 242 122 68 NC_002950:PG0734|3end_nitroreductase_family_protein_784404..784554_POSITIVE 400 290 244 69 20 NC_002950:PG2145|3end_polysaccharide_deacetylase_2253938..2254088_POSITIVE 394 290 241 123 78 NC_002950:PG0143|3end_hydrolase,_carbon-nitrogen_family_165747..165897_NEGATIVE 382 258 216 82 26 NC_002950:PG1007|3end_transcriptional_regulator,_GntR_family_1066518..1066668_NEGATIVE 382 269 228 110 55 NC_002950:PG0508|3end_HAD-superfamily_subfamily_IB_hydrolase,_TIGR01490_548136..548286_NEGATIVE 377 299 251 92 46 NC_002950:PG1411|3end_potassium_uptake_protein_TrkA,_putative_1493481..1493631_NEGATIVE 375 259 216 140 100 NC_002950:PG0520|3end_chaperonin_GroEL_563618..563768_NEGATIVE 369 470 431 114 75 NC_002950:PG1647|3end_cardiolipin_synthetase_1727774..1727924_POSITIVE 367 287 242 117 62 NC_002950:PG0332|3end_transcription_termination_factor_Rho_367675..367825_POSITIVE 362 150 101 51 5 NC_002950:PG1171|3end_oxidoreductase,_putative_1251175..1251325_POSITIVE 362 277 241 77 17 NC_002950:PG0799|3end_hypothetical_protein_854599..854749_POSITIVE 359 260 216 147 100 NC_002950:PG0330|3end_DNA-binding_protein,_histone-like_family_364478..364628_NEGATIVE 352 288 243 151 106 NC_002950:PG0228|3end_DdaH_family_protein_264024..264174_NEGATIVE 351 287 242 91 43 NC_002950:PG2099|3end_ATP-dependent_RNA_helicase,_DEAD/DEAH_box_family_2206649..2206799_NEGATIVE 351 250 203 72 29 NC_002950:PG1782|3end_hypothetical_protein_1871961..1872111_POSITIVE 350 295 252 103 60 NC_002950:PG0752|3end_uracil_phosphoribosyltransferase_798397..798547_POSITIVE