Origin IGS: aatattctccctctattactttatttatttttatatttatattttatatgaaatttaaagaaaagtaaataaaaagaaaattaaaaaagtctttgaaatttttaattcaaagactgtatattgataaaaatggtggagatgacgagagtcgaactcgtgtccgaaatcataatgaccataagcttctacaagtttagtttactattaaatttcgtaataattactcccgtaaacagggctaactaaaactatcctctaaaatgtcccataaacttagagaaatcatttatggtgatctatactagtcaacacctttgaaaaacccgtatagaataagttatccaaggtgtagctgaactaagcagctaaagcgtaatctttgtttccatctaaaagatgtgtttagtctctcacagcgacaagcctgacttgctacctataacctcacaaccccgtcgaaacctttgcatccccatatttaattgtagacttaattatagcactattattaaattttagcaaggattttttagaagataaaaaagagttgttgtaacatttaagctaccaacaactctttgatatagaattaatttata .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9 tataaattaattctatatcaaagagttgttggtagcttaaatgttacaacaactcttttttatcttctaaaaaatccttgctaaaatttaataatagtgctataattaagtctacaattaaatatggggatgcaaaggtttcgacggggttgtgaggttataggtagcaagtcaggcttgtcgctgtgagagactaaacacatcttttagatggaaacaaagattacgctttagctgcttagttcagctacaccttggataacttattctatacgggtttttcaaaggtgttgactagtatagatcaccataaatgatttctctaagtttatgggacattttagaggatagttttagttagccctgtttacgggagtaattattacgaaatttaatagtaaactaaacttgtagaagcttatggtcattatgatttcggacacgagttcgactctcgtcatctccaccatttttatcaatatacagtctttgaattaaaaatttcaaagacttttttaattttctttttatttacttttctttaaatttcatataaaatataaatataaaaataaataaagtaatagagggagaatatt Mask Tandem Repeat Region ================================================ aatattctccctctattactttatttatttttatatttatattttatatgaaatttaaagaaaagtaaataaaaagaaaattaaaaaagtctttgaaatttttaattcaaagactgtatattgataaaaatggtggagatgacgagagtcgaactcgtgtccgaaatcataatgaccataagcttctacaagtttagtttactattaaatttcgtaataattactcccgtaaacagggctaactaaaactatcctctaaaatgtcccataaacttagagaaatcatttatggtgatctatactagtcaacacctttgaaaaacccgtatagaataagttatccaaggtgtagctgaactaagcagctaaagcgtaatctttgtttccatctaaaagatgtgtttagtctctcacagcgacaagcctgacttgctacctataacctcacaaccccgtcgaaacctttgcatccccatatttaattgtagacttaattatagcactattattaaattttagcaaggattttttagaagataaaaaagagttgttgtaacatttaagctaccaacaactctttgatatagaattaatttata Find is-nt database================================================ Query_seq: FN0556:FN0557|FN0556:FN0557:hypothetical protein:hypothetical protein:<-<-:1209091..1209689 599 aatattctccctctattactttatttatttttatatttatattttatatgaaatttaaagaaaagtaaataaaaagaaaattaaaaaagtctttgaaatttttaattcaaagactgtatattgataaaaatggtggagatgacgagagtcgaactcgtgtccgaaatcataatgaccataagcttctacaagtttagtttactattaaatttcgtaataattactcccgtaaacagggctaactaaaactatcctctaaaatgtcccataaacttagagaaatcatttatggtgatctatactagtcaacacctttgaaaaacccgtatagaataagttatccaaggtgtagctgaactaagcagctaaagcgtaatctttgtttccatctaaaagatgtgtttagtctctcacagcgacaagcctgacttgctacctataacctcacaaccccgtcgaaacctttgcatccccatatttaattgtagacttaattatagcactattattaaattttagcaaggattttttagaagataaaaaagagttgttgtaacatttaagctaccaacaactctttgatatagaattaatttata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN0556:FN0557|FN0556:FN0557:hypothetical protein:hypothetical protein:<-<-:1209091..1209689 599 aatattctccctctattactttatttatttttatatttatattttatatgaaatttaaagaaaagtaaataaaaagaaaattaaaaaagtctttgaaatttttaattcaaagactgtatattgataaaaatggtggagatgacgagagtcgaactcgtgtccgaaatcataatgaccataagcttctacaagtttagtttactattaaatttcgtaataattactcccgtaaacagggctaactaaaactatcctctaaaatgtcccataaacttagagaaatcatttatggtgatctatactagtcaacacctttgaaaaacccgtatagaataagttatccaaggtgtagctgaactaagcagctaaagcgtaatctttgtttccatctaaaagatgtgtttagtctctcacagcgacaagcctgacttgctacctataacctcacaaccccgtcgaaacctttgcatccccatatttaattgtagacttaattatagcactattattaaattttagcaaggattttttagaagataaaaaagagttgttgtaacatttaagctaccaacaactctttgatatagaattaatttata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN0556:FN0557|FN0556:FN0557:hypothetical protein:hypothetical protein:<-<-:1209091..1209689 599 aatattctccctctattactttatttatttttatatttatattttatatgaaatttaaagaaaagtaaataaaaagaaaattaaaaaagtctttgaaatttttaattcaaagactgtatattgataaaaatggtggagatgacgagagtcgaactcgtgtccgaaatcataatgaccataagcttctacaagtttagtttactattaaatttcgtaataattactcccgtaaacagggctaactaaaactatcctctaaaatgtcccataaacttagagaaatcatttatggtgatctatactagtcaacacctttgaaaaacccgtatagaataagttatccaaggtgtagctgaactaagcagctaaagcgtaatctttgtttccatctaaaagatgtgtttagtctctcacagcgacaagcctgacttgctacctataacctcacaaccccgtcgaaacctttgcatccccatatttaattgtagacttaattatagcactattattaaattttagcaaggattttttagaagataaaaaagagttgttgtaacatttaagctaccaacaactctttgatatagaattaatttata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aatattctccctctattactttatttatttttatatttatattttatatgaaatttaaagaaaagtaaataaaaagaaaattaaaaaagtctttgaaatttttaattcaaagactgtatattgataaaaatggtggagatgacgagagtcgaactcgtgtccgaaatcataatgaccataagcttctacaagtttagtttactattaaatttcgtaataattactcccgtaaacagggctaactaaaactatcctctaaaatgtcccataaacttagagaaatcatttatggtgatctatactagtcaacacctttgaaaaacccgtatagaataagttatccaaggtgtagctgaactaagcagctaaagcgtaatctttgtttccatctaaaagatgtgtttagtctctcacagcgacaagcctgacttgctacctataacctcacaaccccgtcgaaacctttgcatccccatatttaattgtagacttaattatagcactattattaaattttagcaaggattttttagaagataaaaaagagttgttgtaacatttaagctaccaacaactctttgatatagaattaatttata Predict ORF larger than 30AA ================================================ Protein_Len: 42 Strand: + Start: 69 End: 194 .................................................................... M K R K L K K S L K F L I Q R L Y I D K N G G D D E S R T R V R N H N D H K L L Q V ..................................................................................................................................................................................................................................................................................................................................................................................................................... Protein_Len: 42 Strand: + Start: 118 End: 243 ..................................................................................................................... M L I K M V E M T R V E L V S E I I M T I S F Y K F S L L L N F V I I T P V N R A N .................................................................................................................................................................................................................................................................................................................................................................... Protein_Len: 40 Strand: + Start: 397 End: 516 ............................................................................................................................................................................................................................................................................................................................................................................................................ M C L V S H S D K P D L L P I T S Q P R R N L C I P I F N C R L N Y S T I I K F ................................................................................... aatattctccctctattactttatttatttttatatttatattttatatgaaatttaaagaaaagtaaataaaaagaaaattaaaaaagtctttgaaatttttaattcaaagactgtatattgataaaaatggtggagatgacgagagtcgaactcgtgtccgaaatcataatgaccataagcttctacaagtttagtttactattaaatttcgtaataattactcccgtaaacagggctaactaaaactatcctctaaaatgtcccataaacttagagaaatcatttatggtgatctatactagtcaacacctttgaaaaacccgtatagaataagttatccaaggtgtagctgaactaagcagctaaagcgtaatctttgtttccatctaaaagatgtgtttagtctctcacagcgacaagcctgacttgctacctataacctcacaaccccgtcgaaacctttgcatccccatatttaattgtagacttaattatagcactattattaaattttagcaaggattttttagaagataaaaaagagttgttgtaacatttaagctaccaacaactctttgatatagaattaatttata 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: 88 Start: 494 End: 523 .............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................CTTGCTAAAATTTAATAATAGTGCTATAAT............................................................................ PromScan Matrix: RpoD-17 Strand: - Score: 84 Start: 41 End: 70 ........................................ATTTACTTTTCTTTAAATTTCATATAAAAT................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................. PromScan Matrix: RpoD-17 Strand: - Score: 81 Start: 513 End: 542 ................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................TTTTATCTTCTAAAAAATCCTTGCTAAAAT......................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aatattctccctctattactttatttatttttatatttatattttatatgaaatttaaagaaaagtaaataaaaagaaaattaaaaaagtctttgaaatttttaattcaaagactgtatattgataaaaatggtggagatgacgagagtcgaactcgtgtccgaaatcataatgaccataagcttctacaagtttagtttactattaaatttcgtaataattactcccgtaaacagggctaactaaaactatcctctaaaatgtcccataaacttagagaaatcatttatggtgatctatactagtcaacacctttgaaaaacccgtatagaataagttatccaaggtgtagctgaactaagcagctaaagcgtaatctttgtttccatctaaaagatgtgtttagtctctcacagcgacaagcctgacttgctacctataacctcacaaccccgtcgaaacctttgcatccccatatttaattgtagacttaattatagcactattattaaattttagcaaggattttttagaagataaaaaagagttgttgtaacatttaagctaccaacaactctttgatatagaattaatttata Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 95 HP_score: -7.7 Tail_Score: -5.52347 Start: 89 End: 114 Full_Region: ttttatcaatataca gtctttgaatt aaaa atttcaaagac ttttttaattttctt ........................................................................................gtctttgaattaaaaatttcaaagac..................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................... TransTerm Strand: + Conf: 55 HP_score: -4.3 Tail_Score: -3.84712 Start: 545 End: 577 Full_Region: TTAGAAGATAAAAAA GAGTTGTTGTAAC ATTTAA GCTACCAACAACTC TTTGATATAGAATTA ................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................GAGTTGTTGTAACATTTAAGCTACCAACAACTC...................... Find igs database================================================ Query_seq: FN0556:FN0557|FN0556:FN0557:hypothetical protein:hypothetical protein:<-<-:1209091..1209689 599 aatattctccctctattactttatttatttttatatttatattttatatgaaatttaaagaaaagtaaataaaaagaaaattaaaaaagtctttgaaatttttaattcaaagactgtatattgataaaaatggtggagatgacgagagtcgaactcgtgtccgaaatcataatgaccataagcttctacaagtttagtttactattaaatttcgtaataattactcccgtaaacagggctaactaaaactatcctctaaaatgtcccataaacttagagaaatcatttatggtgatctatactagtcaacacctttgaaaaacccgtatagaataagttatccaaggtgtagctgaactaagcagctaaagcgtaatctttgtttccatctaaaagatgtgtttagtctctcacagcgacaagcctgacttgctacctataacctcacaaccccgtcgaaacctttgcatccccatatttaattgtagacttaattatagcactattattaaattttagcaaggattttttagaagataaaaaagagttgttgtaacatttaagctaccaacaactctttgatatagaattaatttata Intra-Species Hit: Count: 1 Min: 89 Max: 599 Len: 511 Subject: NC_003454_FN0556_FN0557|hypothetical protein:hypothetical protein|NEGATIVE:NEGATIVE|[1209091,1209689]|599 HSP 1 e-value: 0.0 bit: 1013.0 Len: 511 Query Start:89 Query End:599 Subject Strand: POSITIVE Subject Start: 89 Subject End: 599 ........................................................................................gtctttgaaatttttaattcaaagactgtatattgataaaaatggtggagatgacgagagtcgaactcgtgtccgaaatcataatgaccataagcttctacaagtttagtttactattaaatttcgtaataattactcccgtaaacagggctaactaaaactatcctctaaaatgtcccataaacttagagaaatcatttatggtgatctatactagtcaacacctttgaaaaacccgtatagaataagttatccaaggtgtagctgaactaagcagctaaagcgtaatctttgtttccatctaaaagatgtgtttagtctctcacagcgacaagcctgacttgctacctataacctcacaaccccgtcgaaacctttgcatccccatatttaattgtagacttaattatagcactattattaaattttagcaaggattttttagaagataaaaaagagttgttgtaacatttaagctaccaacaactctttgatatagaattaatttata ........................................................................................gtctttgaaatttttaattcaaagactgtatattgataaaaatggtggagatgacgagagtcgaactcgtgtccgaaatcataatgaccataagcttctacaagtttagtttactattaaatttcgtaataattactcccgtaaacagggctaactaaaactatcctctaaaatgtcccataaacttagagaaatcatttatggtgatctatactagtcaacacctttgaaaaacccgtatagaataagttatccaaggtgtagctgaactaagcagctaaagcgtaatctttgtttccatctaaaagatgtgtttagtctctcacagcgacaagcctgacttgctacctataacctcacaaccccgtcgaaacctttgcatccccatatttaattgtagacttaattatagcactattattaaattttagcaaggattttttagaagataaaaaagagttgttgtaacatttaagctaccaacaactctttgatatagaattaatttata Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUCUUUGAAAUUUUUAAUUCAAAGACUGUAUAUUGAUAAAAAUGGUGGAGAUGACGAGAGUCGAACUCGUGUCCGAAAUCAUAAUGACCAUAAGCUUCUACAAGUUUAGUUUACUAUUAAAUUUCGUAAUAAUUACUCCCGUAAACAGGGCUAACUAAAACUAUCCUCUAAAAUGUCCCAUAAACUUAGAGAAAUCAUUUAUGGUGAUCUAUACUAGUCAACACCUUUGAAAAACCCGUAUAGAAUAAGUUAUCCAAGGUGUAGCUGAACUAAGCAGCUAAAGCGUAAUCUUUGUUUCCAUCUAAAAGAUGUGUUUAGUCUCUCACAGCGACAAGCCUGACUUGCUACCUAUAACCUCACAACCCCGUCGAAACCUUUGCAUCCCCAUAUUUAAUUGUAGACUUAAUUAUAGCACUAUUAUUAAAUUUUAGCAAGGAUUUUUUAGAAGAUAAAAAAGAGUUGUUGUAACAUUUAAGCUACCAACAACUCUUUGAUAUAGAAUUAAUUUAUA (((((((((........))))))))).(((.((((((....((((.((...((((....)))).....(((..((((((..(((((....(((((((....)))))))......))))).))))))..............((((...(((((......................((((((((((....((....)).))))))).)))........(((.(((((((.((..(((..((.....))..))).)).))))))).((((.(((((((.((....))...((((((...........))))))..)))))))......))))))).)))))...))))............)))..)))))).((((.((((((........(((((((.((((.((.......))..)))).)))))))....)))))).)))).......(((..((((((((((((((.(......).)).))))))))))))..)))...)))))).))). (-102.00) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAUAAAUUAAUUCUAUAUCAAAGAGUUGUUGGUAGCUUAAAUGUUACAACAACUCUUUUUUAUCUUCUAAAAAAUCCUUGCUAAAAUUUAAUAAUAGUGCUAUAAUUAAGUCUACAAUUAAAUAUGGGGAUGCAAAGGUUUCGACGGGGUUGUGAGGUUAUAGGUAGCAAGUCAGGCUUGUCGCUGUGAGAGACUAAACACAUCUUUUAGAUGGAAACAAAGAUUACGCUUUAGCUGCUUAGUUCAGCUACACCUUGGAUAACUUAUUCUAUACGGGUUUUUCAAAGGUGUUGACUAGUAUAGAUCACCAUAAAUGAUUUCUCUAAGUUUAUGGGACAUUUUAGAGGAUAGUUUUAGUUAGCCCUGUUUACGGGAGUAAUUAUUACGAAAUUUAAUAGUAAACUAAACUUGUAGAAGCUUAUGGUCAUUAUGAUUUCGGACACGAGUUCGACUCUCGUCAUCUCCACCAUUUUUAUCAAUAUACAGUCUUUGAAUUAAAAAUUUCAAAGAC ..........(((((((..((((((((((((.((((......)))))))))))))))).(((((((((((((..((((.(((...(((((((..(((.(((.......))))))..))))))).((((((..((.(((((....((((((.(((..(...((((((((.....((((..(((....(((((((.........)))))))..((....))..)))...))))..))))))))...)...)))))))))...)))))..(((((((.((((...((....))..)))).)))))))..........))...)))))))))....))))..))))))))))))).(((((((.((((((....)))).)).(((((((.......))))))).)))))))..)))))))....(((((....(((((.((((((....)))))).....)))))....)))))...............(((((((((........))))))))) (-126.00) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 697 50 1 229 180 NC_003454:FN0556|5end_hypothetical_protein_1209000..1209230_NEGATIVE 418 74 33 231 185 NC_003454:FN1563|5end_hypothetical_protein_85040..85270_NEGATIVE 339 389 349 223 186 NC_003454:FN1426|5end_Serine_protease_2095462..2095692_NEGATIVE 309 358 314 101 47 NC_003454:FN1591|5end_RNFB-related_protein_103135..103365_NEGATIVE 281 320 275 81 28 NC_003454:FN0421|5end_carbamoyl-phosphate_synthase_small_subunit_1061936..1062166_POSITIVE 266 358 312 210 142 NC_003454:FN1482|5end_Guanosine-3',5'-bis(Diphosphate)_3'-pyrophosphohydrolase_2165992..2166222_NEGATIVE 264 311 273 187 155 NC_003454:FN1126|5end_Acetyltransferase_1770287..1770517_NEGATIVE 262 178 136 85 50 NC_003454:FN1065|5end_hypothetical_protein_1711342..1711572_POSITIVE 262 430 381 150 97 NC_003454:FN0776|5end_asparagine_synthetase_AsnA_1431944..1432174_POSITIVE 257 293 253 70 32 NC_003454:FN1540|5end_Iron-sulfur_cluster-binding_protein_53055..53285_POSITIVE 253 484 441 55 9 NC_003454:FN1538|5end_Arsenical_pump-driving_ATPase_52299..52529_NEGATIVE 252 380 337 46 11 NC_003454:FN0476|5end_transcription_termination_factor_Rho_1123450..1123680_POSITIVE 250 298 257 55 2 NC_003454:FN1265|5end_Outer_membrane_protein_1921331..1921561_POSITIVE 247 380 337 213 169 NC_003454:FN1914|5end_Anti-sigma_F_factor_antagonist_411990..412220_NEGATIVE 247 278 234 188 142 NC_003454:FN1622|5end_Uridylate_kinase_129640..129870_POSITIVE 244 369 327 213 176 NC_003454:FN0909|5end_DNA_repair_protein_radC_1567654..1567884_NEGATIVE 242 363 321 112 63 NC_003454:FN1631|5end_SSU_ribosomal_protein_S14P_135247..135477_NEGATIVE 241 358 323 199 154 NC_003454:FN0082|5end_Ethanolamine_utilization_protein_eutM_720699..720929_POSITIVE 238 303 263 187 160 NC_003454:FN0780|5end_Hypothetical_membrane-spanning_protein_1437490..1437720_NEGATIVE 234 358 317 54 10 NC_003454:FN0006|5end_tRNA_modification_GTPase_644505..644735_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 309 358 314 74 20 NC_003454:FN1592|3end_Na(+)-translocating_NADH-quinone_reductase_subunit_D_103162..103312_NEGATIVE 281 320 275 63 10 NC_003454:FN0420|3end_dihydroorotase_1061998..1062148_POSITIVE 262 430 381 63 10 NC_003454:FN0775|3end_putative_aminopeptidase_2_1431937..1432087_POSITIVE 247 278 234 123 77 NC_003454:FN1621|3end_elongation_factor_Ts_129655..129805_POSITIVE 242 363 321 91 42 NC_003454:FN1632|3end_LSU_ribosomal_protein_L5P_135268..135418_NEGATIVE 234 358 317 48 4 NC_003454:FN0005|3end_Jag_protein_644579..644729_POSITIVE 231 300 252 75 24 NC_003454:FN1158|3end_hypothetical_protein_1814814..1814964_POSITIVE 228 386 348 63 19 NC_003454:FN1495|3end_hypothetical_protein_-89..61_NEGATIVE 228 497 451 76 29 NC_003454:FN0606|3end_Translation_initiation_inhibitor_1261519..1261669_POSITIVE 227 280 248 76 40 NC_003454:FN0950|3end_Precorrin-6X_reductase_1606975..1607125_NEGATIVE 225 170 136 84 43 NC_003454:FN0982|3end_bifunctional_phosphoribosylaminoimidazolecarboxamide_formyltransferase/IMP_cyclohydrolase_1634137..1634287_NEGATIVE 220 178 145 32 1 NC_003454:FN1064|3end_hypothetical_protein_1711369..1711519_POSITIVE 218 295 253 94 46 NC_003454:FN0898|3end_Spore_photoproduct_1558527..1558677_POSITIVE 218 492 452 86 53 NC_003454:FN0039|3end_DNA_primase_(bacterial_type)_and_small_primase-like_proteins_678661..678811_NEGATIVE 217 490 443 83 34 NC_003454:FN0762|3end_hypothetical_protein_1419744..1419894_NEGATIVE 216 357 312 71 20 NC_003454:FN0990|3end_Phosphoribosylformylglycinamidine_synthase_1641679..1641829_NEGATIVE 216 89 46 150 109 NC_003454:FN1553|3end_Transporter_67150..67300_NEGATIVE 214 350 308 98 51 NC_003454:FN0382|3end_hypothetical_protein_1014224..1014374_POSITIVE 214 489 443 55 3 NC_003454:FN1944|3end_Sodium-dependent_tryptophan_transporter_448026..448176_POSITIVE 212 490 446 80 37 NC_003454:FN1800|3end_Peptidyl-prolyl_cis-trans_isomerase_282534..282684_POSITIVE