Origin IGS: gcaaaaacttctaatttatattccccctgcagcaacttgcttgctctgctgcataaccgacacgatcggagccattcgtccgagggggaaaaaccttggttcacaaaggtaacttatttcta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tagaaataagttacctttgtgaaccaaggtttttccccctcggacgaatggctccgatcgtgtcggttatgcagcagagcaagcaagttgctgcagggggaatataaattagaagtttttgc Mask Tandem Repeat Region ================================================ gcaaaaacttctaatttatattccccctgcagcaacttgcttgctctgctgcataaccgacacgatcggagccattcgtccgagggggaaaaaccttggttcacaaaggtaacttatttcta Find is-nt database================================================ Query_seq: PG1370:PG1371|PG1370:PG1371:lysyl-tRNA synthetase:phosphorylase family protein:<-<-:1452320..1452441 122 gcaaaaacttctaatttatattccccctgcagcaacttgcttgctctgctgcataaccgacacgatcggagccattcgtccgagggggaaaaaccttggttcacaaaggtaacttatttcta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG1370:PG1371|PG1370:PG1371:lysyl-tRNA synthetase:phosphorylase family protein:<-<-:1452320..1452441 122 gcaaaaacttctaatttatattccccctgcagcaacttgcttgctctgctgcataaccgacacgatcggagccattcgtccgagggggaaaaaccttggttcacaaaggtaacttatttcta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG1370:PG1371|PG1370:PG1371:lysyl-tRNA synthetase:phosphorylase family protein:<-<-:1452320..1452441 122 gcaaaaacttctaatttatattccccctgcagcaacttgcttgctctgctgcataaccgacacgatcggagccattcgtccgagggggaaaaaccttggttcacaaaggtaacttatttcta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gcaaaaacttctaatttatattccccctgcagcaacttgcttgctctgctgcataaccgacacgatcggagccattcgtccgagggggaaaaaccttggttcacaaaggtaacttatttcta Predict ORF larger than 30AA ================================================ Protein_Len: 32 Strand: + Start: 14 End: 109 ............. M Y I P P A A T C L L C C I T D T I G A I R P R G K N L G S Q R ............. Protein_Len: 33 Strand: - Start: 19 End: 117 .................. I G G A A V Q K S Q Q M V S V I P A M R G L P F F R P E C L Y S M ..... Protein_Len: 34 Strand: - Start: 3 End: 104 .. F V E L K Y E G Q L L K S A R S C L R C S R L W E D S P S F G Q N M .................. gcaaaaacttctaatttatattccccctgcagcaacttgcttgctctgctgcataaccgacacgatcggagccattcgtccgagggggaaaaaccttggttcacaaaggtaacttatttcta 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================================================ gcaaaaacttctaatttatattccccctgcagcaacttgcttgctctgctgcataaccgacacgatcggagccattcgtccgagggggaaaaaccttggttcacaaaggtaacttatttcta Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PG1370:PG1371|PG1370:PG1371:lysyl-tRNA synthetase:phosphorylase family protein:<-<-:1452320..1452441 122 gcaaaaacttctaatttatattccccctgcagcaacttgcttgctctgctgcataaccgacacgatcggagccattcgtccgagggggaaaaaccttggttcacaaaggtaacttatttcta Intra-Species Hit: Count: 1 Min: 1 Max: 122 Len: 122 Subject: NC_002950_PG1370_PG1371|lysyl-tRNA synthetase:phosphorylase family protein|NEGATIVE:NEGATIVE|[1452320,1452441]|122 HSP 1 e-value: 2.0E-63 bit: 242.0 Len: 122 Query Start:1 Query End:122 Subject Strand: POSITIVE Subject Start: 1 Subject End: 122 gcaaaaacttctaatttatattccccctgcagcaacttgcttgctctgctgcataaccgacacgatcggagccattcgtccgagggggaaaaaccttggttcacaaaggtaacttatttcta gcaaaaacttctaatttatattccccctgcagcaacttgcttgctctgctgcataaccgacacgatcggagccattcgtccgagggggaaaaaccttggttcacaaaggtaacttatttcta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GCAAAAACUUCUAAUUUAUAUUCCCCCUGCAGCAACUUGCUUGCUCUGCUGCAUAACCGACACGAUCGGAGCCAUUCGUCCGAGGGGGAAAAACCUUGGUUCACAAAGGUAACUUAUUUCUA ....................((((((((((((((............))))))....((((.....)))).............))))))))..(((((........)))))............ (-32.10) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAGAAAUAAGUUACCUUUGUGAACCAAGGUUUUUCCCCCUCGGACGAAUGGCUCCGAUCGUGUCGGUUAUGCAGCAGAGCAAGCAAGUUGCUGCAGGGGGAAUAUAAAUUAGAAGUUUUUGC (((((((.....(((((.(....).)))))..(((((((.(((((((.((....)).)))).)))....((((((((.(....)...)))))))))))))))............))))))). (-37.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 1089 90 41 181 132 NC_002950:PG1370|5end_lysyl-tRNA_synthetase_1452229..1452459_NEGATIVE 416 90 41 58 7 NC_002950:PG1312|5end_capA_protein,_putative_1390286..1390516_POSITIVE 414 89 41 160 106 NC_002950:PG2034|5end_oxidoreductase,_FAD-binding,_putative_2135701..2135931_NEGATIVE 414 78 32 60 10 NC_002950:PG1675|5end_hypothetical_protein_1760182..1760412_POSITIVE 397 79 36 204 142 NC_002950:PG1855|5end_carboxyl-terminal_protease_1955476..1955706_NEGATIVE 388 100 57 210 152 NC_002950:PG0635|5end_ribosomal_protein_L11_methyltransferase_687773..688003_NEGATIVE 387 88 41 201 145 NC_002950:PG0986|5end_hypothetical_protein_1047426..1047656_POSITIVE 386 88 42 121 58 NC_002950:PG0145|5end_hypothetical_protein_167831..168061_POSITIVE 384 100 51 168 122 NC_002950:PG1333|5end_hypothetical_protein_1415425..1415655_NEGATIVE 377 90 43 124 72 NC_002950:PG1695|5end_hypothetical_protein_1779440..1779670_POSITIVE 363 88 41 139 78 NC_002950:PG1727|5end_yitL_protein_1816709..1816939_POSITIVE 361 78 35 51 1 NC_002950:PG0120|5end_UDP-N-acetylglucosamine_2-epimerase_143004..143234_POSITIVE 358 99 57 211 169 NC_002950:PG1743|5end_2-dehydro-3-deoxyphosphooctonate_aldolase_1828348..1828578_NEGATIVE 354 100 51 83 32 NC_002950:PG2054|5end_lipoprotein_PG3_2152014..2152244_NEGATIVE 354 69 24 75 24 NC_002950:PG0223|5end_exonuclease_257610..257840_NEGATIVE 354 80 31 183 141 NC_002950:PG0086|5end_ATP-dependent_RNA_helicase,_DEAD/DEAH_box_family_102359..102589_NEGATIVE 353 89 44 196 136 NC_002950:PG1754|5end_hypothetical_protein_1839679..1839909_POSITIVE 353 117 71 194 150 NC_002950:PG1688|5end_transcription_elongation_factor_GreA_1774686..1774916_NEGATIVE 353 97 59 46 5 NC_002950:PG1338|5end_umuC_protein_1418246..1418476_POSITIVE 351 80 36 62 17 NC_002950:PG2065|5end_conserved_hypothetical_protein_TIGR00048_2161000..2161230_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 462 86 41 80 36 NC_002950:PG2140|3end_ribosomal_protein_L32_2246399..2246549_POSITIVE 401 68 21 145 105 NC_002950:PG0443|3end_hemagglutinin-related_protein_483147..483297_POSITIVE 383 80 36 85 32 NC_002950:PG1162|3end_ATP:cob(I)alamin_adenosyltransferase,_putative_1241473..1241623_NEGATIVE 363 88 41 129 68 NC_002950:PG1726|3end_PDZ_domain_protein_1816779..1816929_POSITIVE 354 69 24 71 20 NC_002950:PG0224|3end_hypothetical_protein_257614..257764_NEGATIVE 347 80 37 102 51 NC_002950:PG1972|3end_hemagglutinin_protein_HagB_2061203..2061353_POSITIVE 344 88 42 41 1 NC_002950:PG0959|3end_ATP-binding_protein,_Mrp/Nbp35_family_1020023..1020173_NEGATIVE 342 80 31 85 13 NC_002950:PG0439|3end_hypothetical_protein_478810..478960_POSITIVE 342 86 43 88 50 NC_002950:PG0148|3end_sigma-54-dependent_transcriptional_regulator_169654..169804_NEGATIVE 340 106 62 45 1 NC_002950:PG1337|3end_umuD_protein_1418318..1418468_POSITIVE 338 69 21 146 95 NC_002950:PG0198|3end_hypothetical_protein_237501..237651_POSITIVE 338 70 21 148 95 NC_002950:PG0170|3end_methionyl-tRNA_synthetase_191774..191924_POSITIVE 337 78 32 61 2 NC_002950:PG1541|3end_2-amino-4-hydroxy-6-_hydroxymethyldihydropteridine_pyrophosphokinase_1620855..1621005_POSITIVE 336 69 21 108 60 NC_002950:PG1600|3end_hypothetical_protein_1679959..1680109_NEGATIVE 336 78 37 150 105 NC_002950:PG0226|3end_transglutaminase-related_protein_259838..259988_NEGATIVE 335 51 18 69 36 NC_002950:PG0114|3end_hypothetical_protein_137998..138148_POSITIVE 330 89 53 77 31 NC_002950:PG1494|3end_hypothetical_protein_1571234..1571384_POSITIVE 330 88 47 143 102 NC_002950:PG0288|3end_lipoprotein,_putative_323010..323160_POSITIVE 328 89 48 142 90 NC_002950:PG2091|3end_dihydroneopterin_aldolase_2191610..2191760_POSITIVE 328 88 43 82 25 NC_002950:PG1876|3end_hypothetical_protein_1970633..1970783_NEGATIVE