Origin IGS: tcatctcttacctctctttttccctgtcggaaccggacggaaaggcaatagaggaggagaatatttctgatcaagatgaaaaggataataatgatcttgctgccggtt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aaccggcagcaagatcattattatccttttcatcttgatcagaaatattctcctcctctattgcctttccgtccggttccgacagggaaaaagagaggtaagagatga Mask Tandem Repeat Region ================================================ tcatctcttacctctctttttccctgtcggaaccggacggaaaggcaatagaggaggagaatatttctgatcaagatgaaaaggataataatgatcttgctgccggtt Find is-nt database================================================ Query_seq: PG1091:PG1093|PG1091:PG1093:DHH subfamily 1 protein:hypothetical protein:->->:1158153..1158260 108 tcatctcttacctctctttttccctgtcggaaccggacggaaaggcaatagaggaggagaatatttctgatcaagatgaaaaggataataatgatcttgctgccggtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG1091:PG1093|PG1091:PG1093:DHH subfamily 1 protein:hypothetical protein:->->:1158153..1158260 108 tcatctcttacctctctttttccctgtcggaaccggacggaaaggcaatagaggaggagaatatttctgatcaagatgaaaaggataataatgatcttgctgccggtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG1091:PG1093|PG1091:PG1093:DHH subfamily 1 protein:hypothetical protein:->->:1158153..1158260 108 tcatctcttacctctctttttccctgtcggaaccggacggaaaggcaatagaggaggagaatatttctgatcaagatgaaaaggataataatgatcttgctgccggtt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tcatctcttacctctctttttccctgtcggaaccggacggaaaggcaatagaggaggagaatatttctgatcaagatgaaaaggataataatgatcttgctgccggtt Predict ORF larger than 30AA ================================================ Protein_Len: 35 Strand: + Start: 3 End: 107 .. M S Y L S F S L S E P D G K A I E E E N I S D Q D E K D N N D L A A G . Protein_Len: 31 Strand: - Start: 3 End: 95 .. D R V E R K G Q R F R V S L C Y L L L I N R I L I F L I I I M ............. tcatctcttacctctctttttccctgtcggaaccggacggaaaggcaatagaggaggagaatatttctgatcaagatgaaaaggataataatgatcttgctgccggtt 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================================================ tcatctcttacctctctttttccctgtcggaaccggacggaaaggcaatagaggaggagaatatttctgatcaagatgaaaaggataataatgatcttgctgccggtt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PG1091:PG1093|PG1091:PG1093:DHH subfamily 1 protein:hypothetical protein:->->:1158153..1158260 108 tcatctcttacctctctttttccctgtcggaaccggacggaaaggcaatagaggaggagaatatttctgatcaagatgaaaaggataataatgatcttgctgccggtt Intra-Species Hit: Count: 1 Min: 1 Max: 108 Len: 108 Subject: NC_002950_PG1091_PG1093|DHH subfamily 1 protein:hypothetical protein|POSITIVE:POSITIVE|[1158153,1158260]|108 HSP 1 e-value: 4.0E-55 bit: 214.0 Len: 108 Query Start:1 Query End:108 Subject Strand: POSITIVE Subject Start: 1 Subject End: 108 tcatctcttacctctctttttccctgtcggaaccggacggaaaggcaatagaggaggagaatatttctgatcaagatgaaaaggataataatgatcttgctgccggtt tcatctcttacctctctttttccctgtcggaaccggacggaaaggcaatagaggaggagaatatttctgatcaagatgaaaaggataataatgatcttgctgccggtt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCAUCUCUUACCUCUCUUUUUCCCUGUCGGAACCGGACGGAAAGGCAAUAGAGGAGGAGAAUAUUUCUGAUCAAGAUGAAAAGGAUAAUAAUGAUCUUGCUGCCGGUU ...((((((.(((((.(((((((...(((....)))..)))))))....)))))))))))......(((..((((((.(............).))))))....))).. (-25.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AACCGGCAGCAAGAUCAUUAUUAUCCUUUUCAUCUUGAUCAGAAAUAUUCUCCUCCUCUAUUGCCUUUCCGUCCGGUUCCGACAGGGAAAAAGAGAGGUAAGAGAUGA ............(((((..................)))))........((((..(((((.((...((((((((.(....)))).))))).)).)))))...))))... (-21.67) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 434 60 20 51 4 NC_002950:PG1790|5end_hypothetical_protein_1880954..1881184_NEGATIVE 396 60 16 68 13 NC_002950:PG1750|5end_alpha-1,3/4-fucosidase,_putative_1835323..1835553_POSITIVE 370 67 24 80 23 NC_002950:PG0139|5end_membrane-bound_lytic_murein_transglycosylase_D,_putative_163141..163371_NEGATIVE 369 56 11 160 106 NC_002950:PG0124|5end_hypothetical_protein_146234..146464_NEGATIVE 355 60 11 74 22 NC_002950:PG0285|5end_hypothetical_protein_318459..318689_POSITIVE 353 69 23 79 39 NC_002950:PG2095|5end_lipoprotein,_putative_2200617..2200847_NEGATIVE 342 70 28 65 20 NC_002950:PG0926|5end_hypothetical_protein_984634..984864_NEGATIVE 341 57 17 229 192 NC_002950:PG1719|5end_ABC_transporter,_ATP-binding_protein,_MsbA_family_1806749..1806979_POSITIVE 332 64 22 91 48 NC_002950:PG0684|5end_ABC_transporter,_permease_protein,_putative_737648..737878_POSITIVE 331 46 8 144 99 NC_002950:PG1964|5end_bacterial_sugar_transferase_2052910..2053140_POSITIVE 327 58 12 60 3 NC_002950:PG0539|5end_efflux_transporter,_MFP_component,_RND_family_590574..590804_POSITIVE 326 59 11 65 21 NC_002950:PG1861|5end_hypothetical_protein_1960057..1960287_NEGATIVE 323 55 12 225 175 NC_002950:PG0767|5end_4-alpha-glucanotransferase_820533..820763_NEGATIVE 321 58 13 156 114 NC_002950:PG1903|5end_hypothetical_protein_2004221..2004451_NEGATIVE 319 60 14 80 21 NC_002950:PG1021|5end_hypothetical_protein_1083592..1083822_NEGATIVE 319 61 25 185 145 NC_002950:PG0980|5end_hypothetical_protein_1040897..1041127_POSITIVE 319 69 23 212 153 NC_002950:PG0638|5end_tetraacyldisaccharide_4'-kinase_691183..691413_NEGATIVE 319 40 1 229 188 NC_002950:PG0147|5end_hypothetical_protein_169667..169897_NEGATIVE 318 60 12 63 15 NC_002950:PG0320|5end_hypothetical_protein_353409..353639_POSITIVE 317 50 2 81 34 NC_002950:PG1212|5end_TPR_domain_protein_1291392..1291622_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 448 60 14 54 2 NC_002950:PG1791|3end_hypothetical_protein_1880951..1881101_NEGATIVE 392 60 21 133 95 NC_002950:PG0795|3end_hypothetical_protein_849603..849753_POSITIVE 370 67 24 70 13 NC_002950:PG0140|3end_hypothetical_protein_163151..163301_NEGATIVE 368 59 20 87 41 NC_002950:PG0173|3end_transcriptional_regulator,_putative_194388..194538_NEGATIVE 367 70 23 133 87 NC_002950:PG1742|3end_hypothetical_protein_1827506..1827656_POSITIVE 365 61 22 85 47 NC_002950:PG1854|3end_5-formyltetrahydrofolate_cyclo-ligase_family_protein_1953325..1953475_NEGATIVE 354 60 18 107 55 NC_002950:PG1022|3end_hypothetical_protein_1085098..1085248_POSITIVE 353 69 23 71 31 NC_002950:PG2096|3end_hypothetical_protein_2200625..2200775_NEGATIVE 353 60 17 124 84 NC_002950:PG1392|3end_rod_shape-determining_protein_RodA,_putative_1472959..1473109_NEGATIVE 345 60 13 87 31 NC_002950:PG1091|3end_DHH_subfamily_1_protein_1158092..1158242_POSITIVE 342 70 28 65 20 NC_002950:PG0927|3end_conserved_hypothetical_protein_TIGR00150_984634..984784_NEGATIVE 339 60 11 107 56 NC_002950:PG0349|3end_hydrolase,_haloacid_dehalogenase-like_family_385291..385441_POSITIVE 337 45 4 44 4 NC_002950:PG1330|3end_large_conductance_mechanosensitive_channel_protein_1410165..1410315_POSITIVE 332 64 22 64 21 NC_002950:PG0683|3end_ABC_transporter,_permease_protein,_putative_737701..737851_POSITIVE 331 46 8 147 102 NC_002950:PG1963|3end_Sua5/YciO/YrdC/YwlC_family_protein_2052993..2053143_POSITIVE 326 59 11 52 8 NC_002950:PG1862|3end_hypothetical_protein_1960070..1960220_NEGATIVE 319 61 25 70 30 NC_002950:PG0978|3end_shikimate_5-dehydrogenase_1040862..1041012_POSITIVE 317 50 2 68 21 NC_002950:PG1211|3end_hexapeptide_transferase_family_protein_1291459..1291609_POSITIVE 312 46 1 147 104 NC_002950:PG0125|3end_hypothetical_protein_146238..146388_NEGATIVE 309 68 28 111 75 NC_002950:PG0508|3end_HAD-superfamily_subfamily_IB_hydrolase,_TIGR01490_548136..548286_NEGATIVE