Origin IGS: tctctgcgcttcgatcgattaccaatccaagcaaagaggccgcgccaacaggtggcgcggcctctttctcatgttgtgagcccgagaaaagctgcttttctctgattggaaatttgaggattgctttcgtctcgtctctacctttttccactcaaaaggccttcgcctttcgtcaagattttccgactttaagtgtaatccttgtcg .........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 cgacaaggattacacttaaagtcggaaaatcttgacgaaaggcgaaggccttttgagtggaaaaaggtagagacgagacgaaagcaatcctcaaatttccaatcagagaaaagcagcttttctcgggctcacaacatgagaaagaggccgcgccacctgttggcgcggcctctttgcttggattggtaatcgatcgaagcgcagaga Mask Tandem Repeat Region ================================================ tctctgcgcttcgatcgattaccaatccaagcaaagaggccgcgccaacaggtggcgcggcctctttctcatgttgtgagcccgagaaaagctgcttttctctgattggaaatttgaggattgctttcgtctcgtctctacctttttccactcaaaaggccttcgcctttcgtcaagattttccgactttaagtgtaatccttgtcg Find is-nt database================================================ Query_seq: PG0933:PG0934|PG0933:PG0934:translation elongation factor G, putative:hypothetical protein:-><-:992297..992503 207 tctctgcgcttcgatcgattaccaatccaagcaaagaggccgcgccaacaggtggcgcggcctctttctcatgttgtgagcccgagaaaagctgcttttctctgattggaaatttgaggattgctttcgtctcgtctctacctttttccactcaaaaggccttcgcctttcgtcaagattttccgactttaagtgtaatccttgtcg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG0933:PG0934|PG0933:PG0934:translation elongation factor G, putative:hypothetical protein:-><-:992297..992503 207 tctctgcgcttcgatcgattaccaatccaagcaaagaggccgcgccaacaggtggcgcggcctctttctcatgttgtgagcccgagaaaagctgcttttctctgattggaaatttgaggattgctttcgtctcgtctctacctttttccactcaaaaggccttcgcctttcgtcaagattttccgactttaagtgtaatccttgtcg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG0933:PG0934|PG0933:PG0934:translation elongation factor G, putative:hypothetical protein:-><-:992297..992503 207 tctctgcgcttcgatcgattaccaatccaagcaaagaggccgcgccaacaggtggcgcggcctctttctcatgttgtgagcccgagaaaagctgcttttctctgattggaaatttgaggattgctttcgtctcgtctctacctttttccactcaaaaggccttcgcctttcgtcaagattttccgactttaagtgtaatccttgtcg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tctctgcgcttcgatcgattaccaatccaagcaaagaggccgcgccaacaggtggcgcggcctctttctcatgttgtgagcccgagaaaagctgcttttctctgattggaaatttgaggattgctttcgtctcgtctctacctttttccactcaaaaggccttcgcctttcgtcaagattttccgactttaagtgtaatccttgtcg Predict ORF larger than 30AA ================================================ Protein_Len: 33 Strand: + Start: 4 End: 102 ... M R F D R L P I Q A K R P R Q Q V A R P L S H V V S P R K A A F L ......................................................................................................... Protein_Len: 38 Strand: + Start: 92 End: 205 ........................................................................................... M L F S D W K F E D C F R L V S T F F H S K G L R L S S R F S D F K C N P C .. Protein_Len: 60 Strand: + Start: 18 End: 206 ................. M T N P S K E A A P T G G A A S F S C C E P E K S C F S L I G N L R I A F V S S L P F S T Q K A F A F R Q D F P T L S V . Protein_Len: 50 Strand: - Start: 2 End: 151 . E A S R D I V L G L L S A A G V P P A A E K E H Q S G S F L Q K E R I P F K L I A K T E D R G K E M ........................................................ tctctgcgcttcgatcgattaccaatccaagcaaagaggccgcgccaacaggtggcgcggcctctttctcatgttgtgagcccgagaaaagctgcttttctctgattggaaatttgaggattgctttcgtctcgtctctacctttttccactcaaaaggccttcgcctttcgtcaagattttccgactttaagtgtaatccttgtcg 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================================================ tctctgcgcttcgatcgattaccaatccaagcaaagaggccgcgccaacaggtggcgcggcctctttctcatgttgtgagcccgagaaaagctgcttttctctgattggaaatttgaggattgctttcgtctcgtctctacctttttccactcaaaaggccttcgcctttcgtcaagattttccgactttaagtgtaatccttgtcg Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 100 HP_score: -21.8 Tail_Score: -4.08571 Start: 36 End: 64 Full_Region: ACCAATCCAAGCAAA GAGGCCGCGCCA ACAGG TGGCGCGGCCTC TTTCTCATGTTGTGA ...................................GAGGCCGCGCCAACAGGTGGCGCGGCCTC............................................................................................................................................... TransTerm Strand: - Conf: 100 HP_score: -21.8 Tail_Score: -3.96387 Start: 36 End: 64 Full_Region: tcacaacatgagaaa gaggccgcgcca cctgt tggcgcggcctc tttgcttggattggt ...................................gaggccgcgccacctgttggcgcggcctc............................................................................................................................................... Find igs database================================================ Query_seq: PG0933:PG0934|PG0933:PG0934:translation elongation factor G, putative:hypothetical protein:-><-:992297..992503 207 tctctgcgcttcgatcgattaccaatccaagcaaagaggccgcgccaacaggtggcgcggcctctttctcatgttgtgagcccgagaaaagctgcttttctctgattggaaatttgaggattgctttcgtctcgtctctacctttttccactcaaaaggccttcgcctttcgtcaagattttccgactttaagtgtaatccttgtcg Intra-Species Hit: Count: 1 Min: 1 Max: 207 Len: 207 Subject: NC_002950_PG0933_PG0934|translation elongation factor G, putative:hypothetical protein|POSITIVE:NEGATIVE|[992297,992503]|207 HSP 1 e-value: 1.0E-114 bit: 410.0 Len: 207 Query Start:1 Query End:207 Subject Strand: POSITIVE Subject Start: 1 Subject End: 207 tctctgcgcttcgatcgattaccaatccaagcaaagaggccgcgccaacaggtggcgcggcctctttctcatgttgtgagcccgagaaaagctgcttttctctgattggaaatttgaggattgctttcgtctcgtctctacctttttccactcaaaaggccttcgcctttcgtcaagattttccgactttaagtgtaatccttgtcg tctctgcgcttcgatcgattaccaatccaagcaaagaggccgcgccaacaggtggcgcggcctctttctcatgttgtgagcccgagaaaagctgcttttctctgattggaaatttgaggattgctttcgtctcgtctctacctttttccactcaaaaggccttcgcctttcgtcaagattttccgactttaagtgtaatccttgtcg Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCUCUGCGCUUCGAUCGAUUACCAAUCCAAGCAAAGAGGCCGCGCCAACAGGUGGCGCGGCCUCUUUCUCAUGUUGUGAGCCCGAGAAAAGCUGCUUUUCUCUGAUUGGAAAUUUGAGGAUUGCUUUCGUCUCGUCUCUACCUUUUUCCACUCAAAAGGCCUUCGCCUUUCGUCAAGAUUUUCCGACUUUAAGUGUAAUCCUUGUCG ...........((((.((((.((((((.....(((((((((((((((.....)))))))))))))))(((((...)))))...((((((((...)))))))).)))))).)))).(((((((((..............................((((((....)))))).(((..........))).......))))))))))))) (-66.10) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CGACAAGGAUUACACUUAAAGUCGGAAAAUCUUGACGAAAGGCGAAGGCCUUUUGAGUGGAAAAAGGUAGAGACGAGACGAAAGCAAUCCUCAAAUUUCCAAUCAGAGAAAAGCAGCUUUUCUCGGGCUCACAACAUGAGAAAGAGGCCGCGCCACCUGUUGGCGCGGCCUCUUUGCUUGGAUUGGUAAUCGAUCGAAGCGCAGAGA ......(((...(((((((.(((((......)))))..(((((....))))))))))))..........(((..((..(....)...))))).....))).....((((((((...))))))))...(((..........(((((((((((((((.....)))))))))))))))((((.(((((.....))))).))))...))). (-77.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 447 76 31 87 21 NC_002950:PG0452|5end_hypothetical_protein_492879..493109_POSITIVE 432 170 121 72 26 NC_002950:PG0930|5end_hypothetical_protein_987542..987772_NEGATIVE 411 70 25 151 98 NC_002950:PG0767|5end_4-alpha-glucanotransferase_820533..820763_NEGATIVE 411 76 32 71 23 NC_002950:PG0282|5end_ABC_transporter,_ATP-binding_protein_316915..317145_NEGATIVE 408 89 45 105 46 NC_002950:PG1703|5end_MazG_family_protein_1790753..1790983_NEGATIVE 403 80 34 184 125 NC_002950:PG0166|5end_peptidyl-tRNA_hydrolase_188370..188600_NEGATIVE 398 78 36 129 84 NC_002950:PG0026|5end_hypothetical_protein_29234..29464_POSITIVE 394 61 22 72 20 NC_002950:PG1009|5end_hypothetical_protein_1068495..1068725_NEGATIVE 386 70 21 83 34 NC_002950:PG2037|5end_hypothetical_protein_2137812..2138042_NEGATIVE 386 80 31 215 170 NC_002950:PG1946|5end_ABC_3_transporter_family_protein_2032133..2032363_POSITIVE 381 86 41 212 157 NC_002950:PG1043|5end_ferrous_iron_transport_protein_B_1112852..1113082_NEGATIVE 380 86 43 197 146 NC_002950:PG0339|5end_hypothetical_protein_375062..375292_POSITIVE 376 85 44 142 96 NC_002950:PG1403|5end_rhomboid_family_protein_1487039..1487269_NEGATIVE 375 62 27 109 73 NC_002950:PG0039|5end_hypothetical_protein_47637..47867_POSITIVE 369 59 11 211 154 NC_002950:PG0351|5end_hypothetical_protein_386774..387004_POSITIVE 360 80 38 178 134 NC_002950:PG1959|5end_ribosomal_protein_L33_2048405..2048635_NEGATIVE 359 86 42 149 102 NC_002950:PG2146|5end_hypothetical_protein_2253815..2254045_POSITIVE 359 85 41 193 148 NC_002950:PG0636|5end_MATE_efflux_family_protein_689071..689301_NEGATIVE 358 86 42 151 109 NC_002950:PG2033|5end_glutamate_synthase,_small_subunit_2134803..2135033_NEGATIVE 357 61 36 33 11 NC_002950:PG1872|5end_urocanate_hydratase_1968911..1969141_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 621 69 30 61 22 NC_002950:PG0933|3end_translation_elongation_factor_G,_putative_992236..992386_POSITIVE 433 69 35 54 2 NC_002950:PG0707|3end_TonB-dependent_receptor,_putative_761086..761236_NEGATIVE 433 77 31 94 46 NC_002950:PG0686|3end_hypothetical_protein_741131..741281_NEGATIVE 411 62 24 123 84 NC_002950:PG0746|3end_sensor_histidine_kinase_792536..792686_NEGATIVE 408 89 45 87 28 NC_002950:PG1704|3end_thiol:disulfide_interchange_protein_dsbD,_putative_1790771..1790921_NEGATIVE 397 87 41 49 6 NC_002950:PG1675|3end_hypothetical_protein_1760360..1760510_POSITIVE 394 70 22 111 53 NC_002950:PG2037|3end_hypothetical_protein_2137591..2137741_NEGATIVE 394 61 22 58 6 NC_002950:PG1010|3end_ABC_transporter,_ATP-binding_protein_1068509..1068659_NEGATIVE 389 77 31 55 4 NC_002950:PG1809|3end_2-oxoglutarate_oxidoreductase,_gamma_subunit_1905491..1905641_NEGATIVE 386 70 21 86 37 NC_002950:PG2038|3end_N-acetylmuramoyl-L-alanine_amidase,_putative_2137809..2137959_NEGATIVE 386 82 42 52 7 NC_002950:PG1392|3end_rod_shape-determining_protein_RodA,_putative_1472959..1473109_NEGATIVE 378 78 31 151 101 NC_002950:PG0028|3end_2C-methyl-D-erythritol_2,4-cyclodiphosphate_synthase_34431..34581_POSITIVE 377 134 91 60 5 NC_002950:PG2107|3end_thiamine_biosynthesis_protein_ThiH_2215546..2215696_NEGATIVE 376 85 44 110 64 NC_002950:PG1404|3end_rhomboid_family_protein_1487071..1487221_NEGATIVE 374 66 24 63 13 NC_002950:PG0775|3end_acyl-CoA_dehydrogenase_family_protein_827432..827582_NEGATIVE 371 67 29 42 3 NC_002950:PG1297|3end_ribosomal_protein_S1_1377710..1377860_POSITIVE 358 86 42 44 2 NC_002950:PG2034|3end_oxidoreductase,_FAD-binding,_putative_2134910..2135060_NEGATIVE 352 95 51 99 42 NC_002950:PG1855|3end_carboxyl-terminal_protease_1953842..1953992_NEGATIVE 351 70 22 69 9 NC_002950:PG1421|3end_ferredoxin,_4Fe-4S_1506874..1507024_NEGATIVE 349 83 49 151 118 NC_002950:PG0656|3end_50S_ribosomal_protein_L34_706945..707095_NEGATIVE