Origin IGS: tgcccggagtcaagctcagcaaacagcgtggttaaggcttcattaacttacatcacaacaggtttgaggtaaaccaatgaaggtactcatttagtataacactttcagcctacaagtcaataaaaaatgctcaaaaaattgtactttttttaaaaatatcacaggaagataccattttggtaaaaaaatattcggaattctataaataagcaagctattctgtattttatagatgaaatttaaatgaaaaaagagtatgatagatacatactttggaggaatctaaactt .........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 aagtttagattcctccaaagtatgtatctatcatactcttttttcatttaaatttcatctataaaatacagaatagcttgcttatttatagaattccgaatatttttttaccaaaatggtatcttcctgtgatatttttaaaaaaagtacaattttttgagcattttttattgacttgtaggctgaaagtgttatactaaatgagtaccttcattggtttacctcaaacctgttgtgatgtaagttaatgaagccttaaccacgctgtttgctgagcttgactccgggca Mask Tandem Repeat Region ================================================ tgcccggagtcaagctcagcaaacagcgtggttaaggcttcattaacttacatcacaacaggtttgaggtaaaccaatgaaggtactcatttagtataacactttcagcctacaagtcaataaaaaatgctcaaaaaattgtactttttttaaaaatatcacaggaagataccattttggtaaaaaaatattcggaattctataaataagcaagctattctgtattttatagatgaaatttaaatgaaaaaagagtatgatagatacatactttggaggaatctaaactt Find is-nt database================================================ Query_seq: SSA_1774:SSA_1775|SSA_1774:SSA_1775:RRNA methylase, putative:Potassium uptake protein, Trk family, putative:<-->:1761134..1761423 290 tgcccggagtcaagctcagcaaacagcgtggttaaggcttcattaacttacatcacaacaggtttgaggtaaaccaatgaaggtactcatttagtataacactttcagcctacaagtcaataaaaaatgctcaaaaaattgtactttttttaaaaatatcacaggaagataccattttggtaaaaaaatattcggaattctataaataagcaagctattctgtattttatagatgaaatttaaatgaaaaaagagtatgatagatacatactttggaggaatctaaactt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1774:SSA_1775|SSA_1774:SSA_1775:RRNA methylase, putative:Potassium uptake protein, Trk family, putative:<-->:1761134..1761423 290 tgcccggagtcaagctcagcaaacagcgtggttaaggcttcattaacttacatcacaacaggtttgaggtaaaccaatgaaggtactcatttagtataacactttcagcctacaagtcaataaaaaatgctcaaaaaattgtactttttttaaaaatatcacaggaagataccattttggtaaaaaaatattcggaattctataaataagcaagctattctgtattttatagatgaaatttaaatgaaaaaagagtatgatagatacatactttggaggaatctaaactt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1774:SSA_1775|SSA_1774:SSA_1775:RRNA methylase, putative:Potassium uptake protein, Trk family, putative:<-->:1761134..1761423 290 tgcccggagtcaagctcagcaaacagcgtggttaaggcttcattaacttacatcacaacaggtttgaggtaaaccaatgaaggtactcatttagtataacactttcagcctacaagtcaataaaaaatgctcaaaaaattgtactttttttaaaaatatcacaggaagataccattttggtaaaaaaatattcggaattctataaataagcaagctattctgtattttatagatgaaatttaaatgaaaaaagagtatgatagatacatactttggaggaatctaaactt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgcccggagtcaagctcagcaaacagcgtggttaaggcttcattaacttacatcacaacaggtttgaggtaaaccaatgaaggtactcatttagtataacactttcagcctacaagtcaataaaaaatgctcaaaaaattgtactttttttaaaaatatcacaggaagataccattttggtaaaaaaatattcggaattctataaataagcaagctattctgtattttatagatgaaatttaaatgaaaaaagagtatgatagatacatactttggaggaatctaaactt Predict ORF larger than 30AA ================================================ Protein_Len: 37 Strand: + Start: 96 End: 206 ............................................................................................... M T L S A Y K S I K N A Q K I V L F L K I S Q E D T I L V K K Y S E F Y K .................................................................................... Protein_Len: 60 Strand: - Start: 94 End: 282 ............................................................................................. K L R C T L L F H E F F Q V K K L F I V P L Y W K P L F I N P I R Y I L L S N Q I K Y I F N L H F F L I I S V Y K P P M ........ tgcccggagtcaagctcagcaaacagcgtggttaaggcttcattaacttacatcacaacaggtttgaggtaaaccaatgaaggtactcatttagtataacactttcagcctacaagtcaataaaaaatgctcaaaaaattgtactttttttaaaaatatcacaggaagataccattttggtaaaaaaatattcggaattctataaataagcaagctattctgtattttatagatgaaatttaaatgaaaaaagagtatgatagatacatactttggaggaatctaaactt 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================================================ tgcccggagtcaagctcagcaaacagcgtggttaaggcttcattaacttacatcacaacaggtttgaggtaaaccaatgaaggtactcatttagtataacactttcagcctacaagtcaataaaaaatgctcaaaaaattgtactttttttaaaaatatcacaggaagataccattttggtaaaaaaatattcggaattctataaataagcaagctattctgtattttatagatgaaatttaaatgaaaaaagagtatgatagatacatactttggaggaatctaaactt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_1774:SSA_1775|SSA_1774:SSA_1775:RRNA methylase, putative:Potassium uptake protein, Trk family, putative:<-->:1761134..1761423 290 tgcccggagtcaagctcagcaaacagcgtggttaaggcttcattaacttacatcacaacaggtttgaggtaaaccaatgaaggtactcatttagtataacactttcagcctacaagtcaataaaaaatgctcaaaaaattgtactttttttaaaaatatcacaggaagataccattttggtaaaaaaatattcggaattctataaataagcaagctattctgtattttatagatgaaatttaaatgaaaaaagagtatgatagatacatactttggaggaatctaaactt Intra-Species Hit: Count: 1 Min: 1 Max: 290 Len: 290 Subject: NC_009009_SSA_1774_SSA_1775|RRNA methylase, putative:Potassium uptake protein, Trk family, putative|NEGATIVE:POSITIVE|[1761134,1761423]|290 HSP 1 e-value: 1.0E-138 bit: 492.0 Len: 290 Query Start:1 Query End:290 Subject Strand: POSITIVE Subject Start: 1 Subject End: 290 tgcccggagtcaagctcagcaaacagcgtggttaaggcttcattaacttacatcacaacaggtttgaggtaaaccaatgaaggtactcatttagtataacactttcagcctacaagtcaataaaaaatgctcaaaaaattgtacnnnnnnnaaaaatatcacaggaagataccattttggtnnnnnnntattcggaattctataaataagcaagctattctgtattttatagatgaaatttaaatgaaaaaagagtatgatagatacatactttggaggaatctaaactt tgcccggagtcaagctcagcaaacagcgtggttaaggcttcattaacttacatcacaacaggtttgaggtaaaccaatgaaggtactcatttagtataacactttcagcctacaagtcaataaaaaatgctcaaaaaattgtactttttttaaaaatatcacaggaagataccattttggtaaaaaaatattcggaattctataaataagcaagctattctgtattttatagatgaaatttaaatgaaaaaagagtatgatagatacatactttggaggaatctaaactt Inter-species Hit: Count: 2 Min: 1 Max: 108 Len: 108 Subject: smit_SMT_1931_SMT_1932|23S rRNA methyltransferase:K02008 cobalt transport system permease protein|NEGATIVE:NEGATIVE|[1871069,1871260]|192 HSP 1 e-value: 6.0E-26 bit: 119.0 Len: 108 Query Start:1 Query End:108 Subject Strand: POSITIVE Subject Start: 40 Subject End: 147 tgcccggagtcaagctcagcaaacagcgtggttaaggcttcattaacttacatcacaacaggtttgaggtaaaccaatgaaggtactcatttagtataacactttcag...................................................................................................................................................................................... tgcccggagtcaagctcagcaaacagcgtggttaaggcatcgttaacttacctcacaacaggtttgaagtaaatcagcgaaactactttcttagtataacactttcag...................................................................................................................................................................................... Subject: NC_003028_SP_0484_SP_0486|hypothetical protein:RNA methyltransferase, TrmH family|POSITIVE:POSITIVE|[466403,466594]|192 HSP 1 e-value: 6.0E-26 bit: 119.0 Len: 108 Query Start:1 Query End:108 Subject Strand: NEGATIVE Subject Start: 46 Subject End: 153 tgcccggagtcaagctcagcaaacagcgtggttaaggcttcattaacttacatcacaacaggtttgaggtaaaccaatgaaggtactcatttagtataacactttcag...................................................................................................................................................................................... tgcccggagtcaagctcagcaaacagcgtggttaaggcatcgttaacttacctcacaacaggtttgaagtaaatcagcgaaactactttcttagtataacactttcag...................................................................................................................................................................................... Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGCCCGGAGUCAAGCUCAGCAAACAGCGUGGUUAAGGCUUCAUUAACUUACAUCACAACAGGUUUGAGGUAAACCAAUGAAGGUACUCAUUUAGUAUAACACUUUCAG (((...(((.....))).))).......(((((...((((((..(((((..........))))))))))).))))).((((((((((.....))).....))))))). (-21.10) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUGAAAGUGUUAUACUAAAUGAGUACCUUCAUUGGUUUACCUCAAACCUGUUGUGAUGUAAGUUAAUGAAGCCUUAACCACGCUGUUUGCUGAGCUUGACUCCGGGCA .....(((((..((((.....)))).(((((((..(((((.(((.........))).)))))..)))))))........))))).........(((((....))))). (-23.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 973 50 1 141 92 NC_009009:SSA_1774|5end_RRNA_methylase,_putative_1761043..1761273_NEGATIVE 370 40 1 57 7 NC_009009:SSA_2020|5end_hypothetical_protein_2019284..2019514_POSITIVE 343 50 2 55 10 NC_009009:SSA_0385|5end_ABC_transporter,_glycine-betaine/proline_permease_protein,_putative_380250..380480_NEGATIVE 334 39 1 56 12 NC_009009:SSA_0584|5end_hypothetical_protein_575806..576036_POSITIVE 328 39 4 55 25 NC_009009:SSA_0793|5end_DNA-entry_nuclease,_putative_774859..775089_POSITIVE 327 39 1 77 28 NC_009009:SSA_1466|5end_Prephenate_dehydrogenase,_putative_1473111..1473341_NEGATIVE 299 41 4 48 1 NC_009009:SSA_2118|5end_Thiamine_pyrophosphokinase,_putative_2120500..2120730_NEGATIVE 297 46 4 220 177 NC_009009:SSA_0040|5end_Phosphoribosylaminoimidazole_carboxylase,_ATPase_subunit,_putative_46308..46538_POSITIVE 293 37 1 203 170 NC_009009:SSA_1311|5end_Hydrolase,_haloacid_dehalogenase-like_family,_putative_1328393..1328623_NEGATIVE 290 43 4 57 16 NC_009009:SSA_1923|5end_NADPH-q_uinone_reductase_(modulator_of_drug_activity_B),_putative_1912698..1912928_NEGATIVE 290 42 5 100 61 NC_009009:SSA_1725|5end_Branched-chain_amino_acid_ABC_transporter,_ATP-binding_protein,_putative_1711703..1711933_NEGATIVE 290 41 3 60 26 NC_009009:SSA_0551|5end_L-asparaginase,_putative_547293..547523_NEGATIVE 287 42 14 180 152 NC_009009:SSA_0743|5end_Transcriptional_repressor_(arginine_synthesis),_putative_725759..725989_NEGATIVE 280 49 2 175 123 NC_009009:SSA_2340|5end_hypothetical_protein_2342843..2343073_NEGATIVE 280 42 2 230 185 NC_009009:SSA_1076|5end_hypothetical_protein_1094227..1094457_POSITIVE 280 43 5 230 186 NC_009009:SSA_0862|5end_MurM,_putative_854221..854451_NEGATIVE 276 42 1 90 40 NC_009009:SSA_2067|5end_hypothetical_protein_2070254..2070484_POSITIVE 275 48 2 100 45 NC_009009:SSA_1897|5end_Ribosomal_protein_HS6-type_(S12/L30/L7a),_putative_1894450..1894680_NEGATIVE 273 27 3 128 103 NC_009009:SSA_1014|5end_Phosphatidylserine_decarboxylase_proenzyme_2,_putative_1017846..1018076_POSITIVE 273 44 2 62 17 NC_009009:SSA_0200|5end_Bifunctional_folate_synthesis_protein,_putative_198918..199148_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 337 41 1 109 58 NC_009009:SSA_2119|3end_Pentose-5-phosphate-3-epimerase,_putative_2120439..2120589_NEGATIVE 327 39 1 61 12 NC_009009:SSA_1467|3end_Chorismate_synthase,_putative_1473127..1473277_NEGATIVE 300 49 15 107 74 NC_009009:SSA_1280|3end_hypothetical_protein_1301108..1301258_NEGATIVE 290 43 4 64 23 NC_009009:SSA_1924|3end_Transcriptional_regulator,_TetR/AcrR_family,_putative_1912691..1912841_NEGATIVE 290 42 5 100 61 NC_009009:SSA_1726|3end_ABC_transporter_ATP-binding_protein-branched_chain_amino_acid_transport,_putative_1711703..1711853_NEGATIVE 289 39 2 151 113 NC_009009:SSA_0704|3end_Isocitrate_dehydrogenase_[NADP],_putative_690550..690700_POSITIVE 287 46 4 40 1 NC_009009:SSA_2337|3end_hypothetical_protein_2339359..2339509_POSITIVE 286 41 4 75 40 NC_009009:SSA_2206|3end_hypothetical_protein_2207275..2207425_POSITIVE 283 46 2 146 96 NC_009009:SSA_0320|3end_hypothetical_protein_313824..313974_POSITIVE 275 48 2 107 52 NC_009009:SSA_1899|3end_hypothetical_protein_1894443..1894593_NEGATIVE 273 27 3 135 110 NC_009009:SSA_1013|3end_Phosphatidylserine_synthase,_putative_1017933..1018083_POSITIVE 273 44 1 143 76 NC_009009:SSA_0332|3end_hypothetical_protein_326924..327074_POSITIVE 271 39 3 45 2 NC_009009:SSA_1455|3end_Conserved_hypothetical_cytosolic_protein_1461134..1461284_NEGATIVE 270 41 1 48 10 NC_009009:SSA_0271|3end_Glycosylhydrolase,_family_35,_putative_266093..266243_POSITIVE 268 50 4 93 48 NC_009009:SSA_1253|3end_hypothetical_protein_1280976..1281126_NEGATIVE 265 41 1 64 28 NC_009009:SSA_1354|3end_hypothetical_protein_1368555..1368705_NEGATIVE 265 27 1 88 67 NC_009009:SSA_0812|3end_hypothetical_protein_794434..794584_POSITIVE 262 31 1 147 100 NC_009009:SSA_2244|3end_Arsenate_reductase,_putative_2239477..2239627_NEGATIVE 262 46 5 72 28 NC_009009:SSA_1931|3end_Acetyl-coenzyme_A_carboxylase_carboxyl_transferase_subunit_beta,_putative_1918544..1918694_NEGATIVE 262 45 4 76 19 NC_009009:SSA_1409|3end_DTDP-glucose-4,6-dehydratase,_putative_1421209..1421359_NEGATIVE