Origin IGS: aatgatgtatccgttgtacttgagaccggagtgtgcaggattcttctctccaaaatgtacttcgtaagtgtaaattagcttactttgttaagtataaacaaagtagtacagtcggaaaaataaagtatcacaatactcactctaagttaaaatt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aattttaacttagagtgagtattgtgatactttatttttccgactgtactactttgtttatacttaacaaagtaagctaatttacacttacgaagtacattttggagagaagaatcctgcacactccggtctcaagtacaacggatacatcatt Mask Tandem Repeat Region ================================================ aatgatgtatccgttgtacttgagaccggagtgtgcaggattcttctctccaaaatgtacttcgtaagtgtaaattagcttactttgttaagtataaacaaagtagtacagtcggaaaaataaagtatcacaatactcactctaagttaaaatt Find is-nt database================================================ Query_seq: PG1655:PG1656|PG1655:PG1656:hypothetical protein:methylmalonyl-CoA mutase, small subunit:->->:1737445..1737598 154 aatgatgtatccgttgtacttgagaccggagtgtgcaggattcttctctccaaaatgtacttcgtaagtgtaaattagcttactttgttaagtataaacaaagtagtacagtcggaaaaataaagtatcacaatactcactctaagttaaaatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG1655:PG1656|PG1655:PG1656:hypothetical protein:methylmalonyl-CoA mutase, small subunit:->->:1737445..1737598 154 aatgatgtatccgttgtacttgagaccggagtgtgcaggattcttctctccaaaatgtacttcgtaagtgtaaattagcttactttgttaagtataaacaaagtagtacagtcggaaaaataaagtatcacaatactcactctaagttaaaatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG1655:PG1656|PG1655:PG1656:hypothetical protein:methylmalonyl-CoA mutase, small subunit:->->:1737445..1737598 154 aatgatgtatccgttgtacttgagaccggagtgtgcaggattcttctctccaaaatgtacttcgtaagtgtaaattagcttactttgttaagtataaacaaagtagtacagtcggaaaaataaagtatcacaatactcactctaagttaaaatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aatgatgtatccgttgtacttgagaccggagtgtgcaggattcttctctccaaaatgtacttcgtaagtgtaaattagcttactttgttaagtataaacaaagtagtacagtcggaaaaataaagtatcacaatactcactctaagttaaaatt Predict ORF larger than 30AA ================================================ Protein_Len: 40 Strand: + Start: 33 End: 152 ................................ M Q D S S L Q N V L R K C K L A Y F V K Y K Q S S T V G K I K Y H N T H S K L K .. aatgatgtatccgttgtacttgagaccggagtgtgcaggattcttctctccaaaatgtacttcgtaagtgtaaattagcttactttgttaagtataaacaaagtagtacagtcggaaaaataaagtatcacaatactcactctaagttaaaatt 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================================================ aatgatgtatccgttgtacttgagaccggagtgtgcaggattcttctctccaaaatgtacttcgtaagtgtaaattagcttactttgttaagtataaacaaagtagtacagtcggaaaaataaagtatcacaatactcactctaagttaaaatt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PG1655:PG1656|PG1655:PG1656:hypothetical protein:methylmalonyl-CoA mutase, small subunit:->->:1737445..1737598 154 aatgatgtatccgttgtacttgagaccggagtgtgcaggattcttctctccaaaatgtacttcgtaagtgtaaattagcttactttgttaagtataaacaaagtagtacagtcggaaaaataaagtatcacaatactcactctaagttaaaatt Intra-Species Hit: Count: 1 Min: 1 Max: 154 Len: 154 Subject: NC_002950_PG1655_PG1656|hypothetical protein:methylmalonyl-CoA mutase, small subunit|POSITIVE:POSITIVE|[1737445,1737598]|154 HSP 1 e-value: 2.0E-82 bit: 305.0 Len: 154 Query Start:1 Query End:154 Subject Strand: POSITIVE Subject Start: 1 Subject End: 154 aatgatgtatccgttgtacttgagaccggagtgtgcaggattcttctctccaaaatgtacttcgtaagtgtaaattagcttactttgttaagtataaacaaagtagtacagtcggaaaaataaagtatcacaatactcactctaagttaaaatt aatgatgtatccgttgtacttgagaccggagtgtgcaggattcttctctccaaaatgtacttcgtaagtgtaaattagcttactttgttaagtataaacaaagtagtacagtcggaaaaataaagtatcacaatactcactctaagttaaaatt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUGAUGUAUCCGUUGUACUUGAGACCGGAGUGUGCAGGAUUCUUCUCUCCAAAAUGUACUUCGUAAGUGUAAAUUAGCUUACUUUGUUAAGUAUAAACAAAGUAGUACAGUCGGAAAAAUAAAGUAUCACAAUACUCACUCUAAGUUAAAAUU ..(((.((((..((.((((((....((((..(((((.(((........)))....(((((((..((((.((((......))))))))..))))))).........))))).)))).......)))))).)).)))))))............... (-30.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUUUUAACUUAGAGUGAGUAUUGUGAUACUUUAUUUUUCCGACUGUACUACUUUGUUUAUACUUAACAAAGUAAGCUAAUUUACACUUACGAAGUACAUUUUGGAGAGAAGAAUCCUGCACACUCCGGUCUCAAGUACAACGGAUACAUCAUU .............((((((((((((..((((...(((((((((.((((((...(((((.......))))).(((((..........)))))..))))))..))))))))).((..((..........))..)).))))..)).))))).))))) (-30.00) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 354 43 1 231 184 NC_002950:PG2083|5end_hypothetical_protein_2184507..2184737_NEGATIVE 347 49 2 59 18 NC_002950:PG1481|5end_conjugative_transposon_protein_TraG_1558447..1558677_NEGATIVE 331 39 11 212 180 NC_002950:PG0772|5end_hypothetical_protein_824975..825205_POSITIVE 314 48 2 168 118 NC_002950:PG2072|5end_UvrD/REP_helicase_domain_protein_2167369..2167599_POSITIVE 311 54 14 130 96 NC_002950:PG0414|5end_hypothetical_protein_453652..453882_NEGATIVE 297 50 5 89 23 NC_002950:PG1554|5end_hypothetical_protein_1635264..1635494_POSITIVE 296 58 11 75 10 NC_002950:PG0747|5end_sigma-54_dependent_DNA-binding_response_regulator_795294..795524_NEGATIVE 294 47 11 221 184 NC_002950:PG1210|5end_peptidase,_M24_family_1289044..1289274_POSITIVE 290 52 12 133 93 NC_002950:PG2033|5end_glutamate_synthase,_small_subunit_2134803..2135033_NEGATIVE 290 60 11 91 42 NC_002950:PG0608|5end_hypothetical_protein_662945..663175_POSITIVE 288 53 11 55 18 NC_002950:PG2188|5end_diaminopimelate_decarboxylase_2295781..2296011_NEGATIVE 287 60 12 177 121 NC_002950:PG0326|5end_hypothetical_protein_360974..361204_NEGATIVE 285 55 13 212 162 NC_002950:PG1979|5end_hypothetical_protein_2067272..2067502_POSITIVE 285 49 11 47 1 NC_002950:PG0756|5end_hypothetical_protein_805673..805903_NEGATIVE 284 64 23 172 126 NC_002950:PG1072|5end_MutS_family_protein_1138976..1139206_POSITIVE 284 42 11 50 15 NC_002950:PG0539|5end_efflux_transporter,_MFP_component,_RND_family_590574..590804_POSITIVE 282 59 11 99 43 NC_002950:PG1091|5end_DHH_subfamily_1_protein_1157017..1157247_POSITIVE 279 45 2 75 33 NC_002950:PG1649|5end_hypothetical_protein_1730152..1730382_NEGATIVE 279 41 3 214 170 NC_002950:PG1225|5end_ABC_transporter,_ATP-binding_protein_1301385..1301615_POSITIVE 279 52 12 214 179 NC_002950:PG0335|5end_tRNA_delta(2)-isopentenylpyrophosphate_transferase_370706..370936_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 408 37 11 121 95 NC_002950:PG1314|3end_chorismate_synthase_1394362..1394512_NEGATIVE 347 49 2 62 21 NC_002950:PG1482|3end_conjugative_transposon_protein_TraF_1558444..1558594_NEGATIVE 323 49 2 108 43 NC_002950:PG2146|3end_hypothetical_protein_2254650..2254800_POSITIVE 311 54 14 68 34 NC_002950:PG0415|3end_peptidyl-prolyl_cis-trans_isomerase,_PPIC-type_453714..453864_NEGATIVE 309 50 11 41 1 NC_002950:PG0844|3end_hypothetical_protein_905461..905611_POSITIVE 297 50 5 92 26 NC_002950:PG1553|3end_CobN/magnesium_chelatase_family_protein_1635347..1635497_POSITIVE 297 47 2 131 93 NC_002950:PG0841|3end_mobilizable_transposon,_excision_protein,_putative_902781..902931_NEGATIVE 295 65 23 141 104 NC_002950:PG2105|3end_lipoprotein,_putative_2214579..2214729_POSITIVE 290 60 11 60 11 NC_002950:PG0607|3end_hypothetical_protein_662994..663144_POSITIVE 282 51 11 79 33 NC_002950:PG1174|3end_thioesterase_family_protein_1253210..1253360_NEGATIVE 277 48 3 75 27 NC_002950:PG2214|3end_hypothetical_protein_2325301..2325451_NEGATIVE 276 49 2 72 26 NC_002950:PG0515|3end_hypothetical_protein_556363..556513_NEGATIVE 273 66 25 60 21 NC_002950:PG1163|3end_cobyrinic_acid_a,c-diamide_synthase_1242062..1242212_NEGATIVE 271 60 11 149 94 NC_002950:PG0738|3end_cytidine/deoxycytidylate_deaminase_family_protein_786995..787145_POSITIVE 271 54 11 145 105 NC_002950:PG0424|3end_hypothetical_protein_463213..463363_POSITIVE 268 59 11 112 62 NC_002950:PG2076|3end_hypothetical_protein_2177073..2177223_POSITIVE 268 52 11 151 106 NC_002950:PG1444|3end_hypothetical_protein_1529242..1529392_POSITIVE 268 52 11 151 106 NC_002950:PG0829|3end_hypothetical_protein_886270..886420_NEGATIVE 268 50 1 54 6 NC_002950:PG0530|3end_carbamoyl-phosphate_synthase,_large_subunit_579036..579186_POSITIVE 268 51 23 30 1 NC_002950:PG0323|3end_hypothetical_protein_357059..357209_NEGATIVE