Origin IGS: ccttgtagtttgtctttcgagcaaaagtacttataatatgagacctttgcacaataagcagcacttatacagggctgacgcattaaaattaaagttgtatggtcattagttgttgtggtttcattcgaacgagtttcttctgaatatgaggtgttgaagttcagttttgccgattgagagcttttttgttactttgcagtcgctttgcgtaatctctgacaggaaataacgtgcgacctgtgtatattgcgtttagtatttagctaatccaaaaagcaatacaa .........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 ttgtattgctttttggattagctaaatactaaacgcaatatacacaggtcgcacgttatttcctgtcagagattacgcaaagcgactgcaaagtaacaaaaaagctctcaatcggcaaaactgaacttcaacacctcatattcagaagaaactcgttcgaatgaaaccacaacaactaatgaccatacaactttaattttaatgcgtcagccctgtataagtgctgcttattgtgcaaaggtctcatattataagtacttttgctcgaaagacaaactacaagg Mask Tandem Repeat Region ================================================ ccttgtagtttgtctttcgagcaaaagtacttataatatgagacctttgcacaataagcagcacttatacagggctgacgcattaaaattaaagttgtatggtcattagttgttgtggtttcattcgaacgagtttcttctgaatatgaggtgttgaagttcagttttgccgattgagagcttttttgttactttgcagtcgctttgcgtaatctctgacaggaaataacgtgcgacctgtgtatattgcgtttagtatttagctaatccaaaaagcaatacaa Find is-nt database================================================ Query_seq: PG0035:PG0037|PG0035:PG0037:DNA polymerase III, alpha subunit:50S ribosomal protein L19:<-->:46375..46658 284 ccttgtagtttgtctttcgagcaaaagtacttataatatgagacctttgcacaataagcagcacttatacagggctgacgcattaaaattaaagttgtatggtcattagttgttgtggtttcattcgaacgagtttcttctgaatatgaggtgttgaagttcagttttgccgattgagagcttttttgttactttgcagtcgctttgcgtaatctctgacaggaaataacgtgcgacctgtgtatattgcgtttagtatttagctaatccaaaaagcaatacaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG0035:PG0037|PG0035:PG0037:DNA polymerase III, alpha subunit:50S ribosomal protein L19:<-->:46375..46658 284 ccttgtagtttgtctttcgagcaaaagtacttataatatgagacctttgcacaataagcagcacttatacagggctgacgcattaaaattaaagttgtatggtcattagttgttgtggtttcattcgaacgagtttcttctgaatatgaggtgttgaagttcagttttgccgattgagagcttttttgttactttgcagtcgctttgcgtaatctctgacaggaaataacgtgcgacctgtgtatattgcgtttagtatttagctaatccaaaaagcaatacaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG0035:PG0037|PG0035:PG0037:DNA polymerase III, alpha subunit:50S ribosomal protein L19:<-->:46375..46658 284 ccttgtagtttgtctttcgagcaaaagtacttataatatgagacctttgcacaataagcagcacttatacagggctgacgcattaaaattaaagttgtatggtcattagttgttgtggtttcattcgaacgagtttcttctgaatatgaggtgttgaagttcagttttgccgattgagagcttttttgttactttgcagtcgctttgcgtaatctctgacaggaaataacgtgcgacctgtgtatattgcgtttagtatttagctaatccaaaaagcaatacaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ccttgtagtttgtctttcgagcaaaagtacttataatatgagacctttgcacaataagcagcacttatacagggctgacgcattaaaattaaagttgtatggtcattagttgttgtggtttcattcgaacgagtttcttctgaatatgaggtgttgaagttcagttttgccgattgagagcttttttgttactttgcagtcgctttgcgtaatctctgacaggaaataacgtgcgacctgtgtatattgcgtttagtatttagctaatccaaaaagcaatacaa Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: + Start: 82 End: 174 ................................................................................. M K I K V V W S L V V V V S F E R V S S E Y E V L K F S F A D .............................................................................................................. Protein_Len: 32 Strand: - Start: 164 End: 259 ................................................................................................................................................................... N Q R N L A K K N S Q L R K A Y D R V P F L T R G T Y I A N L M ......................... Protein_Len: 33 Strand: - Start: 124 End: 222 ........................................................................................................................... E F S N R R F I L H Q L E T K G I S L K K T V K C D S Q T I E S M .............................................................. Protein_Len: 54 Strand: - Start: 3 End: 164 .. Q L K D K S C F Y K Y Y S V K A C Y A A S I C P Q R M L I L T T H D N T T T T E N S R T E E S Y S T N F N M ........................................................................................................................ ccttgtagtttgtctttcgagcaaaagtacttataatatgagacctttgcacaataagcagcacttatacagggctgacgcattaaaattaaagttgtatggtcattagttgttgtggtttcattcgaacgagtttcttctgaatatgaggtgttgaagttcagttttgccgattgagagcttttttgttactttgcagtcgctttgcgtaatctctgacaggaaataacgtgcgacctgtgtatattgcgtttagtatttagctaatccaaaaagcaatacaa 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================================================ ccttgtagtttgtctttcgagcaaaagtacttataatatgagacctttgcacaataagcagcacttatacagggctgacgcattaaaattaaagttgtatggtcattagttgttgtggtttcattcgaacgagtttcttctgaatatgaggtgttgaagttcagttttgccgattgagagcttttttgttactttgcagtcgctttgcgtaatctctgacaggaaataacgtgcgacctgtgtatattgcgtttagtatttagctaatccaaaaagcaatacaa Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PG0035:PG0037|PG0035:PG0037:DNA polymerase III, alpha subunit:50S ribosomal protein L19:<-->:46375..46658 284 ccttgtagtttgtctttcgagcaaaagtacttataatatgagacctttgcacaataagcagcacttatacagggctgacgcattaaaattaaagttgtatggtcattagttgttgtggtttcattcgaacgagtttcttctgaatatgaggtgttgaagttcagttttgccgattgagagcttttttgttactttgcagtcgctttgcgtaatctctgacaggaaataacgtgcgacctgtgtatattgcgtttagtatttagctaatccaaaaagcaatacaa Intra-Species Hit: Count: 1 Min: 1 Max: 284 Len: 284 Subject: NC_002950_PG0035_PG0037|DNA polymerase III, alpha subunit:50S ribosomal protein L19|NEGATIVE:POSITIVE|[46375,46658]|284 HSP 1 e-value: 1.0E-159 bit: 563.0 Len: 284 Query Start:1 Query End:284 Subject Strand: POSITIVE Subject Start: 1 Subject End: 284 ccttgtagtttgtctttcgagcaaaagtacttataatatgagacctttgcacaataagcagcacttatacagggctgacgcattaaaattaaagttgtatggtcattagttgttgtggtttcattcgaacgagtttcttctgaatatgaggtgttgaagttcagttttgccgattgagagcttttttgttactttgcagtcgctttgcgtaatctctgacaggaaataacgtgcgacctgtgtatattgcgtttagtatttagctaatccaaaaagcaatacaa ccttgtagtttgtctttcgagcaaaagtacttataatatgagacctttgcacaataagcagcacttatacagggctgacgcattaaaattaaagttgtatggtcattagttgttgtggtttcattcgaacgagtttcttctgaatatgaggtgttgaagttcagttttgccgattgagagcttttttgttactttgcagtcgctttgcgtaatctctgacaggaaataacgtgcgacctgtgtatattgcgtttagtatttagctaatccaaaaagcaatacaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CCUUGUAGUUUGUCUUUCGAGCAAAAGUACUUAUAAUAUGAGACCUUUGCACAAUAAGCAGCACUUAUACAGGGCUGACGCAUUAAAAUUAAAGUUGUAUGGUCAUUAGUUGUUGUGGUUUCAUUCGAACGAGUUUCUUCUGAAUAUGAGGUGUUGAAGUUCAGUUUUGCCGAUUGAGAGCUUUUUUGUUACUUUGCAGUCGCUUUGCGUAAUCUCUGACAGGAAAUAACGUGCGACCUGUGUAUAUUGCGUUUAGUAUUUAGCUAAUCCAAAAAGCAAUACAA ...((((.....((..(((.((((((...........((((((((.....(((((((..(((.(((....))))))(((.(((...(((....)))..)))))).....)))))))))))))))..((((......((((.......)))).......))))..)))))))))..))..(((((((.((.....(((((((((...((((.((.(((....))).)).)))))))).)))))......))..(((((.....)))))...)))))))..)))). (-63.02) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUGUAUUGCUUUUUGGAUUAGCUAAAUACUAAACGCAAUAUACACAGGUCGCACGUUAUUUCCUGUCAGAGAUUACGCAAAGCGACUGCAAAGUAACAAAAAAGCUCUCAAUCGGCAAAACUGAACUUCAACACCUCAUAUUCAGAAGAAACUCGUUCGAAUGAAACCACAACAACUAAUGACCAUACAACUUUAAUUUUAAUGCGUCAGCCCUGUAUAAGUGCUGCUUAUUGUGCAAAGGUCUCAUAUUAUAAGUACUUUUGCUCGAAAGACAAACUACAAGG .((((((((..((((((((.....))).))))).))))))))....((((((.(((.(((((......))))).)))....)))))).....(((.............((((.((((..(((..................((((...(((.....)))...))))......(((.....(((((((...............))).))))....)))...)))..)))).)))).((((((((((.........)).))))))))((....)).....))).... (-49.16) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 888 80 31 171 122 NC_002950:PG0035|5end_DNA_polymerase_III,_alpha_subunit_46284..46514_NEGATIVE 598 150 101 229 172 NC_002950:PG1405|5end_hypothetical_protein_1490669..1490899_NEGATIVE 488 139 91 217 169 NC_002950:PG1745|5end_phosphoribulokinase_family_protein_1831024..1831254_NEGATIVE 488 139 91 202 154 NC_002950:PG0278|5end_hypothetical_protein_310047..310277_POSITIVE 453 120 71 221 178 NC_002950:PG2175|5end_hypothetical_protein_2283116..2283346_NEGATIVE 453 120 71 219 176 NC_002950:PG0864|5end_site-specific_recombinase,_resolvase_family_927669..927899_NEGATIVE 424 66 39 184 156 NC_002950:PG0267|5end_arginyl-tRNA_synthetase_299100..299330_POSITIVE 420 156 113 119 80 NC_002950:PG1250|5end_hypothetical_protein_1327846..1328076_NEGATIVE 362 210 162 109 56 NC_002950:PG0753|5end_protease_798301..798531_POSITIVE 342 234 195 196 154 NC_002950:PG0946|5end_ABC_transporter,_ATP-binding_protein_1007396..1007626_NEGATIVE 342 78 37 199 138 NC_002950:PG0033|5end_RmuC_domain_protein_41540..41770_NEGATIVE 327 104 61 189 135 NC_002950:PG0276|5end_hypothetical_protein_308789..309019_NEGATIVE 324 232 195 122 83 NC_002950:PG0517|5end_hypothetical_protein_562097..562327_NEGATIVE 323 210 161 200 146 NC_002950:PG1350|5end_ISPg2,_transposase_1430866..1431096_POSITIVE 323 89 41 182 135 NC_002950:PG0742|5end_antigen_PgaA_790637..790867_NEGATIVE 319 238 198 50 10 NC_002950:PG0996|5end_conserved_hypothetical_protein_TIGR01777_1055592..1055822_POSITIVE 311 209 165 218 181 NC_002950:PG1475|5end_conjugative_transposon_protein_TraN_1551835..1552065_NEGATIVE 311 160 115 221 167 NC_002950:PG0241|5end_lipoprotein,_putative_278214..278444_NEGATIVE 308 240 193 174 128 NC_002950:PG1476|5end_conjugative_transposon_protein_TraM_1553219..1553449_NEGATIVE 307 181 150 149 110 NC_002950:PG1966|5end_hypothetical_protein_2056924..2057154_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 488 139 91 141 93 NC_002950:PG2176|3end_ISPg2,_transposase_2283215..2283365_NEGATIVE 488 139 91 141 93 NC_002950:PG1746|3end_ISPg2,_transposase_1831100..1831250_NEGATIVE 488 139 91 141 93 NC_002950:PG1350|3end_ISPg2,_transposase_1432076..1432226_POSITIVE 488 139 91 141 93 NC_002950:PG0865|3end_ISPg2,_transposase_927766..927916_NEGATIVE 488 139 91 141 93 NC_002950:PG0277|3end_ISPg2,_transposase_310066..310216_POSITIVE 412 66 22 123 77 NC_002950:PG2220|3end_hypothetical_protein_2335368..2335518_POSITIVE 412 66 22 123 77 NC_002950:PG0499|3end_hypothetical_protein_539142..539292_POSITIVE 367 210 168 116 67 NC_002950:PG1837|3end_hemagglutinin_protein_HagA_1936734..1936884_POSITIVE 362 210 162 125 72 NC_002950:PG0752|3end_uracil_phosphoribosyltransferase_798397..798547_POSITIVE 360 66 22 123 77 NC_002950:PG1251|3end_hypothetical_protein_1328212..1328362_POSITIVE 354 66 25 123 82 NC_002950:PG0879|3end_hypothetical_protein_941931..942081_NEGATIVE 343 210 161 52 1 NC_002950:PG0053|3end_hypothetical_protein_64967..65117_NEGATIVE 340 240 193 54 4 NC_002950:PG1392|3end_rod_shape-determining_protein_RodA,_putative_1472959..1473109_NEGATIVE 338 209 161 149 91 NC_002950:PG1975|3end_hemagglutinin_protein_HagC_2064350..2064500_POSITIVE 338 209 161 149 91 NC_002950:PG1972|3end_hemagglutinin_protein_HagB_2061203..2061353_POSITIVE 335 223 182 89 46 NC_002950:PG2037|3end_hypothetical_protein_2137591..2137741_NEGATIVE 323 78 39 77 19 NC_002950:PG0197|3end_hypothetical_protein_235941..236091_NEGATIVE 320 209 164 50 6 NC_002950:PG1133|3end_hypothetical_protein_1214103..1214253_POSITIVE 316 240 193 112 58 NC_002950:PG1757|3end_hypothetical_protein_1843931..1844081_NEGATIVE 300 170 121 137 91 NC_002950:PG0094|3end_outer_membrane_efflux_protein,_putative_109688..109838_NEGATIVE