Origin IGS: catcgcttttgccgcatcgtccttttgaaataagaatacgccggattgctatgtggcttacggctatgcaggctctcagtacacctttctgacataaaaaagtgtgccgaaaacgctgctgaagcgattttcgacacaccctcattccttatgcttatatgaaaagccgcactgcggatagcgtaaactccgaaagacaagatttgaggattccaccacctttgtaatccgctgtgcaaagcaacccgaaggtgcggcccgccatcagcgatgaaattgtcctcggaatagttgttatgatgagtttccccgatctaacagtgcggcttattcctcgtcttctctgtattgcaaagttagcaacattgtttagatttgcaattctttgtttcatcgattttgggt .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9 acccaaaatcgatgaaacaaagaattgcaaatctaaacaatgttgctaactttgcaatacagagaagacgaggaataagccgcactgttagatcggggaaactcatcataacaactattccgaggacaatttcatcgctgatggcgggccgcaccttcgggttgctttgcacagcggattacaaaggtggtggaatcctcaaatcttgtctttcggagtttacgctatccgcagtgcggcttttcatataagcataaggaatgagggtgtgtcgaaaatcgcttcagcagcgttttcggcacacttttttatgtcagaaaggtgtactgagagcctgcatagccgtaagccacatagcaatccggcgtattcttatttcaaaaggacgatgcggcaaaagcgatg Mask Tandem Repeat Region ================================================ catcgcttttgccgcatcgtccttttgaaataagaatacgccggattgctatgtggcttacggctatgcaggctctcagtacacctttctgacataaaaaagtgtgccgaaaacgctgctgaagcgattttcgacacaccctcattccttatgcttatatgaaaagccgcactgcggatagcgtaaactccgaaagacaagatttgaggattccaccacctttgtaatccgctgtgcaaagcaacccgaaggtgcggcccgccatcagcgatgaaattgtcctcggaatagttgttatgatgagtttccccgatctaacagtgcggcttattcctcgtcttctctgtattgcaaagttagcaacattgtttagatttgcaattctttgtttcatcgattttgggt Find is-nt database================================================ Query_seq: PG2089:PG2090|PG2089:PG2090:hypothetical protein:cation efflux family protein:->->:2189965..2190369 405 catcgcttttgccgcatcgtccttttgaaataagaatacgccggattgctatgtggcttacggctatgcaggctctcagtacacctttctgacataaaaaagtgtgccgaaaacgctgctgaagcgattttcgacacaccctcattccttatgcttatatgaaaagccgcactgcggatagcgtaaactccgaaagacaagatttgaggattccaccacctttgtaatccgctgtgcaaagcaacccgaaggtgcggcccgccatcagcgatgaaattgtcctcggaatagttgttatgatgagtttccccgatctaacagtgcggcttattcctcgtcttctctgtattgcaaagttagcaacattgtttagatttgcaattctttgtttcatcgattttgggt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG2089:PG2090|PG2089:PG2090:hypothetical protein:cation efflux family protein:->->:2189965..2190369 405 catcgcttttgccgcatcgtccttttgaaataagaatacgccggattgctatgtggcttacggctatgcaggctctcagtacacctttctgacataaaaaagtgtgccgaaaacgctgctgaagcgattttcgacacaccctcattccttatgcttatatgaaaagccgcactgcggatagcgtaaactccgaaagacaagatttgaggattccaccacctttgtaatccgctgtgcaaagcaacccgaaggtgcggcccgccatcagcgatgaaattgtcctcggaatagttgttatgatgagtttccccgatctaacagtgcggcttattcctcgtcttctctgtattgcaaagttagcaacattgtttagatttgcaattctttgtttcatcgattttgggt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG2089:PG2090|PG2089:PG2090:hypothetical protein:cation efflux family protein:->->:2189965..2190369 405 catcgcttttgccgcatcgtccttttgaaataagaatacgccggattgctatgtggcttacggctatgcaggctctcagtacacctttctgacataaaaaagtgtgccgaaaacgctgctgaagcgattttcgacacaccctcattccttatgcttatatgaaaagccgcactgcggatagcgtaaactccgaaagacaagatttgaggattccaccacctttgtaatccgctgtgcaaagcaacccgaaggtgcggcccgccatcagcgatgaaattgtcctcggaatagttgttatgatgagtttccccgatctaacagtgcggcttattcctcgtcttctctgtattgcaaagttagcaacattgtttagatttgcaattctttgtttcatcgattttgggt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 catcgcttttgccgcatcgtccttttgaaataagaatacgccggattgctatgtggcttacggctatgcaggctctcagtacacctttctgacataaaaaagtgtgccgaaaacgctgctgaagcgattttcgacacaccctcattccttatgcttatatgaaaagccgcactgcggatagcgtaaactccgaaagacaagatttgaggattccaccacctttgtaatccgctgtgcaaagcaacccgaaggtgcggcccgccatcagcgatgaaattgtcctcggaatagttgttatgatgagtttccccgatctaacagtgcggcttattcctcgtcttctctgtattgcaaagttagcaacattgtttagatttgcaattctttgtttcatcgattttgggt Predict ORF larger than 30AA ================================================ Protein_Len: 38 Strand: + Start: 46 End: 159 ............................................. M L C G L R L C R L S V H L S D I K K C A E N A A E A I F D T P S F L M L I ...................................................................................................................................................................................................................................................... Protein_Len: 57 Strand: + Start: 234 End: 404 ......................................................................................................................................................................................................................................... M Q S N P K V R P A I S D E I V L G I V V M M S F P D L T V R L I P R L L C I A K L A T L F R F A I L C F I D F G . Protein_Len: 60 Strand: - Start: 158 End: 394 ............................................................................................................................................................. G G K Y D A T C L L G F T R G A M L S S I T R P I T T I I L K G S R V T R S I G R R R Q I A F N A V N N L N A I R Q K M ........... Protein_Len: 60 Strand: - Start: 3 End: 314 .. V G E N R I S I H F A A S R I A Y V G F S L I Q P N W W R Q L G S H L A V R L H P G G D A I F N D E S Y N N H H T E G M ........................................................................................... Protein_Len: 48 Strand: - Start: 2 End: 145 . D S K G C R G K S I L I R R I A I H S V A I C A R L V G K Q C L F T H R F R Q Q L S K R C V R M .................................................................................................................................................................................................................................................................... catcgcttttgccgcatcgtccttttgaaataagaatacgccggattgctatgtggcttacggctatgcaggctctcagtacacctttctgacataaaaaagtgtgccgaaaacgctgctgaagcgattttcgacacaccctcattccttatgcttatatgaaaagccgcactgcggatagcgtaaactccgaaagacaagatttgaggattccaccacctttgtaatccgctgtgcaaagcaacccgaaggtgcggcccgccatcagcgatgaaattgtcctcggaatagttgttatgatgagtttccccgatctaacagtgcggcttattcctcgtcttctctgtattgcaaagttagcaacattgtttagatttgcaattctttgtttcatcgattttgggt 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================================================ catcgcttttgccgcatcgtccttttgaaataagaatacgccggattgctatgtggcttacggctatgcaggctctcagtacacctttctgacataaaaaagtgtgccgaaaacgctgctgaagcgattttcgacacaccctcattccttatgcttatatgaaaagccgcactgcggatagcgtaaactccgaaagacaagatttgaggattccaccacctttgtaatccgctgtgcaaagcaacccgaaggtgcggcccgccatcagcgatgaaattgtcctcggaatagttgttatgatgagtttccccgatctaacagtgcggcttattcctcgtcttctctgtattgcaaagttagcaacattgtttagatttgcaattctttgtttcatcgattttgggt Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 49 HP_score: -5.2 Tail_Score: -2.88389 Start: 100 End: 141 Full_Region: CTTTCTGACATAAAA AAGTGTGCCGAAAACGCT GCTGA AGCGATTTTCGACACACCC TCATTCCTTATGCTT ...................................................................................................AAGTGTGCCGAAAACGCTGCTGAAGCGATTTTCGACACACCC........................................................................................................................................................................................................................................................................ TransTerm Strand: - Conf: 100 HP_score: -14.4 Tail_Score: -5.36441 Start: 102 End: 139 Full_Region: gcataaggaatgagg gtgtgtcgaaaatcgct tcagc agcgttttcggcacac ttttttatgtcagaa .....................................................................................................gtgtgtcgaaaatcgcttcagcagcgttttcggcacac.......................................................................................................................................................................................................................................................................... Find igs database================================================ Query_seq: PG2089:PG2090|PG2089:PG2090:hypothetical protein:cation efflux family protein:->->:2189965..2190369 405 catcgcttttgccgcatcgtccttttgaaataagaatacgccggattgctatgtggcttacggctatgcaggctctcagtacacctttctgacataaaaaagtgtgccgaaaacgctgctgaagcgattttcgacacaccctcattccttatgcttatatgaaaagccgcactgcggatagcgtaaactccgaaagacaagatttgaggattccaccacctttgtaatccgctgtgcaaagcaacccgaaggtgcggcccgccatcagcgatgaaattgtcctcggaatagttgttatgatgagtttccccgatctaacagtgcggcttattcctcgtcttctctgtattgcaaagttagcaacattgtttagatttgcaattctttgtttcatcgattttgggt Intra-Species Hit: Count: 1 Min: 1 Max: 405 Len: 405 Subject: NC_002950_PG2089_PG2090|hypothetical protein:cation efflux family protein|POSITIVE:POSITIVE|[2189965,2190369]|405 HSP 1 e-value: 0.0 bit: 803.0 Len: 405 Query Start:1 Query End:405 Subject Strand: POSITIVE Subject Start: 1 Subject End: 405 catcgcttttgccgcatcgtccttttgaaataagaatacgccggattgctatgtggcttacggctatgcaggctctcagtacacctttctgacataaaaaagtgtgccgaaaacgctgctgaagcgattttcgacacaccctcattccttatgcttatatgaaaagccgcactgcggatagcgtaaactccgaaagacaagatttgaggattccaccacctttgtaatccgctgtgcaaagcaacccgaaggtgcggcccgccatcagcgatgaaattgtcctcggaatagttgttatgatgagtttccccgatctaacagtgcggcttattcctcgtcttctctgtattgcaaagttagcaacattgtttagatttgcaattctttgtttcatcgattttgggt catcgcttttgccgcatcgtccttttgaaataagaatacgccggattgctatgtggcttacggctatgcaggctctcagtacacctttctgacataaaaaagtgtgccgaaaacgctgctgaagcgattttcgacacaccctcattccttatgcttatatgaaaagccgcactgcggatagcgtaaactccgaaagacaagatttgaggattccaccacctttgtaatccgctgtgcaaagcaacccgaaggtgcggcccgccatcagcgatgaaattgtcctcggaatagttgttatgatgagtttccccgatctaacagtgcggcttattcctcgtcttctctgtattgcaaagttagcaacattgtttagatttgcaattctttgtttcatcgattttgggt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CAUCGCUUUUGCCGCAUCGUCCUUUUGAAAUAAGAAUACGCCGGAUUGCUAUGUGGCUUACGGCUAUGCAGGCUCUCAGUACACCUUUCUGACAUAAAAAAGUGUGCCGAAAACGCUGCUGAAGCGAUUUUCGACACACCCUCAUUCCUUAUGCUUAUAUGAAAAGCCGCACUGCGGAUAGCGUAAACUCCGAAAGACAAGAUUUGAGGAUUCCACCACCUUUGUAAUCCGCUGUGCAAAGCAACCCGAAGGUGCGGCCCGCCAUCAGCGAUGAAAUUGUCCUCGGAAUAGUUGUUAUGAUGAGUUUCCCCGAUCUAACAGUGCGGCUUAUUCCUCGUCUUCUCUGUAUUGCAAAGUUAGCAACAUUGUUUAGAUUUGCAAUUCUUUGUUUCAUCGAUUUUGGGU ..........(((.((..(((....((((((((((((..((((....(((....)))...))))..(((..(((..(((((((.......(((........(((((.((((((((((.....)))).)))))).))))).....................((((((((((((((.((((.(.(.((((((.....(((((..(((((((((.((..((((((((......(((......)))....)))))))).))..(((.....)))........)))))))))....))))).....)))))).).).))))..))))))))))).)))...))).....)))))))...)))..)))..................)))).))))))))..)))..))))) (-116.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACCCAAAAUCGAUGAAACAAAGAAUUGCAAAUCUAAACAAUGUUGCUAACUUUGCAAUACAGAGAAGACGAGGAAUAAGCCGCACUGUUAGAUCGGGGAAACUCAUCAUAACAACUAUUCCGAGGACAAUUUCAUCGCUGAUGGCGGGCCGCACCUUCGGGUUGCUUUGCACAGCGGAUUACAAAGGUGGUGGAAUCCUCAAAUCUUGUCUUUCGGAGUUUACGCUAUCCGCAGUGCGGCUUUUCAUAUAAGCAUAAGGAAUGAGGGUGUGUCGAAAAUCGCUUCAGCAGCGUUUUCGGCACACUUUUUUAUGUCAGAAAGGUGUACUGAGAGCCUGCAUAGCCGUAAGCCACAUAGCAAUCCGGCGUAUUCUUAUUUCAAAAGGACGAUGCGGCAAAAGCGAUG ((((....((...........))..(((...(((......((((((.......))))))...))).......(((.((((((((((((..(((.(((....)))))).........(((((((((((((((((((((((..((.....((((.((....)).(((...)))..))))....))..)))))))))))..........)))).))))))))...........)))))))))))))))......)))..........)))).........(((((((..((((.((((((((.((((((((((.....)))))))))).))))))))))))...((((((.(((............)))...(((((.......)))))...))))))..))))))). (-130.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 509 148 102 179 135 NC_002950:PG1281|5end_hypothetical_protein_1358848..1359078_POSITIVE 440 270 223 60 8 NC_002950:PG0448|5end_hypothetical_protein_488089..488319_POSITIVE 408 80 39 67 23 NC_002950:PG0593|5end_htrA_protein_650362..650592_POSITIVE 405 79 40 225 182 NC_002950:PG0157|5end_regulatory_protein_RecX_179706..179936_POSITIVE 395 290 250 209 177 NC_002950:PG1959|5end_ribosomal_protein_L33_2048405..2048635_NEGATIVE 384 72 40 166 123 NC_002950:PG2170|5end_sugar_transporter_2277974..2278204_NEGATIVE 381 260 213 102 49 NC_002950:PG0362|5end_hypothetical_protein_395301..395531_POSITIVE 379 269 221 161 104 NC_002950:PG1967|5end_TPR_domain_protein_2057168..2057398_POSITIVE 378 269 221 212 151 NC_002950:PG1927|5end_50S_ribosomal_protein_L24_2019557..2019787_NEGATIVE 377 279 231 83 21 NC_002950:PG1992|5end_glucose-inhibited_division_protein_A_2081410..2081640_POSITIVE 366 270 227 211 175 NC_002950:PG1247|5end_3-dehydroquinate_synthase_1324444..1324674_POSITIVE 366 287 245 205 157 NC_002950:PG0241|5end_lipoprotein,_putative_278214..278444_NEGATIVE 365 270 221 180 123 NC_002950:PG0724|5end_prolyl_oligopeptidase_family_protein_775229..775459_POSITIVE 364 79 39 49 7 NC_002950:PG0128|5end_hypothetical_protein_149594..149824_POSITIVE 360 179 132 229 184 NC_002950:PG1720|5end_hypothetical_protein_1808615..1808845_POSITIVE 359 288 241 123 67 NC_002950:PG1409|5end_hypothetical_protein_1493265..1493495_NEGATIVE 356 50 3 72 21 NC_002950:PG2139|5end_hypothetical_protein_2245648..2245878_POSITIVE 353 90 41 213 162 NC_002950:PG1945|5end_hypothetical_protein_2031697..2031927_POSITIVE 351 287 241 61 8 NC_002950:PG2097|5end_ribose-phosphate_pyrophosphokinase_2206462..2206692_NEGATIVE 349 90 45 188 129 NC_002950:PG0803|5end_glucosamine-6-phosphate_deaminase_860518..860748_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 509 148 102 52 8 NC_002950:PG1280|3end_hypothetical_protein_1358801..1358951_POSITIVE 468 148 102 56 12 NC_002950:PG0537|3end_aminoacyl-histidine_dipeptidase_588394..588544_POSITIVE 440 270 223 67 15 NC_002950:PG0447|3end_hypothetical_protein_488176..488326_POSITIVE 427 140 94 62 13 NC_002950:PG0138|3end_malonyl_CoA-acyl_carrier_protein_transacylase_161634..161784_POSITIVE 405 260 212 119 54 NC_002950:PG1649|3end_hypothetical_protein_1730030..1730180_NEGATIVE 391 149 102 79 32 NC_002950:PG0618|3end_alkyl_hydroperoxide_reductase,_C_subunit_671018..671168_POSITIVE 384 72 40 127 84 NC_002950:PG2171|3end_D-isomer_specific_2-hydroxyacid_dehydrogenase_family_protein_2278013..2278163_NEGATIVE 363 140 99 53 7 NC_002950:PG2207|3end_hypothetical_protein_2319142..2319292_NEGATIVE 351 287 241 64 11 NC_002950:PG2098|3end_hypothetical_protein_2206459..2206609_NEGATIVE 349 90 45 149 90 NC_002950:PG0804|3end_flavodoxin_860557..860707_NEGATIVE 348 150 101 68 18 NC_002950:PG0769|3end_fibronectin_type_III_domain_protein_822555..822705_NEGATIVE 348 110 62 150 89 NC_002950:PG0246|3end_hypothetical_protein_281050..281200_NEGATIVE 347 286 241 119 69 NC_002950:PG1389|3end_DNA-binding_protein,_histone-like_family_1470870..1471020_NEGATIVE 346 270 230 130 89 NC_002950:PG0555|3end_DNA-binding_protein,_histone-like_family_611716..611866_NEGATIVE 345 287 246 60 22 NC_002950:PG1495|3end_DNA_topoisomerase_III_1573416..1573566_POSITIVE 344 50 3 111 61 NC_002950:PG1855|3end_carboxyl-terminal_protease_1953842..1953992_NEGATIVE 343 210 166 66 12 NC_002950:PG2190|3end_cell-division_ATP-binding_protein_2297169..2297319_NEGATIVE 343 268 221 151 101 NC_002950:PG1701|3end_glutamine_amidotransferase,_class_II/dipeptidase_1786145..1786295_NEGATIVE 341 87 41 107 56 NC_002950:PG2158|3end_hypothetical_protein_2264473..2264623_POSITIVE 341 342 304 105 64 NC_002950:PG1778|3end_hypothetical_protein_1867922..1868072_POSITIVE