Origin IGS: tgaggaaaagggggcttagaacggcattaaaacgccgtttaagagggtggtaaaatcggagtggttttatcaccctttttacatgtattcgaaggcaattttcagggctggttatgcacgtggttatgcaaagtggttacgcatttttgtaaaagtggttatgcaaaaataggttttgacggggtatgatacagtggggggaaaatactacttttttaatgatattcgcatttatgccaccgatagcccccccctaaatgccaactgtttttgaaactctaccttattaaataaggctatatcaagcactttcctattttcaagggtgttaaagaggggggggatagagaaaagggggagaaagggatgggactggagggttatggtgtatcttctcgttattctttctcgtaccaacgtcctcccttgataactctaaagacgtcta .........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 tagacgtctttagagttatcaagggaggacgttggtacgagaaagaataacgagaagatacaccataaccctccagtcccatccctttctcccccttttctctatcccccccctctttaacacccttgaaaataggaaagtgcttgatatagccttatttaataaggtagagtttcaaaaacagttggcatttaggggggggctatcggtggcataaatgcgaatatcattaaaaaagtagtattttccccccactgtatcataccccgtcaaaacctatttttgcataaccacttttacaaaaatgcgtaaccactttgcataaccacgtgcataaccagccctgaaaattgccttcgaatacatgtaaaaagggtgataaaaccactccgattttaccaccctcttaaacggcgttttaatgccgttctaagcccccttttcctca Mask Tandem Repeat Region ================================================ tgaggaaaagggggcttagaacggcattaaaacgccgtttaagagggtggtaaaatcggagtggttttatcaccctttttacatgtattcgaaggcaattttcagggctggttatgcacgtggttatgcaaagtggttacgcatttttgtaaaagtggttatgcaaaaataggttttgacggggtatgatacagtggggggaaaatactacttttttaatgatattcgcatttatgccaccgatagcccccccctaaatgccaactgtttttgaaactctaccttattaaataaggctatatcaagcactttcctattttcaagggtgttaaagaggggggggatagagaaaagggggagaaagggatgggactggagggttatggtgtatcttctcgttattctttctcgtaccaacgtcctcccttgataactctaaagacgtcta Find is-nt database================================================ Query_seq: PI0327:PI0328|PI0327:PI0328:hypothetical protein:conserved hypothetical protein:->->:309168..309615 448 tgaggaaaagggggcttagaacggcattaaaacgccgtttaagagggtggtaaaatcggagtggttttatcaccctttttacatgtattcgaaggcaattttcagggctggttatgcacgtggttatgcaaagtggttacgcatttttgtaaaagtggttatgcaaaaataggttttgacggggtatgatacagtggggggaaaatactacttttttaatgatattcgcatttatgccaccgatagcccccccctaaatgccaactgtttttgaaactctaccttattaaataaggctatatcaagcactttcctattttcaagggtgttaaagaggggggggatagagaaaagggggagaaagggatgggactggagggttatggtgtatcttctcgttattctttctcgtaccaacgtcctcccttgataactctaaagacgtcta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI0327:PI0328|PI0327:PI0328:hypothetical protein:conserved hypothetical protein:->->:309168..309615 448 tgaggaaaagggggcttagaacggcattaaaacgccgtttaagagggtggtaaaatcggagtggttttatcaccctttttacatgtattcgaaggcaattttcagggctggttatgcacgtggttatgcaaagtggttacgcatttttgtaaaagtggttatgcaaaaataggttttgacggggtatgatacagtggggggaaaatactacttttttaatgatattcgcatttatgccaccgatagcccccccctaaatgccaactgtttttgaaactctaccttattaaataaggctatatcaagcactttcctattttcaagggtgttaaagaggggggggatagagaaaagggggagaaagggatgggactggagggttatggtgtatcttctcgttattctttctcgtaccaacgtcctcccttgataactctaaagacgtcta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI0327:PI0328|PI0327:PI0328:hypothetical protein:conserved hypothetical protein:->->:309168..309615 448 tgaggaaaagggggcttagaacggcattaaaacgccgtttaagagggtggtaaaatcggagtggttttatcaccctttttacatgtattcgaaggcaattttcagggctggttatgcacgtggttatgcaaagtggttacgcatttttgtaaaagtggttatgcaaaaataggttttgacggggtatgatacagtggggggaaaatactacttttttaatgatattcgcatttatgccaccgatagcccccccctaaatgccaactgtttttgaaactctaccttattaaataaggctatatcaagcactttcctattttcaagggtgttaaagaggggggggatagagaaaagggggagaaagggatgggactggagggttatggtgtatcttctcgttattctttctcgtaccaacgtcctcccttgataactctaaagacgtcta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgaggaaaagggggcttagaacggcattaaaacgccgtttaagagggtggtaaaatcggagtggttttatcaccctttttacatgtattcgaaggcaattttcagggctggttatgcacgtggttatgcaaagtggttacgcatttttgtaaaagtggttatgcaaaaataggttttgacggggtatgatacagtggggggaaaatactacttttttaatgatattcgcatttatgccaccgatagcccccccctaaatgccaactgtttttgaaactctaccttattaaataaggctatatcaagcactttcctattttcaagggtgttaaagaggggggggatagagaaaagggggagaaagggatgggactggagggttatggtgtatcttctcgttattctttctcgtaccaacgtcctcccttgataactctaaagacgtcta Predict ORF larger than 30AA ================================================ Protein_Len: 48 Strand: + Start: 26 End: 169 ......................... M K T P F K R V V K S E W F Y H P F Y M Y S K A I F R A G Y A R G Y A K W L R I F V K V V M Q K ....................................................................................................................................................................................................................................................................................... Protein_Len: 44 Strand: + Start: 55 End: 186 ...................................................... M G V V L S P F L H V F E G N F Q G W L C T W L C K V V T H F C K S G Y A K I G F D G V ...................................................................................................................................................................................................................................................................... Protein_Len: 32 Strand: + Start: 176 End: 271 ............................................................................................................................................................................... M T G Y D T V G G K Y Y F F N D I R I Y A T D S P P L N A N C F ................................................................................................................................................................................. Protein_Len: 43 Strand: + Start: 299 End: 427 .......................................................................................................................................................................................................................................................................................................... M S S T F L F S R V L K R G G I E K R G R K G W D W R V M V Y L L V I L S R T N V L P ..................... Protein_Len: 49 Strand: + Start: 301 End: 447 ............................................................................................................................................................................................................................................................................................................ M K H F P I F K G V K E G G D R E K G E K G M G L E G Y G V S S R Y S F S Y Q R P P L I T L K T S . Protein_Len: 60 Strand: - Start: 235 End: 417 .......................................................................................................................................................................................................................................... V S L G G R F A L Q K Q F E V K N F L A I D L V K R N E L T N F L P P I S F L P L F P H S Q L T I T Y R R T I R E R V M ............................... Protein_Len: 35 Strand: - Start: 140 End: 244 ........................................................................................................................................... A N K Y F H N H L F L N Q R P I I C H P S F V V K K I I N A N I G G M ............................................................................................................................................................................................................ Protein_Len: 42 Strand: - Start: 2 End: 127 . L F L P S L V A N F R R K L P H Y F R L P K I V R K V H I R L C N E P S T I C T T M ................................................................................................................................................................................................................................................................................................................................. tgaggaaaagggggcttagaacggcattaaaacgccgtttaagagggtggtaaaatcggagtggttttatcaccctttttacatgtattcgaaggcaattttcagggctggttatgcacgtggttatgcaaagtggttacgcatttttgtaaaagtggttatgcaaaaataggttttgacggggtatgatacagtggggggaaaatactacttttttaatgatattcgcatttatgccaccgatagcccccccctaaatgccaactgtttttgaaactctaccttattaaataaggctatatcaagcactttcctattttcaagggtgttaaagaggggggggatagagaaaagggggagaaagggatgggactggagggttatggtgtatcttctcgttattctttctcgtaccaacgtcctcccttgataactctaaagacgtcta 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================================================ tgaggaaaagggggcttagaacggcattaaaacgccgtttaagagggtggtaaaatcggagtggttttatcaccctttttacatgtattcgaaggcaattttcagggctggttatgcacgtggttatgcaaagtggttacgcatttttgtaaaagtggttatgcaaaaataggttttgacggggtatgatacagtggggggaaaatactacttttttaatgatattcgcatttatgccaccgatagcccccccctaaatgccaactgtttttgaaactctaccttattaaataaggctatatcaagcactttcctattttcaagggtgttaaagaggggggggatagagaaaagggggagaaagggatgggactggagggttatggtgtatcttctcgttattctttctcgtaccaacgtcctcccttgataactctaaagacgtcta Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 100 HP_score: -12.0 Tail_Score: -4.74453 Start: 45 End: 75 Full_Region: AAACGCCGTTTAAGA GGGTGGTAAAATCG GAG TGGTTTTATCACCC TTTTTACATGTATTC ............................................GGGTGGTAAAATCGGAGTGGTTTTATCACCC..................................................................................................................................................................................................................................................................................................................................................................................... TransTerm Strand: - Conf: 58 HP_score: -6.9 Tail_Score: -3.0264 Start: 45 End: 75 Full_Region: gaatacatgtaaaaa gggtgataaaacc actcc gattttaccaccc tcttaaacggcgttt ............................................gggtgataaaaccactccgattttaccaccc..................................................................................................................................................................................................................................................................................................................................................................................... Find igs database================================================ Query_seq: PI0327:PI0328|PI0327:PI0328:hypothetical protein:conserved hypothetical protein:->->:309168..309615 448 tgaggaaaagggggcttagaacggcattaaaacgccgtttaagagggtggtaaaatcggagtggttttatcaccctttttacatgtattcgaaggcaattttcagggctggttatgcacgtggttatgcaaagtggttacgcatttttgtaaaagtggttatgcaaaaataggttttgacggggtatgatacagtggggggaaaatactacttttttaatgatattcgcatttatgccaccgatagcccccccctaaatgccaactgtttttgaaactctaccttattaaataaggctatatcaagcactttcctattttcaagggtgttaaagaggggggggatagagaaaagggggagaaagggatgggactggagggttatggtgtatcttctcgttattctttctcgtaccaacgtcctcccttgataactctaaagacgtcta Intra-Species Hit: Count: 2 Min: 1 Max: 448 Len: 448 Subject: pint_PI0327_PI0328|hypothetical protein:conserved hypothetical protein|POSITIVE:POSITIVE|[309168,309615]|448 HSP 1 e-value: 0.0 bit: 793.0 Len: 448 Query Start:1 Query End:448 Subject Strand: POSITIVE Subject Start: 1 Subject End: 448 tgaggaaaagggggcttagaacggcattaaaacgccgtttaagagggtggtaaaatcggagtggttttatcaccctttttacatgtattcgaaggcaattttcagggctggttatgcacgtggttatgcaaagtggttacgcatttttgtaaaagtggttatgcaaaaataggttttgacggggtatgatacagtggggggaaaatactacttttttaatgatattcgcatttatgccaccgatagnnnnnnnntaaatgccaactgtttttgaaactctaccttattaaataaggctatatcaagcactttcctattttcaagggtgttaaagannnnnnnnatagagaaaagggggagaaagggatgggactggagggttatggtgtatcttctcgttattctttctcgtaccaacgtcctcccttgataactctaaagacgtcta tgaggaaaagggggcttagaacggcattaaaacgccgtttaagagggtggtaaaatcggagtggttttatcaccctttttacatgtattcgaaggcaattttcagggctggttatgcacgtggttatgcaaagtggttacgcatttttgtaaaagtggttatgcaaaaataggttttgacggggtatgatacagtggggggaaaatactacttttttaatgatattcgcatttatgccaccgatagcccccccctaaatgccaactgtttttgaaactctaccttattaaataaggctatatcaagcactttcctattttcaagggtgttaaagaggggggggatagagaaaagggggagaaagggatgggactggagggttatggtgtatcttctcgttattctttctcgtaccaacgtcctcccttgataactctaaagacgtcta Subject: pint_PI1621_PI1622|hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[1545801,1546921]|1121 HSP 1 e-value: 0.0 bit: 729.0 Len: 448 Query Start:1 Query End:448 Subject Strand: POSITIVE Subject Start: 1 Subject End: 448 tgaggaaaagggggcttagaacggcattaaaacgccgtttaagagggtggtaaaatcggagtggttttatcaccctttttacatgtattcgaaggcaattttcagggctggttatgcacgtggttatgcaaagtggttacgcatttttgtaaaagtggttatgcaaaaataggttttgacggggtatgatacagtggggggaaaatactacttttttaatgatattcgcatttatgccaccgatagnnnnnnnntaaatgccaactgtttttgaaactctaccttattaaataaggctatatcaagcactttcctattttcaagggtgttaaagannnnnnnnatagagaaaagggggagaaagggatgggactggagggttatggtgtatcttctcgttattctttctcgtaccaacgtcctcccttgataactctaaagacgtcta tgaggaaaaaggggcttagaacgtcattaaaacgccgtttaagagggtggtaaaatcggagtggttttatcaccctttttacatgtattcgaaggcaattttcaggactggttatgcacgtggttatgcaaagtggttacgcatttttgtaaaagtggttatgcaaaaataggttttgatggggtatgatacagtggggggaaaatactacttttttaatgatattcgcatttatgccaccgatagcccccccctaaatgccacctgtttttgaaactctaccttattaaataacgctatatcaagcactttcctattttcaagggtgttaaagaggggggggatagaaaaaagggggagaaagggatgggactggagggttatggtgtatcttctcgttattcttgctcgtaccaacgtcctcccttgataactctaaagacgtcta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGAGGAAAAGGGGGCUUAGAACGGCAUUAAAACGCCGUUUAAGAGGGUGGUAAAAUCGGAGUGGUUUUAUCACCCUUUUUACAUGUAUUCGAAGGCAAUUUUCAGGGCUGGUUAUGCACGUGGUUAUGCAAAGUGGUUACGCAUUUUUGUAAAAGUGGUUAUGCAAAAAUAGGUUUUGACGGGGUAUGAUACAGUGGGGGGAAAAUACUACUUUUUUAAUGAUAUUCGCAUUUAUGCCACCGAUAGCCCCCCCCUAAAUGCCAACUGUUUUUGAAACUCUACCUUAUUAAAUAAGGCUAUAUCAAGCACUUUCCUAUUUUCAAGGGUGUUAAAGAGGGGGGGGAUAGAGAAAAGGGGGAGAAAGGGAUGGGACUGGAGGGUUAUGGUGUAUCUUCUCGUUAUUCUUUCUCGUACCAACGUCCUCCCUUGAUAACUCUAAAGACGUCUA .(((...(((((((....(((((((........)))))))(((((((((((((((((.....)))))))))))))))))..............(((..(((((..((.((((.((((.....(((((((...((.(..((..(((((((((..........)))))))))..))..).))...)))))))..(((((..........)))))...............))))....)))))).....(((((((((.((((((....((.(((((.......((((((...)))))).....))))).))...............))))))....)))))))))...)))))..((..(((((((((....(((.(((((((........))))))).))).)))))))))...))...)))))))))).....)))............ (-129.51) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAGACGUCUUUAGAGUUAUCAAGGGAGGACGUUGGUACGAGAAAGAAUAACGAGAAGAUACACCAUAACCCUCCAGUCCCAUCCCUUUCUCCCCCUUUUCUCUAUCCCCCCCCUCUUUAACACCCUUGAAAAUAGGAAAGUGCUUGAUAUAGCCUUAUUUAAUAAGGUAGAGUUUCAAAAACAGUUGGCAUUUAGGGGGGGGCUAUCGGUGGCAUAAAUGCGAAUAUCAUUAAAAAAGUAGUAUUUUCCCCCCACUGUAUCAUACCCCGUCAAAACCUAUUUUUGCAUAACCACUUUUACAAAAAUGCGUAACCACUUUGCAUAACCACGUGCAUAACCAGCCCUGAAAAUUGCCUUCGAAUACAUGUAAAAAGGGUGAUAAAACCACUCCGAUUUUACCACCCUCUUAAACGGCGUUUUAAUGCCGUUCUAAGCCCCCUUUUCCUCA ............(((..(..(((((..((((..((((.(((((((......((((((............................))))))....)))))))...((((((((..........(((.......))).(((((((.......(((((((...)))))))...(((.....)))....))))))).))))))))....((((((...((((((...................)))))).....)))))).....)))).))))........(((((((((................(((((.........))))).....((.(((....((....)).....)))...)).....)))))))))(((((.(((((.(.....).))))).))))).((((((((((((....)))))))).))))..))))))..))). (-100.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 361 255 221 120 76 pint:PI2162|5end_conserved_hypothetical_protein_2108796..2109026_POSITIVE 357 425 383 104 60 pint:PI2005|5end_potassium_uptake_protein_1962950..1963180_POSITIVE 353 369 324 93 45 pint:PI1755|5end_RNA_polymerase_sigma-70_factor,_ECF_subfamily_1681930..1682160_POSITIVE 347 378 337 59 5 pint:PI0608|5end_isochorismate_synthase_555487..555717_POSITIVE 346 370 322 113 62 pint:PI1579|5end_penicillin-binding_protein_2_1505713..1505943_POSITIVE 334 412 374 184 152 pint:PI0265|5end_conjugative_transposon_protein,_TraO_257296..257526_POSITIVE 332 369 325 195 150 pint:PI0739|5end_conserved_hypothetical_protein_671794..672024_POSITIVE 332 59 14 170 129 pint:PI0435|5end_30S_ribosomal_protein_S21_406997..407227_POSITIVE 330 50 9 161 123 pint:PI0930|5end_alpha-L-fucosidase_precursor_860977..861207_POSITIVE 329 41 10 134 102 pint:PI0654|5end_K+-dependent_Na+/Ca+_exchanger_related-protein_596283..596513_POSITIVE 320 388 341 146 105 pint:PI1918|5end_uracil-DNA_glycosylase_1861566..1861796_POSITIVE 319 368 322 229 187 pint:PI1548|5end_conserved_hypothetical_protein_1465301..1465531_POSITIVE 318 379 334 48 4 pint:PI1968|5end_hypothetical_protein_1924378..1924608_POSITIVE 316 70 24 182 139 pint:PI2014|5end_conserved_hypothetical_protein_1971471..1971701_POSITIVE 315 254 227 224 184 pint:PI0627|5end_conserved_hypothetical_protein_575618..575848_POSITIVE 315 387 341 114 65 pint:PI0181|5end_conserved_hypothetical_protein_173435..173665_POSITIVE 313 379 334 63 8 pint:PI0668|5end_peptidyl-prolyl_cis-trans_isomerase_SlyD,_FKBP-type_(peptidylprolyl_isomerase)_610216..610446_POSITIVE 312 197 156 105 60 pint:PI1195|5end_hypothetical_protein_1113171..1113401_POSITIVE 308 380 334 166 112 pint:PI1408|5end_glucose-1-phosphate_thymidylyltransferase_1329055..1329285_POSITIVE 308 380 336 68 12 pint:PI0929|5end_copper_homeostasis_protein_860294..860524_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 397 79 41 50 12 pint:PI1621|3end_hypothetical_protein_1545740..1545890_POSITIVE 397 79 41 50 12 pint:PI0327|3end_hypothetical_protein_309107..309257_POSITIVE 368 367 322 54 4 pint:PI1444|3end_protease_ClpB_1368137..1368287_POSITIVE 359 380 333 123 71 pint:PI2095|3end_hypothetical_protein_2050216..2050366_POSITIVE 357 425 383 78 34 pint:PI2004|3end_1-deoxy-D-xylulose_5-phosphate_synthase_1963004..1963154_POSITIVE 354 397 354 143 93 pint:PI0221|3end_DNA_methylase,_site-specific_DNA-methyltransferase_(adenine-specific)_217796..217946_POSITIVE 353 369 324 93 45 pint:PI1754|3end_conserved_hypothetical_protein_1682010..1682160_POSITIVE 346 370 322 60 9 pint:PI1578|3end_rod_shape-determining_protein_1505740..1505890_POSITIVE 345 369 334 65 23 pint:PI1512|3end_hypothetical_protein_1429893..1430043_POSITIVE 325 49 2 93 39 pint:PI0129|3end_hypothetical_protein_121941..122091_POSITIVE 320 388 341 96 55 pint:PI1917|3end_uracil-DNA_glycosylase_1861596..1861746_POSITIVE 314 388 341 143 83 pint:PI0059|3end_peptide_chain_release_factor_RF-2_58171..58321_POSITIVE 308 380 334 147 93 pint:PI1407|3end_conserved_hypothetical_protein_1329116..1329266_POSITIVE 307 358 320 50 14 pint:PI2114|3end_conserved_hypothetical_protein_2064789..2064939_POSITIVE 300 136 93 52 4 pint:PI0906|3end_hypothetical_protein_836008..836158_POSITIVE 297 49 9 151 114 pint:PI0929|3end_copper_homeostasis_protein_861048..861198_POSITIVE 297 380 331 98 47 pint:PI0896|3end_2-oxoglutarate_oxidoreductase,_alpha_subunit_828276..828426_POSITIVE 295 390 349 111 68 pint:PI0696|3end_NADH_pyrophosphatase,_MutT_family_hydrolase_(NAD+_diphosphatase)_633600..633750_POSITIVE 293 360 314 102 57 pint:PI1290|3end_ATP_synthase,_beta_subunit_1204575..1204725_POSITIVE 292 369 325 93 46 pint:PI0489|3end_probable_cardiolipin_synthetase_449108..449258_POSITIVE