Origin IGS: tagtaacaaacccattaaacagtcaaagacgatgaaagaaaaagagtacggctgacatacgagagaagccaccactgaaatccgaaagtaacaacagtattcacccgtcgggaggatatatccaatcctctcggcacaaaacaaagattt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aaatctttgttttgtgccgagaggattggatatatcctcccgacgggtgaatactgttgttactttcggatttcagtggtggcttctctcgtatgtcagccgtactctttttctttcatcgtctttgactgtttaatgggtttgttacta Mask Tandem Repeat Region ================================================ tagtaacaaacccattaaacagtcaaagacgatgaaagaaaaagagtacggctgacatacgagagaagccaccactgaaatccgaaagtaacaacagtattcacccgtcgggaggatatatccaatcctctcggcacaaaacaaagattt Find is-nt database================================================ Query_seq: PI0253:PI0256|PI0253:PI0256:conjugative transposon protein, TraD:conjugative transposon protein, TraE:->->:249034..249183 150 tagtaacaaacccattaaacagtcaaagacgatgaaagaaaaagagtacggctgacatacgagagaagccaccactgaaatccgaaagtaacaacagtattcacccgtcgggaggatatatccaatcctctcggcacaaaacaaagattt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI0253:PI0256|PI0253:PI0256:conjugative transposon protein, TraD:conjugative transposon protein, TraE:->->:249034..249183 150 tagtaacaaacccattaaacagtcaaagacgatgaaagaaaaagagtacggctgacatacgagagaagccaccactgaaatccgaaagtaacaacagtattcacccgtcgggaggatatatccaatcctctcggcacaaaacaaagattt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI0253:PI0256|PI0253:PI0256:conjugative transposon protein, TraD:conjugative transposon protein, TraE:->->:249034..249183 150 tagtaacaaacccattaaacagtcaaagacgatgaaagaaaaagagtacggctgacatacgagagaagccaccactgaaatccgaaagtaacaacagtattcacccgtcgggaggatatatccaatcctctcggcacaaaacaaagattt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tagtaacaaacccattaaacagtcaaagacgatgaaagaaaaagagtacggctgacatacgagagaagccaccactgaaatccgaaagtaacaacagtattcacccgtcgggaggatatatccaatcctctcggcacaaaacaaagattt Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: + Start: 57 End: 149 ........................................................ M R E K P P L K S E S N N S I H P S G G Y I Q S S R H K T K I . Protein_Len: 40 Strand: - Start: 18 End: 137 ................. V T L S S S L F L T R S V Y S L L W W Q F G F T V V T N V R R S S I D L G R P M ............. Protein_Len: 48 Strand: - Start: 1 End: 144 L L L G M L C D F V I F S F S Y P Q C V L S A V V S I R F Y C C Y E G T P L I Y G I R E A C F M ...... tagtaacaaacccattaaacagtcaaagacgatgaaagaaaaagagtacggctgacatacgagagaagccaccactgaaatccgaaagtaacaacagtattcacccgtcgggaggatatatccaatcctctcggcacaaaacaaagattt 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================================================ tagtaacaaacccattaaacagtcaaagacgatgaaagaaaaagagtacggctgacatacgagagaagccaccactgaaatccgaaagtaacaacagtattcacccgtcgggaggatatatccaatcctctcggcacaaaacaaagattt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PI0253:PI0256|PI0253:PI0256:conjugative transposon protein, TraD:conjugative transposon protein, TraE:->->:249034..249183 150 tagtaacaaacccattaaacagtcaaagacgatgaaagaaaaagagtacggctgacatacgagagaagccaccactgaaatccgaaagtaacaacagtattcacccgtcgggaggatatatccaatcctctcggcacaaaacaaagattt Intra-Species Hit: Count: 1 Min: 1 Max: 150 Len: 150 Subject: pint_PI0253_PI0256|conjugative transposon protein, TraD:conjugative transposon protein, TraE|POSITIVE:POSITIVE|[249034,249183]|150 HSP 1 e-value: 5.0E-80 bit: 297.0 Len: 150 Query Start:1 Query End:150 Subject Strand: POSITIVE Subject Start: 1 Subject End: 150 tagtaacaaacccattaaacagtcaaagacgatgaaagaaaaagagtacggctgacatacgagagaagccaccactgaaatccgaaagtaacaacagtattcacccgtcgggaggatatatccaatcctctcggcacaaaacaaagattt tagtaacaaacccattaaacagtcaaagacgatgaaagaaaaagagtacggctgacatacgagagaagccaccactgaaatccgaaagtaacaacagtattcacccgtcgggaggatatatccaatcctctcggcacaaaacaaagattt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAGUAACAAACCCAUUAAACAGUCAAAGACGAUGAAAGAAAAAGAGUACGGCUGACAUACGAGAGAAGCCACCACUGAAAUCCGAAAGUAACAACAGUAUUCACCCGUCGGGAGGAUAUAUCCAAUCCUCUCGGCACAAAACAAAGAUUU ....................((((...................((((((((((.............))))............(....)........))))))....(((((((((((.......)))))))))))..........)))). (-30.52) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAUCUUUGUUUUGUGCCGAGAGGAUUGGAUAUAUCCUCCCGACGGGUGAAUACUGUUGUUACUUUCGGAUUUCAGUGGUGGCUUCUCUCGUAUGUCAGCCGUACUCUUUUUCUUUCAUCGUCUUUGACUGUUUAAUGGGUUUGUUACUA ...........(((..(((((((....(((....)))...((((((.......))))))...)))))))....))).((((((..(((..(((((.....)))))...............(((...)))........)))...)))))). (-29.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 349 90 45 227 182 pint:PI1201|5end_peptidyl-arginine_deiminase_1116598..1116828_POSITIVE 330 87 51 107 60 pint:PI0715|5end_hypothetical_protein_652311..652541_POSITIVE 327 98 51 102 49 pint:PI1535|5end_response_regulator_1454096..1454326_POSITIVE 320 132 95 203 154 pint:PI0336|5end_hypothetical_protein_314499..314729_POSITIVE 301 96 60 120 77 pint:PI0936|5end_conserved_hypothetical_protein_868329..868559_POSITIVE 293 88 50 73 41 pint:PI0932|5end_conserved_hypothetical_protein;_possible_hemin_receptor_863854..864084_POSITIVE 287 69 42 139 110 pint:PI1938|5end_hypothetical_protein_1891854..1892084_POSITIVE 287 147 103 140 94 pint:PI0673|5end_hypothetical_protein_612206..612436_POSITIVE 287 139 101 66 15 pint:PI0365|5end_hypothetical_protein_335721..335951_POSITIVE 286 136 105 41 10 pint:PI0258|5end_conjugative_transposon_protein,_TraG_249722..249952_POSITIVE 281 134 95 170 113 pint:PI2076|5end_hypothetical_protein_2035403..2035633_POSITIVE 280 96 68 127 98 pint:PI0224|5end_conserved_hypothetical_protein_220541..220771_POSITIVE 276 69 24 209 149 pint:PI0918|5end_Fe-S_oxidoreductase,_family_2_847078..847308_POSITIVE 271 89 41 67 24 pint:PI0647|5end_potassium_uptake_protein_587505..587735_POSITIVE 267 136 101 59 24 pint:PI1627|5end_hypothetical_protein_1550445..1550675_POSITIVE 267 143 103 110 57 pint:PI0084|5end_conserved_hypothetical_protein_84195..84425_POSITIVE 266 120 84 107 70 pint:PI1178|5end_histidyl-tRNA_synthetase_1099249..1099479_POSITIVE 265 52 13 87 43 pint:PI0585|5end_conserved_hypothetical_protein_532660..532890_POSITIVE 263 86 49 46 1 pint:PI1043|5end_conserved_hypothetical_protein_960855..961085_POSITIVE 261 110 62 145 100 pint:PI1575|5end_LemA_protein_1501143..1501373_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 349 90 45 151 106 pint:PI1200|3end_carbon-nitrogen_hydrolase/beta-alanine_synthase_1116602..1116752_POSITIVE 327 98 51 92 39 pint:PI1534|3end_ATPase/GTPase_1454166..1454316_POSITIVE 314 84 45 150 114 pint:PI0732|3end_conserved_hypothetical_protein_664367..664517_POSITIVE 287 147 103 84 38 pint:PI0672|3end_conserved_hypothetical_protein_612230..612380_POSITIVE 286 136 105 41 10 pint:PI0257|3end_conjugative_transposon_protein,_TraF_249802..249952_POSITIVE 280 132 100 44 3 pint:PI0335|3end_hypothetical_protein_314420..314570_POSITIVE 280 96 68 89 60 pint:PI0223|3end_topoisomerase_IA_220583..220733_POSITIVE 276 69 24 143 83 pint:PI0917|3end_phosphoglycolate_phosphatase_847092..847242_POSITIVE 268 115 71 42 7 pint:PI0935|3end_collagenase,_protease_868320..868470_POSITIVE 267 78 43 89 49 pint:PI1953|3end_possible_ABC-type_permease_1908582..1908732_POSITIVE 267 136 101 56 21 pint:PI1626|3end_hypothetical_protein_1550522..1550672_POSITIVE 261 110 62 148 103 pint:PI1574|3end_conserved_hypothetical_protein_1501226..1501376_POSITIVE 260 140 91 62 6 pint:PI2027|3end_arginine_decarboxylase_1982130..1982280_POSITIVE 258 137 94 40 3 pint:PI0355|3end_probable__N-acetylmuramoyl-L-alanine_amidase_326698..326848_POSITIVE 257 70 25 135 84 pint:PI1086|3end_pyruvate:ferredoxin_oxidoreductase_1010245..1010395_POSITIVE 256 112 72 99 59 pint:PI1163|3end_single-strand_DNA_binding_protein_1088244..1088394_POSITIVE 255 76 36 58 15 pint:PI0618|3end_acyl-CoA_dehydrogenase_family_protein_569213..569363_POSITIVE 250 85 48 143 109 pint:PI1357|3end_glycosyltransferase_1274259..1274409_POSITIVE 248 137 93 148 96 pint:PI0653|3end_hypothetical_protein_596236..596386_POSITIVE 248 142 103 48 12 pint:PI0603|3end_3-dehydroquinate_synthase_550841..550991_POSITIVE