Origin IGS: cgagatttcattaaatcatttagcgtgcaaaattactaaataaaaataagataggcaatatttcttttatctttaatcttaataatgcctaactgatagaatttatgcta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tagcataaattctatcagttaggcattattaagattaaagataaaagaaatattgcctatcttatttttatttagtaattttgcacgctaaatgatttaatgaaatctcg Mask Tandem Repeat Region ================================================ cgagatttcattaaatcatttagcgtgcaaaattactaaataaaaataagataggcaatatttcttttatctttaatcttaataatgcctaactgatagaatttatgcta Find is-nt database================================================ Query_seq: PI1036:PI1037|PI1036:PI1037:ATP-dependent Lon protease:probable methyltransferase:->->:957058..957167 110 cgagatttcattaaatcatttagcgtgcaaaattactaaataaaaataagataggcaatatttcttttatctttaatcttaataatgcctaactgatagaatttatgcta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI1036:PI1037|PI1036:PI1037:ATP-dependent Lon protease:probable methyltransferase:->->:957058..957167 110 cgagatttcattaaatcatttagcgtgcaaaattactaaataaaaataagataggcaatatttcttttatctttaatcttaataatgcctaactgatagaatttatgcta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI1036:PI1037|PI1036:PI1037:ATP-dependent Lon protease:probable methyltransferase:->->:957058..957167 110 cgagatttcattaaatcatttagcgtgcaaaattactaaataaaaataagataggcaatatttcttttatctttaatcttaataatgcctaactgatagaatttatgcta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 cgagatttcattaaatcatttagcgtgcaaaattactaaataaaaataagataggcaatatttcttttatctttaatcttaataatgcctaactgatagaatttatgcta Predict ORF larger than 30AA ================================================ cgagatttcattaaatcatttagcgtgcaaaattactaaataaaaataagataggcaatatttcttttatctttaatcttaataatgcctaactgatagaatttatgcta 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================================================ cgagatttcattaaatcatttagcgtgcaaaattactaaataaaaataagataggcaatatttcttttatctttaatcttaataatgcctaactgatagaatttatgcta Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PI1036:PI1037|PI1036:PI1037:ATP-dependent Lon protease:probable methyltransferase:->->:957058..957167 110 cgagatttcattaaatcatttagcgtgcaaaattactaaataaaaataagataggcaatatttcttttatctttaatcttaataatgcctaactgatagaatttatgcta Intra-Species Hit: Count: 1 Min: 1 Max: 110 Len: 110 Subject: pint_PI1036_PI1037|ATP-dependent Lon protease:probable methyltransferase|POSITIVE:POSITIVE|[957058,957167]|110 HSP 1 e-value: 3.0E-56 bit: 218.0 Len: 110 Query Start:1 Query End:110 Subject Strand: POSITIVE Subject Start: 1 Subject End: 110 cgagatttcattaaatcatttagcgtgcaaaattactaaataaaaataagataggcaatatttcttttatctttaatcttaataatgcctaactgatagaatttatgcta cgagatttcattaaatcatttagcgtgcaaaattactaaataaaaataagataggcaatatttcttttatctttaatcttaataatgcctaactgatagaatttatgcta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CGAGAUUUCAUUAAAUCAUUUAGCGUGCAAAAUUACUAAAUAAAAAUAAGAUAGGCAAUAUUUCUUUUAUCUUUAAUCUUAAUAAUGCCUAACUGAUAGAAUUUAUGCUA ...(((((....)))))...(((((((...((((.(((..........((.((((((.((((....(((....)))....)))).)))))).))..)))))))))))))) (-16.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAGCAUAAAUUCUAUCAGUUAGGCAUUAUUAAGAUUAAAGAUAAAAGAAAUAUUGCCUAUCUUAUUUUUAUUUAGUAAUUUUGCACGCUAAAUGAUUUAAUGAAAUCUCG ((((.(((((...((.((.((((((.((((..................)))).)))))).)).))....)))))(((....)))..))))...(((((....)))))... (-15.07) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 249 36 1 168 131 pint:PI0435|5end_30S_ribosomal_protein_S21_406997..407227_POSITIVE 224 88 49 89 42 pint:PI0303|5end_hypothetical_protein_286946..287176_POSITIVE 201 108 64 177 122 pint:PI1321|5end_conserved_hypothetical_protein_1239764..1239994_POSITIVE 197 99 53 196 148 pint:PI0975|5end_glycine_dehydrogenase_[decarboxylating]_subunit_2_900798..901028_POSITIVE 190 97 52 102 57 pint:PI0040|5end_conserved_hypothetical_protein_(possible_integral_membrane_protein)_41010..41240_POSITIVE 183 59 14 109 64 pint:PI1153|5end_histidine_kinase_sensor_protein_1077116..1077346_POSITIVE 180 90 46 169 119 pint:PI0768|5end_conserved_hypothetical_protein;_possible_acetyltransferase_704072..704302_POSITIVE 177 78 48 165 135 pint:PI1504|5end_non-specific_DNA-binding_protein_1424318..1424548_POSITIVE 176 109 62 72 24 pint:PI2067|5end_hypothetical_protein_2027760..2027990_POSITIVE 176 94 51 228 179 pint:PI1026|5end_uridine_phosphorylase_942300..942530_POSITIVE 175 108 77 189 159 pint:PI0764|5end_permease_697962..698192_POSITIVE 175 103 67 149 99 pint:PI0585|5end_conserved_hypothetical_protein_532660..532890_POSITIVE 172 37 1 208 166 pint:PI1241|5end_probable_phosphoesterase_1166365..1166595_POSITIVE 170 88 48 202 156 pint:PI0892|5end_acyl-ACP_thioesterase_823131..823361_POSITIVE 169 55 15 200 159 pint:PI2028|5end_shikimate_kinase_1982162..1982392_POSITIVE 167 60 12 225 161 pint:PI0657|5end_conserved_hypothetical_protein_601179..601409_POSITIVE 167 110 74 175 136 pint:PI0433|5end_hypothetical_protein_404724..404954_POSITIVE 165 74 48 134 105 pint:PI1602|5end_conserved_hypothetical_protein;_possible_internalin-related_protein_1531025..1531255_POSITIVE 165 75 39 63 24 pint:PI1027|5end_hypothetical_protein_943197..943427_POSITIVE 165 97 62 52 23 pint:PI0440|5end_transcription_antiterminator_410582..410812_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 224 88 49 82 35 pint:PI0302|3end_hypothetical_protein_287019..287169_POSITIVE 201 108 64 94 39 pint:PI1320|3end_conserved_hypothetical_protein_1239761..1239911_POSITIVE 197 99 53 143 95 pint:PI0973|3end_glycine_dehydrogenase_[decarboxylating]_subunit_1_900825..900975_POSITIVE 194 108 65 120 86 pint:PI0948|3end_hypothetical_protein_881978..882128_POSITIVE 190 97 52 89 44 pint:PI0039|3end_conserved_hypothetical_protein;_possible_integral_membrane_protein_41077..41227_POSITIVE 183 59 14 69 24 pint:PI1152|3end_response_regulator/transcriptional_regulator_RprY_1077156..1077306_POSITIVE 176 94 51 80 31 pint:PI1025|3end_tRNA_modification_GTPase_942232..942382_POSITIVE 175 108 77 149 119 pint:PI0763|3end_thymidine_kinase_698002..698152_POSITIVE 173 107 86 68 48 pint:PI0162|3end_ADP-ribosylglycohydrolase_(ADP-ribosyl-[dinitrogen_reductase]_hydrolase)_157001..157151_POSITIVE 171 107 88 93 73 pint:PI2043|3end_hypothetical_protein_1996257..1996407_POSITIVE 170 95 53 55 13 pint:PI1044|3end_excinuclease_ABC,_subunit_A_964639..964789_POSITIVE 169 55 15 88 47 pint:PI2027|3end_arginine_decarboxylase_1982130..1982280_POSITIVE 167 60 12 99 35 pint:PI0656|3end_peptidase_T_(tripeptide_aminopeptidase)_601133..601283_POSITIVE 167 110 74 44 5 pint:PI0431|3end_Xaa-Pro_aminopeptidase_404673..404823_POSITIVE 165 97 62 34 5 pint:PI0439|3end_conserved_hypothetical_protein;_possible_preprotein_translocase_subunit_SecE_410644..410794_POSITIVE 162 56 23 88 55 pint:PI0319|3end_conserved_hypothetical_protein_302048..302198_POSITIVE 160 65 21 129 83 pint:PI0184|3end_possible_fibronectin_type_III_domain_protein_176516..176666_POSITIVE 159 42 1 116 69 pint:PI1450|3end_hypothetical_protein_1372891..1373041_POSITIVE 159 80 49 82 47 pint:PI1444|3end_protease_ClpB_1368137..1368287_POSITIVE 158 108 62 150 91 pint:PI1004|3end_conserved_hypothetical_protein_926217..926367_POSITIVE