Origin IGS: aattaatcaatgtttatagttgaacatatatttttatcaaaggcaaatataacatttttttttgacttatggtagatgtttgtacttattttgtgttaatttttttgtaaatagtttatttaacaaactttagttggcagaataagtttagtttgcagctaaattagtaatttcgcaaagtttaattt .........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 aaattaaactttgcgaaattactaatttagctgcaaactaaacttattctgccaactaaagtttgttaaataaactatttacaaaaaaattaacacaaaataagtacaaacatctaccataagtcaaaaaaaaatgttatatttgcctttgataaaaatatatgttcaactataaacattgattaatt Mask Tandem Repeat Region ================================================ aattaatcaatgtttatagttgaacatatatttttatcaaaggcaaatataacatttttttttgacttatggtagatgtttgtacttattttgtgttaatttttttgtaaatagtttatttaacaaactttagttggcagaataagtttagtttgcagctaaattagtaatttcgcaaagtttaattt Find is-nt database================================================ Query_seq: PI1079:PI1080|PI1079:PI1080:conserved hypothetical protein:conserved hypothetical protein; possible outer membrane lipoprotein:->->:1000216..1000403 188 aattaatcaatgtttatagttgaacatatatttttatcaaaggcaaatataacatttttttttgacttatggtagatgtttgtacttattttgtgttaatttttttgtaaatagtttatttaacaaactttagttggcagaataagtttagtttgcagctaaattagtaatttcgcaaagtttaattt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI1079:PI1080|PI1079:PI1080:conserved hypothetical protein:conserved hypothetical protein; possible outer membrane lipoprotein:->->:1000216..1000403 188 aattaatcaatgtttatagttgaacatatatttttatcaaaggcaaatataacatttttttttgacttatggtagatgtttgtacttattttgtgttaatttttttgtaaatagtttatttaacaaactttagttggcagaataagtttagtttgcagctaaattagtaatttcgcaaagtttaattt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI1079:PI1080|PI1079:PI1080:conserved hypothetical protein:conserved hypothetical protein; possible outer membrane lipoprotein:->->:1000216..1000403 188 aattaatcaatgtttatagttgaacatatatttttatcaaaggcaaatataacatttttttttgacttatggtagatgtttgtacttattttgtgttaatttttttgtaaatagtttatttaacaaactttagttggcagaataagtttagtttgcagctaaattagtaatttcgcaaagtttaattt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aattaatcaatgtttatagttgaacatatatttttatcaaaggcaaatataacatttttttttgacttatggtagatgtttgtacttattttgtgttaatttttttgtaaatagtttatttaacaaactttagttggcagaataagtttagtttgcagctaaattagtaatttcgcaaagtttaattt Predict ORF larger than 30AA ================================================ aattaatcaatgtttatagttgaacatatatttttatcaaaggcaaatataacatttttttttgacttatggtagatgtttgtacttattttgtgttaatttttttgtaaatagtttatttaacaaactttagttggcagaataagtttagtttgcagctaaattagtaatttcgcaaagtttaattt 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================================================ aattaatcaatgtttatagttgaacatatatttttatcaaaggcaaatataacatttttttttgacttatggtagatgtttgtacttattttgtgttaatttttttgtaaatagtttatttaacaaactttagttggcagaataagtttagtttgcagctaaattagtaatttcgcaaagtttaattt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PI1079:PI1080|PI1079:PI1080:conserved hypothetical protein:conserved hypothetical protein; possible outer membrane lipoprotein:->->:1000216..1000403 188 aattaatcaatgtttatagttgaacatatatttttatcaaaggcaaatataacatttttttttgacttatggtagatgtttgtacttattttgtgttaatttttttgtaaatagtttatttaacaaactttagttggcagaataagtttagtttgcagctaaattagtaatttcgcaaagtttaattt Intra-Species Hit: Count: 1 Min: 1 Max: 188 Len: 188 Subject: pint_PI1079_PI1080|conserved hypothetical protein:conserved hypothetical protein; possible outer membrane lipoprotein|POSITIVE:POSITIVE|[1000216,1000403]|188 HSP 1 e-value: 6.0E-74 bit: 278.0 Len: 188 Query Start:1 Query End:188 Subject Strand: POSITIVE Subject Start: 1 Subject End: 188 aattaatcaatgtttatagttgaacatatatttttatcaaaggcaaatataacannnnnnnnngacttatggtagatgtttgtacttattttgtgttaannnnnnngtaaatagtttatttaacaaactttagttggcagaataagtttagtttgcagctaaattagtaatttcgcaaagtttaattt aattaatcaatgtttatagttgaacatatatttttatcaaaggcaaatataacatttttttttgacttatggtagatgtttgtacttattttgtgttaatttttttgtaaatagtttatttaacaaactttagttggcagaataagtttagtttgcagctaaattagtaatttcgcaaagtttaattt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUUAAUCAAUGUUUAUAGUUGAACAUAUAUUUUUAUCAAAGGCAAAUAUAACAUUUUUUUUUGACUUAUGGUAGAUGUUUGUACUUAUUUUGUGUUAAUUUUUUUGUAAAUAGUUUAUUUAACAAACUUUAGUUGGCAGAAUAAGUUUAGUUUGCAGCUAAAUUAGUAAUUUCGCAAAGUUUAAUUU .........(((((((....))))))).....(((((((.(((((((.............)))).))).)))))))..((((((((((((((((..(((((..((((((((((...))))).)))))....))))))))))))))))(((((.....)))))............)))))......... (-28.62) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAUUAAACUUUGCGAAAUUACUAAUUUAGCUGCAAACUAAACUUAUUCUGCCAACUAAAGUUUGUUAAAUAAACUAUUUACAAAAAAAUUAACACAAAAUAAGUACAAACAUCUACCAUAAGUCAAAAAAAAAUGUUAUAUUUGCCUUUGAUAAAAAUAUAUGUUCAACUAUAAACAUUGAUUAAUU .((((((..((((((................))))))....(((((((.((..........(((((.(((((...))))))))))..........)).)))))))...(((((.((......((((((...(((((...)))))...)))))).....)).)))))............)))))).... (-16.14) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 262 176 132 71 25 pint:PI0727|5end_integrase_659261..659491_POSITIVE 235 179 135 214 157 pint:PI0684|5end_coproporphyrinogen_III_oxidase_619357..619587_POSITIVE 235 179 135 149 92 pint:PI0683|5end_hypothetical_protein_619292..619522_POSITIVE 233 46 9 141 101 pint:PI1055|5end_aspartokinase_974909..975139_POSITIVE 227 161 126 182 153 pint:PI1372|5end_thiamine_monophosphate_kinase_1292899..1293129_POSITIVE 224 163 128 191 154 pint:PI1295|5end_hypothetical_protein_1208636..1208866_POSITIVE 224 163 128 45 8 pint:PI1294|5end_hypothetical_protein_1208490..1208720_POSITIVE 218 177 134 219 176 pint:PI1008|5end_cytochrome_c_nitrite_reductase,_small_subunit_928784..929014_POSITIVE 213 106 67 204 166 pint:PI1300|5end_probable_glycosyltransferase_1213190..1213420_POSITIVE 210 176 132 139 97 pint:PI0896|5end_2-oxoglutarate_oxidoreductase,_alpha_subunit_827138..827368_POSITIVE 205 180 135 160 118 pint:PI2116|5end_fumarate_reductase/succinate_dehydrogenase,_iron-sulfur_protein_2065215..2065445_POSITIVE 204 176 134 193 154 pint:PI1947|5end_hypothetical_protein_1902534..1902764_POSITIVE 202 177 138 197 158 pint:PI2052|5end_hypothetical_protein_2008594..2008824_POSITIVE 202 176 133 105 60 pint:PI0176|5end_hypothetical_protein_168230..168460_POSITIVE 201 158 124 163 128 pint:PI1629|5end_hypothetical_protein_1551707..1551937_POSITIVE 200 97 63 231 193 pint:PI0295|5end_lysine_decarboxylase_276846..277076_POSITIVE 199 180 132 124 82 pint:PI1445|5end_hypothetical_protein_1368403..1368633_POSITIVE 196 159 113 64 27 pint:PI0908|5end_conserved_hypothetical_protein_836870..837100_POSITIVE 194 176 133 44 1 pint:PI1918|5end_uracil-DNA_glycosylase_1861566..1861796_POSITIVE 193 96 52 46 1 pint:PI1837|5end_aspartate_ammonia-lyase_1778953..1779183_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 285 180 132 83 41 pint:PI0953|3end_hypothetical_protein_885390..885540_POSITIVE 285 180 132 141 99 pint:PI0951|3end_hypothetical_protein_885448..885598_POSITIVE 267 175 131 121 74 pint:PI1084|3end_threonyl-tRNA_synthetase_1004690..1004840_POSITIVE 243 180 131 127 78 pint:PI1146|3end_translation_initiation_factor_IF3_1073503..1073653_POSITIVE 235 179 135 149 92 pint:PI0682|3end_hypothetical_protein_619372..619522_POSITIVE 233 46 9 130 90 pint:PI1054|3end_conserved_hypothetical_protein_974978..975128_POSITIVE 230 162 126 66 37 pint:PI1267|3end_probable_integrase_1186475..1186625_POSITIVE 210 176 132 115 73 pint:PI0895|3end_2-oxoglutarate_oxidoreductase,_beta_subunit,_possible_ketoisovalerate_oxidoreductase,__vorA_827194..827344_POSITIVE 207 179 135 89 43 pint:PI1240|3end_probable_Xaa-Pro_dipeptidase_(aminopeptidase_P)_1166272..1166422_POSITIVE 206 170 123 122 81 pint:PI1672|3end_conserved_hypothetical_protein;_possible_DNA-binding_protein,_histone-like_family_1587529..1587679_POSITIVE 200 97 63 111 73 pint:PI0294|3end_conserved_hypothetical_protein_276806..276956_POSITIVE 197 109 66 95 54 pint:PI1011|3end_cytochrome_c_biogenesis_protein_CycY_932989..933139_POSITIVE 196 109 71 108 79 pint:PI0297|3end_hypothetical_protein_277916..278066_POSITIVE 194 94 54 128 83 pint:PI1168|3end_hypothetical_protein_1089922..1090072_POSITIVE 194 94 54 96 51 pint:PI1167|3end_hypothetical_protein_1089890..1090040_POSITIVE 193 162 125 61 33 pint:PI0888|3end_hypothetical_protein_818613..818763_POSITIVE 193 95 62 98 67 pint:PI0583|3end_hypothetical_protein_526276..526426_POSITIVE 189 98 70 124 92 pint:PI2117|3end_fumarate_reductase/succinate_dehydrogenase_flavoprotein_subunit,_C-terminal_2066684..2066834_POSITIVE 189 80 41 89 39 pint:PI1346|3end_hypothetical_protein_1261028..1261178_POSITIVE 189 177 140 114 66 pint:PI1089|3end_conserved_hypothetical_protein_1014040..1014190_POSITIVE