Origin IGS: aagaataagaataaaaatttgtgagagtaataaaaaataattatctttgcattcgttaaaaactgtactctcacagaatgggaaaaattaagaggaaactcaagaaaataaga .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tcttattttcttgagtttcctcttaatttttcccattctgtgagagtacagtttttaacgaatgcaaagataattattttttattactctcacaaatttttattcttattctt Mask Tandem Repeat Region ================================================ aagaataagaataaaaatttgtgagagtaataaaaaataattatctttgcattcgttaaaaactgtactctcacagaatgggaaaaattaagaggaaactcaagaaaataaga Find is-nt database================================================ Query_seq: PI1523:PI1524|PI1523:PI1524:DNA polymerase III, alpha subunit:phosphatidylserine decarboxylase:->->:1445951..1446063 113 aagaataagaataaaaatttgtgagagtaataaaaaataattatctttgcattcgttaaaaactgtactctcacagaatgggaaaaattaagaggaaactcaagaaaataaga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI1523:PI1524|PI1523:PI1524:DNA polymerase III, alpha subunit:phosphatidylserine decarboxylase:->->:1445951..1446063 113 aagaataagaataaaaatttgtgagagtaataaaaaataattatctttgcattcgttaaaaactgtactctcacagaatgggaaaaattaagaggaaactcaagaaaataaga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI1523:PI1524|PI1523:PI1524:DNA polymerase III, alpha subunit:phosphatidylserine decarboxylase:->->:1445951..1446063 113 aagaataagaataaaaatttgtgagagtaataaaaaataattatctttgcattcgttaaaaactgtactctcacagaatgggaaaaattaagaggaaactcaagaaaataaga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aagaataagaataaaaatttgtgagagtaataaaaaataattatctttgcattcgttaaaaactgtactctcacagaatgggaaaaattaagaggaaactcaagaaaataaga Predict ORF larger than 30AA ================================================ aagaataagaataaaaatttgtgagagtaataaaaaataattatctttgcattcgttaaaaactgtactctcacagaatgggaaaaattaagaggaaactcaagaaaataaga 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================================================ aagaataagaataaaaatttgtgagagtaataaaaaataattatctttgcattcgttaaaaactgtactctcacagaatgggaaaaattaagaggaaactcaagaaaataaga Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PI1523:PI1524|PI1523:PI1524:DNA polymerase III, alpha subunit:phosphatidylserine decarboxylase:->->:1445951..1446063 113 aagaataagaataaaaatttgtgagagtaataaaaaataattatctttgcattcgttaaaaactgtactctcacagaatgggaaaaattaagaggaaactcaagaaaataaga Intra-Species Hit: Count: 1 Min: 1 Max: 113 Len: 113 Subject: pint_PI1523_PI1524|DNA polymerase III, alpha subunit:phosphatidylserine decarboxylase|POSITIVE:POSITIVE|[1445951,1446063]|113 HSP 1 e-value: 5.0E-58 bit: 224.0 Len: 113 Query Start:1 Query End:113 Subject Strand: POSITIVE Subject Start: 1 Subject End: 113 aagaataagaataaaaatttgtgagagtaataaaaaataattatctttgcattcgttaaaaactgtactctcacagaatgggaaaaattaagaggaaactcaagaaaataaga aagaataagaataaaaatttgtgagagtaataaaaaataattatctttgcattcgttaaaaactgtactctcacagaatgggaaaaattaagaggaaactcaagaaaataaga Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAGAAUAAGAAUAAAAAUUUGUGAGAGUAAUAAAAAAUAAUUAUCUUUGCAUUCGUUAAAAACUGUACUCUCACAGAAUGGGAAAAAUUAAGAGGAAACUCAAGAAAAUAAGA .................((((((((((((........((((.............)))).......))))))))))))..............(((....)))............ (-20.78) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCUUAUUUUCUUGAGUUUCCUCUUAAUUUUUCCCAUUCUGUGAGAGUACAGUUUUUAACGAAUGCAAAGAUAAUUAUUUUUUAUUACUCUCACAAAUUUUUAUUCUUAUUCUU ..........(((((......)))))............((((((((((..((.....))......((((((....))))))...))))))))))................... (-14.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 304 55 13 160 118 pint:PI0912|5end_conserved_hypothetical_protein_842034..842264_POSITIVE 249 55 14 159 118 pint:PI1165|5end_hypothetical_protein_1089389..1089619_POSITIVE 249 55 14 75 34 pint:PI1166|5end_hypothetical_protein_1089305..1089535_POSITIVE 244 78 41 144 108 pint:PI0190|5end_3-dehydroquinate_dehydratase_II_180618..180848_POSITIVE 221 71 37 76 47 pint:PI0419|5end_conserved_hypothetical_protein_386701..386931_POSITIVE 221 71 37 41 12 pint:PI0418|5end_hypothetical_protein_386666..386896_POSITIVE 212 83 41 193 147 pint:PI1635|5end_hypothetical_protein_1553948..1554178_POSITIVE 210 57 20 51 21 pint:PI1390|5end_hypothetical_protein_1311154..1311384_POSITIVE 208 55 14 192 151 pint:PI1912|5end_possible_DNA_repair_protein_1856364..1856594_POSITIVE 208 81 43 45 18 pint:PI0184|5end_possible_fibronectin_type_III_domain_protein_174355..174585_POSITIVE 208 81 43 37 10 pint:PI0183|5end_hypothetical_protein_174347..174577_POSITIVE 199 67 21 198 150 pint:PI1983|5end_possible_xylanase_1939151..1939381_POSITIVE 199 85 44 77 16 pint:PI1084|5end_threonyl-tRNA_synthetase_1002664..1002894_POSITIVE 196 95 59 66 32 pint:PI0019|5end_conserved_hypothetical_protein_23742..23972_POSITIVE 195 83 41 95 58 pint:PI1516|5end_multidrug_resistance_protein;_HlyD_family_secretion_protein_1434381..1434611_POSITIVE 195 82 44 67 24 pint:PI0705|5end_conserved_hypothetical_protein;_possible_lipoprotein_641274..641504_POSITIVE 193 80 37 121 77 pint:PI2156|5end_conserved_hypothetical_protein;_possible_permease_2102796..2103026_POSITIVE 191 101 63 144 91 pint:PI2078|5end_hypothetical_protein_2036053..2036283_POSITIVE 191 57 11 212 166 pint:PI0882|5end_conserved_hypothetical_protein;_possible_para-aminobenzoate_synthase_component_I_815545..815775_POSITIVE 190 100 51 114 66 pint:PI0722|5end_RNA_polymerase_sigma-70_factor_654473..654703_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 236 97 51 85 32 pint:PI1883|3end_conserved_hypothetical_protein;_possible_surface_protein_1826174..1826324_POSITIVE 221 71 37 151 122 pint:PI0418|3end_hypothetical_protein_386856..387006_POSITIVE 221 71 37 123 94 pint:PI0420|3end_hypothetical_protein_386828..386978_POSITIVE 210 57 20 146 116 pint:PI1390|3end_hypothetical_protein_1311329..1311479_POSITIVE 195 82 44 77 34 pint:PI0704|3end_conserved_hypothetical_protein_641364..641514_POSITIVE 193 80 37 74 30 pint:PI2154|3end_leucyl-tRNA_synthetase_2102829..2102979_POSITIVE 193 51 11 71 30 pint:PI0994|3end_glutaminyl-tRNA_synthetase_920209..920359_POSITIVE 191 101 63 81 28 pint:PI2077|3end_hypothetical_protein_2036070..2036220_POSITIVE 191 84 41 67 19 pint:PI1379|3end_hypothetical_protein_1302292..1302442_POSITIVE 188 81 41 145 96 pint:PI1004|3end_conserved_hypothetical_protein_926217..926367_POSITIVE 185 105 68 56 13 pint:PI1897|3end_conserved_hypothetical_protein_1841235..1841385_POSITIVE 184 107 68 148 110 pint:PI1833|3end_bacterioferritin_comigratory_protein_1774495..1774645_POSITIVE 184 100 52 83 23 pint:PI0593|3end_NAD-specific_glutamate_dehydrogenase_544369..544519_POSITIVE 181 103 75 46 16 pint:PI0282|3end_hypothetical_protein_266826..266976_POSITIVE 179 81 42 151 114 pint:PI1523|3end_DNA_polymerase_III,_alpha_subunit_1445890..1446040_POSITIVE 176 83 41 57 21 pint:PI0336|3end_hypothetical_protein_314806..314956_POSITIVE 174 95 62 83 48 pint:PI1993|3end_thiol_protease/hemagglutinin,_PrtT_precursor_1948992..1949142_POSITIVE 174 83 44 96 60 pint:PI1663|3end_hypothetical_protein_1577347..1577497_POSITIVE 171 80 62 22 3 pint:PI1261|3end_ISPg3-related_transposase,_N-terminal_region_1184074..1184224_POSITIVE 170 98 73 30 5 pint:PI0523|3end_hypothetical_protein_479844..479994_POSITIVE