Origin IGS: tatgctgttgttaatgtttcactgtttataatgttacccttcgtgcaaaggtagtataaagaaaagagataaacaaagaaagtttagcttatttcttataattctcctgttgttcaatactcgtta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taacgagtattgaacaacaggagaattataagaaataagctaaactttctttgtttatctcttttctttatactacctttgcacgaagggtaacattataaacagtgaaacattaacaacagcata Mask Tandem Repeat Region ================================================ tatgctgttgttaatgtttcactgtttataatgttacccttcgtgcaaaggtagtataaagaaaagagataaacaaagaaagtttagcttatttcttataattctcctgttgttcaatactcgtta Find is-nt database================================================ Query_seq: PI0767:PI0768|PI0767:PI0768:possible TonB-dependent receptor:conserved hypothetical protein; possible acetyltransferase:->->:704086..704211 126 tatgctgttgttaatgtttcactgtttataatgttacccttcgtgcaaaggtagtataaagaaaagagataaacaaagaaagtttagcttatttcttataattctcctgttgttcaatactcgtta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI0767:PI0768|PI0767:PI0768:possible TonB-dependent receptor:conserved hypothetical protein; possible acetyltransferase:->->:704086..704211 126 tatgctgttgttaatgtttcactgtttataatgttacccttcgtgcaaaggtagtataaagaaaagagataaacaaagaaagtttagcttatttcttataattctcctgttgttcaatactcgtta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI0767:PI0768|PI0767:PI0768:possible TonB-dependent receptor:conserved hypothetical protein; possible acetyltransferase:->->:704086..704211 126 tatgctgttgttaatgtttcactgtttataatgttacccttcgtgcaaaggtagtataaagaaaagagataaacaaagaaagtttagcttatttcttataattctcctgttgttcaatactcgtta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tatgctgttgttaatgtttcactgtttataatgttacccttcgtgcaaaggtagtataaagaaaagagataaacaaagaaagtttagcttatttcttataattctcctgttgttcaatactcgtta Predict ORF larger than 30AA ================================================ tatgctgttgttaatgtttcactgtttataatgttacccttcgtgcaaaggtagtataaagaaaagagataaacaaagaaagtttagcttatttcttataattctcctgttgttcaatactcgtta 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================================================ tatgctgttgttaatgtttcactgtttataatgttacccttcgtgcaaaggtagtataaagaaaagagataaacaaagaaagtttagcttatttcttataattctcctgttgttcaatactcgtta Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PI0767:PI0768|PI0767:PI0768:possible TonB-dependent receptor:conserved hypothetical protein; possible acetyltransferase:->->:704086..704211 126 tatgctgttgttaatgtttcactgtttataatgttacccttcgtgcaaaggtagtataaagaaaagagataaacaaagaaagtttagcttatttcttataattctcctgttgttcaatactcgtta Intra-Species Hit: Count: 1 Min: 1 Max: 126 Len: 126 Subject: pint_PI0767_PI0768|possible TonB-dependent receptor:conserved hypothetical protein; possible acetyltransferase|POSITIVE:POSITIVE|[704086,704211]|126 HSP 1 e-value: 9.0E-66 bit: 250.0 Len: 126 Query Start:1 Query End:126 Subject Strand: POSITIVE Subject Start: 1 Subject End: 126 tatgctgttgttaatgtttcactgtttataatgttacccttcgtgcaaaggtagtataaagaaaagagataaacaaagaaagtttagcttatttcttataattctcctgttgttcaatactcgtta tatgctgttgttaatgtttcactgtttataatgttacccttcgtgcaaaggtagtataaagaaaagagataaacaaagaaagtttagcttatttcttataattctcctgttgttcaatactcgtta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAUGCUGUUGUUAAUGUUUCACUGUUUAUAAUGUUACCCUUCGUGCAAAGGUAGUAUAAAGAAAAGAGAUAAACAAAGAAAGUUUAGCUUAUUUCUUAUAAUUCUCCUGUUGUUCAAUACUCGUUA ......(((((.(((........))).)))))..........(.(((((((...(((((.((((.(((.(((((.......))))).))).))))))))).....))).)))).)........... (-16.00) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAACGAGUAUUGAACAACAGGAGAAUUAUAAGAAAUAAGCUAAACUUUCUUUGUUUAUCUCUUUUCUUUAUACUACCUUUGCACGAAGGGUAACAUUAUAAACAGUGAAACAUUAACAACAGCAUA .......(((((.......((((((....((((.((((((............)))))).))))))))))....(((((((.....)))))))..........)))))................... (-17.00) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 270 46 1 45 2 pint:PI1586|5end_possible_HesA/MoeB/ThiF_family_protein_1514372..1514602_POSITIVE 266 81 42 79 48 pint:PI1574|5end_conserved_hypothetical_protein_1500325..1500555_POSITIVE 252 67 21 57 11 pint:PI0382|5end_conserved_hypothetical_protein_351510..351740_POSITIVE 249 70 28 149 102 pint:PI0124|5end_outer_membrane_protein/protective_antigen_OMA87_114487..114717_POSITIVE 247 57 18 70 29 pint:PI0713|5end_hypothetical_protein_650294..650524_POSITIVE 246 119 75 65 16 pint:PI2085|5end_conserved_hypothetical_protein_2041100..2041330_POSITIVE 241 82 41 172 116 pint:PI0865|5end_possible_phosphoglycerol_transferase_801637..801867_POSITIVE 236 55 15 67 19 pint:PI1564|5end_surface_antigen_BspA_1483455..1483685_POSITIVE 232 46 2 142 94 pint:PI0420|5end_hypothetical_protein_386551..386781_POSITIVE 232 46 2 128 80 pint:PI0417|5end_hypothetical_protein_386537..386767_POSITIVE 227 46 3 78 31 pint:PI2042|5end_cation-transporting_ATPase_1994175..1994405_POSITIVE 227 46 3 64 17 pint:PI2041|5end_conserved_hypothetical_protein_1994161..1994391_POSITIVE 227 79 38 124 81 pint:PI0935|5end_collagenase,_protease_866297..866527_POSITIVE 226 50 1 109 53 pint:PI1711|5end_ABC_transporter,_ATP-binding_protein_1627597..1627827_POSITIVE 225 52 15 81 50 pint:PI0133|5end_hypothetical_protein_124334..124564_POSITIVE 222 90 44 217 176 pint:PI1971|5end_possible_IS1249-related_transposase_1928027..1928257_POSITIVE 222 90 44 217 176 pint:PI1533|5end_conserved_hypothetical_protein;_possible_transposase_1452667..1452897_POSITIVE 222 90 44 217 176 pint:PI0534|5end_conserved_hypothetical_protein;_possible_transposase_488568..488798_POSITIVE 219 80 32 66 19 pint:PI0716|5end_conserved_hypothetical_protein_652136..652366_POSITIVE 217 69 23 216 166 pint:PI1482|5end_hypothetical_protein_1404179..1404409_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 277 57 15 132 83 pint:PI0191|3end_O-methyltransferase_181785..181935_POSITIVE 249 70 28 83 36 pint:PI0123|3end_outer_membrane_protein,_ompH_family_114501..114651_POSITIVE 247 57 18 53 12 pint:PI0712|3end_conserved_hypothetical_protein;_possible_xylanase_650357..650507_POSITIVE 227 54 13 142 92 pint:PI1688|3end_possible_GTPase_1603903..1604053_POSITIVE 217 69 23 52 2 pint:PI1480|3end_xanthine/uracil_permease_family_protein_1404095..1404245_POSITIVE 211 64 22 58 20 pint:PI1092|3end_conserved_hypothetical_protein_1018611..1018761_POSITIVE 203 68 21 74 14 pint:PI1274|3end_possible_phosphoribosylanthranilate_isomerase_1193604..1193754_POSITIVE 201 48 2 76 34 pint:PI1818|3end_hypothetical_protein_1757270..1757420_POSITIVE 200 44 4 82 36 pint:PI1759|3end_hypothetical_protein_1684386..1684536_POSITIVE 199 46 1 84 48 pint:PI1782|3end_possible_LPS_biosynthesis_protein_1715395..1715545_POSITIVE 198 117 77 119 80 pint:PI1869|3end_hypothetical_protein_1815426..1815576_POSITIVE 198 54 14 135 77 pint:PI1011|3end_cytochrome_c_biogenesis_protein_CycY_932989..933139_POSITIVE 196 56 30 79 55 pint:PI1216|3end_probable_phosphohydrolase_1136111..1136261_POSITIVE 196 69 32 70 32 pint:PI0286|3end_ISPg3-related_transposase_272065..272215_POSITIVE 194 53 13 126 84 pint:PI1373|3end_purine_nucleoside_phosphorylase_(PNP)_1294986..1295136_POSITIVE 194 46 6 54 6 pint:PI0868|3end_exodeoxyribonuclease_VII,_large_subunit_805576..805726_POSITIVE 193 47 3 106 60 pint:PI0798|3end_malonyl_CoA-acyl_carrier_protein_transacylase_736975..737125_POSITIVE 193 56 15 81 46 pint:PI0684|3end_coproporphyrinogen_III_oxidase_620507..620657_POSITIVE 191 55 41 40 26 pint:PI0144|3end_conserved_hypothetical_protein_136597..136747_POSITIVE 190 50 3 100 55 pint:PI0805|3end_conserved_hypothetical_protein_743807..743957_POSITIVE