Origin IGS: caatgccaatgtcagtaatgttttctttatcctcattgttcgttgtttttattttgctgcaaagataactataatataaaaaggtcgaaaattattttcgaccacttctgttattcttttcgacgaaaaagtattttca .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tgaaaatactttttcgtcgaaaagaataacagaagtggtcgaaaataattttcgacctttttatattatagttatctttgcagcaaaataaaaacaacgaacaatgaggataaagaaaacattactgacattggcattg Mask Tandem Repeat Region ================================================ caatgccaatgtcagtaatgttttctttatcctcattgttcgttgtttttattttgctgcaaagataactataatataaaaaggtcgaaaattattttcgaccacttctgttattcttttcgacgaaaaagtattttca Find is-nt database================================================ Query_seq: PI0001:PI0002|PI0001:PI0002:possible Ton-B receptor:conserved hypothetical protein:->->:2973..3111 139 caatgccaatgtcagtaatgttttctttatcctcattgttcgttgtttttattttgctgcaaagataactataatataaaaaggtcgaaaattattttcgaccacttctgttattcttttcgacgaaaaagtattttca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI0001:PI0002|PI0001:PI0002:possible Ton-B receptor:conserved hypothetical protein:->->:2973..3111 139 caatgccaatgtcagtaatgttttctttatcctcattgttcgttgtttttattttgctgcaaagataactataatataaaaaggtcgaaaattattttcgaccacttctgttattcttttcgacgaaaaagtattttca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI0001:PI0002|PI0001:PI0002:possible Ton-B receptor:conserved hypothetical protein:->->:2973..3111 139 caatgccaatgtcagtaatgttttctttatcctcattgttcgttgtttttattttgctgcaaagataactataatataaaaaggtcgaaaattattttcgaccacttctgttattcttttcgacgaaaaagtattttca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 caatgccaatgtcagtaatgttttctttatcctcattgttcgttgtttttattttgctgcaaagataactataatataaaaaggtcgaaaattattttcgaccacttctgttattcttttcgacgaaaaagtattttca Predict ORF larger than 30AA ================================================ Protein_Len: 32 Strand: + Start: 43 End: 138 .......................................... M F L F C C K D N Y N I K R S K I I F D H F C Y S F R R K S I F . caatgccaatgtcagtaatgttttctttatcctcattgttcgttgtttttattttgctgcaaagataactataatataaaaaggtcgaaaattattttcgaccacttctgttattcttttcgacgaaaaagtattttca 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================================================ caatgccaatgtcagtaatgttttctttatcctcattgttcgttgtttttattttgctgcaaagataactataatataaaaaggtcgaaaattattttcgaccacttctgttattcttttcgacgaaaaagtattttca Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 74 HP_score: -9.2 Tail_Score: -2.94206 Start: 82 End: 104 Full_Region: AACTATAATATAAAA AGGTCGAAAA TTA TTTTCGACCA CTTCTGTTATTCTTT .................................................................................AGGTCGAAAATTATTTTCGACCA................................... Find igs database================================================ Query_seq: PI0001:PI0002|PI0001:PI0002:possible Ton-B receptor:conserved hypothetical protein:->->:2973..3111 139 caatgccaatgtcagtaatgttttctttatcctcattgttcgttgtttttattttgctgcaaagataactataatataaaaaggtcgaaaattattttcgaccacttctgttattcttttcgacgaaaaagtattttca Intra-Species Hit: Count: 1 Min: 1 Max: 139 Len: 139 Subject: pint_PI0001_PI0002|possible Ton-B receptor:conserved hypothetical protein|POSITIVE:POSITIVE|[2973,3111]|139 HSP 1 e-value: 2.0E-73 bit: 276.0 Len: 139 Query Start:1 Query End:139 Subject Strand: POSITIVE Subject Start: 1 Subject End: 139 caatgccaatgtcagtaatgttttctttatcctcattgttcgttgtttttattttgctgcaaagataactataatataaaaaggtcgaaaattattttcgaccacttctgttattcttttcgacgaaaaagtattttca caatgccaatgtcagtaatgttttctttatcctcattgttcgttgtttttattttgctgcaaagataactataatataaaaaggtcgaaaattattttcgaccacttctgttattcttttcgacgaaaaagtattttca Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CAAUGCCAAUGUCAGUAAUGUUUUCUUUAUCCUCAUUGUUCGUUGUUUUUAUUUUGCUGCAAAGAUAACUAUAAUAUAAAAAGGUCGAAAAUUAUUUUCGACCACUUCUGUUAUUCUUUUCGACGAAAAAGUAUUUUCA .((((((((((...((((........))))...)))))(((((((...(((((((......)))))))..............((((((((.....)))))))).................)))))))...))))).... (-24.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGAAAAUACUUUUUCGUCGAAAAGAAUAACAGAAGUGGUCGAAAAUAAUUUUCGACCUUUUUAUAUUAUAGUUAUCUUUGCAGCAAAAUAAAAACAACGAACAAUGAGGAUAAAGAAAACAUUACUGACAUUGGCAUUG .(((((....)))))(((((...........((((.((((((((.....)))))))).))))........(((.(((((((..((...................))..).)))))).)))..........))))).... (-21.61) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 307 64 21 205 167 pint:PI1090|5end_tRNA_uracil_5-methyltransferase_1014366..1014596_POSITIVE 301 47 2 159 107 pint:PI2137|5end_RNA_methylase_SpoU_family_2083173..2083403_POSITIVE 275 59 13 190 142 pint:PI1005|5end_hypothetical_protein_926201..926431_POSITIVE 269 60 12 208 170 pint:PI0117|5end_ribonuclease_HI_110731..110961_POSITIVE 254 117 74 175 116 pint:PI0874|5end_conserved_hypothetical_protein_808978..809208_POSITIVE 243 47 4 62 20 pint:PI1461|5end_conserved_hypothetical_protein_1384364..1384594_POSITIVE 243 48 2 117 75 pint:PI1117|5end_glycosyl_transferase,_family_2_1041318..1041548_POSITIVE 243 118 79 70 37 pint:PI1006|5end_conserved_hypothetical_protein_926604..926834_POSITIVE 240 57 16 115 68 pint:PI1326|5end_Na+-driven_multidrug_efflux_pump_1244182..1244412_POSITIVE 237 46 13 222 183 pint:PI0327|5end_hypothetical_protein_308791..309021_POSITIVE 232 126 82 144 93 pint:PI0173|5end_hypothetical_protein_165305..165535_POSITIVE 231 49 3 107 53 pint:PI0411|5end_conserved_hypothetial_protein;_possible_hydrolase_377700..377930_POSITIVE 230 78 32 210 169 pint:PI2108|5end_cell_surface_protein;_possible_cell_surface_antigen_BspA_2059661..2059891_POSITIVE 230 51 12 41 6 pint:PI1353|5end_conserved_hypothetical_protein_1269710..1269940_POSITIVE 229 60 11 209 167 pint:PI1931|5end_alpha_glycan_phosphorylase,_maltodextrin_phosphorylase_1875456..1875686_POSITIVE 229 48 4 56 7 pint:PI0114|5end_hypothetical_protein_108139..108369_POSITIVE 226 67 23 119 82 pint:PI0863|5end_L-asparaginase_I_799437..799667_POSITIVE 224 69 24 142 96 pint:PI0616|5end_electron_transfer_flavoprotein,_beta-subunit_565560..565790_POSITIVE 224 63 27 205 153 pint:PI0559|5end_conserved_hypothetical_protein_507668..507898_POSITIVE 223 59 18 63 27 pint:PI1675|5end_TonB-dependent_outer_membrane_receptor_1588107..1588337_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 275 59 13 126 78 pint:PI1004|3end_conserved_hypothetical_protein_926217..926367_POSITIVE 258 66 22 70 27 pint:PI1932|3end_glycogen_synthase_1879806..1879956_POSITIVE 254 117 74 73 14 pint:PI0873|3end_conserved_hypothetical_protein;_possible_permease_808956..809106_POSITIVE 243 47 4 54 12 pint:PI1460|3end_ribonucleotide_reductase,_alpha_subunit,_N-terminal_region_1384436..1384586_POSITIVE 243 48 2 99 57 pint:PI1116|3end_conserved_hypothetical_protein_1041380..1041530_POSITIVE 237 47 2 106 63 pint:PI0327|3end_hypothetical_protein_309107..309257_POSITIVE 233 46 3 62 24 pint:PI0358|3end_hypothetical_protein_328105..328255_POSITIVE 230 78 32 55 14 pint:PI2105|3end_hypothetical_protein_2059586..2059736_POSITIVE 230 51 12 38 3 pint:PI1352|3end_conserved_hypothetical_protein_1269787..1269937_POSITIVE 229 48 4 102 53 pint:PI0111|3end_hypothetical_protein_108265..108415_POSITIVE 226 45 4 107 68 pint:PI0570|3end_exsB_protein;_possible_aluminum_resistance_protein_515395..515545_POSITIVE 225 38 2 143 107 pint:PI2135|3end_conserved_hypothetical_protein_2083253..2083403_POSITIVE 223 128 81 67 4 pint:PI1143|3end_hypothetical_protein_1070504..1070654_POSITIVE 223 46 4 37 5 pint:PI0944|3end_hypothetical_protein_875249..875399_POSITIVE 219 59 18 97 56 pint:PI0216|3end_transposase/integrase_210416..210566_POSITIVE 217 61 23 62 28 pint:PI2068|3end_hypothetical_protein_2028800..2028950_POSITIVE 215 50 1 75 26 pint:PI2090|3end_thioesterase_family_protein_2048066..2048216_POSITIVE 215 60 12 149 113 pint:PI1870|3end_hypothetical_protein_1815513..1815663_POSITIVE 215 60 12 62 26 pint:PI1869|3end_hypothetical_protein_1815426..1815576_POSITIVE 215 44 1 60 13 pint:PI1049|3end_hypothetical_protein_967341..967491_POSITIVE