Origin IGS: agcaaagaatggcattactgaaaatattattgtgatatatagattcctcatttgcatttataattgtctctaattgcaaagatacgcttttcaagtggcttttccaagaatctaaactttttttca .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tgaaaaaaagtttagattcttggaaaagccacttgaaaagcgtatctttgcaattagagacaattataaatgcaaatgaggaatctatatatcacaataatattttcagtaatgccattctttgct Mask Tandem Repeat Region ================================================ agcaaagaatggcattactgaaaatattattgtgatatatagattcctcatttgcatttataattgtctctaattgcaaagatacgcttttcaagtggcttttccaagaatctaaactttttttca Find is-nt database================================================ Query_seq: PI1160:PI1161|PI1160:PI1161:possible phosphatidylinositol-4-phosphate 5-kinase:conserved hypothetical protein:->->:1085955..1086080 126 agcaaagaatggcattactgaaaatattattgtgatatatagattcctcatttgcatttataattgtctctaattgcaaagatacgcttttcaagtggcttttccaagaatctaaactttttttca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI1160:PI1161|PI1160:PI1161:possible phosphatidylinositol-4-phosphate 5-kinase:conserved hypothetical protein:->->:1085955..1086080 126 agcaaagaatggcattactgaaaatattattgtgatatatagattcctcatttgcatttataattgtctctaattgcaaagatacgcttttcaagtggcttttccaagaatctaaactttttttca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI1160:PI1161|PI1160:PI1161:possible phosphatidylinositol-4-phosphate 5-kinase:conserved hypothetical protein:->->:1085955..1086080 126 agcaaagaatggcattactgaaaatattattgtgatatatagattcctcatttgcatttataattgtctctaattgcaaagatacgcttttcaagtggcttttccaagaatctaaactttttttca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 agcaaagaatggcattactgaaaatattattgtgatatatagattcctcatttgcatttataattgtctctaattgcaaagatacgcttttcaagtggcttttccaagaatctaaactttttttca Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: - Start: 2 End: 94 . C L I A N S F I N N H Y I S E E N A N I I T E L Q L S V S K M ................................ agcaaagaatggcattactgaaaatattattgtgatatatagattcctcatttgcatttataattgtctctaattgcaaagatacgcttttcaagtggcttttccaagaatctaaactttttttca Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ PromScan Matrix: RpoD-17 Strand: + Score: 81 Start: 35 End: 64 ..................................ATATATAGATTCCTCATTTGCATTTATAAT.............................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ agcaaagaatggcattactgaaaatattattgtgatatatagattcctcatttgcatttataattgtctctaattgcaaagatacgcttttcaagtggcttttccaagaatctaaactttttttca Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PI1160:PI1161|PI1160:PI1161:possible phosphatidylinositol-4-phosphate 5-kinase:conserved hypothetical protein:->->:1085955..1086080 126 agcaaagaatggcattactgaaaatattattgtgatatatagattcctcatttgcatttataattgtctctaattgcaaagatacgcttttcaagtggcttttccaagaatctaaactttttttca Intra-Species Hit: Count: 1 Min: 1 Max: 117 Len: 117 Subject: pint_PI1160_PI1161|possible phosphatidylinositol-4-phosphate 5-kinase:conserved hypothetical protein|POSITIVE:POSITIVE|[1085955,1086080]|126 HSP 1 e-value: 2.0E-60 bit: 232.0 Len: 117 Query Start:1 Query End:117 Subject Strand: POSITIVE Subject Start: 1 Subject End: 117 agcaaagaatggcattactgaaaatattattgtgatatatagattcctcatttgcatttataattgtctctaattgcaaagatacgcttttcaagtggcttttccaagaatctaaac......... agcaaagaatggcattactgaaaatattattgtgatatatagattcctcatttgcatttataattgtctctaattgcaaagatacgcttttcaagtggcttttccaagaatctaaac......... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGCAAAGAAUGGCAUUACUGAAAAUAUUAUUGUGAUAUAUAGAUUCCUCAUUUGCAUUUAUAAUUGUCUCUAAUUGCAAAGAUACGCUUUUCAAGUGGCUUUUCCAAGAAUCUAAAC .............(((((.............)))))...(((((((.((.((((((.(((..........))).))))))))..((((.....))))..........)))))))... (-16.02) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUUUAGAUUCUUGGAAAAGCCACUUGAAAAGCGUAUCUUUGCAAUUAGAGACAAUUAUAAAUGCAAAUGAGGAAUCUAUAUAUCACAAUAAUAUUUUCAGUAAUGCCAUUCUUUGCU ...(((((((.(((.....))).............((((((((.(((..........))).)))))).)).)))))))....................(((((.........))))) (-15.00) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 266 108 75 35 2 pint:PI1868|5end_hypothetical_protein_1814638..1814868_POSITIVE 258 102 67 56 16 pint:PI1515|5end_hypothetical_protein_1434101..1434331_POSITIVE 255 87 51 150 113 pint:PI0190|5end_3-dehydroquinate_dehydratase_II_180618..180848_POSITIVE 252 99 54 66 19 pint:PI0824|5end_large_conductance_mechanosensitive_channel_protein_763337..763567_POSITIVE 247 107 72 55 18 pint:PI1779|5end_16S_rRNA_processing_protein_1711335..1711565_POSITIVE 244 98 53 119 82 pint:PI0415|5end_malate_dehydrogenase_385358..385588_POSITIVE 236 99 54 231 198 pint:PI0363|5end_hypothetical_protein_332832..333062_POSITIVE 228 105 64 100 52 pint:PI0617|5end_electron_transfer_flavoprotein,_alpha_subunit_566367..566597_POSITIVE 226 109 64 228 188 pint:PI1272|5end_possible_transcriptional_regulator_1191702..1191932_POSITIVE 222 108 63 73 17 pint:PI2175|5end_RNA_polymerase_sigma-54_2115007..2115237_POSITIVE 217 85 43 66 37 pint:PI1390|5end_hypothetical_protein_1311154..1311384_POSITIVE 214 90 41 111 51 pint:PI1689|5end_conserved_hypothetical_protein_1604310..1604540_POSITIVE 212 103 74 207 164 pint:PI1870|5end_hypothetical_protein_1815302..1815532_POSITIVE 210 98 53 227 184 pint:PI1798|5end__elongation_factor_Ts_1731788..1732018_POSITIVE 210 105 61 223 177 pint:PI0472|5end_50S_ribosomal_protein_L5_438155..438385_POSITIVE 208 99 52 191 143 pint:PI1580|5end_conserved_hypothetical_protein_1507833..1508063_POSITIVE 207 70 24 221 176 pint:PI2053|5end_conserved_hypothetical_protein;_possible_outer_membrane_receptor_protein_2010673..2010903_POSITIVE 207 104 74 48 22 pint:PI1634|5end_conserved_hypothetical_protein_1553179..1553409_POSITIVE 207 86 49 80 38 pint:PI1090|5end_tRNA_uracil_5-methyltransferase_1014366..1014596_POSITIVE 207 99 65 69 43 pint:PI1075|5end_pyruvate_phosphate_dikinase_995828..996058_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 248 59 16 47 1 pint:PI0948|3end_hypothetical_protein_881978..882128_POSITIVE 247 107 72 39 2 pint:PI1778|3end_UDP-N-acetylglucosamine_1-carboxyvinyltransferase_1711399..1711549_POSITIVE 246 109 73 69 32 pint:PI0645|3end_hypothetical_protein_586807..586957_POSITIVE 238 106 76 147 111 pint:PI1891|3end_hypothetical_protein_1835917..1836067_POSITIVE 228 105 64 93 45 pint:PI0616|3end_electron_transfer_flavoprotein,_beta-subunit_566440..566590_POSITIVE 223 105 63 38 2 pint:PI0976|3end_dihydrolipoamide_dehydrogenase_(dihydrolipoyl_dehydrogenanse)_903732..903882_POSITIVE 213 100 51 142 95 pint:PI0447|3end_DNA-directed_RNA_polymerase,_beta'_subunit_421755..421905_POSITIVE 210 105 61 139 93 pint:PI0471|3end_50S_ribosomal_protein_L24_438151..438301_POSITIVE 207 106 67 52 9 pint:PI0684|3end_coproporphyrinogen_III_oxidase_620507..620657_POSITIVE 206 105 64 55 9 pint:PI0999|3end_hypothetical_protein_922812..922962_POSITIVE 205 100 67 64 21 pint:PI0036|3end_glutathione_peroxidase_39289..39439_POSITIVE 204 105 68 57 22 pint:PI1572|3end_hypothetical_protein_1498215..1498365_POSITIVE 200 90 50 51 5 pint:PI0437|3end_conserved_hypothetical_protein;_possible_ribosomal_subunit_interface_protein_408543..408693_POSITIVE 199 108 64 136 88 pint:PI0380|3end_conserved_hypothetical_protein_350541..350691_POSITIVE 198 97 51 145 93 pint:PI1744|3end_chromosome_partitioning_protein_1666620..1666770_POSITIVE 197 110 67 76 28 pint:PI0452|3end_conserved_hypothetical_protein;_possible_surface_antigen_426791..426941_POSITIVE 196 110 64 79 28 pint:PI0893|3end_outer_membrane_protein_41_precursor_825662..825812_POSITIVE 196 104 73 74 33 pint:PI0528|3end_hypothetical_protein_483122..483272_POSITIVE 195 56 12 53 13 pint:PI1802|3end_50S_ribosomal_protein_L13_1734957..1735107_POSITIVE 193 97 54 61 15 pint:PI0717|3end_conserved_hypothetical_protein_653120..653270_POSITIVE