Origin IGS: gtcagttctccttaatactcctgccgatggtttcttcttggcttttgtctctttcataatagaagtgtggtaaaaacgaatattattcataattgttcaaaaataaagtgcgctgtcttta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taaagacagcgcactttatttttgaacaattatgaataatattcgtttttaccacacttctattatgaaagagacaaaagccaagaagaaaccatcggcaggagtattaaggagaactgac Mask Tandem Repeat Region ================================================ gtcagttctccttaatactcctgccgatggtttcttcttggcttttgtctctttcataatagaagtgtggtaaaaacgaatattattcataattgttcaaaaataaagtgcgctgtcttta Find is-nt database================================================ Query_seq: PI0981:PI0982|PI0981:PI0982:outer membrane protein, TonB dependent receptor:hypothetical protein:->->:909451..909571 121 gtcagttctccttaatactcctgccgatggtttcttcttggcttttgtctctttcataatagaagtgtggtaaaaacgaatattattcataattgttcaaaaataaagtgcgctgtcttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI0981:PI0982|PI0981:PI0982:outer membrane protein, TonB dependent receptor:hypothetical protein:->->:909451..909571 121 gtcagttctccttaatactcctgccgatggtttcttcttggcttttgtctctttcataatagaagtgtggtaaaaacgaatattattcataattgttcaaaaataaagtgcgctgtcttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI0981:PI0982|PI0981:PI0982:outer membrane protein, TonB dependent receptor:hypothetical protein:->->:909451..909571 121 gtcagttctccttaatactcctgccgatggtttcttcttggcttttgtctctttcataatagaagtgtggtaaaaacgaatattattcataattgttcaaaaataaagtgcgctgtcttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gtcagttctccttaatactcctgccgatggtttcttcttggcttttgtctctttcataatagaagtgtggtaaaaacgaatattattcataattgttcaaaaataaagtgcgctgtcttta Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: - Start: 1 End: 93 D T R R L V G A S P K K K A K T E K M I S T H Y F R I N N M M ............................ gtcagttctccttaatactcctgccgatggtttcttcttggcttttgtctctttcataatagaagtgtggtaaaaacgaatattattcataattgttcaaaaataaagtgcgctgtcttta 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================================================ gtcagttctccttaatactcctgccgatggtttcttcttggcttttgtctctttcataatagaagtgtggtaaaaacgaatattattcataattgttcaaaaataaagtgcgctgtcttta Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PI0981:PI0982|PI0981:PI0982:outer membrane protein, TonB dependent receptor:hypothetical protein:->->:909451..909571 121 gtcagttctccttaatactcctgccgatggtttcttcttggcttttgtctctttcataatagaagtgtggtaaaaacgaatattattcataattgttcaaaaataaagtgcgctgtcttta Intra-Species Hit: Count: 1 Min: 1 Max: 121 Len: 121 Subject: pint_PI0981_PI0982|outer membrane protein, TonB dependent receptor:hypothetical protein|POSITIVE:POSITIVE|[909451,909571]|121 HSP 1 e-value: 8.0E-63 bit: 240.0 Len: 121 Query Start:1 Query End:121 Subject Strand: POSITIVE Subject Start: 1 Subject End: 121 gtcagttctccttaatactcctgccgatggtttcttcttggcttttgtctctttcataatagaagtgtggtaaaaacgaatattattcataattgttcaaaaataaagtgcgctgtcttta gtcagttctccttaatactcctgccgatggtttcttcttggcttttgtctctttcataatagaagtgtggtaaaaacgaatattattcataattgttcaaaaataaagtgcgctgtcttta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUCAGUUCUCCUUAAUACUCCUGCCGAUGGUUUCUUCUUGGCUUUUGUCUCUUUCAUAAUAGAAGUGUGGUAAAAACGAAUAUUAUUCAUAAUUGUUCAAAAAUAAAGUGCGCUGUCUUUA (.((((.(.(.(((........(((((.((.....))))))).(((..(.(((((......)))).).)..)))...(((((...........))))).....))).).).)))).).... (-15.50) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAAGACAGCGCACUUUAUUUUUGAACAAUUAUGAAUAAUAUUCGUUUUUACCACACUUCUAUUAUGAAAGAGACAAAAGCCAAGAAGAAACCAUCGGCAGGAGUAUUAAGGAGAACUGAC ......(((..(.(((((.........((..((((((...))))))..)).....(((((.....((.......))...(((..............))).)))))..))))).)..))).. (-13.04) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 348 40 4 148 112 pint:PI0068|5end_arginine_repressor_66586..66816_POSITIVE 316 53 18 190 143 pint:PI2140|5end_conserved_hypothetical_protein_2086773..2087003_POSITIVE 295 69 22 75 17 pint:PI1003|5end_conserved_hypothetical_protein_924694..924924_POSITIVE 293 52 15 74 30 pint:PI0529|5end_hypothetical_protein_483026..483256_POSITIVE 286 49 1 207 167 pint:PI1931|5end_alpha_glycan_phosphorylase,_maltodextrin_phosphorylase_1875456..1875686_POSITIVE 286 49 6 175 131 pint:PI0261|5end_conjugative_transposon_protein,_TraK_254065..254295_POSITIVE 284 42 1 41 2 pint:PI1711|5end_ABC_transporter,_ATP-binding_protein_1627597..1627827_POSITIVE 282 49 17 212 179 pint:PI1665|5end_thymidylate_synthase_1578086..1578316_POSITIVE 269 46 2 118 76 pint:PI0113|5end_arginyl-tRNA_synthetase_108371..108601_POSITIVE 269 56 16 169 122 pint:PI0110|5end_ABC_transport_system,_ATP-binding_protein_107136..107366_POSITIVE 266 54 18 208 162 pint:PI2125|5end_D-tyrosyl-tRNA(Tyr)_deacylase_2074450..2074680_POSITIVE 265 49 7 231 179 pint:PI2102|5end_DNA_topoisomerase_IV,_subunit_B_2055706..2055936_POSITIVE 264 50 6 41 5 pint:PI1659|5end_hypothetical_protein_1574725..1574955_POSITIVE 264 44 6 168 126 pint:PI0637|5end_hypothetical_protein_582117..582347_POSITIVE 264 44 6 83 41 pint:PI0636|5end_hypothetical_protein_582032..582262_POSITIVE 260 51 21 228 183 pint:PI0697|5end_5'-nucleotidase_family_protein_633560..633790_POSITIVE 257 50 18 148 119 pint:PI0480|5end_preprotein_translocase,_SecY_subunit_441576..441806_POSITIVE 257 69 22 230 186 pint:PI0447|5end_DNA-directed_RNA_polymerase,_beta'_subunit_417314..417544_POSITIVE 252 42 3 49 2 pint:PI1847|5end_conserved_hypothetical_protein;_possible_integral_membrane_protein_1792006..1792236_POSITIVE 251 46 1 169 128 pint:PI1668|5end_conserved_hypothetical_protein_1580692..1580922_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 348 40 4 68 32 pint:PI0067|3end_hypothetical_protein_66586..66736_POSITIVE 316 53 18 89 42 pint:PI2139|3end_cysteinyl-tRNA_synthetase_2086752..2086902_POSITIVE 316 50 2 151 93 pint:PI0444|3end_50S_ribosomal_protein_L7/L12_413390..413540_POSITIVE 316 50 2 120 62 pint:PI0445|3end_conserved_hypothetical_protein_413359..413509_POSITIVE 293 52 15 90 46 pint:PI0528|3end_hypothetical_protein_483122..483272_POSITIVE 284 42 1 138 99 pint:PI1712|3end_hypothetical_protein_1627774..1627924_POSITIVE 282 49 17 136 103 pint:PI1664|3end_conserved_hypothetical_protein_1578090..1578240_POSITIVE 274 50 2 140 98 pint:PI1227|3end_conserved_hypothetical_protein;_possible_DNA-binding_protein,_histone-like_family_1148974..1149124_POSITIVE 269 56 16 136 89 pint:PI0109|3end_hypothetical_protein_107183..107333_POSITIVE 264 34 1 141 113 pint:PI1136|3end_conserved_hypothetical_protein_1062541..1062691_POSITIVE 263 50 3 87 38 pint:PI0111|3end_hypothetical_protein_108265..108415_POSITIVE 261 50 9 131 95 pint:PI1009|3end_cytochrome_c_nitrite_reductase,_large_subunit_930840..930990_POSITIVE 260 48 6 151 108 pint:PI0260|3end_conjugative_transposon_protein,_TraJ_254122..254272_POSITIVE 258 58 15 77 18 pint:PI0358|3end_hypothetical_protein_328105..328255_POSITIVE 257 50 18 140 111 pint:PI0479|3end_50S_ribosomal_protein_L15_441648..441798_POSITIVE 248 56 12 115 70 pint:PI0368|3end_hypothetical_protein_339985..340135_POSITIVE 246 58 21 48 5 pint:PI2120|3end_hypothetical_protein_2069050..2069200_POSITIVE 245 47 18 111 80 pint:PI2132|3end_hypothetical_protein_2081139..2081289_POSITIVE 244 53 21 64 24 pint:PI0910|3end_possible_sodium_hydrogen_antiporter_(Na+/H+_antiporter)_839544..839694_POSITIVE 244 70 22 136 87 pint:PI0353|3end_hypothetical_protein_325337..325487_POSITIVE