Origin IGS: taaaatctaaaataggaaatagagtatgtcgacttccgcatactctatttttactttatgacactgggtaaaatagtatcataaagctaagtaaaacagcacttattcagcctgaatgagatgttttccgtccgaaacgaaacgattagtttctcagatgtaagataatgcgtacagaatggtggttttgcgtcttttaaaccattcgttaaatattgctaactttaaaatgtttcgcactaaaatttcccccaccaactaataatttgctacatttgcattgttaagcaaagatggaagactgaactgtagacaacttcttaccagcactattctatctgtgaaaaagacagagtacaacgaacttaaacacaatatctaattaataaaatttgcatacaatatggcaaacgagacaaacaacaaggaattccgtattgaaagcgacctc .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gaggtcgctttcaatacggaattccttgttgtttgtctcgtttgccatattgtatgcaaattttattaattagatattgtgtttaagttcgttgtactctgtctttttcacagatagaatagtgctggtaagaagttgtctacagttcagtcttccatctttgcttaacaatgcaaatgtagcaaattattagttggtgggggaaattttagtgcgaaacattttaaagttagcaatatttaacgaatggtttaaaagacgcaaaaccaccattctgtacgcattatcttacatctgagaaactaatcgtttcgtttcggacggaaaacatctcattcaggctgaataagtgctgttttacttagctttatgatactattttacccagtgtcataaagtaaaaatagagtatgcggaagtcgacatactctatttcctattttagatttta Mask Tandem Repeat Region ================================================ taaaatctaaaataggaaatagagtatgtcgacttccgcatactctatttttactttatgacactgggtaaaatagtatcataaagctaagtaaaacagcacttattcagcctgaatgagatgttttccgtccgaaacgaaacgattagtttctcagatgtaagataatgcgtacagaatggtggttttgcgtcttttaaaccattcgttaaatattgctaactttaaaatgtttcgcactaaaatttcccccaccaactaataatttgctacatttgcattgttaagcaaagatggaagactgaactgtagacaacttcttaccagcactattctatctgtgaaaaagacagagtacaacgaacttaaacacaatatctaattaataaaatttgcatacaatatggcaaacgagacaaacaacaaggaattccgtattgaaagcgacctc Find is-nt database================================================ Query_seq: PI1836:PI1837|PI1836:PI1837:conserved hypothetical protein:aspartate ammonia-lyase:->->:1778642..1779092 451 taaaatctaaaataggaaatagagtatgtcgacttccgcatactctatttttactttatgacactgggtaaaatagtatcataaagctaagtaaaacagcacttattcagcctgaatgagatgttttccgtccgaaacgaaacgattagtttctcagatgtaagataatgcgtacagaatggtggttttgcgtcttttaaaccattcgttaaatattgctaactttaaaatgtttcgcactaaaatttcccccaccaactaataatttgctacatttgcattgttaagcaaagatggaagactgaactgtagacaacttcttaccagcactattctatctgtgaaaaagacagagtacaacgaacttaaacacaatatctaattaataaaatttgcatacaatatggcaaacgagacaaacaacaaggaattccgtattgaaagcgacctc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI1836:PI1837|PI1836:PI1837:conserved hypothetical protein:aspartate ammonia-lyase:->->:1778642..1779092 451 taaaatctaaaataggaaatagagtatgtcgacttccgcatactctatttttactttatgacactgggtaaaatagtatcataaagctaagtaaaacagcacttattcagcctgaatgagatgttttccgtccgaaacgaaacgattagtttctcagatgtaagataatgcgtacagaatggtggttttgcgtcttttaaaccattcgttaaatattgctaactttaaaatgtttcgcactaaaatttcccccaccaactaataatttgctacatttgcattgttaagcaaagatggaagactgaactgtagacaacttcttaccagcactattctatctgtgaaaaagacagagtacaacgaacttaaacacaatatctaattaataaaatttgcatacaatatggcaaacgagacaaacaacaaggaattccgtattgaaagcgacctc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI1836:PI1837|PI1836:PI1837:conserved hypothetical protein:aspartate ammonia-lyase:->->:1778642..1779092 451 taaaatctaaaataggaaatagagtatgtcgacttccgcatactctatttttactttatgacactgggtaaaatagtatcataaagctaagtaaaacagcacttattcagcctgaatgagatgttttccgtccgaaacgaaacgattagtttctcagatgtaagataatgcgtacagaatggtggttttgcgtcttttaaaccattcgttaaatattgctaactttaaaatgtttcgcactaaaatttcccccaccaactaataatttgctacatttgcattgttaagcaaagatggaagactgaactgtagacaacttcttaccagcactattctatctgtgaaaaagacagagtacaacgaacttaaacacaatatctaattaataaaatttgcatacaatatggcaaacgagacaaacaacaaggaattccgtattgaaagcgacctc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taaaatctaaaataggaaatagagtatgtcgacttccgcatactctatttttactttatgacactgggtaaaatagtatcataaagctaagtaaaacagcacttattcagcctgaatgagatgttttccgtccgaaacgaaacgattagtttctcagatgtaagataatgcgtacagaatggtggttttgcgtcttttaaaccattcgttaaatattgctaactttaaaatgtttcgcactaaaatttcccccaccaactaataatttgctacatttgcattgttaagcaaagatggaagactgaactgtagacaacttcttaccagcactattctatctgtgaaaaagacagagtacaacgaacttaaacacaatatctaattaataaaatttgcatacaatatggcaaacgagacaaacaacaaggaattccgtattgaaagcgacctc Predict ORF larger than 30AA ================================================ Protein_Len: 33 Strand: + Start: 281 End: 379 ........................................................................................................................................................................................................................................................................................ M L S K D G R L N C R Q L L T S T I L S V K K T E Y N E L K H N I ........................................................................ Protein_Len: 39 Strand: - Start: 262 End: 378 ..................................................................................................................................................................................................................................................................... Y N A V N A N N L L S P L S F Q L C S R V L V I R D T F F V S Y L S S L C L M ......................................................................... Protein_Len: 34 Strand: - Start: 157 End: 258 ............................................................................................................................................................ I Y S L A Y L I T T K R R K F W E N F I A L K L I N R V L I E G V M ................................................................................................................................................................................................. taaaatctaaaataggaaatagagtatgtcgacttccgcatactctatttttactttatgacactgggtaaaatagtatcataaagctaagtaaaacagcacttattcagcctgaatgagatgttttccgtccgaaacgaaacgattagtttctcagatgtaagataatgcgtacagaatggtggttttgcgtcttttaaaccattcgttaaatattgctaactttaaaatgtttcgcactaaaatttcccccaccaactaataatttgctacatttgcattgttaagcaaagatggaagactgaactgtagacaacttcttaccagcactattctatctgtgaaaaagacagagtacaacgaacttaaacacaatatctaattaataaaatttgcatacaatatggcaaacgagacaaacaacaaggaattccgtattgaaagcgacctc 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================================================ taaaatctaaaataggaaatagagtatgtcgacttccgcatactctatttttactttatgacactgggtaaaatagtatcataaagctaagtaaaacagcacttattcagcctgaatgagatgttttccgtccgaaacgaaacgattagtttctcagatgtaagataatgcgtacagaatggtggttttgcgtcttttaaaccattcgttaaatattgctaactttaaaatgtttcgcactaaaatttcccccaccaactaataatttgctacatttgcattgttaagcaaagatggaagactgaactgtagacaacttcttaccagcactattctatctgtgaaaaagacagagtacaacgaacttaaacacaatatctaattaataaaatttgcatacaatatggcaaacgagacaaacaacaaggaattccgtattgaaagcgacctc Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 82 HP_score: -8.6 Tail_Score: -4.0828 Start: 20 End: 47 Full_Region: gtcataaagtaaaaa tagagtatgcgg aag tcgacatactcta tttcctattttagat ...................tagagtatgcggaagtcgacatactcta.................................................................................................................................................................................................................................................................................................................................................................................................................... TransTerm Strand: - Conf: 48 HP_score: -4.3 Tail_Score: -2.71712 Start: 139 End: 153 Full_Region: ttatcttacatctga gaaac taatc gtttc gtttcggacggaaaa ..........................................................................................................................................gaaactaatcgtttc.......................................................................................................................................................................................................................................................................................................... Find igs database================================================ Query_seq: PI1836:PI1837|PI1836:PI1837:conserved hypothetical protein:aspartate ammonia-lyase:->->:1778642..1779092 451 taaaatctaaaataggaaatagagtatgtcgacttccgcatactctatttttactttatgacactgggtaaaatagtatcataaagctaagtaaaacagcacttattcagcctgaatgagatgttttccgtccgaaacgaaacgattagtttctcagatgtaagataatgcgtacagaatggtggttttgcgtcttttaaaccattcgttaaatattgctaactttaaaatgtttcgcactaaaatttcccccaccaactaataatttgctacatttgcattgttaagcaaagatggaagactgaactgtagacaacttcttaccagcactattctatctgtgaaaaagacagagtacaacgaacttaaacacaatatctaattaataaaatttgcatacaatatggcaaacgagacaaacaacaaggaattccgtattgaaagcgacctc Intra-Species Hit: Count: 1 Min: 1 Max: 451 Len: 451 Subject: pint_PI1836_PI1837|conserved hypothetical protein:aspartate ammonia-lyase|POSITIVE:POSITIVE|[1778642,1779092]|451 HSP 1 e-value: 0.0 bit: 894.0 Len: 451 Query Start:1 Query End:451 Subject Strand: POSITIVE Subject Start: 1 Subject End: 451 taaaatctaaaataggaaatagagtatgtcgacttccgcatactctatttttactttatgacactgggtaaaatagtatcataaagctaagtaaaacagcacttattcagcctgaatgagatgttttccgtccgaaacgaaacgattagtttctcagatgtaagataatgcgtacagaatggtggttttgcgtcttttaaaccattcgttaaatattgctaactttaaaatgtttcgcactaaaatttcccccaccaactaataatttgctacatttgcattgttaagcaaagatggaagactgaactgtagacaacttcttaccagcactattctatctgtgaaaaagacagagtacaacgaacttaaacacaatatctaattaataaaatttgcatacaatatggcaaacgagacaaacaacaaggaattccgtattgaaagcgacctc taaaatctaaaataggaaatagagtatgtcgacttccgcatactctatttttactttatgacactgggtaaaatagtatcataaagctaagtaaaacagcacttattcagcctgaatgagatgttttccgtccgaaacgaaacgattagtttctcagatgtaagataatgcgtacagaatggtggttttgcgtcttttaaaccattcgttaaatattgctaactttaaaatgtttcgcactaaaatttcccccaccaactaataatttgctacatttgcattgttaagcaaagatggaagactgaactgtagacaacttcttaccagcactattctatctgtgaaaaagacagagtacaacgaacttaaacacaatatctaattaataaaatttgcatacaatatggcaaacgagacaaacaacaaggaattccgtattgaaagcgacctc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAAAUCUAAAAUAGGAAAUAGAGUAUGUCGACUUCCGCAUACUCUAUUUUUACUUUAUGACACUGGGUAAAAUAGUAUCAUAAAGCUAAGUAAAACAGCACUUAUUCAGCCUGAAUGAGAUGUUUUCCGUCCGAAACGAAACGAUUAGUUUCUCAGAUGUAAGAUAAUGCGUACAGAAUGGUGGUUUUGCGUCUUUUAAACCAUUCGUUAAAUAUUGCUAACUUUAAAAUGUUUCGCACUAAAAUUUCCCCCACCAACUAAUAAUUUGCUACAUUUGCAUUGUUAAGCAAAGAUGGAAGACUGAACUGUAGACAACUUCUUACCAGCACUAUUCUAUCUGUGAAAAAGACAGAGUACAACGAACUUAAACACAAUAUCUAAUUAAUAAAAUUUGCAUACAAUAUGGCAAACGAGACAAACAACAAGGAAUUCCGUAUUGAAAGCGACCUC ..............(((((((((((((((.(....).))))))))))))))).((((((((.((((.......)))).)))))))).(((((...((((..(((((((.....)))))))..((((((((((........(((((...((((...(((((((((((....(((.....)))...)))))))))))...))))...))))).....((((((((....((((((...(((............................))).)))))).....))).))))).))))))))))....))))....................((((((.(((.......))).))))))......)))))........................((((...((((((((....(..............).....))))))))...)))).... (-96.73) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAGGUCGCUUUCAAUACGGAAUUCCUUGUUGUUUGUCUCGUUUGCCAUAUUGUAUGCAAAUUUUAUUAAUUAGAUAUUGUGUUUAAGUUCGUUGUACUCUGUCUUUUUCACAGAUAGAAUAGUGCUGGUAAGAAGUUGUCUACAGUUCAGUCUUCCAUCUUUGCUUAACAAUGCAAAUGUAGCAAAUUAUUAGUUGGUGGGGGAAAUUUUAGUGCGAAACAUUUUAAAGUUAGCAAUAUUUAACGAAUGGUUUAAAAGACGCAAAACCACCAUUCUGUACGCAUUAUCUUACAUCUGAGAAACUAAUCGUUUCGUUUCGGACGGAAAACAUCUCAUUCAGGCUGAAUAAGUGCUGUUUUACUUAGCUUUAUGAUACUAUUUUACCCAGUGUCAUAAAGUAAAAAUAGAGUAUGCGGAAGUCGACAUACUCUAUUUCCUAUUUUAGAUUUUA (((((.(.((((..((((((((......((((..((((..(..(((((.(((....)))..........(((((((((((.((((((....(((((((((((((.......))))))....(.((((...(((.....))).)))).)..(((((((((...(((......(((.......))).......))).)))))))))......))))))).....))))))....)))))))))))...)))))..)..)))))))).......))))))))..............((((((((((.....)))))...)))))..)))).))))))...((((((.....))).))).........(((((((((((((.........)))))))))))))..((((((((((((((.....)).))))))))))))................ (-107.54) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 343 147 101 65 12 pint:PI0696|5end_NADH_pyrophosphatase,_MutT_family_hydrolase_(NAD+_diphosphatase)_632741..632971_POSITIVE 300 145 108 209 176 pint:PI1947|5end_hypothetical_protein_1902534..1902764_POSITIVE 296 330 292 171 127 pint:PI1560|5end_integrase_1476962..1477192_POSITIVE 283 130 83 162 120 pint:PI1033|5end_ATP-dependent_RNA_helicase,_DEAD/DEAH_box_family_950297..950527_POSITIVE 282 339 295 226 174 pint:PI0697|5end_5'-nucleotidase_family_protein_633560..633790_POSITIVE 281 193 152 83 43 pint:PI1279|5end_RNA_polymerase_sigma_factor/ECF_subfamily_(sigma-70)_1195215..1195445_POSITIVE 277 128 85 196 146 pint:PI0589|5end_asparaginyl-tRNA_synthetase_(asparagine--tRNA_ligase)_535491..535721_POSITIVE 275 320 274 103 53 pint:PI0077|5end_hypothetical_protein_76244..76474_POSITIVE 274 426 393 117 73 pint:PI0806|5end_heavy_metal_efflux_pump_743679..743909_POSITIVE 273 42 15 48 23 pint:PI1566|5end_predicted_TPR-repeat-containing_protein_1487570..1487800_POSITIVE 265 435 406 156 124 pint:PI0670|5end_hypothetical_protein_611000..611230_POSITIVE 265 435 406 80 48 pint:PI0669|5end_hypothetical_protein_610924..611154_POSITIVE 265 314 279 88 44 pint:PI0408|5end_hypothetical_protein_374154..374384_POSITIVE 264 155 111 132 88 pint:PI0870|5end_branched-chain_amino_acid_aminotransferase_805933..806163_POSITIVE 263 437 394 102 43 pint:PI1727|5end__ATP-dependent_Clp_protease,_ATP-binding_subunit_1645680..1645910_POSITIVE 262 70 22 99 42 pint:PI1647|5end_hypothetical_protein_1561564..1561794_POSITIVE 262 70 27 112 74 pint:PI0539|5end_hypothetical_protein_493406..493636_POSITIVE 261 311 274 56 8 pint:PI0127|5end_conserved_hypothetical_protein_118683..118913_POSITIVE 260 345 302 162 113 pint:PI0985|5end_aspartyl-tRNA_synthetase_910174..910404_POSITIVE 259 446 402 72 16 pint:PI1095|5end_conserved_hypothetical_protein_1019759..1019989_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 298 208 169 75 39 pint:PI1448|3end_hypothetical_protein_1371832..1371982_POSITIVE 297 332 291 144 100 pint:PI1787|3end_conserved_hypothetical_protein_1719165..1719315_POSITIVE 296 330 292 101 57 pint:PI1559|3end_hypothetical_protein_1476972..1477122_POSITIVE 284 328 293 121 90 pint:PI1237|3end_ATP-dependent_DNA_helicase_1161480..1161630_POSITIVE 281 193 152 88 48 pint:PI1278|3end_ribulose-phosphate_3-epimerase_(pentose-5-phosphate-3-epimerase)_1195300..1195450_POSITIVE 272 134 94 100 51 pint:PI0798|3end_malonyl_CoA-acyl_carrier_protein_transacylase_736975..737125_POSITIVE 270 50 14 74 35 pint:PI1836|3end_conserved_hypothetical_protein_1778581..1778731_POSITIVE 263 128 84 50 3 pint:PI0588|3end_hypothetical_protein_535425..535575_POSITIVE 260 345 302 52 3 pint:PI0984|3end_hypothetical_protein_910144..910294_POSITIVE 259 446 402 61 5 pint:PI1094|3end_recombination_protein_1019828..1019978_POSITIVE 258 66 21 138 84 pint:PI0173|3end_hypothetical_protein_165558..165708_POSITIVE 257 273 233 94 57 pint:PI0434|3end_possible_beta-lactamase_406890..407040_POSITIVE 255 329 286 116 84 pint:PI1947|3end_hypothetical_protein_1902865..1903015_POSITIVE 253 226 182 64 17 pint:PI0729|3end_integrase_661765..661915_POSITIVE 253 191 152 108 65 pint:PI0230|3end_hypothetical_protein_228906..229056_POSITIVE 251 208 169 45 8 pint:PI0672|3end_conserved_hypothetical_protein_612230..612380_POSITIVE 251 133 97 51 11 pint:PI0358|3end_hypothetical_protein_328105..328255_POSITIVE 250 195 153 48 2 pint:PI0261|3end_conjugative_transposon_protein,_TraK_254765..254915_POSITIVE 250 449 404 108 64 pint:PI0188|3end_phosphomethylpyrimidine_kinase_179670..179820_POSITIVE 248 345 301 113 55 pint:PI0695|3end_xanthine/uracil_permease_family_protein_632701..632851_POSITIVE