Origin IGS: ttctttttcttcgacttatttaatatgctgtatcgtttgcaaaaatactaaaaaatatttaacttgccaactaattagctaaaaaacttaaaatatagcacgctgttttctttgttttcggcacacatttggcggttatgtgcagcttttttgcgctta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taagcgcaaaaaagctgcacataaccgccaaatgtgtgccgaaaacaaagaaaacagcgtgctatattttaagttttttagctaattagttggcaagttaaatattttttagtatttttgcaaacgatacagcatattaaataagtcgaagaaaaagaa Mask Tandem Repeat Region ================================================ ttctttttcttcgacttatttaatatgctgtatcgtttgcaaaaatactaaaaaatatttaacttgccaactaattagctaaaaaacttaaaatatagcacgctgttttctttgttttcggcacacatttggcggttatgtgcagcttttttgcgctta Find is-nt database================================================ Query_seq: PI0852:PI0853|PI0852:PI0853:conserved hypothetical protein:glycosyl transferase, group 2 family protein:->->:785496..785654 159 ttctttttcttcgacttatttaatatgctgtatcgtttgcaaaaatactaaaaaatatttaacttgccaactaattagctaaaaaacttaaaatatagcacgctgttttctttgttttcggcacacatttggcggttatgtgcagcttttttgcgctta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI0852:PI0853|PI0852:PI0853:conserved hypothetical protein:glycosyl transferase, group 2 family protein:->->:785496..785654 159 ttctttttcttcgacttatttaatatgctgtatcgtttgcaaaaatactaaaaaatatttaacttgccaactaattagctaaaaaacttaaaatatagcacgctgttttctttgttttcggcacacatttggcggttatgtgcagcttttttgcgctta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI0852:PI0853|PI0852:PI0853:conserved hypothetical protein:glycosyl transferase, group 2 family protein:->->:785496..785654 159 ttctttttcttcgacttatttaatatgctgtatcgtttgcaaaaatactaaaaaatatttaacttgccaactaattagctaaaaaacttaaaatatagcacgctgttttctttgttttcggcacacatttggcggttatgtgcagcttttttgcgctta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttctttttcttcgacttatttaatatgctgtatcgtttgcaaaaatactaaaaaatatttaacttgccaactaattagctaaaaaacttaaaatatagcacgctgttttctttgttttcggcacacatttggcggttatgtgcagcttttttgcgctta Predict ORF larger than 30AA ================================================ ttctttttcttcgacttatttaatatgctgtatcgtttgcaaaaatactaaaaaatatttaacttgccaactaattagctaaaaaacttaaaatatagcacgctgttttctttgttttcggcacacatttggcggttatgtgcagcttttttgcgctta 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: 82 Start: 42 End: 71 .........................................GTTGGCAAGTTAAATATTTTTTAGTATTTT........................................................................................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ttctttttcttcgacttatttaatatgctgtatcgtttgcaaaaatactaaaaaatatttaacttgccaactaattagctaaaaaacttaaaatatagcacgctgttttctttgttttcggcacacatttggcggttatgtgcagcttttttgcgctta Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PI0852:PI0853|PI0852:PI0853:conserved hypothetical protein:glycosyl transferase, group 2 family protein:->->:785496..785654 159 ttctttttcttcgacttatttaatatgctgtatcgtttgcaaaaatactaaaaaatatttaacttgccaactaattagctaaaaaacttaaaatatagcacgctgttttctttgttttcggcacacatttggcggttatgtgcagcttttttgcgctta Intra-Species Hit: Count: 1 Min: 1 Max: 159 Len: 159 Subject: pint_PI0852_PI0853|conserved hypothetical protein:glycosyl transferase, group 2 family protein|POSITIVE:POSITIVE|[785496,785654]|159 HSP 1 e-value: 3.0E-29 bit: 129.0 Len: 65 Query Start:95 Query End:159 Subject Strand: POSITIVE Subject Start: 95 Subject End: 159 ..............................................................................................atagcacgctgttttctttgttttcggcacacatttggcggttatgtgcagcttttttgcgctta ..............................................................................................atagcacgctgttttctttgttttcggcacacatttggcggttatgtgcagcttttttgcgctta HSP 2 e-value: 2.0E-14 bit: 79.8 Len: 40 Query Start:1 Query End:40 Subject Strand: POSITIVE Subject Start: 1 Subject End: 40 ttctttttcttcgacttatttaatatgctgtatcgtttgc....................................................................................................................... ttctttttcttcgacttatttaatatgctgtatcgtttgc....................................................................................................................... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUCUUUUUCUUCGACUUAUUUAAUAUGCUGUAUCGUUUGCAAAAAUACUAAAAAAUAUUUAACUUGCCAACUAAUUAGCUAAAAAACUUAAAAUAUAGCACGCUGUUUUCUUUGUUUUCGGCACACAUUUGGCGGUUAUGUGCAGCUUUUUUGCGCUUA ..................((((.(((..((((.....))))...))).)))).......(((((.(((((.......(((..(((((.......((((....)))).......))))).)))......)))))))))).((((((.....))))))... (-24.56) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAGCGCAAAAAAGCUGCACAUAACCGCCAAAUGUGUGCCGAAAACAAAGAAAACAGCGUGCUAUAUUUUAAGUUUUUUAGCUAAUUAGUUGGCAAGUUAAAUAUUUUUUAGUAUUUUUGCAAACGAUACAGCAUAUUAAAUAAGUCGAAGAAAAAGAA .....(((((((.((((((((((.........)))))))................(((.(((((.......((((....)))).......))))).)))...........))).)))))))...((((................))))........... (-25.23) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 366 138 91 210 151 pint:PI1675|5end_TonB-dependent_outer_membrane_receptor_1588107..1588337_POSITIVE 360 146 103 105 61 pint:PI0703|5end_hypothetical_protein_639655..639885_POSITIVE 328 147 101 186 136 pint:PI2005|5end_potassium_uptake_protein_1962950..1963180_POSITIVE 315 140 96 176 132 pint:PI0753|5end_hypothetical_protein_683391..683621_POSITIVE 303 142 102 130 93 pint:PI0337|5end_hypothetical_protein_314732..314962_POSITIVE 298 147 101 47 6 pint:PI0109|5end_hypothetical_protein_106717..106947_POSITIVE 297 137 97 228 195 pint:PI2016|5end_ribosomal_large_subunit_pseudouridine_synthase_D_1973768..1973998_POSITIVE 296 148 110 208 157 pint:PI2147|5end_GTP-binding_protein_2093263..2093493_POSITIVE 294 146 101 73 23 pint:PI0314|5end_conserved_hypothetical_protein_295552..295782_POSITIVE 292 148 101 195 129 pint:PI1653|5end_hypothetical_protein_1565158..1565388_POSITIVE 287 149 105 206 170 pint:PI0429|5end_hypothetical_protein_396418..396648_POSITIVE 285 146 102 230 178 pint:PI1505|5end_2-amino-4-hydroxy-6-hydroxymethyldihydropteridine_pyrophosphokinase_1424922..1425152_POSITIVE 284 148 102 76 20 pint:PI0168|5end_methionyl-tRNA_synthetase_(methionine--tRNA_ligase)_161181..161411_POSITIVE 283 146 101 174 121 pint:PI0667|5end_hypothetical_protein_610113..610343_POSITIVE 276 147 101 173 128 pint:PI0583|5end_hypothetical_protein_525948..526178_POSITIVE 274 146 101 228 185 pint:PI1851|5end_conserved_hypothetical_protein_1796847..1797077_POSITIVE 274 136 102 228 202 pint:PI0751|5end_conserved_hypothetical_protein_680623..680853_POSITIVE 272 146 101 60 12 pint:PI2096|5end_conserved_hypothetical_protein;_possible_phosphoesterase_2050268..2050498_POSITIVE 270 150 112 74 42 pint:PI1879|5end_uracil_phosphoribosyltransferase_1820671..1820901_POSITIVE 266 134 93 145 103 pint:PI0539|5end_hypothetical_protein_493406..493636_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 319 150 101 101 55 pint:PI0849|3end_hypothetical_protein_783542..783692_POSITIVE 317 146 102 145 99 pint:PI0110|3end_ABC_transport_system,_ATP-binding_protein_107920..108070_POSITIVE 308 145 101 70 25 pint:PI0684|3end_coproporphyrinogen_III_oxidase_620507..620657_POSITIVE 303 142 102 124 87 pint:PI0336|3end_hypothetical_protein_314806..314956_POSITIVE 302 146 104 146 101 pint:PI1775|3end_hypothetical_protein_1708120..1708270_POSITIVE 300 146 104 146 101 pint:PI1774|3end_hypothetical_protein_1707031..1707181_POSITIVE 288 147 102 83 33 pint:PI1651|3end_hypothetical_protein_1564512..1564662_POSITIVE 285 146 102 132 80 pint:PI1504|3end_non-specific_DNA-binding_protein_1424904..1425054_POSITIVE 284 146 102 117 79 pint:PI0967|3end_conserved_hypothetical_protein_896559..896709_POSITIVE 284 148 102 73 17 pint:PI0166|3end_hypothetical_protein_161258..161408_POSITIVE 282 135 101 148 110 pint:PI2004|3end_1-deoxy-D-xylulose_5-phosphate_synthase_1963004..1963154_POSITIVE 271 134 101 149 106 pint:PI1245|3end_hypothetical_protein_1171492..1171642_POSITIVE 267 150 101 122 74 pint:PI0990|3end_GDP-mannose_4,6-dehydratase_915054..915204_POSITIVE 264 149 102 138 87 pint:PI1873|3end_hypothetical_protein_1818419..1818569_POSITIVE 261 138 98 151 101 pint:PI2122|3end_conserved_hypothetical_protein_2070480..2070630_POSITIVE 261 150 101 86 37 pint:PI1636|3end_hypothetical_protein_1554823..1554973_POSITIVE 258 149 109 47 6 pint:PI1579|3end_penicillin-binding_protein_2_1507913..1508063_POSITIVE 254 145 102 149 94 pint:PI1947|3end_hypothetical_protein_1902865..1903015_POSITIVE 253 150 101 89 38 pint:PI1768|3end_conserved_hypothetical_protein_1696639..1696789_POSITIVE 249 145 101 151 99 pint:PI0666|3end_chorismate_synthase_610171..610321_POSITIVE