Origin IGS: cgaaaacttcgttttgctgctgattcgtgggtaaaaaaactaaccgatgatgtcagagtagagccaaacaacccgaaaagcacagcacggatagtattgaaacgaaagtaacagtgcaggttagcctcatttccgatgtgcaaataaatattgtatatatttccttctatacggctatcggtttgttttttcttatgtatatgctttaaatatttgtaaaacctgtgtacctttgcacct .........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 aggtgcaaaggtacacaggttttacaaatatttaaagcatatacataagaaaaaacaaaccgatagccgtatagaaggaaatatatacaatatttatttgcacatcggaaatgaggctaacctgcactgttactttcgtttcaatactatccgtgctgtgcttttcgggttgtttggctctactctgacatcatcggttagtttttttacccacgaatcagcagcaaaacgaagttttcg Mask Tandem Repeat Region ================================================ cgaaaacttcgttttgctgctgattcgtgggtaaaaaaactaaccgatgatgtcagagtagagccaaacaacccgaaaagcacagcacggatagtattgaaacgaaagtaacagtgcaggttagcctcatttccgatgtgcaaataaatattgtatatatttccttctatacggctatcggtttgttttttcttatgtatatgctttaaatatttgtaaaacctgtgtacctttgcacct Find is-nt database================================================ Query_seq: PI0872:PI0873|PI0872:PI0873:hypothetical protein:conserved hypothetical protein; possible permease:->->:807868..808107 240 cgaaaacttcgttttgctgctgattcgtgggtaaaaaaactaaccgatgatgtcagagtagagccaaacaacccgaaaagcacagcacggatagtattgaaacgaaagtaacagtgcaggttagcctcatttccgatgtgcaaataaatattgtatatatttccttctatacggctatcggtttgttttttcttatgtatatgctttaaatatttgtaaaacctgtgtacctttgcacct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI0872:PI0873|PI0872:PI0873:hypothetical protein:conserved hypothetical protein; possible permease:->->:807868..808107 240 cgaaaacttcgttttgctgctgattcgtgggtaaaaaaactaaccgatgatgtcagagtagagccaaacaacccgaaaagcacagcacggatagtattgaaacgaaagtaacagtgcaggttagcctcatttccgatgtgcaaataaatattgtatatatttccttctatacggctatcggtttgttttttcttatgtatatgctttaaatatttgtaaaacctgtgtacctttgcacct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI0872:PI0873|PI0872:PI0873:hypothetical protein:conserved hypothetical protein; possible permease:->->:807868..808107 240 cgaaaacttcgttttgctgctgattcgtgggtaaaaaaactaaccgatgatgtcagagtagagccaaacaacccgaaaagcacagcacggatagtattgaaacgaaagtaacagtgcaggttagcctcatttccgatgtgcaaataaatattgtatatatttccttctatacggctatcggtttgttttttcttatgtatatgctttaaatatttgtaaaacctgtgtacctttgcacct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 cgaaaacttcgttttgctgctgattcgtgggtaaaaaaactaaccgatgatgtcagagtagagccaaacaacccgaaaagcacagcacggatagtattgaaacgaaagtaacagtgcaggttagcctcatttccgatgtgcaaataaatattgtatatatttccttctatacggctatcggtttgttttttcttatgtatatgctttaaatatttgtaaaacctgtgtacctttgcacct Predict ORF larger than 30AA ================================================ Protein_Len: 37 Strand: + Start: 96 End: 206 ............................................................................................... M E T K V T V Q V S L I S D V Q I N I V Y I S F Y T A I G L F F L M Y M L .................................. Protein_Len: 35 Strand: - Start: 56 End: 160 ....................................................... L L A L C G S F C L V S L I S V F T V T C T L R M E S T C I F I T Y M ................................................................................ Protein_Len: 60 Strand: - Start: 3 End: 200 .. S E H T F F S V S S T L T S G F L G F L V A R I T N F R F Y C H L N A E N G I H L Y I N Y I N G E I R S D T Q K K K H M ........................................ cgaaaacttcgttttgctgctgattcgtgggtaaaaaaactaaccgatgatgtcagagtagagccaaacaacccgaaaagcacagcacggatagtattgaaacgaaagtaacagtgcaggttagcctcatttccgatgtgcaaataaatattgtatatatttccttctatacggctatcggtttgttttttcttatgtatatgctttaaatatttgtaaaacctgtgtacctttgcacct 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================================================ cgaaaacttcgttttgctgctgattcgtgggtaaaaaaactaaccgatgatgtcagagtagagccaaacaacccgaaaagcacagcacggatagtattgaaacgaaagtaacagtgcaggttagcctcatttccgatgtgcaaataaatattgtatatatttccttctatacggctatcggtttgttttttcttatgtatatgctttaaatatttgtaaaacctgtgtacctttgcacct Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PI0872:PI0873|PI0872:PI0873:hypothetical protein:conserved hypothetical protein; possible permease:->->:807868..808107 240 cgaaaacttcgttttgctgctgattcgtgggtaaaaaaactaaccgatgatgtcagagtagagccaaacaacccgaaaagcacagcacggatagtattgaaacgaaagtaacagtgcaggttagcctcatttccgatgtgcaaataaatattgtatatatttccttctatacggctatcggtttgttttttcttatgtatatgctttaaatatttgtaaaacctgtgtacctttgcacct Intra-Species Hit: Count: 1 Min: 1 Max: 240 Len: 240 Subject: pint_PI0872_PI0873|hypothetical protein:conserved hypothetical protein; possible permease|POSITIVE:POSITIVE|[807868,808107]|240 HSP 1 e-value: 1.0E-121 bit: 434.0 Len: 240 Query Start:1 Query End:240 Subject Strand: POSITIVE Subject Start: 1 Subject End: 240 cgaaaacttcgttttgctgctgattcgtgggtnnnnnnnctaaccgatgatgtcagagtagagccaaacaacccgaaaagcacagcacggatagtattgaaacgaaagtaacagtgcaggttagcctcatttccgatgtgcaaataaatattgtatatatttccttctatacggctatcggtttgttttttcttatgtatatgctttaaatatttgtaaaacctgtgtacctttgcacct cgaaaacttcgttttgctgctgattcgtgggtaaaaaaactaaccgatgatgtcagagtagagccaaacaacccgaaaagcacagcacggatagtattgaaacgaaagtaacagtgcaggttagcctcatttccgatgtgcaaataaatattgtatatatttccttctatacggctatcggtttgttttttcttatgtatatgctttaaatatttgtaaaacctgtgtacctttgcacct Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CGAAAACUUCGUUUUGCUGCUGAUUCGUGGGUAAAAAAACUAACCGAUGAUGUCAGAGUAGAGCCAAACAACCCGAAAAGCACAGCACGGAUAGUAUUGAAACGAAAGUAACAGUGCAGGUUAGCCUCAUUUCCGAUGUGCAAAUAAAUAUUGUAUAUAUUUCCUUCUAUACGGCUAUCGGUUUGUUUUUUCUUAUGUAUAUGCUUUAAAUAUUUGUAAAACCUGUGUACCUUUGCACCU .(((((....((((((((.(((((((((.(((..........))).)))).)))))))))))))..(((((.((((...(((((...((((..((((((..((....))..)))))).((....)).....)))).))))).........(((((((.(......).)))))))...)))).))))))))))................................(((((....))))).. (-60.50) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGGUGCAAAGGUACACAGGUUUUACAAAUAUUUAAAGCAUAUACAUAAGAAAAAACAAACCGAUAGCCGUAUAGAAGGAAAUAUAUACAAUAUUUAUUUGCACAUCGGAAAUGAGGCUAACCUGCACUGUUACUUUCGUUUCAAUACUAUCCGUGCUGUGCUUUUCGGGUUGUUUGGCUCUACUCUGACAUCAUCGGUUAGUUUUUUUACCCACGAAUCAGCAGCAAAACGAAGUUUUCG .(.(((....(((.....((((((........))))))...)))....((((((((.(((((((....((((((..(((........(((.......))).......(((((((((.((((.......)))).))))))))).......)))...)))))).....(((((....)))))............))))))).))))))))............))).)............... (-47.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 318 130 82 228 164 pint:PI1856|5end_nicotinate-nucleotide_adenylyltransferase_1803203..1803433_POSITIVE 314 140 94 150 101 pint:PI0344|5end_conserved_hypothetical_protein_318178..318408_POSITIVE 311 127 83 79 38 pint:PI0705|5end_conserved_hypothetical_protein;_possible_lipoprotein_641274..641504_POSITIVE 310 117 72 210 168 pint:PI0937|5end_hypothetical_protein_869235..869465_POSITIVE 308 141 101 121 83 pint:PI0092|5end_regulatory_protein_RecX_89080..89310_POSITIVE 303 89 43 64 1 pint:PI0723|5end_conserved_hypothetical_protein_656043..656273_POSITIVE 299 90 53 215 180 pint:PI2138|5end_nicotinate_phosphoribosyltransferase_2083836..2084066_POSITIVE 292 90 44 93 40 pint:PI1650|5end_N-acetylmuramoyl-L-alanine_amidase_1563195..1563425_POSITIVE 288 120 73 221 171 pint:PI0699|5end_conserved_hypothetical_protein_636647..636877_POSITIVE 287 83 42 60 17 pint:PI1477|5end_TonB-dependent_outer_membrane_receptor_1399734..1399964_POSITIVE 284 141 101 78 39 pint:PI1768|5end_conserved_hypothetical_protein_1695456..1695686_POSITIVE 281 148 103 71 29 pint:PI0714|5end_conserved_hypothetical_protein_651345..651575_POSITIVE 280 141 115 31 8 pint:PI1176|5end_endonuclease_III_1098089..1098319_POSITIVE 278 88 45 55 1 pint:PI1263|5end_probable_integrase_1184502..1184732_POSITIVE 273 93 51 105 61 pint:PI0239|5end_conserved_hypothetical_protein_237975..238205_POSITIVE 271 99 53 73 27 pint:PI1820|5end_hypothetical_protein_1759962..1760192_POSITIVE 269 126 81 224 185 pint:PI0673|5end_hypothetical_protein_612206..612436_POSITIVE 269 46 6 231 186 pint:PI0017|5end_thiol-disulfide_isomerase;_thioredoxin_21733..21963_POSITIVE 265 68 25 55 4 pint:PI1933|5end_hypothetical_protein_1879925..1880155_POSITIVE 265 90 45 47 1 pint:PI1639|5end_conserved_hypothetical_protein_1556725..1556955_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 318 130 82 113 49 pint:PI1855|3end_lipopolysaccharide_biosynthesis_protein_1803168..1803318_POSITIVE 311 127 83 89 48 pint:PI0704|3end_conserved_hypothetical_protein_641364..641514_POSITIVE 308 141 101 121 83 pint:PI0090|3end_amidophosphoribosyltransferase_89160..89310_POSITIVE 299 90 53 106 71 pint:PI2137|3end_RNA_methylase_SpoU_family_2083807..2083957_POSITIVE 294 90 45 140 89 pint:PI2018|3end_50S_ribosomal_protein_L34_1975989..1976139_POSITIVE 272 67 26 131 90 pint:PI2147|3end_GTP-binding_protein_2094407..2094557_POSITIVE 269 125 82 150 102 pint:PI0965|3end_hypothetical_protein_894392..894542_POSITIVE 269 46 6 143 98 pint:PI0016|3end_magnesium_chelatase,_subunit_ChlI_21725..21875_POSITIVE 264 128 81 116 62 pint:PI0203|3end_conserved_hypothetical_protein_196064..196214_POSITIVE 263 240 200 141 103 pint:PI0169|3end_hypothetical_protein_164036..164186_POSITIVE 259 87 41 138 85 pint:PI2086|3end_signal_peptidase_I_2043450..2043600_POSITIVE 259 127 83 33 4 pint:PI0273|3end_hypothetical_protein_263284..263434_POSITIVE 259 208 171 112 70 pint:PI0247|3end_conjugative_transposon_protein,_TraA_246232..246382_POSITIVE 258 52 11 62 16 pint:PI2023|3end_hypothetical_protein_1978832..1978982_POSITIVE 255 32 1 110 68 pint:PI1716|3end_hypothetical_protein_1632006..1632156_POSITIVE 255 220 173 80 31 pint:PI0974|3end_hypothetical_protein_899591..899741_POSITIVE 252 204 172 125 98 pint:PI2155|3end_hypothetical_protein_2101052..2101202_POSITIVE 251 127 81 138 88 pint:PI0386|3end_integrase_354640..354790_POSITIVE 250 118 74 57 1 pint:PI0883|3end_para-aminobenzoate_synthase_component_I_817251..817401_POSITIVE 247 204 178 26 1 pint:PI1436|3end_hypothetical_protein_1356232..1356382_POSITIVE