Origin IGS: ttttctttgttttttatgttatttatttcgtgtcgtaatataaaaatcttcaatttcattggcacagttagtgattaaaacatgatattacgataaaaagtttttaatagatgatgcaaaaaagattgaaaacgctgcatggcgatatgttaaaaattcaggatcaggaactgtttttttatttttcctgtcgaatgacgtatctttaccg .........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 cggtaaagatacgtcattcgacaggaaaaataaaaaaacagttcctgatcctgaatttttaacatatcgccatgcagcgttttcaatcttttttgcatcatctattaaaaactttttatcgtaatatcatgttttaatcactaactgtgccaatgaaattgaagatttttatattacgacacgaaataaataacataaaaaacaaagaaaa Mask Tandem Repeat Region ================================================ ttttctttgttttttatgttatttatttcgtgtcgtaatataaaaatcttcaatttcattggcacagttagtgattaaaacatgatattacgataaaaagtttttaatagatgatgcaaaaaagattgaaaacgctgcatggcgatatgttaaaaattcaggatcaggaactgtttttttatttttcctgtcgaatgacgtatctttaccg Find is-nt database================================================ Query_seq: TF0566:TF0567|TF0566:TF0567:hypothetical protein:conserved hypothetical protein; possible periplasmic solute-binding protein:->->:598919..599129 211 ttttctttgttttttatgttatttatttcgtgtcgtaatataaaaatcttcaatttcattggcacagttagtgattaaaacatgatattacgataaaaagtttttaatagatgatgcaaaaaagattgaaaacgctgcatggcgatatgttaaaaattcaggatcaggaactgtttttttatttttcctgtcgaatgacgtatctttaccg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF0566:TF0567|TF0566:TF0567:hypothetical protein:conserved hypothetical protein; possible periplasmic solute-binding protein:->->:598919..599129 211 ttttctttgttttttatgttatttatttcgtgtcgtaatataaaaatcttcaatttcattggcacagttagtgattaaaacatgatattacgataaaaagtttttaatagatgatgcaaaaaagattgaaaacgctgcatggcgatatgttaaaaattcaggatcaggaactgtttttttatttttcctgtcgaatgacgtatctttaccg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF0566:TF0567|TF0566:TF0567:hypothetical protein:conserved hypothetical protein; possible periplasmic solute-binding protein:->->:598919..599129 211 ttttctttgttttttatgttatttatttcgtgtcgtaatataaaaatcttcaatttcattggcacagttagtgattaaaacatgatattacgataaaaagtttttaatagatgatgcaaaaaagattgaaaacgctgcatggcgatatgttaaaaattcaggatcaggaactgtttttttatttttcctgtcgaatgacgtatctttaccg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttttctttgttttttatgttatttatttcgtgtcgtaatataaaaatcttcaatttcattggcacagttagtgattaaaacatgatattacgataaaaagtttttaatagatgatgcaaaaaagattgaaaacgctgcatggcgatatgttaaaaattcaggatcaggaactgtttttttatttttcctgtcgaatgacgtatctttaccg Predict ORF larger than 30AA ================================================ Protein_Len: 33 Strand: + Start: 111 End: 209 .............................................................................................................. M M Q K R L K T L H G D M L K I Q D Q E L F F Y F S C R M T Y L Y .. Protein_Len: 35 Strand: + Start: 107 End: 211 .......................................................................................................... M D D A K K I E N A A W R Y V K N S G S G T V F L F F L S N D V S L P ttttctttgttttttatgttatttatttcgtgtcgtaatataaaaatcttcaatttcattggcacagttagtgattaaaacatgatattacgataaaaagtttttaatagatgatgcaaaaaagattgaaaacgctgcatggcgatatgttaaaaattcaggatcaggaactgtttttttatttttcctgtcgaatgacgtatctttaccg 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================================================ ttttctttgttttttatgttatttatttcgtgtcgtaatataaaaatcttcaatttcattggcacagttagtgattaaaacatgatattacgataaaaagtttttaatagatgatgcaaaaaagattgaaaacgctgcatggcgatatgttaaaaattcaggatcaggaactgtttttttatttttcctgtcgaatgacgtatctttaccg Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF0566:TF0567|TF0566:TF0567:hypothetical protein:conserved hypothetical protein; possible periplasmic solute-binding protein:->->:598919..599129 211 ttttctttgttttttatgttatttatttcgtgtcgtaatataaaaatcttcaatttcattggcacagttagtgattaaaacatgatattacgataaaaagtttttaatagatgatgcaaaaaagattgaaaacgctgcatggcgatatgttaaaaattcaggatcaggaactgtttttttatttttcctgtcgaatgacgtatctttaccg Intra-Species Hit: Count: 1 Min: 1 Max: 173 Len: 173 Subject: tfor_TF0566_TF0567|hypothetical protein:conserved hypothetical protein; possible periplasmic solute-binding protein|POSITIVE:POSITIVE|[598919,599129]|211 HSP 1 e-value: 1.0E-93 bit: 343.0 Len: 173 Query Start:1 Query End:173 Subject Strand: POSITIVE Subject Start: 1 Subject End: 173 ttttctttgttttttatgttatttatttcgtgtcgtaatataaaaatcttcaatttcattggcacagttagtgattaaaacatgatattacgataaaaagtttttaatagatgatgcaaaaaagattgaaaacgctgcatggcgatatgttaaaaattcaggatcaggaactg...................................... ttttctttgttttttatgttatttatttcgtgtcgtaatataaaaatcttcaatttcattggcacagttagtgattaaaacatgatattacgataaaaagtttttaatagatgatgcaaaaaagattgaaaacgctgcatggcgatatgttaaaaattcaggatcaggaactg...................................... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUUCUUUGUUUUUUAUGUUAUUUAUUUCGUGUCGUAAUAUAAAAAUCUUCAAUUUCAUUGGCACAGUUAGUGAUUAAAACAUGAUAUUACGAUAAAAAGUUUUUAAUAGAUGAUGCAAAAAAGAUUGAAAACGCUGCAUGGCGAUAUGUUAAAAAUUCAGGAUCAGGAACUG .((((..(.((((((..((((((((((.(.(((((((((((..............((((((((...))))))))..........)))))))))))....).....))))))))))..)))))).)..)))).((((....))))..............(((.........))) (-32.45) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CAGUUCCUGAUCCUGAAUUUUUAACAUAUCGCCAUGCAGCGUUUUCAAUCUUUUUUGCAUCAUCUAUUAAAAACUUUUUAUCGUAAUAUCAUGUUUUAAUCACUAACUGUGCCAAUGAAAUUGAAGAUUUUUAUAUUACGACACGAAAUAAAUAACAUAAAAAACAAAGAAAA .(((((........))))).........(((..((((((...............))))))....................(((((((((....((((((((((.....)))........)))))))......)))))))))..)))........................... (-15.06) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 287 166 133 181 140 tfor:TF0406|5end_monofunctional_biosynthetic_peptidoglycan_transglycosylase_424245..424475_POSITIVE 280 169 134 81 53 tfor:TF1866|5end_conserved_hypothetical_protein;_possible_transposase_2022272..2022502_POSITIVE 270 170 122 85 26 tfor:TF0094|5end_alpha-glucosidase_103561..103791_POSITIVE 260 144 106 109 75 tfor:TF0704|5end_TPR-repeat-containing_protein_747888..748118_POSITIVE 245 169 134 81 53 tfor:TF1096|5end_conserved_hypothetical_protein_1165065..1165295_POSITIVE 243 145 106 154 112 tfor:TF2821|5end_conserved_hypothetical_protein_3011146..3011376_POSITIVE 243 168 124 202 165 tfor:TF1440|5end_hypothetical_protein_1524599..1524829_POSITIVE 243 170 124 195 161 tfor:TF0313|5end_outer_membrane_protein,_TonB_dependent_receptor_338182..338412_POSITIVE 242 166 124 89 48 tfor:TF3148|5end_hypoxanthine-guanine_phosphoribosyltransferase_3383652..3383882_POSITIVE 239 143 109 36 1 tfor:TF1958|5end_cytidylate_kinase_2108659..2108889_POSITIVE 238 144 111 131 97 tfor:TF0659|5end_RNA_polymerase,_ECF-type_sigma_factor_705428..705658_POSITIVE 236 151 123 75 39 tfor:TF3141|5end_NADH:_ubiquinone_oxidoreductase,_subunit_A_3374667..3374897_POSITIVE 236 147 113 56 18 tfor:TF2780|5end_hypothetical_protein_2966060..2966290_POSITIVE 235 144 109 48 16 tfor:TF2253|5end_conjugative_transposon_protein,_TraG_2424950..2425180_POSITIVE 233 145 110 216 179 tfor:TF1409|5end_outer_membrane_protein_TolC_1485479..1485709_POSITIVE 230 149 110 114 76 tfor:TF1429|5end_S-adenosyl-methyltransferase_1513927..1514157_POSITIVE 227 170 125 195 139 tfor:TF1236|5end_L-rhamnose_isomerase_1320743..1320973_POSITIVE 227 169 122 199 146 tfor:TF0217|5end_50S_ribosomal_protein_L35_242920..243150_POSITIVE 226 150 111 126 77 tfor:TF2333|5end_signal_peptidase_I_2492560..2492790_POSITIVE 225 144 112 201 155 tfor:TF2996|5end_hypothetical_protein_3210802..3211032_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 280 169 134 135 107 tfor:TF1865|3end_conserved_hypothetical_protein;_possible_transposase_2022406..2022556_POSITIVE 270 170 122 62 3 tfor:TF0093|3end_outer_membrane_protein,_TonB_dependent_receptor_103618..103768_POSITIVE 260 144 106 96 62 tfor:TF0703|3end_conserved_hypothetical_protein_747955..748105_POSITIVE 245 169 134 135 107 tfor:TF1095|3end_transposase_1165199..1165349_POSITIVE 243 145 106 128 86 tfor:TF2820|3end_argininosuccinate_synthetase_3011200..3011350_POSITIVE 242 166 124 61 20 tfor:TF3147|3end_adenylate_kinase_3383704..3383854_POSITIVE 235 144 109 48 16 tfor:TF2252|3end_transfer_region-related_protein,_TraF_2425030..2425180_POSITIVE 230 149 110 103 65 tfor:TF1428|3end_conserved_hypothetical_protein_1513996..1514146_POSITIVE 227 169 122 99 46 tfor:TF0216|3end_50S_ribosomal_protein_L20_242900..243050_POSITIVE 226 150 111 99 50 tfor:TF2332|3end_signal_peptidase_I_2492613..2492763_POSITIVE 224 163 133 78 47 tfor:TF2720|3end_conserved_hypothetical_protein_2894941..2895091_POSITIVE 224 168 133 136 94 tfor:TF1184|3end_hypothetical_protein_1269311..1269461_POSITIVE 224 168 133 136 94 tfor:TF1183|3end_hypothetical_protein_1268728..1268878_POSITIVE 222 150 110 136 90 tfor:TF1423|3end_cell_division_protein_(ftsW)_1507323..1507473_POSITIVE 221 149 105 138 95 tfor:TF2530|3end_conserved_hypothetical_protein_2712926..2713076_POSITIVE 220 161 126 46 9 tfor:TF0340|3end_hypothetical_protein_364257..364407_POSITIVE 219 147 105 135 96 tfor:TF2801|3end_outer_membrane_protein,_TonB_dependent_receptor_2989901..2990051_POSITIVE 219 140 99 135 98 tfor:TF2007|3end_uracil_phosphoribosyltransferase_2159327..2159477_POSITIVE 219 149 132 25 4 tfor:TF1908|3end_possible_phosphoglycerate_mutase_2063299..2063449_POSITIVE 219 151 112 47 6 tfor:TF0105|3end_DNA-binding_stress_protein,_Dps_family_113907..114057_POSITIVE