Origin IGS: taagattgcgacgtttcccacatacatcatcacgacgcttgcaccttaatcttcgtatgcaaaaattcttttttctaaaatattctttgtaaaaaccgcccaataaataaaaaaaatgtaattttgtgggaaatcagttagtttcggctgtacgggcttttatcgcttttgcgtcattaaaacaaccatcggccggctaaccgaaatgttttataactaaacaaacaacaatacgatgacaaatacatttatataccgttcacaatgccccattccaatcgggcaatattctttataactacagttactt .........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 aagtaactgtagttataaagaatattgcccgattggaatggggcattgtgaacggtatataaatgtatttgtcatcgtattgttgtttgtttagttataaaacatttcggttagccggccgatggttgttttaatgacgcaaaagcgataaaagcccgtacagccgaaactaactgatttcccacaaaattacattttttttatttattgggcggtttttacaaagaatattttagaaaaaagaatttttgcatacgaagattaaggtgcaagcgtcgtgatgatgtatgtgggaaacgtcgcaatctta Mask Tandem Repeat Region ================================================ taagattgcgacgtttcccacatacatcatcacgacgcttgcaccttaatcttcgtatgcaaaaattcttttttctaaaatattctttgtaaaaaccgcccaataaataaaaaaaatgtaattttgtgggaaatcagttagtttcggctgtacgggcttttatcgcttttgcgtcattaaaacaaccatcggccggctaaccgaaatgttttataactaaacaaacaacaatacgatgacaaatacatttatataccgttcacaatgccccattccaatcgggcaatattctttataactacagttactt Find is-nt database================================================ Query_seq: TF0777:TF0778|TF0777:TF0778:1,4-dihydroxy-2-naphthoate octaprenyltransferase:outer membrane protein, TonB dependent receptor:->->:827114..827423 310 taagattgcgacgtttcccacatacatcatcacgacgcttgcaccttaatcttcgtatgcaaaaattcttttttctaaaatattctttgtaaaaaccgcccaataaataaaaaaaatgtaattttgtgggaaatcagttagtttcggctgtacgggcttttatcgcttttgcgtcattaaaacaaccatcggccggctaaccgaaatgttttataactaaacaaacaacaatacgatgacaaatacatttatataccgttcacaatgccccattccaatcgggcaatattctttataactacagttactt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF0777:TF0778|TF0777:TF0778:1,4-dihydroxy-2-naphthoate octaprenyltransferase:outer membrane protein, TonB dependent receptor:->->:827114..827423 310 taagattgcgacgtttcccacatacatcatcacgacgcttgcaccttaatcttcgtatgcaaaaattcttttttctaaaatattctttgtaaaaaccgcccaataaataaaaaaaatgtaattttgtgggaaatcagttagtttcggctgtacgggcttttatcgcttttgcgtcattaaaacaaccatcggccggctaaccgaaatgttttataactaaacaaacaacaatacgatgacaaatacatttatataccgttcacaatgccccattccaatcgggcaatattctttataactacagttactt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF0777:TF0778|TF0777:TF0778:1,4-dihydroxy-2-naphthoate octaprenyltransferase:outer membrane protein, TonB dependent receptor:->->:827114..827423 310 taagattgcgacgtttcccacatacatcatcacgacgcttgcaccttaatcttcgtatgcaaaaattcttttttctaaaatattctttgtaaaaaccgcccaataaataaaaaaaatgtaattttgtgggaaatcagttagtttcggctgtacgggcttttatcgcttttgcgtcattaaaacaaccatcggccggctaaccgaaatgttttataactaaacaaacaacaatacgatgacaaatacatttatataccgttcacaatgccccattccaatcgggcaatattctttataactacagttactt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taagattgcgacgtttcccacatacatcatcacgacgcttgcaccttaatcttcgtatgcaaaaattcttttttctaaaatattctttgtaaaaaccgcccaataaataaaaaaaatgtaattttgtgggaaatcagttagtttcggctgtacgggcttttatcgcttttgcgtcattaaaacaaccatcggccggctaaccgaaatgttttataactaaacaaacaacaatacgatgacaaatacatttatataccgttcacaatgccccattccaatcgggcaatattctttataactacagttactt Predict ORF larger than 30AA ================================================ Protein_Len: 34 Strand: - Start: 2 End: 103 . L N R R K G C V D D R R K C R L R R I C F N K K R F Y E K Y F G G M ............................................................................................................................................................................................................... taagattgcgacgtttcccacatacatcatcacgacgcttgcaccttaatcttcgtatgcaaaaattcttttttctaaaatattctttgtaaaaaccgcccaataaataaaaaaaatgtaattttgtgggaaatcagttagtttcggctgtacgggcttttatcgcttttgcgtcattaaaacaaccatcggccggctaaccgaaatgttttataactaaacaaacaacaatacgatgacaaatacatttatataccgttcacaatgccccattccaatcgggcaatattctttataactacagttactt 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================================================ taagattgcgacgtttcccacatacatcatcacgacgcttgcaccttaatcttcgtatgcaaaaattcttttttctaaaatattctttgtaaaaaccgcccaataaataaaaaaaatgtaattttgtgggaaatcagttagtttcggctgtacgggcttttatcgcttttgcgtcattaaaacaaccatcggccggctaaccgaaatgttttataactaaacaaacaacaatacgatgacaaatacatttatataccgttcacaatgccccattccaatcgggcaatattctttataactacagttactt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF0777:TF0778|TF0777:TF0778:1,4-dihydroxy-2-naphthoate octaprenyltransferase:outer membrane protein, TonB dependent receptor:->->:827114..827423 310 taagattgcgacgtttcccacatacatcatcacgacgcttgcaccttaatcttcgtatgcaaaaattcttttttctaaaatattctttgtaaaaaccgcccaataaataaaaaaaatgtaattttgtgggaaatcagttagtttcggctgtacgggcttttatcgcttttgcgtcattaaaacaaccatcggccggctaaccgaaatgttttataactaaacaaacaacaatacgatgacaaatacatttatataccgttcacaatgccccattccaatcgggcaatattctttataactacagttactt Intra-Species Hit: Count: 1 Min: 1 Max: 310 Len: 310 Subject: tfor_TF0777_TF0778|1,4-dihydroxy-2-naphthoate octaprenyltransferase:outer membrane protein, TonB dependent receptor|POSITIVE:POSITIVE|[827114,827423]|310 HSP 1 e-value: 1.0E-161 bit: 567.0 Len: 310 Query Start:1 Query End:310 Subject Strand: POSITIVE Subject Start: 1 Subject End: 310 taagattgcgacgtttcccacatacatcatcacgacgcttgcaccttaatcttcgtatgcaaaaattcttttttctaaaatattctttgtaaaaaccgcccaataaatnnnnnnnntgtaattttgtgggaaatcagttagtttcggctgtacgggcttttatcgcttttgcgtcattaaaacaaccatcggccggctaaccgaaatgttttataactaaacaaacaacaatacgatgacaaatacatttatataccgttcacaatgccccattccaatcgggcaatattctttataactacagttactt taagattgcgacgtttcccacatacatcatcacgacgcttgcaccttaatcttcgtatgcaaaaattcttttttctaaaatattctttgtaaaaaccgcccaataaataaaaaaaatgtaattttgtgggaaatcagttagtttcggctgtacgggcttttatcgcttttgcgtcattaaaacaaccatcggccggctaaccgaaatgttttataactaaacaaacaacaatacgatgacaaatacatttatataccgttcacaatgccccattccaatcgggcaatattctttataactacagttactt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAGAUUGCGACGUUUCCCACAUACAUCAUCACGACGCUUGCACCUUAAUCUUCGUAUGCAAAAAUUCUUUUUUCUAAAAUAUUCUUUGUAAAAACCGCCCAAUAAAUAAAAAAAAUGUAAUUUUGUGGGAAAUCAGUUAGUUUCGGCUGUACGGGCUUUUAUCGCUUUUGCGUCAUUAAAACAACCAUCGGCCGGCUAACCGAAAUGUUUUAUAACUAAACAAACAACAAUACGAUGACAAAUACAUUUAUAUACCGUUCACAAUGCCCCAUUCCAAUCGGGCAAUAUUCUUUAUAACUACAGUUACUU ...(((((.((((.(((((((((((((....((((.(.(((.....))).).)))).(((((((((..(((.....)))..))).))))))........................)))))....)))))))).((.((((((..((((((...((..(((((.(((....)))....)))))...))..)))))))))))).))..(((((.......))))).................................)))).....(((((.((....)).)))))................))))).... (-54.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAGUAACUGUAGUUAUAAAGAAUAUUGCCCGAUUGGAAUGGGGCAUUGUGAACGGUAUAUAAAUGUAUUUGUCAUCGUAUUGUUGUUUGUUUAGUUAUAAAACAUUUCGGUUAGCCGGCCGAUGGUUGUUUUAAUGACGCAAAAGCGAUAAAAGCCCGUACAGCCGAAACUAACUGAUUUCCCACAAAAUUACAUUUUUUUUAUUUAUUGGGCGGUUUUUACAAAGAAUAUUUUAGAAAAAAGAAUUUUUGCAUACGAAGAUUAAGGUGCAAGCGUCGUGAUGAUGUAUGUGGGAAACGUCGCAAUCUUA ..(((((....))))).((((....(((((.((....)).))))).(((((.((((.......(((((..((.....(((((((.(((((...(((((((((((..(((((......)))))....)))))).)))))))))))))))))...))..)))))))))...........(((((((((....((((((....((((...(((.((..((((((.(((.....)))))))))....((((((((....))))))))...)).))).....)))).)))))))))))))))..))))).)))). (-70.71) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 355 46 5 183 142 tfor:TF0145|5end_glutamine_synthetase_152446..152676_POSITIVE 350 174 133 70 27 tfor:TF1457|5end_conserved_hypothetical_protein;_possible_transporter_1543229..1543459_POSITIVE 341 176 140 124 81 tfor:TF2660|5end_hypothetical_protein_2833293..2833523_POSITIVE 333 190 146 210 166 tfor:TF2180|5end_phosphoribosylamine--glycine_ligase_2352580..2352810_POSITIVE 333 177 135 215 171 tfor:TF0092|5end_outer_membrane_protein_98889..99119_POSITIVE 332 169 123 127 74 tfor:TF0002|5end_hypothetical_protein_316..546_POSITIVE 328 203 165 59 18 tfor:TF2349|5end_conserved_hypothetical_protein_2513192..2513422_POSITIVE 326 196 151 67 29 tfor:TF1720|5end_conserved_hypothetical_protein_1843679..1843909_POSITIVE 325 197 154 228 173 tfor:TF2276|5end_conserved_hypothetical_protein_2438226..2438456_POSITIVE 323 188 145 195 155 tfor:TF1466|5end_DNA_gyrase_modulator_1555469..1555699_POSITIVE 320 197 151 225 189 tfor:TF2636|5end_glutaminase_2806096..2806326_POSITIVE 319 208 162 220 167 tfor:TF2682|5end_N_utilization_substance_protein_A_2856308..2856538_POSITIVE 318 188 141 59 11 tfor:TF2438|5end_hypothetical_protein_2615781..2616011_POSITIVE 315 187 144 185 135 tfor:TF2009|5end_octaprenyl-diphosphate_synthase_ispB_2162131..2162361_POSITIVE 312 45 2 173 118 tfor:TF1808|5end_DNA_processing_protein_subunit_A_1949356..1949586_POSITIVE 309 170 121 211 164 tfor:TF1812|5end_tryptophan_synthase,_beta_chain_1952696..1952926_POSITIVE 307 166 125 174 136 tfor:TF2226|5end_CTn_excision_protein_2395529..2395759_POSITIVE 306 166 121 131 94 tfor:TF2820|5end_argininosuccinate_synthetase_3009876..3010106_POSITIVE 305 291 251 171 131 tfor:TF2375|5end_conserved_hypothetical_protein_2540953..2541183_POSITIVE 305 174 144 45 9 tfor:TF1811|5end_hypothetical_protein_1952523..1952753_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 350 174 133 48 5 tfor:TF1456|3end_GMP_synthase_1543287..1543437_POSITIVE 320 197 151 150 114 tfor:TF2635|3end_ABC_transporter,_ATP-binding_protein/permease_component_2806101..2806251_POSITIVE 318 197 152 147 95 tfor:TF1838|3end_tRNA/rRNA_methyltransferase_1988745..1988895_POSITIVE 315 203 169 39 2 tfor:TF2348|3end_outer_membrane_protein,_possibly_involved_in_nutrient_binding_2513252..2513402_POSITIVE 306 166 121 131 94 tfor:TF2819|3end_N-acetyl-gamma-glutamylphosphate_reductase_3009956..3010106_POSITIVE 305 197 153 57 5 tfor:TF0413|3end_succinyl-diaminopimelate_desuccinylase_431869..432019_POSITIVE 303 196 153 144 100 tfor:TF2738|3end_30S_ribosomal_protein_S16_2920084..2920234_POSITIVE 303 190 145 147 96 tfor:TF2574|3end_preprotein_translocase_SecY_2745200..2745350_POSITIVE 302 198 153 62 25 tfor:TF1852|3end_prtQ_protein_2006546..2006696_POSITIVE 301 175 134 132 88 tfor:TF0991|3end_probable_NAD(FAD)-dependent_dehydrogenase_1048334..1048484_POSITIVE 300 169 121 114 70 tfor:TF1575|3end_DNA-binding_response_regulator_1685895..1686045_POSITIVE 300 157 114 55 16 tfor:TF0950|3end_ribosomal_large_subunit_pseudouridine_synthase_D_(pseudouridylate_synthase)_(uracil_hydrolyase)_995777..995927_POSITIVE 298 218 171 63 10 tfor:TF2829|3end_conserved_hypothetical_protein_3020661..3020811_POSITIVE 295 210 162 38 4 tfor:TF2092|3end_ribonuclease_III_2261823..2261973_POSITIVE 295 199 154 47 9 tfor:TF0281|3end_hypothetical_protein_309159..309309_POSITIVE 292 166 123 150 98 tfor:TF1335|3end_conserved_hypothetical_protein;_possible_alpha-1,2-mannosidase_family_protein_1418677..1418827_POSITIVE 289 175 135 49 4 tfor:TF2225|3end_CTn_excision_protein_2395602..2395752_POSITIVE 288 47 9 126 90 tfor:TF3105|3end_hypothetical_protein_3338342..3338492_POSITIVE 285 175 143 146 108 tfor:TF2478|3end_hypothetical_protein_2655613..2655763_POSITIVE 283 197 154 147 93 tfor:TF2501|3end_DNA_mismatch_repair_protein_2678183..2678333_POSITIVE