Origin IGS: taacactaagacacatagcgaattgtttcccggaggttatcgctcgcatgtagcgcctctcccgggaaacttcgtttttgcagtgtatagaaaaatatcgttgtgccgttcacctgtactttaagtcgtattttttgaaaagatggcacataaacaggaaaatttatacatttgtcccgtagtaacgtagtaaagaagtaatgtggcaaggtcgtataaactttgtgcttttcactcttctttacgccttaatcattttactgctttactgcatggaatattgaatacttacttataagaaaataagaaatacgaaga .........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 tcttcgtatttcttattttcttataagtaagtattcaatattccatgcagtaaagcagtaaaatgattaaggcgtaaagaagagtgaaaagcacaaagtttatacgaccttgccacattacttctttactacgttactacgggacaaatgtataaattttcctgtttatgtgccatcttttcaaaaaatacgacttaaagtacaggtgaacggcacaacgatatttttctatacactgcaaaaacgaagtttcccgggagaggcgctacatgcgagcgataacctccgggaaacaattcgctatgtgtcttagtgtta Mask Tandem Repeat Region ================================================ taacactaagacacatagcgaattgtttcccggaggttatcgctcgcatgtagcgcctctcccgggaaacttcgtttttgcagtgtatagaaaaatatcgttgtgccgttcacctgtactttaagtcgtattttttgaaaagatggcacataaacaggaaaatttatacatttgtcccgtagtaacgtagtaaagaagtaatgtggcaaggtcgtataaactttgtgcttttcactcttctttacgccttaatcattttactgctttactgcatggaatattgaatacttacttataagaaaataagaaatacgaaga Find is-nt database================================================ Query_seq: TF1327:TF1328|TF1327:TF1328:L-fucose permease:possible cytidylyltransferase:->->:1407256..1407573 318 taacactaagacacatagcgaattgtttcccggaggttatcgctcgcatgtagcgcctctcccgggaaacttcgtttttgcagtgtatagaaaaatatcgttgtgccgttcacctgtactttaagtcgtattttttgaaaagatggcacataaacaggaaaatttatacatttgtcccgtagtaacgtagtaaagaagtaatgtggcaaggtcgtataaactttgtgcttttcactcttctttacgccttaatcattttactgctttactgcatggaatattgaatacttacttataagaaaataagaaatacgaaga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF1327:TF1328|TF1327:TF1328:L-fucose permease:possible cytidylyltransferase:->->:1407256..1407573 318 taacactaagacacatagcgaattgtttcccggaggttatcgctcgcatgtagcgcctctcccgggaaacttcgtttttgcagtgtatagaaaaatatcgttgtgccgttcacctgtactttaagtcgtattttttgaaaagatggcacataaacaggaaaatttatacatttgtcccgtagtaacgtagtaaagaagtaatgtggcaaggtcgtataaactttgtgcttttcactcttctttacgccttaatcattttactgctttactgcatggaatattgaatacttacttataagaaaataagaaatacgaaga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF1327:TF1328|TF1327:TF1328:L-fucose permease:possible cytidylyltransferase:->->:1407256..1407573 318 taacactaagacacatagcgaattgtttcccggaggttatcgctcgcatgtagcgcctctcccgggaaacttcgtttttgcagtgtatagaaaaatatcgttgtgccgttcacctgtactttaagtcgtattttttgaaaagatggcacataaacaggaaaatttatacatttgtcccgtagtaacgtagtaaagaagtaatgtggcaaggtcgtataaactttgtgcttttcactcttctttacgccttaatcattttactgctttactgcatggaatattgaatacttacttataagaaaataagaaatacgaaga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taacactaagacacatagcgaattgtttcccggaggttatcgctcgcatgtagcgcctctcccgggaaacttcgtttttgcagtgtatagaaaaatatcgttgtgccgttcacctgtactttaagtcgtattttttgaaaagatggcacataaacaggaaaatttatacatttgtcccgtagtaacgtagtaaagaagtaatgtggcaaggtcgtataaactttgtgcttttcactcttctttacgccttaatcattttactgctttactgcatggaatattgaatacttacttataagaaaataagaaatacgaaga Predict ORF larger than 30AA ================================================ Protein_Len: 33 Strand: + Start: 23 End: 121 ...................... M F P G G Y R S H V A P L P G N F V F A V Y R K I S L C R S P V L ..................................................................................................................................................................................................... Protein_Len: 34 Strand: + Start: 78 End: 179 ............................................................................. M Q C I E K Y R C A V H L Y F K S Y F L K R W H I N R K I Y T F V P ........................................................................................................................................... Protein_Len: 31 Strand: + Start: 203 End: 295 .......................................................................................................................................................................................................... M A R S Y K L C A F H S S L R L N H F T A L L H G I L N T Y L ....................... Protein_Len: 60 Strand: - Start: 9 End: 209 ........ R L N D S A H L A E G P F S R K Q L T Y F F I T T G N V Q V K L R I K Q F S P V Y V P F N I C K D R L L T T F F Y H P M ............................................................................................................. taacactaagacacatagcgaattgtttcccggaggttatcgctcgcatgtagcgcctctcccgggaaacttcgtttttgcagtgtatagaaaaatatcgttgtgccgttcacctgtactttaagtcgtattttttgaaaagatggcacataaacaggaaaatttatacatttgtcccgtagtaacgtagtaaagaagtaatgtggcaaggtcgtataaactttgtgcttttcactcttctttacgccttaatcattttactgctttactgcatggaatattgaatacttacttataagaaaataagaaatacgaaga 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================================================ taacactaagacacatagcgaattgtttcccggaggttatcgctcgcatgtagcgcctctcccgggaaacttcgtttttgcagtgtatagaaaaatatcgttgtgccgttcacctgtactttaagtcgtattttttgaaaagatggcacataaacaggaaaatttatacatttgtcccgtagtaacgtagtaaagaagtaatgtggcaaggtcgtataaactttgtgcttttcactcttctttacgccttaatcattttactgctttactgcatggaatattgaatacttacttataagaaaataagaaatacgaaga Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF1327:TF1328|TF1327:TF1328:L-fucose permease:possible cytidylyltransferase:->->:1407256..1407573 318 taacactaagacacatagcgaattgtttcccggaggttatcgctcgcatgtagcgcctctcccgggaaacttcgtttttgcagtgtatagaaaaatatcgttgtgccgttcacctgtactttaagtcgtattttttgaaaagatggcacataaacaggaaaatttatacatttgtcccgtagtaacgtagtaaagaagtaatgtggcaaggtcgtataaactttgtgcttttcactcttctttacgccttaatcattttactgctttactgcatggaatattgaatacttacttataagaaaataagaaatacgaaga Intra-Species Hit: Count: 1 Min: 1 Max: 318 Len: 318 Subject: tfor_TF1327_TF1328|L-fucose permease:possible cytidylyltransferase|POSITIVE:POSITIVE|[1407256, 1407573]|318 HSP 1 e-value: 1.0E-180 bit: 630.0 Len: 318 Query Start:1 Query End:318 Subject Strand: POSITIVE Subject Start: 1 Subject End: 318 taacactaagacacatagcgaattgtttcccggaggttatcgctcgcatgtagcgcctctcccgggaaacttcgtttttgcagtgtatagaaaaatatcgttgtgccgttcacctgtactttaagtcgtattttttgaaaagatggcacataaacaggaaaatttatacatttgtcccgtagtaacgtagtaaagaagtaatgtggcaaggtcgtataaactttgtgcttttcactcttctttacgccttaatcattttactgctttactgcatggaatattgaatacttacttataagaaaataagaaatacgaaga taacactaagacacatagcgaattgtttcccggaggttatcgctcgcatgtagcgcctctcccgggaaacttcgtttttgcagtgtatagaaaaatatcgttgtgccgttcacctgtactttaagtcgtattttttgaaaagatggcacataaacaggaaaatttatacatttgtcccgtagtaacgtagtaaagaagtaatgtggcaaggtcgtataaactttgtgcttttcactcttctttacgccttaatcattttactgctttactgcatggaatattgaatacttacttataagaaaataagaaatacgaaga Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAACACUAAGACACAUAGCGAAUUGUUUCCCGGAGGUUAUCGCUCGCAUGUAGCGCCUCUCCCGGGAAACUUCGUUUUUGCAGUGUAUAGAAAAAUAUCGUUGUGCCGUUCACCUGUACUUUAAGUCGUAUUUUUUGAAAAGAUGGCACAUAAACAGGAAAAUUUAUACAUUUGUCCCGUAGUAACGUAGUAAAGAAGUAAUGUGGCAAGGUCGUAUAAACUUUGUGCUUUUCACUCUUCUUUACGCCUUAAUCAUUUUACUGCUUUACUGCAUGGAAUAUUGAAUACUUACUUAUAAGAAAAUAAGAAAUACGAAGA .........((((...((((((..(((((((((..(....((((.......))))...)..))))))))))))))).....((((((((((..........(((((((((((...((((........))))....)))....))))))))............)))))))))))))).((((.....(((((((((.(((((.((((.((((.((((........(((.....))).......))))))))..)))).))))).)))))))))...................(((((......)))))...)))).... (-81.71) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCUUCGUAUUUCUUAUUUUCUUAUAAGUAAGUAUUCAAUAUUCCAUGCAGUAAAGCAGUAAAAUGAUUAAGGCGUAAAGAAGAGUGAAAAGCACAAAGUUUAUACGACCUUGCCACAUUACUUCUUUACUACGUUACUACGGGACAAAUGUAUAAAUUUUCCUGUUUAUGUGCCAUCUUUUCAAAAAAUACGACUUAAAGUACAGGUGAACGGCACAACGAUAUUUUUCUAUACACUGCAAAAACGAAGUUUCCCGGGAGAGGCGCUACAUGCGAGCGAUAACCUCCGGGAAACAAUUCGCUAUGUGUCUUAGUGUUA .....(((((((((((......))))).))))))..((((((..(((.(((((((.(((((..((..(((((((((.(((...(((.....)))....))).)))).))))).))..))))).))))))).)))....((((((.((((......))))))))))...((((((.....((((.....(((........)))....)))).))))))..)))))).......((((((((....(((((((((((((..(...((((.......))))....)..)))))))))..)))).....)))...))))).. (-77.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 420 236 192 214 170 tfor:TF2545|5end_hypothetical_protein_2729053..2729283_POSITIVE 416 74 31 223 174 tfor:TF0696|5end_3-oxoacyl-(acyl-carrier-protein)_reductase_739936..740166_POSITIVE 413 85 41 84 34 tfor:TF2439|5end_conserved_hypothetical_protein_2616380..2616610_POSITIVE 409 70 23 211 158 tfor:TF3003|5end_hypothetical_protein_3220382..3220612_POSITIVE 389 88 41 180 127 tfor:TF2804|5end_conserved_hypothetical_protein_2993494..2993724_POSITIVE 389 86 44 194 155 tfor:TF2584|5end_hypothetical_protein_2751180..2751410_POSITIVE 381 80 32 223 163 tfor:TF1835|5end_possible_dihydroxy-acid_dehydratase_1984201..1984431_POSITIVE 376 69 30 91 35 tfor:TF2224|5end_CTn_excision_protein_2394592..2394822_POSITIVE 376 74 31 54 9 tfor:TF1776|5end_urocanate_hydratase_1914660..1914890_POSITIVE 371 68 29 63 9 tfor:TF0148|5end_conserved_hypothetical_protein_159448..159678_POSITIVE 370 230 187 193 151 tfor:TF1154|5end_RNA_pseudouridylate_synthetase_1235780..1236010_POSITIVE 368 66 23 188 135 tfor:TF2079|5end_permease_2245585..2245815_POSITIVE 367 80 31 130 57 tfor:TF1730|5end_diaminopimelate_decarboxylase_1854670..1854900_POSITIVE 367 80 31 79 6 tfor:TF1732|5end_conserved_hypothetical_protein_1854619..1854849_POSITIVE 366 65 24 182 122 tfor:TF0098|5end_permease_108103..108333_POSITIVE 365 67 31 193 151 tfor:TF0253|5end_conserved_hypothetical_protein_283707..283937_POSITIVE 364 64 29 47 4 tfor:TF2477|5end_phosphatase_2654229..2654459_POSITIVE 362 69 29 86 40 tfor:TF2246|5end_hypothetical_protein_2421288..2421518_POSITIVE 360 67 26 60 20 tfor:TF2518|5end_ATP-dependent_DNA_helicase_2695541..2695771_POSITIVE 359 70 23 45 1 tfor:TF2767|5end_2-oxoglutarate_synthase,_alpha_subunit_2952215..2952445_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 479 70 25 66 21 tfor:TF1327|3end_L-fucose_permease_1407195..1407345_POSITIVE 389 88 41 73 20 tfor:TF2803|3end_dehydrogenase,_possible_NADH-dependent_dehydrogenase_2993467..2993617_POSITIVE 369 75 31 127 80 tfor:TF0970|3end_2-keto-3-deoxygluconate_kinase_1021540..1021690_POSITIVE 367 80 31 98 25 tfor:TF1729|3end_aspartokinase_1854718..1854868_POSITIVE 353 67 25 147 104 tfor:TF2255|3end_transfer_region-related_protein,_TraH_2427961..2428111_POSITIVE 352 59 16 65 16 tfor:TF1683|3end_conserved_hypothetical_protein_1796511..1796661_POSITIVE 350 80 31 148 76 tfor:TF0308|3end_hypothetical_protein_334082..334232_POSITIVE 348 66 31 47 8 tfor:TF2263|3end_transfer_region-related_protein,_TraN_2432964..2433114_POSITIVE 347 66 30 91 59 tfor:TF2556|3end_conserved_hypothetical_protein_2737095..2737245_POSITIVE 343 76 31 49 14 tfor:TF2012|3end_conserved_hypothetical_protein_2168720..2168870_POSITIVE 342 77 31 74 18 tfor:TF1794|3end_possible_glucose-1-phosphatase_1935816..1935966_POSITIVE 341 64 25 48 1 tfor:TF3153|3end_conserved_hypothetical_protein_3389324..3389474_POSITIVE 341 81 41 149 109 tfor:TF3105|3end_hypothetical_protein_3338342..3338492_POSITIVE 340 85 43 51 3 tfor:TF2874|3end_conserved_hypothetical_protein_3065224..3065374_POSITIVE 340 70 25 148 87 tfor:TF1842|3end_hypothetical_protein_1992800..1992950_POSITIVE 336 66 23 42 5 tfor:TF1173|3end_ABC_transporter,_permease_component_1256651..1256801_POSITIVE 333 66 23 149 97 tfor:TF1636|3end_hypothetical_protein_1747414..1747564_POSITIVE 327 68 31 102 61 tfor:TF1311|3end_hypothetical_protein_1388558..1388708_POSITIVE 327 68 31 102 61 tfor:TF1310|3end_hypothetical_protein_1388335..1388485_POSITIVE 326 67 21 131 90 tfor:TF2302|3end_conserved_hypothetical_protein;_possible_outer_membrane_protein_2458063..2458213_POSITIVE