> Sequence data read successfully > Organism codon frequency file read successfully > Mode selected: (p)rotein optimization > Files & libraries read successfully > ------------------------------------------ > Organism used is ecoliK12 > All sequences are OK (nt/AA) > ==================================================================================== > Protein sequence optimization starting... > NOTE: For protein optimization, the sequences file can contain either nucleotide or single letter amino acid sequences. Each sequence should be on a separate line, blank newline entries in the file will result in a read error. The file should contain no other characters than the ones for a sequence. You can have the protein sequences in either amino acid or nucleotide sequence, and sequences in the file are not limited to only one format. The program will automatically translate DNA and/or Protein sequences into a preliminary optimized DNA sequence, which will subsequently be further optimized. If your file is not formatted as such, please press [Ctrl]-C to stop the program and reformat your file. > ========================================== > Sequence 0 is (DNA form): gcgcagcaggtgtatgcgaaaccgacctataaacagtatcgcaactatctgccggataaatggatgaaaggcaacgcgtggattaacgtgatgagcaaaggcgcgtggcgccagtttccgtgcccgatgtgccgcgtgccgaaaggcttttttccgaactatgtgatgtggaacccgggc Translation (initial): aqqvyakptykqyrnylpdkwmkgnawinvmskgawrqfpcpmcrvpkgffpnyvmwnpg Restriction Sites found at following indices to be removed: ['mlui', 'acgcgt', [73]] ['smai', 'cccggg', [173]] ['tspmi', 'cccggg', [173]] ['xmai', 'cccggg', [173]] Codon optimized and and (-) restriction site sequence: gcgcagcaggtgtatgcgaaaccgacctataaacagtatcgcaactatctgccggataaatggatgaaaggcaatgcgtggattaacgtgatgagcaaaggcgcgtggcgccagtttccgtgcccgatgtgccgcgtgccgaaaggcttttttccgaactatgtgatgtggaatccgggc Translation (verification): -good optimization aqqvyakptykqyrnylpdkwmkgnawinvmskgawrqfpcpmcrvpkgffpnyvmwnpg Optimization complete > ========================================== > Sequence 1 is (DNA form): ggcctgagcgcgcgcagctttgatggcctggtgccgacccgccgccatagctttcgccgcattattcgcggccagtaacagccgaccagccgcgtgctgccgaaccgcagcacccgctaa Translation (initial): glsarsfdglvptrrhsfrriirgq*qptsrvlpnrstr* No restriction sites found, only codon optimization needed Codon optimized and and (-) restriction site sequence: ggcctgagcgcgcgcagctttgatggcctggtgccgacccgccgccatagctttcgccgcattattcgcggccagtaacagccgaccagccgcgtgctgccgaaccgcagcacccgctaa Translation (verification): -good optimization glsarsfdglvptrrhsfrriirgq*qptsrvlpnrstr* Optimization complete > ========================================== > Sequence 2 is (DNA form): gaaatgaaaaccgtgattctgaaatgccgctgcgaactgcgctgcaccgcgaaagatattaacaaatgccgcccggatccggaaatgatgcatcgcattccgtgcgtggtgccggaatattgcgcgatg Translation (initial): emktvilkcrcelrctakdinkcrpdpemmhripcvvpeycam Restriction Sites found at following indices to be removed: ['bamhi', 'ggatcc', [74]] ['nsii', 'atgcat', [87]] Codon optimized and and (-) restriction site sequence: gaaatgaaaaccgtgattctgaaatgccgctgcgaactgcgctgcaccgcgaaagatattaacaaatgccgcccggacccggaaatgatgcaccgcattccgtgcgtggtgccggaatattgcgcgatg Translation (verification): -good optimization emktvilkcrcelrctakdinkcrpdpemmhripcvvpeycam Optimization complete > ========================================== > Sequence 3 is (DNA form): cgcgaagtgtgcattttttggaaccatgaagtgatgatggcgtgcaacagcccgcgcgtgtataaattttggagcgcgcagacctgctgcgatattaccatttttgatattattggccattgcgaacgcaccgaaatttattttattctgatggattttcgcgaaccggtgatgaccgcg Translation (initial): revcifwnhevmmacnsprvykfwsaqtccditifdiighcerteiyfilmdfrepvmta Restriction Sites found at following indices to be removed: ['agei', 'accggt', [164]] Codon optimized and and (-) restriction site sequence: cgcgaagtgtgcattttttggaaccatgaagtgatgatggcgtgcaacagcccgcgcgtgtataaattttggagcgcgcagacctgctgcgatattaccatttttgatattattggccattgcgaacgcaccgaaatttattttattctgatggattttcgcgagccggtgatgaccgcg Translation (verification): -good optimization revcifwnhevmmacnsprvykfwsaqtccditifdiighcerteiyfilmdfrepvmta Optimization complete > ========================================== > Sequence 4 is (DNA form): agcgaaaccccgaccccgggcgtgaactggttttgcctggatgattgggtgaccaaatataaactgctgcagagcaccctgattcaggtgtattgggcgtgctttgcgcagtggaaaaacaaaattcgctggatgaaactgcagaaacagaaatttatgcgcgaagcgtgggcgctggtg Translation (initial): setptpgvnwfclddwvtkykllqstliqvywacfaqwknkirwmklqkqkfmreawalv Restriction Sites found at following indices to be removed: ['psti', 'ctgcag', [66, 138]] ['smai', 'cccggg', [14]] ['tspmi', 'cccggg', [14]] ['xmai', 'cccggg', [14]] Codon optimized and and (-) restriction site sequence: agcgaaaccccgacgccgggcgtgaactggttttgcctggatgattgggtgaccaaatataaactgttacagagcaccctgattcaggtgtattgggcgtgctttgcgcagtggaaaaacaaaattcgctggatgaaattacagaaacagaaatttatgcgcgaagcgtgggcgctggtg Translation (verification): -good optimization setptpgvnwfclddwvtkykllqstliqvywacfaqwknkirwmklqkqkfmreawalv Optimization complete > ========================================== > Sequence 5 is (DNA form): agcagcccgcgcattctgtttgcggatccgcagtggccggtggatacccgcccgccgcgctgcagcgtgaccggcacc Translation (initial): ssprilfadpqwpvdtrpprcsvtgt Restriction Sites found at following indices to be removed: ['bamhi', 'ggatcc', [23]] ['psti', 'ctgcag', [59]] Codon optimized and and (-) restriction site sequence: agcagcccgcgcattctgtttgccgatccgcagtggccggtggatacccgcccgccgcgttgcagcgtgaccggcacc Translation (verification): -good optimization ssprilfadpqwpvdtrpprcsvtgt Optimization complete > ========================================== > Sequence 6 is (DNA form): gtgacccagattccgggctgcctggatagcggcaaacatattcagtgcgaagtgtatgattattggctggataaaccggcgtttgtgtataaccgctggcatatggtgcagcgcgtgctgtgccagcagccggaatatgtggcgaaaagccagacctgcgtgcattttttttgctgccgc Translation (initial): vtqipgcldsgkhiqcevydywldkpafvynrwhmvqrvlcqqpeyvaksqtcvhffccr Restriction Sites found at following indices to be removed: ['ndei', 'catatg', [99]] Codon optimized and and (-) restriction site sequence: gtgacccagattccgggctgcctggatagcggcaaacatattcagtgcgaagtgtatgattattggctggataaaccggcgtttgtgtataaccgctggcacatggtgcagcgcgtgctgtgccagcagccggaatatgtggcgaaaagccagacctgcgtgcattttttttgctgccgc Translation (verification): -good optimization vtqipgcldsgkhiqcevydywldkpafvynrwhmvqrvlcqqpeyvaksqtcvhffccr Optimization complete > ========================================== > Sequence 7 is (DNA form): ccgcgcacccgccgccatgcgatggaacgcccgtaactgcgccaggcgattaaaggcaacgtgtgcattacccagaaaaaccgcaaaattggcgaataaatttttagcctgtgcattgaagaatggccgcgcggcggcatgcgccatgcgagc Translation (initial): prtrrhamerp*lrqaikgnvcitqknrkige*ifslcieewprggmrhas Restriction Sites found at following indices to be removed: ['sphi', 'gcatgc', [136]] Codon optimized and and (-) restriction site sequence: ccgcgcacccgccgccatgcgatggaacgcccgtaactgcgccaggcgattaaaggcaacgtgtgcattacccagaaaaaccgcaaaattggcgaataaatttttagcctgtgcattgaagaatggccgcgcggcggtatgcgccatgcgagc Translation (verification): -good optimization prtrrhamerp*lrqaikgnvcitqknrkige*ifslcieewprggmrhas Optimization complete > ========================================== > Sequence 8 is (DNA form): attatgcagaaaccgtgcgatattgataacgaactgaaaaaaattctgagcaaatttattgaaaaccatgtgtttgatattccgcagcataacaaagtgagcaacgatcaggtgggccgctgctggatgttttgcgatcgcccggaacgccagacctttaacatgggcaacatgatgatg Translation (initial): imqkpcdidnelkkilskfienhvfdipqhnkvsndqvgrcwmfcdrperqtfnmgnmmm Restriction Sites found at following indices to be removed: ['pvui', 'cgatcg', [134]] Codon optimized and and (-) restriction site sequence: attatgcagaaaccgtgcgatattgataacgaactgaaaaaaattctgagcaaatttattgaaaaccatgtgtttgatattccgcagcataacaaagtgagcaacgatcaggtgggccgctgctggatgttttgtgatcgcccggaacgccagacctttaacatgggcaacatgatgatg Translation (verification): -good optimization imqkpcdidnelkkilskfienhvfdipqhnkvsndqvgrcwmfcdrperqtfnmgnmmm Optimization complete > ========================================== > Sequence 9 is (DNA form): gtgtttgaagcgcagaaaccgccggtggcgtttctgaccgattgctatcagtggatgaccctgccgagctttgattatcaggtgacctatatgatgaacaacgatgattatgcgattaaa Translation (initial): vfeaqkppvafltdcyqwmtlpsfdyqvtymmnnddyaik No restriction sites found, only codon optimization needed Codon optimized and and (-) restriction site sequence: gtgtttgaagcgcagaaaccgccggtggcgtttctgaccgattgctatcagtggatgaccctgccgagctttgattatcaggtgacctatatgatgaacaacgatgattatgcgattaaa Translation (verification): -good optimization vfeaqkppvafltdcyqwmtlpsfdyqvtymmnnddyaik Optimization complete > ========================================== > Sequence 10 is (DNA form): tatagcgaaagc Translation (initial): yses No restriction sites found, only codon optimization needed Codon optimized and and (-) restriction site sequence: tatagcgaaagc Translation (verification): -good optimization yses Optimization complete > ========================================== > QuitFlush completed, Process Completed.