User:PJ Steiner/Notebook/synthesis/2009/06/03

synthesis

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Synthesizing a RFP for M. florum. Here's the sequence: >MF-RED2 GTTTCTTCGAATTCGCGGCCGCTTCTAGAGTCACACAGGAAAGACTAGATGGCTAGTAGTGAGGATATAATCAAAGAGTT TATGCGTTTTAAAGTTCACATGGAAGGTTCAGTAAACGGACATGAATTTGAAATTGAGGGAGAAGGAGAGGGTCGTCCGT ACGAAGGTACACAAACAGCAAAGTTAAAAGTAACAAAAGGAGGACCTTTACCATTTGCATGGGATATTCTTTCTCCACAA TTTATGTATGGTAGTAAAGCGTATGTTAAACACCCGGCAGATATACCAGACTATTTAAAGTTGAGTTTTCCGGAAGGATT CAAATGGGAACGTGTTATGAATTTTGAAGATGGTGGTGTTGTTACAGTTACTCAAGATAGTAGCTTACAGGATGGTGAAT TTATTTACAAAGTAAAATTACGTGGTACTAACTTCCCGAGCGATGGTCCAGTAATGCAAAAGAAAACTATGGGATGGGAG GCTAGTTCTGAACGTATGTATCCTGAAGACGGTGCTTTAAAAGGAGAAATTAAACAACGTTTGAAACTTAAAGATGGTGG ACACTACGATGCAGAAGTTAAAACTACATATAAAGCTAAAAAGCCTGTTCAGCTTCCGGGTGCTTATAATGTGAATATAA AATTAGATATCACAAGTCATAACGAAGATTATACTATTGTTGAACAGTATGAAAGAGCAGAAGGAAGACATTCTACAGGA GCATAATAATACTAGTAGCGGCCGCTGCAGGTGGATAC This is a bit changed from the one TK sent originally (to remove inverted repeats at the end). Ran a version of bl with the following parameters: (length-min 40) (length-max 60) (overlap-min 10) (overlap-max 20) (repeat-min 8) (buf-size 1) (min-hairpin-stem 6) (min-hairpin-loop 3) (target-tm 45.0) (max-tm-dev 2.5) (primer-conc 0.00001) (salt-conc 0.01) The oligos it gave: > 0-43-f GTTTCTTCGAATTCGCGGCCGCTTCTAGAGTCACACAGGAAAG > 27-70-r TTATATCCTCACTACTAGCCATCTAGTCTTTCCTGTGTGACTC > 50-99-f GGCTAGTAGTGAGGATATAATCAAAGAGTTTATGCGTTTTAAAGTTCAC > 79-132-r TTCAAATTCATGTCCGTTTACTGAACCTTCCATGTGAACTTTAAAACGCATAA > 114-154-f AACGGACATGAATTTGAAATTGAGGGAGAAGGAGAGGGTC > 139-179-r GCTGTTTGTGTACCTTCGTACGGACGACCCTCTCCTTCTC > 163-208-f AAGGTACACAAACAGCAAAGTTAAAAGTAACAAAAGGAGGACCTT > 192-252-r ACCATACATAAATTGTGGAGAAAGAATATCCCATGCAAATGGTAAAGGTCCTCCTTTTGT > 232-272-f CTCCACAATTTATGTATGGTAGTAAAGCGTATGTTAAACA > 252-292-r AGTCTGGTATATCTGCCGGGTGTTTAACATACGCTTTACT > 275-335-f GGCAGATATACCAGACTATTTAAAGTTGAGTTTTCCGGAAGGATTCAAATGGGAACGTGT > 320-377-r TCTTGAGTAACTGTAACAACACCACCATCTTCAAAATTCATAACACGTTCCCATTTG > 357-402-f GTTGTTACAGTTACTCAAGATAGTAGCTTACAGGATGGTGAATTT > 383-439-r TCGGGAAGTTAGTACCACGTAATTTTACTTTGTAAATAAATTCACCATCCTGTAAG > 423-481-f GGTACTAACTTCCCGAGCGATGGTCCAGTAATGCAAAAGAAAACTATGGGATGGGAGG > 466-506-r TCAGGATACATACGTTCAGAACTAGCCTCCCATCCCATAG > 488-528-f TGAACGTATGTATCCTGAAGACGGTGCTTTAAAAGGAGAA > 510-562-r GTCCACCATCTTTAAGTTTCAAACGTTGTTTAATTTCTCCTTTTAAAGCACC > 543-589-f AAACTTAAAGATGGTGGACACTACGATGCAGAAGTTAAAACTACAT > 569-620-r CCCGGAAGCTGAACAGGCTTTTTAGCTTTATATGTAGTTTTAACTTCTGCA > 608-667-f TCAGCTTCCGGGTGCTTATAATGTGAATATAAAATTAGATATCACAAGTCATAACGAAG > 649-699-r TGCTCTTTCATACTGTTCAACAATAGTATAATCTTCGTTATGACTTGTGA > 681-725-f GAACAGTATGAAAGAGCAGAAGGAAGACATTCTACAGGAGCATA > 707-758-r GTATCCACCTGCAGCGGCCGCTACTAGTATTATTATGCTCCTGTAGAATGT Ordered those on 6/2/2009.