User:Morgan L. Paull/Notebook/C.Dog V1.0 - T7 Promoter/2011/07/12

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Checking the sequences for re-picked colonies from the last round of ligations

  • All G12's have GFP and T7, but do not have either Makoff RBS part 1 or part 12.

--> G12 first ligation is no good.

  • All R10's have RFP. Some SNPs in sequencing, but all explainable. Nonetheless, R10.4 appears to be the safest bet from the sequencing results (only SNPs are completely explainable by base repeats). R10.3 is a little funky on the alignment to makoff 10, but probably ok. R10.4 and R10.5 definitely ok. T7 and makoff BD part 1 both present in all three.

--> R10.4 and R10.5 both good to go.

  • Some non-explainable SNPs in the RFP sequence of R20.3, moderately explainable SNPs in RFP of R20.4, and only explainable SNPs in RFP of R20.5 until the very end of the strand (explainable by boundary errors of sequencing?). All have T7, all have BD Makoff part 1, all have Makoff 20.

--> R20.3 and R20.4 probably ok, R20.5 almost certainly ok. CHECK ABOUT BOUNDARY EFFECTS IN SEQUENCING.

  • All of R22-R24 appear are ligated into GFP, with a good GFP match and no RFP match. However they do have a T7 match, a makoff BD part 1 match, and a makoff 22 match.

--> R22-R24 first ligation no good (although it is a fine G22-G24!)