Matt Gethers/CRI, Thailand/Specifications/pIs001/33.SEQ
33.SEQ (pIs001.P1, T7_rev)
Base Number (Sequence File Annotation) = Contig Sequence File Annotation Number + 198 where 198 is the number of trimmed 5' bases.
Base Number (Vector NTI File Annotation) = 5967 - Contig Sequence File Annotation Number
|Base Number (Sequence File Annotation)||Base Number (Vector NTI Annotation)||Theoretical Base||Read Base||Notes|
|213||5953||C||T||I'm not sure a T should be here, but there's no sign of a C - problem|
|236||5930||C||N||Maybe a C - good|
|284||5882||C||N||Maybe a C - good|
|294-295||5872||C||Space||It would be a stretch to say there's a C there - problem|
|320||5845||C||N||Maybe a C - good|
Region of Interest (Vector NTI Annotation): 5318 - 6121 (ATG to TGA)
Lots of truncated 5' and 3' bases - may want to redo alignment with less trimming/manual comparison. Considering the 198 trimmed 3' bases would allow me to complete the region between the forward and reverse primers (~50 bases between the two) while considering the 195 trimmed 5' bases would allow me to see the end of the ORF (~140 bases to end of ORF).