I downloaded an alignment of 35 mammals. I selected a random fragment. In the case of mouse it corresponded to this section:
When I look for that sequence (just the first line of it) using Ensembl BLAST it finds it (despite not in that position) but when I download the data for that region (whether I use ensembl of ncbi) the sequence does not correspond. I then downloaded the full chromosome 2 for the mouse reference genome, then made a search of that sequence and it doesn't appear anywhere. Not even close. What am I missing?
I need that because I want to extract an alignment for that section from other species. Indeed I tried to find a local alignment for the full sequence but the result was terrible. Then I tried with the mouse and same happened. Then I realized that indeed that sequence used in the 35 mammals alignment apparently does not exist in the mouse gemome, despite blast also finds it ... I am lost. Any help would be appreciated.