Multiple sequence alignment - how to align everything to 1 gene sequence?
Your question is not very clear, but I think what you are trying to do is align sequencing results to a reference gene sequence.

Your total gene sequence spans ~2500 bp. It sounds like you have a forward sequence at the start of gene, reading only about 1000 bp and the reverse strand reading in 1000 bp from the end (if this is Sanger sequencing, you likely only have 800-900 bp of accurate base reads by the way). Therefore, you have a gap of about 500 bp in the middle of your gene of interest.

There are (at least) two ways to do the alignment, and I would suggest the manual method if you are trying to verify gene sequencing.

Manual Method:


In a word processing document, paste in your gene-of-interest (or the recombinant gene you are trying to make), as well as the base reads from the forward strand, and the reverse complementof your reverse strand. Make sure you remove any whitespace like line breaks and spaces as this will disrupt the rest of the process.
Manually select a small portion of your forward read (20-30 bp for example) and search for the same "phrase" in your gene-of-interest. If you find it, highlight it in both the sequence it came from and the gene-of-interest so that you know you have already matched them.
Carry on with adjacent bases for the forward strand. Repeat for the reverse complement of the reverse strand.


Semi-Automated Method:


Go to NCBI Blast, and under the heading Basic Blast, click "nucleotide blast".
Check "Align 2 or more sequences."
Enter your Query Sequence as your 1000 bp sequences, entered in FASTA format. FASTA format will allow you to enter multiple sequences, but if you just enter one at a time, that will work perfectly well. Results will only display one at a time anyway.


For example:

&gt; sequence name here
ATCGATCGATCGATCGATCGATCG....



Enter your gene of interest as your Subject Sequence. Format does not matter here, but for consistency, I use FASTA format.
Keep "Highly similar sequences (megablast)" selected. You shouldn't need to play with these parameters, they just change how the alignment method penalizes alignments for gaps and mismatches.
Hit BLAST.
Interpret your results. I've included an example of BLAST results below.




At the top of this window is a schematic, showing exactly how much of the the query sequence aligns with the subject sequence. The longer the line, the more bases align. Similarly, the closer the colour of the line is to right of the scale (e.g., red), then the more continuous the segment is indicating a longer, continuous alignment.

Below the graphic is a table of results. Briefly, the table highlights all possible alignments that the BLAST algorithm has found, including how much coverage there was, confidence of the alignment and length of alignment coverage.

Below the results table, are the detailed results which were summarized in the table. This detailed report shows you exactly which bases align or mismatch, or any gaps. The top line is the subject sequence; the bottom is the query sequence. The other thing to keep in mind here is the Strand line. In this case, it says "Plus/Plus, meaning that the aligned sequences were the forward sense, or plus strand, of each of subject and query sequence, respectively. If you entered a reverse complement sequence instead (such as the reverse sequencing results) then this would change to "Plus/Minus".

From here, you will still need to manually line these results up to your gene of interest to determine exactly which portion of the gene is missing sequence coverage, as well as any mutations that may have cropped up in the cloning process.