Below are insert sequences for all entry clones, and 5' and 3' end sequences for all destination clones. In all cases, we have included sequence up through the appropriate "att shared" sequence--the core sequence that is shared between attL,R,B, and P sites.
These core sequences will overlap between adjacent components of an expression clone, and this overlap can be used to assemble a predicted contig for the expression clone. For instance, using the program Sequencher, just take the insert sequences for your 5', middle, and 3' clones, together with the 5' and 3' ends of your destination clone, and hit "Assemble Automatically" (be sure to set "minimum overlap" to 15 or less in Assembly Parameters).
As an example, here is what the predicted sequence for pDestTol2CG2;bactin:mCherry-IRES-EGFPpA would look like:
<395.pDestTol2CG2 5' thru attR4 shared>
CCACCTAAATTGTAAGCGTTAAT...CAAGCTATCAACTTTGTATAGAAAAGTTG
CAACTTTGTATAGAAAAGTTGAAAATTCCAGTTTGAA...CAGCCTCAAGTTTGTACAAAAAAG
<299.p5E_bactin2_insert> TTTGTACAAAAAAGCAGGCTCCACCATGGT...
<386.pME-mCherry_insert>
<386.pME-mCherry_insert>
...TAAGACCCAGCTTTCTTGTACAAAGT
CTTTCTTGTACAAAGTGGCCGCCCCT...AGGTTTTTTCCAACTTTATTATACA
<389.p3E-IRES-EGFPpA_insert> CAACTTTATTATACATAGTTGATAATTC...CGCACATTTCCCCGAAAAGTG
<395.pDestTol2CG2 3' thru attR3 shared>
