Here is the aligment of my concerning sequence of zebrafish:
tgtgtgtgtgtgtgtgtgtgtgtgtgtgcgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtttgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgcctg . I want to find out how many zebrafish genes have the exact same sequence in their promoter region.i am too silly to do it well by myself.
dear henry,
what you have in your hand is a repeatative sequence. I would suggest you to turn of the low complexity filters, increase the threshold and search in the specific genome if you want exact sequence.
but hardly you will find the exact sequence. But when you get the hits in the blast, kindly verify the position and chromosome number of the hit.
Sometimes in NCBI the same sequence do exist with different identifiers/Accession numbers
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