blastx results: small letters with gray color?

Question

[madiha_shabbir46]

Hi, can anyone help me out to understand results of blastx when we get something like this

Query 2469 ASIFNEMNIDPFVVSDKICPKWGKLFV----DeksiseeeceaegkkkckiLNTSVHPKL 2636 +SI NEMN+D + D+ K+F +E S+ E++ + + KK C LN V K Sbjct 1472 SSICNEMNVDLSLEEDE------KMFTNGVDEENSMLEKKLDHKSKKNCSKLNRKVFTKS 1525

here "eksiseeeceaegkkkcki " why these characters are in small letters and gray color? is it specifying anything unusual? Thanking in anticipation Madiha

[madiha_shabbir46]

oh right, got it...

Thank you MIttu

Answer 1

[mittu1602]

You are seeing the result of automatic filtering of your query for low-complexity sequence. This filter is on for the BLASTN pages to prevent matches that are probably artifacts. The filter substitutes any low-complexity sequence with lowercase grey characters. This allows you to see the sequence that was filtered instead of the "X"s and "N"s of the previous BLAST output. https://blast.ncbi.nlm.nih.gov/blast/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=FAQ#lowercase