Put all the .fasta files in one folder.

grep -l "aggcgaa" fasta_folder/* will print all the file names that have that string. '*' is to search all the files.

If you pipe it to wc -l then you can get the number of files that have that string.

grep -l "aggcgaa" fasta_folder | wc -l

I will leave on you to how to put all the sequences in the tab file into a loop and execute the above command. it should be simple to do.

You can try this. This is assuming that your sequences are in sequences.txt

#!/bin/sh  
awk -F "\t" ' { print $2 } ' sequences.txt > input_sequences.txt
ls data*.fasta > filelist

for sequence in `cat input_sequences.txt`
do
  for file in `cat filelist`
  do
    count=`grep -c "$sequence" $file`
    if [ $count -gt 0 ]; then
      echo "$sequence is present in $file"
    fi
  done
done

It is straight-forward. The first loop is for going through your sequences and the second-inner loop is for going through the files and grep-ing each sequence.

Extending @ashutoshmits' solution, and taking into account the fact that your OP mentions "The list of the 90 sequences is in text format seperated by Tab" (I'm going to assume that this file is named sequences.txt), you could do something like this:

cut -f2 sequences.txt | xargs -I{} grep -l "{}" data*.fasta

The above method cuts the sequences out from the 2nd column and then uses the unix xargs command to iterate through every element from the first pipe and pass it to the grep command (which uses the -l flag to only print the names of the FILEs that contain matches).

In order to speed this up, you can use the GNU Parallel tool, which acts in a fashion similar to xargs, but allows for naive parallelization (making use of as many available processors on your system), running several grep commands at the same time. Here is a example:

cut -f2 sequences.txt | parallel -j5 -k 'grep -l "{}" data*.fasta'

Here the -j5 parameter is instructnig parallel to run 5 grep jobs at a time (adjust according to your liking or let it just use all available cores on your machine) and the -k parameter is instructing it to retain the order of input passed to the command (so that the output is also in the same order; without this parameter, the output order will be jumbled depending on whichever process finishes earlier)