Please excuse me for my fast/paranoid decisions. i get confused easily when i face little problems. I confuse other people also... am sorry for that. I have to build some patience in me. hehehehe :) well, the criteria is to match the alphabets. The alphabets seen in the 3rd column of file2.query should be checked if its available in the 5th(last) column of file1.db. In case, the only common columns are the 2nd and 3rd of file1 and 1st and 2nd column of file2. With this as basis, i compare the alphabets in both the entries(files). For every line in file2, If all (2-seperated by'>') the alphabets (seperated by '/'. can be many, just not 2) are found in file1 at the corresponding line, its reported as a HIT. In the output i needed

1190    31789    A > G    1    2    5    zm1829427
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only in this lines, the "A>G" of file2 matches with "A/G" of file1. The rest is not considered as hit because, the alphabets of file2 in not present in file1. my final decision: the output is:

1190    31277    A > T    1    0    0    -
1190    31607    C > A    0    3    1    -
1190    31629    C > T    0    2    0    -
1190    31789    A > G    1    2    5    zm1829427
1190    31882    A > C    0    4    0    -
1190    31883    T > A    0    4    0    -
1190    31883    T > C    2    2    5    -
1190    32199    C > T    0    1    1    -
1190    32487    T > C    0    1    1    -
1190    32496    A > G    0    3    0    -
Total number of HITS: 1
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