Hi Mike, Thanks for the comment. In the inner loop, after the condition is met, I want to print the result only once. then the loop should continue to check other records to see if it can find the match. Here I have included a partial output of this code. I just need to print the first line. where col 1 and 4 pair and 2 and 3 pair. this is were the condition is met. Then it should find the next match before printing ~4000 junk comparisons. 
CLS_S3_Contig10021      349     349     CLS_S3_Contig10021
CLS_S3_Contig10021      898     349     CLS_S3_Contig10021
CLS_S3_Contig10021      524     349     CLS_S3_Contig10021
CLS_S3_Contig10021      365     349     CLS_S3_Contig10021
CLS_S3_Contig10021      373     349     CLS_S3_Contig10021
CLS_S3_Contig10029      857     349     CLS_S3_Contig10021
CLS_S3_Contig10029      482     349     CLS_S3_Contig10021
CLS_S3_Contig10029      676     349     CLS_S3_Contig10021
CLS_S3_Contig10029      153     349     CLS_S3_Contig10021
CLS_S3_Contig10031      797     349     CLS_S3_Contig10021
CLS_S3_Contig10031      587     349     CLS_S3_Contig10021
CLS_S3_Contig10031      227     349     CLS_S3_Contig10021
CLS_S3_Contig10031      314     349     CLS_S3_Contig10021
CLS_S3_Contig10031      605     349     CLS_S3_Contig10021
CLS_S3_Contig10031      257     349     CLS_S3_Contig10021
CLS_S3_Contig10031      212     349     CLS_S3_Contig10021
CLS_S3_Contig10031      857     349     CLS_S3_Contig10021
CLS_S3_Contig10031      635     349     CLS_S3_Contig10021
CLS_S3_Contig10031      188     349     CLS_S3_Contig10021
CLS_S3_Contig10031      410     349     CLS_S3_Contig10021
CLS_S3_Contig10031      806     349     CLS_S3_Contig10021
CLS_S3_Contig10040      439     349     CLS_S3_Contig10021
CLS_S3_Contig10051      719     349     CLS_S3_Contig10021
CLS_S3_Contig10051      92      349     CLS_S3_Contig10021
CLS_S3_Contig1006       279     349     CLS_S3_Contig10021
CLS_S3_Contig1006       240     349     CLS_S3_Contig10021
CLS_S3_Contig1006       168     349     CLS_S3_Contig10021
CLS_S3_Contig10070      196     349     CLS_S3_Contig10021
CLS_S3_Contig10072      882     349     CLS_S3_Contig10021
CLS_S3_Contig10072      685     349     CLS_S3_Contig10021
CLS_S3_Contig10072      892     349     CLS_S3_Contig10021
CLS_S3_Contig10072      237     349     CLS_S3_Contig10021
CLS_S3_Contig10072      858     349     CLS_S3_Contig10021
CLS_S3_Contig10083      868     349     CLS_S3_Contig10021
CLS_S3_Contig1010       774     349     CLS_S3_Contig10021
CLS_S3_Contig1010       613     349     CLS_S3_Contig10021
CLS_S3_Contig10134      452     349     CLS_S3_Contig10021
CLS_S3_Contig10157      545     349     CLS_S3_Contig10021
CLS_S3_Contig10157      500     349     CLS_S3_Contig10021
CLS_S3_Contig10157      875     349     CLS_S3_Contig10021
CLS_S3_Contig10157      404     349     CLS_S3_Contig10021

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In reply to Re^2: Hash - Compare - Multiple value keys by sesemin
in thread Hash - Compare - Multiple value keys by sesemin

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