How To Make Statistics Of Mismatch And Unpairing Positions Between Mirnas And Their Targets

Dear all, i need to make statistics of mismatch and unpaired positions between miRNAs and their targets. What I have done is that I performed patscan and identified miRNA targets using various patterns ( allowing different mismatch and unpairing numbers ). My patscan result is examplified as below. *An example only* miRNA miR_sequence target_antisense_sequences miR-1 AGCGCU AGCTCT miR-2 AGAGAG AGAAG mIR-3 UGAGC TGAGGC My problem is to make statistics of unparing and mismatch positions. To resolve this problem, I performed batch blast2 to compare miRNAs (query ) and their targets (subject), and output is like below. *concise BLAST Result* miR1 AGCGCU 111 11 AGCTCT miR2 AGAGAG 111 11 AGA-AG miR3 UGAG-C 1111 1 TGAGGC I think it's close, but it's still troublesome to make statistics of mismatch and gap positions. My ideal result is shown below. mismatch_position gap_position miR1 4 0 miR2 0 4 miR3 0 5 I think my analysis is a little bit different from fuzzy matching. My key problem is to calculate mismatch and unpairing positions between miRNAs and their targets. My blast result is close, but i don't know how to statistically summarize where mismatchs and gaps are for many miRNA-target pairs. Could anyone please help me sort this problem? THANK YOU VERY MUCH! ...