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>hsa_circ_0067224|chr3:128345575-128345675-|NM_002950|RPN1  FORWARD
-4.4       6 ..      17   xxxxxxxxxxGTGAC                CAGT ATGC ACT
+G                 AAGATGAGGTTTGTG
...
-2.3       5 ..      26   xxxxxxxxxxxGTGA           C CAGTATGCACTGAAGA
+TGAG G            TTTGTGGACCATGTG
-3.2       4 ..      27   xxxxxxxxxxxxGTG          AC CAGTATGCACTGAAGA
+TGAG GT           TTGTGGACCATGTGT
-1.9       3 ..      28   xxxxxxxxxxxxxGT         GAC CAGTATGCACTGAAGA
+TGAG GTT          TGTGGACCATGTGTT

>hsa_circ_0067224|chr3:128345575-128345675-|NM_002950|RPN1  FORWARD
-4.4       6 ..      17   xxxxxxxxxxGTGAC                CAGT ATGC ACT
+G                 AAGATGAGGTTTGTG
-3.2       4 ..      27   xxxxxxxxxxxxGTG          AC CAGTATGCACTGAAGA
+TGAG GT           TTGTGGACCATGTGT

 
#!/usr/bin/perl 
use strict;
...

close $IN;
close $SIFTED;