Forgive me if this is nonsense but if all your output is going to INTRONS_three then presumably the length of $seq is not 9. So does that mean that this block is not entered ?

if ($intron_from_boundary[$i] >= -6) {
   $left_of_boundary = 3; 
   #$right_of_boundary = 6;
        
   $left_of_boundary = $left_of_boundary - intron_from_bound
+ary[$i]; 
   $new_left = 51 - $left_of_boundary;    
   $seq = substr( $col7[$i], $new_left, 9);
   $matchID = $ID[$i] . "\t" . $intron_from_boundary[$i] 
+. "\t" . "on the negative strand";
}
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Is which case is this $intron_from_boundary[$i] >= -6 the correct test, any number greater or equal to -6 ie. -5, -4, -3 etc or should it be less or equal to -6 ie -7,-8,9 etc
poj