diff --git a/xa2multi.pl b/xa2multi.pl
index fff50fd3..1f4b2d32 100755
--- a/xa2multi.pl
+++ b/xa2multi.pl
@@ -9,7 +9,9 @@
 		print;
 		my @t = split("\t");
 		while ($l =~ /([^,;]+),([-+]\d+),([^,]+),(\d+);/g) {
-			my $mchr = ($t[6] eq $1)? '=' : $t[6]; # FIXME: TLEN/ISIZE is not calculated!
+			my $mchr = ($t[6] eq '=') ? $t[2] : $t[6];
+			my $mchr_ = ($mchr eq $1) ? '=' : $mchr;
+			# FIXME: TLEN/ISIZE is not calculated!
 			my $seq = $t[9];
 			my $phred = $t[10];
 			# if alternative alignment has other orientation than primary, 
@@ -19,7 +21,7 @@
 				$seq =~ tr/ACGTacgt/TGCAtgca/;
 				$phred = reverse $phred;
 			}
-			print(join("\t", $t[0], 0x100|($t[1]&0x6e9)|($2<0?0x10:0), $1, abs($2), 0, $3, @t[6..7], 0, $seq, $phred, "NM:i:$4"), "\n");
+			print(join("\t", $t[0], 0x100|($t[1]&0x6e9)|($2<0?0x10:0), $1, abs($2), 0, $3, $mchr_, $t[7], 0, $seq, $phred, "NM:i:$4"), "\n");
 		}
 	} else { print; }
 }