Sub-optimal alignment reported by ksw in glocal mode

[Nils Homer]

query: CAACCTTGATAATGTCTCCCA
target: CACCACCAACTTGATAATGTCTCCCA

Command:

$ echo -e "CAACCTTGATAATGTCTCCCA\nCACCACCAACTTGATAATGTCTCCCA\n" | ./ksw -s -c -M 1 -a 1 -b 4 -q 6 -r 1 -R
5	0	20	0	25	4M5D17M	CAACCTTGATAATGTCTCCCA	CACCACCAACTTGATAATGTCTCCCA

Alignment:

CAAC-----CTTGATAATGTCTCCCA
||.|     |||||||||||||||||
CACCACCAACTTGATAATGTCTCCCA

Better alignment (score 13):

CAACCTTGATAATGTCTCCCA
||| |||||||||||||||||
CAA-CTTGATAATGTCTCCCA