Alignment #1 Score= 40
TG--CTTAGAACCTAAGATCATAGCC
CTAAAT-TGATGGG-ATGGGACT---
    ^^ ^     ^ ^^         


Alignment #2 Score= 42
TG--CTTAGAAC--CTAAGATCATAGCC
CTAAA-T-TGATGGG-A-TGGGACT---
    ^ ^ ^     ^ ^ ^