I have two alignment ,  how I can automate the process for two o more alignments  only one file?

for example have this two alignment in one file "alignment.ali" :


C; Alignment1
>P1;1efwA
structureX:1efw:162:A:300:A::::
GFVQVETPFLTKSTPEGARDFLVPYR---HEPG----------------LFYALPQSPQL
FKQMLMVAG-LDRYFQIARCFRDEDLRADRQPDFTQLDLEMSFVE--VE-----------
------DVLELNERLMAHVFREALGVELPLPFPRLSYEEAMERYGSDKPDLRFGLELK*
>P1;whi6464
sequence:whi6464:9::186:::::
GFVEVETPVLLKSTPEGAREFLVPTRTSASAPSVKSSIGGGPRESSSQPLFYALPQSPQQ
PKQLLIASGAVDRYYQIAKCFRDEDGRKDRQPEFTQVDLEMAWVSWGIEPSNCSQGDHNV
WRIGGKEVREIIERLIRKIWSTVEGIELPSSFTVMTYEEAMGRFGSDKPDTRFGLEVR*
C; Alignment2
>P1;1cqjD
structureX:1cqj:132:D:284:D::::
CKI--GIQPGHIHKPGKVGIVSRSGTLTYEAVKQTTDYGFGQSTCVGIGGDPIPGSNFID
ILEMFEKDPQTEAIVMIGEIGGSAEEEAAAYIKEH-VTKPVVGYIAGVTAPKGK---RMG
HAGAIIAGGKGTADEKFAALEAAGVKTVRSLADIGEALK*
>P1;whi6880
sequence:whi6880:12::170:::::
CSMMDNIIASKLYRPGSVGYVSKSGGMSNELNNILSLVTNGTYEGIAIGGDRYPGSTFID
HLLRYENDPECKMLVLLGEVGGIEEYRVIEAVKKGLIKKPIVAWAIGTCAKMFTTEVQFG
HAGSMANSDMETADAKNAAMRKAGFIVPDTFEDLPQVLR*


and which is the configuration for file "TOP"?


thanks