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