This program can analyse alignments of two formats - .fasta and .aln. It's no use telling a lot about them...
But every analysed alignment should have either .fasta or .aln format!

Fasta format

		>mlr8250
		-----MPTGYADGRSMTDTVETIDYSKTLYLPQTDFPMRAGLP----EKEPVLVKRWQDM
		D---LYAKLRES---AAG-----RTKYVLHDGPPYANG-NIHIGHALNKILKDVITRSFQ
		MRGYDSTYVPG-WDCHGLPIEWKIEEQYRAKGKNKDEVPV----NEFRKECREFAAHWIT
		>CC0701
		---------MAD-----DATTARDYRETVFLPDTPFPMRAGLP----KKEPEILEGWAAL
		SEKGLYGAVRQKR-QAAG-----APLFVFHDGPPYANG-AIHIGHALNKILKDFVVRSRF
		ALGYDVDYVPG-WDCHGLPIEWKIEEQFRAKGRRKDEVPA----EEFRRECRAYAGGWIE
		>ileS
		---------------------MSDYKSTLNLPETGFPMRGDLA----KREPGMLARWTDD
		D---LYGIIRAA---KKG-----KKTFILHDGPPYANG-SIHIGHSVNKILKDIIVKSKG
		LSGYDSPYVPG-WDCHGLPIELKVEQEYGKPG---EKFTA----AEFRAKCREYAATQVD
		>ZileS
		---------------------MSDYKSTLNLPETGFPMRGDLA----KREPGMLARWTDD
		D---LYGIIRAA---KKG-----KKTFILHDGPPYANG-SIHIGHSVNKILKDIIVKSKG
		LSGYDSPYVPG-WDCHGLPIELKVEQEYGKPD---EKFTA----AEFRAKCREYAATQVD
		>VC0682
		---------------------MSEYKDTLNLPETGFPMRGDLA----KREPEMLQRWYQE
		D---LYGAIRQA---KKG-----KKSFVLHDGPPYANG-DIHIGHALNKILKDVIIKSKT
		LSGFDAPYIPG-WDCHGLPIELMVEKKVGKPG---QKVTA----AEFREKCREYAAGQVE
		>HI0962
		--------------------MTVDYKNTLNLPETSFPMRGDLA----KREPDKXKNWYEK
		N---LYQKIRKA---SKG-----KKSFILHDGPPYANG-NIHIGHAVNKILKDIIIKSKT
		ALGFDSPYIPG-WDCHGLPIELKVEGLVGKPN---EKISA----AEFRQKCREYAAEQVE
		>PM1662
		--------------------MTVDYKNTLNLPETGFPMRGDLA----KREPNMLKSWYEK
		D---LYQKIRQA---SKG-----KKSFILHDGPPYANG-TIHIGHAVNKILKDIIVKSKT
		ALGYDSPYIPG-WDCHGLPIELKVEGLVGKPN---QNISA----AQFREACRQYAAEQVE
		>PA4560
		---------------------MTDYKATLNLPETAFPMKAGLP----QREPETLKFWNDI
		G---LYQKLRAI---GGD-----RPKFVLHDGPPYANG-SIHIGHAVNKILKDIIVRSKT
		LAGYDAPYVPG-WDCHGLPIEHKVETTHGK------NLPA----DKTRELCREYAAEQIE
		>NMB1833
		---------------------MTDYSKTVNLLESPFPMRGNLA----KREPAWLKSWYEQ
		K---RYQKLREI---AKG-----RPKFILHDGPPYANG-DIHIGHAVNKILKDIIIRSKT
		QAGFDAPYVPG-WDCHGLPIEVMVEKLHGK------DMPK----ARFRELCREYAAEQIA
		>NMA0622
		---------------------MTDYSKTVNLLESPFPMRGNLA----KREPAWLKSWYEQ
		K---RYQKLREI---AKG-----RPKFILHDGPPYANG-DIHIGHAVNKILKDIIIRSKT
		QAGFDAPYVPG-WDCHGLPIEVMVEKLHGK------DMPK----ARFRELCREYAAEQIA
		

All sequences follow each other. Declaration of every sequence begins with declaration of the name of this sequence, which is signed by the symbol ">". Then, the sequence declaration itself begins from the new line
No additional information is supposed.

Aln format

		CLUSTAL W (1.74) multiple sequence alignment
		
		
		mlr8250         -----MPTGYADGRSMTDTVETIDYSKTLYLPQTDFPMRAGLP----EKEPVLVKRWQDM
		CC0701          ---------MAD-----DATTARDYRETVFLPDTPFPMRAGLP----KKEPEILEGWAAL
		ileS            ---------------------MSDYKSTLNLPETGFPMRGDLA----KREPGMLARWTDD
		ZileS           ---------------------MSDYKSTLNLPETGFPMRGDLA----KREPGMLARWTDD
		VC0682          ---------------------MSEYKDTLNLPETGFPMRGDLA----KREPEMLQRWYQE
		HI0962          --------------------MTVDYKNTLNLPETSFPMRGDLA----KREPDKXKNWYEK
		PM1662          --------------------MTVDYKNTLNLPETGFPMRGDLA----KREPNMLKSWYEK
		PA4560          ---------------------MTDYKATLNLPETAFPMKAGLP----QREPETLKFWNDI
		NMB1833         ---------------------MTDYSKTVNLLESPFPMRGNLA----KREPAWLKSWYEQ
		NMA0622         ---------------------MTDYSKTVNLLESPFPMRGNLA----KREPAWLKSWYEQ
		                                                                            
		
		mlr8250         D---LYAKLRES---AAG-----RTKYVLHDGPPYANG-NIHIGHALNKILKDVITRSFQ
		CC0701          SEKGLYGAVRQKR-QAAG-----APLFVFHDGPPYANG-AIHIGHALNKILKDFVVRSRF
		ileS            D---LYGIIRAA---KKG-----KKTFILHDGPPYANG-SIHIGHSVNKILKDIIVKSKG
		ZileS           D---LYGIIRAA---KKG-----KKTFILHDGPPYANG-SIHIGHSVNKILKDIIVKSKG
		VC0682          D---LYGAIRQA---KKG-----KKSFVLHDGPPYANG-DIHIGHALNKILKDVIIKSKT
		HI0962          N---LYQKIRKA---SKG-----KKSFILHDGPPYANG-NIHIGHAVNKILKDIIIKSKT
		PM1662          D---LYQKIRQA---SKG-----KKSFILHDGPPYANG-TIHIGHAVNKILKDIIVKSKT
		PA4560          G---LYQKLRAI---GGD-----RPKFVLHDGPPYANG-SIHIGHAVNKILKDIIVRSKT
		NMB1833         K---RYQKLREI---AKG-----RPKFILHDGPPYANG-DIHIGHAVNKILKDIIIRSKT
		NMA0622         K---RYQKLREI---AKG-----RPKFILHDGPPYANG-DIHIGHAVNKILKDIIIRSKT
		                                            : :***  ..             *:       
		
		mlr8250         MRGYDSTYVPG-WDCHGLPIEWKIEEQYRAKGKNKDEVPV----NEFRKECREFAAHWIT
		CC0701          ALGYDVDYVPG-WDCHGLPIEWKIEEQFRAKGRRKDEVPA----EEFRRECRAYAGGWIE
		ileS            LSGYDSPYVPG-WDCHGLPIELKVEQEYGKPG---EKFTA----AEFRAKCREYAATQVD
		ZileS           LSGYDSPYVPG-WDCHGLPIELKVEQEYGKPD---EKFTA----AEFRAKCREYAATQVD
		VC0682          LSGFDAPYIPG-WDCHGLPIELMVEKKVGKPG---QKVTA----AEFREKCREYAAGQVE
		HI0962          ALGFDSPYIPG-WDCHGLPIELKVEGLVGKPN---EKISA----AEFRQKCREYAAEQVE
		PM1662          ALGYDSPYIPG-WDCHGLPIELKVEGLVGKPN---QNISA----AQFREACRQYAAEQVE
		PA4560          LAGYDAPYVPG-WDCHGLPIEHKVETTHGK------NLPA----DKTRELCREYAAEQIE
		NMB1833         QAGFDAPYVPG-WDCHGLPIEVMVEKLHGK------DMPK----ARFRELCREYAAEQIA
		NMA0622         QAGFDAPYVPG-WDCHGLPIEVMVEKLHGK------DMPK----ARFRELCREYAAEQIA
		                  .       . :* **:* *                             .         
                

Aln. file begins with the word "CLUSTAL".
In the very beginning some additional information is included. Every line with such information begins with the symbol "#". Additional information can be only in the beginning of the .aln file.
After this blocks of the alignment are present. Every block is a part of the alignment. All sequences are present in every block; their list and order of following are the same for all blocks. Every block has length 60 positions of alignment.
In every block under the part of alignment some signs can be present. Usually these signs mean type of the position (conservative or semi-conservative). But these signs are not taken into account in this program complex.