Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
_____________________________________________

>P1;d1j3aa-
------------CEEEECCCCCHHHHHHHHHHHHHC------------CCCEEEECHHHCEEEC---------------------CHHHHHHHHHHHCCCCCHHHHHHHHHHCCCCCCCHHHHHHHCCEEECCCCCHHHCCCCCCCCHHHCHHHCCCCCEEEHHHHHHHHCCCC

>P1;d2j01n1
CCCCCCCCCCCCCCEECCCCCCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCCEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHH--------CCCCHHHHHHHHCCCC-CCHHHHHHHCCCEECCCCCCCCCCCCCCCC---------------------------
PSA

>P1;d1j3aa-
------------440030550109400540060026------------5560000102400138---------------------448701650685012440140033302a403486760570193060326228704a59124177031853b926303023008509185

>P1;d2j01n1
977971ab394920011338631580047005103064385425a410113000020360819c526674405547a96b866512056049--------551230032306c303-a6720660261040231691740a853559---------------------------


Translating the sequences
------------CEEEECCCCCHHHHHHHHHHHHHC------------CCCEEEECHHHCEEEC---------------------CHHHHHH********CCHHHHHHHHHHCCCC*CCHHHHHHHCCEEECCCCCHHHCCCCCCCC***************************
************C*EE*CCCCC**HHHHHHHHHH*C************CCC*EE*C***C***C*********************CHHHHHH--------CC**HHHHHHHHCCCC-CCHHHHHHHCC*EECCCCC***CCCCCCCC---------------------------

52161.tem
_________________________________
------------CEEEECCCCCHHHHHHHHHHHHHC------------CCCEEEECHHHCEEEC---------------------CHHHHHH--------CCHHHHHHHHHHCCCC-CCHHHHHHHCCEEECCCCCHHHCCCCCCCC---------------------------




Structural block scores
0	11	-	3.0	P	  75.0  7.2

13	16	E	4.0	M	  1.8  0.5

17	21	C	5.0	H	  2.2  4.6

22	34	H	4.5	M	  2.3  2.6

36	47	-	3.0	P	  75.0  4.4

48	50	C	5.0	H	  5.3  1.7

51	54	E	4.0	M	  0.0  0.0

56	58	H	3.0	P	  2.0  3.0

60	62	E	3.0	P	  1.3  6.0

64	84	-	3.0	P	  75.0  5.6

86	91	H	5.0	H	  4.3  4.0

92	99	-	3.0	P	  3.4  75.0

100	101	C	5.0	H	  4.0  5.0

102	111	H	4.6	H	  1.6  2.0

112	115	C	5.0	H	  4.4  4.6

117	118	C	5.0	H	  7.0  8.2

119	125	H	5.0	H	  3.7  3.3

126	127	C	5.0	H	  6.0  3.5

128	130	E	4.3	M	  2.0  1.3

131	135	C	5.0	H	  3.0  4.2

136	138	H	3.0	P	  5.0  4.0

139	146	C	5.0	H	  4.6  5.7

147	173	-	3.0	P	  4.1  75.0

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