Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
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>P1;d1pp9f-
-----------------------CHHHHHHHHHHHCHHHHCCCHHHHCCC-CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHCCCHHHCCCCCHHHHHHHHHHHHHHHHHHHC----

>P1;d3cx5g-
CCCHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHCHHHHCCCHHHHCCCCCHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHCCCHHHCCCCCHHHHHHHHHHHHHHHHHHCCCCCC
PSA

>P1;d1pp9f-
-----------------------77c7557714421203201260033a4-7a106301730498356605713730750575965157861262660711065317303733677577878----

>P1;d3cx5g-
b6527453866583582894297445867684674311320115003193959205201750489448616713820871774985158942167851651035303701875767776686a8aa


Translating the sequences
-----------------------*HHHHHHHHHHHCHHHHCCCHHHHCCC-CHHHHHHHH*CCHHHHHHHHHHHHHHHHHHHCCCCCCHHHCCCHHHCCCCCHHHHHHHHHHHHHHHHHHHC----
***********************HHHHHHHHHHHHCHHHHCCCHHHHCCC*CHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHCCCHHHCCCCCHHHHHHHHHHHHHHHHHH*C****

81524.tem
_________________________________
-----------------------HHHHHHHHHHHHCHHHHCCCHHHHCCC-CHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHCCCHHHCCCCCHHHHHHHHHHHHHHHHHHHC----




Structural block scores
0	22	-	3.0	P	  75.0  5.8

23	34	H	4.8	H	  5.7  5.8

36	39	H	5.0	H	  1.8  1.8

40	42	C	5.0	H	  1.0  0.7

43	46	H	5.0	H	  2.2  2.0

47	49	C	5.0	H	  5.8  4.3

52	60	H	4.8	H	  3.5  3.4

61	62	C	5.0	H	  2.0  2.0

63	81	H	5.0	H	  4.6  5.1

82	87	C	5.0	H	  5.2  5.3

88	90	H	5.0	H	  7.0  7.0

91	93	C	5.0	H	  3.0  3.0

94	96	H	5.0	H	  4.7  6.7

97	101	C	5.0	H	  1.8  2.6

102	120	H	4.9	H	  5.0  5.1

122	125	-	3.0	P	  75.0  9.9

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