Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
_____________________________________________

>P1;d3cx5c1
------------------------------------------------------------------CCCCCCCCCCCHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCC--CCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHCCCCC

>P1;d4ogqb-
CCCCCCCCCCHHHHHHHHCCCCCCCCCCCIIIIICCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHC-CCCCCCHHHCHHHHHHHHHHHHHHHHHHHHHCCCH-HHC-CCCCCC------------------------------
PSA

>P1;d3cx5c1
------------------------------------------------------------------b9876b97427865102300320285a8605622740670583468246084a--948809325734641481473027003287695447404600730211056212610650365466873bb

>P1;d4ogqb-
b6578276947706732889605a4335476334456564778786878856878886a9a899a78a675a9633785522220252438798606634566577776557738-85a6a55a637a23888787585574226004375-a41-a2046b------------------------------


Translating the sequences
------------------------------------------------------------------CCCCCCCCCCCHHHHHHHHHHH*CCCHHHHHHHHHHHHHHHHHHHHH*C*CCC--C***CHHHHHHHHHHHHHHHHHHHHHCCC****H*HHHHHH******************************
******************************************************************CCCCCCCCCCCHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHC-CCC**CHHHCHHHHHHHHHHHHHHHHHHHHHCCCH-HH*-******------------------------------

81648.tem
_________________________________
------------------------------------------------------------------CCCCCCCCCCCHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHC-CCC--CHHHCHHHHHHHHHHHHHHHHHHHHHCCCH-HHH-HHHHHH------------------------------




Structural block scores
0	65	-	3.0	P	  75.0  6.4

66	76	C	5.0	H	  7.5  6.8

77	88	H	4.8	H	  2.5  3.2

89	91	C	5.0	H	  5.0  6.0

92	113	H	4.9	H	  4.7  5.7

116	118	C	5.0	H	  7.5  7.8

119	120	-	3.0	P	  75.0  8.2

122	124	H	3.0	P	  6.7  7.2

126	146	H	5.0	H	  3.8  5.4

147	149	C	5.0	H	  4.3  4.7

152	154	H	3.0	P	  6.0  5.2

156	161	H	3.0	P	  3.5  5.7

162	191	-	3.0	P	  4.0  75.0

>>>>>>