Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
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>P1;d2g77a1
CCCHHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCCCCCCHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHCHHHHHHHHHHHHHHHHCCCCCCCCC-----CHHHHHHHHHHHHHHHHCCHHHHHHCCCCCHHHCCCHHHHHHHHHHHHHHHHHHHHHHHH----HCCC------------------------------

>P1;d2g77a2
---------------------------------------------------------------------------------------------------------CCHHHHHHHHHHHHHHHHHCHHHHHHHHHCCCCCHHHHHHHHHCCCHHHCCHHHHHHHHH-HHHHHCCCCHHHHHHHHHHHHHHHCHHHHCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHCCC
PSA

>P1;d2g77a1
9a7a87533550482079476074760590096901431404030021900233276298218612740361196035b71a358812630540046024a3500437301500130000002337905046-----60163005101100142056a408405722047108a84122000000100143057479----623b------------------------------

>P1;d2g77a2
---------------------------------------------------------------------------------------------------------d667157108702700560268016206839070430043004330360086a0072047-30882183748500000000001502a6028164750171048050c0777405700640661056276


Translating the sequences
*********************************************************************************************************HCHHHHHHHHHHHHHHHH*C*******-----CHHHHHHHHHHHHHHHHCCHHHHHH*****HHH*CCHHHHHHHHHHHHHHHHHHHHHHHH----H***------------------------------
---------------------------------------------------------------------------------------------------------*CHHHHHHHHHHHHHHHHHCHHHHHHH*****C*HHHHHHHHH***HHHCCHHHHHHHHH-HHHHHCC**HHHHHHHHHHHHHHH*HHHH******HHHH******************************

47923.tem
_________________________________
---------------------------------------------------------------------------------------------------------HCHHHHHHHHHHHHHHHHHCHHHHHHH-----CHHHHHHHHHHHHHHHHCCHHHHHHHHH-HHHHHCCHHHHHHHHHHHHHHHHHHHHHHHH----HHHH------------------------------




Structural block scores
0	104	-	3.0	P	  4.1  75.0

107	123	H	4.9	H	  1.5  3.6

125	131	H	3.0	P	  4.4  3.3

132	136	-	3.0	P	  75.0  5.2

138	153	H	4.5	M	  1.6  2.1

154	155	C	5.0	H	  2.5  4.0

156	164	H	4.3	M	  4.9  4.1

166	170	H	4.2	M	  2.8  4.2

171	172	C	5.0	H	  4.0  4.5

173	196	H	4.6	H	  2.9  2.6

197	200	-	3.0	P	  75.0  4.5

201	204	H	3.5	M	  5.6  3.2

205	234	-	3.0	P	  75.0  3.9

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