Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
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>P1;d1u5ka2
CHHHCHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCEECCCCCCEECCCCCC----------CCCCC------HHHHHHHHH--CCCCCHHHHHH----------CCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHCC

>P1;d2b0oe1
----------------------------------------------CHHHHHHHHHHCC-------CCCCCCCCCCCCCCCEEECCCCCEECHHHHHHHHHHCCCCCCEEECCCCCCCHHHHHHHHHCCHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCCC---------C
PSA

>P1;d1u5ka2
b33869717611400540093006e435880661233036201748502000000002003307082438601745467051105a5020117900a----------57414------860050024--03728293027----------64068a30520071024004420b8907048203

>P1;d2b0oe1
----------------------------------------------a738822750473-------7407600004289031001420000185005005707794070300674a04594085017300650275112415a9a24205592837504800500045660159---------a


Translating the sequences
**********************************************CHHHHHHHHHHHH*******CCCCCCCCCCCCCCCEE*CCCCCEEC*****----------C***C------HHHHHHHHH--*****HHHHHH----------CCCCHHHHHHHHHHHHHHHHHHCC*********C
----------------------------------------------CHHHHHHHHHH**-------CCCCCCCCCCCCCCCEEECCCCCEECHHHHH**********CEEEC******HHHHHHHHH**HHHHHHHH*************CCCCHHHHHHHHHHHH******CC---------C

57863.tem
_________________________________
----------------------------------------------CHHHHHHHHHHHH-------CCCCCCCCCCCCCCCEEECCCCCEECHHHHH----------CEEEC------HHHHHHHHH--HHHHHHHHHHH----------CCCCHHHHHHHHHHHHHHHHHHCC---------C




Structural block scores
0	45	-	3.0	P	  4.1  75.0

47	58	H	4.7	H	  0.3  4.7

59	65	-	3.0	P	  3.0  75.0

66	80	C	5.0	H	  4.1  3.3

81	83	E	4.3	M	  0.7  0.3

84	88	C	5.0	H	  4.5  1.4

89	90	E	5.0	H	  0.5  0.0

92	96	H	3.0	P	  5.3  3.6

97	106	-	3.0	P	  75.0  3.9

108	110	E	3.0	P	  4.0  1.0

112	117	-	3.0	P	  75.0  5.2

118	126	H	5.0	H	  2.8  4.3

127	128	-	3.0	P	  75.0  1.5

129	139	H	3.5	M	  3.9  3.0

140	149	-	3.0	P	  75.0  4.9

150	153	C	5.0	H	  4.0  6.0

154	171	H	4.3	M	  2.9  3.0

172	173	C	5.0	H	  5.8  7.0

174	182	-	3.0	P	  4.2  75.0

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