Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
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>P1;d1iwga5
CEEEEEECHHHHHCCCCCHHHHHHHHHHHCCCCCCCEECCCCCCCCCCCCEECCCCCC-CCCHHHHHCCEEEEECCCEEEEHHHHEEEEEECC

>P1;d1iwga6
CEEEECCCHHHHHHHCCCHHHHHHHHHHHHCCEEEEEEEEC----CEEEEEEECCCHHHCCCHHHHCCCEECC-CCCCCEEHHHCCCEEEECC
PSA

>P1;d1iwga5
741305358930962907484067127632555a2b4617a859a9396557482767-18657401504045497a56010540080553a8

>P1;d1iwga6
5724141459606744053a507742930290555945728----a86454654284742673a115535070-9696505072006355586


Translating the sequences
CEEEEEECHHHHH**CCCHHHHHHHHHHH*CC****EE**C****C****EE*CCC**-CCCHHHHHCCEEEE*CCCEEEEHHHHEEEEEECC
CEEEE**CHHHHHHHCCCHHHHHHHHHHHHCCEEEEEEEEC----CEEEEEEECCCHH*CCCHHHH*CCEE**-CCC**EEHHH***EEEECC

82714.tem
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CEEEEEECHHHHHHHCCCHHHHHHHHHHHHCCEEEEEEEEC----CEEEEEEECCCHH-CCCHHHHHCCEEEE-CCCEEEEHHHHEEEEEECC




Structural block scores
1	6	E	4.3	M	  2.7  3.2

8	14	H	4.4	M	  5.3  5.3

15	17	C	5.0	H	  5.3  3.0

18	29	H	4.8	H	  4.2  4.4

30	31	C	5.0	H	  5.0  4.5

32	39	E	3.5	M	  5.9  5.2

41	44	-	3.0	P	  8.1  75.0

46	52	E	3.6	M	  5.6  5.4

53	55	C	5.0	H	  5.7  4.7

56	57	H	3.0	P	  6.5  5.5

59	61	C	5.0	H	  5.0  5.0

62	66	H	4.6	H	  3.4  4.1

67	68	C	5.0	H	  2.5  4.0

69	72	E	4.0	M	  3.2  3.0

74	76	C	5.0	H	  8.8  8.0

77	80	E	4.0	M	  3.0  4.0

81	84	H	4.5	M	  2.2  2.2

85	90	E	4.3	M	  3.5  4.0

91	92	C	5.0	H	  9.2  7.0

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