Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
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>P1;d1egwa-
C---CCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEECCCCCEEEEECCCCCCC-CCC--------------

>P1;d1mnma-
CCCCCCCCC-CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCEEEEECCCCCEEEEECCCCCHHHHCCHHHHHHHHHCCCCC
PSA

>P1;d1egwa-
d---a97888638789626622777187626816460676a4321241517897425201721579-899--------------

>P1;d1mnma-
b987887a8-73947772564478727652671646068596421222216976242200784544057a269727675768bb


Translating the sequences
C---CCCCC*CCCCHHHHHHHHHHHHHHHHHHHHHHHHH*CCCCEEEEECCCCCEEEEECCCCC**-*CC--------------
C***CCCCC-CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCEEEEECCCCCEEEEECCCCCHH*HCC**************

55455.tem
_________________________________
C---CCCCC-CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCEEEEECCCCCEEEEECCCCCHH-HCC--------------




Structural block scores
1	3	-	3.0	P	  75.0  8.0

4	8	C	5.0	H	  8.5  8.3

10	13	C	5.0	H	  6.0  5.8

14	39	H	4.9	H	  5.2  5.2

40	43	C	5.0	H	  4.9  5.2

44	48	E	5.0	H	  2.6  1.8

49	53	C	5.0	H	  6.4  5.8

54	58	E	5.0	H	  2.6  2.0

59	63	C	5.0	H	  3.2  4.8

64	65	H	3.0	P	  8.0  4.0

68	69	C	5.0	H	  9.0  8.8

70	83	-	3.0	P	  75.0  6.8

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