Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
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>P1;d1iw5a1
C---CCCHHHHHHHHHHHHCCCEEEEEECCCCCCCCEEEEEEECCHHHHCCHHHHHHHHHHHCCCCHHHCC--EEEEEEECHHHHHHCCC---C

>P1;d1ny8a1
CCCCCCCCHHHHHHHHHHCCCCEEEEECC-----CCEEEEEEECCCCCCCCHHHHHHHHHCHHHHHHHHHCCCEEEEEECCHHHHHHHHCCCCC
PSA

>P1;d1iw5a1
a---84626602520375070750708264ab8a41203010017406a457650473057306a236707--406160323a5278859---c

>P1;d1ny8a1
98838271b50351039113096221127-----c5800000006705a377870473044406960592894404020125920771466b82


Translating the sequences
C---CCCHHHHHHHHHHHHCCCEEEEEEC*****CCEEEEEEECCHHHHCCHHHHHHHHHHH****HHH*C--EEEEEEECHHHHHH**C---C
C***CCC*HHHHHHHHHH*CCCEEEEE*C-----CCEEEEEEECC****CCHHHHHHHHH*HHHHHHHHHC**EEEEEE*CHHHHHHHHC***C

82657.tem
_________________________________
C---CCCHHHHHHHHHHHHCCCEEEEEEC-----CCEEEEEEECCHHHHCCHHHHHHHHHHHHHHHHHHHC--EEEEEEECHHHHHHHHC---C




Structural block scores
1	3	-	3.0	P	  75.0  6.3

4	6	C	5.0	H	  6.0  5.7

7	18	H	4.7	H	  3.2  3.4

19	21	C	5.0	H	  4.7  4.0

22	27	E	4.7	H	  3.7  2.3

29	33	-	3.0	P	  8.9  75.0

34	35	C	5.0	H	  2.5  8.8

36	42	E	5.0	H	  0.9  1.1

43	44	C	5.0	H	  4.0  3.0

45	48	H	3.0	P	  5.1  5.6

49	50	C	5.0	H	  4.5  5.0

51	69	H	4.4	M	  4.3  4.5

71	72	-	3.0	P	  75.0  6.5

73	79	E	4.7	H	  2.9  1.6

81	88	H	4.5	M	  6.1  4.4

90	92	-	3.0	P	  75.0  8.5

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