Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
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>P1;d1hwla1
CEEECCEEECCCHHHHHHHHHHHCCHHHHHHHHHHHHCCCC-----CCEEEEEEEEEE-----CCEEEEEEEEECCCCCCHHHHHHHHHHHHHHHHHHCCCCEEEECCCCCCCCCCCCHHHHHHCCC

>P1;d4i6ya2
CEEEEEEEECCC--CHHHHHHHHHH--CHHHHHHHHHHCCHHHHHCCCEEEEEEEEEECCCCCCCEEEEEEEEECCCCCCHHHHHHHHHHHHHHHHHHHC-CEEEEEEECC-----CCCC-------
PSA

>P1;d1hwla1
0101000030385a306703720659803730390025138-----605035040426-----9430200010805b6701b202700650073046416706345331720028493813973815

>P1;d4i6ya2
310030202919--60780374039--43850172026538803868000440505164a2986220101000105b5703b203400520161047009-0605734128-----9374-------


Translating the sequences
CEEE**EEECCC**HHHHHHHHH****HHHHHHHHHH*CC*-----CCEEEEEEEEEE-----CCEEEEEEEEECCCCCCHHHHHHHHHHHHHHHHHH*C*CEEEE***CC*****CCHH*******
CEEEEEEEECCC--*HHHHHHHHHH--*HHHHHHHHHHCCH*****CCEEEEEEEEEE*****CCEEEEEEEEECCCCCCHHHHHHHHHHHHHHHHHHHC-CEEEEEEECC-----CC**-------

55035.tem
_________________________________
CEEEEEEEECCC--HHHHHHHHHHH--HHHHHHHHHHHCCH-----CCEEEEEEEEEE-----CCEEEEEEEEECCCCCCHHHHHHHHHHHHHHHHHHHC-CEEEEEEECC-----CCHH-------




Structural block scores
1	8	E	4.5	M	  0.6  1.0

9	11	C	5.0	H	  3.7  6.3

12	13	-	3.0	P	  7.8  75.0

14	24	H	4.5	M	  3.5  4.3

25	26	-	3.0	P	  8.5  75.0

27	37	H	4.6	H	  2.9  3.5

38	39	C	5.0	H	  2.0  4.0

41	45	-	3.0	P	  75.0  5.0

46	47	C	5.0	H	  3.0  4.0

48	57	E	5.0	H	  2.9  2.5

58	62	-	3.0	P	  75.0  6.7

63	64	C	5.0	H	  6.5  4.0

65	73	E	5.0	H	  1.6  0.6

74	79	C	5.0	H	  4.9  4.8

80	98	H	4.9	H	  3.1  2.6

102	108	E	4.1	M	  3.6  3.7

109	110	C	5.0	H	  4.5  5.0

111	115	-	3.0	P	  2.8  75.0

116	117	C	5.0	H	  6.0  6.0

118	119	H	3.0	P	  4.5  5.5

120	126	-	3.0	P	  5.1  75.0

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