Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
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>P1;d1kyqa2
CEEEEECCCEEEEECCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHCCCHHHCCCCCHHHHHHHHHH-----HHHHHHCCHHHHHHHHHCCCCCCCCCCCCCHHHHHHHCCC

>P1;d6pr1a2
CEEEEEC-CEEEEECCCCCCHHHHHHHHHHHHCCCCC---CHHHHHHHHHHHHHHHHHHCC------CHHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCCCC-------------
PSA

>P1;d1kyqa2
817171aa64835161bd6586602562683767277b913286188338508610773057a81691240475025305-----5721240219402820541676c323a0275960156006

>P1;d6pr1a2
6440607-44534142b98467716653662287177---531403711761594059409------686127401720484a50470116957900640076008490679-------------


Translating the sequences
CEEEEEC*CEEEEECCCCCCHHHHHHHHHHHHHHHHC***CHHHHHHHHHHHHHHHHHHCC******C**HHHHHHHHHH-----HHHHHHCCHHHHHHHHH****CCCCCC*************
CEEEEEC-CEEEEECCCCCCHHHHHHHHHHHH****C---CHHHHHHHHHHHHHHHHHHCC------CHHHHHHHHHHH******HHHHH*CCHHHHHHHHHHHHHCCCCCC-------------

75615.tem
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CEEEEEC-CEEEEECCCCCCHHHHHHHHHHHHHHHHC---CHHHHHHHHHHHHHHHHHHCC------CHHHHHHHHHHHH-----HHHHHHCCHHHHHHHHHHHHHCCCCCC-------------




Structural block scores
1	5	E	5.0	H	  3.4  2.8

9	13	E	5.0	H	  4.2  3.4

14	19	C	5.0	H	  7.2  6.4

20	35	H	4.5	M	  5.1  5.0

37	39	-	3.0	P	  7.2  75.0

41	58	H	5.0	H	  4.7  3.9

59	60	C	5.0	H	  2.5  4.5

61	66	-	3.0	P	  6.9  75.0

68	79	H	4.5	M	  3.1  3.5

80	84	-	3.0	P	  75.0  5.5

85	90	H	4.7	H	  3.5  3.2

91	92	C	5.0	H	  1.0  7.0

93	105	H	4.4	M	  3.8  3.6

106	111	C	5.0	H	  6.2  5.8

112	124	-	3.0	P	  3.6  75.0

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