Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
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>P1;d1ns5a-
-CEEEEEECC-CCHHHHHHHHHHHCCCCC-CCEEEEEECCCCCCCCC---CHHHHHHHHHHC-CCCCC-CCEEEEECCCCCCCCHHHHHHHHHHHHHHCC-CEEEEECCCCCCCHHHHHHCCEEECCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCC-

>P1;d1o6da1
-CEEEEEECCC-CHHHHHHHHHHHHHHCCCCCEEEEEECCCCCC------CHHHHHC-CHHHHHCCCCCCCEEEEECCCCEECCHHHHHHHHHHHHHHCC-CEEEEECCCCCCCHHHHHHCCEEEECCCCCCCHHHHHHHHHHHHHHHHHHHCCC----

>P1;d4faka1
CEEEEEEECCCCCHHHHHHHHHHHHHHCCCCEEEEEEECCCCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCEEEEECCCCEECCHHHHHHHHHHHHHCCCCEEEEEECCCCCCCHHHHHHCCEEEECCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCC
PSA

>P1;d1ns5a-
-210000154-a6970685045126403a-94052420646a259a3---478711560173-28209-a2100002570770726600610550692a4-300000008470077058404230003a882513510240011003020304b4824-

>P1;d1o6da1
-5020000170-89605841861165055016030330825499------7596015-00520083219c0100001461550628610820560466a3-3000000054804970283054200138882931400130042025003514c5----

>P1;d4faka1
23000000080747724730751384066108051330742926ab17b86276124500730385078900000025a1652716300920662086a363000000062700760392051300129872632310140022002001215a3b23b


Translating the sequences
-CEEEEEECC-CCHHHHHHHHHHH***CC-CCEEEEEECCCCCCCCC---CHHHHHHHHHH*-*CCCC-CCEEEEECCCC**CCHHHHHHHHHHHHHHCC-CEEEEECCCCCCCHHHHHHCCEEE*CCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCC-
-CEEEEEECCC-CHHHHHHHHHHHHHHCCCCCEEEEEECCCCCC------CHHHHH*-*HHHHHCCCCCCCEEEEECCCCEECCHHHHHHHHHHHHHHCC-CEEEEECCCCCCCHHHHHHCCEEEECCCCCCCHHHHHHHHHHHHHHHHHHHCCC----
**EEEEEECCCCCHHHHHHHHHHHHHHCCCC*EEEEEECCCCCCCCC****HHHHHHHHHHHHH*CCCCCCEEEEECCCCEECCHHHHHHHHHHHHH*CC**EEEEECCCCCCCHHHHHHCCEEEECCCCCCCHHHHHHHHHHHHHHHHHHH*CCCCC*

75217-4.tem
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-CEEEEEECCCCCHHHHHHHHHHHHHHCCCCCEEEEEECCCCCCCCC---CHHHHHHHHHHHHHCCCCCCCEEEEECCCCEECCHHHHHHHHHHHHHHCC-CEEEEECCCCCCCHHHHHHCCEEEECCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCC-




Structural block scores
2	7	E	5.0	H	  0.3  0.3  0.0

8	12	C	4.6	H	  20.1  18.2  3.8

13	26	H	4.8	H	  4.1  4.3  4.1

27	31	C	4.6	H	  20.3  3.4  4.2

32	37	E	5.0	H	  2.2  1.5  2.0

38	46	C	4.7	H	  6.2  29.1  5.9

47	49	-	4.0	M	  75.0  75.0  8.8

51	63	H	4.5	M	  9.5  8.3  3.1

64	70	C	4.7	H	  15.2  5.1  5.3

71	75	E	5.0	H	  0.2  0.2  0.0

76	79	C	5.0	H	  3.5  3.0  4.6

80	81	E	4.0	M	  7.0  5.0  5.5

82	83	C	5.0	H	  3.5  3.0  4.5

84	97	H	4.9	H	  3.4  3.9  3.5

98	99	C	5.0	H	  7.2  6.8  6.8

102	106	E	5.0	H	  0.0  0.0  0.0

107	113	C	5.0	H	  2.7  3.0  2.1

114	119	H	5.0	H	  5.2  4.8  4.5

120	121	C	5.0	H	  2.0  2.5  2.5

122	125	E	4.8	H	  1.2  1.5  1.0

126	132	C	5.0	H	  5.2  5.6  5.0

133	151	H	5.0	H	  1.4  1.8  1.3

152	157	C	4.3	M	  5.6  41.1  5.8

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