Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
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>P1;d1ou8a-
-----CCCCHHHHHHHHHHHHHHC-------CCCEEEEEECCCCCCCCC--HHHCCCCEEEEECCCCCCEEEEECCCEEEEEEEECCEEEEEEEEHHHEEEEEECCCCCEEECCCCHHHC

>P1;d2nysa1
CCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCEEEEECCCCCCCCCCCHHHHCC--CCCEEEC-CCCCC-CCC-CEEEEEEEECCEEEEEEEEHHHEEEEEEHHHCEEEECCC-----
PSA

>P1;d1ou8a-
-----a718006503731740485-------921020102073a90700--96328b540403029a40791514693020416199645603010000300305466602809739617

>P1;d2nysa1
6a6587677367514404840213876806ba310302020629707064049449--8440303-89147-824-8003000328a5604030108004203021594517096-----


Translating the sequences
-----****HHHHHHHHHHHHHHC-------CCCEEEEEECCCCCCCCC--HHHCC**EEEEE*C*CCCEE*EEC*CEEEEEEEECCEEEEEEEEHHHEEEEEE***C*EEECCC*****
*****HHHHHHHHHHHHHHHH**C*******CCCEEEEE*CCCCCCCCC**HHHCC--***EEEC-CCC**-**C-CEEEEEEEECCEEEEEEEEHHHEEEEEEHHHCEEEECCC-----

101738.tem
_________________________________
-----HHHHHHHHHHHHHHHHHHC-------CCCEEEEEECCCCCCCCC--HHHCC--EEEEEEC-CCCEE-EEC-CEEEEEEEECCEEEEEEEEHHHEEEEEEHHHCEEEECCC-----




Structural block scores
0	4	-	3.0	P	  75.0  7.1

5	22	H	4.3	M	  4.1  4.2

24	30	-	3.0	P	  75.0  6.6

31	33	C	5.0	H	  4.0  4.8

34	39	E	4.7	H	  0.8  1.2

40	48	C	5.0	H	  4.1  4.1

49	50	-	3.0	P	  75.0  2.0

51	53	H	5.0	H	  6.0  5.7

54	55	C	5.0	H	  5.0  6.5

56	57	-	3.0	P	  8.2  75.0

58	63	E	3.7	M	  1.8  3.2

66	68	C	5.0	H	  4.8  6.0

69	70	E	3.0	P	  8.0  5.5

72	73	E	3.0	P	  3.0  5.0

77	84	E	5.0	H	  2.1  1.0

85	86	C	5.0	H	  9.0  9.2

87	94	E	5.0	H	  3.1  2.4

95	97	H	5.0	H	  0.0  2.7

98	103	E	5.0	H	  1.0  1.5

104	106	H	3.0	P	  5.0  2.7

108	111	E	4.5	M	  4.0  4.2

112	114	C	5.0	H	  5.3  5.0

115	119	-	3.0	P	  5.2  75.0

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