Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
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>P1;d1t6t1-
CCCHHHHHHHHHHHCCCCEEEECCHHHHHHHHCCC--CCCEEECCC-CCHHHHHCCCCCCC--EEEECCCCCHHHHHHHHCC-HHHHHCCCEEECHHHHHHHHCCCCCHHHC---------------------

>P1;d2fcja1
CC------------CCCEEEEECCHHHHHHHHHHCCCCCEEEECCCCCCHHHHHHHHHHCCCCEEEEECCCCHHHHHHHHHHHHHCC--CCEEECCCC------CCCCCCCCCHHHHHHHHHHCCCCCCHHHC
PSA

>P1;d1t6t1-
18539401840383068000003388046203746--07302116c-3957401707c739--4000001147704810564-830554907022810530462a1540550---------------------

>P1;d2fcja1
aa------------93520000268803620470062705020087817487067118718a3500000132a60760071056205--606106069------8463045026510050057190604a813


Translating the sequences
CC************CCC*EEEECCHHHHHHHH**C--CC*EEECCC-CCHHHHH*****CC--EEEE*CCCCHHHHHHHH**-HHHH**CCEEECHHH******CCCCHHHC---------------------
CC------------CCCEEEEECCHHHHHHHHHHC**CCEEEECCC*CCHHHHHHHHHHCC**EEEEECCCCHHHHHHHHHH*HH**--CCEEEC***------CCCC***C*********************

110455.tem
_________________________________
CC------------CCCEEEEECCHHHHHHHHHHC--CCEEEECCC-CCHHHHHHHHHHCC--EEEEECCCCHHHHHHHHHH-HHHH--CCEEECHHH------CCCCHHHC---------------------




Structural block scores
0	1	C	5.0	H	  4.5  10.5

2	13	-	3.0	P	  4.0  75.0

14	16	C	5.0	H	  4.7  5.7

17	21	E	4.6	H	  0.0  0.4

22	23	C	5.0	H	  3.0  4.0

24	33	H	4.6	H	  4.2  3.8

35	36	-	3.0	P	  75.0  4.0

37	38	C	5.0	H	  3.5  3.5

39	42	E	4.5	M	  1.5  1.8

43	45	C	5.0	H	  6.5  5.0

47	48	C	5.0	H	  6.0  4.0

49	58	H	4.0	M	  5.0  4.9

59	60	C	5.0	H	  6.0  4.5

61	62	-	3.0	P	  75.0  6.8

63	67	E	4.6	H	  0.8  1.0

68	71	C	5.0	H	  1.5  1.5

72	81	H	4.6	H	  4.2  3.8

83	86	H	4.0	M	  4.0  3.2

87	88	-	3.0	P	  4.5  75.0

89	90	C	5.0	H	  4.5  3.0

91	93	E	5.0	H	  3.0  2.3

95	97	H	3.0	P	  3.0  5.0

98	103	-	3.0	P	  3.3  75.0

104	107	C	5.0	H	  5.1  5.2

108	110	H	3.0	P	  3.3  3.0

112	132	-	3.0	P	  75.0  3.5

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