Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
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>P1;d3og2a3
CCCHHHEECCCCCCCCCCHHHCCCCC--CCCCCEEECCCEEEEEEEECCEEEEEEECCCCCCEEEECCCCCCCEEEECCEEECCEECCCCCEEECCCCC

>P1;d5ifpa3
CCCHHHEECCCEECCC--CCCCCCCHHHHHCCCEEECCCEEEEEEEECCEEEEEEECCCCEEEEEECCCCCCCEEEECCEEECCEECCCCCEEEEECCC
PSA

>P1;d3og2a3
79977642614237ab9739705699--b271040310630560629c530405040687250203a12ab06502049762a1754a8710307071a

>P1;d5ifpa3
79976533601015aa--6845a759a56851050204630530117c400104041775070304a02a807401057872b194697720405275a


Translating the sequences
CCCHHHEECCC**CCC**HHHCCCC*--**CCCEEECCCEEEEEEEECCEEEEEEECCCC**EEEECCCCCCCEEEECCEEECCEECCCCCEEE**CCC
CCCHHHEECCCEECCC--***CCCCH**HHCCCEEECCCEEEEEEEECCEEEEEEECCCCEEEEEECCCCCCCEEEECCEEECCEECCCCCEEEEECCC

117100.tem
_________________________________
CCCHHHEECCCEECCC--HHHCCCCH--HHCCCEEECCCEEEEEEEECCEEEEEEECCCCEEEEEECCCCCCCEEEECCEEECCEECCCCCEEEEECCC




Structural block scores
0	2	C	5.0	H	  8.3  8.3

3	5	H	5.0	H	  6.7  6.0

6	7	E	5.0	H	  3.0  3.0

8	10	C	5.0	H	  3.7  2.3

11	12	E	3.0	P	  2.5  0.5

13	15	C	5.0	H	  9.7  8.7

16	17	-	3.0	P	  8.0  75.0

18	20	H	3.0	P	  6.3  6.0

21	24	C	5.0	H	  5.0  6.9

26	27	-	3.0	P	  75.0  7.8

28	29	H	3.0	P	  6.8  7.0

30	32	C	5.0	H	  2.7  2.0

33	35	E	5.0	H	  2.3  2.3

36	38	C	5.0	H	  2.3  3.3

39	46	E	5.0	H	  3.9  2.5

47	48	C	5.0	H	  8.8  8.2

49	55	E	5.0	H	  2.3  1.3

56	59	C	5.0	H	  5.2  5.0

60	65	E	4.3	M	  2.0  2.3

66	72	C	5.0	H	  5.9  5.4

73	76	E	5.0	H	  1.8  1.2

77	78	C	5.0	H	  6.5  6.0

79	81	E	5.0	H	  5.0  5.7

82	83	C	5.0	H	  5.8  6.2

84	85	E	5.0	H	  6.0  6.5

86	90	C	5.0	H	  6.1  6.2

91	95	E	4.2	M	  2.0  2.2

96	98	C	5.0	H	  6.2  7.5

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