Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
_____________________________________________

>P1;d2ot2a1
CCCCEEEEEEEEC--CCEEEEECCCCEEEEECCCCCCCCCCCCCCCCCEEEECCCCEEEEECHHHHHHHHHHHHHHCCCCCCCHHHHHCCCC

>P1;d2z1ca1
-CCCCCEEEEEEE--CCEEEEECCCCC-CEECCCCC------CCCCCCEEEEECCEEEEEECHHHHHHHHHHHHHHCCC-------------

>P1;d3d3ra1
-CCCCCEEEEEEECCCCEEEEEECCEEEEEECCCCCCCC------CCCEECCCCCC-CCCCCHHHHHHHHHHHHHHHHHHC-----------
PSA

>P1;d2ot2a1
8522300204619--a760502019854501075193608886505631020457403522a3760684373265684776a6164899977

>P1;d2z1ca1
-585200403619--a6402033d995-70504626------a0756120116b8403430878507624772885577-------------

>P1;d3d3ra1
-ba34604015159a8530202188665746264a8927------64462659b49-7a966887368469878778887a-----------


Translating the sequences
*CCC**EEEEEE*--CCEEEEECCCCEEEEECCCCCCCC***CCCCCCEEEECCCCEEEEECHHHHHHHHHHHHHHCCC*C***********
-CCCCCEEEEEEE--CCEEEEECCCC*-*EECCCCC------CCCCCCEEEE*CC*EEEEECHHHHHHHHHHHHHHCCC-------------
-CCCCCEEEEEEE**CCEEEEE*CC*EEEEECCCCCCCC------CCCEE**CCCC-****CHHHHHHHHHHHHHH****C-----------

159127.tem
_________________________________
-CCCCCEEEEEEE--CCEEEEECCCCEEEEECCCCCCCC---CCCCCCEEEECCCCEEEEECHHHHHHHHHHHHHHCCC*C-----------




Structural block scores
1	5	C	4.6	H	  2.4  4.0  7.0

6	12	E	4.9	H	  3.1  3.3  2.3

13	14	-	4.0	M	  75.0  75.0  9.8

15	16	C	5.0	H	  8.8  8.2  6.5

17	21	E	5.0	H	  2.6  1.8  1.4

22	25	C	4.5	M	  4.5  8.6  5.8

26	30	E	4.4	M	  3.0  18.4  5.6

31	38	C	4.6	H	  3.9  30.4  6.1

39	41	-	4.0	M	  8.0  75.0  75.0

42	47	C	4.5	M	  4.2  4.9  39.8

48	51	E	4.5	M	  0.8  1.0  4.8

52	55	C	4.5	M	  5.0  7.4  8.4

56	60	E	4.0	M	  2.4  2.0  21.5

62	75	H	5.0	H	  4.7  5.4  6.9

76	78	C	4.0	M	  6.3  6.3  8.0

81	91	-	4.0	M	  7.0  75.0  75.0

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