Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
_____________________________________________

>P1;d1syxb-
---------CCEEEEECCCCCCCCCEEEEEHHHHHHHHHCCCCCCCCEEEECCCCCCCCEEHHHCCHHHHC

>P1;d1wh2a1
CCCCCCCCCCCCEEEECC---CCCEEEEECHHHHHHHHHCCCCCCCCEEEECCCCHHHCEEHHHH-CCC--
PSA

>P1;d1syxb-
---------b3401105756ba2834962508503523759606a0030243978c071640591607737

>P1;d1wh2a1
da9782658655020417---9574313200650563195970798140012c484a50440550-286--


Translating the sequences
---------CCEEEEECC***CCC*EEEEEHHHHHHHHHCCCCCCCCEEEECCCC***CEEHHH**HHH**
*********CC*EEEECC---CCCEEEEE*HHHHHHHHHCCCCCCCCEEEECCCCHHHCEEHHHH-***--

55277.tem
_________________________________
---------CCEEEEECC---CCCEEEEEEHHHHHHHHHCCCCCCCCEEEECCCCHHHCEEHHHH-HHH--




Structural block scores
0	8	-	3.0	P	  75.0  7.7

9	10	C	5.0	H	  7.2  5.5

11	15	E	4.6	H	  1.2  2.2

16	17	C	5.0	H	  6.0  4.0

18	20	-	3.0	P	  7.5  75.0

21	23	C	5.0	H	  6.8  7.0

24	29	E	4.3	M	  4.8  2.2

30	38	H	5.0	H	  3.7  3.9

39	46	C	5.0	H	  4.6  5.8

47	50	E	5.0	H	  2.2  1.2

51	54	C	5.0	H	  6.8  6.6

55	57	H	3.0	P	  6.5  6.5

59	60	E	5.0	H	  5.0  4.0

61	64	H	4.5	M	  3.8  2.5

66	68	H	3.0	P	  4.7  5.3

69	70	-	3.0	P	  5.0  75.0

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