Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
_____________________________________________

>P1;d1bxya-
CCEEEEEECCCCCCCCHHHHHHHHHHCCCCCCCEEEEECCHHHHHHHHHCCCCEEEEEEC------------------------------------------------------------------------------------------------

>P1;d1vq8w1
--CEEEEECCCCCCCCHHHHHHHHHCCCCCCCEEEEECCCHHHHHHHHHCHHHEEEECCCHHHHHHHHHHHCCCCCCCCCCCHHHHHHHCCCCCHHHHHHHHHCCCCCCHHHCCCCCEECCCCCCCCCCCCCCHHHCCCCEECCHHHHHHHHHHCC
PSA

>P1;d1bxya-
8620203025429a2698247007504066571444152579257218507700636848------------------------------------------------------------------------------------------------

>P1;d1vq8w1
--01000003669b088713500470305742100002468847a316404710000505390035005330305aab79066810376082a4146008001437050660702110505614c826739644a6a0001609496017005305


Translating the sequences
**EEEEEECCCCCCCCHHHHHHHHHHCCCCCC*EEEEECCHHHHHHHHHC***EEEEEEC------------------------------------------------------------------------------------------------
--*EEEEECCCCCCCCHHHHHHHHH*CCCCCCEEEEE*CCHHHHHHHHHCHHHEEEE**C************************************************************************************************

55129.tem
_________________________________
--EEEEEECCCCCCCCHHHHHHHHHHCCCCCCEEEEEECCHHHHHHHHHCHHHEEEEEEC------------------------------------------------------------------------------------------------




Structural block scores
0	1	-	3.0	P	  7.0  75.0

2	7	E	4.7	H	  1.2  0.2

8	15	C	5.0	H	  5.1  5.4

16	25	H	4.8	H	  4.2  3.5

26	31	C	5.0	H	  4.7  3.5

32	37	E	4.3	M	  3.2  0.5

38	39	C	5.0	H	  3.5  5.0

40	48	H	5.0	H	  5.1  5.7

50	52	H	3.0	P	  4.7  4.0

53	58	E	4.3	M	  4.5  0.8

60	155	-	3.0	P	  75.0  3.9

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