Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
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>P1;d1dq3a2
CCCEECCCHHHHHHHHHCCC-CEEEEEC---CEEEEEEC-CEEEECCCHHHHCCEEHHHHHHHHHHHHHHHCCHHHHHHHHHHC

>P1;d1whza-
----CCCCHHHHHHHHHHCC-CEECCCC---CEEEEECCCCCEEEEE--CCCCCCCHHHHHHHHHHC---CCCHHHHHHC----

>P1;d2hjja1
----CCCCHHHHHHHHHHCCCEEEECCCCCCCEEEEECCCCCEEEEECCC-----CCCHHHHHHHHHHCCCCCCC---------
PSA

>P1;d1dq3a2
cc82264809814820671a-070558c---54010109-a5515085023554014530270064027226576038305814

>P1;d1whza-
----3316063004004638-054649b---7414021768340401--066c6075a105300740---8074860681----

>P1;d2hjja1
----251849807742a319005154594a50300022773755552315-----476027308911891426b9---------


Translating the sequences
*****CCCHHHHHHHHH*CC-CEEE**C---CEEEEE*C-C*EEE**C****CC**HHHHHHHHHHHH***CCHHHHHH*****
----CCCCHHHHHHHHHHCC-CEE*CCC---CEEEEECCCCCEEEEE--C**CC*CHHHHHHHHHH*---CCCHHHHHH*----
----CCCCHHHHHHHHHHCC**EEECCC***CEEEEECCCCCEEEEEC*C-----C**HHHHHHHHHH**CCC**---------

54786.tem
_________________________________
----CCCCHHHHHHHHHHCC-CEEECCC---CEEEEECCCCCEEEEEC*C**CC*CHHHHHHHHHHHH**CCCHHHHHH*----




Structural block scores
0	3	-	4.0	M	  8.8  75.0  75.0

4	7	C	4.8	H	  5.0  3.2  4.0

8	17	H	4.9	H	  4.5  2.3  5.5

18	19	C	5.0	H	  5.8  5.5  5.0

22	24	E	4.7	H	  4.0  5.0  3.7

25	27	C	4.3	M	  8.5  8.2  6.0

28	30	-	4.0	M	  75.0  75.0  6.5

32	36	E	5.0	H	  1.2  2.2  1.0

37	41	C	4.4	M	  19.9  5.0  5.2

42	46	E	4.6	H	  3.8  1.8  4.4

50	51	*	2.7	P	  4.0  6.0  75.0

52	53	C	4.0	M	  4.5  9.2  75.0

56	67	H	4.7	H	  2.8  9.2  4.3

68	69	*	2.7	P	  4.5  75.0  5.0

70	72	C	4.7	H	  4.3  5.0  4.0

73	78	H	4.0	M	  4.5  5.3  53.4

80	83	-	4.0	M	  4.5  75.0  75.0

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