Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
_____________________________________________

>P1;d1k28a1
--CCCCEEEEEEEEC---CCCCCCCCEEEEEC-CCCCCCCCCCCCCCCCHHHCCEEEECCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCCCEEEEEECCCEECCCCCCCCCCCCCCCCCCCCCEECC

>P1;d2p5zx1
CCCCCCCEEEEECCCCCCCCC-CCCCEEEECCCCCCC-----------CCCCEEEECC-------------------CCCCEEEEEEHHHCCCCEEEEEEC-----------------------------
PSA

>P1;d1k28a1
--aa65703000024---80669602010005-a311341a67b95022175061061527b706679c729848a132123040203258377020284456518953757502002745225758549

>P1;d2p5zx1
66839b4440503198a0444-a6232203034b938-----------8a82233069-------------------709230102068231741513365-----------------------------


Translating the sequences
--CCCCEEEEEEEEC---CCC*CCCCEEEEEC-CCCC***********CHHH**EEEE*******************CCCCEEEEEE***CCCCEEEEEEC*****************************
**CCCC*EEEEE**C***CCC-CCCCEEEE*C*CCCC-----------C***EEEE**-------------------CCCCEEEEEEHHHCCCCEEEEEEC-----------------------------

69255.tem
_________________________________
--CCCCEEEEEEEEC---CCC-CCCCEEEEEC-CCCC-----------CHHHEEEEEE-------------------CCCCEEEEEEHHHCCCCEEEEEEC-----------------------------




Structural block scores
0	1	-	3.0	P	  75.0  6.0

2	5	C	5.0	H	  8.0  7.9

6	13	E	4.2	M	  1.5  2.6

15	17	-	3.0	P	  75.0  6.2

18	20	C	5.0	H	  4.7  4.0

22	25	C	5.0	H	  4.2  5.4

26	30	E	4.6	H	  0.2  1.4

33	36	C	5.0	H	  3.9  7.9

37	47	-	3.0	P	  5.4  75.0

49	51	H	3.0	P	  4.3  6.8

52	57	E	3.7	M	  2.3  3.8

58	76	-	3.0	P	  6.4  75.0

77	80	C	5.0	H	  2.0  4.5

81	86	E	5.0	H	  1.5  1.0

87	89	H	3.0	P	  3.3  5.3

90	93	C	5.0	H	  6.2  3.8

94	99	E	5.0	H	  2.7  3.2

101	129	-	3.0	P	  4.6  75.0

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