Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
_____________________________________________

>P1;d1ig0a1
CEEEEEECCCCEEEECCHHHHHHHEEEEEEECCCCCEEEEEEECCCCCCEEEEECCCCCCCEEEECCCCCCEEEEEECCCEEEEEEECHHHHHHHC

>P1;d1ig3a1
CEEEEEECCEEEEEECCCC---CEEEEEEEECCCCCEEEEEEECCCCCCCCEEECCCC-CCEEEECCCCCCEEEEEECCCEEEEEEECC-------
PSA

>P1;d1ig0a1
925644085613417074621630024000206b7503042072046426825016a68412780404496303020534020203056a428728

>P1;d1ig3a1
754664073872616077b---712a4000106a5507604070066308844006c6-511680315a6430204043302011056b-------


Translating the sequences
CEEEEEECC**EEEECCHH***H*EEEEEEECCCCCEEEEEEECCCCCCEEEEECCCC*CCEEEECCCCCCEEEEEECCCEEEEEEECH*******
CEEEEEECCEEEEEECC**---*EEEEEEEECCCCCEEEEEEECCCCCC**EEECCCC-CCEEEECCCCCCEEEEEECCCEEEEEEEC*-------

63862.tem
_________________________________
CEEEEEECCEEEEEECCHH---HEEEEEEEECCCCCEEEEEEECCCCCCEEEEECCCC-CCEEEECCCCCCEEEEEECCCEEEEEEECH-------




Structural block scores
1	6	E	5.0	H	  3.5  4.2

7	8	C	5.0	H	  6.5  5.0

9	14	E	4.3	M	  3.7  5.0

15	16	C	5.0	H	  3.5  3.5

17	18	H	3.0	P	  5.0  9.2

19	21	-	3.0	P	  3.0  75.0

23	30	E	4.8	H	  1.0  2.3

31	35	C	5.0	H	  5.9  5.3

36	42	E	5.0	H	  2.3  3.4

43	48	C	5.0	H	  3.0  2.5

49	53	E	4.2	M	  4.2  4.8

54	57	C	5.0	H	  5.9  6.1

59	60	C	5.0	H	  2.5  3.0

61	64	E	5.0	H	  4.2  3.8

65	70	C	5.0	H	  4.5  4.9

71	76	E	5.0	H	  1.3  1.5

77	79	C	5.0	H	  4.0  3.3

80	86	E	5.0	H	  1.0  1.3

89	95	-	3.0	P	  5.9  75.0

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