Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
_____________________________________________

>P1;d1ei5a1
CCCCCCCCEEEECCCCCCEEEEECC-CCCEEEC-CC----CCEECEEEECCEEECC-----------CCEEEEEC---CEEEEEEHHHCEEEEEC----

>P1;d1ei5a2
CCCCCCCCEEEEECCCCEEEEEEEECCEEEEEEEECCEECCCEECEEEECCEEEEEECCCCCCCCCEEEEEEEECCCCCEEEEEEC-CEEEEEEEECCC
PSA

>P1;d1ei5a1
b5607503a5050992854010462-a103050-2b----842605035944051a-----------5040517b---7604021995b350803----

>P1;d1ei5a2
5a075504020207a6822020337c86030031397973a32406240622020218949a89129424050518a061020108-656636051456


Translating the sequences
CCCCCCCCEEEE*CCCC*EEEEE**-C**EEE*-*C----CCEECEEEECCEEE**-----------**EEEEEC---CEEEEEEH*H*EEEEE*----
CCCCCCCCEEEEECCCCEEEEEEEE*CEEEEEE*EC****CCEECEEEECCEEEEE***********EEEEEEEC***CEEEEEE*-*EEEEEEE****

50886.tem
_________________________________
CCCCCCCCEEEEECCCCEEEEEEEE-CEEEEEE-EC----CCEECEEEECCEEEEE-----------EEEEEEEC---CEEEEEEH-HEEEEEEE----




Structural block scores
0	7	C	5.0	H	  4.7  4.6

8	12	E	4.6	H	  4.1  0.8

13	16	C	5.0	H	  7.0  7.9

17	24	E	4.2	M	  2.8  2.4

27	32	E	4.0	M	  1.5  2.0

36	39	-	3.0	P	  75.0  6.5

40	41	C	5.0	H	  6.0  6.8

42	43	E	5.0	H	  4.0  3.0

45	48	E	5.0	H	  3.2  3.0

49	50	C	5.0	H	  6.5  4.0

51	55	E	4.2	M	  4.1  1.2

56	66	-	3.0	P	  75.0  6.4

67	73	E	4.4	M	  3.1  2.9

75	77	-	3.0	P	  75.0  6.2

79	84	E	5.0	H	  2.2  0.7

88	94	E	4.4	M	  4.4  4.4

95	98	-	3.0	P	  75.0  4.0

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