Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
_____________________________________________

>P1;d2hg4a4
--------CCEEEEEEECCCCCCHHHHHHHHHHHHCCCCCHHHHHHHHHHCCCCC----CEEEEEEECHHHHHHHHHHHHCCCCCCCEEEEECC---C

>P1;d2vz8a5
CCCCCCCCCCEEEEEEECCH---HHHHHHHHHHHCCCC--CHHHHHHHHHHHCCCCCCCCEEEEEEECC-------CC-------CCEEEEECCCCCC
PSA

>P1;d2hg4a4
--------a51604001776a5374057105503746955188106514467665----52404040528701700400163694a60868629---c

>P1;d2vz8a5
a9585169733505001667---840463063046539--52930881396084628732231403086-------b4-------c4371872669a7


Translating the sequences
--------CCEEEEEEECC****HHHHHHHHHHHHCCC**HHHHHHHHHH**CCC----CEEEEEEECH*******HH*******CCEEEEECC---C
********CCEEEEEEECCH---HHHHHHHHHHH*CCC--*HHHHHHHHHHHCCC****CEEEEEEEC*-------**-------CCEEEEECC***C

310590.tem
_________________________________
--------CCEEEEEEECCH---HHHHHHHHHHHHCCC--HHHHHHHHHHHHCCC----CEEEEEEECH-------HH-------CCEEEEECC---C




Structural block scores
0	7	-	3.0	P	  75.0  6.7

8	9	C	5.0	H	  7.8  5.0

10	16	E	5.0	H	  1.7  2.0

17	18	C	5.0	H	  7.0  6.0

20	22	-	3.0	P	  6.2  75.0

23	34	H	4.8	H	  3.7  3.7

35	37	C	5.0	H	  6.3  5.7

38	39	-	3.0	P	  5.0  75.0

40	51	H	4.5	M	  4.2  4.5

52	54	C	5.0	H	  5.7  6.0

55	58	-	3.0	P	  75.0  5.0

60	66	E	5.0	H	  2.0  1.9

69	75	-	3.0	P	  3.3  75.0

76	77	H	3.0	P	  2.0  7.8

78	84	-	3.0	P	  4.1  75.0

85	86	C	5.0	H	  8.2  8.2

87	91	E	5.0	H	  5.6  5.2

92	93	C	5.0	H	  5.5  4.0

94	96	-	3.0	P	  75.0  8.5

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