Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
_____________________________________________

>P1;d2ekna-
CCCCCCCCCCCCEEEEEEEEEEEECCHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCEEEEEEEEEEC--CCEEEEEEEEEEEECCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEEEEEEEEEC------

>P1;d3jqka-
CCCCCCCCCCCCEEEEEEEEEEEECCHHHHHHHHHC---CCCHHHHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEEEEECCCCEEEEEEEEEEEECCCCHHHHHHHHHHHHHHHHHHHCCCCC-------CCEEEEEEEEEEECCCCCCEEC
PSA

>P1;d2ekna-
d8948816837502020103020202570062056960746902540473046005602654841170615306070622--84201010202062220034002100430061025104620319767345051462423533557------

>P1;d3jqka-
97746819a685571102000004057700450375---784028503720350066029548512607056070503126a642030302050403220340031004300610350049717-------c07226232221143a866475


Translating the sequences
CCCCCCCCCCCCEEEEEEEEEEEECCHHHHHHHHHC***CCCHHHHHHHHHHHHHHHHHHHCCCCCCCCEEEEEEEEEE*--CCEEEEEEEEEEEECCCCHHHHHHHHHHHHHHHHHHHHHHHC*******CCEEEEEEEEEEEEEC------
CCCCCCCCCCCCEEEEEEEEEEEECCHHHHHHHHHC---CCCHHHHHHHHHHHHHHHHHHHCCCCCCCC**EEEEEEEEE**CCEEEEEEEEEEEECCCCHHHHHHHHHHHHHHHHHHH****C-------CCEEEEEEEEEEE**C******

55040.tem
_________________________________
CCCCCCCCCCCCEEEEEEEEEEEECCHHHHHHHHHC---CCCHHHHHHHHHHHHHHHHHHHCCCCCCCCEEEEEEEEEEE--CCEEEEEEEEEEEECCCCHHHHHHHHHHHHHHHHHHHHHHHC-------CCEEEEEEEEEEEEEC------




Structural block scores
0	11	C	5.0	H	  6.7  6.7

12	23	E	5.0	H	  1.0  1.7

24	25	C	5.0	H	  1.0  2.5

26	34	H	5.0	H	  3.4  3.7

36	38	-	3.0	P	  4.3  75.0

39	41	C	5.0	H	  6.3  6.3

42	60	H	5.0	H	  3.1  3.3

61	68	C	5.0	H	  3.9  4.1

69	79	E	4.5	M	  2.9  2.6

80	81	-	3.0	P	  75.0  8.2

82	83	C	5.0	H	  6.0  5.0

84	95	E	5.0	H	  1.3  1.6

96	99	C	5.0	H	  1.0  1.8

100	122	H	4.7	H	  1.9  2.3

124	130	-	3.0	P	  5.3  75.0

131	132	C	5.0	H	  2.5  6.2

133	145	E	4.7	H	  3.7  2.8

147	152	-	3.0	P	  75.0  6.0

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