Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
_____________________________________________

>P1;d2rcfa1
CEEEEEEEECCCCCCCCCCCC--CCEEEEECCCCCC----CEEEEECCCCCCCCEEEEEECCHHHHHCCCCCCCCCEEEEEECCCCCC--------

>P1;d4jw0a-
CEEEEEEEEECCCCCCHHHCCCCEEEEEEECC-CCCEEEEEEEEEECCCCCCCCEEEEEEHHHHHHCCCCCCCCCCEEEEEECCEEEECCEEEEEC

>P1;d5l37a-
CEEEEEEEEECCCCCCCCCCC--CEEEEEEECCCCC----EEEEEECCCCCCCCEEEEEECHHHHHCCCCCCCCCCEEEEEECC------------

>P1;d6jy5a-
CEEEEEEEECCCCCCCHHHCC--CCEEEEECC-CCC----EEEEECCCCCCCCCEEEEEECHHHHH----CCCCCCEEEEEECC------------
PSA

>P1;d2rcfa1
56702025529a3b37b619a--3510001576b19----55300013908562203013a97046207688121910034336598b--------

>P1;d4jw0a-
5520205354949c277517a05104030024-40854876230108490977200301385404759a06a25080003520762648c673264

>P1;d5l37a-
646020255493aa48ba02b--461120303c657----42400025a0a7846030148a7018619aa704080004552c------------

>P1;d6jy5a-
686040546394a9268725b--261010237-858----44400024906564304037a67036----6526191002334b------------


Translating the sequences
CEEEEEEEE*CCCCCC***CC--C*EEEEECC*CCC----*EEEEECCCCCCCCEEEEEEC*HHHH*CCCCCCCCCEEEEEECC****--------
CEEEEEEEE*CCCCCC***CC****EEEEECC-CCC****EEEEEECCCCCCCCEEEEEE*HHHHH*CCCCCCCCCEEEEEECC************
CEEEEEEEE*CCCCCC***CC--C*EEEEE*C*CCC----EEEEEECCCCCCCCEEEEEECHHHHH*CCCCCCCCCEEEEEECC------------
CEEEEEEEE*CCCCCC***CC--C*EEEEECC-CCC----EEEEE*CCCCCCCCEEEEEECHHHHH----CCCCCCEEEEEECC------------

159133.tem
_________________________________
CEEEEEEEE*CCCCCC***CC--C*EEEEECC*CCC----EEEEEECCCCCCCCEEEEEECHHHHH*CCCCCCCCCEEEEEECC****--------




Structural block scores
1	8	E	5.0	H	  3.4  2.8  3.0  4.1

10	15	C	5.0	H	  7.3  7.2  7.5  6.8

16	18	*	1.0	P	  6.2  4.3  7.3  5.7

19	20	C	5.0	H	  9.8  8.8  6.8  8.2

21	22	-	4.3	M	  75.0  2.5  75.0  75.0

25	29	E	5.0	H	  0.4  1.4  1.4  0.8

30	31	C	4.7	H	  6.0  3.0  1.5  5.0

33	35	C	5.0	H	  7.2  4.0  6.0  7.0

36	39	-	4.3	M	  75.0  6.0  75.0  75.0

40	45	E	4.8	H	  2.2  2.0  1.7  2.0

46	53	C	5.0	H	  4.2  5.8  5.9  4.5

54	59	E	5.0	H	  1.5  1.2  2.3  2.8

61	65	H	4.9	H	  5.2  4.0  5.3  4.4

67	75	C	4.8	H	  4.7  5.7  5.6  28.2

76	81	E	5.0	H	  1.8  1.7  2.3  1.5

82	83	C	5.0	H	  4.5  3.5  7.2  7.8

84	87	*	3.5	M	  8.4  4.5  75.0  75.0

88	95	-	4.3	M	  75.0  6.1  75.0  75.0

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