Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
_____________________________________________

>P1;d1d1ra1
------------------------CC-CCCCEEEEECCCCCCCCEEEEECCCCCHHHHHHHHHHHHHCCCCCCEEEC-----CEEEEECCCHHHHHHHHHHHCC----CCCCCCC

>P1;d2if1a1
CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC-CCCCCEECCC-CCCCCCHHHHHHHHHHCCCCEEEECCCCCCCEEEECCCCHHHHHHHHHHCCCCCHHHCCCCCC
PSA

>P1;d1d1ra1
------------------------b9-70404054836daab7020304b0638995067106505881b9046295-----7602178463a60572086481----816329c

>P1;d2if1a1
9b989d99a9778599a8c7bb9898a7a304050237b9-6501000230-66a276850153038418280644728717500103561365016005319007772232406


Translating the sequences
------------------------CC-CCCCEEEEECCCC*CCCEEEEECC*CCHHHHHHHHHHHHH*CCCC*EEEC-----CEEEEECCCHHHHHHHHHHHCC----*CCCCCC
************************CC*CCCC*****CCCC-CCC**EE*CC-CC****HHHHHHHHHHCCCCEEEEC*****CEEEE*CCCHHHHHHHHHH*CC****HCCCCCC

55159.tem
_________________________________
------------------------CC-CCCCEEEEECCCC-CCCEEEEECC-CCHHHHHHHHHHHHHHCCCCEEEEC-----CEEEEECCCHHHHHHHHHHHCC----HCCCCCC




Structural block scores
0	23	-	3.0	P	  75.0  9.2

24	25	C	5.0	H	  10.2  8.5

27	30	C	5.0	H	  2.8  5.1

31	35	E	3.0	P	  4.2  2.2

36	39	C	5.0	H	  8.2  7.6

41	43	C	5.0	H	  6.2  3.7

44	48	E	3.8	M	  1.8  0.6

49	50	C	5.0	H	  5.8  1.5

52	53	C	5.0	H	  5.5  6.0

54	67	H	4.3	M	  4.9  4.5

68	71	C	5.0	H	  5.4  4.8

72	75	E	4.5	M	  5.2  3.5

77	81	-	3.0	P	  75.0  5.0

83	87	E	4.6	H	  3.2  0.8

88	90	C	5.0	H	  6.0  4.0

91	101	H	4.8	H	  4.7  2.7

102	103	C	5.0	H	  4.5  4.5

104	107	-	3.0	P	  75.0  5.2

109	114	C	5.0	H	  5.6  2.8

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