Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
_____________________________________________

>P1;d1wfea1
-------------------------------CCCCCCCCCCCCCCCCCCEECCCCCCCCEEC--CCEECCCCCCEECHHHCCCCCCCCC------CCCCCCCCCCCCCCCCC

>P1;d1wffa1
CCCCCCCCCCCCCCCCC-------------------------------CCCCCC--CCCCCCCCCCEECC-CCCEECCCCCCHHHHCCCCCCCCCCCCCCCCCCC------C

>P1;d1wfpa1
-----------------CCCCCCCCCCCCCC--------------CCCCCCCCC--CCCCCCC-CCEECC-CCCEECCCCCCCCCCCCCCCCCCCC----------------
PSA

>P1;d1wfea1
-------------------------------ba8bb9a8a78a97a675380328a0b5618--7135074085100582472840806------53b79778b799aa9c9

>P1;d1wffa1
da9a599989999699a-------------------------------935074--536706c9503805-186200582461620a0c5a49638886b6aab9------c

>P1;d1wfpa1
-----------------ba98b85107b946--------------a19343024--356707b-904705-180200583454940b0b5a299a8----------------


Translating the sequences
-------------------------------**************CCCC**CCC**CCC**C--CCEECC*CCCEEC***CCCCCCCCC------CCCCCCCCCC******C
*****************-------------------------------CCCCCC--CCCCCCC*CCEECC-CCCEECCCCCC****CCCCCCCCCCCCCCCCCCC------C
-----------------**************--------------CCCCCCCCC--CCCCCCC-CCEECC-CCCEECCCCCCCCCCCCCCCCCCCC----------------

118310.tem
_________________________________
---------------------------------------------CCCCCCCCC--CCCCCCC-CCEECC-CCCEECCCCCCCCCCCCCCCCCCCCCCCCCCCCC------C




Structural block scores
0	44	-	4.0	M	  54.6  50.1  53.9

45	53	C	4.4	M	  4.9  28.1  4.1

54	55	-	4.0	M	  9.2  75.0  75.0

56	62	C	4.6	H	  15.2  5.6  5.6

64	65	C	5.0	H	  4.0  2.5  4.5

66	67	E	5.0	H	  4.0  5.5  5.5

68	69	C	5.0	H	  3.5  2.5  2.5

71	73	C	5.0	H	  4.3  5.0  3.0

74	75	E	5.0	H	  0.5  1.0  1.0

76	104	C	4.2	M	  20.0  6.3  27.4

105	110	-	4.0	M	  10.1  75.0  75.0

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