Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
_____________________________________________

>P1;d1tiga-
--------CCEEEEEECCCCCHHHHHHHHHHHHHHHHCCCEEEEEEECCCCCCCHHHHHHHHHHHHHHHCCCCEEEEEEEEEECCEEEEEEEECCC-

>P1;d2m71a1
------CCCCCEEEEEECCCCHHHHHHHHHHHHHHHCCCCCEEEEEECCCCHHHCCHHHHHHHHHHHHHHCCCEEECCCCEEECCEEEEEEEECC-C

>P1;d6vrja-
CCCCCCCCCCCEEEEECCCCCHHHHHHHHHHHHHHHHHCCCEEEEECCCCCHHHHHHHHHHHHHHHHHHHHCCCEEEEEEEEECCEEEEEEECCCCC
PSA

>P1;d1tiga-
--------a7534070519096850632265036205630303010608a85a515630481045019306720535370546b3201010104c8-

>P1;d2m71a1
------aa87426150325174b406720640243076822030303069a41864820371065027404860554660628b6201020314a-a

>P1;d6vrja-
d39a9b863765514080907a941972163026306821403000418b8697268505510760354057605435737778940202022579c


Translating the sequences
--------CC*EEEEECCCCCHHHHHHHHHHHHHHHHCCC*EEEEEECCCC***HHHHHHHHHHHHHHH*CCCEEEEEEEEEECCEEEEEEEECCC-
------CCCCCEEEEE*CCCCHHHHHHHHHHHHHHH*CCCCEEEEEECCCCHHH**HHHHHHHHHHHHHHCCCEEE****EEECCEEEEEEEECC-C
******CCCCCEEEEECCCCCHHHHHHHHHHHHHHHH*CCCEEEEE*CCCCHHHHHHHHHHHHHHHHHHH*CC*EEEEEEEEECCEEEEEEE*CCCC

55200.tem
_________________________________
------CCCCCEEEEECCCCCHHHHHHHHHHHHHHHHCCCCEEEEEECCCCHHHHHHHHHHHHHHHHHHHCCCEEEEEEEEEECCEEEEEEEECCCC




Structural block scores
0	5	-	4.0	M	  75.0  75.0  9.4

6	10	C	4.4	M	  34.5  8.0  6.0

11	15	E	5.0	H	  2.8  2.8  3.0

16	20	C	4.8	H	  4.8  3.6  4.8

21	36	H	4.9	H	  3.7  3.8  4.3

37	40	C	4.5	M	  3.0  4.5  3.8

41	46	E	4.8	H	  1.7  1.5  1.2

47	50	C	5.0	H	  6.6  6.4  7.1

51	69	H	4.7	H	  3.7  3.6  4.2

70	72	C	4.7	H	  5.0  6.0  6.0

73	82	E	4.5	M	  3.8  4.2  4.8

83	84	C	5.0	H	  7.2  8.8  8.5

85	92	E	4.9	H	  0.6  1.1  1.5

93	96	C	4.5	M	  24.9  25.0  8.4

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