Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
_____________________________________________

>P1;d1914a1
--CCCHHHHHHHHHHHHHHCCC--CCEEEEEEECCCC-----EEEEEEECCCC-EEEEEECCHHHHHHHHHHHHHHHHHHHCCCCCCC

>P1;d1914a2
CCEECHHHHHHHHHHHHHHCCCCCCCEEEEEEECCCCCCCCCEEEEEEECCCC-EEEEEEE-CCCHHHHHHHHHHHHHHHCCCCCC-C

>P1;d2w9ja-
C-CCCHHHHHHHHHHHHHC------CCEEEEEEC-------CEEEEEEECCCCCEEEEEEE-HHHHHHHHHHHHHCCCCCC-------
PSA

>P1;d1914a1
--38517501630491057549--7050436658848-----51103002785-51316176a80683066023406644869ab9ac

>P1;d1914a2
366192960161036016605a98708176885cc8a9887923204020983-5000102-7944a906861581287265a999-9

>P1;d2w9ja-
b-53829501640130269------c2837675b-------813202051cb385010207-6a53a60484256278299-------


Translating the sequences
--CCCHHHHHHHHHHHHHHCCC--CCEEEEEEECCCC-----EEEEEEECCCC-EEEEEE**HHHHHHHHHHHHHHHHHH*CCCCC*C
C***CHHHHHHHHHHHHHHCCC**CCEEEEEEECCCC****CEEEEEEECCCC-EEEEEEE-***HHHHHHHHHHHHHHHCCCCCC-C
C-CCCHHHHHHHHHHHHH*------C*EEEEEEC-------CEEEEEEECCCC*EEEEEEE-HHHHHHHHHHHHH*****C-------

54762.tem
_________________________________
C-CCCHHHHHHHHHHHHHHCCC--CCEEEEEEECCCC----CEEEEEEECCCC-EEEEEEE-HHHHHHHHHHHHHHHHHHCCCCCC-C




Structural block scores
2	4	C	4.3	M	  5.3  5.3  5.3

5	18	H	4.9	H	  3.5  3.4  3.4

19	21	C	4.0	M	  6.0  5.2  75.0

22	23	-	4.0	M	  75.0  8.5  75.0

24	25	C	4.5	M	  3.5  3.5  43.8

26	32	E	4.9	H	  4.1  6.1  5.4

33	36	C	4.2	M	  7.0  10.9  59.1

37	40	-	4.0	M	  75.0  8.0  75.0

42	48	E	5.0	H	  1.4  1.9  1.9

49	52	C	5.0	H	  5.5  5.0  7.0

54	60	E	4.9	H	  3.4  1.1  2.1

62	79	H	4.6	H	  4.2  5.4  5.4

80	85	C	4.0	M	  9.0  8.1  64.0

>>>>>>