Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
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>P1;d1q8ka2
CCEEEEEEECEEECCCCCCHHHHHHHHHHHHCCC---CCC-CEEEEEEECCEEEEEEEECCHHHHHHHHHHHHHHHHHHHHCCCEEECCCCCCEEECCHHHHCCHHHHCCHHHCCCCCCCC

>P1;d2qn6b-
-CEEEEEEEEEEECCCCCHHHHHHHHHHHHCCHHHHCCCEEEEEEEECCCCEEEEEEEECCHHHHHHHHHHHHHHHHHHHHHCCEEEEEC-------------------------------
PSA

>P1;d1q8ka2
a11604000204076860780276016102b317---ad1-70809563754030203077596015106900540464048690508465625142a858878859a59b689aa6b7b9

>P1;d2qn6b-
-735323302060c2874761163017503760675192047070463a53513000106568305501930173037108638090652-------------------------------


Translating the sequences
*CEEEEEEE*EEECCCCC*HHHHHHHHHHHHC**---CC*-*EEEEEEECCEEEEEEEECCHHHHHHHHHHHHHHHHHHHH*CCEEE**C*******************************
-CEEEEEEEEEEECCCCCHHHHHHHHHHHH*CHH***CCE*EEEEEE**CCEEEEEEEECCHHHHHHHHHHHHHHHHHHHHHCCEEEEEC-------------------------------

110993.tem
_________________________________
-CEEEEEEEEEEECCCCCHHHHHHHHHHHHHCHH---CCE-EEEEEEEECCEEEEEEEECCHHHHHHHHHHHHHHHHHHHHHCCEEEEEC-------------------------------




Structural block scores
2	12	E	4.8	H	  1.5  2.5

13	17	C	5.0	H	  5.4  6.7

18	30	H	4.7	H	  4.0  3.6

32	33	H	3.0	P	  4.0  3.0

34	36	-	3.0	P	  75.0  4.3

37	38	C	5.0	H	  12.0  5.5

41	48	E	4.2	M	  4.8  4.7

49	50	C	5.0	H	  6.0  4.0

51	58	E	5.0	H	  1.5  1.2

59	60	C	5.0	H	  7.0  5.5

61	81	H	4.9	H	  3.7  3.6

82	83	C	5.0	H	  7.5  5.5

84	88	E	4.2	M	  3.4  4.0

90	120	-	3.0	P	  7.3  75.0

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