Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
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>P1;d1mlaa2
CCEEEEEEECCCHHHHHHHHHHHCCCCCEEEEEEEECCEEEEEEEHHHHHHHHHHHHHCCCCEEEECCCC

>P1;d1nm2a2
-CEEEEEEEECCHHHHHHHHHHC----CCEEEEEEECCEEEEEEEHHHHHHHHHCCCC-CEEEEEECC--

>P1;d2hg4a5
---CEEEE-CCCHHHHHHHHHHHC-C-CEEEEEEEECCEEEEEECCCHHHHHHHHHHHHCC-CEECCCCC
PSA

>P1;d1mlaa2
a932301034075820570087037c27051355469450002334500730183068590662683957

>P1;d1nm2a2
-a664030441639602710471----70723465a9570002556a3065068720a-a0770463a--

>P1;d2hg4a5
---52050-0035a5057208519-a-2071456659750205475720560173066582-7085486b


Translating the sequences
*CEEEEEEECCCHHHHHHHHHHHC*C*CEEEEEEEECCEEEEEEEHHHHHHHHHHHHH*CC*EEEECCCC
-CEEEEEEE*CCHHHHHHHHHH*----C*EEEEEEECCEEEEEEEHHHHHHHHH****-C**EEEECC--
---*EEEE-CCCHHHHHHHHHHHC-C-CEEEEEEEECCEEEEEE***HHHHHHHHHHH*CC-*EE*CCCC

55048.tem
_________________________________
-CEEEEEEECCCHHHHHHHHHHHC-C-CEEEEEEEECCEEEEEEEHHHHHHHHHHHHH*CC*EEEECCCC




Structural block scores
2	8	E	4.6	H	  1.7  3.3  23.1

9	11	C	4.7	H	  3.7  3.7  1.0

12	22	H	4.9	H	  3.8  3.6  4.4

28	35	E	4.9	H	  3.6  4.7  4.2

36	37	C	5.0	H	  6.5  7.0  8.0

38	44	E	4.9	H	  1.9  2.7  3.3

45	57	H	4.5	M	  3.5  4.9  3.7

59	60	C	4.5	M	  4.5  5.2  5.0

62	65	E	4.5	M	  5.5  4.2  5.0

66	69	C	4.5	M	  6.0  40.9  7.4

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