Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
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>P1;d1ln4a1
CCCCHHHHHHHHHHHCCCCCCEEECCCCCCHHHHHHHHHHHHHHCEEEEEECCCCHHHHHHHHHHHHHHHCCEEEEEECCEEEEECCCCC-CCCCCCC

>P1;d1rq8a-
C-CCHHHHHHHHHHHHHCCEEEEECCCCCCHHHHHHHHHHHHHCCEEEEEECCCCHHHHHHHHHHHHHHCCEEEEEECCCEEEEEECCCCCCCCCCC-
PSA

>P1;d1ln4a1
39178822640493096493407057a316ab1276047105740001040318678414710520276080040505c310000122b8-5327028

>P1;d1rq8a-
5-07872374046506c292207056a3086a2268058306b6200003043a979407800870184080320422922000004699e5a1704-


Translating the sequences
C*CCHHHHHHHHHHH**CC**EEECCCCCCHHHHHHHHHHHHHHCEEEEEECCCCHHHHHHHHHHHHHHHC*EEEEEECCEEEEE*CCCC-CCCCCC*
C-CCHHHHHHHHHHHHHCCEEEEECCCCCCHHHHHHHHHHHHH*CEEEEEECCCCHHHHHHHHHHHHHH*CEEEEEE*CCEEEEEECCCC*CCCCCC-

75471.tem
_________________________________
C-CCHHHHHHHHHHHHHCCEEEEECCCCCCHHHHHHHHHHHHHHCEEEEEECCCCHHHHHHHHHHHHHHHCEEEEEEECCEEEEEECCCC-CCCCCC-




Structural block scores
2	3	C	5.0	H	  4.0  3.5

4	16	H	4.7	H	  4.7  5.0

17	18	C	5.0	H	  6.5  5.5

19	23	E	4.2	M	  2.8  2.2

24	29	C	5.0	H	  5.4  5.4

30	43	H	4.9	H	  4.7  5.3

45	50	E	5.0	H	  0.8  0.5

51	54	C	5.0	H	  4.5  6.6

55	69	H	4.9	H	  3.6  4.2

71	77	E	4.4	M	  2.0  1.9

78	79	C	5.0	H	  7.8  5.5

80	85	E	4.7	H	  0.3  0.3

86	89	C	5.0	H	  5.9  7.0

91	96	C	5.0	H	  3.2  4.6

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