Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
_____________________________________________

>P1;d2vy6a2
--CCCCCCCCEEEEEECCHHHCCCEEHHHHHHCCCCCEEEEEEECCEEEEEEECCCCC--------------

>P1;d5d9ac1
CCCHHHHCCCEEECC--CCCCCCCCCHHHHHCCCCCCCEEEECCCCCEEEEEECCCCCCCCHHHHHHHHHHC
PSA

>P1;d2vy6a2
--567a41a702028943983590255a6089086153000619ab6111022278a8--------------

>P1;d5d9ac1
996557814806447--883a07516575069288663040439a773501314788748a67787868789


Translating the sequences
--C****CCCEEEEE**CHHHCCCEEHHHHHHCCCCCEEEEEEECCEEEEEEECCCCC--------------
**CHHHHCCCEEE**--C***CCC**HHHHH*CCCCC*EEEE**CC*EEEEEECCCCC**************

160453.tem
_________________________________
--CHHHHCCCEEEEE--CHHHCCCEEHHHHHHCCCCCEEEEEEECCEEEEEEECCCCC--------------




Structural block scores
0	1	-	3.0	P	  75.0  9.0

3	6	H	3.0	P	  6.9  6.2

7	9	C	5.0	H	  6.2  4.3

10	14	E	4.2	M	  2.4  4.2

15	16	-	3.0	P	  6.5  75.0

18	20	H	3.0	P	  6.7  7.2

21	23	C	5.0	H	  4.7  4.0

24	25	E	3.0	P	  3.5  3.5

26	31	H	4.7	H	  6.4  5.3

32	36	C	5.0	H	  4.0  6.0

37	43	E	4.1	M	  2.7  3.3

44	45	C	5.0	H	  11.0  8.8

46	52	E	4.7	H	  1.9  2.9

53	57	C	5.0	H	  7.1  6.8

58	71	-	3.0	P	  75.0  7.4

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