Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
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>P1;d1ataa-
CCCCCCCCCCEEECCCC-CCCCCC-CCCCCCCCCCCCCEEECCCCCCEEEECC--CEEEECCCCCC

>P1;d1ccva-
--CCC-CCCEEEEEEECCCCCCCC-CCCCCCCCCCCEEEEEEC--CCCEEECC--CEEECHHHC--

>P1;d1eaic-
CCCCC-CCCCEEECCCC-CCCCCCCCCCCCCCCCCCCCEEECCHHHCEEECCC--CCEEEHHHCC-

>P1;d1hx2a-
--CCCCCCCEEEECCCCCCCCCCCCCCCCCCCCCCCCCEEEEC--CCCEECCCCCCCEECCCCC--
PSA

>P1;d1ataa-
b6a91b87156318402-210449-648472c8946858430219341042aa--770354a516c

>P1;d1ccva-
--9b0-585143386024422319-75756647a943722304--b81153d9--740453a96--

>P1;d1eaic-
55b80-79514328516-34252937aa5846a953a3421022c582223b7--760244971b-

>P1;d1hx2a-
--96a13721521850172200263593740087752840004--7400046882750443863--


Translating the sequences
**CCC*CCC*EEECCCC-CCCCCC-CCCCCCCCCCCCCEEE*C**CC*EE*CC--C*EE****C**
--CCC-CCC*EEE***C*CCCCCC-CCCCCCCCCCC**EEE*C--CC*EE*CC--C*EE****C--
**CCC-CCC*EEECCCC-CCCCCC*CCCCCCCCCCCCCEEE*C***C*EE*CC--C*EE****C*-
--CCC*CCC*EEECCCC*CCCCCC*CCCCCCCCCCCCCEEE*C--CC*EE*CC**C*EE****C--

57567.tem
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**CCC*CCC*EEECCCC*CCCCCC*CCCCCCCCCCCCCEEE*C**CC*EE*CC--C*EE****C*-




Structural block scores
0	1	*	3.5	M	  8.8  75.0  5.0  75.0

2	4	C	5.0	H	  6.8  6.8  6.5  8.5

6	8	C	5.0	H	  5.3  6.0  7.0  4.0

10	12	E	5.0	H	  3.3  3.3  3.0  2.7

13	16	C	4.5	M	  3.5  4.0  5.0  3.5

18	23	C	5.0	H	  3.3  3.5  4.2  2.0

25	37	C	4.9	H	  6.4  6.2  7.1  5.0

38	40	E	5.0	H	  5.0  2.3  2.3  1.3

43	44	*	3.5	M	  5.0  75.0  7.2  75.0

45	46	C	4.7	H	  3.5  9.8  6.5  5.5

48	49	E	5.0	H	  2.0  3.0  2.0  0.0

51	52	C	5.0	H	  10.5  11.2  9.2  7.0

53	54	-	4.3	M	  75.0  75.0  75.0  5.0

57	58	E	5.0	H	  1.5  2.0  1.0  2.0

59	62	*	1.0	P	  6.1  6.9  6.0  5.2

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