Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
_____________________________________________

>P1;d1j8ea-
CCCCCC-CCEEECC--CCCEEEHHHCCCCCCCCCCCHHHCHHHHCCC

>P1;d1v9u5-
----CCCCCC-CCCCCCCCCCCHHHCCCCCCCCCCCHHHC--CCCC-

>P1;d1xfea2
CCCCCCCCCEEECC--CCCEEECCCCCCCCCCCCCCCCCCCCCCC--

>P1;d2fcwb1
--CCCC-CCEEECC--CCCEEEHHHCCCCCCCCCCCCCCC--CCC-C

>P1;d2gtlm2
--CCCC--CEEECCCCCCCEEEHHHCCCCCCCCCCCCCCCHHHHC--
PSA

>P1;d1j8ea-
db9607-a732609--667204595124a742094600049823686

>P1;d1v9u5-
----489974-6041a78902368473397720a546116--b2cc-

>P1;d1xfea2
c98b0a29742507--576334573434a76007443003a971d--

>P1;d2fcwb1
--7a06-b623607--437013785344976209421028--927-a

>P1;d2gtlm2
--8a0a--9353053b57211459413499830750102599029--


Translating the sequences
**CCCC-CCEEECC--CCCEEEHHHCCCCCCCCCCC***C****C**
----CC*CC*-*CC**CCC***HHHCCCCCCCCCCC***C--CCC*-
**CCCC*CCEEECC--CCCEEE***CCCCCCCCCCCCCCC**CCC--
--CCCC-CCEEECC--CCCEEEHHHCCCCCCCCCCCCCCC--CCC-*
--CCCC--CEEECC**CCCEEEHHHCCCCCCCCCCCCCCC****C--

57424.tem
_________________________________
--CCCC-CCEEECC--CCCEEEHHHCCCCCCCCCCCCCCC**CCC--




Structural block scores
0	1	-	3.8	M	  12.5  75.0  10.8  75.0  75.0

2	5	C	4.8	H	  5.5  40.5  7.5  5.9  7.2

7	8	C	4.8	H	  8.8  8.0  8.0  8.8  42.0

9	11	E	4.5	M	  3.7  28.3  3.7  3.7  3.7

12	13	C	5.0	H	  4.5  2.0  3.5  3.5  2.5

14	15	-	3.8	M	  75.0  5.8  75.0  75.0  7.2

16	18	C	5.0	H	  6.3  8.0  6.0  4.7  4.7

19	21	E	4.5	M	  2.0  1.7  3.3  1.3  2.0

22	24	H	4.5	M	  6.3  6.0  5.0  6.7  6.0

25	39	C	4.8	H	  3.6  4.8  3.7  4.1  3.8

40	41	*	3.0	P	  8.5  75.0  9.8  75.0  9.0

42	44	C	4.2	M	  3.7  8.7  7.2  6.0  3.7

45	46	-	3.8	M	  7.0  43.8  75.0  42.8  75.0

>>>>>>