Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
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>P1;d1baza-
C-CCCCCCCCCCHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHC--C---CCCC-------------------------

>P1;d1irqa-
--CCCCCCCCCCHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHCCC---CC---------------------------

>P1;d1mnta-
CCCCCCCCCCCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHCCCCCCCCCCCHHHHCCCCHHHC--------------

>P1;d1x93a1
C---CCCCCCCCHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHC----------------------------------

>P1;d1xrxa1
------CCCCCCHHHHHHHHCCCCCCCCC-HHHHHHCCCC----------------------------------------

>P1;d1y9ba1
CCC-CCCCCCCCHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHC

>P1;d2bsqe1
---CCCCCCCCCHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHCCC---CHHHHHHHHHHHCCCCCCCCCCC------
PSA

>P1;d1baza-
b-a9898a4a3677536715730865a383b40264663664296--8---74c8-------------------------

>P1;d1irqa-
--b9b69b8a47a75477365607677a62473357775662575559---76---------------------------

>P1;d1mnta-
baaa5a8b58077854571365076594a0a5015334655873589837a521276455744776--------------

>P1;d1x93a1
c---9a887a3787857825820984a6328522666657468989----------------------------------

>P1;d1xrxa1
------a98a38ba57871574368ab17-7750554798----------------------------------------

>P1;d1y9ba1
9a9-97778a48894578248418869c63a7346846575674677667777878667877738966a72877778977

>P1;d2bsqe1
---ba8768b4799547725960964b483830364367576879598---78b5567665884a66a99989d------


Translating the sequences
*-**CCCCCCCCHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHH*--*---****-------------------------
--**CCCCCCCCHHHHHHHHHHHHH*CCCHHHHHHHHHHHHHHH****---**---------------------------
****CCCCCCCCHHHHHHHHHHHHH*CCC*HHHHHHHHHHHHH***********************--------------
*---CCCCCCCCHHHHHHHHHHH**CCCCHHHHHHHHHHHHHHH**----------------------------------
------CCCCCCHHHHHHHH*****CCCC-HHHHHH****----------------------------------------
***-CCCCCCCCHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHH************************************
---*CCCCCCCCHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHH****---***********************------

47598.tem
_________________________________
*-**CCCCCCCCHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHH****---***************--------------




Structural block scores
2	3	*	3.1	M	  9.8  10.2  10.5  75.0  75.0  42.0  43.2

4	11	C	4.9	H	  7.4  8.4  6.9  7.9  24.9  7.6  7.8

12	24	H	4.8	H	  5.0  5.7  4.9  5.9  6.4  5.8  6.0

25	28	C	4.8	H	  6.6  7.6  7.1  5.9  7.5  8.4  6.9

29	43	H	4.7	H	  4.8  5.1  4.4  5.5  28.8  5.7  5.1

44	47	*	2.5	P	  41.0  6.0  7.5  41.8  75.0  6.5  7.8

48	50	-	4.2	M	  75.0  75.0  6.8  75.0  75.0  6.7  75.0

51	65	*	3.5	M	  57.1  65.9  4.8  75.0  75.0  7.0  6.9

66	79	-	4.4	M	  75.0  75.0  75.0  75.0  75.0  7.0  37.4

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