Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
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>P1;d1khda1
--CHHHHHHHHCCCCCCHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHCCCCCC

>P1;d1uoua1
CCCC-CHHHHHCCCCCCHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHCCCHHHHHHHHHHHHCCCC---

>P1;d2elca1
---CCHHHHHHCCCCCCHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHCCC--

>P1;d4eada1
CCHHHHHHHHHCCCCCCHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHCCCHHHHHHHHHHHHCCCC-CC
PSA

>P1;d1khda1
--36800530467520759304501201259608b94374056207818457407602630686459899

>P1;d1uoua1
6a06-01640653750659003810714679708a923850661287580998066037506754ab---

>P1;d2elca1
---460061035453084820350141134a5069a427706710681835840660155058847a9--

>P1;d4eada1
841650144055275066a20440061355a708aa34750761287470787055137406633a8-5a


Translating the sequences
--***HHHHHHCCCCCCHHHHHHHHHHH*CCCCCHHHHHHHHHHHHHHCCCHHHHHHHHHHHH*CCC***
****-*HHHHHCCCCCCHHHHHHHHHHHH*CCCCHHHHHHHHHHHHHHCCCHHHHHHHHHHHH*CCC---
---**HHHHHHCCCCCCHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHCCCHHHHHHHHHHHH**CC*--
*****HHHHHHCCCCCCHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHCCCHHHHHHHHHHHH*CCC-**

47648.tem
_________________________________
*****HHHHHHCCCCCCHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHCCCHHHHHHHHHHHH*CCC***




Structural block scores
0	4	*	2.5	P	  33.4  19.5  47.0  4.8

5	10	H	4.9	H	  2.0  2.8  1.7  2.3

11	16	C	5.0	H	  4.5  4.3  4.2  4.2

17	28	H	4.9	H	  2.7  3.7  2.7  3.5

29	33	C	4.9	H	  5.6  6.2  5.1  6.1

34	47	H	5.0	H	  4.8  5.2  4.9  5.4

48	50	C	5.0	H	  5.7  5.7  5.3  4.7

51	62	H	5.0	H	  4.1  4.8  4.0  4.3

64	66	C	4.8	H	  6.0  8.7  7.2  7.2

67	69	*	3.5	M	  8.7  75.0  53.0  30.2

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