Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
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>P1;d2gboa1
CCHHHHHHHHHHHHHHHHHHCCHHHHHCCCHHHHHHHHHHHHHHCCHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHCC----

>P1;d2odma-
C--CCHHHHHHHHHHHHHHHHHHHHHHCCC----CCCHHHHHHHCCHHHHHHHHHHHCCCCCHHHHHHCC-HHHHHHHCCCCC
PSA

>P1;d2gboa1
989778876664875566674866a88938898777786866788995377046216587289a60874333576988a----

>P1;d2odma-
8--b4782367037206711830552287b----988458506847915540470285940667406616-41771275137b


Translating the sequences
C**HHHHHHHHHHHHHHHHH**HHHHHCCC****HHHHHHHHHHCCHHHHHHHHHHHCCCCCHHHHHHHH*HHHHHH*C----
C--**HHHHHHHHHHHHHHHHHHHHHHCCC----***HHHHHHHCCHHHHHHHHHHHCCCCCHHHHHH**-HHHHHHHC****

140404.tem
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C--HHHHHHHHHHHHHHHHHHHHHHHHCCC----HHHHHHHHHHCCHHHHHHHHHHHCCCCCHHHHHHHH-HHHHHHHC----




Structural block scores
1	2	-	3.0	P	  8.5  75.0

3	26	H	4.7	H	  6.6  4.2

27	29	C	5.0	H	  6.7  8.8

30	33	-	3.0	P	  8.0  75.0

34	43	H	4.4	M	  7.0  6.1

44	45	C	5.0	H	  8.5  5.5

46	56	H	5.0	H	  4.5  4.1

57	61	C	5.0	H	  6.0  4.8

62	69	H	4.5	M	  5.9  4.5

71	77	H	4.7	H	  6.6  4.1

79	82	-	3.0	P	  75.0  5.6

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