Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
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>P1;d1oksa1
-CCHHHHHHHHHHCCCCHHHHHHC-CHHHHCCCHHHHHHHHC-CCCCCC----

>P1;d1r4ga-
CCCHHHHHHHHHHCCCCHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHCCCCC
PSA

>P1;d1oksa1
-4747608731981a377771771-7418829a9b5167137-068639----

>P1;d1r4ga-
a98a5525660482918aa645803641780a89a71662266043574989b


Translating the sequences
-CCHHHHHHHHHHCCCCHHHHHH*-*HHHHCCCHHHHHHHH*-*****C----
*CCHHHHHHHHHHCCCCHHHHHHH*HHHH*CCC*HHHHHHHH*HHHHHC****

101089.tem
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-CCHHHHHHHHHHCCCCHHHHHHH-HHHHHCCCHHHHHHHHH-HHHHHC----




Structural block scores
1	2	C	5.0	H	  5.5  8.5

3	12	H	5.0	H	  5.3  5.2

13	16	C	5.0	H	  5.4  5.0

17	23	H	4.7	H	  5.3  6.3

25	29	H	4.2	M	  5.6  5.2

30	32	C	5.0	H	  7.2  6.2

33	41	H	4.6	H	  5.6  5.5

43	47	H	3.0	P	  4.6  3.8

49	52	-	3.0	P	  75.0  9.4

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