Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
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>P1;d1doqa-
-CCCCCCCCCHHHHCCCHHHHHHHHHCCCCCHHHHHHCCHHHHCCCCCCCHHHHHHHHHHHHHHCCCCCC-------------

>P1;d1z3eb1
---CCCCCCCHHHCCCCHHHHHHHHHCCCCCHHHHHCCCHHHHHCCCCCCHHHHHHHHHHHHHCCCCCC--------------

>P1;d3k4ga-
CCCCHHHHCCHHHHCCCHHHHHHC-CCCCCCHHHHHHCCHHHHC-CCCCC--CCCCC--CCHHHCCCCCCCCCCCCCCCCCCC
PSA

>P1;d1doqa-
-8b29907430560901a803820573c1720620250779307a08709a8037205700671719607-------------

>P1;d1z3eb1
---7831735056090597025004838053065016335830671980aa9007404720872a2806--------------

>P1;d3k4ga-
a98782265518409079602810-6270750020032569504-2760a--00b40--20983a17153909a173a9aaad


Translating the sequences
-CCCCCCCCCHHHHCCCHHHHHHHHHCCCCCHHHHHHCCHHHHCCCCCCCHHHHHHHHHHHHHHCCCCCC-------------
---CCCCCCCHHH*CCCHHHHHHHHHCCCCCHHHHH*CCHHHH*CCCCCCHHHHHHHHHHHHH*CCCCC--------------
*CCC****CCHHHHCCCHHHHHH*-*CCCCCHHHHHHCCHHHHC-CCCCC--*****--**HHHCCCCCC*************

47789.tem
_________________________________
-CCCCCCCCCHHHHCCCHHHHHHHHHCCCCCHHHHHHCCHHHHCCCCCCCHHHHHHHHHHHHHHCCCCCC-------------




Structural block scores
1	9	C	4.3	M	  5.9  20.4  5.8

10	13	H	4.8	H	  2.8  2.8  3.2

14	16	C	5.0	H	  3.3  4.7  5.3

17	25	H	4.7	H	  4.8  3.9  11.9

26	30	C	5.0	H	  5.1  3.8  4.2

31	36	H	4.8	H	  2.5  3.0  0.8

37	38	C	5.0	H	  3.5  3.0  3.5

39	42	H	5.0	H	  4.8  4.0  5.0

43	49	C	4.7	H	  5.9  5.9  14.9

50	63	H	4.1	M	  4.0  4.3  24.1

64	69	C	4.8	H	  5.0  16.9  4.6

70	82	-	4.0	M	  75.0  75.0  8.0

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