Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
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>P1;d2a73b3
--CCCCCHHHHCCCCCC-HHHHHHHHHHHCCCCCCCCHHHHCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCC

>P1;d4p3aa1
CHHHHHHHHHHHHCCCCCHHHHHHHHHHHCCCC-CCCHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHCC---
PSA

>P1;d2a73b3
--942975387117727-8924800540067185a260761287197a88017013600630662265596a

>P1;d4p3aa1
888316540761076287771371045006548-92818500772875780470145004203603768---


Translating the sequences
--*****HHHH**CCCC-HHHHHHHHHHHCCCC*CCCHHHH*CCCCCCHHHHHHHHHHHHHHHHH**CC***
**HHHHHHHHHHHCCCC*HHHHHHHHHHHCCCC-CCCHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHCC---

47686.tem
_________________________________
--HHHHHHHHHHHCCCC-HHHHHHHHHHHCCCC-CCCHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHCC---




Structural block scores
0	1	-	3.0	P	  75.0  8.0

2	12	H	3.7	M	  5.1  3.7

13	16	C	5.0	H	  5.8  5.8

18	28	H	5.0	H	  3.6  3.2

29	32	C	5.0	H	  5.5  5.8

34	36	C	5.0	H	  6.2  6.3

37	41	H	4.6	H	  3.2  2.8

42	47	C	5.0	H	  7.1  6.0

48	66	H	4.8	H	  3.4  3.2

67	68	C	5.0	H	  5.0  7.0

69	71	-	3.0	P	  8.5  75.0

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