Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
_____________________________________________

>P1;d2c0ga1
CCCCCCCHHHC-CHHHC-CHHHHCCCCC-----CCCCCCCCCCCHHHHHHHHHHHHHHCHHHC--CHHHHC-CCCC-CCCCCC--CCCC-HHHHHHCCCCCCCCCC

>P1;d5v8za1
---CHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHCCCC-------
PSA

>P1;d2c0ga1
79110804740-70002-669706311a-----289296774420710060064027652a10--12a605-6399-a39b95--6074-110062030a8453a9

>P1;d5v8za1
---18605800250062a98a516812750663198079933610520160064027676a1077117506641766618aa63842650180042057-------


Translating the sequences
***C***HHH*-*HHHC-CHHHH*****-----***CC******HHHHHHHHHHHHHHCHHH*--*HHHH*-****-CCC***--****-HHHHHHCCC*******
---CHHHHHHH*HHHHC*CHHHHHHHHH*****HHHCCHHHHHHHHHHHHHHHHHHHHC**HH**HHHHHH*HHHH*CCCHHH**HHHH*HHHHH*CCC-------

47933.tem
_________________________________
---CHHHHHHH-HHHHC-CHHHHHHHHH-----HHHCCHHHHHHHHHHHHHHHHHHHHCHHHH--HHHHHH-HHHH-CCCHHH--HHHH-HHHHHHCCC-------




Structural block scores
0	2	-	3.0	P	  5.7  75.0

4	10	H	3.9	M	  3.3  3.9

12	15	H	4.5	M	  1.8  2.8

19	27	H	3.9	M	  4.8  5.4

28	32	-	3.0	P	  75.0  4.0

33	35	H	3.0	P	  6.3  6.0

36	37	C	5.0	H	  5.5  3.5

38	57	H	4.4	M	  3.5  3.5

59	62	H	3.5	M	  3.4  4.4

63	64	-	3.0	P	  75.0  7.0

65	70	H	4.3	M	  4.1  3.3

72	75	H	3.0	P	  6.8  4.5

77	79	C	5.0	H	  7.5  5.0

80	82	H	3.0	P	  8.5  9.0

83	84	-	3.0	P	  75.0  5.5

85	88	H	3.0	P	  4.2  4.2

90	95	H	4.7	H	  1.7  2.5

96	98	C	5.0	H	  1.0  4.0

99	105	-	3.0	P	  7.1  75.0

>>>>>>