Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
_____________________________________________

>P1;d1i4ja-
-----------CCEEEEEEEECCCHHHHHHHHHHHCCCCHHHHHHHHHHCC------------------------------CCCHHHHHHHHHHHHHHHHHCCCCCHHHEEEEEEEEEEEEEECCC---CCCCCCCCCEEEEEEEEEEEECCCC

>P1;d1vq8r1
CCCCCCCCCHHHEEEEEEEEECCCHHHHHHHHHHHCCCCHHHHHHHHHHHHCCCCCEECCCCCCCCCCCCCCCCCCCEECCHHHHHHHHHHHHHHHHHHHH-CCCCHHHCEEEEEEEEEEEEECCEEECHHHCEEECCEEEEEEEEEEECC---
PSA

>P1;d1i4ja-
-----------660313266180207404600540424506602720681a------------------------------470184045005600630377490748401023050660515516---a9b81784565002000100259b7

>P1;d1vq8r1
419264b07795004010463403263020004305733046038106302757400104623bc0a72b60ab35005405700500250096018505a-49180840303103033274587647599b7325713320000000446---


Translating the sequences
-----------**EEEEEEEECCCHHHHHHHHHHHCCCCHHHHHHHHHH**------------------------------***HHHHHHHHHHHHHHHHH*CCCCHHHEEEEEEEEEEEEEECC*---***C***CCEEEEEEEEEEEEC***
***********HEEEEEEEEECCCHHHHHHHHHHHCCCCHHHHHHHHHHHH******************************HHHHHHHHHHHHHHHHHHHH-CCCCHHH*EEEEEEEEEEEEECCE***HHHCEEECCEEEEEEEEEEE*C---

54843.tem
_________________________________
-----------HEEEEEEEEECCCHHHHHHHHHHHCCCCHHHHHHHHHHHH------------------------------HHHHHHHHHHHHHHHHHHHH-CCCCHHHEEEEEEEEEEEEEECCE---HHHCEEECCEEEEEEEEEEEEC---




Structural block scores
0	10	-	3.0	P	  75.0  5.5

12	20	E	4.8	H	  3.1  2.0

21	23	C	5.0	H	  3.3  2.3

24	34	H	5.0	H	  2.7  1.8

35	38	C	5.0	H	  3.8  4.5

39	50	H	4.7	H	  4.0  2.8

51	80	-	3.0	P	  75.0  4.6

81	100	H	4.7	H	  3.1  3.4

102	105	C	5.0	H	  5.0  5.5

106	108	H	5.0	H	  5.3  4.0

109	122	E	4.9	H	  2.4  2.4

123	124	C	5.0	H	  3.0  7.5

126	128	-	3.0	P	  75.0  5.3

129	131	H	3.0	P	  10.3  9.8

133	135	E	3.0	P	  5.3  3.3

136	137	C	5.0	H	  4.5  4.0

138	149	E	4.8	H	  1.3  1.3

151	153	-	3.0	P	  9.2  75.0

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