Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
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>P1;d1e3pa1
------CCHHHHHHHHHHHHHHHHHHCC--CCCHHHHHHHHHHHHHHHHCCCCCCCCC-CHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCC---

>P1;d1whua1
CCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCC----CCCCCC
PSA

>P1;d1e3pa1
------2785038302800565047005--366798175317704750586037716a-36a306500630176027714975653431696---

>P1;d1whua1
b987990296017302710483026109733967a46751366057602840485169186630320055028602640577747----83b99b


Translating the sequences
------CCHHHHHHHHHHHHHHHHHH**--CCCHHHHHHHHHHHHHHHH****CCCCC-CHHHHHHHHHHHHHHHHHHHHHHCCC****CCC---
******CCHHHHHHHHHHHHHHHHHHHH**CCC*****HHHHHHHHHHHHHHHCCCCC*CHHHHHHHHHHHHHHHHHHHHH*CCC----CCC***

46915.tem
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------CCHHHHHHHHHHHHHHHHHHHH--CCCHHHHHHHHHHHHHHHHHHHHCCCCC-CHHHHHHHHHHHHHHHHHHHHHHCCC----CCC---




Structural block scores
0	5	-	3.0	P	  75.0  8.9

6	7	C	5.0	H	  4.5  1.0

8	27	H	4.8	H	  3.5  3.5

28	29	-	3.0	P	  75.0  5.0

30	32	C	5.0	H	  5.0  6.0

33	52	H	4.1	M	  4.7  4.6

53	57	C	5.0	H	  6.3  5.8

60	81	H	4.9	H	  4.1  3.5

82	84	C	5.0	H	  5.3  6.0

85	88	-	3.0	P	  2.8  75.0

89	91	C	5.0	H	  7.0  7.5

92	94	-	3.0	P	  75.0  9.8

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