Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
_____________________________________________

>P1;d1hc7a3
CEECCC--HHHHHHHCCC--CCEEECCCCCHHHHHHHHHHHCCEEEECCCCCCCCCCCCCCCCCCCCCCCCEEEECCC

>P1;d1nj1a2
CEECCC--HHHHHHHHHHHCCCEEEEECCCHHHHHHHHHHHCCEEEEEE---ECCCCCCCCCCCCCC--EEEEEECCC

>P1;d1nj8a2
CEECCCCCHHHHHHHCCCCCCEEEEECC-HHHCCHHHHHHHCCCEEEEEECC---------------CCEEEEEECCC
PSA

>P1;d1hc7a3
555077--1820560069--95020000149513540563170324732a947827370032757044510010142c

>P1;d1nj1a2
6470a5--19404600565983000110058900730295070514837---75c577001376703--31020034d

>P1;d1nj8a2
41519725294039208856b2000327-96427980395060405453748---------------a961000064d


Translating the sequences
CEECCC--HHHHHHHCCC--CCEEE*CCCCHHHHHHHHHHHCCEEEE***CC*CCCCCCCCCCCCCCCC**EEEECCC
CEECCC--HHHHHHH****CCCEEEE*CCCHHHHHHHHHHHCCEEEEEE---*CCCCCCCCCCCCCC--EEEEEECCC
CEECCC**HHHHHHHCCC*CC*EEEECC-*HH**HHHHHHHCC*EEEEE*CC---------------CCEEEEEECCC

64586.tem
_________________________________
CEECCC--HHHHHHHCCC*CCCEEEECCCCHHHHHHHHHHHCCEEEEEE*CC*CCCCCCCCCCCCCCCCEEEEEECCC




Structural block scores
1	2	E	5.0	H	  5.0  5.5  3.0

3	5	C	5.0	H	  4.7  5.2  5.7

6	7	-	4.0	M	  75.0  75.0  3.5

8	14	H	5.0	H	  3.1  3.4  4.1

15	17	C	4.0	M	  5.0  3.7  5.3

19	21	C	4.3	M	  29.7  6.7  6.5

22	25	E	4.8	H	  0.5  0.2  0.8

26	29	C	4.2	M	  1.2  1.5  23.2

30	40	H	4.8	H	  3.8  3.9  4.8

41	42	C	5.0	H	  3.5  3.5  3.0

43	48	E	4.5	M	  3.5  4.7  3.5

50	51	C	4.0	M	  6.5  75.0  6.0

53	68	C	4.0	M	  4.0  13.3  66.8

69	74	E	4.7	H	  0.5  1.0  1.2

75	77	C	5.0	H	  6.2  6.8  7.8

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