Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
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>P1;d1hkya1
CC----CCCCC--CCCCCC---CCCCCCCCCCCCHHHHHHHHCCCC----CCCCCEECC--CCCCCCC----CCCCCCCCCCCCCEECCCCCCCCCC

>P1;d1i8na-
CEEECCCCEEEEEECCCCC---HHH-EEECCCCCHHHHC-CCCCCC-CCCCCCEEEEECCCCCEEEECCCCCCHHHCC-CCCCCEEEEEEEC--CC-

>P1;d3hmsa-
--CCCHHH-EEEEEEEEEEECCCCCCCEEEECCCHHHHHHHHHHCCCCCCCCCEEEEECCCCEEEEECC-CCCCCCEEEEEEEEEEEEEE-HHHCC-
PSA

>P1;d1hkya1
ba----a7479--833216---a0a12351718729605740773a----617210038--4502002----95971744748904003a73a96ac

>P1;d1i8na-
76448a5220325612303---991-0651826548701-20192a-88470300004465720310436a043a416-792750100016a--2b-

>P1;d3hmsa-
--a42195-06426510053648925244651a6244001601629b0615030000047652020010-0033b507566274200100-57319-


Translating the sequences
C*----CC***--*CCCCC---CCCCC**CCCCCHHHHHHHHCCCC----CCC**EE*C--CC****C----CCCCCC*CCCCC*EE****C**CC*
C***C*CC*EEEEECCCCC---***-*EECCCCCHHHH*-**CCCC-CCCCCCEEEEECCCCCEEEECC*CCC***CC-CCCCCEEEEEE*C--CC-
--**C***-EEEEE********CCCCCEE**CCCHHHHHHHH**CC*CCCCCCEEEEECCCC*EEEECC-CCCCCC********EEEEEE-***CC-

57414.tem
_________________________________
C***C*CC*EEEEECCCCC---CCCCCEECCCCCHHHHHHHHCCCC-CCCCCCEEEEECCCCCEEEECC-CCCCCCCC*CCCCCEEEEEE*C**CC-




Structural block scores
1	3	*	2.7	P	  53.5  4.7  29.8

6	7	C	4.0	M	  8.8  3.5  7.0

9	13	E	4.0	M	  34.8  3.2  3.6

14	18	C	4.0	M	  3.0  1.8  2.2

19	21	-	4.0	M	  75.0  75.0  4.3

22	26	C	4.0	M	  4.8  18.8  5.2

27	28	E	4.0	M	  4.0  5.5  4.0

29	33	C	4.6	H	  4.8  4.4  5.7

34	41	H	4.5	M	  4.1  12.1  2.1

42	45	C	4.5	M	  6.9  5.6  4.5

47	52	C	4.5	M	  39.8  5.0  2.5

53	57	E	4.4	M	  1.2  0.8  0.0

58	62	C	4.4	M	  33.4  4.8  4.8

63	66	E	4.0	M	  0.5  1.0  0.5

67	68	C	4.5	M	  38.5  3.5  0.5

70	77	C	4.1	M	  23.5  4.9  3.7

79	83	C	4.0	M	  6.4  6.0  5.0

84	89	E	4.3	M	  2.9  0.3  0.5

92	93	*	2.7	P	  9.8  75.0  5.0

94	95	C	5.0	H	  8.2  6.8  5.0

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