Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
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>P1;d2blkb1
CCEEEECCCCCCCCC-CCCCCEEEEECHHHHHHHHHHHHHCCCEEECCCCHHHHHHHHHHHCCCCCCCCCCCC-CCCCEEEECC-CCCCCCCCCC-CHHHHHCCCCCCCCEEEEE--

>P1;d2j6ba1
-CEEEECCCCCCCCCCCCCEEEEEEECHHHHHHHHHHC----CEEECCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCEEEEEEECCCCCCCCCCCCHHHHHHH---CEEEEEEEEE
PSA

>P1;d2blkb1
94000157368a249-591a26476061850164046339594041001756008002400a1a093573934-69a0210001-768179c4a2-6484044376840203104--

>P1;d2j6ba1
-30100163731268b4a07173650857504610584----813000038000500381072a05346581403691300003156a27bc530762850580---4110301308


Translating the sequences
*CEEEECCCCCCCCC-CCC**EEEEECHHHHHHHHHHH****CEEECCCCHHHHHHHHHHHCCCCCCCCCCCC-CCCCEEEE**-CCCCCCCCCC-CHHHHH*****C**EEEEE--
-CEEEECCCCCCCCC*CCCEEEEEEECHHHHHHHHHH*----CEEECCCCHHHHHHHHHHHCCCCCCCCCCCC*CCCCEEEEEE*CCCCCCCCCC*CHHHHHHH---CEEEEEEE**

143602.tem
_________________________________
-CEEEECCCCCCCCC-CCCEEEEEEECHHHHHHHHHHH----CEEECCCCHHHHHHHHHHHCCCCCCCCCCCC-CCCCEEEEEE-CCCCCCCCCC-CHHHHHHH---CEEEEEEE--




Structural block scores
2	5	E	5.0	H	  0.2  0.2

6	14	C	5.0	H	  6.1  4.1

16	18	C	5.0	H	  5.0  4.8

19	25	E	4.4	M	  5.1  4.1

27	37	H	4.8	H	  3.5  4.1

38	41	-	3.0	P	  6.5  75.0

43	45	E	5.0	H	  1.7  1.3

46	49	C	5.0	H	  2.0  0.8

50	60	H	5.0	H	  2.3  2.3

61	72	C	5.0	H	  5.4  4.6

74	77	C	5.0	H	  6.4  4.8

78	83	E	4.3	M	  0.7  1.0

85	94	C	5.0	H	  6.7  6.2

97	103	H	4.4	M	  3.9  4.0

104	106	-	3.0	P	  7.0  75.0

108	114	E	4.4	M	  1.4  1.3

115	116	-	3.0	P	  75.0  4.0

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