Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
_____________________________________________

>P1;d1n10a1
C-CCEEEECCCCCCCEEEEEEECCCCCCCEEEEEEEECCCCCCEECCCCCCCCEEEECCCCCCCCEEEEEEECCCCEEEEEEEECCCCCCCEEEEC--

>P1;d3ft1a1
CCEEEEEECCCCCCCEEEEEEEEECCCCCEEEEEEECCCCCCCEECEEECC-EEEEECCCCCCCCEEEEEEECCCCEEEEEEEECCCCCCCCEECCCC
PSA

>P1;d1n10a1
8-51101026b0754300020461c573915400031696992370764a972031818850622000101069975441730047c073443153--

>P1;d3ft1a1
6060302039a067520102070637c16026010215a3a81270755bb-2000529860603000303068646211650045a064764172a5


Translating the sequences
C-**EEEECCCCCCCEEEEEEE**CCCCCEEEEEEEECCCCCCEEC***CC**EEEECCCCCCCCEEEEEEECCCCEEEEEEEECCCCCCCEEEEC--
C*EEEEEECCCCCCCEEEEEEEEECCCCCEEEEEEE*CCCCCCEECEEECC-EEEEECCCCCCCCEEEEEEECCCCEEEEEEEECCCCCCC*EE*C**

49590.tem
_________________________________
C-EEEEEECCCCCCCEEEEEEEEECCCCCEEEEEEEECCCCCCEECEEECC-EEEEECCCCCCCCEEEEEEECCCCEEEEEEEECCCCCCCEEEEC--




Structural block scores
2	7	E	4.3	M	  1.3  1.8

8	14	C	5.0	H	  5.1  5.8

15	23	E	4.6	H	  1.8  2.0

24	28	C	5.0	H	  7.3  5.9

29	36	E	4.8	H	  1.8  1.5

37	42	C	5.0	H	  6.8  6.3

43	44	E	5.0	H	  5.0  4.5

46	48	E	3.0	P	  5.7  5.7

49	50	C	5.0	H	  9.8  11.5

52	56	E	4.6	H	  2.8  1.4

57	64	C	5.0	H	  4.0  4.2

65	71	E	5.0	H	  0.3  0.9

72	75	C	5.0	H	  7.8  6.0

76	83	E	5.0	H	  3.0  2.6

84	90	C	5.0	H	  5.4  5.2

91	94	E	4.0	M	  3.2  4.5

96	97	-	3.0	P	  75.0  7.8

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