Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
_____________________________________________

>P1;d1vq8h1
CCHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEEECCCEEEEHHHHHHHHHHHHHHHHHHHCCCCCCEEEECCCCCEEEEECCCCCCCCCCEE--EEEEEEECCCCEEEEEEECCCCHHHHHHHHHHHHHHCCCCEEC-----------

>P1;d2j01q1
---------------CCCCCCCCCCCCCCCCCCCC---CCCCCC--CEEEECCCEEEEHHHHHHHHHHHHHHCC------CCCEEEECCCCCEEECCCCCCCCCCCCCCCCCEEEEEECCCCEEEEEECCC--HHHHHHHHHHHHHHCCCCEEEECCCCCCCC-C

>P1;d2pa2a1
------------------------------------CCCCCCCCEEEEEEECCCEEEEHHHHHHHHHHHHHHHHHHHCCC-CEEEEECCC------------------C--CCCEEEECCCCEEEEEEECHHHHHHHHHHHHHHHHHCCCCEEEEEECCCCCCCC
PSA

>P1;d1vq8h1
664541462768623666709c03c47066170156a373a50526110304730002143024005101610473088923010204250700011357a89a27071--2100020648440000103891274044005503650207072-----------

>P1;d2j01q1
---------------a979235a6a719c1a7052---602703--2001055332024620650342048309------a336033208171030644a8889b30703642400202233000002b27--584035005300640408162475a97798-d

>P1;d2pa2a1
------------------------------------8755950310000203451504282044034202720281088a-405040107------------------6--16460606774300000057925730230065028407460506138819888a


Translating the sequences
***************CCCCCCCCCCCCCCCCCCCC*CCCCCCCCEEEEEEECCCEEEEHHHHHHHHHHHHHHHHHHHCCCCCCEEEECCCCCEEE**CCCCCCCCCC**--*EEEEEECCCCEEEEEEECC**HHHHHHHHHHHHHHCCCCEE*-----------
---------------CCCCCCCCCCCCCCCCCCCC---CCCCCC--*EEEECCCEEEEHHHHHHHHHHHHHH**------CCCEEEECCCCCEEE**CCCCCCCCCC*C**CEEEEEECCCCEEEEEE*CC--HHHHHHHHHHHHHHCCCCEEEE**CCCCCC-C
------------------------------------CCCCCCCCEEEEEEECCCEEEEHHHHHHHHHHHHHHHHHHHCCC-C*EEEECCC------------------C--C**EEEECCCCEEEEEEEC***HHHHHHHHHHHHHHCCCCEEEE**CCCCCC*C

54686.tem
_________________________________
---------------CCCCCCCCCCCCCCCCCCCC-CCCCCCCCEEEEEEECCCEEEEHHHHHHHHHHHHHHHHHHHCCCCCCEEEECCCCCEEE**CCCCCCCCCC*C--CEEEEEECCCCEEEEEEECC**HHHHHHHHHHHHHHCCCCEEEE**CCCCCC-C




Structural block scores
0	14	-	4.0	M	  4.7  75.0  75.0

15	34	C	4.0	M	  5.0  6.4  75.0

36	43	C	4.8	H	  5.5  21.0  5.2

44	50	E	4.6	H	  1.9  21.9  0.4

51	53	C	5.0	H	  4.7  4.3  4.0

54	57	E	5.0	H	  0.5  1.8  2.5

58	76	H	4.7	H	  2.2  14.8  2.7

77	82	C	4.2	M	  5.0  40.2  17.6

83	86	E	5.0	H	  0.8  3.0  2.2

87	91	C	4.6	H	  3.6  3.6  31.6

92	94	E	4.0	M	  0.0  1.3  75.0

95	96	*	2.7	P	  1.0  3.0  75.0

97	106	C	4.0	M	  6.2  6.6  75.0

109	110	-	4.0	M	  75.0  4.5  75.0

112	117	E	4.7	H	  0.5  1.3  3.7

118	121	C	5.0	H	  5.5  2.5  6.0

122	128	E	4.9	H	  0.7  1.9  0.4

129	130	C	4.5	M	  5.5  4.5  6.0

131	132	*	2.7	P	  5.0  75.0  5.5

133	146	H	5.0	H	  3.2  3.1  3.2

147	150	C	5.0	H	  2.2  3.0  4.2

151	154	E	4.5	M	  21.0  3.2  2.8

155	156	*	2.7	P	  75.0  6.0  2.0

157	162	C	4.0	M	  75.0  8.4  7.0

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