Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
_____________________________________________

>P1;d2d00a1
----CEEEECHHHHHHHHHC--------CC-EEEECC---CHHHHHHHHHHHHHHCCCCCEEECCCCCCCHHHHHHHHC--CCCCCCCCCCCCCHHHHHCCCCHHHHHHHHHHHHHCCCCCC

>P1;d2i4ra1
----CEEEECHHHHHCC-CC--------CCCCEEECC---CHHHHHHHHHHHHHCCCCCEEEC-CCCCCCCC--CCCCC--CCEECCCC---------------------------------

>P1;d6wlzn-
CCCEEEEECCHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCEEEEEEEHHHHCCCHHHHHCCCCCCCEEEEECCCCCCCCCC---CCCCCCCCCCCC---------
PSA

>P1;d2d00a1
----4010055950674587--------a5-603207---6575017212605555b1a71505990256595076316--758b798a281a56960789a84624336214653986497

>P1;d2i4ra1
----3000035920792-87--------b29412506---568502700530383b70a3012-76172057--a142b--42615556---------------------------------

>P1;d6wlzn-
9265400002793158348a71054397763133116a7265850241156028595134011003002602610381889915060234a5775567---502946937b95---------


Translating the sequences
----CEEEECHHHHHHHHHC--------CC-*EEECC---CHHHHHHHHHHHHH*CCCC*EEE*CCCCCC*HHHHH**C--CC**CCCCCCCCC*******CC*******************
----CEEEECHHHHH**-*C--------CCCCEEECC---CHHHHHHHHHHHHHCCCCCEEE*-CCCCCCC*--**CCC--CCEECCCC---------------------------------
*****EEE*CHHHHHHHHH*********CCCC***CC***CHHHHHHHHHHHHHCCC**EEEE*****CCCHHHHHCCC**CCEE***CCCCCC****---CC**********---------

159468.tem
_________________________________
----CEEEECHHHHHHHHHC--------CCCCEEECC---CHHHHHHHHHHHHHCCCCCEEEE*CCCCCCCHHHHHCCC--CCEECCCCCCCCC****---CC**********---------




Structural block scores
0	3	-	4.0	M	  75.0  75.0  5.5

5	8	E	4.8	H	  0.2  0.0  0.0

10	18	H	4.6	H	  5.4  13.0  5.3

20	27	-	4.0	M	  75.0  75.0  4.5

28	31	C	4.5	M	  24.1  6.6  4.2

32	34	E	4.0	M	  1.7  2.7  2.3

35	36	C	5.0	H	  3.5  3.0  3.5

37	39	-	4.0	M	  75.0  75.0  6.5

41	53	H	5.0	H	  3.5  3.6  3.6

54	58	C	4.4	M	  6.6  6.4  4.6

59	62	E	4.5	M	  3.2  1.5  1.5

64	70	C	4.3	M	  5.1  4.0  1.6

71	75	H	4.0	M	  5.4  33.7  2.4

76	78	C	4.3	M	  3.3  5.8  5.7

79	80	-	4.0	M	  75.0  75.0  8.5

81	82	C	5.0	H	  6.0  3.0  5.0

83	84	E	4.0	M	  9.8  3.5  2.5

85	93	C	4.1	M	  6.8  44.0  4.9

94	97	*	2.7	P	  5.2  75.0  5.8

98	100	-	4.0	M	  8.0  75.0  75.0

101	102	C	4.0	M	  9.2  75.0  2.5

103	112	*	2.7	P	  3.5  75.0  6.5

113	121	-	4.0	M	  6.3  75.0  75.0

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