Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
_____________________________________________

>P1;d1sska1
CCCCCCCCCCCCCCCCCCCC----CCCCCCCCEEEECCC--CCCCCCCCCCCCCCCCCCCCCCEEEEEEECCCCCCCCCCCCCCCCEEEEEEECCCCCCCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEECCCCCCCC

>P1;d2geca1
-----------------CCCCCCCCCCCCCCCCEEECCCCCCCCCCC-CCCCCCCCCCCHHHCEEEEEEEEEEECC-CCCCEEEEEEEEEEECCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCC-CCCCCCCCEECCCCCC--
PSA

>P1;d1sska1
baab8a977b7878896d95----a7554102000264a--55070399610050280035040000743676382ab784653432030310034072746543c6b51102229b08837355045538b9a90430701c90922780630369bae

>P1;d2geca1
-----------------98797b3b64301000020485b0660808-4200052b80865210000335623486-62a7542230030000210113b26345a591010012a90638340b180155974a551030-963104b405288269--


Translating the sequences
*****************CCC----CCCCCCCCEEEECCC--CCCCCC*CCCCCCCCCCC***CEEEEEEE****CC*CCCC*****EEEEEEECCCCCCCCCCCCCCCCEEEE*CCCCCCCCCCCCCCCCCCCCCCCCCCC*CCCCCCCCEECCCCCC**
-----------------CCC****CCCCCCCC*EEECCC**CCCCCC-CCCCCCCCCCCHHHCEEEEEEEEEEECC-CCCCEEEEEEEEEEE*CCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCC-CCCCCCCCEECCCCCC--

110304.tem
_________________________________
-----------------CCC----CCCCCCCCEEEECCC--CCCCCC-CCCCCCCCCCCHHHCEEEEEEEEEEECC-CCCCEEEEEEEEEEEECCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCC-CCCCCCCCEECCCCCC--




Structural block scores
0	16	-	3.0	P	  8.8  75.0

17	19	C	5.0	H	  9.2  8.0

20	23	-	3.0	P	  75.0  7.6

24	31	C	5.0	H	  4.3  3.2

32	35	E	4.5	M	  0.5  0.5

36	38	C	5.0	H	  6.8  5.7

39	40	-	3.0	P	  75.0  5.8

41	46	C	5.0	H	  3.3  4.7

48	58	C	5.0	H	  2.8  3.7

59	61	H	3.0	P	  2.7  4.3

63	73	E	4.3	M	  3.3  2.4

74	75	C	5.0	H	  5.0  7.0

77	80	C	5.0	H	  7.6  6.4

81	92	E	4.0	M	  2.5  1.6

93	108	C	5.0	H	  5.0  4.1

109	113	E	4.6	H	  1.2  0.4

114	140	C	5.0	H	  5.2  4.5

142	149	C	5.0	H	  6.2  4.8

150	151	E	5.0	H	  3.0  2.5

152	157	C	5.0	H	  5.4  5.8

158	159	-	3.0	P	  12.5  75.0

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