Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
_____________________________________________

>P1;d2bkya-
C-CEEECC-C-CCHHHHHHHHHHHHHCCCCEEEEEEECCHHHHHHHHHHHHHHHCCCCCEEEEEEEEEEEEEECCCCCEEEEEEEEEEEEEC----------

>P1;d2bkyx-
CCEEEECC-CCCCHHHHHHHHHHHHHCCCCEEEEEEECCHHHHHHHHHHHHHHH-HHHHEEEEEEEEEEEEEC-----CEEEEEEEEEEEECC---------

>P1;d2q3va-
CCCEEECCCCCCCHHHHHHHHHHCC--CCCEEEEEEEC-CHHHHHHHHHHHHHC---CCEEEEEC-CEEEEEC-----CEEEEEEEEEEEECCCCCCCCCC-

>P1;d7dl8c-
-CCCCCCC-CC-HHHHHHHHHHHHHHCC-CCEEEEEEHHHHHHHHHHHHHHHHC---CCEECCEEECC------------CCCEEEEEEEECCCHHHHCCCC
PSA

>P1;d2bkya-
9-420708-a-77235107502620a683730003066a22930550042038632596041344477634447b67857726213000444----------

>P1;d2bkyx-
a4442306-694736500440272067a37201010189138204601640394-38810523756665465b-----978261120305448---------

>P1;d2q3va-
983406086b936474007302725--53830200043-329205401620487---31153664-576374a-----87443404010330951973988-

>P1;d7dl8c-
-9c59897-6b-438650550155047a-651513267b529105400620394---7006248786a------------664413030431b707942489


Translating the sequences
C-CEEECC-C-CCHHHHHHHHHHHHHCCCCEEEEEEEC*HHHHHHHHHHHHHH****CCEEEEEEE*EEEEE*******EEEEEEEEEEEEC----------
CC*EEECC-CCCCHHHHHHHHHHHHHCCCCEEEEEEEC*HHHHHHHHHHHHHH*-****EEEEEEE*EEEEE*-----*EEEEEEEEEEEECC---------
CCCEEECC*CCCCHHHHHHHHHH**--CCCEEEEEEEC-*HHHHHHHHHHHHH*---CCEEEEE*-*EEEEE*-----*EEEEEEEEEEEECC********-
-CC***CC-CC-*HHHHHHHHHHHHHCC-C*EEEEEE**HHHHHHHHHHHHHH*---CCEE**EEE**------------***EEEEEEEECC*********

82704.tem
_________________________________
CCCEEECC-CCCCHHHHHHHHHHHHHCCCCEEEEEEEC*HHHHHHHHHHHHHH*-**CCEEEEEEE*EEEEE*-----*EEEEEEEEEEEECC********-




Structural block scores
0	2	C	4.3	M	  29.3  6.2  6.7  32.2

3	5	E	4.3	M	  3.0  3.0  3.3  7.3

6	7	C	5.0	H	  4.0  3.0  4.0  8.0

9	12	C	4.5	M	  24.9  6.5  7.4  24.1

13	25	H	4.8	H	  3.3  3.0  8.9  3.6

26	29	C	4.7	H	  6.0  6.9  22.8  24.6

30	36	E	4.9	H	  1.7  0.7  1.3  3.3

39	52	H	5.0	H	  3.1  3.4  3.3  3.3

55	56	*	3.5	M	  3.5  5.5  75.0  75.0

57	58	C	4.3	M	  7.5  4.5  2.0  3.5

59	65	E	4.6	H	  2.9  4.0  14.3  5.0

67	71	E	4.3	M	  4.8  5.2  5.4  62.1

73	77	-	4.3	M	  7.9  75.0  75.0  75.0

79	90	E	4.8	H	  3.0  3.2  2.8  9.1

91	92	C	4.7	H	  39.5  6.0  4.5  6.2

93	100	*	3.5	M	  75.0  75.0  6.2  5.1

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