Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
_____________________________________________

>P1;d1a1yi-
-----CCCCHHHCCCCHHHHHHHHHHHCCCCEEEEEECCCCCCCCCCCCEEEEEECC-CCCCCCCCEEC

>P1;d1csei-
------CCCHHHCCCCHHHHHHHHHHHCCCCEEEEEECCCCCCCCCEEEEEEEEEECCCCEECCCCEEE

>P1;d1vbwa-
CCCCCCCCCHHHCCCCHHHHHHHHHHHCCCCEEEEEECCCCCCCCCCCCEEEEEECC-CCCCCCCCEEC
PSA

>P1;d1a1yi-
-----575046047541960473047306609063264c4a298466941010113a-97401530601

>P1;d1csei-
------55056037250860572086516716250343b292895868700102145b67303540811

>P1;d1vbwa-
a937745406a158360960464038407607033163b5a2896642610102037-96402550503


Translating the sequences
-----CCCCHHHCCCCHHHHHHHHHHHCCCCEEEEEECCCCCCCCCCCCEEEEEECC-CCCCCCCCEEC
------CCCHHHCCCCHHHHHHHHHHHCCCCEEEEEECCCCCCCCC***EEEEEE*C*CC**CCCCEE*
*****CCCCHHHCCCCHHHHHHHHHHHCCCCEEEEEECCCCCCCCCCCCEEEEEECC-CCCCCCCCEEC

54654.tem
_________________________________
-----CCCCHHHCCCCHHHHHHHHHHHCCCCEEEEEECCCCCCCCCCCCEEEEEECC-CCCCCCCCEEC




Structural block scores
0	4	-	4.0	M	  75.0  75.0  7.3

5	8	C	4.8	H	  4.2  21.2  3.2

9	11	H	5.0	H	  3.3  3.7  5.8

12	15	C	5.0	H	  5.0  4.2  5.5

16	26	H	5.0	H	  4.0  4.3  4.0

27	30	C	5.0	H	  3.0  3.8  3.2

31	36	E	5.0	H	  4.3  3.3  3.3

37	48	C	4.8	H	  6.6  6.5  6.1

49	54	E	5.0	H	  0.7  0.7  0.7

55	56	C	4.5	M	  6.8  4.5  5.0

58	65	C	4.8	H	  3.6  3.5  3.9

66	67	E	5.0	H	  3.0  4.5  2.5

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