Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
_____________________________________________

>P1;d1gl0i-
--CCCCCCEEECCCCEEEECCCC-CEEECCCCCCC

>P1;d3tvji-
CCCCCCCCEEEECCEEEEECCCCCCEEECCCCCCC
PSA

>P1;d1gl0i-
--9184a6568653150604891-6171696b1b9

>P1;d3tvji-
c3918475526563140606a51650926a791aa


Translating the sequences
--CCCCCCEEE*CC*EEEECCCC-CEEECCCCCCC
**CCCCCCEEEECCEEEEECCCC*CEEECCCCCCC

57283.tem
_________________________________
--CCCCCCEEEECCEEEEECCCC-CEEECCCCCCC




Structural block scores
0	1	-	3.0	P	  75.0  7.8

2	7	C	5.0	H	  6.4  5.7

8	11	E	4.5	M	  6.2  4.5

12	13	C	5.0	H	  4.0  4.5

14	18	E	4.6	H	  2.4  2.2

19	22	C	5.0	H	  5.5  5.6

25	27	E	5.0	H	  3.0  3.7

28	34	C	5.0	H	  7.7  7.8

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