Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
_____________________________________________

>P1;d1x4sa1
----CCCCEECCCCCCCCCCEECEECCCCC-CEECCHHHHHHHCCCCCCCC----------

>P1;d2d8qa1
CCCCCCCCCCCCCCC----CCCCEECCCCCCCEECCHHHHHHCHHHHHHHCCCCCCCCCCC

>P1;d2jw6a-
---------CCCCCC----CCCCEECCCCCCCEECCHHHHHHHHHHHCCCCCCCC------
PSA

>P1;d1x4sa1
----aa934609317ab7677085404549-13015791079058317b68----------

>P1;d2d8qa1
c99b78b73502445----6a098508606b230278813864598048809846abc798

>P1;d2jw6a-
---------407347----a9186506715524013860176336905760888d------


Translating the sequences
----CCCC**CCCCC****C**CEECCCCC-CEECCHHHHHHH****CCCC----------
****CCCC*CCCCCC----CCCCEECCCCCCCEECCHHHHHH*HHHH***CCCCC******
---------CCCCCC----CCCCEECCCCCCCEECCHHHHHHHHHHHCCCCCCCC------

144232.tem
_________________________________
----CCCC*CCCCCC----CCCCEECCCCCCCEECCHHHHHHHHHHHCCCCCCCC------




Structural block scores
0	3	-	4.0	M	  75.0  10.5  75.0

4	7	C	4.0	M	  8.2  8.4  75.0

9	14	C	4.8	H	  4.3  3.3  4.2

15	18	-	4.0	M	  8.8  75.0  75.0

19	22	C	4.5	M	  5.5  6.4  7.1

23	24	E	5.0	H	  4.5  6.5  5.5

25	31	C	4.9	H	  14.0  4.8  3.7

32	33	E	5.0	H	  1.5  1.5  2.0

34	35	C	5.0	H	  3.0  4.5  2.0

36	46	H	4.5	M	  4.5  5.5  4.5

47	54	C	4.1	M	  41.6  5.9  6.9

55	60	-	4.0	M	  75.0  9.8  75.0

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