Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
_____________________________________________

>P1;d2k49a1
--------CEECCCEECCEEECCCCCEEEEC-CCCCCHHHHHHHHHHHHHHCCCCCCCCCC

>P1;d2k49a2
C-CCEEEEEECCCCCEEEEEECCCCCEEEEC-CCCCCHHHHHHHHHHHHHHCCCHHHCCC-

>P1;d3bida1
----CEEEEECCCCCEEEEEECCCCCEEEEC-CCCCCHHHHHHHHHHHHCCCCCCCCCCC-

>P1;d6q2za-
CCCEEEEEEECCCCCEEEEEEECCCCEEEECCCCCCCHHHHHHHHHHHHCCCCCCCCCCC-
PSA

>P1;d2k49a1
--------66399930211653ba8655651-b729687625944664679686b8977aa

>P1;d2k49a2
b-905142742ba722302123095744652-a43a759705921743785565977697-

>P1;d3bida1
----6242452a8642312314a97645540-92294696067206656757b958999a-

>P1;d6q2za-
a9706152453a6942103213886543431a725867950546157467845969baae-


Translating the sequences
--------*E*CCC*E**EEECCCCCEEEEC-CCCCCHHHHHHHHHHHH**CCCCCCCCC*
*-***EEEEECCCCCEEEEEECCCCCEEEEC-CCCCCHHHHHHHHHHHH**CCC***CCC-
----*EEEEECCCCCEEEEEECCCCCEEEEC-CCCCCHHHHHHHHHHHH**CCCCCCCCC-
*****EEEEECCCCCEEEEEE*CCCCEEEEC*CCCCCHHHHHHHHHHHH**CCCCCCCCC-

160113.tem
_________________________________
*-***EEEEECCCCCEEEEEECCCCCEEEEC-CCCCCHHHHHHHHHHHH**CCCCCCCCC-




Structural block scores
2	4	*	3.1	M	  75.0  4.7  52.0  4.3

5	9	E	4.4	M	  47.4  3.6  3.4  3.4

10	14	C	4.7	H	  6.6  6.6  6.1  6.5

15	20	E	4.8	H	  2.5  1.7  2.0  1.5

21	25	C	4.9	H	  7.8  4.8  7.3  6.0

26	29	E	5.0	H	  5.2  4.8  4.5  3.5

32	36	C	5.0	H	  7.1  7.0  5.2  5.6

37	48	H	5.0	H	  5.6  4.9  4.9  4.9

49	50	*	1.0	P	  8.0  6.5  6.0  7.5

51	59	C	4.8	H	  8.1  6.8  8.7  8.9

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