Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
_____________________________________________

>P1;d4uw2a5
------CCC--CCCEEEEECCCCCCCCCCCC-CCEEEEEC-------CCCEEEEECCCCCCCCCCCCEEEEECCCCCCCCCCCC-------

>P1;d6ifka5
CCHHHHHHHCCCCCEEEEEC----CCCEEEECCEEEEEECHHHCCCCCCCEEEEECCCCC-------CCEEEC-CCCCCCCCCHHHHCCCC
PSA

>P1;d4uw2a5
------c76--8250203164a69c157637-81022246-------65630312448a4c2589a07252365a5a69798a7-------

>P1;d6ifka5
99368536715a46110106----94426449a31220047842972926613024597a-------805354-b687646983597678c


Translating the sequences
------***--CCCEEEEEC****CCC****-C*EEEEEC-------CCCEEEEECCCCC*******EEEEEC*CCCCCCCCC*-------
******HHH**CCCEEEEEC----CCCEEEE*CEEEEEEC*******CCCEEEEECCCCC-------**EEEC-CCCCCCCCCH*******

418772.tem
_________________________________
------HHH--CCCEEEEEC----CCCEEEE-CEEEEEEC-------CCCEEEEECCCCC-------EEEEEC-CCCCCCCCCH-------




Structural block scores
0	5	-	3.0	P	  75.0  6.7

6	8	H	3.0	P	  8.5  5.3

9	10	-	3.0	P	  75.0  3.0

11	13	C	5.0	H	  5.0  6.8

14	18	E	5.0	H	  1.2  0.6

20	23	-	3.0	P	  7.4  75.0

24	26	C	5.0	H	  6.2  5.7

27	30	E	3.0	P	  5.8  4.0

33	38	E	4.7	H	  1.8  1.3

40	46	-	3.0	P	  75.0  5.6

47	49	C	5.0	H	  5.7  5.7

50	54	E	5.0	H	  1.8  2.4

55	59	C	5.0	H	  6.1  7.1

60	66	-	3.0	P	  6.7  75.0

67	71	E	4.2	M	  3.8  4.2

74	82	C	5.0	H	  8.4  7.3

84	90	-	3.0	P	  75.0  7.8

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