Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
_____________________________________________

>P1;d1nh2c-
CCCCCCEEEEEEEEEEEECCEEEEEEEEEEEEECCEEEEEEEEEEEEECC--

>P1;d1nh2d2
CCCCEEEEEEEEEEEEEECCEEEEEEEEEEEEEECEEEEEEEEEEEEECCCC

>P1;d1nvpd2
C---CCEEEEEEEEEEEECCEEEEEEEEEEEECC--CEEEEEEEEEEE---C
PSA

>P1;d1nh2c-
9a9b8653616767365993545231350504578766818726466699--

>P1;d1nh2d2
d99485428384467748a435330148071446b65673a53635575a9a

>P1;d1nvpd2
9---84649284667748a93413213804255b--4754a7263557---a


Translating the sequences
CCCCCCEEEEEEEEEEEECCEEEEEEEEEEEEECCEEEEEEEEEEEEECC--
CCCC**EEEEEEEEEEEECCEEEEEEEEEEEEE*CEEEEEEEEEEEEECC*C
C---CCEEEEEEEEEEEECCEEEEEEEEEEEE*C--*EEEEEEEEEEE---C

50784.tem
_________________________________
CCCCCCEEEEEEEEEEEECCEEEEEEEEEEEEECCEEEEEEEEEEEEECC-C




Structural block scores
0	5	C	4.2	M	  9.0  8.1  41.0

6	17	E	5.0	H	  5.3  5.4  5.9

18	19	C	5.0	H	  6.0  7.2  9.8

20	32	E	4.9	H	  3.2  3.3  3.2

33	34	C	4.0	M	  7.5  8.8  43.2

35	47	E	4.8	H	  5.6  5.5  10.8

48	49	C	4.0	M	  9.0  7.8  75.0

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