Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
_____________________________________________

>P1;d2l7pa1
CC-CCCCCCCCCCCCEEEEECCC--CCCEEEEECCC-CCCCCCCCCCCHHHCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCCCCCCCCC--

>P1;d2rr4a1
CCCC-------CCCCCCEEECCCCCCCCEEECCCCCCHHHCC--CCCCHHHCCCCCCCCCCCCCCCCC------------------------CCC
PSA

>P1;d2l7pa1
96-b3ba9647a4a920014046--37420505191-0661596960203604488405294912365740134005a1b78b6a9a94b899--

>P1;d2rr4a1
976a-------a067512150468b04150306562149813--ba00084054952573a3731978------------------------bad


Translating the sequences
CC-C*******CCCCEEEEECCC--CCCEEEEECCC-***CC**CCCCHHHCCCCCCCCCCCCCCCCH************************C--
CC*C-------CCCC**EEECCC**CCCEEE**CCC*HHHCC--CCCCHHHCCCCCCCCCCCCCCCC*------------------------C**

310596.tem
_________________________________
CC-C-------CCCCEEEEECCC--CCCEEEEECCC-HHHCC--CCCCHHHCCCCCCCCCCCCCCCCH------------------------C--




Structural block scores
0	1	C	5.0	H	  7.5  8.0

4	10	-	3.0	P	  7.3  75.0

11	14	C	5.0	H	  8.5  5.9

15	19	E	4.2	M	  1.4  2.8

20	22	C	5.0	H	  3.3  3.3

23	24	-	3.0	P	  75.0  9.8

25	27	C	5.0	H	  4.7  1.7

28	32	E	4.2	M	  2.4  2.8

33	35	C	5.0	H	  3.7  4.3

37	39	H	3.0	P	  4.0  7.0

40	41	C	5.0	H	  3.0  2.0

42	43	-	3.0	P	  7.5  75.0

44	47	C	5.0	H	  4.2  5.5

48	50	H	5.0	H	  3.0  4.0

51	66	C	5.0	H	  4.3  5.0

68	91	-	3.0	P	  6.3  75.0

93	94	-	3.0	P	  75.0  12.0

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