Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
_____________________________________________

>P1;d3s3na3
CCCCCCEEEECCCCCCCCCCCCCCCEEEEEEEECCEEEEECCCC-CEEEEEHHHEEECCCC

>P1;d4fw1a2
CCCCCCEEEEECCC-----CCEEEEEEEEEE-CCCEEEEEECCCCCEEEEEHHHEEECC--

>P1;d6t6ea1
CC-CCEEEEECCCCC----CCCEEEEEEEEE-CCCEEEEEEC--CEEEEEEHHHEEEEEC-
PSA

>P1;d3s3na3
7086645011429a289a77525740404723776302041670-86550427603627ab

>P1;d4fw1a2
b6a60640204597-----872555010263-8a960000249676336132720461a--

>P1;d6t6ea1
34-890403024694----883305050273-5b9302041c--a653703381062574-


Translating the sequences
CCCCCCEEEECCCCC****CCC***EEEEEE**CCEEEEE*CCC-CEEEEEHHHEEECCC*
CCCCCCEEEE*CCC-----CC*EEEEEEEEE-CCCEEEEEECCCCCEEEEEHHHEEECC--
CC-CC*EEEECCCCC----CCCEEEEEEEEE-CCCEEEEEEC--C*EEEEEHHHEEE**C-

50122.tem
_________________________________
CCCCCCEEEECCCCC----CCCEEEEEEEEE-CCCEEEEEECCCCCEEEEEHHHEEECCC-




Structural block scores
0	5	C	4.7	H	  5.2  6.7  16.5

6	9	E	5.0	H	  1.8  1.5  1.8

10	14	C	4.6	H	  5.5  20.0  5.0

15	18	-	4.0	M	  8.6  75.0  75.0

19	21	C	4.7	H	  4.7  5.7  6.3

22	30	E	4.7	H	  3.7  3.0  2.8

32	34	C	4.7	H	  6.7  9.2  8.5

35	40	E	4.8	H	  1.7  1.3  1.7

41	45	C	4.2	M	  19.2  6.4  35.8

46	50	E	5.0	H	  4.0  3.2  3.6

51	53	H	5.0	H	  5.0  3.7  4.0

54	56	E	5.0	H	  3.0  3.3  2.7

57	59	C	4.0	M	  6.5  28.8  5.3

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