Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
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>P1;d1ru0a-
CCCCCCCC--CCCCCCCCCEECCCCCCEEEEEEC-CHHHHHHHHHHHHHHHHHHCCCCEEEEECCEEEEEECCCCCCCCCCCCC-CHHHHHHHHCC--

>P1;d1usma-
----------------CCCEE---CCCEEEEEECCCHHHHHHHHHHHHHHHHHHCCCCEEEEECCEEEEEECCCCCCCCCHHHHHHHHHHHHCCCC--

>P1;d2ebba-
-CCCHHHHHHHHHCCC-CCEEECCC-EEEEEEECCCHHHHHHHHHHHHHHHHHCCCCCEEEEECCEEEEEECCCCCCCCCHHHHHHHHHHHHHHHHHC
PSA

>P1;d1ru0a-
76068932--417a09390753a95400313041-75a70690154068207829050527177340301010a5390006200-00620380188--

>P1;d1usma-
----------------58074---543000109164565046007506600762915062514715010003399492038304400630171278--

>P1;d2ebba-
-51788517721981a-60744884-30116060a64850420274057307a381606152973200030018838002640040075026116707


Translating the sequences
*CCC****--***CCCCCCEE*CCCCCEEEEEEC-CHHHHHHHHHHHHHHHHHHCCCCEEEEECCEEEEEECCCCCCCCC****-*HHHHHHHHCC--
----------------CCCEE---CCCEEEEEECCCHHHHHHHHHHHHHHHHHHCCCCEEEEECCEEEEEECCCCCCCCCHHHHHHHHHHHH**CC--
-CCC*********CCC-CCEE*CCC-*EEEEEECCCHHHHHHHHHHHHHHHHH*CCCCEEEEECCEEEEEECCCCCCCCCHHHHHHHHHHHHHH****

55248.tem
_________________________________
-CCC****--***CCCCCCEE*CCCCCEEEEEECCCHHHHHHHHHHHHHHHHHHCCCCEEEEECCEEEEEECCCCCCCCCHHHHHHHHHHHHHHCC--




Structural block scores
1	3	C	4.0	M	  4.0  75.0  4.3

4	7	*	2.7	P	  5.5  75.0  5.5

8	9	-	4.0	M	  75.0  75.0  7.0

10	12	*	2.7	P	  4.0  75.0  4.0

13	18	C	4.3	M	  5.2  39.7  16.8

19	20	E	5.0	H	  6.0  5.5  5.5

22	26	C	4.2	M	  5.7  32.4  19.6

27	32	E	5.0	H	  1.8  1.7  2.3

33	35	C	4.7	H	  27.7  3.7  5.5

36	53	H	4.9	H	  4.5  3.6  4.0

54	57	C	5.0	H	  3.5  3.8  3.8

58	62	E	5.0	H	  4.4  3.6  4.6

63	64	C	5.0	H	  5.0  4.0  5.0

65	70	E	5.0	H	  1.3  1.0  0.8

71	79	C	5.0	H	  3.2  4.7  3.3

80	93	H	4.4	M	  7.4  2.8  2.6

94	95	C	4.0	M	  8.0  7.5  6.5

96	97	-	4.0	M	  75.0  75.0  3.5

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