Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
_____________________________________________

>P1;d2odka1
-CEEEHHHHHHCHHHHHHHHHHC-CCEEEEECCEEEEEECCHHHHHHHHHHC-------------------------------

>P1;d3d55a-
-CEEEHHHHHHCHHHHHHHHHHHCCCEEEECCC-CCEEECCHHHHHHHHHHHHHCCCHHHHHHHHHHHCC-------------

>P1;d7bwfb1
CEEEEHHHHHHCHHHHHHHHHHHCCCEEEECCCCCCEEECCHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHCCCCCCCCCC
PSA

>P1;d2odka1
-740468509756a505710657-3303206aa6647432277556775888-------------------------------

>P1;d3d55a-
-780447608865a5058305854750726199-a77323096356787766755748625556866988-------------

>P1;d7bwfb1
4373968407945970574066573202033c78837421088357744666647778b437737747437868839a7b8a9


Translating the sequences
-CEEEHHHHHHCHHHHHHHHHH*-CCEEEE*CC***EEECCHHHHHHHHHH*-------------------------------
-CEEEHHHHHHCHHHHHHHHHHHCCCEEEECCC-CCEEECCHHHHHHHHHHHHH*CCHHHHHHHHHHH**-------------
**EEEHHHHHHCHHHHHHHHHHHCCCEEEECCC*CCEEECCHHHHHHHHHHHHH*CCHHHHHHHHHHH***************

143120.tem
_________________________________
-CEEEHHHHHHCHHHHHHHHHHHCCCEEEECCC*CCEEECCHHHHHHHHHHHHH*CCHHHHHHHHHHH**-------------




Structural block scores
2	4	E	5.0	H	  2.7  4.0  6.3

5	10	H	5.0	H	  5.8  5.5  5.7

12	22	H	4.9	H	  4.8  5.0  4.9

23	25	C	4.7	H	  27.0  5.3  4.0

26	29	E	5.0	H	  1.2  3.8  1.2

30	32	C	4.7	H	  9.0  6.3  7.5

34	35	C	4.0	M	  5.0  8.8  5.5

36	38	E	5.0	H	  4.7  4.0  4.3

39	40	C	5.0	H	  2.0  1.5  0.5

41	53	H	4.8	H	  17.2  6.3  5.7

55	56	C	4.0	M	  75.0  5.5  7.0

57	67	H	4.0	M	  75.0  6.0  6.2

68	69	*	2.7	P	  75.0  8.0  3.5

70	82	-	4.0	M	  75.0  75.0  8.1

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