Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
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>P1;d2qi2a1
CEEEEEEC----CCC-EEEEECCCCHHHHHHHHHCCCCCEEEEEEC-CCEEEEEEEEEEECCCCCCCEEEEEEECCC-----------CCEEEEEECCCCEEEEEC-CCCHHHHHHHHHHCC

>P1;d2vgna1
-CEEEEEECCCCCCCEEEEECCCCHHHHHHHHCCCCCCCEEEEEECCCCEEEEEEEEEEEEE-CCCEEEEEEEECCCCCCCCCCCCCCCCEEEEECCCCCCEEEEECCCCC-CCHHHHHCCC
PSA

>P1;d2qi2a1
05227358----975-11102046580042045003a505031255-a77813030570707695750404031456-----------895540504363401031-905982272076029

>P1;d2vgna1
-61461844aa69200402010456710610330057602020337ab25501040562525-a75302030302619677006a17776711050537430102079089-726207633b


Translating the sequences
*EEEEEE*----CCC-EEEEECCC*HHHHHHHHHCCCCCEEEEEEC-CCEEEEEEEEEEE***CCC*EEEEEEECCC-----------CCEEEEEECCCCEEEEE*-CCCH*HHHHHHHHCC
-*EEEEEE****CCC*EEEE*CCCHHHHHHHH**CCCCCEEEEEEC*CCEEEEEEEEEEEEE-CCCEEEEEEEECCC***********CCEEEEE*CCCC*EEEEE*CCC*-**HHHHH*CC

159065.tem
_________________________________
-EEEEEEE----CCC-EEEEECCCHHHHHHHHHHCCCCCEEEEEEC-CCEEEEEEEEEEEEE-CCCEEEEEEEECCC-----------CCEEEEEECCCCEEEEEE-CCCH-HHHHHHHHCC




Structural block scores
1	7	E	4.4	M	  4.6  4.3

8	11	-	3.0	P	  75.0  7.8

12	14	C	5.0	H	  7.0  3.7

16	20	E	4.6	H	  1.0  1.4

21	23	C	5.0	H	  3.3  3.0

24	33	H	4.4	M	  2.8  2.7

34	38	C	5.0	H	  3.7  3.6

39	44	E	5.0	H	  2.7  1.7

47	48	C	5.0	H	  8.8  6.8

49	61	E	4.7	H	  3.7  3.1

63	65	C	5.0	H	  7.0  7.5

66	73	E	4.8	H	  2.1  1.4

74	76	C	5.0	H	  5.0  3.0

77	87	-	3.0	P	  75.0  5.5

88	89	C	5.0	H	  8.5  6.5

90	95	E	4.7	H	  3.2  2.3

96	99	C	5.0	H	  4.0  4.8

100	105	E	4.3	M	  1.5  1.0

107	109	C	5.0	H	  4.7  5.7

112	119	H	4.2	M	  3.2  4.1

120	121	C	5.0	H	  5.5  7.2

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