Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
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>P1;d1b0na1
--CCHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHC

>P1;d1b0nb-
CCCCHHHHHHHHHHHHCCCCHHHHHHHHHHC------
PSA

>P1;d1b0na1
--58a865755756794c5698657755854766876

>P1;d1b0nb-
bb778864554561876a5668726665855------


Translating the sequences
--CCHHHHHHHHHHHHCCCCHHHHHHHHHHH******
**CCHHHHHHHHHHHHCCCCHHHHHHHHHH*------

47406.tem
_________________________________
--CCHHHHHHHHHHHHCCCCHHHHHHHHHHH------




Structural block scores
0	1	-	3.0	P	  75.0  11.5

2	3	C	5.0	H	  6.5  7.0

4	15	H	5.0	H	  6.7  5.6

16	19	C	5.0	H	  6.9  6.9

20	30	H	4.8	H	  6.3  5.8

31	36	-	3.0	P	  6.7  75.0

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