Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
_____________________________________________

>P1;d1ucsa-
-------CCCEEEECCCCCCCCCCCHHHEEEECCC--CCCCCHHHHHHHC-CCCCCCCCCCCCCCCHHHCCCCC

>P1;d1vlia1
--CHHHHCCCEEEECCCCCCCCCCCCCCEEEECCCCCCCCCCHHHHHHHHCCCCCCCCCCCCCCCCHHHCCCCC

>P1;d2wqpa2
CHHHHHHHCCEEEECCCCCCCCCCCCCCEEEECCCC--CCCCHHHHHHHC-CCCCCCCCCCCCCCCHHHCC---
PSA

>P1;d1ucsa-
-------5720000545046734067810334638--8300417216704-72504440575410258103c1c

>P1;d1vlia1
--87777475000045608794405891033570cb4920152622a70178460257073750055400686a

>P1;d2wqpa2
878656627200004570767570438106266419--04155b428703-75401580864430679016---


Translating the sequences
-------CCCEEEECCCCCCCCCCC***EEEECCC--CCCCCHHHHHHHC-CCCCCCCCCCCCCCCHHHCCCCC
--*HHHHCCCEEEECCCCCCCCCCCCCCEEEECCCC*CCCCCHHHHHHH**CCCCCCCCCCCCCCCHHHCCCCC
***HHHH*CCEEEECCCCCCCCCCCCCCEEEECCCC--CCCCHHHHHHHC-CCCCCCCCCCCCCCCHHHCC---

51269.tem
_________________________________
--*HHHHCCCEEEECCCCCCCCCCCCCCEEEECCCC-CCCCCHHHHHHHC-CCCCCCCCCCCCCCCHHHCCCCC




Structural block scores
0	1	-	4.0	M	  75.0  75.0  7.5

3	6	H	4.0	M	  75.0  7.0  5.8

7	9	C	4.7	H	  4.7  5.3  3.7

10	13	E	5.0	H	  0.0  0.0  0.0

14	27	C	4.8	H	  4.3  5.0  4.6

28	31	E	5.0	H	  2.5  2.8  3.5

32	35	C	4.8	H	  23.0  7.8  5.0

37	41	C	4.8	H	  3.0  3.4  17.0

42	48	H	5.0	H	  3.4  4.2  5.4

51	65	C	5.0	H	  3.3  3.9  4.1

66	68	H	5.0	H	  4.7  3.0  5.3

69	73	C	4.4	M	  5.8  6.1  46.4

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