Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
_____________________________________________

>P1;d1pp9e2
-CHHHCCCCCCCCCCCHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCC

>P1;d1q90r-
---------------------------CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC----C

>P1;d3cx5e2
CCCCC--CCCCCCCCCC---------CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCC---
PSA

>P1;d1pp9e2
-79788987865a85575145a866598239826885777778788977866846767887898579967

>P1;d1q90r-
---------------------------b98957775566678787b75786768878a8979688----9

>P1;d3cx5e2
85aa8--7776888758---------b7596696776786894898878697776768877897aab---


Translating the sequences
-C*****CCCCCCCCC***************HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCC**C
---------------------------CCCC**HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC----C
*C***--CCCCCCCCC*---------*CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH**CCCC---

81502.tem
_________________________________
-C***--CCCCCCCCC*---------*CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCC--C




Structural block scores
2	4	*	2.7	P	  8.0  75.0  9.7

5	6	-	4.0	M	  8.5  75.0  75.0

7	15	C	4.0	M	  6.9  75.0  7.0

17	25	-	4.0	M	  5.6  75.0  75.0

27	30	C	4.0	M	  5.5  9.4  6.8

31	62	H	4.9	H	  7.0  7.2  7.3

63	66	C	4.5	M	  7.2  41.5  9.9

67	68	-	4.0	M	  7.5  75.0  75.0

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