Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
_____________________________________________

>P1;d1vzma-
-CCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCCCCC

>P1;d2pf1a2
------CCCHHHHHHHHHCCCCC-CCHHHHHHHHCCC---

>P1;d6r2wl1
CCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCC--C
PSA

>P1;d1vzma-
-aa18ba3280650b3a70641996905601453368264

>P1;d2pf1a2
------68993766645705b25-a5995376347aa---

>P1;d6r2wl1
8ca96869544506a094062287870791288247b--c


Translating the sequences
-CCCCCCCCCCCCCCCCCCCC*****HHHHHHHH*CC**C
------CCC*********CCCCC-CCHHHHHHHHCCC---
*CCCCCCCCCCCCCCCCCCCCCC*CCHHHHHHHHCCC--C

57630.tem
_________________________________
-CCCCCCCCCCCCCCCCCCCCCC*CCHHHHHHHHCCC--C




Structural block scores
1	22	C	4.3	M	  5.8  21.6  5.8

24	25	C	4.0	M	  7.5  7.8  7.5

26	33	H	5.0	H	  3.0  5.8  4.6

34	36	C	4.7	H	  5.7  9.3  7.5

37	38	-	4.0	M	  4.0  75.0  75.0

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