Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
_____________________________________________

>P1;d1lpba1
-------------CCCCCCCCCCCCCCHHHCCC-CCEE-C----CCCCCCCEECCCCC

>P1;d1lpba2
CCCEEECC---CCCC---CCCCCCCC------CCEEEECCCCHHHHHHCCCEEEEEEC

>P1;d2kraa1
-------------C-----CCCCCCCCHHHCCCCEECCCC----CCCCCCCCCEECCC

>P1;d2kraa2
CCCCCCCCCCCCCCCCCCCCCCCCCC------CCCEEEEEC--------CEEEEE---
PSA

>P1;d1lpba1
-------------6b77a06485507a471052-7306-4----879958140476aa

>P1;d1lpba2
48860029---074b---82739409------ad15055b66981464050325048a

>P1;d2kraa1
-------------a-----a85170876b60ba7420530----a75692423375be

>P1;d2kraa2
69830347134892a795b2a49007------ab290655b--------85330b---


Translating the sequences
-------------CC***CCCCCCCC******C-**EE-C----****CCCEE****C
********---**CC---CCCCCCCC------CC*EEE*C********CCCEEEE**C
-------------C-----CCCCCCC******CC*E***C----****CCC**EE**C
*************CC***CCCCCCCC------CC*EEE***--------C*EEEE---

57190.tem
_________________________________
********---**CC***CCCCCCCC******CC*EEE*C*---****CCCEEEE**C




Structural block scores
0	7	*	3.5	M	  75.0  4.6  75.0  5.0

8	10	-	4.3	M	  75.0  75.0  75.0  2.7

11	12	*	3.5	M	  75.0  3.5  75.0  8.5

13	14	C	4.7	H	  8.8  7.8  42.8  6.2

15	17	*	3.5	M	  8.2  75.0  75.0  7.0

18	25	C	4.9	H	  4.4  5.2  14.3  5.5

26	31	*	3.5	M	  4.6  75.0  7.0  75.0

32	33	C	4.7	H	  38.5  12.0  8.8  11.0

35	37	E	4.3	M	  3.0  3.3  2.3  5.0

41	43	-	4.3	M	  75.0  7.7  75.0  75.0

44	47	*	2.3	P	  8.2  3.8  7.1  75.0

48	50	C	4.5	M	  4.7  1.7  5.0  29.3

51	54	E	4.3	M	  3.8  2.5  3.8  4.4

55	56	*	2.3	P	  8.2  6.0  8.2  75.0

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