Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
_____________________________________________

>P1;d1e0ga-
CCCEEEECCCCCHHHHHHHCCCCHHHHHHHCCCCC--CCCCCEEEECCCC---

>P1;d4a1ia1
CE-EEECCCCCCHHHHHHHHCCCHHHHHHHCH-HHHHCCCCCCEEEECC---C

>P1;d4uz3a2
CCCEEECCCCCCHHHHHHHCCCCHHHHHHHHC-CCCCCCCCCCEEECCCHHHC

>P1;d5buma-
-CCEEECCCCCCHHHHHHHCCCCHHHHHHCCCCCCHHHCCCCCEEECCC----

>P1;d5k2la-
CCEEEECCCCCCHHHHHHHHCCCHHHHHHHCCCCCCCCCCCCCEEEECC----
PSA

>P1;d1e0ga-
b45406079c3628610992a0717205733a918--917473602050b---

>P1;d4a1ia1
74-527078b0739600862817394049218-909981837350202c---5

>P1;d4uz3a2
369526067b160830076090618002611a-1a659086725070099c51

>P1;d5buma-
-17525069c2607600673a28373057218c062a607863601048----

>P1;d5k2la-
a83525067c1607400782a17494047407b2649809573506025----


Translating the sequences
CCCEEE*CCCCCHHHHHHHCCCCHHHHHHHCCCCC--CCCCC*EEECCC*---
C*-EEECCCCCCHHHHHHH*CCCHHHHHHHC*-****CCCCCCEEE*CC---*
CCCEEECCCCCCHHHHHHHCCCCHHHHHHH*C-CC**CCCCCCEEECCC****
-CCEEECCCCCCHHHHHHHCCCCHHHHHH*CCCCC***CCCCCEEECCC----
CC*EEECCCCCCHHHHHHH*CCCHHHHHHHCCCCC**CCCCCCEEE*CC----

54106.tem
_________________________________
CCCEEECCCCCCHHHHHHHCCCCHHHHHHHCCCCC**CCCCCCEEECCC----




Structural block scores
0	2	C	4.4	M	  6.8  28.7  6.0  27.7  7.2

3	5	E	5.0	H	  3.3  4.7  4.3  4.0  4.0

6	11	C	4.9	H	  6.2  5.6  5.2  5.9  5.4

12	18	H	5.0	H	  5.0  4.6  3.4  3.7  3.7

19	22	C	4.7	H	  4.9  4.5  3.8  5.9  5.1

23	29	H	4.9	H	  3.6  4.4  2.6  3.9  4.6

30	34	C	4.4	M	  6.3  18.6  19.6  5.5  5.3

35	36	*	2.1	P	  75.0  9.0  5.5  6.2  6.5

37	42	C	4.8	H	  5.2  5.0  5.3  5.0  5.3

43	45	E	5.0	H	  2.7  2.3  4.0  2.3  3.7

46	48	C	4.6	H	  1.7  4.8  3.0  4.0  2.3

49	52	-	4.2	M	  59.1  57.5  6.9  75.0  75.0

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