Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
_____________________________________________

>P1;d1e0na-
-------------CCEEEEECC--CCEEEEECCCCEEECCCC------

>P1;d1eg3a3
CCCHHHHHCCCC-CCEEEEECC-CCCEEEEECCCCEEECC--------

>P1;d1o6wa2
CCCHHHHHHHHHHHCCEEEECC-CCCEEEEECCCCEEECCCC-CCCCC

>P1;d1ywia1
-------------CCEEEEEEC-CCEEEEEECCCCEEECCCC------

>P1;d2ho2a1
---------CCCCCCEEEEECC-C-CEEEEECCCCCEECCCCCC----

>P1;d2itka1
-----------CCCCEEEEECCCCCCEEEEECCCCCEECCCCC-----

>P1;d4n7fa1
----------CCCCCEEEEECC-CCCEEEEECCCCEEECCCCCC----

>P1;d4rexa1
---CCCCCCCCCCCCEEEEECC-CCCEEEEECCCCEEECCCHHHHHCC
PSA

>P1;d1e0na-
-------------b3346574b--985134067784535769------

>P1;d1eg3a3
4a7399449629-933512119-a663213168798556a--------

>P1;d1o6wa2
9aa877468208537043254b-7755213048495737a23-8167a

>P1;d1ywia1
-------------963566709-7456314146767636984------

>P1;d2ho2a1
---------c703b4173385b-8-73214245665436860a8----

>P1;d2itka1
-----------23901553619a4765203066675444860c-----

>P1;d4n7fa1
----------a23a41435519-985420105888652591149----

>P1;d4rexa1
---b6078a5814b9162354b-878120425a597736a1105896b


Translating the sequences
-------------CCEEEEECC--CCEEEEECCCCEEECCCC------
************-CCEEEEECC-CCCEEEEECCCCEEECC--------
**************C*EEEECC-CCCEEEEECCCCEEECCCC-*****
-------------CCEEEEE*C-CC*EEEEECCCCEEECCCC------
---------****CCEEEEECC-C-CEEEEECCCC*EECCCC**----
-----------**CCEEEEECC*CCCEEEEECCCC*EECCCC*-----
----------***CCEEEEECC-CCCEEEEECCCCEEECCCC**----
---**********CCEEEEECC-CCCEEEEECCCCEEECCC*******

51045.tem
_________________________________
---**********CCEEEEECC-CCCEEEEECCCCEEECCCC**----




Structural block scores
0	2	-	4.3	M	  75.0  7.2  10.0  75.0  75.0  75.0  75.0  75.0

3	12	*	3.5	M	  75.0  13.0  5.5  75.0  47.2  60.5  54.0  6.1

13	14	C	4.8	H	  7.2  6.0  5.0  7.5  7.8  4.5  7.2  10.2

15	19	E	4.9	H	  5.0  2.4  2.8  5.4  4.4  4.0  3.6  3.4

20	21	C	4.8	H	  7.8  5.0  7.8  4.5  8.2  5.0  5.0  7.8

23	25	C	4.7	H	  30.7  7.5  6.3  5.3  30.0  5.7  7.3  7.7

26	30	E	5.0	H	  2.6  2.0  2.2  3.0  2.4  2.0  1.4  1.8

31	34	C	5.0	H	  7.0  7.5  6.2  5.8  5.2  6.2  7.2  7.4

35	37	E	4.8	H	  4.0  6.0  5.0  5.3  4.0  4.3  4.3  5.7

38	41	C	4.8	H	  6.8  41.6  5.6  6.8  5.0  4.5  4.0  4.6

42	43	*	3.4	M	  75.0  75.0  41.5  75.0  9.2  43.8  6.5  2.5

44	47	-	4.3	M	  75.0  75.0  6.1  75.0  75.0  75.0  75.0  8.6

>>>>>>