Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
_____________________________________________

>P1;d1e88a3
-CC-CEEEC-CCEEECCCEEEEEECC--CCEEEEEECC--C-CCEEECC------------------------------

>P1;d1o9aa1
CCC-CEECC--CCEECCCCEEEEEEC--CEEEEEECCCCCC-CCEEEECC-----------------------------

>P1;d1tpga2
CCCCCCCCCCCCCCCCCCCEEEEECCCCCCEEEEECCC---CCCCCCEECCCC--------------------------

>P1;d1u5ma1
CCCCCEECC--CCEECCCCEECCC-----CCEEEEEECC---EEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC

>P1;d2cg7a2
C-CCEEECCCCCCEEECCCEEEEEECC--EEEEEEEEECCCCEEEEECCC-----------------------------
PSA

>P1;d1e88a3
-a5-31508-585525665807166a--c490300063--c-837285c------------------------------

>P1;d1o9aa1
997-5071c--878294a57174659--86313040402b8-82616749-----------------------------

>P1;d1tpga2
aa673161974a7817565316652994c412404045---07451634949b--------------------------

>P1;d1u5ma1
c77330948--7763849451527-----75620005b0---7472581b0383792c85931a4133612449b8aaa

>P1;d2cg7a2
b-754060722675165848161548a--452504050689270605589-----------------------------


Translating the sequences
-CC-CEE*C-CC*EECCC*EEEEE*C--CCEEEEEECC--C-CCEEE*C------------------------------
CCC-CEECC--CCEECCCCEEEEE*C--C*EEEEE*CCC*C-CCEEEECC-----------------------------
CCCCC**CC*CCC**CCCCEEEEE*C**CCEEEEE*CC---*CC***E*C***--------------------------
CCCCCEECC--CCEECCCCEE***-----C*EEEEE*CC---**EEEECC*****************************
C-CC*EECC*CCCEE*CCCEEEEE*C*--*EEEEEE**C*C***EEE*CC-----------------------------

57603.tem
_________________________________
CCCCCEECC-CCCEECCCCEEEEE*C--CCEEEEEECCC-C-CCEEEECC-----------------------------




Structural block scores
0	4	C	4.5	M	  33.7  21.0  7.4  6.5  20.5

5	6	E	4.5	M	  3.0  3.5  3.5  4.5  3.0

7	8	C	4.8	H	  4.0  6.8  5.0  6.0  3.5

10	12	C	4.6	H	  6.0  30.0  7.2  29.7  5.0

13	14	E	4.5	M	  3.5  5.0  4.5  4.5  3.0

15	18	C	4.8	H	  5.5  7.1  5.8  6.2  5.8

19	23	E	4.7	H	  4.4  5.0  4.2  4.0  4.2

26	27	-	4.2	M	  75.0  75.0  6.5  75.0  42.8

28	29	C	4.0	M	  8.2  7.0  8.2  41.0  39.5

30	35	E	4.7	H	  2.0  1.8  1.8  2.2  2.7

36	38	C	4.2	M	  28.0  2.0  28.0  5.5  3.7

42	43	C	3.8	M	  5.5  5.0  5.5  5.5  3.5

44	47	E	4.3	M	  5.5  5.0  3.8  5.5  4.0

48	49	C	4.5	M	  43.8  6.5  6.5  6.2  8.5

50	78	-	4.4	M	  75.0  75.0  68.1  5.8  75.0

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