Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
_____________________________________________

>P1;d1e6ta-
CCCCCCEEEECCCC-CCCEEEEEEEC--HHHCEEEECC-CCCCCCCEEEEEEECCCC-CEEEEEEEEEEEEEEEEEECCEEEEEEEEEEEEEEEEEEECCCCHHHHHHHHHHHHHHHCCCCHHHHHHHCCCCCC-

>P1;d1qbea-
C-CCCCEEECCCCCCCCCEEEEEEEEECCCCEEEEEECCCCHHHCCEEEEEEEC----CCEEEEEEEEEEEEEC------CCCEEEEEEEEEEEEEECCCCCHHHHHHHHHHHHHHHHCH-HHHHHHCCCCCCC-

>P1;d2quda1
C--CCEEEEEE---CCEEEEEEEEEECC--CCEEEECCCCCCCCCCEEEEEEEECCCCCEEEEEEEEEEEEECCC-----CCCCEEEEEEEEEEEEEECCCCHHHHHHHHHHHHHHHHCH-HHHHHHHHCCCCCC
PSA

>P1;d1e6ta-
b8c276441476a9-ab224052266--6a9511110b-455610130123365169-6332343311506655656c987553047165573524053718b853783678478668aa475161887b4a6a-

>P1;d1qbea-
c-837556459469858624052495588772231033c276930341343549----7846333444405088------ca39368386554416166907996458566646855837-625536668686c-

>P1;d2quda1
a--67354468---ca65440112456a--6441101488685010412116544c77714435453261324a9-----ca38355373454535253b28896466574857764759-41844566948496


Translating the sequences
C*CCCCEEEECCCC-CCCEEEEEEE*--***CEEEECC-CCCCCCCEEEEEEECCCC-CEEEEEEEEEEEEEE**********EEEEEEEEEEEEEEECCCCHHHHHHHHHHHHHHH*C**HHHHHHHCCCCCC-
C-CCCCEEE*CCCCCCCCEEEEEEEE*C**C*EEEE*CCCC***CCEEEEEEEC----C*EEEEEEEEEEEEEC------CCCEEEEEEEEEEEEEE*CCCCHHHHHHHHHHHHHHHHCH-HHHHHH*CCCCCC-
C--CC*EEEE*---CC**EEEEEEEE*C--CCEEEECCCCCCCCCCEEEEEEE*CCC*CEEEEEEEEEEEEE*C*-----CCC*EEEEEEEEEEEEEECCCCHHHHHHHHHHHHHHHHCH-HHHHHHH*CCCCC*

55405.tem
_________________________________
C-CCCCEEEECCCCCCCCEEEEEEEE*C**CCEEEECCCCCCCCCCEEEEEEECCCC-CEEEEEEEEEEEEEEC*-----CCCEEEEEEEEEEEEEEECCCCHHHHHHHHHHHHHHHHCH-HHHHHHHCCCCCC-




Structural block scores
2	5	C	4.5	M	  6.9  5.8  22.8

6	9	E	4.8	H	  3.2  5.0  4.8

10	17	C	4.1	M	  16.4  6.9  33.4

18	25	E	4.9	H	  3.4  3.9  2.6

28	29	*	2.7	P	  8.2  7.5  75.0

30	31	C	4.0	M	  7.0  4.5  5.0

32	35	E	5.0	H	  1.0  1.5  1.5

36	45	C	4.5	M	  10.8  4.8  4.1

46	52	E	5.0	H	  2.6  3.4  2.9

53	56	C	4.0	M	  5.2  58.5  6.9

59	72	E	4.9	H	  3.2  4.0  3.4

75	79	-	4.0	M	  8.1  75.0  75.0

80	82	C	4.0	M	  5.7  8.7  8.7

83	97	E	4.9	H	  3.8  5.0  4.5

98	101	C	5.0	H	  4.8  5.5  6.1

102	117	H	4.9	H	  6.6  6.2  6.2

121	127	H	4.9	H	  5.1  4.7  4.6

128	133	C	4.8	H	  8.2  7.8  6.7

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