Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
_____________________________________________

>P1;d2a73b6
CCEEEEEEEECCEECCCCCCCCCCCEEEECCCCCCCCCCCCCCEEEEEEEC-CCEEEEEEECCCCCCCEEEEEECCCCCCEEEEEECCCCCEEEECC-CCCCEEEEEEEEEEECC

>P1;d3cu7ad
C-CEEEEEEEEEEECCCCCCCCCCCCEEECCCCCCCCCCCCCCEEEEEEECCCCCCCCCEEECCCCCCCCCCCCCCC-CCCCCEECCCCCCEEECCCCCCCCEEEEEEEEEECCC
PSA

>P1;d2a73b6
a07547360073501067b28b83161905508085207b26040501050-8060402060433b95151704696b4353225176222050405-7605140303030206b

>P1;d3cu7ad
a-958644932240005147a8523643051851a5108a3915030403067020604020376a63262603696-3756524075712010209641020407042203257


Translating the sequences
C*EEEEEEEE**EECCCCCCCCCCCEEEECCCCCCCCCCCCCCEEEEEEEC-CCEEEEEEE*CCCCCCEEEEEECCC*CCEEEEEECCCCCEEEECC-CCCCEEEEEEEEEEECC
C-*EEEEEEEEEEECCCCCCCCCCC*EEECCCCCCCCCCCCCCEEEEEEEC*CC*****EEECCCCCC******CCC-CC***EE*CCCCCEEE*CC*CCCCEEEEEEEEEE*CC

254131.tem
_________________________________
C-EEEEEEEEEEEECCCCCCCCCCCEEEECCCCCCCCCCCCCCEEEEEEEC-CCEEEEEEEECCCCCCEEEEEECCC-CCEEEEEECCCCCEEEECC-CCCCEEEEEEEEEEECC




Structural block scores
2	13	E	4.5	M	  3.9  4.7

14	24	C	5.0	H	  5.4  4.1

25	28	E	4.5	M	  4.0  3.2

29	42	C	5.0	H	  4.2  4.9

43	49	E	5.0	H	  2.1  2.1

52	53	C	5.0	H	  4.0  3.5

54	61	E	3.5	M	  2.2  1.8

62	67	C	5.0	H	  5.9  5.9

68	73	E	3.0	P	  3.0  3.2

74	76	C	5.0	H	  7.0  7.0

78	79	C	5.0	H	  3.5  5.0

80	85	E	3.7	M	  3.0  3.7

86	90	C	5.0	H	  3.8  4.4

91	94	E	4.5	M	  2.2  0.8

95	96	C	5.0	H	  2.5  4.5

98	101	C	5.0	H	  4.5  1.8

102	112	E	4.8	H	  1.5  2.2

113	114	C	5.0	H	  8.8  6.0

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