Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
_____________________________________________

>P1;d1m1ha2
CCCCCCCEEEEEEECCCCHHHHHHHHHHHHHHCCCHHHEEEEECCCC----------------CCCCCEEEEEECCC-----HHHHHHHHCCCCEEEECEEC-CEECEECHHHHHHHHHHCCC------

>P1;d1nz8a-
-----CCEEEEEECCCCCHHHHHHHHHHHHHHHCCCCCCCEEECCEEEEEEECCCCCEEEEEEECCCCEEEEEECCCCCCCCCHHHHHHCCCCCCCCCCCCCC-CCEECCHHHHHHHHHHHCCCC----

>P1;d2k06a-
CCCCCCCEEEEEEECCCCHHHHHHHHHHHHHHHCCCCCEEEEECCCCCCCC-CCCCCCCCCCCCCCCCEEEEEECCC-----HHHHHHHHHCCCEEEECCCCCCCCCCCCHHHHHHHHHHHHHCCCCCC
PSA

>P1;d1m1ha2
8a9687150010305695095025204720684a06b2054021022----------------a3242300020515-----b601500380530730419c-78043166940671365188------

>P1;d1nz8a-
-----a45010020688708802850685067570792033113022556775bb973676565335130001030b3a982660091068051066336996-6063168a606801530535f----

>P1;d2k06a-
ba88764400004065b5045019107610575b15a203632204794b5-a72c8a9559391241400020313-----960170065054134027897770641879507622952b949576b


Translating the sequences
CCCCCCCEEEEEEECCCCHHHHHHHHHHHHHH*CC***EEEEECCCC----------------CCCCCEEEEEECCC-----HHHHHHHHCCCCEEEEC**C-C**CE*CHHHHHHHHHH*CC------
-----CCEEEEEE*CCCCHHHHHHHHHHHHHHHCCCCC**EEECC*******CCCCC*******CCCCEEEEEECCC******HHHHHH*CCCC****CCCCC-CC*ECCHHHHHHHHHHHCCCC----
CCCCCCCEEEEEEECCCCHHHHHHHHHHHHHHHCCCCCEEEEECCCC****-CCCCC******CCCCCEEEEEECCC-----HHHHHHHH*CCCEEEECCCCCCCCC*CCHHHHHHHHHHH**CC****

82679.tem
_________________________________
CCCCCCCEEEEEEECCCCHHHHHHHHHHHHHHHCCCCCEEEEECCCC****-CCCCC******CCCCCEEEEEECCC-----HHHHHHHHCCCCEEEECCCCCCCCCECCHHHHHHHHHHHCCCC----




Structural block scores
0	6	C	4.3	M	  7.1  55.6  7.9

7	13	E	4.9	H	  1.3  1.1  1.1

14	17	C	5.0	H	  6.2  7.2  6.9

18	32	H	4.9	H	  3.6  4.5  3.4

33	37	C	4.4	M	  6.0  5.0  6.0

38	42	E	4.6	H	  2.2  1.6  2.8

43	46	C	4.5	M	  1.2  1.8  3.2

47	50	*	2.7	P	  75.0  5.8  7.4

52	56	C	4.0	M	  75.0  8.8  8.0

57	62	*	2.7	P	  75.0  5.5  6.9

63	67	C	4.8	H	  4.3  3.4  3.4

68	73	E	5.0	H	  0.8  0.7  1.0

74	76	C	5.0	H	  3.7  4.8  2.3

77	81	-	4.0	M	  75.0  6.5  75.0

82	89	H	4.8	H	  3.3  3.5  3.6

90	93	C	4.8	H	  4.0  3.5  3.5

94	97	E	4.0	M	  2.5  3.8  2.0

98	106	C	4.2	M	  13.4  13.3  5.9

108	109	C	4.5	M	  3.5  3.5  4.5

110	120	H	4.9	H	  4.4  4.3  4.9

121	124	C	4.0	M	  41.5  8.9  8.4

125	128	-	4.0	M	  75.0  75.0  7.4

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