Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
_____________________________________________

>P1;d1l6pa-
CCCCCCCCCHHHHEEEEEEEECCEEEEEEEECCCEEEEHHHCEEEEEEEE-ECCCCCCCCEEEEECCCE-EEEECCEEEEEEEEE-EEEEEEEEEEEECEEECCCEECCCEEEEEECCCCCC----

>P1;d6dnva1
----CCCCCHHHHEEEEEEEECCEEEEEEEECCCEEEEHHHCEEEEECCCCCCCCEECCCEEEEECCCEEEEEECCEEEEEEECCCCCCCCEEEEEEECEEECCCEECCCEEEEEEECCCEEECCC
PSA

>P1;d1l6pa-
9994a372626700407360975804010605a40000163070624807-05b18147177381a456-300039505070406-2057b0303000100042730074243506085096----

>P1;d6dnva1
----da434266002020606aa004050503970000272050708479004a28259069370724782300267030504146b0b57040303010003724117416140607a5952526


Translating the sequences
****CCCCCHHHHEEEEEEEECCEEEEEEEECCCEEEEHHHCEEEEEEEE-ECCC**CCCEEEEECCCE-EEEECCEEEEEEEEE-EEEEEEEEEEEECEEECCCEECCCEEEEEE*CCC**----
----CCCCCHHHHEEEEEEEECCEEEEEEEECCCEEEEHHHCEEEEE*****CCCEECCCEEEEECCCE*EEEECCEEEEEEE********EEEEEEECEEECCCEECCCEEEEEEECCCEE****

74863.tem
_________________________________
----CCCCCHHHHEEEEEEEECCEEEEEEEECCCEEEEHHHCEEEEEEEE-ECCCEECCCEEEEECCCE-EEEECCEEEEEEEEE-EEEEEEEEEEEECEEECCCEECCCEEEEEEECCCEE----




Structural block scores
0	3	-	3.0	P	  7.8  75.0

4	8	C	5.0	H	  5.7  7.0

9	12	H	5.0	H	  3.8  3.5

13	20	E	5.0	H	  3.6  2.0

21	22	C	5.0	H	  6.0  10.5

23	30	E	5.0	H	  2.4  1.8

31	33	C	5.0	H	  6.5  6.3

34	37	E	5.0	H	  0.0  0.0

38	40	H	5.0	H	  3.3  3.7

42	49	E	4.2	M	  4.2  5.0

52	54	C	5.0	H	  5.8  5.5

55	56	E	3.0	P	  4.5  5.0

57	59	C	5.0	H	  4.0  4.7

60	64	E	5.0	H	  5.2  5.0

65	67	C	5.0	H	  6.5  4.3

70	73	E	5.0	H	  0.8  1.2

74	75	C	5.0	H	  6.0  4.0

76	84	E	4.6	H	  3.0  2.7

86	97	E	4.2	M	  2.6  3.8

99	101	E	5.0	H	  0.0  0.0

102	104	C	5.0	H	  4.3  4.0

105	106	E	5.0	H	  1.5  2.5

107	109	C	5.0	H	  3.7  4.0

110	116	E	4.7	H	  2.9  2.6

117	119	C	5.0	H	  4.3  7.5

120	121	E	3.0	P	  7.5  7.0

122	125	-	3.0	P	  75.0  3.8

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