Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
_____________________________________________

>P1;d1roca1
-CCEEEEEEEECCCCEECCCCEEEEEEEEECCCCCCCEEEEEEECCCCCCCCCCEEEEEEEECCCCCEEEEEEEEECCCCHHHCCCHHHHCCEEEEEEEEECCEEEEEEEEEEEEEECCHHHHHCCCCCCCHHHEEEEECCCCCEEEECCCCCC-

>P1;d6a6ya-
CCCEEEEEEEECCCEEECCCCEEEEEEEEECCCCCCCEEEEEEEECCCC---CCEEEEEEEECCCCCEEEEEEEEECCCCHHHCCHHHCCEEEEEEEEEEECCEEEEEEEEEEEEEECCHHHHHCCCCCCCHHHEEEEECCCCCEEEECCCCCCC
PSA

>P1;d1roca1
-5104147160281517054302020203066907430303020302a7190463405257208075862524050800549402420088403020000058320030106030604769146833aa050930404033a8282374c1914-

>P1;d6a6ya-
742060450503336130544030101030456074401020202033a---a44405435207067745417050910606817470028400010000049730040103050304768347952a82327401040448536457470903b


Translating the sequences
-CCEEEEEEEECCC*EECCCCEEEEEEEEECCCCCCCEEEEEEE*CCCC***CCEEEEEEEECCCCCEEEEEEEEECCCCHHHCC*HHHH**EEEEEEEEECCEEEEEEEEEEEEEECCHHHHHCCCCCCCHHHEEEEECCCCCEEEECCCCCC-
*CCEEEEEEEECCCEEECCCCEEEEEEEEECCCCCCCEEEEEEEECCCC---CCEEEEEEEECCCCCEEEEEEEEECCCCHHHCCHHH**EEEEEEEEEEECCEEEEEEEEEEEEEECCHHHHHCCCCCCCHHHEEEEECCCCCEEEECCCCCC*

101546.tem
_________________________________
-CCEEEEEEEECCCEEECCCCEEEEEEEEECCCCCCCEEEEEEEECCCC---CCEEEEEEEECCCCCEEEEEEEEECCCCHHHCCHHHHHEEEEEEEEEEECCEEEEEEEEEEEEEECCHHHHHCCCCCCCHHHEEEEECCCCCEEEECCCCCC-




Structural block scores
1	2	C	5.0	H	  3.0  3.0

3	10	E	5.0	H	  2.9  2.5

11	13	C	5.0	H	  3.7  3.0

14	16	E	4.3	M	  4.3  3.3

17	20	C	5.0	H	  3.0  3.2

21	29	E	5.0	H	  1.0  0.9

30	36	C	5.0	H	  5.0  4.3

37	44	E	4.8	H	  1.4  0.9

45	48	C	5.0	H	  4.9  4.1

49	51	-	3.0	P	  3.3  75.0

52	53	C	5.0	H	  5.0  7.2

54	61	E	5.0	H	  3.5  3.4

62	66	C	5.0	H	  4.0  4.0

67	75	E	5.0	H	  3.6  3.7

76	79	C	5.0	H	  3.2  4.0

80	82	H	5.0	H	  5.7  4.7

83	84	C	5.0	H	  1.0  4.0

85	89	H	3.8	M	  2.8  2.6

90	100	E	4.6	H	  1.5  1.2

101	102	C	5.0	H	  6.5  6.5

103	116	E	5.0	H	  1.7  1.9

117	118	C	5.0	H	  5.5  5.5

119	123	H	5.0	H	  5.2  5.6

124	130	C	5.0	H	  5.7  5.6

131	133	H	5.0	H	  4.0  4.3

134	138	E	5.0	H	  1.6  1.0

139	143	C	5.0	H	  5.3  4.8

144	147	E	5.0	H	  5.0  5.5

148	153	C	5.0	H	  5.2  3.8

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