Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
_____________________________________________

>P1;d2ywqa1
-CCCEEEEECCCCCHHHHHHHHHHHHHHHHCCCC-CCCEEEEEECC----CEEEEEEEEECCEEEEEEEEECCHHHHHHHHHHHHHHHHHHCC-----------------

>P1;d3tqma-
-CE-E-EEECCCCCHHHHHHHHHHHCCCCCCHHHCCEEEEEEEEEC---CEEEEEEEEEECCEEEEEEECCCC-CHHHHHC-CHHHHHHHHHHCC---------------

>P1;d3v2cy-
-CC-EEEEECCCCCHHHHHHHHHHHHHHHHHCCCCEEEEEEEECCC---CCEEEEEEEEECCEEEEEEEEE-CHHHHHHHHHHHHHHHHHHHHHCCCCCC----------

>P1;d4fyla1
-CE-EEEEECCCCCHHHHHHHHHHHHHHCCCCCCEEEEEEEEEEEC---CEEEEEEEEEECCEEEEEEEEECCHHHHHHHHHHHHHHHHHHC------------------

>P1;d6qbza-
CCCCCCEEEECCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCEEEECCCCCCEEEEEEECCCCEEEEEECCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCC
PSA

>P1;d2ywqa1
-a155040691905a81463057206306621b6-a003000044a----50301020605d4513041428714300450075026404738-----------------

>P1;d3tqma-
-82-6-607c2b16971582045307607213a5066030413469---a54004050406b63171605286-5600430-7504640662688---------------

>P1;d3v2cy-
-b2-8050690a1589137302620550771917138030202748---9421040506046650614065-61550055008402940562157a4a8a----------

>P1;d4fyla1
-91-6060681a2497138305520780588187077030302257---942001020407a350514043970440045016403640784------------------

>P1;d6qbza-
a2625170607657761765046203700660a907401040405075c9205010302023240406387750450055019403650565266586356a794a779b


Translating the sequences
-CC*EEEEECCCCCHHHHHHHHHHHHHHH*CCCC-C**EEEEEE*C----CEEEEEEEEECCEEEEEEEEECCHHHHHHHHHHHHHHHHHH**-----------------
-C*-E-EEECCCCCHHHHHHHHHHH****CC***CCEEEEEEEEEC---C*EEEEEEEEECCEEEEEEE**CC-*HHHHH*-*HHHHHHHHHH**---------------
-CC-EEEEECCCCCHHHHHHHHHHHHHHH**CCCC*EEEEEEE**C---CCEEEEEEEEECCEEEEEEEEE-CHHHHHHHHHHHHHHHHHHHH*******----------
-C*-EEEEECCCCCHHHHHHHHHHHHHH*CCCCC**EEEEEEEEEC---C*EEEEEEEEECCEEEEEEEEECCHHHHHHHHHHHHHHHHHH*------------------
*CC***EEE*CCCCHHHHHHHHHHHHHHHCCCCCCC******EEE****CC*EEEEEEE*CC*EEEEEE**CCHHHHHHHHHHHHHHHHHHHH*****************

69754.tem
_________________________________
-CC-EEEEECCCCCHHHHHHHHHHHHHHHCCCCCCCEEEEEEEEEC---CCEEEEEEEEECCEEEEEEEEECCHHHHHHHHHHHHHHHHHHHH**---------------




Structural block scores
1	2	C	4.4	M	  5.8  5.0  6.8  5.0  4.0

4	8	E	4.7	H	  3.0  18.8  3.8  3.6  3.8

9	13	C	4.9	H	  4.8  6.6  5.1  5.1  5.0

14	28	H	4.8	H	  4.1  4.3  3.9  4.2  3.6

29	35	C	4.2	M	  16.0  3.9  4.1  5.6  5.5

36	44	E	4.3	M	  1.2  3.0  2.9  2.4  2.0

46	48	-	4.5	M	  75.0  75.0  75.0  75.0  8.2

49	50	C	4.2	M	  40.0  7.8  6.5  6.5  5.5

51	59	E	4.9	H	  1.3  1.9  2.0  1.0  1.2

60	61	C	5.0	H	  9.2  8.8  5.0  8.8  2.5

62	70	E	4.7	H	  2.7  3.4  3.7  2.8  3.8

71	72	C	4.8	H	  7.5  7.0  40.5  8.0  6.0

73	92	H	4.8	H	  3.1  10.7  3.1  6.8  3.2

93	94	*	3.0	P	  75.0  8.0  6.0  75.0  6.0

95	109	-	4.3	M	  75.0  75.0  52.9  75.0  7.2

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