Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
_____________________________________________

>P1;d1fs1a1
----------------------CCCCCHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHC-CHHHC-------------------------------------------------------

>P1;d1nexb1
-------------CCCCHHHHC----CHHHHHHHHCCCCHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHCCCCCCCCHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHCC--C

>P1;d1p22a1
------------CCCCCHHHHCHHHCCHHHHHHHHCCCCHHHHHHHHHHCHHHHHHHHHCC-HHHHHHHHHHC-CCHHHHHHHHCCCHHHHCCCCCHHHHHHHHHHHHHHHHHHHHCCC

>P1;d2ovrb1
CCHHHHHHHHCCCCCCCCCCCC----CHHHHHHHHCCCCHHHHHHHCCCCHHHHHHHC-CCHHHHHHHCCCCCC-------CCCCCCCCCCCCCCCCHHHHHHHHHHHHHHC-------
PSA

>P1;d1fs1a1
----------------------77b3669702950583957408702a5382277107-3a804-------------------------------------------------------

>P1;d1nexb1
-------------aa7670443----638501650384905504901a56a5227103603500451037391166971a81287037526a464211024002540662588868--9

>P1;d1p22a1
------------7965570322088a55640174048370930570195583233003603-00340014316-868405601985810850495065026115704722674568877

>P1;d2ovrb1
8207601871518948391072----63a60286046371950381175271240000-128104700675818-------82477889a978056021120126467578a-------


Translating the sequences
----------------------****CHHHHHHHHCCCCHHHHHHH*CCCHHHHHHH*-C*HH*-------------------------------------------------------
-------------CCCC****C----CHHHHHHHHCCCCHHHHHHH*CCCHHHHHHH**CCHHHHHHH****C******************CCC***HHHHHHHHHHHHHH*****--*
------------*CCCC****C****CHHHHHHHHCCCCHHHHHHH***CHHHHHHH**CC-HHHHHH****C-*****************CCC***HHHHHHHHHHHHHH********
*************CCCC****C----CHHHHHHHHCCCCHHHHHHH*CCCHHHHHHH*-CCHHHHHHH****C*-------**********CCC***HHHHHHHHHHHHHH*-------

81383.tem
_________________________________
------------*CCCC****C****CHHHHHHHHCCCCHHHHHHH*CCCHHHHHHH**CCHHHHHHH****C******************CCC***HHHHHHHHHHHHHH*****--*




Structural block scores
0	11	-	4.3	M	  75.0  75.0  75.0  3.8

13	16	C	4.3	M	  75.0  8.5  6.2  6.0

17	20	*	2.3	P	  75.0  3.8  3.0  4.2

22	25	*	3.5	M	  7.1  75.0  6.6  75.0

27	34	H	5.0	H	  4.8  3.5  3.4  4.4

35	38	C	5.0	H	  6.2  6.0  5.5  5.0

39	45	H	5.0	H	  4.4  3.3  3.4  3.9

47	49	C	4.5	M	  6.2  7.2  6.3  4.7

50	56	H	5.0	H	  3.9  3.9  2.7  2.0

57	58	*	2.2	P	  41.0  4.5  4.5  37.5

59	60	C	4.7	H	  6.8  1.5  1.5  1.5

61	67	H	4.4	M	  44.6  2.1  11.7  2.9

68	71	*	2.3	P	  75.0  5.5  2.2  6.5

73	90	*	2.8	P	  75.0  5.0  8.7  33.6

91	93	C	4.3	M	  75.0  6.8  4.3  5.0

94	96	*	2.3	P	  75.0  2.3  3.7  3.7

97	110	H	4.3	M	  75.0  2.6  3.4  3.7

111	115	*	3.3	M	  75.0  7.6  6.0  62.1

116	117	-	4.3	M	  75.0  75.0  7.5  75.0

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