Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
_____________________________________________

>P1;d1mvfd-
----------------------------------------------------------------------------CCCCCCCCCCCCCCHHHHHHCCCCCCCCCEEECCEEECCCC--------------------

>P1;d1n0ea1
CCCCEEEECCCCCCEEECCCHHHHHCCCEEECCCCCCCCCEECCHHHHHHHHHHHCCCCCCCHHHHHHHHHHHCCCCEEECCCCCEEECCHHHHHHCCCCCCEEEEECCCCEEEEEHHHHHHHHHCCCCHHHHHHCC

>P1;d1yfba-
C------------------------CCCCCCCCCCCCCCCCCCCHHHHHHCCCCC--------------------------------------------CCCEEEEEECCEEEEEECCCC-----------------
PSA

>P1;d1mvfd-
----------------------------------------------------------------------------b9679ac77349259962864a099a526876997543738--------------------

>P1;d1n0ea1
60685272604a731060169048208840000306660000022611671458078555968a145327602720671904b5130602a6018307087600010567101001373154457946699456968

>P1;d1yfba-
a------------------------a996a6a6975b85657227733793a18a--------------------------------------------a464364858a755246387d-----------------


Translating the sequences
----------------------------------------------------------------------------C***CCCCC***CCHHHHHHCCCCCC***EEECCEEE***C--------------------
C************************CCC***CCCCCCCCC**CCHHHHHH**************************C***CCCCC***CCHHHHHHCCCCCCEEEEE*CC*EEEEE*********************
C------------------------CCC***CCCCCCCCC**CCHHHHHH*****--------------------------------------------CCCEEEEEECCEEEEEEC***-----------------

89447.tem
_________________________________
C------------------------CCC***CCCCCCCCC**CCHHHHHH*****---------------------C***CCCCC***CCHHHHHHCCCCCCEEEEEECCEEEEEEC***-----------------




Structural block scores
1	24	-	4.0	M	  75.0  4.1  75.0

25	27	C	4.0	M	  75.0  5.3  9.5

28	30	*	2.7	P	  75.0  1.3  7.5

31	39	C	4.0	M	  75.0  2.3  7.6

40	41	*	2.7	P	  75.0  0.0  6.0

42	43	C	4.0	M	  75.0  1.0  2.0

44	49	H	4.0	M	  75.0  3.8  6.0

50	54	*	2.7	P	  75.0  3.6  6.6

55	75	-	4.0	M	  75.0  4.9  75.0

77	79	*	2.7	P	  7.3  5.7  75.0

80	84	C	4.0	M	  9.2  4.3  75.0

85	87	*	2.7	P	  5.3  3.0  75.0

88	89	C	4.0	M	  3.5  1.0  75.0

90	95	H	4.0	M	  6.7  4.8  75.0

96	101	C	4.5	M	  7.2  4.7  40.9

102	107	E	4.3	M	  5.7  1.0  5.0

108	109	C	5.0	H	  9.0  6.5  9.2

110	115	E	4.3	M	  4.8  0.5  4.8

117	119	*	2.7	P	  75.0  3.7  9.5

120	136	-	4.0	M	  75.0  6.2  75.0

>>>>>>