Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
_____________________________________________

>P1;d2gtlm1
CHHHCCCCEEEEEEEECCCCCCCCEEEEEEEEEECCCCCCCCCCCEEEEEEEECCCC-CCCEEEEEEEEEEECCCCEEEEEECCCCCCCCEEEECCCCCCCEEEEEEEECCCCEEEEEEEEEEC-

>P1;d2gtln1
CHHHCCCCEEEEEEEECCCCCCCCEEEEEEEEEEECCCCCCCCEEEEEEEECEEECCCCEEECCEEEEEEEECCCCEEEEEECCCCCCCEEEEECCCCCCCEEEEEEECCCCCCEEEEEEEEECC

>P1;d2gtlo1
--CCCCCCEEEEEEEEECCCCCCCCEEEEEEEEEEECCCCCCEEEEEEEEEEECCCCCCCCEEEEEEEEEEECCCCEEEECCCCC-CCEEEEEEECCCCCCEEEEEEEECCCCEEEEEEEEEC--
PSA

>P1;d2gtlm1
58008691202350607324c1950604020560645a8556204050202023559-877435160532023b83203040389375100002074a53540303003297565004060528-

>P1;d2gtln1
58007491302450506234b1a60303020651645a855630405030305066b9aa542318053301395330103249a8b2200103084c35640301004698575004050624b

>P1;d2gtlo1
--1084b360505244071162509602020672945a967431604030407166a978682515180302575440305213a-45100205062a5374040300428586410302052--


Translating the sequences
CHHHCCCCEEEEEEEECCCCCCCCEEEEEEEEEE*CCCCCCCC**EEEEEEEECCCC-CCCEEEEEEEEEEECCCCEEEEEECCCCCCC*EEEECCCCCCCEEEEEEEECCCCEEEEEEEEEEC-
CHHHCCCCEEEEEEEECCCCCCCCEEEEEEEEEEECCCCCCCCEEEEEEEE*E**CCCC**E**EEEEEEEECCCCEEEEEECCCCCCCEEEEECCCCCCCEEEEEEE*CCCC*EEEEEEEEEC*
--**CCCCEEEEEEEE*CCCCCCC*EEEEEEEEEE*CCCCCC*EEEEEEEEEECCCCCCCCEEEEEEEEEEECCCCEEEE**CCC-CC*EEEEE*CCCCCCEEEEEEEECCCCEEEEEEEEE*--

141480.tem
_________________________________
CHHHCCCCEEEEEEEECCCCCCCCEEEEEEEEEEECCCCCCCCEEEEEEEEEECCCCCCCCEEEEEEEEEEECCCCEEEEEECCCCCCCEEEEECCCCCCCEEEEEEEECCCCEEEEEEEEEEC-




Structural block scores
1	3	H	4.0	M	  2.7  2.7  25.3

4	7	C	5.0	H	  6.0  5.2  6.6

8	15	E	5.0	H	  2.2  2.4  3.2

16	23	C	4.9	H	  5.4  5.5  2.8

24	34	E	4.8	H	  2.6  2.4  3.9

35	42	C	4.8	H	  5.7  5.8  6.1

43	52	E	4.7	H	  1.5  2.0  2.5

53	60	C	4.4	M	  14.9  7.3  6.7

61	71	E	4.8	H	  2.8  2.7  3.2

72	75	C	5.0	H	  6.4  5.0  5.2

76	81	E	4.7	H	  1.5  1.5  2.3

82	88	C	4.7	H	  5.1  6.7  14.2

89	93	E	4.8	H	  0.4  0.8  1.4

94	100	C	4.9	H	  4.9  5.5  4.8

101	108	E	4.9	H	  1.6  1.5  1.9

109	112	C	5.0	H	  5.8  7.0  5.8

113	122	E	4.8	H	  2.8  2.9  2.3

>>>>>>