Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
_____________________________________________

>P1;d2g7ja1
CCCCHHHHHHHHHHCCCEEEEECCCEEEEEECCEEEEEECCCCCCCCCEECCCCCHHHHCCCCCCCCCCEEC----CCCCCCCCCCCCCC-CCCEECEECCC---CHHHHHHHHHHHCCC---

>P1;d2od0a1
C--CHHHHCCHHHHHCCCEEEC-CCCEEEEECCEEEEEEC------CEEEEECC-HHHHHHHHHCCCCCCEEEECC-------------EEEECCEEECCHHHHHCHHHHHHHHHHHHHHHHC
PSA

>P1;d2g7ja1
85061720141046290853473d4030033b944000035088053000020717a505840833573322----83071921583b58-43110000116---458304720860067---

>P1;d2od0a1
9--6147407206409817388-551530206a3000018------65000102-8a41773486a690124679b-------------856604113058932846a602520440074048


Translating the sequences
C**CHHHHHHHHHH*CCEEEEE*CCEEEEEECCEEEEEEC******C*EE**CC*HHHH*****CCCCCEE*----**************-**CEE*EEC**---CHHHHHHHHHHH***---
C--CHHHH**HHHHHCC*EEE*-CC*EEEEECCEEEEEEC------CEEEEECC-HHHHHHHHHCCCCC*EE****-------------E*EEC*EEE*CHH***CHHHHHHHHHHHHHH***

159894.tem
_________________________________
C--CHHHHHHHHHHHCCEEEEE-CCEEEEEECCEEEEEEC------CEEEEECC-HHHHHHHHHCCCCCEEE-----------------E-EECEEEEECHH---CHHHHHHHHHHHHHH---




Structural block scores
1	2	-	3.0	P	  2.5  75.0

4	14	H	4.5	M	  2.5  3.2

15	16	C	5.0	H	  4.5  8.5

17	21	E	4.2	M	  5.4  5.4

23	24	C	5.0	H	  8.8  5.0

25	30	E	4.7	H	  1.5  1.8

31	32	C	5.0	H	  10.2  8.2

33	38	E	5.0	H	  1.3  0.7

40	45	-	3.0	P	  4.3  75.0

47	51	E	3.8	M	  0.4  1.2

52	53	C	5.0	H	  3.5  1.0

55	63	H	3.9	M	  5.3  5.8

64	68	C	5.0	H	  4.2  6.3

69	71	E	3.7	M	  2.3  2.3

72	88	-	3.0	P	  21.4  59.3

91	92	E	3.0	P	  3.5  6.0

94	98	E	3.8	M	  0.2  1.8

100	101	H	3.0	P	  3.5  8.5

102	104	-	3.0	P	  75.0  4.3

106	119	H	4.6	H	  4.0  3.6

120	122	-	3.0	P	  75.0  4.0

>>>>>>