Reading input alignment file to find conserved blocks of secondary structure

The input structure based alignment from Comparer
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>P1;d1r5la1
--------------------------CCCHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHCHHHHCCCCCC----

>P1;d4uyba1
--------------CCCCCCCCCHHHHHHHHHHHHHHCCC-HHHCCC-CCHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHC--CHHHHHHCC---

>P1;d6slda1
CHHHHCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHC--CCCCC-CCHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHC--CHHHHHHHHHHC
PSA

>P1;d1r5la1
--------------------------47309302520774914977371669000700654a252840163056406628625870767587----

>P1;d4uyba1
--------------55063c41399256117503840861-175068-2457100610254a14397036303821750666--62474a989---

>P1;d6slda1
894875838467c3a6010520879245107702630594--c2873-02441005003449162b4018303531652776--71266966878c


Translating the sequences
--------------------------***HHHHHHHHHH***CCCCC*CCHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHC***H*****C----
--------------CCCCCCCCCHHHHHHHHHHHHHH**C-***CCC-CCHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHC--CHHHHHHC*---
**************CCCCCCCCCHHHHHHHHHHHHHHHHC--CCCCC-CCHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHC--CHHHHHH*****

46938.tem
_________________________________
--------------CCCCCCCCCHHHHHHHHHHHHHHHHC-*CCCCC-CCHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHC--CHHHHHHC*---




Structural block scores
0	13	-	4.0	M	  75.0  75.0  6.6

14	22	C	4.0	M	  75.0  4.4  3.6

23	38	H	4.5	M	  17.1  4.6  4.2

42	46	C	4.6	H	  6.0  5.2  6.5

48	49	C	5.0	H	  3.5  3.0  1.0

50	59	H	5.0	H	  3.3  2.7  2.1

60	63	C	5.0	H	  5.4  4.9  5.0

64	80	H	5.0	H	  3.9  4.1  4.0

82	83	-	4.0	M	  6.5  75.0  75.0

85	90	H	4.2	M	  5.5  6.1  5.0

93	95	-	4.0	M	  75.0  75.0  9.2

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