Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1gtda- ---CCCEEEEEECCC-CCHHHHHHHHH-HHHHCCCCCCCCCCEEEECC-CCCCHHHHHHHHH-CCCC----------------------CCCCCC--------------CEEEEEECCC------------------------------------- >P1;d1t3ta3 ---CEEEEEEEEC--CCHHHHHHHHHH-HHCCCCCCCEEEEEEEEEEEECCCCCHHHHHHHHHHCCCCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHCCCCCEEEEEEEEEEEEECCCCCHHHHHHHHHCCCCCCCCEEECCHHHHHHHHCC >P1;d1t4aa- ---CEEEEEEEECCCCCCHHHHHHHHH-HHCCCCCCCCCCCCCC-CEECCCC-CCCHHHHHH-CCCC----------------------CCCCCC--------------CEEEEEEEEC------------------------------------- >P1;d1vq3a1 CCEEEEEEEEEECCCCCCHHHHHHHHH-CCCCCCCCCCCCCCEEEEEEEECC-C-CCHHHHC-CIII----------------------IICCCC--------------CEEEEEEEC-------------------------------------- >P1;d2zw2a- -CEEEEEEEEEECCCCCCHHHHHHHHHCHHHHCCCCCCCCCEEEEEEEEECCCHHHHHHHHHHHHHHC---------------------CCCCCC--------------CEEEEEEEEEEC----------------------------------- PSA >P1;d1gtda- ---7003050524ab-82670675376-346797847a2532734657-82a5583058615-5048----------------------820638--------------5271726098------------------------------------- >P1;d1t3ta3 ---9023180410--249652841275-0884a070550001200002064908b8247606920567b2876a46542000013c6527207711760394807204100202011040a60797217502630268883311743640660078 >P1;d1t4aa- ---3402030613ba2a0770784287-4379778387233274-4582a86-c67366305-4057----------------------920739--------------5161626159------------------------------------- >P1;d1vq3a1 6652600030144aa272680554353-3866b5838924425636240529-6-8047603-4088----------------------820679--------------305280675-------------------------------------- >P1;d2zw2a- -410401020324ab460570564276714883a9596251365333619075685026605640467---------------------731649--------------335151506527----------------------------------- Translating the sequences ---C**EEEEEECCC-CCHHHHHHHHH-HH**CCCCCCCCCCEEEE**-CCCC*HHHHHHHH-CCCC----------------------CCCCCC--------------CEEEEEE***------------------------------------- ---CEEEEEEEEC--CC*HHHHHHHHH-HHCCCCCCC*****EEEEEEECCCCCHHHHHHHH**CCC*******************************************EEEEEEEE************************************** ---CEEEEEEEECCCCCCHHHHHHHHH-HHCCCCCCCCCCCC**-*EE*CCC-C**HHHHHH-CCCC----------------------CCCCCC--------------CEEEEEEEE*------------------------------------- ****EEEEEEEECCCCCCHHHHHHHHH-**CCCCCCCCCCCCEEEEEEE*CC-C-**HHHH*-C***----------------------**CCCC--------------CEEEEEEE*-------------------------------------- -***EEEEEEEECCCCCCHHHHHHHHH*HH**CCCCCCCCC*EEEEEEE*CCC*HHHHHHHH******---------------------CCCCCC--------------CEEEEEEEE***----------------------------------- 82697.tem _________________________________ ---CEEEEEEEECCCCCCHHHHHHHHH-HHCCCCCCCCCCCCEEEEEEECCCCCHHHHHHHH-CCCC----------------------CCCCCC--------------CEEEEEEEE*------------------------------------- Structural block scores 0 2 - 4.0 M 75.0 75.0 75.0 5.7 26.7 4 11 E 4.9 H 1.9 2.4 2.0 1.8 1.5 12 17 C 4.7 H 18.5 27.5 6.2 6.0 6.0 18 26 H 5.0 H 5.2 4.4 5.6 4.3 4.7 28 29 H 4.5 M 3.5 4.0 3.5 5.5 2.5 30 41 C 4.5 M 5.9 3.4 5.5 5.7 5.8 42 48 E 4.4 M 15.3 0.6 15.0 3.7 3.9 49 53 C 4.4 M 6.1 5.4 22.4 19.4 5.4 54 61 H 4.6 H 4.5 5.6 4.5 12.9 4.0 63 66 C 3.8 M 4.2 3.2 4.0 5.0 3.5 67 88 - 4.5 M 75.0 4.7 75.0 75.0 71.9 89 94 C 4.3 M 4.5 4.0 5.0 5.3 5.0 95 108 - 4.5 M 75.0 3.7 75.0 75.0 75.0 110 117 E 4.8 H 4.2 0.8 3.5 4.1 3.2 119 155 - 4.5 M 75.0 4.2 75.0 75.0 71.2 >>>>>>