Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1h8la1 --CEEEEEEEC------CCCCCCCCCEEEECCEE--EEEECCCCCEEEECCCC---EEEEEEEECCCCCCEEEEEEECCC----CCEECCEEECCC------------- >P1;d1uwya1 --CEEEEEECC------C-CCCCCCCEEEECCCCCCCCCCCCCCCEEEECCCC---EEEEEEEECCCCCCEEEEEEECCCCCCCCCEECCEECCCCCCCCCCCCCCCCC >P1;d5m0yb1 CEEEEEEEECCCCCCHHHHHHHHCCCEEEECCCC--CEEECCCCCEEEEEEECCCCCEEEEEEECCCCCCEEEEEECCC--------EEECCCCCCCEECCCCCC---- PSA >P1;d1h8la1 --004030303------63780158030503a4b--7536076802061a0a5---751703041a91553446070669----923414050649------------- >P1;d1uwya1 --002330204------7-773156020005757323263057702060a093---7614020306d3a53716070488599a3427450604365a826967388a5 >P1;d5m0yb1 601010201064b258933482135030303c2a--333606750305066035a377020405295157462617538--------8261165a9113073767---- Translating the sequences --CEEEEEE*C------C*CCCCCCCEEEECC**--*EEECCCCCEEEECCCC---EEEEEEEECCCCCCEEEEEEECCC----CCEECCEE*CCC------------- --CEEEEEECC------C-CCCCCCCEEEECCCC**C***CCCCCEEEECCCC---EEEEEEEECCCCCCEEEEEEECCC****CCEECCEECCCCC**CCCCCC**** ***EEEEEECC************CCCEEEECCCC--CEEECCCCCEEEE***C****EEEEEEECCCCCCEEEEEE*CC--------E****CCCCC**CCCCCC---- 49464.tem _________________________________ --CEEEEEECC------C*CCCCCCCEEEECCCC--CEEECCCCCEEEECCCC---EEEEEEEECCCCCCEEEEEEECCC----CCEECCEECCCCC**CCCCCC---- Structural block scores 0 1 - 4.0 M 75.0 75.0 3.0 3 8 E 5.0 H 1.7 1.7 0.7 9 10 C 4.5 M 1.5 2.0 3.0 11 16 - 4.0 M 75.0 75.0 6.6 19 25 C 4.4 M 4.1 4.1 3.3 26 29 E 5.0 H 2.0 0.5 1.5 30 33 C 4.5 M 7.2 6.0 7.0 34 35 - 4.0 M 75.0 2.5 75.0 37 39 E 4.0 M 4.7 3.7 4.0 40 44 C 5.0 H 4.2 3.8 3.6 45 48 E 5.0 H 2.2 2.0 2.0 49 52 C 4.2 M 6.5 5.6 3.8 53 55 - 4.0 M 75.0 75.0 6.2 56 63 E 4.9 H 3.4 2.9 3.1 64 69 C 5.0 H 5.2 6.3 4.8 70 76 E 4.9 H 3.4 3.4 4.4 77 79 C 4.7 H 7.0 6.7 28.7 80 83 - 4.0 M 75.0 8.4 75.0 84 85 C 4.0 M 5.5 3.5 75.0 86 87 E 4.5 M 3.5 4.5 41.5 88 89 C 4.0 M 2.5 4.5 4.0 90 91 E 4.0 M 2.5 3.0 1.0 92 96 C 4.6 H 18.8 3.6 6.3 97 98 * 2.7 P 75.0 9.2 2.0 99 104 C 4.0 M 75.0 5.5 5.0 105 108 - 4.0 M 75.0 7.9 75.0 >>>>>>