Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1cbya- CCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHHHHHHHHHHHCCCC--CCCCCHHHHHHHHCCCC--CEEEEEEEEEEEEEEEEEHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHCCCCHHHHCCCCCEEEECCCC-CCEEEEEEEEEEECCCCCCCEEEEEEEEEEEEECC-CHHHHCCCCCCCEEEEEEEEEEEEEEEECCCCCCCHHHHHCCCCCCCC >P1;d1pp0a- ----------------------CCCEEEECCCHHHHHHHHHHHHHHHCCEEEECCEEEECHHHHHHHHHCCCCCCEEEEEEEEEEEEEEEEEHHHHHHHHHHHHHHHCCCCCC----HHHHHHHHHHHHCCHHHHCCCCCEEEEEECCCCEEEEEEEEEEEEECCC--CEEEEEEEEEEEEECCCCHHHHCCCCCCCEEEEEEEEEEEEEEEECCCC-CC------------- PSA >P1;d1cbya- ba9898878589696a4944294203221205741410024001000800479--73306185037008506--90813431363005661403600750272068005390928702730371045000803814a45204137367-940001000000000a2099300000000203052-42770071739451505030000001161863b478861373417b13 >P1;d1pp0a- ----------------------7202422905a604600730160014216668a3230418504620781a4a307444135263a55514035007500730362067007----5970251038002406821a291011334ba772010100000014569--33010000003020506747702a0758363601030000002044908-04------------- Translating the sequences **********************CCCEEEEECCHHHHHHHHHHHHHHHHH****--****CHHHHHHHH*CCC--CEEEEEEEEEEEEEEEEEHHHHHHHHHHHHHHHHCCCCC****HHHHHHHHHH**CCHHHHCCCCCEEEE**CC-C*EEEEEEEEEEE*CCC**CEEEEEEEEEEEEECC-CHHHHCCCCCCCEEEEEEEEEEEEEEEECCCC*CC************* ----------------------CCCEEEE*CCHHHHHHHHHHHHHHH**EEEE**EEEECHHHHHHHHHCCC**CEEEEEEEEEEEEEEEEEHHHHHHHHHHHHHHH*CCCCC----HHHHHHHHHHHHCCHHHHCCCCCEEEEEECC*CEEEEEEEEEEEEECCC--CEEEEEEEEEEEEECC*CHHHHCCCCCCCEEEEEEEEEEEEEEEECCCC-CC------------- 55676.tem _________________________________ ----------------------CCCEEEEECCHHHHHHHHHHHHHHHHHEEEE--EEEECHHHHHHHHHCCC--CEEEEEEEEEEEEEEEEEHHHHHHHHHHHHHHHHCCCCC----HHHHHHHHHHHHCCHHHHCCCCCEEEEEECC-CEEEEEEEEEEEEECCC--CEEEEEEEEEEEEECC-CHHHHCCCCCCCEEEEEEEEEEEEEEEECCCC-CC------------- Structural block scores 0 21 - 3.0 P 7.5 75.0 22 24 C 5.0 H 2.0 3.0 25 29 E 4.6 H 2.0 3.8 30 31 C 5.0 H 2.5 2.5 32 48 H 4.8 H 1.9 3.0 49 52 E 3.0 P 5.0 4.8 53 54 - 3.0 P 75.0 9.2 55 58 E 3.0 P 3.2 2.0 60 68 H 4.8 H 3.6 3.7 69 71 C 5.0 H 3.7 6.5 72 73 - 3.0 P 75.0 7.2 75 91 E 5.0 H 3.2 4.1 92 107 H 4.9 H 2.9 2.6 108 112 C 5.0 H 5.2 4.0 113 116 - 3.0 P 4.2 75.0 117 128 H 4.7 H 2.7 3.3 129 130 C 5.0 H 4.0 3.0 131 134 H 5.0 H 3.0 4.0 135 139 C 5.0 H 5.1 4.7 140 145 E 4.3 M 3.0 2.0 146 147 C 5.0 H 6.5 11.0 150 162 E 4.7 H 0.4 0.7 163 165 C 5.0 H 4.2 6.7 166 167 - 3.0 P 4.5 75.0 169 181 E 5.0 H 0.6 0.7 182 183 C 5.0 H 3.5 2.5 186 189 H 5.0 H 4.0 4.5 190 196 C 5.0 H 4.4 5.1 197 212 E 5.0 H 1.7 1.6 213 216 C 5.0 H 4.5 5.2 218 219 C 5.0 H 5.5 2.0 220 232 - 3.0 P 4.9 75.0 >>>>>>