Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d3a9sa2 CCEEEEEEEEECHHHHHHHHCCCCCHHHCCCEEEECCCCCCCHHHHCCEEECCEEECCCHHHCCHHHHHHHHHCCEEEECCCCCCC-CCCEEEECCCCCCCEEEEEEEEEECCCEEEEEEEEEEECCCCHHHHHHHHHCCCCCCCCEEEEECCCCCHHHCCHHHHHHCC----CCCEEEEEECCCHHHHHHHHHHCCCCEEECCCCHHHCCCCHHHHHHCCCCHHHHHHHHHHHC >P1;d4f2da2 -CCC-CEEEEECCC--------------CCCEEEECCC-CCCHHHCCC-------------------------CCEEEECCCCCCCCCCCEEEECCCCC-EEEEEEEEEEC-CCCEEEEEEEEEECCCCC--CCC-----CCCCCCEEEEECC-------CHHHHHHHHHHCCCCCCCEEECCCCCCC-CCCCC-CCCEEEEECC---CCC-HHHHHH-----HHHHHHHHHCC- PSA >P1;d3a9sa2 4606020332033830570072707c50470000001508033200020369971001497517a605740563075370478649-c58601204040602000134275ab3540100000200704980143016501220000001042488c106506202650----7293050133230482036007551004010057860904a4057257a6363003500863 >P1;d4f2da2 -404-13564576a--------------c420020022-704460044-------------------------a2764558489aa9b52504205046-48010204162-a81501000104029178--837-----a332000004020-------6052035018408047406002767184-56508-7810101017---916-288043-----61673687249- Translating the sequences *CEE*EEEEEECHH**************CCCEEEECCC*CCCHHHHCC*************************CCEEEECCCCCCC-CCCEEEECCCCC**EEEEEEEEEE*CCEEEEEEEEEEECCCCH**HHH*****CCCCCCEEEEECC*******CHHHHHH**----CCCEEEEEECCCHHH*HHHHH*CCC*EEE*CC***HCC**HHHHH*****HHHHHHHHHHH* -C**-*EEEEEC**--------------CCCEEEECCC-CCCHHH*CC-------------------------CCEEEECCCCCCC*CCCEEEECCCCC-EEEEEEEEEE*-CC*EEEEEEEEEECCCC*--***-----CCCCCCEEEEECC-------CHHHHHHHH****CCC**EEE*CCC***-*****-CCCEEEEECC---*CC-HHHHHH-----HHHHHHHHH**- 50443.tem _________________________________ -CEE-EEEEEECHH--------------CCCEEEECCC-CCCHHHHCC-------------------------CCEEEECCCCCCC-CCCEEEECCCCC-EEEEEEEEEEE-CCEEEEEEEEEEECCCCH--HHH-----CCCCCCEEEEECC-------CHHHHHHHH----CCCEEEEEECCCHHH-HHHHH-CCCEEEEECC---HCC-HHHHHH-----HHHHHHHHHHH- Structural block scores 2 3 E 3.0 P 3.0 2.0 5 10 E 4.7 H 1.7 4.0 12 13 H 3.0 P 5.5 8.2 14 27 - 3.0 P 4.0 75.0 28 30 C 5.0 H 3.7 6.2 31 34 E 5.0 H 0.0 0.5 35 37 C 5.0 H 2.0 1.3 39 41 C 5.0 H 3.7 3.7 42 45 H 4.5 M 1.2 2.5 46 47 C 5.0 H 1.0 4.0 48 72 - 3.0 P 4.5 75.0 73 74 C 5.0 H 1.5 6.2 75 78 E 5.0 H 5.5 5.5 79 85 C 5.0 H 5.4 7.9 87 89 C 5.0 H 8.5 6.2 90 93 E 5.0 H 2.2 2.8 94 98 C 5.0 H 1.6 3.0 100 110 E 4.6 H 2.2 2.5 112 113 C 5.0 H 7.2 9.2 114 124 E 4.8 H 1.1 1.1 125 128 C 5.0 H 2.8 4.8 130 131 - 3.0 P 4.0 75.0 132 134 H 3.0 P 2.7 6.0 135 139 - 3.0 P 2.4 75.0 140 145 C 5.0 H 0.8 3.1 146 150 E 5.0 H 0.2 0.8 151 152 C 5.0 H 3.0 1.0 153 159 - 3.0 P 5.6 75.0 161 168 H 4.5 M 2.6 2.0 169 172 - 3.0 P 75.0 5.0 173 175 C 5.0 H 6.0 3.7 176 181 E 4.0 M 2.0 2.0 182 184 C 5.0 H 2.7 6.7 185 187 H 3.0 P 4.0 4.3 189 193 H 3.0 P 1.8 4.8 195 197 C 5.0 H 3.7 5.3 198 202 E 4.2 M 1.0 0.4 203 204 C 5.0 H 0.0 4.0 205 207 - 3.0 P 6.7 75.0 209 210 C 5.0 H 4.5 3.5 212 217 H 4.7 H 5.1 4.2 218 222 - 3.0 P 6.1 75.0 223 233 H 4.6 H 3.1 5.4 >>>>>>