Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1l5xa1 -CEEEECCCCCCCHHHHHHHHHHHHHCCEEEEEECCCCCCCCCCCCCCCCCCCEEECCCCEEEEECCCHHHHHHHHHH-HHC-CCCCEEEEEEEECCCCCHHHHCCCHHHHHHHHHHHCCCCEEEEEECCCCCHHHHCCHHHHHCCHHHHHHHHHHHHHCCCCCCEEEEECCCCCCCCC-CEEECCCCCCCCCCCCEEEECCCCCEEEECCCCCC--CCCCCCHHHHHHCCCCEEEEEECCCCCCCCCCCCCCCCCCCCHHHHHHHC >P1;d2phja- CEEEEECCCCCCCHHHHHHHHHHCCCCEEEEEEECCCCCCCCCCCCCCCCCC-EEEEECCEEEECCCCHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCH-HHHHHCHHHHHHHHHHHCCCCEEEEEEECCC------CCCHHHHHHHHHHHHHHHHHHCCCCCEEEEEEEECCCHHHCCEEEECCCCCCCCEEEEEEEECCCCCEEEEEEEECCCCCCCCCCHHHHHH-CCEEEEEEEECCCCC----------HHHHHHHHHHHC PSA >P1;d1l5xa1 -1000000210713003001520580880300004443a61a3640885919662609c1605002010000053029-918-670600000013600005320670000100120063a0400000120851951496a4029114004000310286917603010000039178a1-4042070285030b544564399785456467553--a18670002001647300001141487a869a374480176185026406 >P1;d2phja- 530000000036060041025305913600000015505b7b1a23897816-16537830200250100000120056118694050000001333100-4408710002003103414030000002499------b04192004001400671278706a500100000245366057338063093126564455537977455772543407717660002002-422001041825948----------694477657679 Translating the sequences -*EEEECCCCCCCHHHHHHHHHHHHHC*EEEEEECCCCCCCCCCCCCCCCCC*EEE**CCEEEEECCCHHHHHHHHHH-HHC-CCCCEEEEEEEECCCC**HHH**CHHHHHHHHHHHCCCCEEEEEE*CCC******CHHHHH**HHHHHHHHHHHHHCCCCC*EEEEE**CCC***C-*EEECCCCCCCC****EEEECCCCCEEEE****CC--CCCCCCHHHHHH*CC*EEEEEE*CCCCC**************HHHHHHHC *EEEEECCCCCCCHHHHHHHHHH***CEEEEEEECCCCCCCCCCCCCCCCCC-EEEEECCEEEE*CCCHHHHHHHHHH***C*CCCCEEEEEEE*CCCCH-HHHHHCHHHHHHHHHHHCCCCEEEEEEECCC------C**HHHHHHHHHHHHHHHHHHCCCCCEEEEEEEECCCHHHC*EEEECCCCCCCCEEEEEEEECCCCCEEEEEEEECC**CCCCCCHHHHHH-CCEEEEEEEECCCCC----------HHHHHHHHHHHC 64167.tem _________________________________ -EEEEECCCCCCCHHHHHHHHHHHHHCEEEEEEECCCCCCCCCCCCCCCCCC-EEEEECCEEEEECCCHHHHHHHHHH-HHC-CCCCEEEEEEEECCCCH-HHHHHCHHHHHHHHHHHCCCCEEEEEEECCC------CHHHHHHHHHHHHHHHHHHHHCCCCCEEEEEEEECCCHHHC-EEEECCCCCCCCEEEEEEEECCCCCEEEEEEEECC--CCCCCCHHHHHH-CCEEEEEEEECCCCC----------HHHHHHHHHHHC Structural block scores 1 5 E 4.6 H 0.2 0.6 6 12 C 5.0 H 1.6 1.3 13 25 H 4.5 M 2.1 2.8 27 33 E 4.7 H 1.6 0.9 34 51 C 5.0 H 5.3 5.6 53 57 E 4.2 M 4.6 4.4 58 59 C 5.0 H 6.8 5.5 60 64 E 4.6 H 2.2 0.8 65 67 C 5.0 H 1.0 2.0 68 77 H 5.0 H 1.9 0.8 79 80 H 3.0 P 5.0 1.0 83 86 C 5.0 H 4.8 4.5 87 94 E 4.8 H 0.5 0.5 95 98 C 5.0 H 1.5 1.8 101 105 H 4.2 M 3.6 4.6 107 117 H 5.0 H 0.9 1.2 118 121 C 5.0 H 4.4 2.0 122 128 E 4.7 H 0.4 0.3 129 131 C 5.0 H 4.3 7.3 132 137 - 3.0 P 4.8 75.0 139 158 H 4.6 H 2.8 2.8 159 163 C 5.0 H 4.6 5.7 164 171 E 4.2 M 0.5 0.1 172 174 C 5.0 H 4.3 3.7 175 177 H 3.0 P 8.5 5.0 180 183 E 4.5 M 2.5 5.2 184 191 C 5.0 H 3.1 3.0 192 199 E 4.0 M 4.9 5.0 200 204 C 5.0 H 7.2 6.6 205 212 E 4.0 M 5.2 4.9 213 214 C 5.0 H 4.0 3.5 215 216 - 3.0 P 75.0 3.5 217 222 C 5.0 H 5.4 4.5 223 228 H 5.0 H 0.5 0.7 230 231 C 5.0 H 5.5 3.0 232 239 E 4.5 M 1.1 2.0 240 244 C 5.0 H 6.1 5.6 245 254 - 3.0 P 6.0 75.0 255 265 H 4.3 M 3.6 6.2 >>>>>>