Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1ewfa1 ---------------------------------CCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCEEEECCCC---------------------CCCEEEEEEEECCCCCCCCEEEEEECCCEEEEEEEEEEEEEEEEEEECCCCEEEEEEEEEEEEEEEEECEEECCCCEEECCCCEEEEECCEEEEECCC----HHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHCHHHHHCCCCCEEECCCCCEEECCCCCC----CCCCC------ >P1;d1ewfa2 CCCCCCCCCCCCCC---CCCCC-CCCCCCCCCCCCCEEEEEEHHHHHHHHHHHHHC-------CCCEEEEEHHHCCCCCCCCCCHHHHHCCCCCHHHH--CCCCCEEE-EEECCCCCEEEEECCEEEEEC--EEEEEEEEECCCCCEEEEEEEEEECCEEEEEEECC----CEEEE-----EEEECCCEEEEEEECCC--------CCC---HHHHHHHHHHHHHHHCHHHHHHHHHHC-EECCCC----CCEEEEEEEEEEECCEEEEEEEEEEC- >P1;d4m4da2 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCC--------------CEEEEEHHHCCCCCCCCCCCCCCCCCCCCHHHH--CCCCEEEE-EEEEEECCCCCCCCCEEEECC--EEEEEEEEECCCCCEEEEEEEEEEEEEEEEEEEEC----CEEEE-----EEEEEEEEEEEEEECCC--------CCC---HHHHHHHHHHHHHHCHHHHHHHHHHHC-EECCCC----CCEEEEEEEEEECCCCEEEEEEEEECC PSA >P1;d1ewfa1 ---------------------------------c4c688957597167407591660371047004616440949---------------------75180003706066050480705134a71141206802003150606787264806040430503040140579513030808706070930607085----b70a302700363029602940272018205710855334742755272756995457412776----38088------ >P1;d1ewfa2 75977958722779---a0748-51a382724772651300020211023123165-------7636220518303a708230308200720350475--15916010-303177317040368401242--52303010237986322003020604060706166----43001-----40317805072460507--------906---184038006200441213541642570-280417----76151573425126400010012565- >P1;d4m4da2 a6967858b25478aa5879368459390771871650131142577373a--------------464423285069b1b130305404500550285--24727001-402145164735661101222--51411010227798543002010313051317078----53020-----60435605072250707--------906---295037414631553504715733580-350308----961304703023394021000327558 Translating the sequences ---------------------------------CCC*****CHHHHHHHHHHHHH********CCC*EEEE***C---------------------********EEE*****CCC**EEEECCCEEEEE***EEEEEEEEE**CCC*EEEEEEEEEEEEEEEEE*E*****CEEE******EEE*CEEEEE***----**************HHHHHHHHHHHHHHHHHHHHHH*HHH****CCC*****CC*EEE******----*****------ CCCCCCCCCCCCCC---CCCCC-CCCCCCCCCCCCCEEEEE*HHHHHHHHHHHHH*-------CCCEEEEEHHHCCCCCCCCCC*****CCCCCHHHH--CCCC*EEE-EEECCCCCEEEE*CCEEEEEC--EEEEEEEEECCCCCEEEEEEEEEE**EEEEEEE*C----CEEEE-----EEEEC**EEEEEEECCC--------CCC---HHHHHHHHHHHHHHH*HHHHHHHHHHC-EECCCC----CCEEEEEEEEEE*CC*EEEEEEEEEC- CCCCCCCCCCCCCC***CCCCC*CCCCCCCCCCCCCEEEEEC*********--------------CEEEEEHHHCCCCCCCCCC*****CCCCCHHHH--CCCCEEEE-EEE***CC****CCCEEEE*C--EEEEEEEEECCCCCEEEEEEEEEEEEEEEEEEEEC----CEEEE-----EEEE*EEEEEEEEECCC--------CCC---HHHHHHHHHHHHHH*HHHHHHHHHHHC-EECCCC----CCEEEEEEEEEE*CC*EEEEEEEEEC* 55394.tem _________________________________ CCCCCCCCCCCCCC---CCCCC-CCCCCCCCCCCCCEEEEECHHHHHHHHHHHHH*-------CCCEEEEEHHHCCCCCCCCCC*****CCCCCHHHH--CCCCEEEE-EEECCCCCEEEECCCEEEEEC--EEEEEEEEECCCCCEEEEEEEEEEEEEEEEEEEEC----CEEEE-----EEEECEEEEEEEEECCC--------CCC---HHHHHHHHHHHHHHHHHHHHHHHHHHC-EECCCC----CCEEEEEEEEEE*CC*EEEEEEEEEC- Structural block scores 0 13 C 4.0 M 75.0 6.5 6.9 14 16 - 4.0 M 75.0 75.0 8.7 17 21 C 4.0 M 75.0 5.9 6.6 23 35 C 4.2 M 59.9 5.0 5.2 36 40 E 4.0 M 7.2 1.8 2.0 42 54 H 4.0 M 5.2 1.8 26.8 56 62 - 4.0 M 3.1 75.0 75.0 63 65 C 4.3 M 1.3 5.3 51.3 66 70 E 4.8 H 4.2 3.0 3.8 71 73 H 4.0 M 4.3 4.0 5.0 74 83 C 4.1 M 68.4 3.6 4.6 84 88 * 2.7 P 75.0 2.0 2.6 89 93 C 4.0 M 75.0 3.4 3.0 94 97 H 4.0 M 40.5 4.0 3.8 98 99 - 4.0 M 4.5 75.0 75.0 100 103 C 4.0 M 0.8 4.0 3.8 104 107 E 4.5 M 3.2 1.8 2.0 109 111 E 4.0 M 3.7 2.0 2.0 112 116 C 4.0 M 3.8 3.8 3.4 117 120 E 4.0 M 2.2 2.8 4.8 121 123 C 4.7 H 7.2 5.7 4.3 124 128 E 4.8 H 1.8 2.2 1.2 130 131 - 4.0 M 7.0 75.0 75.0 132 140 E 5.0 H 1.9 1.8 1.7 141 145 C 4.6 H 5.6 6.6 6.6 146 165 E 4.8 H 2.7 2.4 2.3 167 170 - 4.0 M 6.5 75.0 75.0 172 175 E 4.8 H 1.5 1.0 1.2 176 180 - 4.0 M 4.6 75.0 75.0 181 184 E 4.8 H 3.2 2.0 3.2 186 194 E 4.3 M 11.6 3.6 3.0 195 197 C 4.0 M 75.0 4.0 4.7 198 205 - 4.0 M 5.1 75.0 75.0 206 208 C 4.0 M 1.0 5.0 5.0 209 211 - 4.0 M 3.0 75.0 75.0 212 237 H 4.9 H 3.7 3.1 4.1 240 241 E 4.0 M 4.5 5.0 4.0 242 245 C 4.8 H 4.8 3.0 2.8 246 249 - 4.0 M 5.0 75.0 75.0 250 251 C 5.0 H 9.0 6.5 7.5 252 261 E 4.3 M 4.8 3.4 2.3 263 264 C 4.0 M 75.0 5.0 6.5 266 274 E 4.0 M 36.3 1.7 2.2 >>>>>>