Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1n4ka2 ------CCCEEEEEEC----CCCEEEEEEECC-----CCEEEEEECCCC-CCHHHCCCHHHCEEEEECC-------------------------------------------------CEEEEECCCCCEEEEEE-------CCCEEEEEECCCC--CHHHCEEEEC---------------CCEEEECCCCEEEEEEEEECCCCCCCCCEEEEEEECCCCCCCCEEEEEC------- >P1;d1t9fa1 CCCCCCCCCEEEEEEC----CCCCEEEEEEEECCCCCCCEEEEEEC--------CCCCHHHCEEEEECCCC--------------------------------CCC---CCCCCCCCCEEEEEECCCCCEEEEEE-EECCCCCCCEEEEEECCCCCCCHHHCEEEECC------CCCCCCCCEEEEEECCCCCEEEEEEEECCCCCC--CCEEEEEECCCCCCCCEEEECCC------ >P1;d1xzza1 --CCCCCCCEEEEEEEC---CCCEEEEECC------CCCCCEEECHHHCCCCCCCCCHHHHCEEEECCCCCHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCEEEEEEEEEECCCCCCCEEEEEEC---CCCHHHCEEEEECCCCCCCCCCCCCCCEEEEEECCCCCCEEEEEEECC-CCC--CCEEEEECCCC---CEEEEEEC------- >P1;d3im6a- ---CCCCCCEEEEEEEECCCCEEEEEECCCC-------CCCCEEE---EC---CCCCHHHCCEEEEEEECHHHHHHHHHHC------------------------------CCCCCCCEEEEEECCCCCEEEECC--C-----CCEEEEEECCCC--CCCCEEEEEECC---CCCCCCCCCCEEEEEECCCCCEEEEEEC------C--CCEEEEEECCC---CCEEEEC-------- >P1;d3mala- --CCCCCCCEEEEEEC----CCCCEEEEEEEECCCCCCCEEEEEEC--------CCCCHHHCEEEECCCCC--------------------------------CCC---CCCCCCCCCEEEEEECCCCCEEEEEE-EECCCCC-CEEEEEECCCCCCCHHHCEEEEECCC----CCCCCCCCEEEEEECCCCCEEEEEEEECCCCCC--CCEEEEEECCCCHHHCEEEEEEECCCCCC PSA >P1;d1n4ka2 ------3782010103----526100003528-----963300043196-b61651448402031462a-------------------------------------------------52103034353100068-------5382002027708--7730104136---------------710010541701020196210675a723012000168439702023473------- >P1;d1t9fa1 b862020332000100----7360100019360b411531000007--------67636300020111295--------------------------------a17---88410508640101033251000019-5400408821000021459605620003030c------c74034726020401505000000a65168718--42100000a845b2030403608------ >P1;d1xzza1 --950301240000034---7160000018------6a3520002294243a850a51700103011414092066248151b688547715750461566165327645853050251000102307210002684604229a02201047---60440010303126a83767520313120202015044101005450a-636--2011000281b---00020345------- >P1;d3im6a- ---406383602020506397450000062d-------9440401---51---8165680010102402437205652787------------------------------91030020000303616110002a--8-----823200038728--83300000422a---48574064a3400010032712020336------b--86150201895---1504033-------- >P1;d3mala- --64000002000202----6261100019450c920530100024--------97a163030102226b4--------------------------------b56---70310635230100055243000027-4702326-410000215596167101040202ab----68203372501020440500000175328a922--71000001574663000102408149349 Translating the sequences ------CCCEEEEEEC----CCCEEEEEEE**-----CCEEEEEEC***-*****CCCHHHCEEEEECC-------------------------------------------------*EEEEECCCCCEEEEEE-------CCCEEEEEECCCC--CHHHCEEEE*---------------**EEEECCCC*EEEEEEEECCCCCC**C*EEEEEECCCC**CCEEEEEC------- **CCCCCCCEEEEEEC----CCC*EEEEEE******CCCEEEEEEC--------CCCCHHHCEEEEECCCC--------------------------------***---CCCCCCCCCEEEEEECCCCCEEEEEE-EECCCCCCCEEEEEECCCCCCCHHHCEEEE*C------CCCCCCCCEEEEEECCCCCEEEEEEEECCCCCC--CCEEEEEECCCC**CCEEEE*C*------ --CCCCCCCEEEEEE**---CCCEEEEE**------CCC**EEE**********CCC*HHHCEEEE*CCCC**************************************CCCCCCCCCEEEEEECCCC*EEEEEE*EECCCCCCCEEEEEEC---CCCHHHCEEEEECC*****CCCCCCCCEEEEEECCCCC*EEEEEEECC-CCC--CCEEEEE*CCC---C*EEEEEC------- ---CCCCCCEEEEEE*****C**EEEE****-------C***EEE---**---*CCC*HH*CEEEEE**C***********------------------------------CCCCCCCEEEEEECCCCCEEEE**--*-----CCEEEEEECCCC--C****EEEEECC---**CCCCCCCCEEEEEECCCCCEEEEEE*------C--CCEEEEEECCC---CCEEEE*-------- --CCCCCCCEEEEEEC----CCC*EEEEEE******CCCEEEEEEC--------CCCCHHHCEEEE*CCCC--------------------------------***---CCCCCCCCCEEEEEECCCCCEEEEEE-EECCCCC-CEEEEEECCCCCCCHHHCEEEEECC*----CCCCCCCCEEEEEECCCCCEEEEEEEECCCCCC--CCEEEEEECCCC***CEEEEE******** 82109.tem _________________________________ --CCCCCCCEEEEEEC----CCCEEEEEEE**----CCCEEEEEEC--*----*CCCCHHHCEEEEECCCC--------------------------------***---CCCCCCCCCEEEEEECCCCCEEEEEE-EECCCCCCCEEEEEECCCCCCCHHHCEEEEECC-----CCCCCCCCEEEEEECCCCCEEEEEEEECCCCCC--CCEEEEEECCCC**CCEEEEEC------- Structural block scores 0 1 - 4.5 M 75.0 9.8 75.0 75.0 75.0 2 8 C 4.7 H 45.4 2.3 2.9 14.1 1.4 9 14 E 5.0 H 0.7 0.5 0.7 1.7 0.7 16 19 - 4.3 M 75.0 75.0 57.2 4.5 75.0 20 22 C 4.7 H 4.3 5.3 4.7 5.3 4.7 23 29 E 4.4 M 1.3 1.6 1.3 1.1 1.7 30 31 * 2.5 P 5.0 4.5 75.0 44.2 4.5 32 35 - 3.8 M 75.0 4.1 75.0 75.0 5.9 36 38 C 4.6 H 30.0 3.0 6.5 53.0 2.7 39 44 E 4.4 M 1.7 0.2 1.5 2.2 0.5 46 47 - 3.8 M 5.0 75.0 6.5 75.0 75.0 49 52 - 3.8 M 23.4 75.0 6.4 56.5 75.0 54 57 C 4.6 H 3.5 5.5 4.1 4.5 6.9 58 60 H 4.8 H 4.0 3.0 2.3 2.7 3.0 62 66 E 4.8 H 2.8 0.8 1.0 1.4 1.0 67 70 C 4.4 M 40.6 4.2 2.2 2.2 5.9 71 102 - 4.3 M 75.0 75.0 4.8 53.1 75.0 103 105 * 3.0 P 75.0 6.2 3.3 75.0 7.5 106 108 - 4.5 M 75.0 75.0 5.7 75.0 75.0 109 117 C 4.4 M 75.0 4.4 3.7 18.3 3.0 118 123 E 4.9 H 1.8 1.0 0.3 0.5 0.7 124 128 C 4.9 H 3.6 2.8 2.8 3.4 3.8 129 134 E 4.8 H 2.5 1.7 1.5 2.2 1.5 136 137 E 4.2 M 75.0 4.5 5.0 41.5 5.5 138 144 C 4.4 M 45.1 3.1 3.9 55.0 13.1 145 150 E 5.0 H 1.0 0.5 1.5 1.3 0.5 151 157 C 4.6 H 25.6 4.3 34.6 26.1 4.7 158 160 H 4.5 M 3.3 2.7 1.3 2.0 2.7 162 166 E 4.8 H 2.8 1.2 1.4 1.2 1.2 167 168 C 4.3 M 75.0 43.8 4.0 6.2 6.2 169 173 - 4.1 M 75.0 75.0 6.9 47.4 62.3 174 181 C 4.5 M 75.0 4.9 2.8 4.9 3.9 182 187 E 4.8 H 1.5 2.0 1.0 0.8 1.3 188 192 C 4.9 H 3.4 2.2 2.8 2.6 2.6 193 200 E 4.8 H 2.6 2.7 2.0 11.4 2.0 201 206 C 4.5 M 4.9 5.2 16.8 64.4 5.6 207 208 - 4.5 M 4.5 75.0 75.0 75.0 75.0 209 210 C 4.8 H 1.5 3.0 1.0 7.0 4.0 211 216 E 4.9 H 0.7 0.2 0.7 1.5 0.2 217 220 C 4.8 H 5.2 6.9 23.9 24.2 5.5 221 222 * 3.0 P 8.0 6.8 75.0 75.0 4.5 223 224 C 4.5 M 1.0 1.5 0.0 3.0 0.0 225 229 E 4.8 H 3.2 2.6 1.8 2.0 1.4 231 237 - 4.4 M 75.0 65.4 75.0 75.0 5.4 >>>>>>