Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1bu8a1 -----CEEEEEEEEEEC------CCCEEEEEEEEEEECC--------EECCCEEEEE-----EEECCCCEEEEEEEEC---CCCCCEEEEEEEEE------CCCEEEEEEEEEC-CCCCEEEEECCCCCCCC----CCEEEEEC--- >P1;d1ca1a2 CCCCCCCEEEEEEEECCCC----CCCCCCEEEEEEEECC--------CCEEEEECCCC---CCCCCCCCEEEEEEECCCCCCCHHHEEEEEEEEECCCCCCCCCCEEEEEEEECC--EEEEEEECCCCCCCC----CEEECC----- >P1;d2p0ma2 ------CEEEEEEEECCCC----CCCCCCEEEEEEEECC--------CEEEEEEEE-------CCCCCCEEEEEEECC---CCCCCEEEEEEEEECCC-CCCCEEEEEEEEEECCCCCCCEEEEEEEEECCC----CCEEEECC--- >P1;d3pzwa1 -------CEEEEEEEEEHHHCCHHHHCCCCEEEEEEEEEEECCCCCEEECCCEECCEEECCCCCCCCCCEEEEEEECCCHHHC--CEEEEEEEECCC----CCEEEEEEEEEC-----CCEEEEEEEEECCHHHCCCCEEEECCCCC >P1;d3v98a1 -------CEEEEEEECCCC----CCCCCCEEEEEEEECC--------CCCCCEECCC-----CCCCCCCEEEEEECCC---CCCCCEEEEEEEEECCC-CCCCEEEEEEEEECCC--CCEEEEEEEEEECCC----CCEEEECC--- PSA >P1;d1bu8a1 -----655040103031------8761925020002066--------8507424036-----9505194613520503---35056053010004------5400045020329-9756523031a832546----53020653--- >P1;d1ca1a2 2aa6305602040100769----7000703010003058--------57423130552---e7106443525040708567144830530103044577934401041030302a--641154805630835----643504----- >P1;d2p0ma2 ------8413010100758----9010904020201056--------760707321-------50646664526271a---7802504404020726a-963302021000303a6b4b4140305440676----a4230652--- >P1;d3pzwa1 -------72501010115a44c39702c82000201055545a9981432742105431a837828b311003040708b822--701003020428----61010230204a-----d21607052305128639a42417066a9 >P1;d3v98a1 -------305020000759----6020402020002066--------4306623048-----6608542524270816---4a07804304040656b-9833010320005039--766240305540508----84030853--- Translating the sequences -----**EEEEEEEE*C------CCC***EEEEEEEECC--------*ECCCEE***-----***CCCCEEEEEEE*C---CCCCCEEEEEEEEE------CC*EEEEEEEEEC-**CCEEEEE*****CCC----CCEEEE*C--- *******EEEEEEEECCCC----CCCCCCEEEEEEEECC--------C****EECC**---*CCCCCCCEEEEEEECC***CC***EEEEEEEEECCC*CCCC**EEEEEEEECC--**EEEEE*****CCC----C*EE**----- ------*EEEEEEEECCCC----CCCCCCEEEEEEEECC--------CE***EE**-------CCCCCCEEEEEEECC---CCCCCEEEEEEEEECCC-CCCCEEEEEEEEEECC**CC*EEEEEEEEECCC----CCEEEECC--- -------*EEEEEEE***********CCC*EEEEEEE***********ECCCEECC******CCCCCCCEEEEEEECC****C--CEEEEEEEE*CC----CCEEEEEEEEE*-----C*EEEEEEEEECC*****CCEEEECC*** -------*EEEEEEECCCC----CCCCCCEEEEEEEECC--------C*CCCEECC*-----CCCCCCCEEEEEE*CC---CCCCCEEEEEEEEECCC-CCCCEEEEEEEEE*CC--CCEEEEEEEEEECCC----CCEEEECC--- 49723.tem _________________________________ ------*EEEEEEEECCCC----CCCCCCEEEEEEEECC--------CECCCEECC*-----CCCCCCCEEEEEEECC---CCCCCEEEEEEEEECCC-CCCCEEEEEEEEEECC--CCEEEEEEEEEECCC----CCEEEECC--- Structural block scores 0 5 - 4.4 M 63.5 5.3 75.0 75.0 75.0 7 14 E 4.8 H 1.6 1.6 1.2 2.0 1.2 15 18 C 4.1 M 38.5 5.5 5.0 4.4 5.2 19 22 - 4.5 M 75.0 75.0 75.0 5.9 75.0 23 28 C 4.5 M 5.5 2.3 3.2 6.4 2.0 29 36 E 4.9 H 1.1 0.9 1.1 0.6 0.8 37 38 C 4.5 M 6.0 6.5 5.5 5.0 6.0 39 46 - 4.5 M 75.0 75.0 75.0 6.4 75.0 49 51 C 3.8 M 3.7 3.0 2.3 4.3 4.0 52 53 E 5.0 H 3.0 2.0 5.0 1.5 2.5 54 55 C 3.8 M 1.5 2.5 1.5 2.5 2.0 57 61 - 4.2 M 75.0 48.3 75.0 5.1 75.0 62 68 C 4.7 H 4.7 3.6 14.6 5.8 4.4 69 75 E 4.9 H 3.1 3.3 4.6 1.1 4.0 76 77 C 4.8 H 1.5 4.0 5.8 3.5 3.5 78 80 - 3.8 M 75.0 6.0 75.0 9.2 75.0 81 85 C 4.4 M 3.8 4.0 4.4 32.2 5.9 86 94 E 4.9 H 1.4 1.8 2.3 1.1 2.3 95 97 C 4.4 M 75.0 5.3 6.2 28.3 7.5 99 102 C 4.6 H 39.8 5.0 5.2 39.2 5.8 103 112 E 4.7 H 1.6 1.2 0.8 2.2 1.1 113 114 C 4.3 M 42.0 6.2 6.8 75.0 6.0 115 116 - 3.8 M 8.0 75.0 8.8 75.0 75.0 117 118 C 4.3 M 5.5 5.0 7.8 44.2 6.5 119 128 E 4.3 M 3.8 3.3 2.5 2.6 2.9 129 131 C 4.8 H 5.0 5.3 6.3 2.7 4.3 132 135 - 4.5 M 75.0 75.0 75.0 6.5 75.0 136 137 C 4.8 H 4.0 5.0 7.2 7.2 6.0 138 141 E 4.8 H 2.0 3.0 2.8 3.5 2.8 142 143 C 4.3 M 4.0 75.0 3.5 3.0 4.0 144 146 - 4.5 M 75.0 75.0 75.0 8.5 75.0 >>>>>>