Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1txvb5 ----CCEEEEEECCCCCCCCC---------CCCCCCCCCCCCEEEEEECC------CCEEEEEEEEECCCEEEECCCCCEEEEEEEECCCCCEEE-------------------------CCCCCCCCCCCCEEEEEEEEEECCCCC------CCCEEEEEEEC------------------CCCCCEEEEEEECCCCCCCCC >P1;d4g1ma3 CCCCCCCEEEEECCCCCCEECCC-------------EEEEEEEEEEEECC----CCCCCEEEEEECCC----------CEEEEEECC-----------CCCCCCCCEEEEECCCCCCEEEEEEEC-CCCCCCEEEEEEEEEEECCCC-----CCCEEEEEEEEECCCC----------CCC--CCCCEEEEEEEE-------- >P1;d4g1ma4 -CCCCEEEEEEEECCEEEECCCCCCCCCCCCCHHHHCCEEEEEEEEEECCC---CCCCEEEEEEEEEEECC----CCCCEEEEEEEEECCEEEEECCCCCCCCCCCCCEEECCCCCEEEEEEEEECCCCCCEEEEEEEEEEECHHHHHCCCCCCCCEEEEEEEEEEEEECCCCCCCCCCEE--EEEEEEEEEEECC----CCC >P1;d5ffga2 -CEEEEEEEEEEECCEEECCCCCCCCCCCC----CCCCEEEEEEEEEEECCCCCCCEEEEEEEEECCCCCC--CCCCCCEEECC-----------------------------CCCCEEEEEEEEEC--CCCCEEEEEEEEECCH--HHCCCCCCCEEEEEEEEECCCCCCCCCCCCCEECCCCCCEEEEEEEEE-------- PSA >P1;d1txvb5 ----a03176334690488c7---------b6a79422011130303063------642371605023060316920b20707140213697546-------------------------a44309b0783320304050507621b------55724020206------------------b1612030403052889a86a >P1;d4g1ma3 8c434070407078394606348-------------61803040302044----52056030104028----------305054007-----------9589135180824779b7220106087-408554524000302050759-----a590050202040408----------675--407535160803-------- >P1;d4g1ma4 -180705060606475060417b18549a1831910033030202030506---11026020405001228----a410000071616540a070538112580659565010c6061050306075057661020303000102002a098756310030304040340147b6849526--8455030403168----869 >P1;d5ffga2 -25060805050456705087472315b4a----a510004030003061a9a026704030302004717--ab362000006-----------------------------65326364904041--58a5512513000365--950a43a230001040502385032a8774061388574524550406-------- Translating the sequences ----C*EEEEEE*CC****CC---------******CC****EEEEEECC------CCEEEEEEE**C*C*****CCCCEEEEEE**********-------------------------******CCCCCCEEEEEEEEEECC***------CCCEEEEEEE*------------------*CCC*EEEEEEE********* *C**C**EEEEE*CC*****CCC-------------**EEEEEEEEEECC----CCCC*EEEEEE**C----------CEEEEEE**-----------***************CCC*EEEEEEE*-CCCCCCEEEEEEEEEE*C***-----CCC*EEEEEEEE****----------***--CCC*EEEEEEE*-------- -C**C*EEEEEE*CC****CCCC*************CCEEEEEEEEEECC*---CCCCEEEEEEE****C*----CCCCEEEEEE****************************CCC*EEEEEEE**CCCCC*EEEEEEEEEEC*********CCCCEEEEEEEE*****************--****EEEEEEE**----*** -C****EEEEEE*CC****CCCC*******----**CCEEEEEEEEEE*C****CC**EEEEEEE**C*C*--**CCCCEEE**-----------------------------CCC*EEEEEEE**C--CCC*EEEEEEEEECC*--*****CCCCEEEEEEEE*******************CCC*EEEEEEE*-------- 69179.tem _________________________________ -C**C*EEEEEE*CC****CCCC*************CCEEEEEEEEEECC*---CCCCEEEEEEE**C*C*--**CCCCEEEEEE**********---***************CCC*EEEEEEE**CCCCCCEEEEEEEEEECC********CCCCEEEEEEEE*****************-*CCC*EEEEEEE**----*** Structural block scores 2 3 * 2.3 P 75.0 3.5 4.0 2.5 6 11 E 4.9 H 3.8 3.0 2.8 3.0 13 14 C 5.0 H 7.5 5.5 5.5 5.5 15 18 * 1.0 P 5.0 4.8 2.8 3.0 19 22 C 4.5 M 42.4 5.2 5.9 6.5 23 35 * 3.3 M 44.1 75.0 4.7 27.1 36 37 C 4.3 M 2.0 3.5 1.5 0.5 38 47 E 4.7 H 1.2 2.0 1.3 1.0 48 49 C 4.7 H 4.5 4.0 2.5 3.5 51 53 - 4.3 M 75.0 75.0 75.0 6.5 54 57 C 4.3 M 40.0 3.0 1.0 3.8 58 64 E 4.9 H 3.4 2.0 2.4 1.7 65 66 * 1.0 P 1.0 1.0 0.0 0.0 71 72 - 4.3 M 2.0 75.0 75.0 75.0 73 74 * 3.5 M 7.5 75.0 75.0 11.0 75 78 C 4.5 M 3.9 57.0 3.9 2.8 79 84 E 4.7 H 3.2 2.3 1.3 13.5 85 94 * 3.3 M 4.3 60.7 4.0 75.0 95 97 - 4.3 M 75.0 75.0 5.3 75.0 98 112 * 3.5 M 75.0 5.1 3.6 75.0 113 115 C 4.3 M 75.0 9.2 6.2 4.7 117 123 E 4.3 M 35.2 2.4 2.1 4.6 124 125 * 1.6 P 4.5 41.0 3.5 2.0 126 131 C 4.7 H 5.4 4.3 4.8 29.1 132 141 E 4.9 H 1.9 1.6 0.9 2.2 142 143 C 4.3 M 6.5 2.5 0.5 4.5 144 151 * 2.9 P 48.7 49.5 3.9 22.9 152 155 C 4.7 H 23.0 6.1 5.2 4.6 156 163 E 4.9 H 2.0 1.6 1.4 1.2 164 180 * 3.0 P 75.0 45.9 4.4 4.1 183 185 C 4.3 M 2.7 3.7 5.7 5.3 187 193 E 5.0 H 1.4 3.3 1.6 2.9 194 195 * 2.2 P 3.5 39.0 7.0 40.5 196 199 - 4.3 M 8.9 75.0 75.0 75.0 200 202 * 3.5 M 8.2 75.0 7.7 75.0 >>>>>>