Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1stma- -----------------CC--CCEEEEEEEEEC---CCCC-CEEEEEHHH--CHHHHHCCCCCEEEEEEEEEEEEC----CCEEEEEEECCCCCC--------------------------CCCEECCCEEEC-------CCCEEEEECCCCCCCCCC-CCCCCCC---CEEEEEEEECCCCCCCCCCEEEEEEEEEEECCCCCCCC >P1;d1vtz0- ----------CHHHHHHHHHHCCCCEEEEEEEEEEECCCCCEEEECCCCCCCCCCCCCCCCCEEEEEEEEEEEEEECCCCCEEEEEEEEEECCCCCCCCCHHHHCCCCCCCCCCCHHHHHCCCEEEEEEEEEEECCCCCCEEEEEEEEECC---EEECCCCCCCHHHCCCCCEEEEEEE---CCCCCEEEEEEEEEEECC------- >P1;d4oq9a- CCCCCCCCCCCCCCCCCCC--CCEEEEEEEEEE---CCCC-CCEEEEHHHHCCHHHCCCCCCEEEEEEEEEEECCCCCCCCCCEEEEEECCCC-------------------------------CCCCCCEEEECC--CCCCCCEEEEECCHHHCCEE-CC----C---CEEEEEEECCC---------EEEEEEEEEEE------- PSA >P1;d1stma- -----------------a6--a54426052826---0615-553303042--0640591a2220102202040306----58020201010194a--------------------------803330952709-------79564260609a823730-8080755---220000203188a84902905050201040243789af >P1;d1vtz0- ----------9897578762672731518284663602480502300040336b765208a460604303040403047650100000010250907207163006736281a32680294830511420406043a88354545163807---3030464746580003000000000---417504030302010009------- >P1;d4oq9a- c6a8b77988aa86a5688--674725051418---077b-61450303401389180681920202305030359039a5502030200268-------------------------------a5296442370a--75965032106049932752-56----a---13001030105---------40102030306------- Translating the sequences -----------------CC--CCEEEEEEEEE*---CCCC-CEEEEEHHH--CHHH**CCCC*EEEEEEEEEEEEC----CCEEEEEEECCCCCC--------------------------CC*EECCCEEE*-------CCCEEEEE*CC***CC*C-CCCCC*C---CEEEEEEEECC**CCCCC*EEEEEEEEEEEC******* ----------C**********CC**EEEEEEEE***CCCC**EEE******CC***CCCCCCEEEEEEEEEEEEE*CCCCC*EEEEEEE**CCCC**************************CC*EE***EEEEECC**CC***EEEEEECC---**EC*CCCCC*****C**EEEEEE*---CCCCC*EEEEEEEEEE*C------- **********C******CC--CCEEEEEEEEEE---CCCC-C*EEEEHHH*CCHHHCCCCCCEEEEEEEEEEE**CCCCCCC*EEEEEECCCC-------------------------------**CCC*EEEECC--CCCCC*EEEEECC***CCE*-CC----C---CEEEEEEE*CC---------EEEEEEEEEE*------- 88650.tem _________________________________ ----------C******CC--CCEEEEEEEEEE---CCCC-CEEEEEHHH*CCHHHCCCCCCEEEEEEEEEEEEECCCCCCCEEEEEEECCCCCC--------------------------CC*EECCCEEEEECC--CCCCCEEEEEECC***CCEC-CCCCC*C---CEEEEEEEECC--CCCCC*EEEEEEEEEEEC------- Structural block scores 0 9 - 4.0 M 75.0 75.0 8.8 11 16 * 2.7 P 75.0 7.3 7.7 17 18 C 4.0 M 8.2 6.5 8.0 19 20 - 4.0 M 75.0 4.0 75.0 21 22 C 5.0 H 7.8 4.5 6.5 23 32 E 4.7 H 3.9 4.5 3.7 33 35 - 4.0 M 75.0 5.0 75.0 36 39 C 5.0 H 3.0 3.5 6.4 42 46 E 4.4 M 2.8 1.0 2.6 47 49 H 4.0 M 2.0 1.3 2.3 51 52 C 4.5 M 37.5 4.5 2.0 53 55 H 4.0 M 3.3 8.2 6.0 56 61 C 4.7 H 4.9 4.9 5.3 62 74 E 4.8 H 1.2 2.3 1.9 75 81 C 4.1 M 45.6 3.6 5.9 82 88 E 4.9 H 0.7 0.1 1.0 89 94 C 4.3 M 4.2 2.8 27.7 95 120 - 4.0 M 75.0 4.0 75.0 121 122 C 4.0 M 4.0 5.5 75.0 124 125 E 4.0 M 3.0 3.0 7.8 126 128 C 4.0 M 4.7 2.3 5.7 129 133 E 4.4 M 18.6 2.0 4.0 134 135 C 4.0 M 75.0 3.5 5.2 136 137 - 4.0 M 75.0 9.2 75.0 138 142 C 4.0 M 34.2 5.0 6.4 143 148 E 4.7 H 4.0 4.5 2.0 149 150 C 5.0 H 4.5 3.5 2.0 151 153 * 2.7 P 6.8 75.0 7.0 154 155 C 4.0 M 5.0 1.5 4.5 159 163 C 4.4 M 4.6 5.4 47.2 166 168 - 4.0 M 75.0 0.0 75.0 170 177 E 4.6 H 0.9 0.0 1.0 178 179 C 4.0 M 4.5 37.5 2.5 180 181 - 4.0 M 9.2 75.0 75.0 182 186 C 4.0 M 4.6 3.4 75.0 188 198 E 4.8 H 1.5 0.8 8.0 200 206 - 4.0 M 9.1 75.0 75.0 >>>>>>