Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1qd1a1 CCEEEECCEECCCCCHHHHHHHHHHHH----CCCCCEEEEEEEECCCCEEEEEEEE-CHHH--HHHHHHHHHHHHHHHCCHHHCCCCCCCCCCEEEEEEEEEECCCHHHHHHHHHHHHHHHHHHHCCCEEEEECCCCCHHHCCHHHHHCCHHHHHHHHCCCHHHCCCCCCCCCCCCCCCEEEEECC--- >P1;d1qd1a2 ---CCEEEEEEECCCHHHHHHHHHHHCCCCCCCCCEEE-EEEEECCCCEEEEEEEECCCCCCCHHHHHHHHHHHHHHC--------------CCCEEEEEEEC----CCCHHHHHHHHHHHHHHHCC-CCC-----------CHHHHHHHHHHHHCCCCCC----------CCCHH-----HHCHHHHC PSA >P1;d1qd1a1 7420201010010667a1042026204----8094061562715785100302011-6082--0040004003203740404808173400000000001146b08182016004500540064170000004500578c166175017831630370075a816002145722540000000048--- >P1;d1qd1a2 ---74030000051767304600370347125075040-604229749100010403415400014002002620885--------------a150410306a----500260023007301863b3-828-----------6584307101830305318----------70539-----6201534a Translating the sequences ***EEE**EE**CCCHHHHHHHHHHHH----CCCC*EE*EEEEECCCCEEEEEEEE-CHHH--HHHHHHHHHHHHHHH**************CEEEEEEEEEE****HHHHHHHHHHHHHHHHHHCC*EEE***********CHHHHH**HHHHHHHHCCC**********CCC*******EEE**--- ---**EEEEEEECCCHHHHHHHHHHH*****CCCCEEE-EEEEECCCCEEEEEEEE*C*****HHHHHHHHHHHHHH*--------------C**EEEEEEE*----***HHHHHHHHHHHHHHHCC-***-----------CHHHHHHHHHHHH***CCC----------CCCHH-----***HH*** 55116.tem _________________________________ ---EEEEEEEEECCCHHHHHHHHHHHH----CCCCEEE-EEEEECCCCEEEEEEEE-CHHH--HHHHHHHHHHHHHHH--------------CEEEEEEEEEE----HHHHHHHHHHHHHHHHHHCC-EEE-----------CHHHHHHHHHHHHHHHCCC----------CCCHH-----EEEHH--- Structural block scores 0 2 - 3.0 P 4.3 75.0 3 11 E 3.7 M 0.6 1.6 12 14 C 5.0 H 4.0 4.3 15 26 H 4.8 H 3.2 3.2 27 30 - 3.0 P 75.0 3.5 31 34 C 5.0 H 5.2 4.2 35 37 E 4.3 M 2.3 1.3 39 43 E 5.0 H 4.2 2.8 44 47 C 5.0 H 5.2 7.2 48 55 E 5.0 H 0.9 0.8 58 60 H 3.0 P 3.3 3.3 61 62 - 3.0 P 75.0 0.0 63 77 H 4.9 H 1.8 2.5 78 91 - 3.0 P 2.8 75.0 93 102 E 4.4 M 1.2 3.0 103 106 - 3.0 P 5.1 75.0 107 124 H 4.7 H 2.6 2.6 125 126 C 5.0 H 3.5 7.2 128 130 E 3.0 P 0.0 6.0 131 141 - 3.0 P 4.4 75.0 143 157 H 4.3 M 3.5 3.2 158 160 C 5.0 H 4.0 4.0 161 170 - 3.0 P 3.8 75.0 171 173 C 5.0 H 3.7 4.0 174 175 H 3.0 P 4.5 6.0 176 180 - 3.0 P 0.0 75.0 181 183 E 3.0 P 0.0 2.7 184 185 H 3.0 P 6.0 3.0 186 188 - 3.0 P 75.0 5.8 >>>>>>