Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1uz5a2 ---CCCCHHHHHHHHHHCCCCC-CEEEEEHHHCCCCCCCCCEECCCCCCCCCEECCCEEEECHHHHCCCCCCCCEEEEEEEEECCCCCCCCCCCCCEEEEECCCCCCCCCCCEEEEHHHCEEEC--------CEEEECCCCCCCCCEECCCCCCCCCCEEECCCCCCCHHHHHHHHHCCCCEEEEECC >P1;d2nqra2 ----CCCHHHHHHHHHHHCCCCCCEEEEEHHHCCCCCCCCCEECCCCCCCCCEECCCEEEECHHHHHHC-----CCCCEEEEECCCCCCCCCCCCCCEEEECCCCCCCCCCCEEEEHHHEEECC--------CCEEECCCCCCCCCEECCCCCCCCCCEEECCCCCCCCCCHHHHHHCCCCEEEEECC >P1;d6fgca1 CCCCCCCHHHHHHHHHHHCCCC-CEEEEEHHHCCCCCCCCCEECCCCCCCCCEECCCEEEECHHHCC-------EEEEEEEEECCCCCCCCCCCCCEEEEECCCCCCCCCCCEEEEHHHEEEEEECCCCCCEEEEEECCCCCCCCCEECCCCCCCCCCEEECCCCCCCHHHHHHHHHHCCCEEEEECC PSA >P1;d1uz5a2 ---9a47875555577779983-943415187077130054150442204344043500002061059059a8226062264058c5707370786300302530400850400054860664b--------c202039307533204650662867630076637079731730670a296040358 >P1;d2nqra2 ----b7698735877687788597554141960611400540505522266310245000023911869-----71053243055b93277a05960002026601109a0400036730674b--------82050438087222065615817486612646250398115405509295030258 >P1;d6fgca1 7a98b58896466587676796-9347140670551401430606644043200435000020a224-------63170262066b770a550656400404650000830500046720631642b8497151040446086722035506407685301667370479218304306245030346 Translating the sequences ---CCCCHHHHHHHHHH*CCCC-CEEEEEHHHCCCCCCCCCEECCCCCCCCCEECCCEEEECHHHHC*C*****EEEEEEEEECCCCCCCCCCCCCEEEEECCCCCCCCCCCEEEEHHH*EEEC--------CEEEECCCCCCCCCEECCCCCCCCCCEEECCCCCCCHHHHHHHHHCCCCEEEEECC ----CCCHHHHHHHHHHHCCCC*CEEEEEHHHCCCCCCCCCEECCCCCCCCCEECCCEEEECHHHH**C-----****EEEEECCCCCCCCCCCCC*EEEECCCCCCCCCCCEEEEHHHEEE*C--------C*EEECCCCCCCCCEECCCCCCCCCCEEECCCCCCC***HHHHHHCCCCEEEEECC ***CCCCHHHHHHHHHHHCCCC-CEEEEEHHHCCCCCCCCCEECCCCCCCCCEECCCEEEECHHH*C-------EEEEEEEEECCCCCCCCCCCCCEEEEECCCCCCCCCCCEEEEHHHEEEE**********EEEECCCCCCCCCEECCCCCCCCCCEEECCCCCCCHHHHHHHHH*CCCEEEEECC 63882.tem _________________________________ ---CCCCHHHHHHHHHHHCCCC-CEEEEEHHHCCCCCCCCCEECCCCCCCCCEECCCEEEECHHHHC*C-----EEEEEEEEECCCCCCCCCCCCCEEEEECCCCCCCCCCCEEEEHHHEEEEC--------CEEEECCCCCCCCCEECCCCCCCCCCEEECCCCCCCHHHHHHHHHCCCCEEEEECC Structural block scores 0 2 - 4.0 M 75.0 75.0 8.8 3 6 C 4.8 H 7.6 24.9 8.1 7 17 H 4.9 H 6.2 6.8 6.5 18 21 C 5.0 H 7.2 7.0 7.0 24 28 E 5.0 H 3.4 3.8 3.8 29 31 H 5.0 H 5.3 5.3 4.3 32 40 C 5.0 H 3.0 2.3 2.6 41 42 E 5.0 H 3.0 2.5 3.0 43 51 C 5.0 H 2.6 3.4 3.2 52 53 E 5.0 H 2.0 0.5 0.0 54 56 C 5.0 H 4.0 3.7 4.0 57 60 E 5.0 H 0.0 0.0 0.0 62 65 H 4.8 H 1.8 3.5 3.6 69 73 - 4.0 M 6.9 75.0 75.0 74 82 E 4.6 H 3.1 2.8 3.0 83 95 C 5.0 H 5.8 6.2 5.8 96 100 E 4.8 H 1.2 0.4 1.6 101 111 C 5.0 H 2.8 3.6 2.8 112 115 E 5.0 H 1.2 0.8 1.0 116 118 H 5.0 H 6.0 5.3 5.0 119 122 E 4.5 M 4.0 4.2 2.5 124 131 - 4.0 M 75.0 75.0 5.8 133 136 E 4.8 H 1.0 1.8 1.2 137 145 C 5.0 H 3.9 4.0 4.3 146 147 E 5.0 H 2.0 3.0 1.5 148 157 C 5.0 H 5.2 5.1 4.6 158 160 E 5.0 H 1.0 3.0 1.3 161 167 C 5.0 H 5.1 3.7 4.7 168 176 H 4.7 H 4.8 4.2 4.1 177 180 C 4.8 H 5.4 5.0 3.0 181 185 E 5.0 H 2.6 2.0 2.2 186 187 C 5.0 H 6.5 6.5 5.0 >>>>>>