Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1bdfa2 -CEEEEEEEECCCCCCCCCCCCCCCCHHHHHHHHHCCCEECC-------------------CCCEEEEEEEEEC------------------CEEEEHHHCCC--CC---------CCEECC-----CCCEEEEECCCCCEEEEEEEEEECCCEECCCCCCCCCCEECC >P1;d1twfc2 CEEEEEEEEEEEE--------CCCCCHHHHHHHHHCCCEEECCHHHCCCCCCCCC--CCCCCCCEEEEEEEEECCCC--------------CCEEEEHHHEEECC--CCC---CCCEEEECCCCCCCCCCEEEEE-CCCCEEEEEEEEEEECCCCCHHHCC-------- >P1;d4c2mc2 CEEEEEEEEEEEE--------CCCCCHHHHHHHHHHCCEEC-CHHHCCCCCCCCCHHHHCCCCCCEEEEEEEECEECCCCCCCCCCHHHHEECCEEEHHHCEEECCCCHHHHCCCCCCEECC-----CCCEEEEC-CCCCEEEEEEEEEEECCCCCHHHCC-------- PSA >P1;d1bdfa2 -7000140405b0875a372a006140650073029060708-------------------8674140407374------------------5640205204a--3c---------406156-----47230030667b050403020335986653ac3206040416 >P1;d1twfc2 5100035061731--------60936596037301405021720970721760a3--a7334800020206250878--------------a5330204307161--813---b1500513394a8721540050-8572304030002004597591027-------- >P1;d4c2mc2 5200024041650--------60927585026401505070-539306506794689611525100100061706627a15ac1a526421570101052070435a7079506a5605036-----48340050-52b33020402000152b7591056-------- Translating the sequences -*EEEEEEEE***********CCCCCHHHHHHHHHCCCEECC-------------------CCCEEEEEEEEEC------------------CEEEEHHHC**--CC---------CCEECC-----CCCEEEEE*CCCCEEEEEEEEEE*CC**C***CC******** CEEEEEEEEEEEE--------CCCCCHHHHHHHHHCCCEE*CCHHHCCCCCCCCC--**CCCCCEEEEEEEEEC**C--------------*CEEEEHHH*EE*C--C**---CCC**EECC*****CCCEEEEE-CCCCEEEEEEEEEEECCCCCHHHCC-------- CEEEEEEEEEEEE--------CCCCCHHHHHHHHH*CCEEC-CHHHCCCCCCCCC****CCCCC*EEEEEEEEC**C***************C*EEEHHHCEE*CCCC*****CCCCCEECC-----CCCEEEE*-CCCCEEEEEEEEEEECCCCCHHHCC-------- 56553.tem _________________________________ CEEEEEEEEEEEE--------CCCCCHHHHHHHHHCCCEECCCHHHCCCCCCCCC--**CCCCCEEEEEEEEEC**C--------------*CEEEEHHHCEE*CCCC**---CCCCCEECC-----CCCEEEEE-CCCCEEEEEEEEEEECCCCCHHHCC-------- Structural block scores 1 12 E 4.7 H 2.7 2.2 2.0 13 20 - 4.0 M 6.6 75.0 75.0 21 25 C 5.0 H 2.2 4.8 4.8 26 34 H 5.0 H 2.6 3.8 3.4 35 37 C 4.7 H 5.0 3.0 3.3 38 39 E 5.0 H 3.5 1.0 3.5 40 42 C 4.0 M 27.7 3.3 26.7 43 45 H 4.0 M 75.0 5.3 5.0 46 54 C 4.0 M 75.0 4.1 4.8 55 56 - 4.0 M 75.0 75.0 8.5 57 58 * 2.7 P 75.0 8.8 3.5 59 63 C 4.6 H 34.2 3.6 2.8 64 72 E 4.9 H 3.3 1.9 1.7 74 75 * 2.7 P 75.0 7.5 6.0 77 90 - 4.0 M 75.0 75.0 5.6 93 96 E 4.8 H 3.0 2.0 0.5 97 99 H 5.0 H 2.3 2.3 2.3 101 102 E 4.0 M 7.2 4.0 3.5 104 107 C 4.0 M 41.4 39.8 6.4 108 109 * 2.7 P 75.0 2.0 3.5 110 112 - 4.0 M 75.0 75.0 4.7 113 117 C 4.0 M 45.8 3.5 5.5 118 119 E 5.0 H 3.5 3.0 2.5 120 121 C 5.0 H 5.5 3.0 4.5 122 126 - 4.0 M 75.0 7.7 75.0 127 129 C 5.0 H 4.3 2.7 5.0 130 134 E 4.8 H 1.2 1.8 1.8 136 139 C 5.0 H 6.1 5.5 5.4 140 150 E 4.9 H 2.3 1.1 1.1 151 155 C 4.6 H 6.8 6.0 6.1 156 158 H 4.0 M 8.7 3.3 3.3 159 160 C 5.0 H 2.5 4.5 5.5 161 168 - 4.0 M 2.6 75.0 75.0 >>>>>>