Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1k8kd1 CCCCCCCCHHHHHHHHHHHHHHHHC--------------CCCC----------CCEEEEEECCCEEEEEECHHHCCCEEEEEEECC----CHHHHHCCCHHHHHH--HHHHHH--EEC-CCC---------------CCCEEEEEECCCCCC-CHHHHHHHHHCHHHHC-------------------------------- >P1;d1k8kd2 ----------CHHHHHHHHHHHHHCCC-------------------------CCCCEEEEEECCEEEEEEEC---CCCEEEEEEEECCCHHHHHHHHHHHHHHHCHHHCCCCCCEEEEEECCCCHHHCCCCCCCCCCEEEEEEEECHHHHCCCCHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCC >P1;d1k8kf- -------CCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHCCCHHHCCCCEEEECCCCCEEEEEEC---CCEEEEEEECCCCCHHHHHHHHHHHHHHHHCCC---CCCCCCCCCCC---------------CCCEEEEEEHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC------- PSA >P1;d1k8kd1 6aa6563165027106710841559--------------6929----------7074516277905010103b9553201000209----407834786058406--7207a3--13b-43b---------------a1200020407903b-73a7105400102600-------------------------------- >P1;d1k8kd2 ----------65a10460051165355-------------------------c4b2244715b501010204---57401010001086891083048306733664996943220414156029707b4b065673100011003561057932981087035017501630653376556757876567667777869a >P1;d1k8kf- -------59549501560472088106076280554a94333002335178116945414169713010100---30001000104265a307510862056117408---a260026822b---------------b13000201051057396760043006004403750662377587768887669877------- Translating the sequences *******C**HHHHHHHHHHHHHHC--------------CCC*----------CC*EEEEECCCEEEEEE*****CCEEEEEEECC----*HHHHH***HHHHHH--H*****--EEC-CCC---------------CCCEEEEEE****CC-CHHHHHHHHHCHHHH*-------------------------------- ----------*HHHHHHHHHHHHHCCC-------------------------CCCCEEEEE*CCEEEEEEEC---CC*EEEEEE**CCCHHHHHHHHHHHHHHH***H***CCC*EE***CC******************EEEEE*HHHHCCCCHHHHHHHH*CHHHHHHHHHHHHHHHHHHHHHHHHHHHH********* -------C**HHHHHHHHHHHHHH*CC************CCC**********CCCCEEEE*CCC*EEEEEEC---CCEEEEEEECCCCCHHHHHHHHHHHHHHHH***---CCC***C*CCC---------------CCCEEEEEEHHHH**CCHHHHHHHHH*HHHHHHHHHHHHHHHHHHHHHHHHHHHH**------- 69645.tem _________________________________ -------C**HHHHHHHHHHHHHHCCC------------CCC*---------CCCCEEEEECCCEEEEEEEC---CCEEEEEEECCCCCHHHHHHHHHHHHHHHH**H***CCC*EEC*CCC---------------CCCEEEEEEHHHHCCCCHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHH**------- Structural block scores 0 6 - 4.0 M 6.7 75.0 75.0 8 9 * 2.7 P 5.5 75.0 7.0 10 23 H 4.9 H 3.4 3.6 4.2 24 26 C 4.0 M 53.0 4.3 2.3 27 38 - 4.0 M 75.0 75.0 5.0 39 41 C 4.0 M 5.7 75.0 3.0 43 51 - 4.0 M 75.0 75.0 3.3 52 55 C 4.5 M 22.2 7.5 5.0 56 60 E 4.8 H 3.6 3.6 3.0 61 63 C 4.7 H 7.7 7.2 7.3 64 70 E 4.7 H 1.0 0.6 0.9 72 74 - 4.0 M 8.5 75.0 75.0 75 76 C 5.0 H 4.0 6.0 1.5 77 83 E 4.9 H 0.7 0.9 0.3 84 88 C 4.0 M 46.8 3.0 3.4 89 104 H 4.6 H 9.1 4.3 3.9 105 106 * 2.7 P 75.0 5.0 2.0 108 110 * 2.7 P 3.0 8.0 75.0 111 113 C 4.0 M 29.5 3.0 6.2 115 116 E 4.0 M 2.0 2.0 1.0 119 121 C 4.7 H 6.2 4.0 5.2 122 136 - 4.0 M 75.0 5.3 75.0 137 139 C 4.0 M 4.5 0.3 5.2 140 145 E 4.8 H 1.0 0.8 0.5 146 149 H 4.0 M 4.0 3.0 1.5 150 153 C 4.2 M 24.1 6.0 6.0 154 162 H 4.9 H 3.4 4.2 2.9 164 191 H 4.1 M 61.9 4.8 5.2 192 193 * 2.7 P 75.0 6.5 7.0 194 200 - 4.0 M 75.0 7.8 75.0 >>>>>>