Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1iu8a- -CCEEEEEECCCCCCCCCHHHHHHHHHHHH-CC---CEEEEEECCCHHHHHHHHHHHHHHHCCCEEEEEEECCCCCCEEEECEEECCEECCCCCCCCCCCEEECCCCCCCCEEECCCCHHHHHHHHHHCCCCEEEECCCCCCHHHHHHHHHHHHHHHHCCCCEEEEEEECCCHHHCCCCC----CCCCCCHHHHHHHHHHHHHHHHHHHHHCCCC---- >P1;d3giua- --CEEEEEECCCCCCCCCHHHHHHHHCCC-EEC-CEEEEEEEECCCHHHHHHHHHHHHHHCCCCEEEEEEECCCCCCCEECCEEECCEECCCCCCCCCCCEEECCCCCCCCEEECCCCCCC-CHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCCEEEEEEECCCHHHHCCCC----CCCC-CHHHHHHHHHHHHHCCCCCCCCCCCCCCCC >P1;d5z48a1 CCEEEEEEECCCCCCCCCHHHHHHHHHCCCEEHHHEEEEEEEECCCHHHHHHHHHHHHHHHCCCEEEEEEECCCCCCEEEECEEECEECCCCCCCCCCCCCCEECCCCCCCEEECCCCHHHHHHHHHHCCCCEEEECCCCCCHHHHHHHHHHHHHHHCCCCCCEEEEEECCCHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHC---------- PSA >P1;d1iu8a- -140000003315b1b30004400830285-08---30302201000640384047105625020000000135364000021041403085403485325763028c15a318050205700530574a04060168092101000000002015569105100000000046118a3a----b131043830150031004202840676579---- >P1;d3giua- --30000002214b1a2000230036088-707-935041340200075027305710775806000000010539100003105130308230438430566302980482170300111-0320376a150602370841010000000010243646a0200000001046019c38----b131-53a502600301052049982574b1668c >P1;d5z48a1 742000000441481420002500870572908b6150303302020860084047105639050000000114365010042040301093504686425856058b03b31705021730183089290507027709320101000200120555a6b3200000000054018315b9679145262920040041003100753---------- Translating the sequences -CCEEEEEECCCCCCCCCHHHHHHHHH***-*C---*EEEEEECCCHHHHHHHHHHHHHHHCCCEEEEEEECCCCCCEEEECEEECCEECCCCCCCCCCCEEECCCCCCCCEEECCCCHHHHHHHHHHCCCCEEEECCCCCCHHHHHHHHHHHHHHH*CCCCEEEEEEECCCHHH*CCCC----CCCCCCHHHHHHHHHHHHHHHHHH***CCCC---- --CEEEEEECCCCCCCCCHHHHHHHH*CC-EEC-*EEEEEEEECCCHHHHHHHHHHHHHH*CCCEEEEEEECCCCCC*EE*CEEECCEECCCCCCCCCCCEEECCCCCCCCEEECCCC***-*HHHHHCCCC****CCCCCCHHHHHHHHHHHHHHHCCCCCEEEEEEECCCHHHHCCCC----CCCC-CHHHHHHHHHHHHH*****C**CCCC**** *C*EEEEEECCCCCCCCCHHHHHHHHHCC*EE***EEEEEEEECCCHHHHHHHHHHHHHHHCCCEEEEEEECCCCCCEEEECEEEC*E*CCCCCCCCCCC**E*CCCCCCCEEECCCCHHHHHHHHHHCCCCEEEECCCCCCHHHHHHHHHHHHHHHCCCCC*EEEEEECCCHHHH**CC****CCCCCCHHHHHHHHHHHHHHHHHHC---------- 53182.tem _________________________________ -CCEEEEEECCCCCCCCCHHHHHHHHHCC*EEC-*EEEEEEEECCCHHHHHHHHHHHHHHHCCCEEEEEEECCCCCCEEEECEEECCEECCCCCCCCCCCEEECCCCCCCCEEECCCCHHHHHHHHHHCCCCEEEECCCCCCHHHHHHHHHHHHHHHCCCCCEEEEEEECCCHHHHCCCC----CCCCCCHHHHHHHHHHHHHHHHHHC**CCCC---- Structural block scores 1 2 C 4.0 M 2.5 39.0 3.0 3 8 E 5.0 H 0.0 0.0 0.0 9 17 C 5.0 H 4.3 3.8 3.1 18 26 H 4.9 H 2.1 1.6 2.4 27 28 C 4.0 M 5.0 8.0 6.0 30 31 E 4.0 M 37.5 3.5 4.5 35 42 E 4.8 H 10.6 2.5 1.9 43 45 C 5.0 H 0.3 0.7 1.3 46 60 H 4.9 H 3.3 3.7 3.5 61 63 C 5.0 H 2.3 4.7 4.7 64 70 E 5.0 H 0.0 0.0 0.0 71 76 C 5.0 H 3.7 3.2 3.3 77 80 E 4.5 M 0.0 0.0 0.2 82 84 E 5.0 H 1.7 2.0 2.0 85 86 C 4.5 M 2.5 2.0 1.5 87 88 E 4.5 M 1.5 1.5 0.5 89 99 C 5.0 H 3.8 3.2 4.3 100 102 E 4.3 M 6.0 5.7 6.0 103 110 C 4.9 H 5.2 4.2 5.6 111 113 E 5.0 H 4.0 3.3 3.7 114 117 C 5.0 H 1.8 0.8 1.8 118 127 H 4.5 M 3.2 9.3 4.0 128 131 C 5.0 H 4.6 5.6 4.0 132 135 E 4.0 M 1.8 2.0 2.2 136 141 C 5.0 H 4.3 3.8 4.7 142 156 H 5.0 H 0.9 0.7 1.1 157 161 C 4.8 H 4.2 5.3 7.2 162 168 E 4.9 H 0.1 0.3 0.3 169 171 C 5.0 H 0.0 0.3 0.0 172 175 H 4.8 H 3.0 2.8 2.5 176 179 C 4.5 M 8.0 8.1 4.2 180 183 - 4.0 M 75.0 75.0 8.4 184 189 C 4.8 H 3.4 16.1 4.5 190 207 H 4.7 H 2.4 3.3 2.1 209 210 * 2.7 P 6.5 3.5 75.0 211 214 C 4.0 M 6.8 5.9 75.0 215 218 - 4.0 M 75.0 8.1 75.0 >>>>>>