Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1cfea- --------------------------------------------CCCHHHHHHHHHHHHHHCC-------CC------CCEECHHHHHHHHHHHHHHHHCCCCCCC----------CCCEEEECCCC----CCCCHHHHHHHCCCCCCCCCCCCCCCCCC---CCCHHHHHHCCCCCEEEEEEEECC---CCCEEEEEEEECCCCCC----CCCCC--- >P1;d1qnxa1 CCHHHCCCCCCCCCHHHHCCCCCCCCCCCEEEEECCCHHHH---HHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCEECHHHHHHHHHHHCC----CCCCCC--CCCCCCCCCCEEEEEEEEECCCCCCCHHHHHHHHHHHHHHCCCC-CCHH-HCCHHHHHHHHHHCCCCCCEEEEEEEEEEECCEEEEEEEEEEECCCCC----CCCCCCCCC >P1;d1smba- -----------------------------------------CHHHHHHHHHHHHHHHHHHHCC-------CCCCC-CCHH--HHHHHHHHHHHHHH----CCCCCCHHHHC-----CCCEEEEEEC----CCCCHHHHHHHHHHHHHHCCCC-----CCCCCHHHHHHHHHHCCCCCEEEEEEEECC---CCCEEEEEEEECCCCCCCCCHHHHHCCCC >P1;d1xtaa1 ----------------------------------CCCHHHCCCCHHHHHHHHHHHHHHHHCCC--------CCCCCCCCCEECHHHHHHHHHHHCC----CCCCCCCHHHCEECCEECEEEEEEEC----CCCCHHHHHHHHHHHHHHEECCCEECCCCCC---CHHHHHHCCCCCCEEEEEEEECCCCCC-CEEEEEEEECCCCC--CCCCCCCCCCC PSA >P1;d1cfea- --------------------------------------------555590014004400752a-------07------60821890166059206844c6073523----------c200000342b----722033006701627600558a6713cc4---91650100005508300013160a---5061000000255005b----92610--- >P1;d1qnxa1 87058190796560002438676180cc2724634079633---7402710160024006160830760603306406607129301400200000----075650--60110872401000013157778137026005300520540217-6706-706695013000000070410000002033995110000000031024----894500756 >P1;d1smba- -----------------------------------------8a77801740260026109609-------04608-1972--06303610660086----58475054177-----8740010407----6607073003401722980529-----826469b0230000004505500001140a---590000000064202479b8508700364 >P1;d1xtaa1 ----------------------------------374a5040749802830161004007608--------4804405705106501610362074----24176057961416955010002306----a033046004401425650514722378b27---06200000035043000000505a296-21000000022028--ab643400758 Translating the sequences --------------------------------------------***HHHHHHHHHHHHH*CC-------CC------CCEECHHHHHHHHHHH******CCCCCC----------CC*EEEE**C*----CCC*HHHHHHH******CCCC*****CCC---***HHHHH*CCCCCEEEEEEEECC---C*CEEEEEEEECCCCC*----CCCCC--- *****************************************---HHHHHHHHHHHHHHH**CC*******CCCCC*CCCCEECHHHHHHHHHHH**----CCCCCC--**C*****CC*EEEEEE*****CCCCHHHHHHHHHHHHHHCCCC-****-*CC****HHHHHH*CCCCCEEEEEEEE********EEEEEEEECCCCC----*CCCCCCCC -----------------------------------------***HHHHHHHHHHHHHHHH*CC-------CCCCC-CC**--*HHHHHHHHHHH**----CCCCCC****C-----CC*EEEEEEC----CCCCHHHHHHHHHHHHHHCCCC-----CCCC****HHHHHH*CCCCCEEEEEEEECC---C*CEEEEEEEECCCCC*********CCCC ----------------------------------**********HHHHHHHHHHHHHHHH*CC--------CCCC*CCCCEECHHHHHHHHHHH**----CCCCCC****C******C*EEEEEEC----CCCCHHHHHHHHHHHHHH**CC*****CCCC---*HHHHHH*CCCCCEEEEEEEECC***C-CEEEEEEEECCCCC--***CCCCCCCC 55797.tem _________________________________ ----------------------------------**********HHHHHHHHHHHHHHHH*CC-------CCCCC*CCCCEECHHHHHHHHHHH**----CCCCCC****C*****CC*EEEEEEC*---CCCCHHHHHHHHHHHHHHCCCC*****CCCC****HHHHHH*CCCCCEEEEEEEECC***C*CEEEEEEEECCCCC*-***CCCCCCCC Structural block scores 0 33 - 4.3 M 75.0 4.9 75.0 75.0 34 43 * 3.5 M 75.0 25.7 55.0 4.5 44 59 H 4.8 H 3.1 2.5 3.3 3.1 61 62 C 5.0 H 6.2 3.0 4.5 4.0 63 69 - 4.3 M 75.0 4.3 75.0 75.0 70 74 C 4.4 M 46.4 2.4 3.6 18.2 76 79 C 4.3 M 39.0 3.0 4.8 3.0 80 81 E 4.3 M 5.0 4.0 75.0 3.0 83 93 H 5.0 H 4.2 1.7 2.8 2.7 94 95 * 1.0 P 7.0 0.0 7.0 5.5 96 99 - 4.3 M 6.6 75.0 75.0 75.0 100 105 C 5.0 H 3.3 3.8 4.8 3.3 106 109 * 2.9 P 75.0 39.0 4.2 6.8 111 115 * 3.5 M 75.0 3.6 75.0 5.0 116 117 C 4.7 H 7.2 2.0 7.5 2.5 119 124 E 4.8 H 1.2 0.7 0.8 0.8 127 129 - 4.3 M 75.0 7.0 75.0 75.0 130 133 C 4.8 H 21.5 4.8 4.8 4.1 134 147 H 4.6 H 2.9 2.3 3.3 2.9 148 151 C 4.7 H 4.5 2.5 4.0 2.5 152 156 * 2.5 P 5.5 18.8 75.0 4.2 157 160 C 4.5 M 26.0 22.0 5.0 7.1 161 164 * 2.6 P 40.0 5.0 6.6 56.2 165 170 H 4.9 H 2.0 0.7 0.8 1.3 172 176 C 5.0 H 3.6 2.2 2.8 2.4 177 184 E 5.0 H 1.8 0.4 1.4 1.0 185 186 C 4.3 M 5.2 1.5 5.2 2.5 187 189 * 3.5 M 75.0 7.0 75.0 7.2 193 200 E 5.0 H 0.4 0.0 0.8 0.1 201 205 C 5.0 H 3.0 2.0 2.4 2.8 208 210 * 3.1 M 75.0 52.7 8.2 9.3 211 218 C 4.4 M 30.4 4.5 3.5 3.9 >>>>>>