Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1ou0a- --------------CHHHHH-CCC-CCCCC-CCHHHHHHHHHHCCHHHHHHEEECCCCCCCC-HHHHHCCEEEECCC-CCCCCCCHHHHHHCEEEECCCCHHHHC-CCCCCCCHHHHHHHHCCCCC-CEEEEECCCHHHHHHCC--CCCC-CCCCCCEEECCCCCHHHHHHHHHHHHCC-CCEEEECCCCCCHHHHHHHHHHHH-HHC >P1;d4au1a- CCCCCCCHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHCCCCHHHHEEECCCHHHHHHHHHHCCCCEEECCHHHHHHCCHHHCCCCCCEECCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEECCCHHHHHHHHHHCCCCCCCCCCEEEECCCCCCCHHHHHHHHHHHCCCCEEEECCCCCCHHHHHHHHHHHHCCCC PSA >P1;d1ou0a- --------------97a505-806-8a388-422002200621936701740433b603921-51048101000025-0497071720463070201273a4067-07869354100003206434-60000006115006005--0566-534600000004487703700890381a-030000475502360001000000-620 >P1;d4au1a- aa97476995558630760386080a50684123000000221a4260064050098007401710382110000168005605591023a0602022628703830982a456200002304740770000006115004100700868903303000000547a404700540095701300004764021700100000004794 Translating the sequences --------------*HHHHH-*CC-CCCC*-**HHHHHHHHHHCCHHHHHHEEECCC*****-HHHHHCCEEEECC*-****CC*HHHHHHCEEEECCCCHHHH*-****CCCHHHHHHHH*****-CEEEEECCCHHHHHH**--CCCC-CCCCC*EEECCCCCHHHHHHHHHHHH*C-CCEEEECCCCCCHHHHHHHHHHHH-HHC **************HHHHHH*HCC*CCCCH*HHHHHHHHHHHHCC**HHHHEEECCCHHHHH*HHHH*CC*EEECCH*HHHHCCHHH****C*EE*CCCC**HHH*HHHHCCCHHHHHHHHHHHHH*C*EEEECCCHHHHHHHH**CCCC*CCCCCEEEECCCCC**HHHHHHHHHHHC*CCEEEECCCCCCHHHHHHHHHHHH***C 63965.tem _________________________________ --------------HHHHHH-HCC-CCCCH-HHHHHHHHHHHHCCHHHHHHEEECCCHHHHH-HHHHHCCEEEECCH-HHHHCCHHHHHHHCEEEECCCCHHHHH-HHHHCCCHHHHHHHHHHHHH-CEEEEECCCHHHHHHHH--CCCC-CCCCCEEEECCCCCHHHHHHHHHHHHHC-CCEEEECCCCCCHHHHHHHHHHHH-HHC Structural block scores 0 13 - 3.0 P 75.0 7.2 14 19 H 4.7 H 6.1 3.2 22 23 C 5.0 H 3.0 4.0 25 28 C 5.0 H 7.4 5.4 31 42 H 4.7 H 1.8 0.9 43 44 C 5.0 H 6.0 7.2 45 50 H 4.3 M 4.2 3.0 51 53 E 5.0 H 2.3 1.7 54 56 C 5.0 H 6.8 5.7 57 61 H 3.0 P 3.0 2.2 63 67 H 4.6 H 3.6 3.8 68 69 C 5.0 H 0.5 1.5 70 73 E 4.5 M 0.2 0.2 74 75 C 5.0 H 1.0 0.5 78 81 H 3.0 P 5.0 2.8 82 83 C 5.0 H 3.5 2.5 84 90 H 3.6 M 3.3 4.4 92 95 E 4.0 M 2.2 2.0 96 99 C 5.0 H 3.2 3.0 100 104 H 3.8 M 5.5 5.2 106 109 H 3.0 P 5.2 4.8 110 112 C 5.0 H 5.7 6.5 113 125 H 4.2 M 2.1 2.2 128 132 E 4.6 H 0.0 0.0 133 135 C 5.0 H 2.3 2.3 136 143 H 4.5 M 2.1 1.4 144 145 - 3.0 P 75.0 3.5 146 149 C 5.0 H 4.2 5.5 151 155 C 5.0 H 3.6 1.8 156 159 E 4.5 M 0.0 0.0 160 164 C 5.0 H 3.2 3.2 165 177 H 4.5 M 4.1 3.7 180 181 C 5.0 H 1.5 2.0 182 185 E 5.0 H 0.0 0.0 186 191 C 5.0 H 3.8 3.8 192 203 H 5.0 H 0.8 0.8 205 206 H 3.0 P 4.0 8.0 >>>>>>