Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d3zs3a- CEEEEEECCCCCCEEEEEECCCCCCCCCCCCCCCCCCEEEEECCCCEE-EEEEEEEEEEECCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEEEC--HHHCCEEEEEECCCCCCCCEEEEEECCCCCCCCEEECCCHHHHCCHHHEEECCCCCEEEECCHHHHHCCHHHHCCCCCCCHHHCCCCHHHHHHHHHCCCCCCCCCCCCCCCCEECCCCEEEEEECC >P1;d4bcta- CCEEEEECCCCCEEEEEEC--------CEEEEECCCCEEEECCCCCCCCEEEEEEEEEEECCCCCEEEEECCCC-CCCCCC-CCCCCCCCEEEEEEEEE-CC-EEEEEEECCCCCCCCEEEEECCC-CCCCCEEECCCHHHHCCHHHEEC------CEECCHHHHHCCHHHHCCCC-----CCCCCHHHHHHHHHCCCCCCCCCCHHHCCEEEECCCCEEEEECC PSA >P1;d3zs3a- 150203050792010001077b5930a310050626444308064503-130000140864b67605050020813744061520831000040302--6c87605000003300010010305b17a51550304350185038402350b7652000310320366251105682666a506428114202730560101331a74a4010367040302022 >P1;d4bcta- 0303030406510100024--------4004505585415060ba627b010000180a06c72667050000a-222608-64081000003010648-98-3030100022000010101043b-a1870050337047502960418------50010023247657110967-----a1531a1051015306401012405a603030439040301022 Translating the sequences CEEEEEECCCCC*EEEEEE********C*****CCCCEEEEECCCCEE-EEEEEEEEEEECCCCCEEEEECCCC*CCCCCC*CCCCCCCCEEEEEE*--*HH**EEEEEECCCCCCCCEEEEEECC*CCCCCEEECCCHHHHCCHHHEEE******EEECCHHHHHCCHHHHCCCC*****HCCCCHHHHHHHHHCCCCCCCCCC***CC*EE*CCCEEEEEECC C*EEEEECCCCCEEEEEE*--------CEEEEECCCCEEEE*CCCC***EEEEEEEEEEECCCCCEEEEECCCC-CCCCCC-CCCCCCCCEEEEEEE**-**-EEEEEEECCCCCCCCEEEEE*CC-CCCCCEEECCCHHHHCCHHHEE*------*EECCHHHHHCCHHHHCCCC-----*CCCCHHHHHHHHHCCCCCCCCCCHHHCCEEEECCC*EEEEECC 49870.tem _________________________________ CEEEEEECCCCCEEEEEEE--------CEEEEECCCCEEEEECCCCEE-EEEEEEEEEEECCCCCEEEEECCCC-CCCCCC-CCCCCCCCEEEEEEE---HH-EEEEEEECCCCCCCCEEEEEECC-CCCCCEEECCCHHHHCCHHHEEE------EEECCHHHHHCCHHHHCCCC-----HCCCCHHHHHHHHHCCCCCCCCCCHHHCCEEEECCCEEEEEECC Structural block scores 1 6 E 4.7 H 1.7 1.5 7 11 C 5.0 H 4.6 3.2 12 18 E 4.4 M 0.3 1.0 19 26 - 3.0 P 6.6 75.0 28 32 E 3.0 P 1.2 1.8 33 36 C 5.0 H 4.5 5.8 37 41 E 4.6 H 3.8 3.2 42 45 C 5.0 H 3.8 7.0 46 47 E 3.0 P 1.5 4.5 49 59 E 5.0 H 2.1 1.9 60 64 C 5.0 H 6.9 6.7 65 69 E 5.0 H 2.0 3.6 70 73 C 5.0 H 2.5 2.6 75 80 C 5.0 H 4.0 3.3 82 89 C 5.0 H 2.4 2.4 90 96 E 4.7 H 1.3 1.4 97 99 - 3.0 P 52.0 29.0 100 101 H 3.0 P 10.2 8.5 103 109 E 4.7 H 1.6 1.0 110 117 C 5.0 H 0.9 0.6 118 123 E 4.7 H 1.5 1.0 124 125 C 5.0 H 6.2 7.2 127 131 C 5.0 H 5.3 5.3 132 134 E 5.0 H 1.0 1.7 135 137 C 5.0 H 4.0 4.3 138 141 H 5.0 H 3.5 4.0 142 143 C 5.0 H 1.5 1.0 144 146 H 5.0 H 4.0 5.0 147 149 E 4.3 M 3.3 4.3 150 155 - 3.0 P 5.2 75.0 156 158 E 4.3 M 0.0 1.7 159 160 C 5.0 H 2.0 0.5 161 165 H 5.0 H 1.6 2.2 166 167 C 5.0 H 6.0 6.5 168 171 H 5.0 H 2.2 3.5 172 175 C 5.0 H 4.8 5.5 176 180 - 3.0 P 6.1 75.0 182 185 C 5.0 H 3.0 2.5 186 194 H 5.0 H 3.1 2.9 195 204 C 5.0 H 2.0 1.8 205 207 H 3.0 P 7.2 7.2 208 209 C 5.0 H 7.2 1.5 210 213 E 4.0 M 1.0 1.8 214 216 C 5.0 H 4.3 4.0 217 222 E 4.7 H 1.5 1.3 223 224 C 5.0 H 2.0 2.0 >>>>>>