Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d2bjqa1 C--CCCCCCEEEEEECCCCCCHHHCCCCHHHCCEECCCCCEECCEEEEEEECCEEEEEEEEECCCCCEEEEEEECCEEECCH-HH-CEEEEEECCC------HHHCCCCCEEEEHHHHCC--CCCCEECCCC----CEEEEEEECCCCCEEEEEEECCCCEEECCCCCCCCCEEHHHHHHCEEEEE--------- >P1;d2bjqa2 -----CCCCEEEEEECCCCCC--CCCCCCCCCC---------CCEEEEEEECCEEEEEEEEEEC-CEEEEEEEECCEEECCCCCCCCEEEEEECCCCCHHHHHHHHCCEEEEEEHHHHHCCC--CEEECCCC----CEEEEEEECCCCCEEEEEEECCCCEEEEEECCEEEEEECHHHHHCEEEEEECCCCCC-- >P1;d2bjra2 CCCCCCCCCEEEEEECCCCCCCCCEECCHHHCCCCCCCCCCCCCEEEEEEECCEEE-EEEEEEC-CEEEEEEEECCEEECC--CC-CEEEEEEECC------CCCCCEEEEECCHHHHHHHHHCCEEECCCCCCCCCCEEEEEEEC-CEEEEEEEECCCCEEEEEECCEEEEEEHHHHCCC-CEEEEECCCCCCC PSA >P1;d2bjqa1 e--9648a15138161447017a560210085505027a6624010001519b2100000232b784020100197722368-60-8703000125------594141605013067047--689350063a----600000054b94100000002554400004987123349a6027030001--------- >P1;d2bjqa2 -----8490713516055612--a211507b29---------501000042898110000356a-83030000389501485a70a55010011527554602762601020420523968a--3010041a----50000007096774000103157620100298802645aa60362400001165078-- >P1;d2bjra2 995a3439141281716281097461030285507008c0453010001427a100-100157c-8702000026861249--90-9803000317------6a41003050160540382a566200022529624101000419-9310011010774400002986053174860470-00005219b1907 Translating the sequences C--CCCCCCEEEEEECCCCCC***CCCCHHHCC**CCCCC**CCEEEEEEECCEEEEEEEEE*C*C*EEEEEEECCEEECC*-**-CEEEEEECCC------HHHCCC**EEEEHHHH*C--*CC*EECCCC----CEEEEEEECCCCCEEEEEEECCCCEEE***CC****EEHHHHHHCEEEEE--------- -----CCCCEEEEEECCCCCC--CCCCC***CC---------CCEEEEEEECCEEEEEEEEEEC-CEEEEEEEECCEEECC**CC*CEEEEEECCC******HHH*CCEEEEEEHHHHHC**--CEEECCCC----CEEEEEEECCCCCEEEEEEECCCCEEEEEECCEEEEEE*HHHHHCEEEEEE*CCCCC-- C**CCCCCCEEEEEECCCCCC**C**CCHHHCC**CCCCC**CCEEEEEEECCEEE-EEEEEEC-CEEEEEEEECCEEECC--CC-CEEEEEE*CC------***CC*EEEE**HHHHH****CCEEECCCC****C*EEEEEE*C-C*EEEEEEECCCCEEEEEECCEEEEEEHHHH**C-*EEEE*CCCCC** 141739.tem _________________________________ C--CCCCCCEEEEEECCCCCC**CCCCCHHHCC**CCCCC**CCEEEEEEECCEEEEEEEEEEC-CEEEEEEEECCEEECC*-CC-CEEEEEECCC------HHHCCCEEEEEEHHHHHC***CCEEECCCC----CEEEEEEECCCCCEEEEEEECCCCEEEEEECCEEEEEEHHHHHHCEEEEEE*CCCCC-- Structural block scores 1 2 - 4.0 M 75.0 75.0 7.0 3 8 C 4.7 H 6.4 28.5 5.1 9 14 E 5.0 H 4.0 3.8 3.8 15 20 C 5.0 H 2.8 3.2 3.0 21 22 * 2.7 P 8.8 75.0 8.0 23 27 C 4.4 M 2.8 3.9 2.8 28 30 H 4.0 M 2.7 6.2 3.3 31 32 C 5.0 H 5.0 5.5 5.0 33 34 * 2.7 P 2.5 75.0 3.5 35 39 C 4.0 M 5.1 75.0 4.1 40 41 * 2.7 P 4.0 75.0 4.5 42 43 C 5.0 H 2.0 2.5 1.5 44 50 E 5.0 H 1.1 1.0 1.1 51 52 C 5.0 H 10.2 8.5 8.8 53 62 E 4.8 H 1.0 2.4 9.0 66 73 E 4.9 H 1.0 1.1 1.4 74 75 C 5.0 H 8.0 8.5 7.0 76 78 E 5.0 H 3.7 2.0 3.0 79 80 C 5.0 H 4.5 6.0 6.5 83 84 C 4.0 M 3.0 3.5 4.5 87 92 E 5.0 H 1.7 1.2 1.8 93 95 C 4.7 H 2.7 2.7 3.7 96 101 - 4.0 M 75.0 4.5 75.0 102 104 H 4.0 M 6.0 5.0 6.8 105 107 C 4.3 M 2.0 2.7 0.3 108 113 E 4.3 M 2.5 1.5 2.5 114 118 H 4.8 H 3.4 3.8 2.4 120 122 * 2.7 P 52.0 31.2 5.8 123 124 C 4.5 M 8.5 39.0 6.0 125 127 E 4.7 H 2.7 0.3 0.7 128 131 C 5.0 H 4.9 3.9 2.2 132 135 - 4.0 M 75.0 75.0 4.8 137 143 E 4.9 H 0.7 1.0 0.9 144 148 C 4.4 M 5.9 5.8 19.4 149 155 E 5.0 H 0.0 1.1 0.6 156 159 C 5.0 H 4.0 4.8 4.5 160 165 E 4.5 M 1.3 0.8 1.0 166 167 C 5.0 H 8.5 8.5 8.5 168 173 E 4.3 M 3.3 4.2 3.7 174 179 H 4.5 M 5.8 6.0 4.8 181 186 E 4.5 M 13.2 0.8 13.3 188 192 C 4.0 M 75.0 5.2 6.3 193 194 - 4.0 M 75.0 75.0 3.5 >>>>>>