Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1xi3a- -------CCCC--CCEEECCCCC----CCCCCC-CCCCCCCEEEECC----------CCCHHHHHHHCC-HHHHHHHC-CEEEEECCHHHHHHHCCCEEEECC-CCCHHHHHHHCC-CCEEEEEECCHHHHC-CCCCCCCEEEEECCCCCC-----CCCCHHHHHHHHHH--HCCCEEEECCCCCCCC-CCHHHCCCEEEECHHHHCCC---CCHHHHC-CHHHHHC-- >P1;d2tpsa1 CCCCCHHHHHHHCCEEEEECHHHCCCCHHHHHHHHHHHCCCEEEECCCCC------CCCCHHHHHHHHHHHHHHHHHHCCCEEEECCHHHHHHHCCCEEEECCCCCCHHHHHHHHC-CCEEEEEECCHHHHHHHHHHCCCEEEECCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCEEEECCCCCCCCHHHHHCCCCEEEECHHHHCCCCHHHHHHHHHHHHHHHHHHC >P1;d3o63a1 ----CHHHHHHHCCEEEEECCCCCCCCHHHHHHHHHHCCCCEEEECCCCCHHHHHHCCCCHHHHHHHHHHHHHHHHHCCCEEEEECCHHHHHHHCCCEEEECCCCCCHHHHHHHCCCCCEEEEEECCHHHHHHHHHCCCCEEEECCCCCCC------CCCCHHHHHHHHC--CCCCEEEECCCCCCCHHHHHHCCCCCEEECHHHHCCCCHHHHHHHHHHHHHCC---- PSA >P1;d1xi3a- -------c25a--0000000373----905106-0071403000040----------d07683066105-00930573-130002430600450703000025-335165039506-b02000201539404-039560400200103754-----a53065a6055015--2021000314055930-5008170100002820043b---1108603-106713f-- >P1;d2tpsa1 a94184960271010000001310a67224006500702010000104ba------b049b86255004602700983a110000341800381905001033a25606801850b-320000302629205503703000010000272a248626a42727104402859170000032405393024005130000000420062a60263046046206732993 >P1;d3o63a1 ----836720670200000100214a3057003300205000000406804028655808496138106401700553a000001340600650a000000329245194037406980000220455a3078139660100000302759------9125270064028--892110032304294064018040420003520152b7155205703850573---- Translating the sequences -------****--C*EEE*CCCC----******-***CCCCEEEECC----------CCCHHHHHHH**-HHHHHHHC-CEEEEECCHHHHHHHCCCEEEECC-CCCHHHHHHHCC-CCEEEEEECCHHHH*-***CCCCEEEE*CCCCCC-----CCCC*HHHHHHHHH--*CCCEEEECCCCCCCC-**HH*CCCEEEECHHHHCCC---**HHHH*-*HHHHH*-- ****CHHHHHHHCCEEEEEC***CCCCHHHHHHHHHH*CCCEEEECCCCC------CCCCHHHHHHHHHHHHHHHHH*CC*EEEECCHHHHHHHCCCEEEECCCCCCHHHHHHH*C-CCEEEEEECCHHHHHHHHH*CCCEEEECCCCCCC*****CCCCC*HHHHHHHH**CCCCEEEECCCCCCCCHHHHHCCCCEEEECHHHHCCCCHHHHHHHHHHHHHHHH*** ----CHHHHHHHCCEEEEECCCCCCCCHHHHHHHHHHCCCCEEEECCCCC******CCCCHHHHHHHHHHHHHHHHHCCCEEEEECCHHHHHHHCCCEEEECCCCCCHHHHHHHCC*CCEEEEEECCHHHHHHHHHCCCCEEEECCCCCCC------CCCCHHHHHHHH*--CCCCEEEECCCCCCC*HHHHHCCCC*EEECHHHHCCCCHHHHHHHHHHHHH**---- 51391.tem _________________________________ ----CHHHHHHHCCEEEEECCCCCCCCHHHHHHHHHHCCCCEEEECCCCC------CCCCHHHHHHHHHHHHHHHHHCCCEEEEECCHHHHHHHCCCEEEECCCCCCHHHHHHHCC-CCEEEEEECCHHHHHHHHHCCCCEEEECCCCCCC-----CCCCCHHHHHHHHH--CCCCEEEECCCCCCCCHHHHHCCCCEEEECHHHHCCCCHHHHHHHHHHHHHHHH*-- Structural block scores 0 3 - 4.0 M 75.0 6.1 75.0 5 11 H 4.0 M 36.4 4.1 4.4 12 13 C 4.5 M 37.5 0.5 1.0 14 18 E 4.6 H 0.0 0.0 0.0 19 26 C 4.1 M 39.1 3.6 2.7 27 36 H 4.0 M 10.3 2.6 2.0 37 40 C 4.8 H 2.0 0.8 1.2 41 44 E 5.0 H 0.0 0.0 0.0 45 49 C 4.4 M 45.8 5.4 3.6 50 55 - 4.0 M 75.0 75.0 4.2 56 59 C 4.8 H 23.9 6.1 5.2 60 76 H 4.8 H 7.9 4.3 3.5 77 79 C 4.3 M 26.3 4.8 4.5 80 84 E 4.8 H 1.0 0.2 0.2 85 86 C 5.0 H 3.5 3.5 3.5 87 93 H 5.0 H 2.1 3.0 2.4 94 96 C 5.0 H 3.3 4.7 3.5 97 100 E 5.0 H 0.0 0.2 0.0 101 106 C 4.8 H 15.5 4.9 4.2 107 113 H 5.0 H 4.1 4.0 4.0 114 115 C 4.5 M 3.0 5.8 3.0 117 118 C 5.0 H 5.8 2.5 4.0 119 124 E 5.0 H 0.7 0.5 0.7 125 126 C 5.0 H 3.0 4.0 4.5 127 135 H 4.4 M 11.9 3.7 5.2 136 139 C 4.8 H 3.8 0.8 3.2 140 143 E 5.0 H 0.5 0.2 0.0 144 150 C 4.9 H 2.9 3.1 3.7 151 155 - 4.0 M 75.0 4.4 75.0 156 160 C 4.6 H 4.9 5.9 18.4 161 169 H 4.8 H 4.2 3.1 3.2 170 171 - 4.0 M 75.0 7.0 75.0 172 175 C 4.8 H 1.2 2.0 5.0 176 179 E 5.0 H 0.8 0.8 1.0 180 187 C 4.9 H 3.4 3.2 3.0 188 192 H 4.4 M 17.6 2.2 3.8 193 196 C 4.8 H 2.2 1.0 2.0 197 200 E 4.8 H 0.0 0.0 0.5 202 205 H 5.0 H 2.5 1.5 2.0 206 209 C 4.8 H 23.4 6.1 6.4 210 225 H 4.4 M 16.4 3.2 8.2 227 228 - 4.0 M 75.0 6.0 75.0 >>>>>>