Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d2b0aa1 --CEEECCCCCC--CCCCC--CCCCCEEEEEEEC----CEEEEEEECCCCCCCEEECHHHHCCCCC---CCCHHHCEEEEEEEEECC---------CCCCCCCCCCCEEEEECCHHHHCCCHHHHHCCCCCC-CHHHHHHCCCCEEEECCCCCCC-----HHHHHHHHHCCCEEEECCCHHHHHHCCCEEEEEEEECCCCCCCEEEEEEEEEC-- >P1;d3krva- CCCEEECCCCCCCCCCCHHHCHHHCCEEEEEEE---C-CEEEEEEECCCCCCCEEECCHHHCC---CCCCCCCCCC-EEEEEEEECCCCCCEECHHHHCCCCCCCCCEEEEECHHHHCC-CC-CCCCCEECHHHHHHHHHHCCCEEEECCCCCCC-CCCCCHHHHHHHHCCCEEEECCC--CCCCCCEEEEEEEEECCCCCCCEEEEEEEEEEC- >P1;d4coga- --CEEECCCCCCCCCCCCC--CCCCCEEEEEECCCCCCCCCEEEEECCCCCCCEEECHHHCCCCCCCHHHCCHHHH-EEEEEEEECCCCCCEECHHHHHHHCCCCCCEEEEECCCCCCCCCC-CCCCCEECHHHHHHHHHCCCCEEEECCCCCCCCCCCCCHHHHHHHHCCCEEECCCC--CCCCCCEEEEEECCCCCCCCCCEEECCCEEEECC PSA >P1;d2b0aa1 --8524010934--51146--b46707436687a----c8663755132200000010430a3a26---810855405240200119---------806b5a01a0300001042072135a6008340a06-00750183c040000000001a-----68414400354000000016207603765040206067468230020602033-- >P1;d3krva- b67425012735590303464783206663849---b-a568395813440000010096209---9941046a30-317010140270954025930482706782000010500539-70-56800001460062007360100000112002-72b96202720292200000002--049065860403050685532300006030239- >P1;d4coga- --85340018354912135--b34805364374573b1866536562012010000033312aa152005176810-4250100203a15830635205a40bc013000010279033a92-35a000023800330174a0400000020004192973400440443901000202--0390557302020406958943002070204539 Translating the sequences --CEEECCCCCC--CCCCC--CCCCCEEEEEEEC----CEEEEEEECCCCCCCEEECHHHHCCCCC---CCCHHHC*EEEEEEEECC---------**CCCCCCCCCEEEEECCHHH*CCC*****CC**C*-*HHHHHHCCCCEEEECCCCCCC-----*HHHHHHHHCCCEEEECCC******CC*EEEEEEEECCCCCCCEEEEEEEEE*-- **CEEECCCCCCCCCCC*******CCEEEEEEE---C-CEEEEEEECCCCCCCEEEC*HHHCC---C**CCC***C-EEEEEEEECCCCCCEECHHHHCCCCCCCCCEEEEEC*HHHCC-CC-CCCCCEECHHHHHHHHH*CCCEEEECCCCCCC-CCCCCHHHHHHHHCCCEEEECCC--CCCCCCEEEEEEEEECCCCCCCEEEEEEEEEEC- --CEEECCCCCCCCCCCCC--CCCCCEEEEEE*C**C*C**EEEEECCCCCCCEEECHHH*CCCCCC***CCHHH*-EEEEEEEECCCCCCEECHHHH***CCCCCCEEEEECC***CCCCC-CCCCCEECHHHHHHHHHCCCCEEEECCCCCCC*CCCCCHHHHHHHHCCCEEE*CCC--CCCCCCEEEEEE***CCCCCCCEEE***EEEEC* 102198.tem _________________________________ --CEEECCCCCCCCCCCCC--CCCCCEEEEEEEC--C-CEEEEEEECCCCCCCEEECHHHHCCCCCC**CCCHHHC-EEEEEEEECCCCCCEECHHHHCCCCCCCCCEEEEECCHHHCCCCC-CCCCCEECHHHHHHHHHCCCCEEEECCCCCCC-CCCCCHHHHHHHHCCCEEEECCC--CCCCCCEEEEEEEEECCCCCCCEEEEEEEEEEC- Structural block scores 0 1 - 4.0 M 75.0 8.8 75.0 3 5 E 5.0 H 3.7 3.7 4.0 6 18 C 4.7 H 14.2 3.2 3.2 19 20 - 4.0 M 75.0 5.0 75.0 21 25 C 4.4 M 5.7 4.0 5.3 26 32 E 4.9 H 5.9 6.0 4.6 34 35 - 4.0 M 75.0 75.0 5.0 39 45 E 4.7 H 5.7 6.3 5.3 46 52 C 5.0 H 1.1 1.7 0.9 53 55 E 5.0 H 0.0 0.3 0.0 57 60 H 4.5 M 1.8 4.2 2.5 61 66 C 4.3 M 17.8 40.5 5.2 67 68 * 2.7 P 75.0 6.5 0.0 69 71 C 4.7 H 3.0 1.7 4.3 72 74 H 4.0 M 6.0 6.5 5.0 77 84 E 5.0 H 1.8 2.1 1.8 85 90 C 4.3 M 51.7 3.8 4.6 91 92 E 4.0 M 75.0 2.0 1.5 94 97 H 4.0 M 39.5 4.2 2.5 98 106 C 4.7 H 5.3 4.9 5.3 107 111 E 5.0 H 0.2 0.2 0.2 112 113 C 4.5 M 2.0 2.5 1.0 114 116 H 4.0 M 3.0 1.7 5.3 117 121 C 4.4 M 4.3 18.8 5.5 123 127 C 4.4 M 3.0 3.8 3.7 128 129 E 4.0 M 5.2 0.0 0.0 131 139 H 4.7 H 11.3 2.8 2.8 140 143 C 4.8 H 4.9 2.5 4.6 144 147 E 5.0 H 0.0 0.0 0.0 148 154 C 5.0 H 1.6 0.9 0.9 156 160 C 4.0 M 61.2 7.1 6.0 161 168 H 5.0 H 3.0 3.0 2.5 169 171 C 5.0 H 3.0 1.3 4.0 172 175 E 4.8 H 0.0 0.0 0.2 176 178 C 5.0 H 0.3 0.7 1.3 179 180 - 4.0 M 4.0 75.0 75.0 181 186 C 4.3 M 3.8 4.0 3.7 187 195 E 4.6 H 2.6 2.9 2.0 196 202 C 5.0 H 5.1 4.6 6.3 203 212 E 4.6 H 1.6 1.4 2.0 >>>>>>