Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d2o6pa1 ---------------------------CEEEEEEEEEECCCCCCCHHHHHCCCCEEEEEECCEEEEEEEEECHHHEEEEEEC---C--EECEEEEEECC-CCEEEEEEEECCCEEEEEEEEEEEEEEEEC-CEEEEEEEEEEEEEEEECCCCCCC >P1;d3qzma1 ------------------------CCEEEEEECEEEEECCCCCCCHHHHHCCCCEEEEEECCEEEEEEEEECHHHEEEEEEECCCCCEECEEEEEEECC-CCEEEEEEEECCCCCEEEEEEEEEE----HHH---CEEEEEEEEEEECCCCCCCC >P1;d3rtla1 ------------------------CCEEEEECCEEEEECCCCCCCHHHHHCCCCCEEEEECCEEEEEEEEECHHHEEEEEEC---C--EECEEEEEECC-CCEEEEEEECCCCCCEEEEEEEEEE----HHH---CEEEEEEEEEEECC------ >P1;d4fc3e- CCCCCCCCCHHHHCCCCCCCCCCCCCCCEEEECEEEECCCCCCCHHHHHCCCCCEEEEEECCEEEEEEEECCCCCEEEEEEEECC-EECCC-CCEEECCC-CEEEEEEECCCCCCEEEEEEEEEEC--------CEEEEEEEEEEEECCCCCC-- >P1;d4h8qa- -------------------------CCEEEEEEEEEEECCCCCCCHHHHHCCCCEEEEEECCEEEEEEEECCHHHEEEEEEEEC-CEEEECEEEEEECC-CCEEEEEEEECCCCCCEEEEEEEEE----HHH--C-EEEEEEEEEEEECCCC--- >P1;d4mypa- -----------------------CCCCEEEEECEEEEECCCCCCCHHHHHCCCCEEEEEECCEEEEEEEECCCCCEEEEEEEEC-CEEEECEEEEEECC-CCEEEEEEECCCCCCCEEEEEEEEEEE---CC--EEEEEEEEEEEEEC-CCC--- >P1;d4ympa- ----------------------------CEEEEEEEECCCCCCCCHHHHHEE-EEEEEEECCEEEEEEEEECHHHEEEEEEC-----CEECEEEEEECCCCCEEEEEEEECCCCCCEEEEEEEEEC-------CCCEEEEEEEEEEEEECC--CC PSA >P1;d2o6pa1 ---------------------------668509030174747841a22930434060324a850101020241610530104---9--59183375699-64102000307404640516031506565a-987543557540003040279194 >P1;d3qzma1 ------------------------5a4434604040156b487409116405251401156860201020340730441602079a880817347348a-5421202040628252030502122----6a7---a365643020208540270e >P1;d3rtla1 ------------------------a08746726010144978540801830633021041aa63000040441741610304---a--960621765b9-744310005168c374050502241----8a7---94605530101258------ >P1;d4fc3e- ba34501700240072681355a3a1a855516070317797517304400334020024a9502000003605203302021ca-64070-030124a5-320202040676176030200045a--------d645519302040584057-- >P1;d4h8qa- -------------------------94864602060063938741a037305340404169b533030304318204602035a-9825707327468a-5421303020a71763150303121----996--a-445854010305185b--- >P1;d4mypa- -----------------------b3a5762404040252b78771913930634070506996130102033182034030328-a735708436367b-6331402020561a7316010433486---ac--86571766020307-a0a--- >P1;d4ympa- ----------------------------75403050165b678608135216-8140347aa54102030530620520214-----295083474488970323021408627631303011426-------a63466544010102255--a9 Translating the sequences ---------------------------*EEEE*EEEEECCCCCCCHHHHHCCCCEEEEEECCEEEEEEEE*CHHHEEEEEE*---C--EECEEEEEECC-CCEEEEEEE*CCC***EEEEEEEEE*****-*****EEEEEEEEEEE*CCCC*** ------------------------*C**EEEE*EEEEECCCCCCCHHHHHCCCCEEEEEECCEEEEEEEE*CHHHEEEEEE****C**E**EEEEEECC-CCEEEEEEE*CCCCC*EEEEEEEEE----***---*EEEEEEEEEEE*CCCC*** ------------------------*C**EEE**EEEEECCCCCCCHHHHHCCCC*EEEEECCEEEEEEEE*CHHHEEEEEE*---C--EECEEEEEECC-CCEEEEEEE*CCCCC*EEEEEEEEE----***---*EEEEEEEEEEE*C------ *************************C**EEEE*EEEE*CCCCCC*HHHH*CCCCEEEEEECCEEEEEEEE*C***EEEEEE****-****C-**EEECC*-CEEEEEEE*CCCCC*EEEEEEEEE*--------**EEEEEEEEEEE*CCCC*-- -------------------------C**EEEE*EEEEECCCCCCCHHHHHCCCCEEEEEECCEEEEEEEE*CHHHEEEEEE***-C**EECEEEEEECC-CCEEEEEEE*CCCCC*EEEEEEEEE----***--*-EEEEEEEEEEE*CCCC--- -----------------------**C**EEEE*EEEEECCCCCCCHHHHHCCCCEEEEEECCEEEEEEEE*C***EEEEEE***-C**EECEEEEEECC-CCEEEEEEE*CCCCC*EEEEEEEEE**---**--**EEEEEEEEEEE*-CCC--- ----------------------------*EEE*EEEE*CCCCCCCHHHHH**-*EEEEEECCEEEEEEEE*CHHHEEEEEE*-----*EECEEEEEECC*CCEEEEEEE*CCCCC*EEEEEEEEE*-------***EEEEEEEEEEE**CC--** 158911.tem _________________________________ ------------------------*C**EEEE*EEEEECCCCCCCHHHHHCCCCEEEEEECCEEEEEEEE*CHHHEEEEEE***-C**EECEEEEEECC-CCEEEEEEE*CCCCC*EEEEEEEEE*---***--**EEEEEEEEEEE*CCCC*** Structural block scores 0 23 - 4.6 H 75.0 75.0 75.0 4.1 75.0 72.4 75.0 26 27 * 2.1 P 40.5 4.0 7.5 9.2 6.0 6.0 75.0 28 31 E 4.8 H 4.8 3.2 4.8 4.0 4.0 3.0 4.0 33 37 E 4.8 H 2.2 2.0 1.2 2.2 2.4 2.2 2.4 38 44 C 4.9 H 5.0 5.8 5.3 6.1 5.0 6.2 6.2 45 49 H 4.9 H 5.3 4.2 4.0 2.2 4.7 5.0 3.8 50 53 C 4.6 H 2.8 3.0 3.0 2.5 3.0 3.2 22.5 54 59 E 4.9 H 2.5 2.0 1.3 1.3 2.5 3.0 3.2 60 61 C 5.0 H 9.2 7.0 10.5 9.8 10.2 9.0 10.5 62 69 E 5.0 H 1.1 1.4 1.6 0.9 2.1 1.6 1.9 72 74 H 4.2 M 2.7 3.3 4.0 2.3 3.7 3.7 2.7 75 80 E 5.0 H 1.5 2.5 1.8 1.3 2.0 1.7 1.7 81 83 * 2.4 P 51.3 3.0 51.3 5.2 6.2 4.3 51.3 86 87 * 2.8 P 75.0 8.0 75.0 5.0 5.0 5.0 38.5 88 89 E 4.4 M 7.0 4.0 7.5 3.5 6.0 6.0 7.0 91 96 E 4.8 H 5.3 4.7 4.5 13.5 4.8 5.0 5.0 97 98 C 5.0 H 9.0 9.2 10.2 7.2 9.2 9.2 8.0 100 101 C 4.8 H 5.0 4.5 5.5 39.0 4.5 4.5 3.5 102 108 E 5.0 H 0.9 1.6 1.9 1.4 1.6 1.7 2.1 110 114 C 4.8 H 4.2 4.6 7.3 5.4 6.3 5.9 5.8 116 124 E 5.0 H 2.3 1.7 2.1 1.6 1.8 2.4 1.7 126 128 - 4.5 M 5.3 75.0 75.0 75.0 75.0 52.0 75.0 129 131 * 2.9 P 31.5 7.8 8.5 75.0 8.0 32.7 75.0 132 133 - 4.4 M 7.5 75.0 75.0 75.0 75.0 75.0 42.8 134 135 * 2.1 P 4.5 42.8 42.0 9.8 42.8 7.0 4.5 136 146 E 5.0 H 2.9 2.8 2.5 3.0 3.1 3.4 2.8 148 151 C 4.5 M 4.5 2.8 58.2 4.2 6.4 24.0 21.8 152 154 * 3.7 M 4.7 7.2 75.0 52.3 75.0 75.0 31.5 >>>>>>