Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1iq4a- CCHHHHHHHHCHHHHHHHHHCCCCHHHCCCEEEEEEEEECCCCCCCHHHHHHHHHHHHHHHCC-----CCEEEECCCCCCCCCCCCCCEEEEEEEECHHHHHHHHHHHHHCCHHHCCCCCCCCCCCCCCCCEEEEEECCHHHCCCCCHH--HCCCCCCEEEEEEECCC---------------------------CHHHHHHHHHHHCCCCCC >P1;d1vq8d1 ----------------------CCCCCCCEEEEEEEEEECCCC--------CCHHHHHHHCCC-----CCEEEECCCCCCCCCCCCCCEEEEEEEECCHHHHHHHHH----HHHHC----CCCHHHCCCCCCEEEC----------------------CEEEEEEECHHHHHHCCC-------CCCCCCCHHHCCCHHHHHHHHHCCCCCCC- >P1;d2nrqa1 -------------------------------CEEEEEEEECC----CCCHHHHHHHHHHHCCCHHHHCCCEEEEEECCCC------CEEEEEEECC--CCCCCHHHHHHCCCCCCCCCCCCC--CCEE-CCEEEEEECHHHHHHHCCCCCCC--CCCCEEEEEECCCCC--CCCCCCCC---------------------------------- >P1;d2nwua1 ---------------------------------CEEEEEECC----CCCHHHHHHHHHCCC-----CC--CCCC----C--------CCEEEEEEECCHHHHHHHHHHHHHC-CCHHHHHHHC-CCCCC-CEEEE-CCHHHHHC-CCCCCC------CCCEEEECC----CHHHHHHHHCCCEECCEECCCCCCCCC---------------- >P1;d2ogka1 ----------------------------CEEEEEEEEEEECC----CCCHHHHC-CCHHHCC-----CCCCCEEE------------CCEEEEEEECCHHHHHHHCCHHHHHHHHCC-HHHHHHHHCCCCCEEEEEECHHHHHC-CCCCCCC--CCCCEEEEEEEECCCCCHHHHHHHCC--------------------------------- >P1;d2pzza1 --------------------------------CEEEEEEECC----CCCHHHHHHHHHHHCC----CC--EEEEEECCC--------CCEEEEEEEC---CCHHHHHHHHHC-CCHHHHC-CCCCC-CC-CEEEEEECHHHHHC-CCCCCCCCC-CCCEEEEEECCC--CCCCCHHHHHCCCCCCCCC-CC---------------------- >P1;d2wnya- --------------------------CCCCEEEEEEEEEECC----CCCHHHHHHHHCCCCC----CCCCEEEEEECHHH------CEEEEEEEEECCHHHHH---HHHHHHHHHHCCCHHHCHHHCCCCCEEEEEEEHHHHHC-CCCCEEC--CCCEEEEEEEECCCCCCHHHHHHHHHHHC------------------------------ >P1;d3c9ga- -----------------------------CCCCEEEEEECCC----CCCHHHHHHHHHHHCC----CC--EEEECC------------CCEEEEEEC---CCHHHHHHHHHC-CCCHHHHHHHHHCCCC-CCEEEEECHHHHCC-CCCCCCCCCCCCCEEEEECC----CCCCHHHHHHCCCC--CCCCCC---------------------- PSA >P1;d1iq4a- 5270453137600540385291956860050420103070a4048668417403600350093-----9073251885a96ba835712300402059750150014014500353882811449504880104070a20100330578--80873330503020409---------------------------52710320043060205a >P1;d1vq8d1 ----------------------a78746151020203142481--------b13a50484074-----90743738963d99267761310040305a830660079----01571----a027a405a5020318----------------------35040200018274253a-------a7378068934054940274038692957- >P1;d2nrqa1 -------------------------------65040204056----a373940180037004820770835366656997------7522304007--771060162016304591060472--9167-c4412020006402666401039--966001020139688--92733a73---------------------------------- >P1;d2nwua1 ---------------------------------500203155----a25488037005400-----54--5775----c--------9364040207205005401720267-7308502730-6229a-75051-05172037-460506------505050607----61850020000506b773438592076---------------- >P1;d2ogka1 ----------------------------0503105030204a----a2548601-0062002-----2b1a2735------------76140504067a93066002028409b327-03940871049631030402074048-7601129--9b410304030217940490057108--------------------------------- >P1;d2pzza1 --------------------------------3020404022----9153660360034003----60--90814859a--------9401042507---217302710373-7209600-30593-99-82050401062047-540617519-330020304079--957182166001618b774-3a---------------------- >P1;d2wnya- --------------------------a87404003020202c----a253960160043004----90709559471876------67020053506679106---60084028206b30840571038701050403074027-5505025--9a400304050309666572026405810------------------------------ >P1;d3c9ga- -----------------------------a413030304149----a246770170043004----60--90924a------------723050506---517400400172-7429602720474399-65020203063045-27060287a3b100301005----93796005200068--76d438---------------------- Translating the sequences *********************************EEEEEE*CC*******HHHHHHHHHHH*C*-----**EEEE***************EEEEEEEC*****HHHHHHHH****************CCC*CEEEEEEC*HHH*C*CC**--****CCCEEEEEE**C*---------------------------****************** ----------------------***********EEEEEE*CC*--------**HHHHHHHCC*-----**EEEE***************EEEEEEEC*****HHHHH----*****----******CCC*C*EEE*----------------------*EEEEE**C*********-------*****************************- -------------------------------**EEEEEE*CC----CCCHHHHHHHHHHHCC*****C**EEEE******------***EEEEE**--*****HHHHHH*************--****-*CEEEEEECHHHH***CCCC***--*CCCEEEEEE**C**--********---------------------------------- ---------------------------------*EEEEE*CC----CCCHHHHHHHHH**C-----*C--****----*--------**EEEEEEEC*****HHHHHHHH**-**********-**CCC-CEEEE-*CHHHH*C-CCCC**------C**EEEE**----***************************---------------- ----------------------------*****EEEEEE*CC----CCCHHHH*-**HHHCC-----C****EE*------------**EEEEEEEC*****HHH**HHH*******-********CCC*CEEEEEECHHHH*C-CCCC***--*CCCEEEEEE**C*************--------------------------------- --------------------------------*EEEEEE*CC----CCCHHHHHHHHHHHCC----*C--EEEE*****--------**EEEEEEEC---**HHHHHHHH**-*******-*****-CC-CEEEEEECHHHH*C-CCCC*****-CCCEEEEEE**C--*******************-**---------------------- --------------------------*******EEEEEE*CC----CCCHHHHHHHH***CC----*C**EEEE******------***EEEEEEEC*****H---HHHH****************CCC*CEEEEEE*HHHH*C-CCCC***--*CC*EEEEEE**C****************------------------------------ -----------------------------****EEEEEE*CC----CCCHHHHHHHHHHHCC----*C--EEEE**------------**EEEEEEC---**HHHHHHHH**-*************CCC-C*EEEEECHHHH*C-CCCC******CCCEEEEE**----**************--******---------------------- 55282.tem _________________________________ --------------------------*******EEEEEE*CC----CCCHHHHHHHHHHHCC*---*C**EEEE******------***EEEEEEEC*****HHHHHHHH****************CCC*CEEEEEECHHHH*C-CCCC******CCCEEEEEE**C************************----**---------------- Structural block scores 0 25 - 4.6 H 4.2 64.7 75.0 75.0 75.0 75.0 75.0 75.0 26 32 * 3.0 P 2.4 2.7 55.1 75.0 22.7 64.7 4.8 34.8 33 38 E 5.0 H 1.8 1.7 1.7 1.7 1.7 1.7 1.2 1.7 40 41 C 5.0 H 7.2 6.0 5.5 5.0 7.2 2.0 7.2 6.5 42 45 - 4.6 H 4.5 56.5 75.0 75.0 75.0 75.0 75.0 75.0 46 48 C 4.4 M 6.0 75.0 6.8 5.8 5.8 5.0 5.8 5.5 49 59 H 4.6 H 2.6 17.9 3.2 3.5 9.3 2.8 2.9 3.2 60 61 C 4.7 H 4.5 3.5 2.0 37.5 1.0 1.5 2.0 2.0 63 65 - 4.7 H 75.0 75.0 3.0 75.0 75.0 75.0 75.0 75.0 68 69 * 2.9 P 4.5 4.5 5.5 75.0 6.2 75.0 3.5 75.0 70 73 E 4.5 M 4.2 5.2 5.0 6.0 5.6 4.5 7.0 5.0 74 79 * 2.6 P 6.9 7.1 7.0 64.6 63.3 18.6 5.5 52.4 80 85 - 4.3 M 7.3 6.7 75.0 75.0 75.0 75.0 75.0 75.0 86 88 * 2.0 P 3.3 3.3 4.7 29.0 29.3 29.3 4.3 52.3 89 95 E 4.9 H 1.3 1.1 2.3 2.3 2.0 1.7 2.1 2.1 97 101 * 1.9 P 4.4 5.5 18.0 1.4 5.9 45.6 4.6 46.2 102 109 H 4.6 H 1.9 30.9 2.8 2.6 3.0 2.9 30.6 2.0 110 125 * 1.5 P 4.1 26.4 12.6 12.9 9.0 12.8 3.8 8.6 126 128 C 4.6 H 4.0 5.2 29.3 7.2 4.3 31.0 3.7 7.0 131 136 E 4.7 H 2.0 14.8 1.5 14.3 1.3 1.8 1.7 1.5 138 141 H 4.6 H 0.8 75.0 2.5 2.5 2.8 2.0 2.8 2.2 145 148 C 4.6 H 5.0 75.0 2.8 3.8 3.5 3.8 3.8 3.8 149 154 * 2.9 P 28.8 75.0 28.5 51.0 28.5 16.3 27.7 5.1 155 157 C 4.5 M 3.0 75.0 4.0 51.7 5.5 2.0 4.8 4.2 158 163 E 4.8 H 1.7 2.3 0.7 2.7 1.7 1.5 2.0 0.7 164 165 * 1.4 P 2.0 0.0 6.0 3.5 1.0 3.5 1.5 40.0 167 190 * 2.9 P 72.2 25.7 46.3 12.6 36.6 13.7 27.8 16.5 191 194 - 4.3 M 75.0 4.0 75.0 4.0 75.0 75.0 75.0 75.0 195 196 * 3.9 M 3.5 4.5 75.0 6.5 75.0 75.0 75.0 75.0 197 212 - 4.3 M 2.7 9.4 75.0 75.0 75.0 75.0 75.0 75.0 >>>>>>