Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1knxa2 CCCEEEEEEEEEEC-----CEEEEEEECCCCCHHHHHHHHHCC---CCEEEEEEEEEEEEEC-CEEEEEECCCCCCEEEEC------------------------------------------------------------------CCEEEEHHHHHC---HHHCCCCEEEEEEEEEECC----------------CCCCCCCCCEEEECCEEEEEEEEECCC---------------------------------------------------------------------------------------------------------CCCHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHC >P1;d1ko7a2 CEEEEEECEEEEEC-----CEEEEEEECCCCCHHHHHHHHHHC---CCEEEECCEEEEEECCCCCEEEECCHHHCCEEEEC------------------------------------------------------------------CCEEEEHHHHHC---HHHCCCEEECCEEEEEEC------------------------CEEEEECCEEEEEEEEECCC---------------------------------------------------------------------------------------------------------CCCHHHHHHHHHHHHHHHHCCCCHHHHHHHHHC------- >P1;d2olra1 --CEEECEEEEECC------CEEEEECCCCCCHHHHHCCC------CCEEEECCCEEEEC-----CEEEECCC-EEEEECCCCC--CCHHHHHCCCCCCEEECCEECC--CCEECCCCC------------------------CCCCCEEEEEHHHCCCCCCC--CCEECCEEEEEEEECCCCCCCCCEEECCHHHHHHHHHHCEECCCCCCCCCCCCCEECHHHCHHHCCCCHHHHHHHHCCHH---HHC-CEEEEEEC-CCCCCCCCCC---CCHHHHHHHHHCCHHHHCCEEECCCCEEECC----CCCCCCCCCCHHHHCCCHHHHHHHHHHHHHHHHHHHHHHC-CCHHHHHHHHHCCCC---- >P1;d3tqfa- --CEEEECEEEECC-----C-CEEEEECCCCCHHHHHHHHHHC---CCEEEECCEEEEEECC-CCEEEECCCCCCCEEEEC------------------------------------------------------------------CCEEEEHHHHHC---HHHCCCEEECCEEEEEECCCCCCC-----------CCCCCCEEEEEEECCEEEEEEEEECCC---------------------------------------------------------------------------------------------------------CCCHHHHHHHHHHHHHHCC----HHHHHHHHCCC------ >P1;d4gmua2 --CEEECCEEEEEECCCCCEEEEEEECCCCCCHHHHHCCCCCCCCCEEEEEECCCEEEEECCCCCEEEECCCC-EEEEECCCCCCCCCHHHHHHCCCCCEEECCEEECCCCEECCCCCCCCCCCCCEECCCCCEECCCCCCCCCCCCCEEEEEHHHCCCCCCCCCCCCCEEEEEEEEECCCCCCC-CCEEECCCHHHHHHHHHCCEEECC---------EECHHHCCCCCCCCHHHHHHHHHHHHHCCCCCCCEEEEECCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCCEEEECC-EEEECCCCCCCCCCCCCCHHHHHCCCHHHHHHHHHHHHHHHHHHCHHHC-C-HHHHHHHHHHHHHHHCC PSA >P1;d1knxa2 3a345380000105-----800000218ac1511500260074---903000073010045b-95010401981605071a------------------------------------------------------------------b68603038434---8800495030400020458----------------a46652955557234150212313247---------------------------------------------------------------------------------------------------------c371043016006305516795160667477667676897 >P1;d1ko7a2 25635450000104-----600000209a90401510240074---90400006405040377730203018a32320619------------------------------------------------------------------c68513047528---780237422040003068------------------------95426023060324215278---------------------------------------------------------------------------------------------------------b45104300610541543679636875777759------- >P1;d2olra1 --505020000039------60000001840301200005------60400003400038-----9003043a-3050301707--5163066014a70823603559--762317328------------------------63860104021700950179--71626405100000000000000002079600300000001024086a58526260200004871966245118302218---91a-04000000-02105a8407---4202200300074302922450400504007----807b076101027217458604940460063048208612-958915805710054---- >P1;d3tqfa- --a56270000003-----8-00004169b1322500230073---a13000174040445a-b40002049a74140609------------------------------------------------------------------b57504028638---9a10394320500010233854b4-----------a65952125426038380420114139---------------------------------------------------------------------------------------------------------b671244016105824745----88886988887------ >P1;d4gmua2 --4050000000021387520100000068040230000704088050100004405060388030204013a-3060301800782020016007780816500606868310580658279c2603026a88176749830046502050307103210620728700303000000404710-000000260200000001002639---------41000014351a66107005400600849806203000000113198775004151200000300021039692056120-031048a20429b0ba055840161638205600540472077505a41-1-92065106406530574 Translating the sequences **CEEEE*EEEEEC-----CEEEEEEECCCCCHHHHHHHHH*C---CCEEEE**EEEEEE*C-C*EEEE*CCC*CCEEEEC------------------------------------------------------------------CCEEEEHHHHHC---HHHCCC*EEEEEEEEEECC----------------******CC*EEEECCEEEEEEEEECCC---------------------------------------------------------------------------------------------------------CCCHHHHHHHHHHHHHHHHC*CCHHHHHHHHH******** ***EEEECEEEEEC-----CEEEEEEECCCCCHHHHHHHHH*C---CCEEEECCEEEEEECC*CCEEEECC***CCEEEEC------------------------------------------------------------------CCEEEEHHHHHC---HHHCCCEEE**EEEEEEC------------------------CEEEEECCEEEEEEEEECCC---------------------------------------------------------------------------------------------------------CCCHHHHHHHHHHHHHHHHC*CCHHHHHHHHHC------- --CEEE**EEEE*C------*EEEEE*CCCCCHHHHH***------CCEEEECC*EEEE*-----*EEE*CCC-**EEE*C***--**********************--*********------------------------****C*EEEEHHH**C****--CC*E**EEEEEEEECCCCCC******************C*E****CC*******EEC***********************---***-********-**********---*******************************----***********************HHHHHHHHHHHHHHHHC-CCHHHHHHHHHC***---- --CEEEECEEEE*C-----C-*EEEEECCCCCHHHHHHHHH*C---CCEEEECCEEEEEECC-CCEEEECCCC*CCEEEEC------------------------------------------------------------------CCEEEEHHHHHC---HHHCCCEEE**EEEEEECCCCCC*-----------********EEEEECCEEEEEEEEECCC---------------------------------------------------------------------------------------------------------CCCHHHHHHHHHHHHHH**----HHHHHHHH*C*------ --CEEE*CEEEEE*******EEEEEE*CCCCCHHHHH*****C*****EEEECC*EEEEECC*CCEEEECCCC-**EEE*C******************************************************************C*EEEEHHH**C******CCC*EEEEEEEEE*CCCCCC-*****************CCEEE**---------EEC*****************************************************************************-********************************HHHHHHHHHHHH*HHHC-C-HHHHHHHHH******** 53795.tem _________________________________ --CEEEECEEEEEC-----CEEEEEEECCCCCHHHHHHHHH*C---CCEEEECCEEEEEECC-CCEEEECCCC*CCEEEEC------------------------------------------------------------------CCEEEEHHHHHC---HHHCCCEEEEEEEEEEECCCCCC------------******CCEEEEECCEEEEEEEEECCC---------------------------------------------------------------------------------------------------------CCCHHHHHHHHHHHHHHHHC-CCHHHHHHHHHC***---- Structural block scores 0 1 - 3.8 M 6.8 3.5 75.0 75.0 75.0 3 6 E 4.7 H 5.0 4.2 1.8 5.0 1.2 8 12 E 4.8 H 0.2 0.2 0.6 0.0 0.0 14 18 - 4.5 M 75.0 75.0 75.0 75.0 4.8 20 26 E 4.6 H 0.4 0.3 0.9 11.4 0.1 27 31 C 5.0 H 7.4 6.5 3.2 6.1 3.6 32 40 H 4.5 M 1.7 1.4 9.2 1.6 1.3 43 45 - 4.5 M 75.0 75.0 75.0 75.0 5.3 46 47 C 4.5 M 4.5 4.5 3.0 5.8 2.5 48 51 E 5.0 H 0.8 1.0 1.0 0.8 0.2 52 53 C 4.5 M 3.5 3.0 1.5 4.0 2.0 54 59 E 4.7 H 1.3 2.2 2.5 2.7 2.5 60 61 C 4.3 M 8.2 5.0 75.0 7.8 5.5 63 64 C 4.3 M 7.0 5.0 75.0 7.8 1.5 65 68 E 4.9 H 1.2 1.2 3.0 0.5 1.5 69 72 C 4.5 M 4.5 4.9 4.4 5.9 3.6 74 75 C 3.8 M 3.0 2.5 1.5 2.5 1.5 76 79 E 4.7 H 3.2 2.2 2.0 2.5 2.2 81 146 - 4.1 M 75.0 75.0 34.3 75.0 4.3 147 148 C 4.4 M 8.8 9.2 0.5 8.2 1.0 149 152 E 5.0 H 4.2 4.2 1.5 4.0 2.0 153 157 H 4.5 M 3.6 3.6 3.4 3.8 2.2 159 161 - 3.8 M 75.0 75.0 2.7 75.0 2.3 162 164 H 4.0 M 5.3 5.0 53.0 6.8 3.0 165 167 C 4.8 H 4.3 4.0 4.7 4.0 5.7 168 178 E 4.5 M 1.6 1.9 1.6 1.5 0.5 179 184 C 4.4 M 52.2 63.8 0.0 5.8 2.7 185 196 - 3.8 M 75.0 75.0 2.0 69.1 7.1 197 202 * 2.1 P 5.6 75.0 0.5 6.2 0.0 203 204 C 3.9 M 7.0 42.0 0.0 1.5 0.5 205 209 E 4.2 M 4.8 3.4 1.4 3.4 4.0 210 211 C 4.5 M 3.5 2.5 7.0 5.5 75.0 212 220 E 4.3 M 2.0 2.6 4.9 2.6 58.9 221 223 C 4.2 M 4.3 5.7 0.7 4.3 0.0 224 328 - 3.9 M 75.0 75.0 11.4 75.0 3.9 329 331 C 3.8 M 7.5 6.8 4.3 8.2 3.7 332 347 H 4.9 H 2.6 2.7 3.2 3.4 3.8 350 351 C 4.3 M 3.0 4.5 7.0 75.0 38.0 352 360 H 4.9 H 5.4 6.6 4.9 7.9 3.7 362 364 * 2.7 P 6.7 75.0 3.0 52.3 4.7 365 368 - 3.8 M 7.5 75.0 75.0 75.0 4.0 >>>>>>